Publications

Adkinson, NF, Bochner, BS, Burks, AW, Busse, WW, Holgate, ST, Lemanske, RF & O'Hehir, RE 2013, Middleton's Allergy: Principles and Practice: Eighth Edition.
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Boasting a worldwide reputation as the leading text in allergy and immunology, Middletons Allergy continues its steadfast tradition of providing comprehensive coverage of state-of-the-art basic science, as well as authoritative guidance on the clinical concepts of day-to-day diagnosis and management of allergic disorders. Offering timely information that's suited for clinicians and researchers alike, Middleton's is a user-friendly and versatile source for the knowledge you need to provide optimal care to your patients!. 'A valuable source of reference and pre-sifted information ...the editors are to be commending in keeping the book up-to-date and clinically valuable.' Reviewed by: Imnunology News Date: March 2015.

Baldeaux, J & Platen, E 2013, Functionals of Multidimensional Diffusions with Applications to Finance, 1, Springer International Publishing, Germany.
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This research monograph provides an introduction to tractable multidimensional diffusion models, where transition densities, Laplace transforms, Fourier transforms, fundamental solutions or functionals can be obtained in explicit form. The book also provides an introduction to the use of Lie symmetry group methods for diffusions, which allows to compute a wide range of functionals. Besides the well-known methodology on affine diffusions it presents a novel approach to affine processes with applications in finance. Numerical methods, including Monte Carlo and quadrature methods, are discussed together with supporting material on stochastic processes. Applications in finance, for instance, on credit risk and credit valuation adjustment are included in the book. The functionals of multidimensional diffusions analyzed in this book are significant for many areas of application beyond finance. The book is aimed at a wide readership, and develops an intuitive and rigorous understanding of the mathematics underlying the derivation of explicit formulas for functionals of multidimensional diffusions.

De Silva, KSB & Xu, X 2013, Graphene/Graphene oxide doped magnesium diboride superconductors, 1, LAP LAMBERT Academic Publishing, Germany.

Blanes, L, Coltro, WKT, Saito, RM, do Lago, CL, Roux, C & Doble, P 2013, 'Practical Considerations for the Design and Implementation of High‐Voltage Power Supplies for Capillary and Microchip Capillary Electrophoresis' in Carlos, DGA, Karin, YCT & Emanuel, C (eds), Capillary Electrophoresis and Microchip Capillary Electrophoresis, Wiley, Chichester, pp. 67-75.
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Capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) are powerful analytical techniques used to analyze chemical and biological samples. For both techniques sample injection and separation are two crucial steps that depend on a reliable high-voltage power supply (HVPS) to ensure reproducible separations. Therefore, the source of high voltage (HV) is considered to be the heart for these instruments. Separation of the analytes occurs due to the influence of an applied potential difference between electrodes placed at the ends of the capillary or channel. As a consequence, the components present in the plug of injection are driven toward the detector. This book chapter is a comprehensive source of information of HVPS for CE and MCE. This chapter covers topics as such as fundamentals of HV, electroosmotic flow control, construction of bipolar HVPS from unipolar HVPS, commercially available HVPS and DC/DC converters, alternative sources of HV, HVPS controllers for MCE, and strategies to measure HV. The chapter also includes practical and safety considerations that can be helpful for development of new CE and MCE instrumentation

Chen, H & Morris, MJ 2013, 'Mammalian target of rapamycin (mTOR): Structure, signaling pathways and biological effects' in Berhardt, LV (ed), Advances in Medicine and Biology Volume 68, Nova Science Publishers, New York, pp. 145-158.
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The mammalian target of rapamycin (mTOR) is a highly conserved member of the phosphoinositide 3-kinase (PI3K) related kinase protien family and functions as a cellular sensor of changes in ambient glucose and amino acid levels; critical for cellular proliferation and differentiation. There are two multiprotein complexes of mTOR signalling components, as mTOR complex 1 (mTORC1) and mTORC2. Only mTORC1 appears to be nutrient dependent. In response to low intracellular energy availability, mTORC1 stabilizes and reduces the activity of mTOR. On the other hand, conditions of nutrient abundance promote its activity. However, such mechanisms have only been reported in either cell line models or lean animals; and hence their application to human states is yet to be determined.

Choi, AH, Matinlinna, JP, Heness, G & Ben-Nissan, B 2013, 'Nanocomposites for biomedical and dental applications' in Handbook of Functional Nanomaterials, Nova Publishing, New York, pp. 149-172.
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During the last decade, there has been a major increase in the interest of nanostructured materials in advanced technologies such as biomedical and dental technology. Nanostructured materials are associated with a variety of uses within the bio-medical field, for example, nanoparticles in drug-delivery system, in biomaterial science and diagnostic systems and in regenerative medicine. By definition, a biomaterial is a nondrug substance that is ideal for inclusion in systems that replace or extend the function of bodily tissues or organs. The key factors in the clinical success of any biomaterial are its biocompatibility and biofunctionality, both of which are related directly to tissue/implant interface interactions. Nanocomposites can be described as a heterogeneous combination of two or more materials, in which at least one of those materials should be on a nanometer-scale. By using the composite approach, it is possible to manipulate the mechanical properties such as strength and modulus of the composites closer to those of natural bone, with the help of secondary substitution phases. Currently, the most common composite materials used for clinical applications are those selected from a handful of available and well-characterized biocompatible ceramics and the combination with metals and polymers as composites and hybrids. This approach is currently being explored in the development of a new generation of nanocomposites with a widened range of biomedical and dental applications. The aim of this chapter is to provide information relating to the use of nanocomposites for biomedical and dental applications. An overview on the basis of biomaterials will be followed by some of past and present research into the use of nanocomposites in biomedical and dental applications.

Cranfield, CG 2013, 'Techniques for investigating the mechanosensitivity of ion channels' in Encyclopedia of Biophysics, Springer, USA, pp. 1-4.

Cranfield, CG, Kloda, A, Petrov, E, Battle, A, Nomura, T, Rohde, PR, Cox, C & Martinac, B 2013, 'Mechanosensitivity of Ion Channels' in Encyclopedia of Biophysics, Springer Berlin Heidelberg, pp. 1433-1440.
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Darling, A & Stoye, J 2013, 'Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface' in Algorithms in Bioinformatics, pp. VI-VI.

Hennige, SJ, Suggett, DJ, Hepburn, LJ, Pugsley, A, Crabbe, J & Smith, DJ 2013, 'Coral reefs of the Wakatobi: Processes of reef growth and loss' in Marine Research and Conservation in the Coral Triangle, Nova, USA, pp. 27-44.
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Coral reef accretion (net reef growth) is the result of complex and dynamic interactions between reef building organisms, bioeroders and the environment. Coral calcification often forms the 'measureable' portion of net reef growth, and is dependent upon the successful symbiotic relationship between cnidaria and photosynthetic dinoflagellate microalgae (Symbiodinium spp.). Light is thus a crucial resource for coral growth. Processes of reef loss include abiotic (storms, disturbance events and climate change) and biotic (bioeroders and corralivores) factors. To assess reef accretion, an understanding of the relationship between coral growth and loss, environmental variables and biotic eroders is vital. Reef systems that have both high biodiversity and varied environmental conditions are prime 'study grounds' to assess these complex interactions. An important example is the Wakatobi National Park (WNP), which is a centre for biodiversity but also has active long-term projects across a range of environments. This chapter examines the underlying physiology of the coral symbiotic relationship, and how this relates to reef growth by using studies from both the WNP and other systems. Understanding these processes remains a critical first step in any reef management strategy plan, but current methods by which reef growth can be assessed often lack the resolution and accuracy needed to relate to changes of environment. Consequently, this chapter discusses benefits and limitations of certain techniques used to assess reef growth. Ultimately, accurate coral growth measurements will improve our ability to model future ecosystem change, and should therefore be a priority research area to support future reef management and conservation strategies. Processes of reef loss are then discussed with regard to the impact of bioeroders, environmental perturbations and anthropogenic stressors upon primary and secondary reef framework. © 2010 by Nova Science Publishers, Inc. Al...

Kumari, P, Kumar, M, Reddy, CRK & Jha, B 2013, 'Algal lipids, fatty acids and sterols' in Functional Ingredients from Algae for Foods and Nutraceuticals, Elsevier, USA, pp. 87-134.
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Algae are photosynthetic organisms with ubiquitous distribution and contain varied forms of lipids owing to their extreme habitat diversity. This chapter presents detailed information on the structure and distribution of lipids, fatty acids and sterols in algae together with the genes and enzymes involved in their metabolism. The developments in acclimatory roles of lipids, fatty acids and sterols in response to changes in environmental factors such as nutrients, light, temperature and salinity have been discussed. Further, the current status of lipidomics in algae has also been discussed presuming its promising implications in elucidation of novel lipids and understanding of complex metabolic pathways. © 2013 Woodhead Publishing Limited All rights reserved.

Li, Y, Larkum, A, Schliep, M, Kühl, M, Neilan, B & Chen, M 2013, 'Newly Isolated Chl d-Containing Cyanobacteria' in Kuang, T, Lu, C & Zhang, L (eds), Advanced Topics in Science and Technology in China, Springer Berlin Heidelberg, Beijing, pp. 686-690.
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Stromatolites are sedimentary structures formed by microbial mats that are typically found in limestone-or dolostone-rich environments. Shark Bay, Australia, has abundant examples of living marine stromatolites. Although the stromatolites from Shark Bay are only about 20003000 years old, they are similar to fossilized evidence of life found on Earth up to 3.5 billion years ago. Using infra-red light centred at 720 nm, new chlorophyll d-containing microorganisms were isolated from the living stromatolites (collected from Shark Bay, Western Australia) and red algae on mangrove pneumatophores (collected from the Georges River, Sydney, Australia) and enriched in KES+ seawater medium. Microscopic examination of the red-light enriched cultures confirmed that they are Acaryochloris-like cyanobacteria. Using cyanobacterial-specific 16S rRNA gene primers, we obtained almost full length sequences of 16S rDNA from the newly isolated Chl d-containing cyanobacteria. The sequences shared 98% identity with Acaryochloris marina MBIC11017. Interestingly, the strain isolated from stromatolites (designated as ssball1 strain) was more similar to Acaryochloris sp CR111A while the strain isolated from Georges River (designated as Mangrove1 strain) was more closely related to Acaryochloris sp CCMEE 5401, which was isolated from an inland lake, Salton Sea in California,. Pigment composition of the newly isolated strains were determined using HPLC, However, no obvious differences were noted. Chl d was the major photopigment while Chl a was present as a minor photopigment, about 2%3.5 % of the total chlorophyll.

M., A, Anne, M, Jun, G, Tao, C, A, B, Chng, E, M., L, Ting, J, Elgundi, Z, An, T, Lutherborrow, M, Torpy, F, K., D, E., B & M., G 2013, 'Insulin Trafficking in a Glucose Responsive Engineered Human Liver Cell Line is Regulated by the Interaction of ATP-Sensitive Potassium Channels and Voltage-Gated Calcium Channels' in Molina, FM (ed), Gene Therapy - Tools and Potential Applications, InTech, Rijeka, Croatia, pp. 703-726.
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Type I diabetes is caused by the autoimmune destruction of pancreatic beta (â) cells [1]. Current treatment requires multiple daily injections of insulin to control blood glucose levels. Tight glucose control lowers, but does not eliminate, the onset of diabetic complications, which greatly reduce the quality and longevity of life for patients. Transplantation of pancreatic tissue as a treatment is restricted by the scarcity of donors and the requirement for lifelong immunosuppression to preserve the graft, which carries adverse side-effects. This is of particular concern as Type 1 diabetes predominantly affects children. Lack of glucose control could be overcome by genetically engineering 'an artificial â-cell' that is capable of synthesising, storing and secreting insulin in response to metabolic signals. The donor cell type must be readily accessible and capable of being engineered to synthesise, process, store and secrete insulin under physiological conditions.

Martinac, B, Rohde, PR, Cranfield, CG & Nomura, T 2013, 'Patch Clamp Electrophysiology for the Study of Bacterial Ion Channels in Giant Spheroplasts of E. coli' in Methods in Molecular Biology, Humana Press, pp. 367-380.
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Martinac, B, Rohde, PR, Cranfield, CG & Nomura, T 2013, 'Patch clamp electrophysiology for the study of bacterial ion channels in giant spheroplasts of E. coli.' in Anne Delcour (ed), Methods in Molecular Biology - Bacterial Cell Surfaces, Springer, USA, pp. 367-380.
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Ion channel studies have been focused on ion channels from animal and human cells over many years. Based on the knowledge acquired, predominantly over the last 20 years, a large diversity of ion channels exists in cellular membranes of prokaryotes as well. Paradoxically, most of what is known about the structure of eukaryotic ion channels is based on the structure of bacterial channels. This is largely due to the suitability of bacterial cells for functional and structural studies of biological macromolecules in a laboratory environment. Development of the 'giant spheroplast' preparation from E. coli cells was instrumental for functional studies of ion channels in the bacterial cell membrane. Here we describe detailed protocols used for the preparation of giant spheroplasts as well as protocols used for the patch-clamp recording of native or heterologously expressed ion channels in E. coli spheroplast membrane.

Martinez, E, Djordjevic, S, Stokes, HW & Chowdhury, PR 2013, 'Mobilized integrons: Team players in the spread of antibiotic resistance genes' in Uri Gophna (ed), Lateral Gene Transfer in Evolution, Springer, New York, pp. 79-103.
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Integrons possess a site-specific recombination system and comprise a family of elements that are broadly distributed amongst the Proteobacteria. The units of capture into these elements are gene cassettes, which normally comprise of only a single gene along with an attachment site recognized by the recombination system. The class 1 integron has at least two features that distinguishes it from most other members of the integron family of integrase elements. The first of these is that they are located on mobile elements as opposed to being fixed in the chromosome and the second is that most of the associated gene cassettes include genes that encode antibiotic resistance. The linkage of the class 1 integron to mobile elements was an important step since it has meant that diverse molecular processes act cooperatively to disseminate resistance genes in Gram-negative bacteria. The selection for resistance in the antibiotic era has now led to an enormous diversity of elements that in many cases has resulted in conjugation, transposition, and site-specific recombination processes combining to spread large clusters of resistance genes. All these processes existed in nature prior to the antibiotic era but the level and extent of cooperation did not. Here we discuss how some of these complex class 1-associated mobile resistance regions evolved and their ramifications for the management of the antibiotic resistance problem.

Martinez, E, Djordjevic, S, Stokes, HW & Roy Chowdhury, P 2013, 'Mobilized Integrons: Team Players in the Spread of Antibiotic Resistance Genes' in Lateral Gene Transfer in Evolution, Springer New York, pp. 79-103.
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McCauley, J, Zivanovic, A & Skropeta, D 2013, 'Bioassays for Anticancer Activities' in Methods in Molecular Biology, Humana Press, pp. 191-205.
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O’Mara, ML & Deplazes, E 2013, 'Polypeptide and Protein Modeling for Drug Design' in Encyclopedia of Computational Neuroscience, Springer New York, pp. 1-9.
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Rahman, MA, Hassler, C, Hasegawa, H & Lim, R 2013, 'Ecotoxicology of arsenic in the freshwater environment: Consequences and risk assessment' in Andrea Masotti (ed), Arsenic: Sources, Environmental Impact, Toxicity and Human Health - A Medical Geology Perspective, Nova Science Publishers, New York, USA, pp. 85-103.
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Arsenic is a known environmental toxicant and it occurs in the environment from natural and anthropogenic sources. Arsenic is one of the important environmental issues because of its occurrence, bioaccumulation, toxicity, and trophic transfer in the freshwater food chain. Aquatic organisms accumulate, retain, and transform arsenic when exposed to it through water, their diet, and other routes. Since arsenic toxicity mostly depends on its chemical forms, measurement of arsenic speciation in aquatic organisms is particularly important in assessing the ecological risks of the element. Arsenate (As(V)) comprises the major part of total arsenic in oxic waters. Phytoplankton take up As(V) and subsequently convert it to arsenite (As(III)) and then to less toxic dimethylarsinic acid (DMAA), monomethylarsonic acid (MMAA), and higher order organoarsenicals. Phytoplankton are thought to convert inorganic arsenic species to methylarsenicals and to other organoarsenic compounds (lipids and arsenosugars) to reduce the toxic effects of inorganic arsenicals. Since phytoplankton are a major food source for the organisms of higher trophic levels in the aquatic systems, arsenic is biotransferred from lower to higher trophic levels; while biomagnification of the element in aquatic food chain is not consistent. Other important arsenic forms found in aquatic organisms include arsenocholine (AsC), arsenobetaine (AsB) and arsenosugars (AsS). This review discusses the bioaccumulation, biotransformation, and trophic transfer (biomagnification or diminution) of arsenic in the aquatic food chains in relation to its ecotoxicological risks in the freshwater environment. © 2013 by Nova Science Publishers, Inc. All rights reserved.

Robertson, J & Roux, C 2013, 'Fiber: Protocols for Examination' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 124-128.
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Fiber: Protocols for Examination

Robertson, J & Roux, C 2013, 'Fibers: Overview' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 109-112.
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The forensic examination of fibers requires an understanding of many facets of the forensic process from the crime scene to the laboratory and, ultimately, the courts. Fiber examination has the potential to contribute forensic intelligence at the investigative stage, especially in helping to answer the `what happened question. The role of the crime scene examiner in recognizing the potential of fiber evidence is stressed in this article, as `evidence not recovered is evidence lost. The technical and scientific examination of fibers as well as the interpretation of recovered fibers in the forensic context is considered.

Roux, C & Robertson, J 2013, 'Interpretation of Fiber Evidence' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 155-160.
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Because of their size and their particular nature, fibers probably constitute the ultimate example of trace evidence. Although fibers are easily transferred during a criminal event and a large pool of techniques can be applied for their characterization, the interpretation of an apparent `fiber match remains one of the most difficult challenges in the forensic examination of trace evidence. However, knowledge in this area has significantly improved over the past 25 years. Nowadays, a wealth of empirical data can be used by forensic scientists to determine the value of fiber evidence in the context of a case. In addition, logical and statistical frameworks can also assist them in this endeavor. This article reviews the state of the art in this topic

Roux, C & Robertson, J 2013, 'Trace Evidence Overview' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 279-285.
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The forensic examination of trace evidence requires an understanding of the many facets of the forensic process from the crime scene to the laboratory and, ultimately, the courts. Trace evidence examination has the potential to contribute forensic intelligence at the investigative stage, especially in helping to answer the `what happened question. The role of the crime scene examiner in recognizing the potential value of trace evidence is stressed in this article as `evidence not recovered is evidence lost. The technical and scientific examination of trace evidence as well as the interpretation of recovered trace evidence in the forensic context is considered.

Roux, C & Robertson, J 2013, 'Transfer' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 113-116.
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Fibers are easily transferred according to the Locard's exchange principle and, as a result, are commonly found in criminal cases. This article reviews the factors that have an effect on fiber transfer and explains fiber transfer mechanisms. This topic is pivotal to the interpretation of fiber evidence.

Roux, C, Hales, S, Morelato, M & Olinder, S 2013, 'Plastic Bag Striations' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 8-15.
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This article presents and reviews the examination of plastic bags in forensic science, and more specifically, the use and value of some of their physical features often known as `plastic bag striations. This is also presented with a view to exploit such information from an intelligence perspective.

Roux, C, Robertson, J & Palmer, R 2013, 'Persistence and Recovery' in Siegel, JA & Saukko, PJ (eds), Encyclopedia of Forensic Sciences, Elsevier, Waltham, pp. 117-123.
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Fibers are easily transferred according to the Locard's exchange principle and, as a result, are commonly found in criminal cases. This article provides an overview of fiber persistence and the significance of this topic in the interpretation of fiber evidence. It also presents a critical review of common methods used to recover fibers

Roux, CP & Robertson, J 2013, 'Professional standards, public protection and the administration of justice' in Fraser, J & Williams, R (eds), Handbook of Forensic Science, Willan, Cullompton, pp. 580-605.
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Scudder, N & Saw, B 2013, 'Health and Safety' in Encyclopedia of Forensic Sciences, Elsevier, pp. 535-541.
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The health and safety of people at work are vitally important. The health and safety of forensic practitioners, who have to contend with a unique range of hazards, pose a challenge for both practitioners and management. While there are a myriad of hazards to deal with, effective controls of the risks can be undertaken, provided a systematic process is in place.Forensic practitioners work within the office and laboratory, as well as external environments outside of the control of management. Forensic practitioners can respond to major crime scenes in residential, corporate, industrial, and public places, ranging from a murder in a park to a postblast scene or an international deployment involving Disaster Victim Identification. The diverse role performed by forensic practitioners has challenged health and safety in this unique environment.This article discusses the value of documented risk assessments, introduces the concept of dynamic risk assessments and hierarchy of controls, besides providing specific information about a range of hazards identified in the laboratory and in the field.

Siegel, JA, Saukko, PJ, Houck, MM, Cattaneo, C, Arrigo, B, Butler, JM, Carracedo, A, Roux, C, Daeid, NN, Crispino, F, Fraser, J, Fisher, BAJ, Epstein, J, Robertson, J, Lewis, SW, Langenburg, G, Bowen, RT, Drummer, OH, Pollak, S, Pollanen, M, Rogers, M, Found, B & Batterman, S 2013, 'Section Editors' in Encyclopedia of Forensic Sciences, Elsevier, pp. ix-x.
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Soole, KL & Menz, RI 2013, 'ATP in Plant Mitochondria: Substrates, Inhibitors, and Uncouplers' in Encyclopedia of Biological Chemistry, Elsevier, pp. 141-144.
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Voyer, M, Dreher, T, Gladstone, W & Goodall, H 2013, 'Dodgy science or global necessity?: Local media reporting of marine parks' in Lester, L & Hutchins, B (eds), Global Crises and the MediaEnvironmental Conflict and the Media, Peter Lang Publishing, New York, USA, pp. 153-168.
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Has the hype associated with the «revolutionary» potential of the World Wide Web and digital media for environmental activism been muted by the past two decades of lived experience? What are the empirical realities of the prevailing media landscape? Using a range of related disciplinary perspectives, the contributors to this book analyze and explain the complicated relationship between environmental conflict and the media. They shine light on why media are central to historical and contemporary conceptions of power and politics in the context of local, national and global issues and outline the emerging mixture of innovation and reliance on established strategies in environmental campaigns. With cases drawn from different sections of the globe Australia, the United Kingdom, the United States, Europe, Latin America, China, Japan, the Pacific Islands, Africa the book demonstrates how conflicts emanate from and flow across multiple sites, regions and media platforms and examines the role of the media in helping to structure collective discussion, debate and decision-making.

Abboud, M, Puglisi, DA, Davies, BN, Rybchyn, M, Whitehead, NP, Brock, KE, Cole, L, Gordon-Thomson, C, Fraser, DR & Mason, RS 2013, 'Evidence for a Specific Uptake and Retention Mechanism for 25-Hydroxyvitamin D (25OHD) in Skeletal Muscle Cells', Endocrinology, vol. 154, no. 9, pp. 3022-3030.
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Little is known about the mechanism for the prolonged residence time of 25-hydroxyvitamin D (25OHD) in blood. Several lines of evidence led us to propose that skeletal muscle could function as the site of an extravascular pool of 25OHD. In vitro studies investigated the capacity of differentiated C2 murine muscle cells to take up and release 25OHD, in comparison with other cell types and the involvement of the membrane protein megalin in these mechanisms. When C2 cells are differentiated into myotubes, the time-dependent uptake of labeled 25OHD is 2–3 times higher than in undifferentiated myoblasts or nonmuscle osteoblastic MG63 cells (P < .001). During in vitro release experiments (after 25OHD uptake), myotubes released only 32% ± 6% stored 25OHD after 4 hours, whereas this figure was 60% ± 2% for osteoblasts (P < .01). Using immunofluorescence, C2 myotubes and primary rat muscle fibers were, for the first time, shown to express megalin and cubilin, endocytotic receptors for the vitamin D binding protein (DBP), which binds nearly all 25OHD in the blood. DBP has a high affinity for actin in skeletal muscle. A time-dependent uptake of Alexafluor-488-labeled DBP into mature muscle cells was observed by confocal microscopy. Incubation of C2 myotubes (for 24 hours) with receptor-associated protein, a megalin inhibitor, led to a 40% decrease in 25OHD uptake (P < .01). These data support the proposal that 25OHD, after uptake into mature muscle cells, is held there by DBP, which has been internalized via membrane megalin and is retained by binding to actin.

Abraham, J, Champod, C, Lennard, C & Roux, C 2013, 'Modern statistical models for forensic fingerprint examinations: A critical review', FORENSIC SCIENCE INTERNATIONAL, vol. 232, no. 1-3, pp. 131-150.
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Over the last decade, the development of statistical models in support of forensic fingerprint identification has been the subject of increasing research attention, spurned on recently by commentators who claim that the scientific basis for fingerprint identification has not been adequately demonstrated. Such models are increasingly seen as useful tools in support of the fingerprint identification process within or in addition to the ACE-V framework. This paper provides a critical review of recent statistical models from both a practical and theoretical perspective. This includes analysis of models of two different methodologies: Probability of Random Correspondence (PRC) models that focus on calculating probabilities of the occurrence of fingerprint configurations for a given population, and Likelihood Ratio (LR) models which use analysis of corresponding features of fingerprints to derive a likelihood value representing the evidential weighting for a potential source.

Abraham, J, Champod, C, Lennard, C & Roux, C 2013, 'Spatial analysis of corresponding fingerprint features from match and close non-match populations', FORENSIC SCIENCE INTERNATIONAL, vol. 230, no. 1-3, pp. 87-98.
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The development of statistical models for forensic fingerprint identification purposes has been the subject of increasing research attention in recent years. This can be partly seen as a response to a number of commentators who claim that the scientific basis for fingerprint identification has not been adequately demonstrated. In addition, key forensic identification bodies such as ENFSI [1] and IAI [2] have recently endorsed and acknowledged the potential benefits of using statistical models as an important tool in support of the fingerprint identification process within the ACE-V framework. In this paper, we introduce a new Likelihood Ratio (LR) model based on Support Vector Machines (SVMs) trained with features discovered via morphometric and spatial analyses of corresponding minutiae configurations for both match and close non-match populations often found in AFIS candidate lists. Computed LR values are derived from a probabilistic framework based on SVMs that discover the intrinsic spatial differences of match and close non-match populations. Lastly, experimentation performed on a set of over 120,000 publicly available fingerprint images (mostly sourced from the National Institute of Standards and Technology (NIST) datasets) and a distortion set of approximately 40,000 images, is presented, illustrating that the proposed LR model is reliably guiding towards the right proposition in the identification assessment of match and close non-match populations. Results further indicate that the proposed model is a promising tool for fingerprint practitioners to use for analysing the spatial consistency of corresponding minutiae configurations.

Afzal, S, Daoud, WA & Langford, SJ 2013, 'Photostable Self-Cleaning Cotton by a Copper(II) Porphyrin/TiO₂ Visible-Light Photocatalytic System', ACS Applied Materials & Interfaces, vol. 5, no. 11, pp. 4753-4759.
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Afzal, S, Daoud, WA & Langford, SJ 2013, 'Visible-light self-cleaning cotton by metalloporphyrin-sensitized photocatalysis', Applied Surface Science, vol. 275, pp. 36-42.
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Ajani, P, Brett, S, Krogh, M, Scanes, P, Webster, G & Armand, L 2013, 'The risk of harmful algal blooms (HABs) in the oyster-growing estuaries of New South Wales, Australia', Environmental Monitoring and Assessment, vol. 185, no. 6, pp. 5295-5316.
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Ajani, P, Murray, S, Hallegraeff, G, Brett, S & Armand, L 2013, 'First reports of Pseudo-nitzschia micropora and P-hasleana (Bacillariaceae) from the Southern Hemisphere: Morphological, molecular and toxicological characterization', PHYCOLOGICAL RESEARCH, vol. 61, no. 3, pp. 237-248.
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Pseudo-nitzschia H. Peragallo is a marine diatom genus found worldwide in polar, temperate, subtropical and tropical waters. It includes toxigenic representatives that produce domoic acid (DA), a neurotoxin responsible for Amnesic Shellfish Poisoning. In this study we characterized two species of Pseudo-nitzschia collected from Port Stephens and the Hawkesbury River (south eastern Australia) previously unreported from Australian waters. Clonal isolates were sub-sampled for (i) light and transmission electron microscopy; (ii) DNA sequencing, based on the nuclear-encoded partial large subunit ribosomal RNA gene and internal transcribed spacer (ITS)-ITS1, 5.8S and ITS2 rDNA regions and, (iii) DA production as measured by liquid chromatography-mass spectrometry. Morphological and molecular data unambiguously revealed the species to be Pseudo-nitzschia micropora Priisholm, Moestrup & Lundholm (Port Stephens) and Pseudo-nitzschia hasleana Lundholm (Hawkesbury River). This is the first report of the occurrence of these species from the Southern Hemisphere and the first report of P.?micropora in warm-temperate waters. Cultures of P.?micropora, tested for DA production for the first time, proved to be non-toxic. Similarly, no detectable toxin concentrations were observed for P.?hasleana. Species resolution and knowledge on the toxicity of local Pseudo-nitzschia species has important implications for harmful algal bloom monitoring and management.

Ajani, P, Murray, S, Hallegraeff, G, Lundholm, N, Gillings, M, Brett, S & Armand, L 2013, 'THE DIATOM GENUS PSEUDO-NITZSCHIA (BACILLARIOPHYCEAE) IN NEW SOUTH WALES, AUSTRALIA: MORPHOTAXONOMY, MOLECULAR PHYLOGENY, TOXICITY, AND DISTRIBUTION', JOURNAL OF PHYCOLOGY, vol. 49, no. 4, pp. 765-785.
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Species belonging to the potentially harmful diatom genus Pseudo-nitzschia, isolated from 16 localities (31 sampling events) in the coastal waters of south-eastern Australia, were examined. Clonal isolates were characterized by (i) light and transmission electron microscopy; (ii) phylogenies, based on sequencing of nuclear-encoded ribosomal deoxyribonucleic acid (rDNA) regions and, (iii) domoic acid (DA) production as measured by liquid chromatographymass spectrometry (LC-MS/MS). Ten taxa were unequivocally confirmed as Pseudo-nitzschia americana, P. arenysensis, P. calliantha, P. cuspidata, P. fraudulenta, P. hasleana, P. micropora, P. multiseries, P. multistriata, and P. pungens. An updated taxonomic key for south-eastern Australian Pseudo-nitzschia is presented. The occurrence of two toxigenic species, P. multistriata (maximum concentration 11 pg DA per cell) and P. cuspidata (25.4 pg DA per cell), was documented for the first time in Australia. The Australian strains of P. multiseries, a consistent producer of DA in strains throughout the world, were nontoxic. Data from 5,888 water samples, collected from 31 oyster-growing estuaries (2,000 km coastline) from 2005 to 2009, revealed 310 regulatory exceedances for Total Pseudo-nitzschia, resulting in six toxic episodes. Further examination of high-risk estuaries revealed that the P. seriata group had highest cell densities in the austral summer, autumn, or spring (species dependent), and lowest cell densities in the austral winter, while the P. delicatissima group had highest in winter and spring

Alexander, TJ & Gladstone, W 2013, 'Assessing the effectiveness of a long-standing rocky intertidal protected area and its contribution to the regional conservation of species, habitats and assemblages', AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS, vol. 23, no. 1, pp. 111-123.
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The acceptance of reserves as a useful management strategy relies on evidence of their effectiveness in preserving stocks of harvested species and conserving biodiversity. A history of ad hoc decisions in terrestrial and marine protected area planning has meant that many of these areas are contributing inefficiently to conservation goals. The conservation value of existing protected areas should be assessed when planning the placement of additional areas in a reserve network. This study tested (1) the effectiveness of protection for intertidal molluscs of a marine reserve (Bouddi Marine Extension, NSW, Australia) established in 1971, and (2) the contribution of the protected area to the conservation of regional species, assemblages, and habitats. The shell length and population density of one harvested (Cellana tramoserica), and three non-harvested species (Bembicium nanum, Morula marginalba, Nerita atramentosa) of intertidal molluscs were examined in the protected area and two reference locations over two seasons. The heavily collected limpet C. tramoserica was significantly larger in the protected area and was the only species to exhibit a significant difference. No species significantly differed in population density between the protected area and reference locations. Temporally replicated surveys of macro-molluscs at 21 locations over 75?km of coastline identified that the existing protected area included 50% of species, two of five assemblage types and 19 of 20 intertidal rocky shore habitats surveyed in the study region. Reservation of a further three rocky reefs would protect a large proportion of species (71%), a representative of each assemblage and all habitat types. Despite originally being selected in the absence of information on regional biodiversity, the protected area is today an effective starting point for expansion to a regional network of intertidal protected areas.

Allen-Hall, A & McNevin, D 2013, 'Non-cryogenic forensic tissue preservation in the field: a review', Australian Journal of Forensic Sciences, vol. 45, no. 4, pp. 450-460.
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Ammit, AJ 2013, 'Glucocorticoid insensitivity as a source of drug targets for respiratory disease', Current Opinion in Pharmacology, vol. 13, no. 3, pp. 370-376.
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Ang, KCS & van Reyk, D 2013, ''Teach me chemistry like a ladder and make it real'-barriers and motivations students face in learning chemistry for bioscience', International Journal of Innovation in Science and Mathematics Education, vol. 21, no. 2, pp. 1-12.
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Students enrolled in the Bachelor of Nursing program come with diverse academic abilities, age, language skills and experience. Many enrol without any prior knowledge of the supporting sciences including chemistry. Moreover, whilst some do possess such prior knowledge, they may have had a substantial break since they last studied chemistry. This paper draws from surveys and interviews conducted to investigate students' prior knowledge of chemistry and experiences around learning. These were first year students enrolled in a core unit of anatomy and physiology for which, albeit implicitly some prior knowledge of chemistry is assumed. It explores barriers and motivations to learning chemistry and offers insights into what students need in order to gain a mastery of the foundational chemical principles that underlie anatomy and physiology. This research is of considerable importance given that the teaching of anatomy and physiology relies heavily on foundation-level chemistry knowledge. It is of great significance if students can be better supported in the successful learning, retention and completion of their nursing studies. Insights reveal that problems stem from various factors including length of time since their last chemistry studies, language difficulties, students' interests and motivations in the subject, pace and structure of sessions, relevance of information and the students' ability to manage the amount of content. This informs future practice suggesting that it is important to scaffold the learning for all students in a structured and relevant manner. Additionally, it supports the development and provision of resources to support students transitioning into higher education from diverse backgrounds.

Asatryan, AA, Botten, LC, Fang, K, Fan, S & McPhedran, RC 2013, 'Local density of states of chiral Hall edge states in gyrotropic photonic clusters', PHYSICAL REVIEW B, vol. 88, no. 3.
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We have constructed the Green's tensor for two-dimensional gyrotropic photonic clusters and have calculated their optical local density of states (LDOS). For clusters that support the chiral Hall edge states we calculate the LDOS as a function of wavelength, position, size, and shape of the cluster. It is shown that the LDOS of Hall edge states is a strong function of the cluster shape and position. The LDOS can be orders of magnitude higher at the edges of the cluster compared to the free space value while it vanishes towards the cluster center. It is shown that the LDOS in such photonic clusters can withstand a very strong disorder due to their topological protection. The spatial profiles of chiral Hall edge modes, their quality factors, and their excitations have been calculated. Both gyroelectric and gyromagnetic (ferrite) clusters have been treated. © 2013 American Physical Society.

Austin, C, Smith, TM, Bradman, A, Hinde, K, Joannes-Boyau, R, Bishop, D, Hare, DJ, Doble, P, Eskenazi, B & Arora, M 2013, 'Barium distributions in teeth reveal early-life dietary transitions in primates', NATURE, vol. 498, no. 7453, pp. 216-+.
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Early-life dietary transitions reflect fundamental aspects of primate evolution and are important determinants of health in contemporary human populations. Weaning is critical to developmental and reproductive rates; early weaning can have detrimental health effects but enables shorter inter-birth intervals, which influences population growth. Uncovering early-life dietary history in fossils is hampered by the absence of prospectively validated biomarkers that are not modified during fossilization. Here we show that large dietary shifts in early life manifest as compositional variations in dental tissues. Teeth from human children and captive macaques, with prospectively recorded diet histories, demonstrate that barium (Ba) distributions accurately reflect dietary transitions from the introduction of mother's milk through the weaning process. We also document dietary transitions in a Middle Palaeolithic juvenile Neanderthal, which shows a pattern of exclusive breastfeeding for seven months, followed by seven months of supplementation. After this point, Ba levels in enamel returned to baseline prenatal levels, indicating an abrupt cessation of breastfeeding at 1.2 years of age. Integration of Ba spatial distributions and histological mapping of tooth formation enables novel studies of the evolution of human life history, dietary ontogeny in wild primates, and human health investigations through accurate reconstructions of breastfeeding history. © 2013 Macmillan Publishers Limited. All rights reserved.

Ayub, A, Ashfaq, UA, Idrees, S & Haque, A 2013, 'Global Consensus Sequence Development and Analysis of Dengue NS3 Conserved Domains', BioResearch Open Access, vol. 2, no. 5, pp. 392-396.
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Baffour, B, Brown, JJ & Smith, PWF 2013, 'An investigation of triple system estimators in censuses', Statistical Journal of the IAOS, vol. 29, no. 1, pp. 53-68.
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The value of a census cannot be overstated, given that no other data resource provides such detailed information about the population. Further, censuses are often the only historical data source to map out change over time due the consistency of questions asked. However, it is often the most expensive undertaking-other than going to war-that a country embarks on. Countries are thus seeking more cost-effective alternatives. This paper details some exploratory research into one such alternative, based on capture-recapture methods. Capture recapture methods have been used for population estimation for decades, but the focus has been on dual system estimation. Dual system measurement of the population has been criticized for its reliance on the independence assumption between the two systems. This assumption is untestable, and failure introduces bias into the estimates of the population. The most logical improvement of dual system estimation is triple system estimation. In this paper, a simulation study is carried out to compare the performance of different dual and triple system estimators of the population size under various dependency scenarios. Performance is explored through both the bias and variability. The study shows that the dual system estimator copes well with dependence, provided the coverage of both lists are reasonably high. In addition, although the triple system estimators yield less biased estimates of the population, the dual system estimator is shown to be robust enough to cope with low levels of dependence.

Bahl, J, Krauss, S, Kühnert, D, Fourment, M, Raven, G, Pryor, SP, Niles, LJ, Danner, A, Walker, D, Mendenhall, IH, Su, YCF, Dugan, VG, Halpin, RA, Stockwell, TB, Webby, RJ, Wentworth, DE, Drummond, AJ, Smith, GJD & Webster, RG 2013, 'Influenza A Virus Migration and Persistence in North American Wild Birds', PLoS Pathogens, vol. 9, no. 8, pp. e1003570-e1003570.
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Baird, ME, Ralph, PJ, Rizwi, F, Wild-Allen, K & Steven, ADL 2013, 'A dynamic model of the cellular carbon to chlorophyll ratio applied to a batch culture and a continental shelf ecosystem', LIMNOLOGY AND OCEANOGRAPHY, vol. 58, no. 4, pp. 1215-1226.
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A novel parameterization of the dynamical relationship between cellular carbon (C) and chlorophyll (Chl) is developed using a Chl synthesis term that includes the physiological status of the cell and the effect of packaging of pigments within cells. The geometric derivation highlights the non-linear relationship between Chl content and absorption due to the package effect. When parameterized for a generic 3 mm radius phytoplankton cell, the model reproduces the magnitude and daily variations of C: Chl and C: nitrogen ratios of the diatom Skeletonema costatum in published laboratory experiments. The parameterization is then applied in a three-dimensional biogeochemical model containing three phytoplankton classes in the coastal waters off southeast Tasmania, Australia, which demonstrates the behavior of the dynamic Chl parameterization over a range of light- and nutrient-limiting environments for phytoplankton of different sizes and growth rates. The model produces C: Chl ratios of , 1220 (weight : weight) and , 6080 for phytoplankton communities dominated by fast-growing small and fast-growing large cells, respectively, close to the ratios of 17 and 76 observed at two sampling stations during periods with diatom- and flagellate-dominated communities. Throughout the simulation, community C: Chl ratios generally vary between 12 and 200, which is similar to the range observed globally. In the new parameterization, C: Chl ratios are most influenced by the package effect for light-limited, slow-growing large microalgae, with physiological processes becoming important for smaller, nutrient-limited, fast-growing microalgae.

Baldeaux, J & Platen, E 2013, 'Credit Derivative Evaluation and CVA under the Benchmark Approach', Asia-Pacific Financial Markets, vol. 22, no. 3, pp. 305-331.
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In this paper, we discuss how to model credit risk under the benchmark approach. Firstly we introduce an affine credit risk model. We then show how to price credit default swaps (CDSs) and introduce credit valuation adjustment (CVA) as an extension of CDSs. In particular, our model can capture right-way - and wrong-way exposure. This means, we capture the dependence structure of the default event and the value of the transaction under consideration. For simple contracts, we provide closed-form solutions. However, due to the fact that we allow for a dependence between the default event and the value of the transaction, closed-form solutions are difficult to obtain in general. Hence we conclude this paper with a reduced form model, which is more tractable.

Baldeaux, JF, Grasselli, M & Platen, E 2013, 'Pricing Currency Derivatives Under the Benchmark Approach', Journal of Banking and Finance, vol. 53, pp. 34-48.
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This paper considers the realistic modelling of derivative contracts on exchange rates. We propose a stochastic volatility model that recovers not only the typically observed implied volatility smiles and skews for short dated vanilla foreign exchange options but allows one also to price payoffs in foreign currencies, lower than possible under classical risk neutral pricing, in particular, for long dated derivatives. The main reason for this important feature is the strict supermartingale property of benchmarked savings accounts under the real world probability measure, which the calibrated parameters identify under the proposed model. Using a real dataset on vanilla option quotes, we calibrate our model on a triangle of currencies and find that the risk neutral approach fails for the calibrated model, while the benchmark approach still works.

Balogh, ZJ, McIlroy, DJ, Smith, DW & Hansbro, PM 2013, 'The origin and the role of mitochondrial DNA in postinjury inflammation', Journal of Critical Care, vol. 28, no. 6, pp. 1099-1100.
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Banihashemi, N & Yalçın Kaya, C 2013, 'Inexact Restoration for Euler Discretization of Box-Constrained Optimal Control Problems', Journal of Optimization Theory and Applications, vol. 156, no. 3, pp. 726-760.
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Banks, CC, Elder, M & Willis, GA 2013, 'Simple groups of automorphisms of trees determined by their actions on finite subtrees', Journal of Group Theory, vol. 18, pp. 235-261.
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We introduce the notion of the $k$-closure of a group of automorphisms of alocally finite tree, and give several examples of the construction. We showthat the $k$-closure satisfies a new property of automorphism groups of treesthat generalises Tits' Property $P$. We prove that, apart from some degeneratecases, any non-discrete group acting on a tree with this property contains anabstractly simple subgroup.

Barba‐Bon, A, Costero, AM, Parra, M, Gil, S, Martínez‐Máñez, R, Sancenón, F, Gale, PA & Hiscock, JR 2013, 'Neutral 1,3‐Diindolylureas for Nerve Agent Remediation', Chemistry – A European Journal, vol. 19, no. 5, pp. 1586-1590.
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Barbosa, SS, Klanten, SO, Puritz, JB, Toonen, RJ & Byrne, M 2013, 'Very fine-scale population genetic structure of sympatric asterinid sea stars with benthic and pelagic larvae: influence of mating system and dispersal potential', Biological Journal of the Linnean Society, vol. 108, no. 4, pp. 821-833.
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Barnes, RJ, Bandi, RR, Wong, WS, Barraud, N, McDougald, D, Fane, A, Kjelleberg, S & Rice, SA 2013, 'Optimal dosing regimen of nitric oxide donor compounds for the reduction ofPseudomonas aeruginosabiofilm and isolates from wastewater membranes', Biofouling, vol. 29, no. 2, pp. 203-212.
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Membrane fouling by bacterial biofilms remains a key challenge for membrane-based water purification systems. Here, the optimal biofilm dispersal potential of three nitric oxide (NO) donor compounds, viz. sodium nitroprusside, 6-(2-hydroxy-1-methyl-2-nitrosohydrazino)-N-methyl-1-hexanamine (MAHMA NONOate) and 1-(hydroxy-NNO-azoxy)-L-proline, disodium salt, was investigated using Pseudomonas aeruginosa PAO1 as a model organism. Dispersal was quantitatively assessed by confocal microscopy [bacterial cells and the components of the extracellular polymeric substances (EPS) (polysaccharides and extracellular DNA)] and colony-forming unit counts. The three NO donor compounds had different optimal exposure times and concentrations, with MAHMA NONOate being the optimal NO donor compound. Biofilm dispersal correlated with a reduction in both bacterial cells and EPS. MAHMA NONOate also reduced single species biofilms formed by bacteria isolated from industrial membrane bioreactor and reverse osmosis membranes, as well as in isolates combined to generate mixed species biofilms. The data present strong evidence for the application of these NO donor compounds for prevention of biofouling in an industrial setting. © 2013 Copyright Taylor and Francis Group, LLC.

Barraud, N, Buson, A, Jarolimek, W & Rice, SA 2013, 'Mannitol Enhances Antibiotic Sensitivity of Persister Bacteria in Pseudomonas aeruginosa Biofilms', PLoS ONE, vol. 8, no. 12, pp. e84220-e84220.
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Bateman, JE, Dalgliesh, R, Duxbury, DM, Helsby, WI, Holt, SA, Kinane, CJ, Marsh, AS, Rhodes, NJ, Schooneveld, EM, Spill, EJ & Stephenson, R 2013, 'The OSMOND detector', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, vol. 698, pp. 168-176.
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Beckett, EL, Stevens, RL, Jarnicki, AG, Kim, RY, Hanish, I, Hansbro, NG, Deane, A, Keely, S, Horvat, JC, Yang, M, Oliver, BG, van Rooijen, N, Inman, MD, Adachi, R, Soberman, RJ, Hamadi, S, Wark, PA, Foster, PS & Hansbro, PM 2013, 'A new short-term mouse model of chronic obstructive pulmonary disease identifies a role for mast cell tryptase in pathogenesis', Journal of Allergy and Clinical Immunology, vol. 131, no. 3, pp. 752-762.e7.
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Background: Cigarette smoke-induced chronic obstructive pulmonary disease (COPD) is a life-threatening inflammatory disorder of the lung. The development of effective therapies for COPD has been hampered by the lack of an animal model that mimics the human disease in a short timeframe. Objectives: We sought to create an early-onset mouse model of cigarette smoke-induced COPD that develops the hallmark features of the human condition in a short time-frame. We also sought to use this model to better understand pathogenesis and the roles of macrophages and mast cells (MCs) in patients with COPD. Methods: Tightly controlled amounts of cigarette smoke were delivered to the airways of mice, and the development of the pathologic features of COPD was assessed. The roles of macrophages and MC tryptase in pathogenesis were evaluated by using depletion and in vitro studies and MC protease 6-deficient mice. Results: After just 8 weeks of smoke exposure, wild-type mice had chronic inflammation, mucus hypersecretion, airway remodeling, emphysema, and reduced lung function. These characteristic features of COPD were glucocorticoid resistant and did not spontaneously resolve. Systemic effects on skeletal muscle and the heart and increased susceptibility to respiratory tract infections also were observed. Macrophages and tryptase-expressing MCs were required for the development of COPD. Recombinant MC tryptase induced proinflammatory responses from cultured macrophages. Conclusion: A short-term mouse model of cigarette smoke-induced COPD was developed in which the characteristic features of the disease were induced more rapidly than in existing models. The model can be used to better understand COPD pathogenesis, and we show a requirement for macrophages and tryptase-expressing MCs. © 2013 American Academy of Allergy, Asthma & Immunology.

Behrendt, L, Staal, M, Cristescu, SM, Harren, FJM, Schliep, M, Larkum, AWD & Kühl, M 2013, 'Reactive oxygen production induced by near-infrared radiation in three strains of the Chl d-containing cyanobacterium Acaryochloris marina', F1000Research, vol. 2, pp. 44-44.
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Cyanobacteria in the genus Acaryochloris have largely exchanged Chl a with Chl d, enabling them to harvest near-infrared-radiation (NIR) for oxygenic photosynthesis, a biochemical pathway prone to generate reactive oxygen species (ROS). In this study, ROS production under different light conditions was quantified in three Acaryochloris strains (MBIC11017, HICR111A and the novel strain CRS) using a real-time ethylene detector in conjunction with addition of 2-keto-4-thiomethylbutyric acid, a substrate that is converted to ethylene when reacting with certain types of ROS. In all strains, NIR was found to generate less ROS than visible light (VIS). More ROS was generated if strains MBIC11017 and HICR111A were adapted to NIR and then exposed to VIS, while strain CRS demonstrated the opposite behavior. This is the very first study of ROS generation and suggests that Acaryochloris can avoid a considerable amount of light-induced stress by using NIR instead of VIS for its photosynthesis, adding further evolutionary arguments to their widespread appearance.

Belov, PA, Slobozhanyuk, AP, Filonov, DS, Yagupov, IV, Kapitanova, PV, Simovski, CR, Lapine, M & Kivshar, YS 2013, 'Broadband isotropic mu-near-zero metamaterials', APPLIED PHYSICS LETTERS, vol. 103, no. 21.
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Natural diamagnetism, while being a common phenomenon, is limited to permeability values close to unity. Artificial diamagnetics, to the contrary, can be engineered to provide much lower values and may even possess an effective permeability close to zero. In this letter, we provide an experimental confirmation of the possibility to obtain extremely low permeability values by manufacturing an isotropic metamaterial composed of conducting cubes. We show that the practical assembly is quite sensitive to fabrication tolerances and demonstrate that permeability of about μ = 0.15 is realisable. © 2013 AIP Publishing LLC.

Ben-Nissan, B, Choi, AH & Bendavid, A 2013, 'Mechanical properties of inorganic biomedical thin films and their corresponding testing methods', Surface and Coatings Technology, vol. 233, no. 1, pp. 39-48.
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Coatings on implants are aimed to achieve some or all of the improvements in abrasion, corrosion resistance, metal ion release protection, increased bioactivity, biocompatibility, and ultimately an improved environment and structure for new bone attachme

Bera, A & Pal, AJ 2013, 'Molecular rectifiers based on donor/acceptor assemblies: effect of orientation of the components' magnetic moments', Nanoscale, vol. 5, no. 14, pp. 6518-6518.
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We perform density functional theory (DFT) calculations on molecular junctions consisting of a single molecule between two Au(111) electrodes. The molecules consist of an alkane or aryl bridge connecting acceptor, donor or thiol endgroups in various combinations. The molecular geometries are optimized and wavefunctions and eigenstates of the junction calculated using the DFT method, and then the electron transport properties for the junction are calculated within the non-equilibrium Green's function (NEGF) formalism. The currentvoltage or i(V) characteristics for the various molecules are then compared. Rectification is observed for these molecules, particularly for the donorbridgeacceptor case where the bridge is an alkane, with rectification being in the same direction as the original findings of Aviram and Ratner (1974 Chem. Phys. Lett. 29 27783), at least for relatively large negative and positive applied bias. However, at smaller bias rectification is in the opposite direction and is attributed to the lowest unoccupied orbital associated with the acceptor group.

Bilton, K, Hammer, L & Zaslawski, C 2013, 'Contemporary Chinese Pulse Diagnosis: A Modern Interpretation of an Ancient and Traditional Method', Journal of Acupuncture and Meridian Studies, vol. 6, no. 5, pp. 227-233.
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Braasch, K, de la Hunty, M, Deppe, J, Spindler, X, Cantu, AA, Maynard, P, Lennard, C & Roux, C 2013, 'Nile red: Alternative to physical developer for the detection of latent fingermarks on wet porous surfaces?', FORENSIC SCIENCE INTERNATIONAL, vol. 230, no. 1-3, pp. 74-80.
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This paper describes the application of a luminescent lipid stain, nile red, for the development of latent fingermarks on porous surfaces. An optimised formulation is presented that provides rapid development of latent fingermarks on porous surfaces that are or have been wet. A comparison with physical developer (PD), the method of choice to enhance such fingermarks, indicated that nile red was a simpler and more stable technique for the development of fingermarks. The nile red formulation showed similar performance to PD across a range of substrates and ageing conditions, although PD still showed greater sensitivity on five-year-old examination booklets used in a pseudo-operational study. The pseudo-operational trial also indicated that nile red consistently developed different fingermarks to those enhanced by PD, suggesting that it preferentially targets a different fraction of the latent fingermark deposit. Significantly, the compatibility of nile red in a detection sequence with indanedione-zinc, ninhydrin and PD is reported. © 2013 Elsevier Ireland Ltd.

Bradfield, LA & Balleine, BW 2013, 'Hierarchical and binary associations compete for behavioral control during instrumental biconditional discrimination.', Journal of Experimental Psychology: Animal Behavior Processes, vol. 39, no. 1, pp. 2-13.
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Bradfield, LA, Bertran-Gonzalez, J, Chieng, B & Balleine, BW 2013, 'The Thalamostriatal Pathway and Cholinergic Control of Goal-Directed Action: Interlacing New with Existing Learning in the Striatum', Neuron, vol. 79, no. 1, pp. 153-166.
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Bradfield, LA, Hart, G & Balleine, BW 2013, 'The role of the anterior, mediodorsal, and parafascicular thalamus in instrumental conditioning', Frontiers in Systems Neuroscience, vol. 7, no. OCT.
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The traditional animal model of instrumental behavior has focused almost exclusively on structures within the cortico-striatal network and ignored the contributions of various thalamic nuclei despite large and specific connections with each of these structures. One possible reason for this is that the thalamus has been conventionally viewed as a mediator of general processes, such as attention, arousal and movement, that are not easily separated from more cognitive aspects of instrumental behavior. Recent research has, however, begun to separate these roles. Here we review the role of three thalamic nuclei in instrumental conditioning: the anterior thalamic nuclei (ANT), the mediodorsal (MD), and parafascicular thalamic nuclei (PF). Early research suggested that ANT might regulate aspects of instrumental behavior but, on review, we suggest that the types of tasks used in these studies were more likely to recruit Pavlovian processes. Indeed lesions of ANT have been found to have no effect on performance in instrumental free-operant tasks. By contrast the mediodorsal thalamus (MD) has been found to play a specific and important role in the acquisition of goal-directed action. We propose this role is related to its connections with prelimbic cortex (PL) and present new data that directly implicates this circuit in the acquisition of goal-directed actions. Finally we review evidence suggesting the PF, although not critical for the acquisition or performance of instrumental actions, plays a specific role in regulating action flexibility. © 2013 Bradfield, Hart and Balleine.

Bradfield, LA, Hart, G & Balleine, BW 2013, 'The role of the anterior, mediodorsal, and parafascicular thalamus in instrumental conditioning', FRONTIERS IN SYSTEMS NEUROSCIENCE, vol. 7.
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Brading, P, Warner, ME, Smith, DJ & Suggett, DJ 2013, 'Contrasting modes of inorganic carbon acquisition amongst Symbiodinium (Dinophyceae) phylotypes', New Phytologist, vol. 200, no. 2, pp. 432-442.
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SummaryGrowing concerns over ocean acidification have highlighted the need to critically understand inorganic carbon acquisition and utilization in marine microalgae. Here, we contrast these characteristics for the first time between two genetically distinct dinoflagellate species of the genus Symbiodinium (phylotypes A13 and A20) that live in symbiosis with reef‐forming corals.Both phylotypes were grown in continuous cultures under identical environmental conditions. Rubisco was measured using quantitative Western blots, and radioisotopic 14C uptake was used to characterize light‐ and total carbon dioxide (TCO2)‐dependent carbon fixation, as well as inorganic carbon species preference and external carbonic anhydrase activity.A13 and A20 exhibited similar rates of carbon fixation despite cellular concentrations of Rubisco being approximately four‐fold greater in A13. The uptake of CO2 over was found to support the majority of carbon fixation in both phylotypes. However, A20 was also able to indirectly utilize by first converting it to CO2 via external carbonic anhydrase.These results show that adaptive differences in inorganic carbon acquisition have evolved within the Symbiodinium genus, which thus carries fundamental impl...

Brito, BP, Perez, AM, Jamal, SM, Belsham, GJ, Pauszek, SJ, Ahmed, Z & Rodriguez, LL 2013, 'Foot-and-Mouth Disease Virus Serotype O Phylodynamics: Genetic Variability Associated with Epidemiological Factors in Pakistan', Transboundary and Emerging Diseases, vol. 60, no. 6, pp. 516-524.
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Browne, EC, Langford, SJ & Abbott, BM 2013, 'Synthesis and effects of conjugated tocopherol analogues on peptide nucleic acid hybridisation', Organic & Biomolecular Chemistry, vol. 11, no. 39, pp. 6744-6744.
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Bryant, C, Suen, H, Brown, R, Yang, S, Favaloro, J, Aklilu, E, Gibson, J, Ho, PJ, Iland, H, Fromm, P, Woodland, N, Nassif, N, Hart, D & Joshua, DE 2013, 'Long-term survival in multiple myeloma is associated with a distinct immunological profile, which includes proliferative cytotoxic T-cell clones and a favourable Treg/Th17 balance', BLOOD CANCER JOURNAL, vol. 3, no. 9, pp. 1-7.
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Despite improved outcomes in multiple myeloma (MM), a cure remains elusive. However, even before the current therapeutic era, 5% of patients survived 410 years and we propose that immune factors contribute to this longer survival. We identified patients attending our clinic, who had survived 410 years (n>20) and analysed their blood for the presence of T-cell clones, T-regulatory cells (Tregs) and T helper 17 (Th17) cells. These results were compared with MM patients with shorter follow-up and age-matched healthy control donors. The frequency of cytotoxic T-cell clonal expansions in patients with o10 years follow-up (MM patients) was 54% (n>144), whereas it was 100% (n>19/19) in the long-survivors (LTS-MM). T-cell clones from MM patients proliferated poorly in vitro, whereas those from LTS-MM patients proliferated readily (median proliferations 6.1% and 61.5%, respectively (Po0.0001)). In addition, we found significantly higher Th17 cells and lower Tregs in the LTS-MM group when compared with the MM group. These results indicate that long-term survival in MM is associated with a distinct immunological profile, which is consistent with decreased immune suppression. © 2013 Macmillan Publishers Limited.

Burke, C, Liu, M, Britton, W, Triccas, JA, Thomas, T, Smith, AL, Allen, S, Salomon, R & Harry, E 2013, 'Harnessing Single Cell Sorting to Identify Cell Division Genes and Regulators in Bacteria', PLOS ONE, vol. 8, no. 4, pp. 1-13.
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Cell division is an essential cellular process that requires an array of known and unknown proteins for its spatial and temporal regulation. Here we develop a novel, high-throughput screening method for the identification of bacterial cell division genes and regulators. The method combines the over-expression of a shotgun genomic expression library to perturb the cell division process with high-throughput flow cytometry sorting to screen many thousands of clones. Using this approach, we recovered clones with a filamentous morphology for the model bacterium, Escherichia coli. Genetic analysis revealed that our screen identified both known cell division genes, and genes that have not previously been identified to be involved in cell division. This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development. © 2013 Burke et al.

Busschaert, N & Gale, PA 2013, 'Small‐Molecule Lipid‐Bilayer Anion Transporters for Biological Applications', Angewandte Chemie International Edition, vol. 52, no. 5, pp. 1374-1382.
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AbstractThe development of small‐molecule lipid‐bilayer anion transporters for potential future use in channel replacement therapy for the treatment of diseases caused by dysregulation of anion transport (such as cystic fibrosis), and in treating cancer by perturbing chemical gradients within cells, thus triggering apoptosis, is an area of intense current interest. This Minireview looks at recent developments in the design of small‐molecule transmembrane anion transporters and focuses on the progress so far in employing these compounds in biological systems.

Busschaert, N, Bradberry, SJ, Wenzel, M, Haynes, CJE, Hiscock, JR, Kirby, IL, Karagiannidis, LE, Moore, SJ, Wells, NJ, Herniman, J, Langley, GJ, Horton, PN, Light, ME, Marques, I, Costa, PJ, Félix, V, Frey, JG & Gale, PA 2013, 'Towards predictable transmembrane transport: QSAR analysis of anion binding and transport', Chemical Science, vol. 4, no. 8, pp. 3036-3036.
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Cai, H, An, X, Cui, J, Li, J, Wen, S, Li, K, Shen, M, Zheng, L, Zhang, G & Shi, X 2013, 'Facile Hydrothermal Synthesis and Surface Functionalization of Polyethyleneimine-Coated Iron Oxide Nanoparticles for Biomedical Applications', ACS Applied Materials & Interfaces, vol. 5, no. 5, pp. 1722-1731.
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Campos, GEP, Moran, MS, Huete, A, Zhang, Y, Bresloff, C, Huxman, TE, Eamus, D, Bosch, DD, Buda, AR, Gunter, SA, Scalley, TH, Kitchen, SG, McClaran, MP, McNab, WH, Montoya, DS, Morgan, JA, Peters, DPC, Sadler, EJ, Seyfried, MS & Starks, PJ 2013, 'Ecosystem resilience despite large-scale altered hydroclimatic conditions', NATURE, vol. 494, no. 7437, pp. 349-352.
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Climate change is predicted to increase both drought frequency and duration, and when coupled with substantial warming, will establish a new hydroclimatological model for many regions. Large-scale, warm droughts have recently occurred in North America, Africa, Europe, Amazonia and Australia, resulting in major effects on terrestrial ecosystems, carbon balance and food security. Here we compare the functional response of above-ground net primary production to contrasting hydroclimatic periods in the late twentieth century (1975-1998), and drier, warmer conditions in the early twenty-first century (2000-2009) in the Northern and Southern Hemispheres. We find a common ecosystem water-use efficiency (WUE e: Above-ground net primary production/ evapotranspiration) across biomes ranging from grassland to forest that indicates an intrinsic system sensitivity to water availability across rainfall regimes, regardless of hydroclimatic conditions. We found higher WUE e in drier years that increased significantly with drought to a maximum WUE e across all biomes; and a minimum native state in wetter years that was common across hydroclimatic periods. This indicates biome-scale resilience to the interannual variability associated with the early twenty-first century drought - that is, the capacity to tolerate low, annual precipitation and to respond to subsequent periods of favourable water balance. These findings provide a conceptual model of ecosystem properties at the decadal scale applicable to the widespread altered hydroclimatic conditions that are predicted for later this century. Understanding the hydroclimatic threshold that will break down ecosystem resilience and alter maximum WUE e may allow us to predict land-surface consequences as large regions become more arid, starting with water-limited, low-productivity grasslands. © 2013 Macmillan Publishers Limited. All rights reserved.

Carey, AJ, Huston, WM, Cunningham, KA, Hafner, LM, Timms, P & Beagley, KW 2013, 'Characterization of In Vitro Chlamydia muridarum Persistence and Utilization in an In Vivo Mouse Model of Chlamydia Vaccine', American Journal of Reproductive Immunology, vol. 69, no. 5, pp. 475-485.
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ProblemChlamydia trachomatis genital tract infections are easily treated with antibiotics; however, the majority of infections are asymptomatic and therefore untreated, highlighting the need for a vaccine. Because most infections are asymptomatic, vaccination could potentially be administered to individuals who may have an acute infection at that time. In such individuals, the effect of vaccination on the existing infection is unknown; however, one potential outcome could be the development of a persistent infection. In vitro chlamydial persistence has been well characterized in various strains; however, there have been no reported studies in C. muridarum.Method of StudyWe performed ultrastructural characterization and transcriptome analysis of selected genes. We then used the transcriptional profiles of the selected genes to examine whether intranasal immunization of mice during an active genital infection would induce persistence in the upper reproductive tract of female mice.Results and ConclusionsWe found that persistence developed in the oviducts of mice as a result of immunization. This is a significant finding, not only because it is the first time that C. muridarum persistence has been characterized in vitro, but also due to the fact that there is a minimal characterization of in vivo persistence of any chlamydial species. This highlights the importance of the timing of vaccination in individuals.

Carrillo, MC, Rowe, CC, Szoeke, C, Masters, CL, Ames, D, O'Meara, T, Macaulay, SL, Milner, A, Ellis, KA, Maruff, P, Rainey‐Smith, SR, Martins, RN, Bain, LJ & Head, RJ 2013, 'Research and standardization in Alzheimer's trials: Reaching international consensus', Alzheimer's & Dementia, vol. 9, no. 2, pp. 160-168.
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Alzheimer's disease (AD) is an epidemic facing the entire world. Increased knowledge gained during the past 25 years indicates that AD falls along a clinical and neuropathological spectrum represented as a continuum that extends from preclinical disease in which there are no symptoms, through early symptomatic phases, and finally to AD dementia. The Alzheimer's research community recognizes that imaging, body fluids, and cognitive biomarkers contribute to enhanced diagnostic confidence for AD. There has also been emerging consensus regarding the use of AD biomarkers in clinical trials. The use of biomarkers in clinical trials and practice is hampered by the lack of standardization. In response to the emerging need for standardization, an international meeting of AD researchers was held in Melbourne, Australia, in March 2012 to bring together key researchers, clinicians, industry, and regulatory stakeholders with the aim of generating consensus on standardization and validation of cognitive, imaging, and fluid biomarkers, as well as lifestyle parameters used in research centers worldwide.

Carroll, RJ, Delaigle, A & Hall, P 2013, 'Unexpected properties of bandwidth choice when smoothing discrete data for constructing a functional data classifier', Annals of Statistics, vol. 41, no. 6, pp. 2739-2767.
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The data functions that are studied in the course of functional data analysisare assembled from discrete data, and the level of smoothing that is used isgenerally that which is appropriate for accurate approximation of theconceptually smooth functions that were not actually observed. Existingliterature shows that this approach is effective, and even optimal, when usingfunctional data methods for prediction or hypothesis testing. However, in thepresent paper we show that this approach is not effective in classificationproblems. There a useful rule of thumb is that undersmoothing is oftendesirable, but there are several surprising qualifications to that approach.First, the effect of smoothing the training data can be more significant thanthat of smoothing the new data set to be classified; second, undersmoothing isnot always the right approach, and in fact in some cases using a relativelylarge bandwidth can be more effective; and third, these perverse results arethe consequence of very unusual properties of error rates, expressed asfunctions of smoothing parameters. For example, the orders of magnitude ofoptimal smoothing parameter choices depend on the signs and sizes of terms inan expansion of error rate, and those signs and sizes can vary dramaticallyfrom one setting to another, even for the same classifier.

Castorina, A, D’Amico, AG, Scuderi, S, Leggio, GM, Drago, F & D’Agata, V 2013, 'Dopamine D3 receptor deletion increases tissue plasminogen activator (tPA) activity in prefrontal cortex and hippocampus', Neuroscience, vol. 250, pp. 546-556.
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Ceh, J, Kilburn, MR, Cliff, JB, Raina, J, van Keulen, M & Bourne, DG 2013, 'Nutrient cycling in early coral life stages: Pocillopora damicornis larvae provide their algal symbiont (Symbiodinium) with nitrogen acquired from bacterial associates', Ecology and Evolution, vol. 3, no. 8, pp. 2393-2400.
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AbstractThe waters surrounding coral reef ecosystems are generally poor in nutrients, yet their levels of primary production are comparable with those reported from tropical rain forests. One explanation of this paradox is the efficient cycling of nutrients between the coral host, its endosymbiotic alga Symbiodinium and a wide array of microorganisms. Despite their importance for the animals' fitness, the cycling of nutrients in early coral life stages and the initial establishment of partnerships with the microbes involved in these processes has received little scrutiny to date. Nitrogen is an essential but limited nutrient in coral reef ecosystems. In order to assess the early nutrient exchange between bacteria and corals, coral larvae of the species Pocillopora damicornis were incubated with two coral‐associated bacteria (Alteromonas sp., or Vibrio alginolyticus), prelabeled with the stable nitrogen isotope 15N. The incorporation and translocation of nitrogen from Vibrio‐ and Alteromonas bacteria into P. damicornis coral larvae and specifically into the coral‐symbiotic Symbiodinium were detected by nanoscale secondary ion mass spectrometry (NanoSIMS). A significant increase in the amount of enriched 15N (two to threefold compared to natural abundance) was observed in P. damicornis larvae within 8 h of incubation for both bacterial treatments (one‐way ANOVA, F5,53 = 18.03, P = 0.004 for Alteromonas sp. and

Cervenka, J, Lau, DWM, Dontschuk, N, Shimoni, O, Silvestri, L, Ladouceur, F, Duvall, SG & Prawer, S 2013, 'Nucleation and Chemical Vapor Deposition Growth of Polycrystalline Diamond on Aluminum Nitride: Role of Surface Termination and Polarity', Crystal Growth & Design, vol. 13, no. 8, pp. 3490-3497.
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We have investigated the growth and atomic interface structures of diamond on aluminum nitride (AlN). The two-step chemical vapor deposition technique is used to control diamond nucleation density, crystal size, and AlN surface orientation and polarity. Highly uniform diamond layers with a nucleation density in the range of 105-1011 cm-2 and a grain size of 0.1-5 μm are fabricated. Crystallographically abrupt interfaces between polycrystalline diamond and single-crystal AlN(0001) layers have been observed via high-resolution transmission electron microscopy and electron energy-loss spectroscopy. A majority of the diamond crystals have been found to have the diamond(111)/AlN(0001) interface relationship. Atomistic models of the bonding mechanism at the heterointerface are used to elucidate experimental observations and the role of hydrogen plasma on the growth of diamond on AlN. Nonpolar and semipolar AlN surfaces have been found to have higher resistance to process plasma and led to better crystallinity of the diamond/AlN heterointerfaces. These results underline the potential of nonpolar and semipolar AlN surfaces for the growth of high-crystal quality diamond/AlN heterointerfaces. © 2013 American Chemical Society.

Červený, J, Sinetova, MA, Valledor, L, Sherman, LA & Nedbal, L 2013, 'Ultradian metabolic rhythm in the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142', Proceedings of the National Academy of Sciences, vol. 110, no. 32, pp. 13210-13215.
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The unicellular cyanobacterium Cyanothece sp. American Type Culture Collection (ATCC) 51142 is capable of performing oxygenic photosynthesis during the day and microoxic nitrogen fixation at night. These mutually exclusive processes are possible only by temporal separation by circadian clock or another cellular program. We report identification of a temperature-dependent ultradian metabolic rhythm that controls the alternating oxygenic and microoxic processes of Cyanothece sp. ATCC 51142 under continuous high irradiance and in high CO 2 concentration. During the oxygenic photosynthesis phase, nitrate deficiency limited protein synthesis and CO 2 assimilation was directed toward glycogen synthesis. The carbohydrate accumulation reduced overexcitation of the photosynthetic reactions until a respiration burst initiated a transition to microoxic N 2 fixation. In contrast to the circadian clock, this ultradian period is strongly temperature-dependent: 17 h at 27 °C, which continuously decreased to 10 h at 39 °C. The cycle was expressed by an oscillatory modulation of net O 2 evolution, CO 2 uptake, pH, fluorescence emission, glycogen content, cell division, and culture optical density. The corresponding ultradian modulation was also observed in the transcription of nitrogenase-related nifB and nifH genes and in nitrogenase activities. We propose that the control by the newly identified metabolic cycle adds another rhythmic component to the circadian clock that reflects the true metabolic state depending on the actual...

Çetin, U, Novikov, A & Shiryaev, AN 2013, 'Bayesian Sequential Estimation of a Drift of Fractional Brownian Motion', Sequential Analysis, vol. 32, no. 3, pp. 288-296.
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We solve explicitly a Bayesian sequential estimation problem for the drift parameter μ of a fractional Brownian motion under the assumptions that a prior density of μ is Gaussian and that a penalty function is quadratic or Dirac-delta. The optimal stopping time for this case is deterministic. © 2013 Copyright Taylor and Francis Group, LLC.

Chan, CW, Deadman, BJ, Manley-Harris, M, Wilkins, AL, Alber, DG & Harry, E 2013, 'Analysis of the flavonoid component of bioactive New Zealand mānuka (Leptospermum scoparium) honey and the isolation, characterisation and synthesis of an unusual pyrrole', Food Chemistry, vol. 141, no. 3, pp. 1772-1781.
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The flavonoid components of New Zealand mānuka (Leptospermum scoparium) honey have been quantified in a series of 31 honeys of varying non-peroxide antibacterial activity to clarify discrepancies between previous studies reported in the literature. Total flavonoid content was 1.16 mg/100 g honey. The principal flavonoids present were pinobanksin, pinocembrin, luteolin and chrysin and together these represented 61% of the total flavonoid content. 1, 2-formyl-5-(2-methoxyphenyl)-pyrrole, which was weakly correlated with the non-peroxide antibacterial activity, was isolated from the flavonoid fraction and separately synthesised. 1 did not display inhibitory activity against Staphylococcus aureus in vitro and thus the origin of the correlation, which is still unknown, is not a direct contribution. © 2013 Elsevier Ltd.

Chan, CY-Y, Kendig, M, Boakes, RA & Rooney, K 2013, 'Low-volume exercise can prevent sucrose-induced weight gain but has limited impact on metabolic measures in rats', European Journal of Nutrition, vol. 52, no. 7, pp. 1721-1732.
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Chavez-Dozal, A, Gorman, C, Erken, M, Steinberg, PD, McDougald, D & Nishiguchi, MK 2013, 'Predation Response of Vibrio fischeri Biofilms to Bacterivorus Protists', Applied and Environmental Microbiology, vol. 79, no. 2, pp. 553-558.
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ABSTRACT Vibrio fischeri proliferates in a sessile, stable community known as a biofilm, which is one alternative survival strategy of its life cycle. Although this survival strategy provides adequate protection from abiotic factors, marine biofilms are still susceptible to grazing by bacteria-consuming protozoa. Subsequently, grazing pressure can be controlled by certain defense mechanisms that confer higher biofilm antipredator fitness. In the present work, we hypothesized that V. fischeri exhibits an antipredator fitness behavior while forming biofilms. Different predators representing commonly found species in aquatic populations were examined, including the flagellates Rhynchomonas nasuta and Neobodo designis (early biofilm feeders) and the ciliate Tetrahymena pyriformis (late biofilm grazer). V. fischeri biofilms included isolates from both seawater and squid hosts ( Euprymna and Sepiola species). Our results demonstrate inhibition of predation by biofilms, specifically, isolates from seawater. Additionally, antiprotozoan behavior was observed to be higher in late biofilms, particularly toward the ciliate T...

Chejara, DR, Kondaveeti, S, Prasad, K & Siddhanta, AK 2013, 'Studies on the structure–property relationship of sodium alginate based thixotropic hydrogels', RSC Advances, vol. 3, no. 36, pp. 15744-15744.
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Chen, C, Greene, AM, Robertson, AW, Baethgen, WE & Eamus, D 2013, 'Scenario development for estimating potential climate change impacts on crop production in the North China Plain', INTERNATIONAL JOURNAL OF CLIMATOLOGY, vol. 33, no. 15, pp. 3124-3140.
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It is important to investigate potential changes in temperature, precipitation and solar radiation for assessing the impacts of future climate change on agricultural production for specific regions. In this study, climate scenarios of precipitation, temperature and solar radiation for the North China Plain (NCP) were constructed in terms of stochastic daily weather sequences. A nonhomogeneous hidden Markov model (NHMM) was used to downscale daily precipitation projections at 32 stations during winter wheat and summer maize growing seasons for a baseline (19662005) and a 21st century (20802099) A1B scenario, using selected general circulation models (GCMs). A climatological seasonal cycle of regional-averaged daily reanalysis precipitation was used as input to the down-scaling for the baseline simulation; this input was then scaled by the precipitation changes from GCM projections to generate down-scaled stochastic simulations of precipitation in the 21st century. Temperature was generated using a weakly stationary generating process, conditional on precipitation occurrence, with 21st century additive changes taken from the GCMs at the regional scale. Three hypotheses about changes in solar radiation (-20%, 0% and 20%) were made considering the large uncertainty in its future change. The down-scaled simulations exhibit station increases in the mean daily rainfall of 13.969.7% in the scenarios driven by the GCM with the projected largest and multi-model mean precipitation increase for the wheat season, with changes of 0.429.9% for the maize season. In the scenario driven by the GCM with the largest projected precipitation decrease, the simulated rainfall decreases at all stations, with changes ranging from -24.6 to -0.1% for the wheat and maize seasons, respectively. Temperature increases by about 3.7?°C for the wheat season and 3.6?°C for the maize season.

Chen, H, Dorrigan, A, Saad, S, Hare, DJ, Cortie, MB & Valenzuela, SM 2013, 'In Vivo Study of Spherical Gold Nanoparticles: Inflammatory Effects and Distribution in Mice', PLOS ONE, vol. 8, no. 2, pp. 1-8.
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Objectives: Gold nanoparticles (AuNPs) of 21 nm have been previously well characterized in vitro for their capacity to target macrophages via active uptake. However, the short-term impact of such AuNPs on physiological systems, in particular resident macrophages located in fat tissue in vivo, is largely unknown. This project investigated the distribution, organ toxicity and changes in inflammatory cytokines within the adipose tissue after mice were exposed to AuNPs. Methods: Male C57BL/6 mice were injected intraperitoneally (IP) with a single dose of AuNPs (7.85 μg AuNPs/g). Body weight and energy intake were recorded daily. Tissues were collected at 1 h, 24 h and 72 h post-injection to test for organ toxicity. AuNP distribution was examined using electron microscopy. Proinflammatory cytokine expression and macrophage number within the abdominal fat pad were determined using real-time PCR. Results: At 72 hours post AuNP injection, daily energy intake and body weight were found to be similar between Control and AuNP treated mice. However, fat mass was significantly smaller in AuNP-treated mice. Following IP injection, AuNPs rapidly accumulated within the abdominal fat tissue and some were seen in the liver. A reduction in TNFα and IL-6 mRNA levels in the fat were observed from 1 h to 72 h post AuNP injection, with no observable changes in macrophage number. There was no detectable toxicity to vital organs (liver and kidney). Conclusion: Our 21 nm spherical AuNPs caused no measurable organ or cell toxicity in mice, but were correlated with significant fat loss and inhibition of inflammatory effects. With the growing incidence of obesity and obesity-related diseases, our findings offer a new avenue for the potential development of gold nanoparticles as a therapeutic agent in the treatment of such disorders. © 2013 Chen et al.

Chen, L, Ge, Q, Black, JL, Deng, L, Burgess, JK & Oliver, BGG 2013, 'Differential Regulation of Extracellular Matrix and Soluble Fibulin-1 Levels by TGF-β1 in Airway Smooth Muscle Cells', PLoS ONE, vol. 8, no. 6, pp. e65544-e65544.
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Fibulin-1 (FBLN-1) is a secreted glycoprotein that is associated with extracellular matrix (ECM) formation and rebuilding. Abnormal and exaggerated deposition of ECM proteins is a hallmark of many fibrotic diseases, such as chronic obstructive pulmonary disease (COPD) where small airway fibrosis occurs. The aim of this study was to investigate the regulation of FBLN-1 by transforming growth factor beta 1 (TGF-β1) (a pro-fibrotic stimulus) in primary human airway smooth muscle (ASM) cells from volunteers with and without COPD. Human ASM cells were seeded at a density of 1×104 cells/cm2, and stimulated with or without TGF-β1 (10 ng/ml) for 72 hours before FBLN-1 deposition and soluble FBLN-1 were measured. Fold change in FBLN-1 mRNA was measured at 4, 8, 24, 48, 72 hours. In some experiments, cycloheximide (0.5 μg/ml) was used to assess the regulation of FBLN-1 production. TGF-β1 decreased the amount of soluble FBLN-1 both from COPD and non-COPD ASM cells. In contrast, the deposition of FBLN-1 into the ECM was increased in ASM cells obtained from both groups. TGF-β1 did not increase FBLN-1 gene expression at any of the time points. There were no differences in the TGF-β1 induced FBLN-1 levels between cells from people with or without COPD. Cycloheximide treatment, which inhibits protein synthesis, decreased both the constitutive release of soluble FBLN-1, and TGF-β1 induced ECM FBLN-1 deposition. Furthermore, in cycloheximide treated cells addition of soluble FBLN-1 resulted in incorporation of FBLN-1 into the ECM. Therefore the increased deposition of FBLN-1 by ASM cells into the ECM following treatment with TGF-β1 is likely due to incorporation of soluble FBLN-1 rather than de-novo synthesis. © 2013 Chen et al.

Chen, Q, Li, K, Wen, S, Liu, H, Peng, C, Cai, H, Shen, M, Zhang, G & Shi, X 2013, 'Targeted CT/MR dual mode imaging of tumors using multifunctional dendrimer-entrapped gold nanoparticles', Biomaterials, vol. 34, no. 21, pp. 5200-5209.
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Chen, S, Bao, P, Xiao, L & Wang, G 2013, 'Large-scale and low cost synthesis of graphene as high capacity anode materials for lithium-ion batteries', CARBON, vol. 64, no. 1, pp. 158-169.
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Graphene has emerged as an intriguing and attractive functional material for a wide range of applications, owing to its unique physical, chemical and mechanical properties. Herein, we report large-scale production of high quality single crystalline graphene sheets based on the ambient pressure chemical vapor deposition (APCVD) method using acetylene (C2H2) as the carbon source and coral-like iron with body-centered-cubic structure as the catalyst. The process can be scaled up for large quantity production at a low cost. The optimum APCVD temperature has been identified to be 850 C, which is much lower than that catalyzed by other metals. Transmission electron microscopy (TEM), atomic force microscopy, Raman spectroscopy and X-ray photoemission spectroscopy characterizations show the single crystalline and high quality nature of the as-prepared graphene produced by the bottom-up APCVD approach. A new horizontal 'dissolution-deposition-growth' mechanism is proposed and verified by high resolution TEM. When applied as anode materials in lithium ion batteries, graphene sheets exhibited a high lithium storage capacity and an excellent cyclability. The capability of preparing crystalline graphene on a large scale with low cost opens an avenue for technological applications of graphene in many fields. © 2013 Elsevier Ltd. All rights reserved.

Chen, SK, Tan, KY, Halim, AS, Xu, X, De Silva, KSB, Yeoh, WK, Dou, SX, Kursumovic, A & MacManus-Driscoll, JL 2013, 'Reaction method control of impurity scattering in C-doped MgB2: proving the role of defects besides C substitution level', SUPERCONDUCTOR SCIENCE & TECHNOLOGY, vol. 26, no. 12.
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Chen, X, Suwarno, SR, Chong, TH, McDougald, D, Kjelleberg, S, Cohen, Y, Fane, AG & Rice, SA 2013, 'Dynamics of biofilm formation under different nutrient levels and the effect on biofouling of a reverse osmosis membrane system', Biofouling, vol. 29, no. 3, pp. 319-330.
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Pseudomonas aeruginosa PAO1 wild type and a mucoid derivative (FRD1) which over produces alginate were used to foul reverse osmosis (RO) membranes. When operated at a constant flux, biofilm formation on the RO membrane resulted in a slow rise in transmembrane pressure (TMP) of 22% for the initial four days of operation, followed by a sharp increase of 159% over the following two days. The initial slow increase in TMP was probably due to the formation of a biofilm on the membrane surface, which then accelerated the rate of biofouling through the effect of concentration polarization. At later stages of operation, most of the bacterial biomass consisted of dead cells. The amount of extracellular polymeric substances appeared to correlate positively with the number of dead cells. The results indicate that prolonging the initial stage of slow TMP increase and avoiding the latter stage of accelerated TMP increase would provide a sustainable operation of the RO system. These results suggest that nutrient limitation could reduce biofilm accumulation and delay the increase in TMP. © 2013 Copyright Taylor and Francis Group, LLC.

Chen, Y, Liu, L, Wang, M, Wang, C, Hu, X & Wang, G 2013, 'Self-made non-enzymatic silver electrode from recordable CDs for fast detection of glucose in blood', Sensors and Actuators B: Chemical, vol. 177, pp. 555-561.
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An electrochemical sensor based on a self-made electrode from recordable CDs was developed for the non-enzymatic detection of glucose by chronoamperometry. We discussed the amperometric current response of glucose with the change of potential, pH and electrode area, and determined the optimum detection conditions. The current response measurements were performed in a phosphate buffered solution (pH 6.5) with a potential of -0.50 V, and presented a linearity over the range of 0.5-13 mmol/L (r = 0.996). The experimental results of the designed sensor demonstrate that this method has merits such as simple operation, low cost and rapid responses. The results of detecting glucose in blood samples were satisfactory. © 2012 Elsevier B.V.

Chen, Y-H, Chatterjee, N & Carroll, RJ 2013, 'Using shared genetic controls in studies of gene-environment interactions', Biometrika, vol. 100, no. 2, pp. 319-338.
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With the advent of modern genomic methods to adjust for population stratification, the use of external or publicly available controls has become an attractive option for reducing the cost of large-scale case-control genetic association studies. In this article, we study the estimation of joint effects of genetic and environmental exposures from a case-control study where data on genome-wide markers are available on the cases and a set of external controls while data on environmental exposures are available on the cases and a set of internal controls. We show that under such a design, one can exploit an assumption of gene-environment independence in the underlying population to estimate the gene-environment joint effects, after adjustment for population stratification. We develop a semiparametric profile likelihood method and related pseudolikelihood and working likelihood methods that are easy to implement in practice. We propose variance estimators for the methods based on asymptotic theory. Simulation is used to study the performance of the methods, and data from a multi-centre genome-wide association study of bladder cancer is further used to illustrate their application.

Choi, AH, Ben-Nissan, B, Matinlinna, JP & Conway, RC 2013, 'Current Perspectives: Calcium Phosphate Nanocoatings and Nanocomposite Coatings in Dentistry', JOURNAL OF DENTAL RESEARCH, vol. 92, no. 10, pp. 853-859.
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The purpose of coatings on implants is to achieve some or all of the improvements in biocompatibility, bioactivity, and increased protection from the release of harmful or unnecessary metal ions. During the last decade, there has been substantially incre

Choi, AH, Matinlinna, J & Ben-Nissan, B 2013, 'Effects of micromovement on the changes in stress distribution of partially stabilized zirconia (PS-ZrO₂) dental implants and bridge during clenching: A three-dimensional finite element analysis', Acta Odontologica Scandinavica, vol. 71, no. 1, pp. 72-81.
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Objective. This investigation aims to evaluate the changes in stress magnitudes and distributions on Partially Stabilized Zirconia (PS-ZrO2) dental implants and bridges and on the mandible caused by fibrous encapsulations during clenching. Materials and methods. Four 3.26 mm diameter PS-ZrO2 dental implants with lengths of 12 mm were modelled and placed in the second premolar and first molar region on both sides of the mandible model. A rigid zirconia bridge with a thickness of 0.5 mm connects the PS-ZrO2 dental implants placed in the second premolar and first molar. Four periodontal ligament (PDL) case studies were examined: PDL in the second premolars; PDL in the first molars; PDL in both the second premolars and first molars; and no PDL present. Results. The results reveal the magnitudes and distributions of stresses on the dental implants and connecting bridges were governed by the PDLs. A significant drop in stress levels were recorded when the PDL encapsulates the roots of the dental implants. Of the four PDL case studies, it was found that when the PDLs are present in both the second premolars and first molars the lowest stress magnitudes are generated. The analysis also revealed that, during the healing process after implant insertion and the result of fibrous encapsulation, the dental implant system will experience a varying amount of stress levels. Conclusion. This study was intended to produce more insight into the influence of the PDL on the changes in stress distribution on the dental implant system during clenching.

Choi, S, Ton-That, C, Phillips, MR & Aharonovich, I 2013, 'Observation of whispering gallery modes from hexagonal ZnO microdisks using cathodoluminescence spectroscopy', APPLIED PHYSICS LETTERS, vol. 103, no. 17.
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Zinc oxide hexagonal microdisks with diameters ranging from 3 μm up to 15 μm were fabricated by thermal chemical vapour deposition. Optical characterisation of ZnO microdisks was performed using low temperature (80 K) cathodoluminescence (CL) imaging and spectroscopy. The microdisks exhibited green luminescence locally distributed near the hexagonal boundary of the ZnO microdisks. High resolution CL spectra of the ZnO microdisks revealed whispering gallery modes (WGMs) emission. The experimentally observed WGMs were in excellent agreement with the predicted theoretical positions calculated using a plane wave model. This work could provide the means for ZnO microdisk devices operating in the green spectral range. © 2013 AIP Publishing LLC.

Chou, J, Green, DW, Singh, K, Hao, J, Ben-Nissan, B & Milthorpe, B 2013, 'Adipose Stem Cell Coating of Biomimetic β-TCP Macrospheres by Use of Laboratory Centrifuge', BioResearch Open Access, vol. 2, no. 1, pp. 67-71.
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Biomimetic materials such as coral exoskeletons possess unique architectural structures with a uniform and interconnected porous network that can be beneficial as a scaffold material. In addition, these marine structures can be hydrothermally converted to calcium phosphates, while retaining the original structural properties. The ability of biomaterials to stimulate the local microenvironment is one of the main focuses in tissue engineering, and directly coating the scaffold with stem cells facilitates future potential applications in therapeutics and regenerative medicine. In this article we describe a new and simple method that uses a laboratory centrifuge to coat hydrothermally derived beta-tricalcium phosphate macrospheres from coral exoskeleton with stem cells. In this research the optimal seeding duration and speed were determined to be 1 min and 700 g. Scanning electron micrographs showed complete surface coverage by stem cells within 7 days of seeding. This study constitutes an important step toward achieving functional tissue-engineered implants by increasing our understanding of the influence of dynamic parameters on the efficiency and distribution of stem cell attachment to biomimetic materials and how stem cells interact with biomimetic materials. © Copyright 2013, Mary Ann Liebert, Inc. 2013.

Chou, J, Hao, J, Ben-Nissan, B, Milthorpe, B & Otsuka, M 2013, 'Coral Exoskeletons as a Precursor Material for the Development of a Calcium Phosphate Drug Delivery System for Bone Tissue Engineering', Biological and Pharmaceutical Bulletin, vol. 36, no. 11, pp. 1662-1665.
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With the global rise in aging of populations, the occurrence of osteoporosis will continue to increase. Biomaterial and pharmaceutical scientists continue to develop innovative strategies and materials to address this disease. In this article, we describe a new perspective and approach into the use of coral exoskeletons as a precursor material to synthesize a calcium phosphate-based drug delivery system. Studies detailing the methodology of the conversion methods and the strategies and approach for the development of these novel drug delivery systems are described. Furthermore, in vivo studies in osteoporotic mice using a drug loaded and chemically modified version of the biomimetic delivery system showed significant cortical and cancellous bone increases. These studies support the notion and the rationale for future research and development of the use of coral exoskeletons as materials for drug delivery applications. © 2013 The Pharmaceutical Society of Japan.

Chou, J, Hao, J, Hatoyama, H, Ben-Nissan, B, Milthorpe, B & Otsuka, M 2013, 'The Therapeutic Effect on Bone Mineral Formation from Biomimetic Zinc Containing Tricalcium Phosphate (ZnTCP) in Zinc-Deficient Osteoporotic Mice', PLoS ONE, vol. 8, no. 8, pp. e71821-e71821.
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The aim of this study was to evaluate the therapeutic efficacy of biomimetic zinc-containing tricalcium phosphate (ZnTCP) produced by hydrothermally converting calcium carbonate exoskeletons from foraminifera, in the treatment of osteoporotic mice. X-Ray powder diffraction showed crystallographic structures matching JCPDS profile for tricalcium phosphate. Mass spectroscopy used to calculate total composition amount showed similar amount of calcium (5×104 μg/g) and phosphate (4×104ppm) after conversion and the presence of zinc (5.18×103 μg/g). In vitro zinc release showed no release in PBS buffer and <1% zinc release in 7 days. In vivo evaluation was done in ovariectomized mice by implanting the ZnTCP samples in the soft tissues near the right femur bone for four weeks. Thirty ddY mice (5 weeks old, average weight of 21 g) were divided into six experimental groups (normal, sham, OVX, β-TCP, ZnTCP and direct injection of zinc). CT images were taken every two weeks where the bone mineral density (BMD) and bone mineral content (BMC) were calculated by software based on CT images. The ZnTCP group exhibits cortical and cancellous bone growth of 45% and 20% respectively. While sham, OVX and β-TCP suffered from bone loss. A correlation was made between the significant body weight increase in ZnTCP with the significant increase in plasma zinc level compared with OVX. The presented results indicate that biomimetic ZnTCP were effective in preventing and treating bone loss in osteoporotic mice model. © 2013 Chou et al.

Chou, J, Hao, J, Kuroda, S, Bishop, D, Ben-Nissan, B, Milthorpe, B & Otsuka, M 2013, 'Bone Regeneration of Rat Tibial Defect by Zinc-Tricalcium Phosphate (Zn-TCP) Synthesized from Porous Foraminifera Carbonate Macrospheres', Marine Drugs, vol. 11, no. 12, pp. 5148-5158.
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Foraminifera carbonate exoskeleton was hydrothermally converted to biocompatible and biodegradable zinc-tricalcium phosphate (Zn-TCP) as an alternative biomimetic material for bone fracture repair. Zn-TCP samples implanted in a rat tibial defect model for eight weeks were compared with unfilled defect and beta-tricalcium phosphate showing accelerated bone regeneration compared with the control groups, with statistically significant bone mineral density and bone mineral content growth. CT images of the defect showed restoration of cancellous bone in Zn-TCP and only minimal growth in control group. Histological slices reveal bone in-growth within the pores and porous chamber of the material detailing good bone-material integration with the presence of blood vessels. These results exhibit the future potential of biomimetic Zn-TCP as bone grafts for bone fracture repair. © 2013 by the authors; licensee MDPI.

Chou, J, Ito, T, Bishop, D, Otsuka, M, Ben-Nissan, B & Milthorpe, B 2013, 'Controlled Release of Simvastatin from Biomimetic β-TCP Drug Delivery System', PLoS ONE, vol. 8, no. 1, pp. e54676-e54676.
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Simvastatin have been shown to induce bone formation and there is currently a urgent need to develop an appropriate delivery system to sustain the release of the drug to increase therapeutic efficacy whilst reducing side effects. In this study, a novel drug delivery system for simvastatin by means of hydrothermally converting marine exoskeletons to biocompatible beta-tricalcium phosphate was investigated. Furthermore, the release of simvastatin was controlled by the addition of an outer apatite coating layer. The samples were characterized by x-ray diffraction analysis, fourier transform infrared spectroscopy, scanning electron microscopy and mass spectroscopy confirming the conversion process. The in-vitro dissolution of key chemical compositional elements and the release of simvastatin were measured in simulated body fluid solution showing controlled release with reduction of approximately 25% compared with un-coated samples. This study shows the potential applications of marine structures as a drug delivery system for simvastatin. © 2013 Chou et al.

Chou, J, Ito, T, Otsuka, M, Ben-Nissan, B & Milthorpe, B 2013, 'Simvastatin-Loaded beta-TCP Drug Delivery System Induces Bone Formation and Prevents Rhabdomyolysis in OVX Mice', ADVANCED HEALTHCARE MATERIALS, vol. 2, no. 5, pp. 678-681.
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Bone formation and regeneration is a prolonged process that requires a slow drug release system to assist in the long-term recovery. A drug-delivery system is developed that allows for the controlled release of simvastin, without exhibiting the side effects associated with high concentrations of simvastatin, and is still capable of inducing constant bone formation.

Chou, J, Ito, T, Otsuka, M, Ben-Nissan, B & Milthorpe, B 2013, 'The Controlled Release of Simvastatin from Biomimetic Macrospheres', BIOCERAMICS 24, vol. 529-530, no. 1, pp. 461-464.
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Simvastatin has been shown to succesfully stimulate bone regeneration and attention has being focussed on developing appropriate delivery carriers for its release. The challenge of deliverying therapeutic concentration of pharmaceutical compunds has being the centre of focus in drug delivery developments. This study examines the in-vivo effects of simvastatin released from β-TCP macrospheres derived from coral exoxskeletons. The results indicates that the controlled release of simvastatin can promote bone formation comparable with direct injection. Furthermore the results showed that the release of simvastatin delivery rates can be controlled by additional coating of an apatite coating. Analysis by CT scans, SEM, amount of new bone formed and mechanical strength tests, showed that by controlling the release of simvastatin bone formation can be stimulated to a therapeutic level. © (2013) Trans Tech Publications, Switzerland.

Chua, SL, Tan, SY-Y, Rybtke, MT, Chen, Y, Rice, SA, Kjelleberg, S, Tolker-Nielsen, T, Yang, L & Givskov, M 2013, 'Bis-(3′-5′)-Cyclic Dimeric GMP Regulates Antimicrobial Peptide Resistance in Pseudomonas aeruginosa', Antimicrobial Agents and Chemotherapy, vol. 57, no. 5, pp. 2066-2075.
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ABSTRACT Bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is an intracellular second messenger that controls the lifestyles of many bacteria. A high intracellular level of c-di-GMP induces a biofilm lifestyle, whereas a low intracellular level of c-di-GMP stimulates dispersal of biofilms and promotes a planktonic lifestyle. Here, we used the expression of different reporters to show that planktonic cells, biofilm cells, and cells dispersed from biofilms (DCells) had distinct intracellular c-di-GMP levels. Proteomics analysis showed that the low intracellular c-di-GMP level of DCells induced the expression of proteins required for the virulence and development of antimicrobial peptide resistance in Pseudomonas aeruginosa . In accordance with this, P. aeruginosa cells with low c-di-GMP levels were found to be more resistant to colistin than P. aeruginosa cells with high c-di-GMP levels. This finding contradicts the current dogma stating that dispersed cells are inevitably more susceptible to antibiotics than their sessile counterparts.

Clark, JS, Poore, AGB, Ralph, PJ & Doblin, MA 2013, 'POTENTIAL FOR ADAPTATION IN RESPONSE TO THERMAL STRESS IN AN INTERTIDAL MACROALGA', JOURNAL OF PHYCOLOGY, vol. 49, no. 4, pp. 630-639.
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Understanding responses of marine algae to changing ocean temperatures requires knowledge of the impacts of elevated temperatures and the likelihood of adaptation to thermal stress. The potential for rapid evolution of thermal tolerance is dependent on the levels of heritable genetic variation in response to thermal stress within a population. Here, we use a quantitative genetic breeding design to establish whether there is a heritable variation in thermal sensitivity in two populations of a habitat-forming intertidal macroalga, Hormosira banksii (Turner) Descaisne. Gametes from multiple parents were mixed and growth and photosynthetic performance were measured in the resulting embryos, which were incubated under control and elevated temperature (20°C and 28°C). Embryo growth was reduced at 28°C, but significant interactions between male genotype and temperature in one population indicated the presence of genetic variation in thermal sensitivity. Selection for more tolerant genotypes thus has the ability to result in the evolution of increased thermal tolerance. Furthermore, genetic correlations between embryos grown in the two temperatures were positive, indicating that those genotypes that performed well in elevated temperature also performed well in control temperature. Chlorophyll a fluorescence measurements showed a marked decrease in maximum quantum yield of photosystem II (PSII) under elevated temperature. There was an increase in the proportion of energy directed to photoinhibition (nonregulated nonphotochemical quenching) and a concomitant decrease in energy used to drive photochemistry and xanthophyll cycling (regulated nonphotochemical quenching). However, PSII performance between genotypes was similar, suggesting that thermal sensitivity is related to processes other than photosynthesis. © 2013 Phycological Society of America.

Cleverly, J, Boulain, N, Villalobos-Vega, R, Grant, N, Faux, R, Wood, C, Cook, PG, Yu, Q, Leigh, A & Eamus, D 2013, 'Dynamics of component carbon fluxes in a semi-arid Acacia woodland, central Australia', JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, vol. 118, no. 3, pp. 1168-1185.
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Vast areas in the interior of Australia are exposed to regular but infrequent periods of heavy rainfall, interspersed with long periods at high temperatures, but little is known of the carbon budget of these remote areas or how they respond to extreme precipitation. In this study, we applied three methods to partition net ecosystem photosynthesis into gross primary production (GPP) and ecosystem respiration (Re) during two years of contrasting rainfall. The first year was wet (>250 mm above average rainfall), while little precipitation fell during the second year (>100 mm below average). During the first year of study, rates of GPP were large (793 g C m^-2 yr^-1) in this semi-arid Mulga (Acacia aneura) and grass savanna due to complementary photosynthetic responses by the canopy and C4 understorey to cycles of heavy rainfall. Patterns in GPP during the summer and autumn matched those in leaf area index (LAI), photosynthetic activity, and autotrophic respiration. During the dry year, small but positive photosynthetic uptake by Mulga contributed to the neutral carbon budget (GPP / Re = 1.06 ± 0.03). Small rates of photosynthesis by evergreen Mulga when dry were supported by storage of soil moisture above a relatively shallow hardpan. Little soil organic matter (1.1%) was available to support heterotrophic respiration (Rh) without input of fresh substrate. The two largest sources of Re in this study were autotrophic respiration by the seasonal understorey and Rh through decomposition of fresh organic matter supplied by the senescent understorey. © 2013. American Geophysical Union. All Rights Reserved.

Clifton, LA, Skoda, MWA, Daulton, EL, Hughes, AV, Le Brun, AP, Lakey, JH & Holt, SA 2013, 'Asymmetric phospholipid: lipopolysaccharide bilayers; a Gram-negative bacterial outer membrane mimic', Journal of The Royal Society Interface, vol. 10, no. 89, pp. 20130810-20130810.
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The Gram-negative bacterial outer membrane (OM) is a complex and highly asymmetric biological barrier but the small size of bacteria has hindered advances in in vivo examination of membrane dynamics. Thus, model OMs, amenable to physical study, are important sources of data. Here, we present data from asymmetric bilayers which emulate the OM and are formed by a simple two-step approach. The bilayers were deposited on an SiO 2 surface by Langmuir–Blodgett deposition of phosphatidylcholine as the inner leaflet and, via Langmuir–Schaefer deposition, an outer leaflet of either Lipid A or Escherichia coli rough lipopolysaccharides (LPS). The membranes were examined using neutron reflectometry (NR) to examine the coverage and mixing of lipids between the bilayer leaflets. NR data showed that in all cases, the initial deposition asymmetry was mostly maintained for more than 16 h. This stability enabled the sizes of the headgroups and bilayer roughness of 1,2-dipalmitoyl- sn -glycero-3-phosphocholine and Lipid A, Rc-LPS and Ra-LPS to be clearly resolved. The results show that rough LPS can be manipulated like phospholipids and used to fabricate advanced asymmetric bacterial membrane models using well-known bilayer deposition techniques. Such models will enable OM dynamics and interactions to be studied under in vivo -like conditions.

Coenen, MJJ, den Boer, D, van den Bruele, FJ, Habets, T, Timmers, KAAM, van der Maas, M, Khoury, T, Panduwinata, D, Crossley, MJ, Reimers, JR, van Enckevort, WJP, Hendriksen, BLM, Elemans, JAAW & Speller, S 2013, 'Polymorphism in porphyrin monolayers: the relation between adsorption configuration and molecular conformation', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 15, no. 30, pp. 12451-12458.
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Self-assembled monolayers of meso-5,10,15,20-tetrakis(undecyl)porphyrin copper(ii) on a graphite/1-octanoic acid interface have been studied by Scanning Tunnelling Microscopy. Four distinct polymorphs were observed, varying in their unit cell size. Arrays of unit cells of the various polymorphs seamlessly connect to each other via shared unit cell vectors. The monolayers are not commensurate, but coincident with the underlying graphite substrate. The seamless transition between the polymorphs is proposed to be the result of an adaptation of the molecular conformations in the polymorphs and at the boundaries, which is enabled by the conformational freedom of the alkyl tails of these molecules. This journal is © the Owner Societies 2013.

Collison, A, Siegle, JS, Hansbro, NG, Kwok, C-T, Herbert, C, Mattes, J, Hitchins, M, Foster, PS & Kumar, RK 2013, 'Epigenetic changes associated with disease progression in a mouse model of childhood allergic asthma', Disease Models & Mechanisms, vol. 6, no. 4, pp. 993-1000.
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Summary Development of asthma in childhood is linked to viral infections of the lower respiratory tract in early life, with subsequent chronic exposure to allergens. Progression to persistent asthma is associated with a Th2-biased immunological response and structural remodelling of the airways. The underlying mechanisms are unclear, but could involve epigenetic changes. To investigate this, we employed a recently developed mouse model in which self-limited neonatal infection with a pneumovirus, followed by sensitisation to ovalbumin via the respiratory tract and low-level chronic challenge with aerosolised antigen, leads to development of an asthmatic phenotype. We assessed expression of microRNA by cells in the proximal airways, comparing changes over the period of disease progression, and used target prediction databases to identify genes likely to be up- or downregulated as a consequence of altered regulation of microRNA. In parallel, we assessed DNA methylation in pulmonary CD4+ T cells. We found that a limited number of microRNAs exhibited marked up- or downregulation following early-life infection and sensitisation, for many of which the levels of expression were further changed following chronic challenge with the sensitizing antigen. Targets of these microRNAs included genes involved in immune or inflammatory responses (e.g. Gata3, Kitl) and in tissue remodelling (e.g. Igf1, Tgfbr1), as well as genes for various transcription factors and signalling proteins. In pulmonary CD4+ T cells, there was significant demethylation at promoter sites for interleukin-4 and interferon-γ, the latter increasing following chronic challenge. We conclude that, in this model, progression to an asthmatic phenotype is linked to epigenetic regulation of genes associated with inflammation and structural remodelling, and with T-cell commitment to a Th2 immunological response. Epigenetic changes associated with this pattern...

Constable, EC & Gale, PA 2013, 'Celebrating the 100th Anniversary of the Nobel Prize in Chemistry awarded to Alfred Werner', Chemical Society Reviews, vol. 42, no. 4, pp. 1427-1427.
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Cooper, ER, McGrath, KCY & Heather, AK 2013, 'In Vitro Androgen Bioassays as a Detection Method for Designer Androgens', SENSORS, vol. 13, no. 2, pp. 2148-2163.
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Androgens are the class of sex steroids responsible for male sexual characteristics, including increased muscle mass and decreased fat mass. Illicit use of androgen doping can be an attractive option for those looking to enhance sporting performance and/or physical appearance. The use of in vitro bioassays to detect androgens, especially designer or proandrogens, is becoming increasingly important in combating androgen doping associated with nutritional supplements. The nutritional sports supplement market has grown rapidly throughout the past decade. Many of these supplements contain androgens, designer androgens or proandrogens. Many designer or proandrogens cannot be detected by the standard highly-sensitive screening methods such as gas chromatography-mass spectrometry because their chemical structure is unknown. However, in vitro androgen bioassays can detect designer and proandrogens as these assays are not reliant on knowing the chemical structure but instead are based on androgen receptor activation. For these reasons, it may be advantageous to use routine androgen bioassay screening of nutraceutical samples to help curb the increasing problem of androgen doping. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Cortie, MB, Coutts, MJ, Ton-That, C, Dowd, A, Keast, VJ & McDonagh, AM 2013, 'On the Coalescence of Nanoparticulate Gold Sinter Ink', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 117, no. 21, pp. 11377-11384.
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We examine the mechanism by which thiol-protected gold nanoparticle inks can sinter at surprisingly low temperatures. At room temperature the sample is comprised of randomly close-packed gold nanoparticles of about 2.3 nm diameter with a ligand shell of about 0.2 nm effective thickness. As the particles are heated through 80 C they begin to coarsen, reaching about 10 nm diameter at 180 C. Upon further heating, rapid sintering and grain growth occurs at a temperature that depends on environment and heating rate. Sintering in vacuum requires a higher temperature than in oxidizing environments. Mass spectrometry in the former case is consistent with volatile species such as C 4H9, C2SH, and C2H4 being displaced, whereas XPS shows that the exposed surface of the Au is rich in C and S. However, when sintering is performed in the presence of even trace O 2, it is the Au-S bond that is cleaved, and the sintering temperature is lowered by up to 50 C. In this case mass spectrometry shows the generation of alkane and thiol fragments, some S2 and H2S, and oxidized sulfur-containing species, whereas XPS shows that C and S on the Au surface is much reduced. © 2013 American Chemical Society.

Cortie, MB, Nafea, EH, Chen, H, Valenzuela, SM, Ting, SRS, Sonvico, F & Milthorpe, B 2013, 'Nanomedical research in Australia and New Zealand', NANOMEDICINE, vol. 8, no. 12, pp. 1999-2006.
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Although Australia and New Zealand have a combined population of less than 30 million, they have an active and interlinked community of nanomedical researchers. This report provides a synopsis and update on this network with a view to identifying the main topics of interest and their likely future trajectories. In addition, our report may also serve to alert others to opportunities for joint projects. Australian and New Zealand researchers are engaged in most of the possible nanomedical topics, but the majority of interest is focused on drug and nucleic acid delivery using nanoparticles or nanoporous constructs. There are, however, smaller programs directed at hyperthermal therapy and radiotherapy, various kinds of diagnostic tests and regenerative technologies. © 2013 Future Medicine Ltd.

Craddock, MJ & Hogan, JA 2013, 'The Fractional Clifford-Fourier Kernel', JOURNAL OF FOURIER ANALYSIS AND APPLICATIONS, vol. 19, no. 4, pp. 683-711.
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The Clifford-Fourier transform was introduced by Brackx, De Schepper and Sommen who subsequently computed its kernel in dimension d=2. Here we compute the kernel of a fractional version of the transform when d=2 and 4. In doing so we solve appropriate wa

Croak, BM, Crowther, MS, Webb, JK & Shine, R 2013, 'Movements and Habitat Use of an Endangered Snake, Hoplocephalus bungaroides (Elapidae): Implications for Conservation', PLOS ONE, vol. 8, no. 4, pp. 1-10.
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A detailed understanding of how extensively animals move through the landscape, and the habitat features upon which they rely, can identify conservation priorities and thus inform management planning. For many endangered species, information on habitat use either is sparse, or is based upon studies from a small part of the species' range. The broad-headed snake (Hoplocephalus bungaroides) is restricted to a specialized habitat (sandstone outcrops and nearby forests) within a small geographic range in south-eastern Australia. Previous research on this endangered taxon was done at a single site in the extreme south of the species' geographic range. We captured and radio-tracked 9 adult broad-headed snakes at sites in the northern part of the species' distribution, to evaluate the generality of results from prior studies, and to identify critical habitat components for this northern population. Snakes spent most of winter beneath sun-warmed rocks then shifted to tree hollows in summer. Thermal regimes within retreat-sites support the hypothesis that this shift is thermally driven. Intervals between successive displacements were longer than in the southern snakes but dispersal distances per move and home ranges were similar. Our snakes showed non-random preferences both in terms of macrohabitat (e.g., avoidance of some vegetation types) and microhabitat (e.g., frequent use of hollow-bearing trees). Despite many consistencies, the ecology of this species differs enough between southern and northern extremes of its range that managers need to incorporate information on local features to most effectively conserve this threatened reptile. © 2013 Croak et al.

Croak, BM, Webb, JK & Shine, R 2013, 'The benefits of habitat restoration for rock-dwelling velvet geckos Oedura lesueurii', JOURNAL OF APPLIED ECOLOGY, vol. 50, no. 2, pp. 432-439.
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Summary: Worldwide, efforts to restore habitat quality are rarely matched by efforts to evaluate the effects of those restoration attempts. Simply documenting usage of the newly created habitats by biota is not enough, because such areas may serve as sink populations. We need to monitor viability (growth, survival, reproduction) of individuals that colonize the newly created habitat, compared with conspecifics in non-restored areas. In the Sydney region in south-eastern Australia, humans have degraded sandstone rock outcrops by removing natural rocks for landscaping urban gardens. We restored degraded rock outcrops by placing artificial rocks at sites where natural rocks had been removed. We measured growth rates and survival in velvet geckos Oedura lesueurii at control and restored sites over a 2-year period. Gecko growth rates were unaffected by habitat restoration, but restoring sites with artificial rocks increased the overall numbers of lizards detected (both adults and juveniles). The apparent survival rates of adult male lizards (as estimated using mark) were not significantly affected by habitat restoration. However, apparent survival rates of juvenile geckos were higher at restored sites than at unrestored sites. Synthesis and applications. Habitat restoration using artificial rocks has had measurable conservation benefits on these degraded rocky outcrops. Quantifying those benefits in terms of species' survival and growth rates enables management decisions about habitat restoration to be based upon evidence rather than wishful thinking or untested intuition. Habitat restoration using artificial rocks has had measurable conservation benefits on these degraded rocky outcrops. Quantifying those benefits in terms of species' survival and growth rates enables management decisions about habitat restoration to be based upon evidence rather than wishful thinking or untested intuition. © 2013 British Ecological Society.

Cruz, RDL, Meza, C, Arribas-Gil, A & Carroll, RJ 2013, 'Bayesian Regression Analysis of Data with Random Effects Covariates from Nonlinear Longitudinal Measurements', Journal of Multivariate Analysis, vol. 143, pp. 94-106.
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Joint models for a wide class of response variables and longitudinalmeasurements consist on a mixed-effects model to fit longitudinal trajectorieswhose random effects enter as covariates in a generalized linear model for theprimary response. They provide a useful way to asses association between thesetwo kinds of data, which in clinical studies are often collected jointly on aseries of individuals and may help understanding, for instance, the mechanismsof recovery of a certain disease or the efficacy of a given therapy. The mostcommon joint model in this framework is based on a linear mixed model for thelongitudinal data. However, for complex datasets the linearity assumption maybe too restrictive. Some works have considered generalizing this setting withthe use of a nonlinear mixed-effects model for the longitudinal trajectoriesbut the proposed estimation procedures based on likelihood approximations havebeen shown De la Cruz et al. (2011) to exhibit some computational efficiencyproblems. In this article we propose an MCMC-based estimation procedure in thejoint model with a nonlinear mixed-effects model for the longitudinal data anda generalized linear model for the primary response. Moreover, we consider thatthe errors in the longitudinal model may be correlated. We apply our method tothe analysis of hormone levels measured at the early stages of pregnancy thatcan be used to predict normal versus abnormal pregnancy outcomes. We alsoconduct a simulation study to asses the importance of modelling correlatederrors and quantify the consequences of model misspecification.

Cui, PH, Rawling, T, Gillani, TB, Bourget, K, Wang, X-S, Zhou, F & Murray, M 2013, 'Anti-proliferative actions of N′-desmethylsorafenib in human breast cancer cells', Biochemical Pharmacology, vol. 86, no. 3, pp. 419-427.
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d The multi-kinase inhibitor sorafenib is used for the treatment of renal and hepatic carcinomas and is undergoing evaluation for treatment of breast cancer in combination with other agents. Cytochrome P450 (CYP) 3A4 converts sorafenib to multiple metabo

Cunningham, K, Stansfield, SH, Patel, P, Menon, S, Kienzle, V, Allan, JA & Huston, WM 2013, 'The IL-6 response to Chlamydia from primary reproductive epithelial cells is highly variable and may be involved in differential susceptibility to the immunopathological consequences of chlamydial infection', BMC IMMUNOLOGY, vol. 14, no. 1.
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Background: Chlamydia trachomatis infection results in reproductive damage in some women. The process and factors involved in this immunopathology are not well understood. This study aimed to investigate the role of primary human cellular responses to chlamydial stress response proteases and chlamydial infection to further identify the immune processes involved in serious disease sequelae.Results: Laboratory cell cultures and primary human reproductive epithelial cultures produced IL-6 in response to chlamydial stress response proteases (CtHtrA and CtTsp), UV inactivated Chlamydia, and live Chlamydia. The magnitude of the IL-6 response varied considerably (up to 1000 pg ml-1) across different primary human reproductive cultures. Thus different levels of IL-6 production by reproductive epithelia may be a determinant in disease outcome. Interestingly, co-culture models with either THP-1 cells or autologous primary human PBMC generally resulted in increased levels of IL-6, except in the case of live Chlamydia where the level of IL-6 was decreased compared to the epithelial cell culture only, suggesting this pathway may be able to be modulated by live Chlamydia. PBMC responses to the stress response proteases (CtTsp and CtHtrA) did not significantly vary for the different participant cohorts. Therefore, these proteases may possess conserved innate PAMPs. MAP kinases appeared to be involved in this IL-6 induction from human cells. Finally, we also demonstrated that IL-6 was induced by these proteins and Chlamydia from mouse primary reproductive cell cultures (BALB/C mice) and mouse laboratory cell models.Conclusions: We have demonstrated that IL-6 may be a key factor for the chlamydial disease outcome in humans, given that primary human reproductive epithelial cell culture showed considerable variation in IL-6 response to Chlamydia or chlamydial proteins, and that the presence of live Chlamydia (but not UV killed) during co-culture resulted in a reduced IL-6...

Cvitanovic, C, Wilson, SK, Fulton, CJ, Almany, GR, Anderson, P, Babcock, RC, Ban, NC, Beeden, RJ, Beger, M, Cinner, J, Dobbs, K, Evans, LS, Farnham, A, Friedman, KJ, Gale, K, Gladstone, W, Grafton, Q, Graham, NAJ, Gudge, S, Harrison, PL, Holmes, TH, Johnstone, N, Jones, GP, Jordan, A, Kendrick, AJ, Klein, CJ, Little, LR, Malcolm, HA, Morris, D, Possingham, HP, Prescott, J, Pressey, RL, Skilleter, GA, Simpson, C, Waples, K, Wilson, D & Williamson, DH 2013, 'Critical research needs for managing coral reef marine protected areas: Perspectives of academics and managers', Journal of Environmental Management, vol. 114, pp. 84-91.
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Marine protected areas (MPAs) are a primary policy instrument for managing and protecting coral reefs. Successful MPAs ultimately depend on knowledge-based decision making, where scientific research is integrated into management actions. Fourteen coral reef MPA managers and sixteen academics from eleven research, state and federal government institutions each outlined at least five pertinent research needs for improving the management of MPAs situated in Australian coral reefs. From this list of 173 key questions, we asked members of each group to rank questions in order of urgency, redundancy and importance, which allowed us to explore the extent of perceptional mismatch and overlap among the two groups. Our results suggest the mismatch among MPA managers and academics is small, with no significant difference among the groups in terms of their respective research interests, or the type of questions they pose. However, managers prioritised spatial management and monitoring as research themes, whilst academics identified climate change, resilience, spatial management, fishing and connectivity as the most important topics. Ranking of the posed questions by the two groups was also similar, although managers were less confident about the achievability of the posed research questions and whether questions represented a knowledge gap. We conclude that improved collaboration and knowledge transfer among management and academic groups can be used to achieve similar objectives and enhance the knowledge-based management of MPAs.

D’Amico, AG, Castorina, A, Leggio, GM, Drago, F & D’Agata, V 2013, 'Hippocampal Neurofibromin and Amyloid Precursor Protein Expression in Dopamine D3 Receptor Knock-out Mice Following Passive Avoidance Conditioning', Neurochemical Research, vol. 38, no. 3, pp. 564-572.
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D’Amico, AG, Scuderi, S, Leggio, GM, Castorina, A, Drago, F & D’Agata, V 2013, 'Increased Hippocampal CREB Phosphorylation in Dopamine D3 Receptor Knockout Mice Following Passive Avoidance Conditioning', Neurochemical Research, vol. 38, no. 12, pp. 2516-2523.
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D’Amico, AG, Scuderi, S, Saccone, S, Castorina, A, Drago, F & D’Agata, V 2013, 'Antiproliferative Effects of PACAP and VIP in Serum-Starved Glioma Cells', Journal of Molecular Neuroscience, vol. 51, no. 2, pp. 503-513.
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Dafforn, KA, Kelaher, BP, Simpson, SL, Coleman, MA, Hutchings, PA, Clark, GF, Knott, NA, Doblin, MA & Johnston, EL 2013, 'Polychaete Richness and Abundance Enhanced in Anthropogenically Modified Estuaries Despite High Concentrations of Toxic Contaminants', PLOS ONE, vol. 8, no. 9, pp. 1-10.
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Ecological communities are increasingly exposed to multiple chemical and physical stressors, but distinguishing anthropogenic impacts from other environmental drivers remains challenging. Rarely are multiple stressors investigated in replicated studies over large spatial scales (.1000 kms) or supported with manipulations that are necessary to interpret ecological patterns. We measured the composition of sediment infaunal communities in relation to anthropogenic and natural stressors at multiple sites within seven estuaries. We observed increases in the richness and abundance of polychaete worms in heavily modified estuaries with severe metal contamination, but no changes in the diversity or abundance of other taxa. Estuaries in which toxic contaminants were elevated also showed evidence of organic enrichment. We hypothesised that the observed response of polychaetes was not a `positive response to toxic contamination or a reduction in biotic competition, but due to high levels of nutrients in heavily modified estuaries driving productivity in the water column and enriching the sediment over large spatial scales. We deployed defaunated field-collected sediments from the surveyed estuaries in a small scale experiment, but observed no effects of sediment characteristics (toxic or enriching). Furthermore, invertebrate recruitment instead reflected the low diversity and abundance observed during field surveys of this relatively `pristine estuary. This suggests that differences observed in the survey are not a direct consequence of sediment characteristics (even severe metal contamination) but are related to parameters that covary with estuary modification such as enhanced productivity from nutrient inputs and the diversity of the local species pool. This has implications for the interpretation of diversity measures in large-scale monitoring studies in which the observed patterns may be strongly influenced by many factors that covary with anthropogenic modification.

Dahan-Pasternak, N, Nasereddin, A, Kolevzon, N, Pe'er, M, Wong, W, Shinder, V, Turnbull, L, Whitchurch, CB, Elbaum, M, Gilberger, TW, Yavin, E, Baum, J & Dzikowski, R 2013, 'PfSec13 is an unusual chromatin-associated nucleoporin of Plasmodium falciparum that is essential for parasite proliferation in human erythrocytes', JOURNAL OF CELL SCIENCE, vol. 126, no. 14, pp. 3055-3069.
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In Plasmodium falciparum, the deadliest form of human malaria, the nuclear periphery has drawn much attention due to its role as a subnuclear compartment involved in virulence gene expression. Recent data have implicated components of the nuclear envelope in regulating gene expression in several eukaryotes. Special attention has been given to nucleoporins that compose the nuclear pore complex (NPC). However, very little is known about components of the nuclear envelope in Plasmodium parasites. Here we characterize PfSec13, an unusual nucleoporin of P. falciparum, which shows unique structural similarities suggesting that it is a fusion between Sec13 and Nup145C of yeast. Using super resolution fluorescence microscopy (3D-SIM) and in vivo imaging, we show that the dynamiclocalization of PfSec13 during parasites' intra-erythrocytic development corresponds with that of the NPCs and that these dynamics are associated with microtubules rather than with F-actin. In addition, PfSec13 does not co-localize with the heterochormatin markers HP1 and H3K9me3, suggesting euchromatic location of the NPCs. The proteins associated with PfSec13 indicate that this unusual Nup is involved in several cellular processes. Indeed, ultrastructural and chromatin immunoprecipitation analyses revealed that, in addition to the NPCs, PfSec13 is found in the nucleoplasm where it is associated with chromatin. Finally, we used peptide nucleic acids (PNA) to downregulate PfSec13 and show that it is essential for parasite proliferation in human erythrocytes. © 2013. Published by The Company of Biologists Ltd.

Dalton, JP, Robinson, MW, Mulcahy, G, O'Neill, SM & Donnelly, S 2013, 'Immunomodulatory molecules of Fasciola hepatica: Candidates for both vaccine and immunotherapeutic development', VETERINARY PARASITOLOGY, vol. 195, no. 3-4, pp. 272-285.
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The liver fluke, Fasciola hepatica, causes fascioliasis in domestic animals (sheep, cattle), a global disease that is also an important infection of humans. As soon as the parasite invades the gut wall its interaction with various host immune cells (e.g. dendritic cells, macrophages and mast cells) is complex. The parasite secretes a myriad of molecules that direct the immune response towards a favourable non-protective Th2-mediate/regulatory environment. These immunomodulatory molecules, such as cathepsin L peptidase (FhCL1), are under development as the first generation of fluke vaccines. However, this peptidase and other molecules, such as peroxiredoxin (FhPrx) and helminth defence molecule (FhHDM-1), exhibit various immunomodulatory properties that could be harnessed to help treat immune-related conditions in humans and animals. © 2013 Elsevier B.V.

D'Amico, AG, Castorina, A, Leggio, GM, Imbesi, R, Drago, F & D'Agata, V 2013, 'Dopamine D3 receptor knockout mice exhibit increased hippocampal cAMP response element binding protein (CREB) following acquisition of passive avoidance memory', Italian Journal of Anatomy and Embryology, vol. 118, no. 2 SUPPL.

Danforn, L 2013, 'Number and Necessity of Tests Performed In the Last Week of Life of a Cancer Patient', Journal of Geriatrics and Palliative Care, vol. 1, no. 1.
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Davies, KM, Hare, DJ, Cottam, V, Chen, N, Hilgers, L, Halliday, G, Mercer, JFB & Double, KL 2013, 'Localization of copper and copper transporters in the human brain', METALLOMICS, vol. 5, no. 1, pp. 43-51.
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Disturbances in brain copper result in rare and severe neurological disorders and may play a role in the pathogenesis and progression of multiple neurodegenerative diseases. Our current understanding of mammalian brain copper transport is based on model systems outside the central nervous system and no data are available regarding copper transport systems in the human brain. To address this deficit, we quantified regional copper concentrations and examined the distribution and cellular localization of the copper transport proteins Copper transporter 1, Atox1, ATP7A, and ATP7B in multiple regions of the human brain using inductively coupled plasma-mass spectrometry, Western blot and immunohistochemistry. We identified significant relationships between copper transporter levels and brain copper concentrations, supporting a role for these proteins in copper transport in the human brain. Interestingly, the substantia nigra contained twice as much copper than that in other brain regions, suggesting an important role for copper in this brain region. Furthermore, ATP7A levels were significantly greater in the cerebellum, compared with other brain regions, supporting an important role for ATP7A in cerebellar neuronal health. This study provides novel data regarding copper regulation in the human brain, critical to understand the mechanisms by which brain copper levels can be altered, leading to neurological disease.

Davis, J, Short, K, Wuhrer, R, Phillips, MR, Lumpkin, GR & Whittle, KR 2013, 'Electron backscatter diffraction characterization of plasma immersion ion implantation effects in stainless steel', NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS, vol. 295, pp. 38-41.
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In these experiments plasma immersion ion implantation is utilised to simulate some of the radiation effects in a nuclear reactor environment. Scanning electron microscopy using the angular selective backscatter detector has revealed observable changes in crystallographic contrast after irradiation with helium ions. Further studies using electron backscatter diffraction in both plan and cross section view allow us to visualize the extent and depth of damage and observe differences in the behavior of different crystalline phases present in several grades of stainless steel. © 2012 Elsevier B.V. All rights reserved.

De Silva, KSB, Aboutalebi, SH, Xu, X, Wang, XL, Li, WX, Konstantinov, K & Dou, SX 2013, 'A significant improvement in both low- and high-field performance of MgB2 superconductors through graphene oxide doping', SCRIPTA MATERIALIA, vol. 69, no. 6, pp. 437-440.
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De Silva, KSB, Xu, X, Gambir, S, Wong, DCK, Li, WX & Hu, QY 2013, 'Effect of Sintering Temperature on the Superconducting Properties of Graphene Doped MgB2', IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY, vol. 23, no. 3.
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de Sterke, CM, Kabakova, IV, Uddin, I, Jeyaratnam, J & Malomed, BA 2013, 'Spontaneous symmetry breaking in a double-defect nonlinear grating', Physical Review A, vol. 88, no. 3.
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Delmas, S, Duggin, IG & Allers, T 2013, 'DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii', MOLECULAR MICROBIOLOGY, vol. 87, no. 1, pp. 168-179.
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In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination

Deng, W, Buzas, DM, Ying, H, Robertson, M, Taylor, J, Peacock, WJ, Dennis, ES & Helliwell, C 2013, 'Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes', BMC GENOMICS, vol. 14.
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Dennis, PG, Seymour, J, Kumbun, K & Tyson, GW 2013, 'Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients', The ISME Journal, vol. 7, no. 8, pp. 1661-1664.
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Abstract Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes.

Diep, AL, Lang, JM, Darling, AE, Eisen, JA & Coil, DA 2013, 'Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria )', Genome Announcements, vol. 1, no. 3, pp. 198-204.
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ABSTRACT Here, we present the draft genome sequence of an actinobacterium, Dietzia sp. strain UCD-THP, isolated from a residential toilet handle. The assembly contains 3,915,613 bp. The genome sequences of only two other Dietzia species have been published, those of Dietzia alimentaria and Dietzia cinnamea .

Dietmann, A, Millonig, A, Combes, V, Couraud, P-O, Kachlany, SC & Grau, GE 2013, 'Effects of Aggregatibacter actinomycetemcomitans leukotoxin on endothelial cells', Microbial Pathogenesis, vol. 61-62, pp. 43-50.
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Aggregatibacter actinomycetemcomitans is a human pathogen that produces leukotoxin (LtxA) as a major virulence factor. In this study the effect of LtxA on microvascular endothelial cell viability and phenotype was studied. High doses of single LtxA treatment (500ng/ml to 5μg/ml) significantly and irreversibly decreased cell proliferation and induced apoptosis, as assessed by tetrazolium salt and annexin V assay, respectively. Apoptosis was partially inhibited by the pan-caspase inhibitor, z-VAD-fmk. LtxA caused a cell cycle arrest in the G2/M phase after 72h. Between 500ng/ml and 5μg/ml, after long- or short-term stimulation LtxA increased the expression of ICAM-1 and VCAM-1, as well as the percentages of endothelial cells expressing these adhesion molecules. Thus, A.actinomycetemcomitans LtxA has substantial pro-inflammatory effects on human brain endothelial cells by upregulation of ICAM-1 and VCAM-1. Furthermore, LtxA in higher concentration was found to decrease proliferation and induces apoptosis in microvascular endothelial cells. •LtxA has anti-proliferative effects on endothelial cells.•LtxA induces a G2/M phase cell cycle arrest in endothelial cells.•LtxA induces apoptosis in endothelial cells.•LtxA increased expression of ICAM-1 and VCAM-1 in endothelial cells. © 2013 The Authors.

Ding, Y, Zhang, Y, Peng, T, Lu, Y, Jin, D, Ren, Q, Liu, Y, Han, J & Xi, P 2013, 'Observation of mesenteric microcirculatory disturbance in rat by laser oblique scanning optical microscopy', SCIENTIFIC REPORTS, vol. 3.
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Ischemia-reperfusion (I/R) injury model has been widely applied to the study of microcirculation disturbance. In this work, we used laser oblique scanning optical microscopy (LOSOM) to observe the microcirculation system in the mesentery of rat model. Utilizing a localized point-scanning detection scheme, high-contrast images of leukocytes were obtained. The extended detection capability facilitated both the automatic in vivo cell counting and the accurate measurement of the rolling velocity of leukocytes. Statistical analysis of the different treatment groups suggested that the distinction between I/R and sham groups with time lapse is significant.

Djordjevic, SP, Stokes, HW & Chowdhury, PR 2013, 'Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota', Frontiers in Microbiology, vol. 4, no. 86, pp. 1-12.
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Multiple antibiotic resistant pathogens represent a major clinical challenge in both human and veterinary context. It is now well-understood that the genes that encode resistance are context independent. That is, the same gene is commonly present in otherwise very disparate pathogens in both humans and production and companion animals, and among bacteria that proliferate in an agricultural context. This can be true even for pathogenic species or clonal types that are otherwise confined to a single host or ecological niche. It therefore follows that mechanisms of gene flow must exist to move genes from one part of the microbial biosphere to another. It is widely accepted that lateral (or horizontal) gene transfer (L(H)GT) drives this gene flow. LGT is relatively well-understood mechanistically but much of this knowledge is derived from a reductionist perspective. We believe that this is impeding our ability to deal with the medical ramifications of LGT. Resistance genes and the genetic scaffolds that mobilize them in multiply drug resistant bacteria of clinical significance are likely to have their origins in completely unrelated parts of the microbial biosphere.

Donovan, C, Royce, SG, Esposito, J, Tran, J, Ibrahim, ZA, Tang, MLK, Bailey, S & Bourke, JE 2013, 'Differential Effects of Allergen Challenge on Large and Small Airway Reactivity in Mice', PLoS ONE, vol. 8, no. 9, pp. e74101-e74101.
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The relative contributions of large and small airways to hyperresponsiveness in asthma have yet to be fully assessed. This study used a mouse model of chronic allergic airways disease to induce inflammation and remodelling and determine whether in vivo hyperresponsiveness to methacholine is consistent with in vitro reactivity of trachea and small airways. Balb/C mice were sensitised (days 0, 14) and challenged (3 times/week, 6 weeks) with ovalbumin. Airway reactivity was compared with saline-challenged controls in vivo assessing whole lung resistance, and in vitro measuring the force of tracheal contraction and the magnitude/rate of small airway narrowing within lung slices. Increased airway inflammation, epithelial remodelling and fibrosis were evident following allergen challenge. In vivo hyperresponsiveness to methacholine was maintained in isolated trachea. In contrast, methacholine induced slower narrowing, with reduced potency in small airways compared to controls. In vitro incubation with IL-1/TNFα did not alter reactivity. The hyporesponsiveness to methacholine in small airways within lung slices following chronic ovalbumin challenge was unexpected, given hyperresponsiveness to the same agonist both in vivo and in vitro in tracheal preparations. This finding may reflect the altered interactions of small airways with surrounding parenchymal tissue after allergen challenge to oppose airway narrowing and closure. © 2013 Donovan et al.

Dossou, KB, Botten, LC & Poulton, CG 2013, 'Semi-analytic impedance modeling of three-dimensional photonic and metamaterial structures', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, vol. 30, no. 10, pp. 2034-2047.
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We define the concept of an impedance matrix for three-dimensional (3D) photonic and metamaterial structures relative to a reference medium and show that it satisfies a matrix generalization of the basic algebraic properties of the wave impedance between homogeneous media. This definition of the impedance matrix is motivated by the structure of the Fresnel reflection and transmission matrices at the interface between the media. In the derivation of the Fresnel scattering matrices, the field in each medium is expressed by a Bloch mode expansion, with field matching at the interface being undertaken in a least-squares manner by exploiting a biorthogonality relation between primal and adjoint Bloch modes. A semi-analytic technique, based on the impedance matrix, is developed for modeling the scattering of light by 3D periodic photonic and metamaterial structures. The advantages (in design and intuition) of the formalism are demonstrated through two applications. © 2013 Optical Society of America.

Dowse, R, Tang, D, Palmer, CG & Kefford, BJ 2013, 'Risk assessment using the species sensitivity distribution method: Data quality versus data quantity', ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, vol. 32, no. 6, pp. 1360-1369.
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Species sensitivity distributions (SSDs) are cumulative distributions of measures of species sensitivity to a stressor or toxicant, and are used to estimate concentrations that will protect p% of a community (PCp). There is conflict between the desire to use high-quality sensitivity data in SSDs, and to construct them with a large number of species forming a representative sample. Trade-offs between data quality and quantity were investigated using the effects of increasing salinity on the macroinvertebrate community from the Hunter River catchment, in eastern Australia. Five SSDs were constructed, representing five points along a continuum of data quality versus data quantity and representativeness. This continuum was achieved by the various inclusion/exclusion of censored data, nonmodeled data, and extrapolation from related species. Protective concentrations were estimated using the Burr type III distribution, Kaplan-Meier survival function, and two Bayesian statistical models. The dominant taxonomic group was the prime determinant of protective concentrations, with an increase in PC95 values resulting from a decrease in the proportion of Ephemeropteran species included in the SSD. In addition, decreases in data quantity in a SSD decreased community representativeness. The authors suggest, at least for salinity, that the inclusion of right censored data provides a more representative sample of species that reflects the natural biotic assemblage of an area to be protected, and will therefore improve risk assessment

Duchene, D, Klanten, SO, Munday, PL, Herler, J & van Herwerden, L 2013, 'Phylogenetic evidence for recent diversification of obligate coral-dwelling gobies compared with their host corals', Molecular Phylogenetics and Evolution, vol. 69, no. 1, pp. 123-132.
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Dunlop, RA, Cox, PA, Banack, SA & Rodgers, KJ 2013, 'The Non-Protein Amino Acid BMAA Is Misincorporated into Human Proteins in Place of L-Serine Causing Protein Misfolding and Aggregation', PLOS ONE, vol. 8, no. 9, pp. 1-8.
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Mechanisms of protein misfolding are of increasing interest in the aetiology of neurodegenerative diseases characterized by protein aggregation and tangles including Amyotrophic Lateral Sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), Lewy Body Dementia (LBD), and Progressive Supranuclear Palsy (PSP). Some forms of neurodegenerative illness are associated with mutations in genes which control assembly of disease related proteins. For example, the mouse sticky mutation sti, which results in undetected mischarging of tRNAAla with serine resulting in the substitution of serine for alanine in proteins causes cerebellar Purkinje cell loss and ataxia in laboratory animals. Replacement of serine 422 with glutamic acid in tau increases the propensity of tau aggregation associated with neurodegeneration. However, the possibility that environmental factors can trigger abnormal folding in proteins remains relatively unexplored. We here report that a non-protein amino acid, β-N-methylamino-L-alanine (BMAA), can be misincorporated in place of l-serine into human proteins. We also report that this misincorporation can be inhibited by l-serine. Misincorporation of BMAA into human neuroproteins may shed light on putative associations between human exposure to BMAA produced by cyanobacteria and an increased incidence of ALS. © 2013 Dunlop et al.

Edson, J, Brooks, EM, McLaren, C, Robertson, J, McNevin, D, Cooper, A & Austin, JJ 2013, 'A quantitative assessment of a reliable screening technique for the STR analysis of telogen hair roots', Forensic Science International: Genetics, vol. 7, no. 1, pp. 180-188.
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Eftekhari, P, Hajizadeh, S, Reza Raoufy, M, Reza Masjedi, M, Yang, M, Hansbro, N, Li, JJ & Foster, PS 2013, 'Preventive effect of N-acetylcysteine in a mouse model of steroid resistant acute exacerbation of asthma', EXCLI Journal, vol. 12, pp. 184-192.
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Oxidative stress appears to have an important role in glucocorticoid insensitivity, as a crucial problem in asthma therapy. We studied the preventive effect of antioxidant N-acetylcysteine (NAC) on the airway hyper-responsiveness (AHR) and the accumulation of inflammatory cells in the airways in an animal model of steroid resistant acute exacerbation of asthma. Systemically sensitized Balb/C mice were exposed to Ovalbumin aerosol on days 13, 14, 15 and 16, followed by intratracheal lipopolysaccharide (LPS) to induce acute exacerbation. NAC (intraperitoneal, 320 mg/kg 30 min before and 12 hours after each challenge) reduced hyperresponsiveness with/out dexamethasone. LPS application caused neutrophilia in bronchoalveolar lavage fluid (BALF) and eosinophil count was higher than respective control in BALF as well as neutrophils after dexamethasone treatment. NAC significantly decreased neutrophil and eosinophil count in BALF as well as inflammatory cytokines (IL-13 and IL-5).We concluded that addition of NAC to asthma therapy has beneficial preventive effects in an animal model of steroid resistant acute exacerbation of asthma.

Egan, S, Harder, T, Burke, C, Steinberg, P, Kjelleberg, S & Thomas, T 2013, 'The seaweed holobiont: understanding seaweed-bacteria interactions', FEMS MICROBIOLOGY REVIEWS, vol. 37, no. 3, pp. 462-476.
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Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich diversity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the diversity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept. © 2012 Federation of European Microbiological Societies.

Eggleton, BJ, Poulton, CG & Pant, R 2013, 'Inducing and harnessing stimulated Brillouin scattering in photonic integrated circuits', Advances in Optics and Photonics, vol. 5, no. 4, pp. 536-536.
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We review recent progress in inducing and harnessing stimulated Brillouin scattering (SBS) in integrated photonic circuits. Exciting SBS in a chip-scale device is challenging due to the stringent requirements on materials and device geometry. We discuss these requirements, which include material parameters, such as optical refractive index and acoustic velocity, and device properties, such as acousto-optic confinement. Recent work on SBS in nano-photonic waveguides and micro-resonators is presented, with special attention paid to photonic integration of applications such as narrow-linewidth lasers, slowand fast-light, microwave signal processing, Brillouin dynamic gratings, and nonreciprocal devices. © 2013 Optical Society of America.

Ehsan, B, Haque, A, Younas, M, Shaheen, T, Huma, T, Sattar, S, Idrees, S & Iqbal, Z 2013, 'Assessment of genomic diversity of cotton (gossypium hirsutum) genotypes using simple sequence repeats markers through genetic analysis software', International Journal of Agriculture and Biology, vol. 15, no. 5, pp. 968-972.
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The present study was designed to evaluate genetic diversity among twenty cotton genotypes by employing thirty one SSR markers that were reported from Brookheaven National Laboratories. Out of thirty-one primers, six SSR primers were found polymorphic at different SSR loci. Maximum number of loci (33), were amplified by MNH-93, while minimum (22) by 238-F. Total percentage of informative loci was 36.8%. Genetic diversity matrix of these genotypes was calculated by NTSYS-pc 2.2 software. Genetic similarity coefficients ranged from 0.474 to 0.974. The highest dissimilarity (0.474) was observed between genotype 298-F and CIM-496. Cluster analysis as performed using un-weighted pair group method of arithmetic average algorithm showed that Nei and Li's coefficients ranged from 0.63 to 0.97. The dendrogram of cotton lines showed two major clusters except 238-F forming an out-group from other genotypes, thus showing maximum dissimilarity. Genotypes MNH-93 and K-68/9 showed maximum similarity coefficient of 0.97. Information obtained from the present study can be used to select divergent parents for future breeding programs. © 2013 Friends Science Publishers.

Eilenberger, F, Kabakova, IV, de Sterke, CM, Eggleton, BJ & Pertsch, T 2013, 'Cavity Optical Pulse Extraction: ultra-short pulse generation as seeded Hawking radiation', Scientific Reports, vol. 3, no. 1.
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El-Assaad, F, Wheway, J, Mitchell, AJ, Lou, J, Hunt, NH, Combes, V & Grau, GER 2013, 'Cytoadherence of Plasmodium berghei-Infected Red Blood Cells to Murine Brain and Lung Microvascular Endothelial Cells In Vitro', Infection and Immunity, vol. 81, no. 11, pp. 3984-3991.
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ABSTRACT Sequestration of infected red blood cells (iRBC) within the cerebral and pulmonary microvasculature is a hallmark of human cerebral malaria (hCM). The interaction between iRBC and the endothelium in hCM has been studied extensively and is linked to the severity of malaria. Experimental CM (eCM) caused by Plasmodium berghei ANKA reproduces most features of hCM, although the sequestration of RBC infected by P. berghei ANKA (PbA-iRBC) has not been completely delineated. The role of PbA-iRBC sequestration in the severity of eCM is not well characterized. Using static and flow cytoadherence assays, we provide the first direct in vitro evidence for the binding of PbA-iRBC to murine brain and lung microvascular endothelial cells (MVEC). We found that basal PbA-iRBC cytoadherence to MVECs was significantly higher than that of normal red blood cells (NRBC) and of RBC infected with P. berghei K173 (PbK173-iRBC), a strain that causes noncerebral malaria (NCM). MVEC prestimulation with tumor necrosis factor (TNF) failed to promote any further significant increase in mixed-stage iRBC adherence. Interestingly, enrichment of the blood for mature parasites significantly increased PbA-iRBC binding to the MVECs prestimulated with TNF, while blockade of VCAM-1 reduced this adhesion. Our study provides evidence for the firm, flow-resistant binding to endothelial cells of iRBC from strain ANKA-infe...

Elbadawi, C, Toth, M & Lobo, CJ 2013, 'Pure Platinum Nanostructures Grown by Electron Beam Induced Deposition', ACS Applied Materials & Interfaces, vol. 5, no. 19, pp. 9372-9376.
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Platinum has numerous applications in catalysis, nanoelectronics, and sensing devices. Here we report a method for localized, mask-free deposition of high-purity platinum that employs a combination of room-temperature, direct-write electron beam induced deposition (EBID) using the precursor Pt(PF3)4, and low temperature (≤400 C) postgrowth annealing in H2O. The annealing treatment removes phosphorus contaminants through a thermally activated pathway involving dissociation of H2O and the subsequent formation of volatile phosphorus oxides and hydrides that desorb during annealing. The resulting Pt is indistinguishable from pure Pt films by wavelength dispersive X-ray spectroscopy (WDS). © 2013 American Chemical Society.

Elder, M & Taback, J 2013, '$\mathcal C$-graph automatic groups', JOURNAL OF ALGEBRA, vol. 413, pp. 289-319.
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We generalize the notion of a graph automatic group introduced byKharlampovich, Khoussainov and Miasnikov (arXiv:1107.3645) by replacing theregular languages in their definition with more powerful language classes. Fora fixed language class $\mathcal C$, we call the resulting groups $\mathcalC$-graph automatic. We prove that the class of $\mathcal C$-graph automaticgroups is closed under change of generating set, direct and free product forcertain classes $\mathcal C$. We show that for quasi-realtime counter-graphautomatic groups where normal forms have length that is linear in the geodesiclength, there is an algorithm to compute normal forms (and therefore solve theword problem) in polynomial time. The class of quasi-realtime counter-graphautomatic groups includes all Baumslag-Solitar groups, and the free group ofcountably infinite rank. Context-sensitive-graph automatic groups are shown tobe a very large class, which encompasses, for example, groups with unsolvableconjugacy problem, the Grigorchuk group, and Thompson's groups $F,T$ and $V$.

Elder, M, Rechnitzer, A & Rensburg, EJJV 2013, 'Random sampling of trivials words in finitely presented groups', Experimental Mathematics, vol. 24, pp. 391-409.
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We describe a novel algorithm for random sampling of freely reduced wordsequal to the identity in a finitely presented group. The algorithm is based onMetropolis Monte Carlo sampling. The algorithm samples from a stretchedBoltzmann distribution \begin{align*}\pi(w) &= (|w|+1)^{\alpha} \beta^{|w|}\cdot Z^{-1} \end{align*} where $|w|$ is the length of a word $w$, $\alpha$ and$\beta$ are parameters of the algorithm, and $Z$ is a normalising constant. Itfollows that words of the same length are sampled with the same probability.The distribution can be expressed in terms of the cogrowth series of the group,which then allows us to relate statistical properties of words sampled by thealgorithm to the cogrowth of the group, and hence its amenability. We have implemented the algorithm and applied it to several grouppresentations including the Baumslag-Solitar groups, some free products studiedby Kouksov, a finitely presented amenable group that is not subexponentiallyamenable (based on the basilica group), and Richard Thompson's group $F$.

Erken, M, Lutz, C & McDougald, D 2013, 'The Rise of Pathogens: Predation as a Factor Driving the Evolution of Human Pathogens in the Environment', Microbial Ecology, vol. 65, no. 4, pp. 860-868.
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Bacteria in the environment must survive predation from bacteriophage, heterotrophic protists, and predatory bacteria. This selective pressure has resulted in the evolution of a variety of defense mechanisms, which can also function as virulence factors. Here we discuss the potential dual function of some of the mechanisms, which protect against heterotrophic protists, and how predation pressure leads to the evolution of pathogenicity. This is in accordance with the coincidental evolution hypothesis, which suggests that virulence factors arose as a response to other selective pressures, for example, predation rather than for virulence per se. In this review we discuss some of those environmental factors that may be associated with the rise of pathogens in the marine environment. In particular, we will discuss the role of heterotrophic protists in the evolution of virulence factors in marine bacteria. Finally, we will discuss the implications for expansion of current pathogens and emergence of new pathogens. © 2013 The Author(s).

Evans, SJ, Renison, CA, Williams, DBG & Muller, A 2013, 'P,P-Bis[4-(dimethylamino)phenyl]-N,N-bis(propan-2-yl)phosphinic amide', Acta Crystallographica Section E Structure Reports Online, vol. 69, no. 2, pp. o195-o195.
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The molecular structure of the title compound, C22H34N3OP, adopts a distorted tetrahedral geometry at the P atom, with the most noticeable distortion being for the O—P—N angle [117.53 (10)°]. An effective cone angle of 187° was calculated for the compound. In the crystal, weak C—H...O interactions create infinite chains along [100], whereas C—H...π interactions propagating in [001] generate a herringbone motif.

Evans, SJ, Renison, CA, Williams, DBG & Muller, A 2013, 'rac-[2-(Dicyclohexylphosphanyl)phenyl](phenyl)phosphinic diisopropylamide–borane hemihydrate', Acta Crystallographica Section E Structure Reports Online, vol. 69, no. 2, pp. o282-o283.
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In the title compound, C30H48BNOP2·0.5H2O, the water molecule is disordered about an inversion centre. Both phosphorus atoms shows distortions in their tetrahedral environments with the cyclohexyl substituents disordered over two orientations in a 0.851 (3):0.149 (3) occupancy ratio. The crystal structure is assembledviaO—H...O interactions between pairs of phosphininc amide molecules and water molecules, creating hydrogen-bonded dimers with graph-setR24(8) along [001]. Weak C—H...O interactions are also observed.

Exton, DA, Suggett, DJ, McGenity, TJ & Steinke, M 2013, 'Chlorophyll‐normalized isoprene production in laboratory cultures of marine microalgae and implications for global models', Limnology and Oceanography, vol. 58, no. 4, pp. 1301-1311.
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We used laboratory cultures of marine microalgae to investigate the effects of growth conditions and their taxonomic position on the production of isoprene, a gas that has major effects on atmospheric chemistry and provides stress tolerance to many primary producers. Isoprene was quantified from 21 microalgal strains sampled during exponential growth, using purge‐and‐trap pre‐concentration and gas chromatography with flame‐ionization detection. Isoprene production rates varied by two orders of magnitude between strains (0.03–1.34 µmol [g chlorophyll a]−1 h−1), and were positively correlated with temperature (r2 = 0.52, p < 0.001, n = 59). Three distinct sea surface temperature (SST)‐dependent relationships were found between isoprene and chlorophyll a (µmol [g chlorophyll a]−1 h−1), an improvement in resolution over the single relationship used in previous models: for three polar strains grown at −1°C (slope = 0.03, R2 = 0.76, p < 0.05, n = 9), nine strains grown at 16°C (slope = 0.24, R2 = 0.43, p < 0.05, n = 27 with Dunaliella tertiolecta excluded), and eight strains grown at 26°C (slope = 0.39, R2 = 0.15, p < 0.05, n = 24). We then used a simple model that applied the SST‐dependent nature of isoprene production to three representative bioregions for the growth temperatures used in this study. This approach yielded an est...

Fahimnia, B, Sarkis, J, Dehghanian, F, Banihashemi, N & Rahman, S 2013, 'The impact of carbon pricing on a closed-loop supply chain: an Australian case study', JOURNAL OF CLEANER PRODUCTION, vol. 59, no. 1, pp. 210-225.
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Concerns about industrial and supply chain implications on our natural environment have existed for decades. Climate change and greenhouse gas emissions have caused countries to implement various instruments ranging from taxes, permits and voluntary incentives to required regulatory policies. Given this environment, we develop a unified optimization model for a closed-loop supply chain in which the carbon emission is expressed in terms of dollar carbon cost. This study is one of the first to evaluate the forward and reverse supply chain influences on the carbon footprint. A comparative analysis is completed with a decomposition of cost and environmental influences across supply chain functions. We utilize data from a company located in Australia, where the government is currently introducing a carbon pricing scheme. We find that variations in cost and environmental impacts occur over ranges of carbon pricing. Characteristics and patterns of the numerical results over these ranges provide insights for corporate key strategies and potential additional government policies. These results and implications are analyzed along with limitations and directions for future research. © 2013 Elsevier Ltd. All rights reserved.

Faiz, A, Tjin, G, Harkness, L, Weckmann, M, Bao, S, Black, JL, Oliver, BGG & Burgess, JK 2013, 'The Expression and Activity of Cathepsins D, H and K in Asthmatic Airways', PLoS ONE, vol. 8, no. 3, pp. e57245-e57245.
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Tumstatin is an anti-angiogenic collagen IV α3 fragment, levels of which are reduced in the airways of asthmatics. Its reduction may be due to the degradation by extracellular matrix (ECM) proteases. Cathepsins play a role in ECM remodelling, with cathepsin D, H and K (CTSD, CTSH and CTSK) being associated with lung diseases. CTSD modulates the NC1 domains of collagen molecules including tumstatin, while CTSH and CTSK are involved in ECM degradation. The role of these cathepsins in the regulation of tumstatin in the lung has not previously been examined. We demonstrated that CTSB, D, F, H, K, L and S mRNA was expressed in the airways. Quantification of immunohistochemistry showed that there is no difference in the global expression of CTSD, CTSH and CTSK between asthmatics and non-asthmatics. CTSD and CTSK, but not CTSH had the capacity to degrade tumstatin. No difference was observed in the activity of CTSD and H in bronchoalveolar lavage fluid of asthmatic and non-asthmatics, while CTSK was undetectable. This indicates that while CTSD possesses the potential to directly regulate tumstatin, and thus angiogenesis through this mechanism however, it is not likely to be involved in the dysregulation of tumstatin found in asthmatic airways. © 2013 Faiz et al.

Farrell, H, Brett, S, Ajani, P & Murray, S 2013, 'Distribution of the genus Alexandrium (Halim) and paralytic shellfish toxins along the coastline of New South Wales, Australia', MARINE POLLUTION BULLETIN, vol. 72, no. 1, pp. 133-145.
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Blooms of Alexandrium species, in particular the species Alexandrium catenella, accounted for more than 50% of algal related, shellfish aquaculture harvest zone closures in New South Wales (NSW) Australia since 2005. While there are indications that species of Alexandrium are more abundant than they were formerly, there is little data available on the spatial and temporal distribution and abundance of the genus in NSW. A six and a half year dataset comprising a total of 8649 fortnightly samples from 31 estuaries spread over 2000. km of NSW coastline was analysed. The greatest abundances of Alexandrium spp. were observed during the austral Spring and Summer, in estuaries in the mid and southern latitudes of the state. In identifying these high risk zones, we propose variables such as season, temperature, rainfall and estuarine flushing to be targeted in intensive site specific studies, to support the development of predictive tools for resource managers. © 2013 Elsevier Ltd.

Fatima-Shad, K 2013, 'Peripheral markers of Alzheimer's disease: Surveillance of white blood cells', Synapse (New York), vol. 67, no. 8, pp. 541-543.
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Inflammation is part of the complex biological response of vascular tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. This is a mechanism of innate immunity, which may cause an increase in the number of monocytes and neutrophils circulating in the blood. Literature indicated that chronic inflammation might be a factor in developing neurological problems, including Alzheimer’s, Parkinson’s and other similar illnesses. Our main objective is to identify peripheral markers of Alzheimer’s disease and for that purpose; we are looking at the profile of white blood cells focusing on monocytes, neutrophils, lymphocytes and basophils. Twenty-seven patients of Alzheimer’s disease (AD), diagnosed by magnetic resonance imaging and neuropsychological tests were observed for their blood profile. Key observations during this study were that the levels of monocytes in the blood of the diagnosed AD patients were high irrespective of their age and sex. For those patients whose monocytes were in normal range their neutrophil levels were significantly high. Whereas blood levels of lymphocytes and basophils were found to be constantly low. Escalated levels of monocytes and neutrophils are hallmarks of chronic inflammation and may be precursor to Alzheimer’s disease. A low lymphocyte count specifies that the body’s resistance to fight infection is substantially reduced, whereas low basophil levels indicates their over utilization due to chronic allergic inflammatory condition. Future studies involved closer look at the cytokines produced by these white blood cells especially TNF IL-1, and IL-12, which are products of monocytes. Likewise, blood glucose and creatinine levels were high whereas calcium ions were low. Our studies indicated that white blood cells along with other inflammatory byproducts may act as peripheral markers for early diagnosis of Alzheimer’s disease.

Feary, DA, Burt, JA, Bauman, AG, Al Hazeem, S, Abdel-Moati, MA, Al-Khalifa, KA, Anderson, DM, Amos, C, Baker, A, Bartholomew, A, Bento, R, Cavalcante, GH, Chen, CA, Coles, SL, Dab, K, Fowler, AM, George, D, Grandcourt, E, Hill, R, John, DM, Jones, DA, Keshavmurthy, S, Mahmoud, H, Tapeh, MMO, Mostafavi, PG, Naser, H, Pichon, M, Purkis, S, Riegl, B, Samimi-Namin, K, Sheppard, C, Samiei, JV, Voolstra, CR & Wiedenmann, J 2013, 'Critical research needs for identifying future changes in Gulf coral reef ecosystems', MARINE POLLUTION BULLETIN, vol. 72, no. 2, pp. 406-416.
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Expert opinion was assessed to identify current knowledge gaps in determining future changes in Arabian/Persian Gulf (thereafter `Gulf) coral reefs. Thirty-one participants submitted 71 research questions that were peer-assessed in terms of scientific importance (i.e., filled a knowledge gap and was a research priority) and efficiency in resource use (i.e., was highly feasible and ecologically broad). Ten research questions, in six major research areas, were highly important for both understanding Gulf coral reef ecosystems and also an efficient use of limited research resources. These questions mirrored global evaluations of the importance of understanding and evaluating biodiversity, determining the potential impacts of climate change, the role of anthropogenic impacts in structuring coral reef communities, and economically evaluating coral reef communities. These questions provide guidance for future research on coral reef ecosystems within the Gulf, and enhance the potential for assessment and management of future changes in this globally significant region.

Fierro, AO & Leslie, LM 2013, 'Links between Central West Western Australian Rainfall Variability and Large-Scale Climate Drivers', Journal of Climate, vol. 26, no. 7, pp. 2222-2246.
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AbstractOver the past century, and especially after the 1970s, rainfall observations show an increase (decrease) of the wet summer (winter) season rainfall over northwest (southwest) Western Australia. The rainfall in central west Western Australia (CWWA), however, has exhibited comparatively much weaker coastal trends, but a more prominent inland increase during the wet summer season. Analysis of seasonally averaged rainfall data from a group of stations, representative of both the coastal and inland regions of CWWA, revealed that rainfall trends during the 1958–2010 period in the wet months of November–April were primarily associated with El Niño–Southern Oscillation (ENSO), and with the southern annular mode (SAM) farther inland. During the wet months of May–October, the Indian Ocean dipole (IOD) showed the most robust relationships. Those results hold when the effects of ENSO or IOD are excluded, and were confirmed using a principal component analysis of sea surface temperature (SST) anomalies, rainfall wavelet analyses, and point-by-point correlations of rainfall with global SST anomaly fields. Although speculative, given their long-term averages, reanalysis data suggest that from 1958 to 2010 the increase in CWWA inland rainfall largely is attributable to an increasing cyclonic anomaly trend over CWWA, bringing onshore moist tropical flow to the Pilbara coast. During May–October, the flow anomaly exhibits a transition from an onshore to offshore flow regime in the 2001–10 decade, which is consistent with the observed weaker drying trend during this period.

Finkelstein, DI, George, JL, Adlard, PA, Masters, CL, Hare, DJ, Doble, PA, Gautier, E, Parsons, J, Kok, G, Huggins, P, Barnham, KJ, Bush, AI & Cherny, RA 2013, 'PBT434, a novel 8-hydroxyquinazolinone, preserves nigro-striatal circuitry, improves motor performance and inhibits alpha synuclein accumulation in animal models of Parkinson's disease by modulation of iron homeostasis', MOVEMENT DISORDERS, vol. 28, pp. S369-S369.

Fletcher, S, Van Hal, S, Andresen, D, McLaws, M-L, Stark, D, Harkness, J & Ellis, J 2013, 'Gastrointestinal pathogen distribution in symptomatic children in Sydney, Australia', Journal of Epidemiology and Global Health, vol. 3, no. 1, pp. 11-11.
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There is limited information on the causes of paediatric diarrhoea in Sydney. This cross-sectional study used clinical and microbiological data to describe the clinical features and pathogens associated with gastrointestinal illnesses for children presenting to two major public hospitals in Sydney with diarrhoea, for the period January 2007December 2010. Of 825 children who tested positive for an enteric pathogen, 430 medical records were reviewed. Adenovirus, norovirus and rotavirus were identified in 20.8%, 20.3% and 21.6% of reviewed cases, respectively. Younger children were more likely to have adenovirus and norovirus compared with rotavirus (P = 0.001). More viruses were detected in winter than in the other three seasons (P = 0.001). Rotavirus presented a distinct seasonal pattern with the lowest rates occurring in the warm months and peaking in the cooler months. Adenovirus showed a less consistent monthly trend, and norovirus detection increased in the cooler months (P = 0.008). A decline in the number of rotavirus cases was observed after mid-2008. The majority of childhood diarrhoeal illnesses leading to hospital presentations in Sydney are caused by enteric viruses with most infections following clear seasonal patterns. However, a sustained decrease in the incidence of rotavirus infections has been observed over the study period.

Fletcher, SM, McLaws, M-L & Ellis, JT 2013, 'Prevalence of Gastrointestinal Pathogens in Developed and Developing Countries: Systematic Review and Meta-Analysis', Journal of Public Health Research, vol. 2, no. 1, pp. jphr.2013.e9-jphr.2013.e9.
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Diarrhoeal illness is a leading cause of child mortality and morbidity worldwide. There are no precise or current estimates of the types and prevalence of pathogens associated with diarrheal illnesses in developed and developing settings. This systematic review assessed data from 60 studies published in the English language from five developing regions and developed countries worldwide to provide regional estimates of enteric pathogens affecting children. The random-effect method was used to establish the weighted average prevalence of pathogens in adults and children for each region. Significantly more pathogens were reported by studies from developing regions compared with Organisation for Economic Co-operation and Development countries (P<0.016). The identification rates of pathogens from community based and hospital based studies were similar (58.5% and 58.1% respectively, P<0.619). The overall detection of enteric pathogens in developing countries was higher in adults (74.8%; 95% CI 63.1-83.8%) compared with children (56.7%; 95% CI 53.0-60.4%) (P<0.001). Rotavirus was the most frequently detected pathogen in all regions with the highest rate, 24.8% (95% CI 18.0-33.1%), detected in the developed countries. This systematic review is the first to provide an estimate of the prevalence of enteric pathogens associated with diarrhoeal illnesses in adults and children in developed and developing settings. While pathogen detection rate is greater in developing regions the consistently high prevalence of rotavirus in both developed and developing settings underscores the urgent need for access to rotavirus vaccines. Increased travel between developing and developed countries increases disease risk, and hence developed countries have a vested interest in supporting vaccine accessibility in developing settings.

Foster, PS, Plank, M, Collison, A, Tay, HL, Kaiko, GE, Li, J, Johnston, SL, Hansbro, PM, Kumar, RK, Yang, M & Mattes, J 2013, 'The emerging role of microRNAs in regulating immune and inflammatory responses in the lung', Immunological Reviews, vol. 253, no. 1, pp. 198-215.
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SummaryChronic inflammatory diseases of the lung are leading causes of morbidity and mortality worldwide. Many of these disorders can be attributed to abnormal immune responses to environmental stimuli and infections. As such, understanding the innate host defense pathways and their regulatory systems will be critical to developing new approaches to treatment. In this regard, there is increasing interest in the role of microRNAs (miRNAs) in the regulation of pulmonary innate host defense responses and the inflammatory sequelae in respiratory disease. In this review, we discuss recent findings that indicate an important role for miRNAs in the regulation in mouse models of various respiratory diseases and in host defense against bacterial and viral infection. We also discuss the potential utility and limitations of targeting these molecules as anti‐inflammatory strategies and also as a means to improve pathogen clearance from the lung.

Fowler, AM & Booth, DJ 2013, 'Seasonal Dynamics of Fish Assemblages on Breakwaters and Natural Rocky Reefs in a Temperate Estuary: Consistent Assemblage Differences Driven by Sub-Adults', PLoS ONE, vol. 8, no. 9, pp. e75790-e75790.
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Development of infrastructure around cities is rapidly increasing the amount of artificial substrate (termed artificial reef, 'AR') in coastal marine habitats. However, effects of ARs on marine communities remain unknown, because it is unclear whether ARs can maintain similar communities to natural reefs. We investigated whether well-established (> 30 years old) breakwaters could consistently approximate fish assemblages on interspersed rocky reefs in a temperate estuary over 6 consecutive seasons using regular visual surveys between June 2009 (winter) and November 2010 (spring). We examined whether assemblage differences between reef types were driven by differences in juvenile recruitment, or were related to differences in older life-stages. Assemblages on both reef types were dominated by juveniles (61% of individuals) and sub-adults (34% of individuals). Seasonal fluctuations in assemblage parameters (species richness, diversity, sub-adult abundance) were similar between reef types, and levels of species diversity and assemblage composition were generally comparable. However, abundance and species richness were consistently higher (1.9-7.6 and 1.3-2.6 times, respectively) on breakwaters. These assemblage differences could not be explained by differences in juvenile recruitment, with seasonal patterns of recruitment and juvenile species found to be similar between reef types. In contrast, abundances of sub-adults were consistently higher (1.1-12 times) at breakwaters, and assemblage differences appeared to be driven by this life-stage. Our results indicate that breakwaters in temperate estuaries are capable of supporting abundant and diverse fish assemblages with similar recruitment process to natural reefs. However, breakwaters may not approximate all aspects of natural assemblage structure, with differences maintained by a single-life stage in some cases. © 2013 Fowler, Booth et al.

Frederiksen, M, Bochenkov, VE, Cortie, MB & Sutherland, DS 2013, 'Plasmon Hybridization and Field Confinement in Multilayer Metal-Dielectric Nanocups', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 117, no. 30, pp. 15782-15789.
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Large-area arrays of dispersed multilayer gold-dielectric nanocups were fabricated by colloidal lithography and studied by extinction spectroscopy. Hybridization of the elemental plasmons of the individual nanocups gave rise to new resonance peaks in the visible and near-infrared regions of the extinction spectrum. Transmission electron microscopy was used to confirm the fabricated structure geometry, and the optical properties of the arrays were studied by UV-vis-NIR spectroscopy and finite-difference time-domain (FDTD) simulations. The nature of the resonances was elucidated from Efield plots and charge plots showing clear hybridized modes. We observe a dominant hybridized dipolar mode combining a bonding and antibonding mode at the two caps. A high-energy antibonding (antisymmetric) quadrupolar mode of an individual nanocup is revealed through hybridization with an elemental mode on the second nanocup. A lowenergy tunable cavity mode with a very small mode volume is observed in the near-IR range.

Fung, KY, Mangan, NE, Cumming, H, Horvat, JC, Mayall, JR, Stifter, SA, De Weerd, N, Roisman, LC, Rossjohn, J, Robertson, SA, Schjenken, JE, Parker, B, Gargett, CE, Nguyen, HPT, Carr, DJ, Hansbro, PM & Hertzog, PJ 2013, 'Interferon-ε Protects the Female Reproductive Tract from Viral and Bacterial Infection', Science, vol. 339, no. 6123, pp. 1088-1092.
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A Role for IFN-ɛ Type I interferons (IFNs) are critical cytokines involved in host defense against pathogens, particularly viruses. IFN-ɛ is an IFN-like gene encoded within the type I IFN locus in mice and humans whose function has not been characterized. Fung et al. (p. 1088 ) created mice with a genetic deletion in Ifn -ɛ and found that, like other type I IFNs, IFN-ɛ signals through the IFN-α receptors 1 and 2. However, unlike these other cytokines, which are primarily expressed by immune cells and are induced upon immune cell triggering, IFN-ɛ was expressed exclusively by epithelial cells of the female reproductive tract in both mice and humans and its expression was hormonally regulated. IFN-ɛ–deficient mice were more susceptible to infection with herpes simplex virus 2 and Chlamydia muridarum , two common sexually transmitted pathogens.

Fung, T, Wang, JJJ & Seneta, E 2013, 'Contaminated Variance–Mean mixing model', Computational Statistics & Data Analysis, vol. 67, pp. 258-267.
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The Generalised Normal Variance-Mean (GNVM) model in which the mixing random variable is Gamma distributed is considered. This model generalises the popular Variance-Gamma (VG) distribution. This GNVM model can be interpreted as the addition of noise to a (skew) VG base. The discussion is based on goodness of fit criteria and on parameter estimation. The conclusion is that the shape of the VG distribution can be adjusted in a favourable way by adding noise. © 2013 Elsevier B.V. All rights reserved.

Gale, PA, Pérez-Tomás, R & Quesada, R 2013, 'Anion Transporters and Biological Systems', Accounts of Chemical Research, vol. 46, no. 12, pp. 2801-2813.
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Gao, C, Jin, X, Yan, X, An, P, Zhang, Y, Liu, L, Tian, H, Liu, W, Yao, X & Tang, Y 2013, 'A small molecular fluorescent sensor for highly selectivity of zinc ion', Sensors and Actuators B: Chemical, vol. 176, pp. 775-781.
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Gao, F, Pant, R, Li, E, Poulton, CG, Choi, D-Y, Madden, SJ, Luther-Davies, B & Eggleton, BJ 2013, 'On-chip high sensitivity laser frequency sensing with Brillouin mutually-modulated cross-gain modulation', Optics Express, vol. 21, no. 7, pp. 8605-8605.
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We report the first demonstration of a photonic-chip laser frequency sensor using Brillouin mutually-modulated cross-gain modulation (MMXGM). A large sensitivity (∼9.5 mrad/kHz) of the modulation phase shift to probe carrier frequency is demonstrated at a modulation frequency of 50 kHz using Brillouin MMXGM in a ∼7 cm long chalcogenide rib waveguide. © 2013 Optical Society of America.

Garby, TJ, Walter, MR, Larkum, AWD & Neilan, BA 2013, 'Diversity of cyanobacterial biomarker genes from the stromatolites of Shark Bay, Western Australia', Environmental Microbiology, vol. 15, no. 5, pp. 1464-1475.
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SummaryFamilies of closely related chemical compounds, which are relatively resistant to degradation, are often used as biomarkers to help trace the evolutionary history of early groups of organisms and the environments in which they lived. Biomarkers derived from hopanoid variations are particularly useful in determining bacterial community compositions. 2‐Methylhopananoids have been thought to be diagnostic for cyanobacteria, and 2‐methylhopanes in the geological record are taken as evidence for the presence of cyanobacteria‐containing communities at the time of sediment deposition. Recently, however, doubt has been cast on the validity of 2‐methylhopanes as cyanobacterial biomarkers, since non‐cyanobacterial species have been shown to produce significant amounts of 2‐methylhopanoids. This study examines the diversity of hpnP, the hopanoid biosynthesis gene coding for the enzyme that methylates hopanoids at the C2 position. Genomic DNA isolated from stromatolite‐associated pustular and smooth microbial mat samples from Shark Bay, Western Australia, was analysed for bacterial diversity, and used to construct an hpnP clone library. A total of 117 partial hpnP clones were sequenced, representing 12 operational taxonomic units (OTUs). Phylogenetic analysis showed that 11 of these OTUs, representing 115 sequences, cluster within the cyanobacterial clade. We conclude that the dominant types of microorganisms with the detected capability of producing 2‐methylhopanoids within pustular and smooth microbial mats in Shark Bay are cyanobacteria.

Garces, E, Alacid, E, Rene, A, Petrou, K & Simo, R 2013, 'Host-released dimethylsulphide activates the dinoflagellate parasitoid Parvilucifera sinerae', ISME JOURNAL, vol. 7, no. 5, pp. 1065-1068.
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Parasitoids are a major top-down cause of mortality of coastal harmful algae, but the mechanisms and strategies they have evolved to efficiently infect ephemeral blooms are largely unknown. Here, we show that the generalist dinoflagellate parasitoid Parvilucifera sinerae (Perkinsozoa, Alveolata) is activated from dormancy, not only by Alexandrium minutum cells but also by culture filtrates. We unequivocally identified the algal metabolite dimethylsulphide (DMS) as the density-dependent cue of the presence of potential host. This allows the parasitoid to alternate between a sporangium-hosted dormant stage and a chemically-activated, free-living virulent stage. DMS-rich exudates of resistant dinoflagellates also induced parasitoid activation, which we interpret as an example of coevolutionary arms race between parasitoid and host. These results further expand the involvement of dimethylated sulphur compounds in marine chemical ecology, where they have been described as foraging cues and chemoattractants for mammals, turtles, birds, fish, invertebrates and plankton microbes.© 2013 International Society for Microbial Ecology All rights reserved.

Garcia, TP, Muller, S, Carroll, RJ, Dunn, TN, Thomas, AP, Adams, SH, Pillai, SD & Walzem, RL 2013, 'Structured variable selection with q-values', Biostatistics, vol. 14, no. 4, pp. 695-707.
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When some of the regressors can act on both the response and other explanatory variables, the already challenging problem of selecting variables when the number of covariates exceeds the sample size becomes more difficult. A motivating example is a metabolic study in mice that has diet groups and gut microbial percentages that may affect changes in multiple phenotypes related to body weight regulation. The data have more variables than observations and diet is known to act directly on the phenotypes as well as on some or potentially all of the microbial percentages. Interest lies in determining which gut microflora influence the phenotypes while accounting for the direct relationship between diet and the other variables. A new methodology for variable selection in this context is presented that links the concept of q-values from multiple hypothesis testing to the recently developed weighted Lasso. © The Author 2013. Published by Oxford University Press. All rights reserved.

Gauci, VJ, Padula, MP & Coorssen, JR 2013, 'Coomassie blue staining for high sensitivity gel-based proteomics', Journal of Proteomics, vol. 90, no. 1, pp. 96-106.
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Gel electrophoresis, particularly one- (1DE) and two-dimensional electrophoresis (2DE), remain among the most widely used top-down methods for resolving and analysing proteomes. Detection of the resulting protein maps relies on staining (i.e. colloidal coomassie blue (CCB) or SYPRO Ruby (SR), in addition to many others). Fluorescent in-gel protein stains are generally preferred for higher sensitivity, reduced background, and wider dynamic range. Although traditionally used for densitometry, CBB has fluorescent properties. Indeed, infrared detection of CCB stained protein was comparable to SR, with BioSafe (Bio-Rad) and the Neuhoff formulation (NCCB) identified as potentially superior to SR; a minor sensitivity issue encountered in gel-resolved proteomes; might have been due to the unified staining protocol used. Here the staining protocol for both CCB formulations was optimised, yielding improved selectivity without affecting sensitivity; the resulting linear dynamic range was similar for BioSafe and NCCB and somewhat better than SR. 2D gel-based analyses of mouse brain and Arabidopsis thaliana (leaf) proteomes indicated markedly superior spot detection using the NCCB formulation. Thus more sensitive, quantitative in-gel protein analyses can be achieved using NCCB, at a fraction of the cost. This article is part of a Special Issue entitled: From Genome to Proteome: Open Innovations. © 2013 Elsevier B.V.

Gazioglu, S, Wei, J, Jennings, EM & Carroll, RJ 2013, 'A Note on Penalized Regression Spline Estimation in the Secondary Analysis of Case-Control Data', Statistics in Biosciences, vol. 5, no. 2, pp. 250-260.
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Primary analysis of case-control studies focuses on the relationship between disease (D) and a set of covariates of interest (Y,X). A secondary application of the case-control study, often invoked in modern genetic epidemiologic association studies, is to investigate the interrelationship between the covariates themselves. The task is complicated due to the case-control sampling, and to avoid the biased sampling that arises from the design, it is typical to use the control data only. In this paper, we develop penalized regression spline methodology that uses all the data, and improves precision of estimation compared to using only the controls. A simulation study and an empirical example are used to illustrate the methodology. © 2013 International Chinese Statistical Association.

Gentle, AR, Dybdal, KL & Smith, GB 2013, 'Polymeric mesh for durable infra-red transparent convection shields: Applications in cool roofs and sky cooling', SOLAR ENERGY MATERIALS AND SOLAR CELLS, vol. 115, pp. 79-85.
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Polyethylene (PE) mesh is shown to strongly suppress convective gain at night and to have a high black body transmittance, making it suited to use in radiative cooling. Advantages over previous non-porous cover systems include; self-supporting for large areas, good mechanical stability, low cost, retractable, and a long outdoor lifetime. This study compares performance with a PE mesh cover to that of an impermeable PE cover and to no cover. Convective suppression and net cooling for different wind speeds and ambient temperatures are examined. The impact of such a mesh on night sky cooling rates for a mesh over water, then over a roof is presented. For the roof the associated rise in surface temperature is also measured and modelled in the daytime. Effective permeabilities are not the same as geometric permeability. They are extracted by comparing simulation results with data and are found to depend only weakly on wind speed. They are most sensitive to magnitude and sign of the difference between roof and ambient temperatures. They differ significantly between night and day, that is for convective warming and cooling respectively. © 2013 Elsevier B.V. All rights reserved.

Gentle, AR, Smith, GB & Watkins, SE 2013, 'Discharge amplified photo-emission from ultra-thin films applied to tuning work function of transparent electrodes in organic opto-electronic devices', APPLIED SURFACE SCIENCE, vol. 285, no. PARTB, pp. 110-114.
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A novel photoemission technique utilising localised discharge amplification of photo-yield is reported. It enables fast, accurate measurement of work function and ionisation potential for ultra-thin buffer layers vacuum deposited onto single and multilayer transparent conducting electrodes for organic solar cells and OLED's. Work function in most traditional transparent electrodes has to be raised to maximise charge transfer while high transmittance and high conductance must be retained. Results are presented for a range of metal oxide buffers, which achieve this goal. This compact photo-yield spectroscopy tool with its fast turn-around has been a valuable development aid since ionisation potential can vary significantly as deposition conditions change slightly, and as ultra-thin films grow. It has also been useful in tracking the impact of different post deposition cleaning treatments along with some storage and transport protocols, which can adversely reduce ionisation potential and hence subsequent device performance. © 2013 Elsevier B.V. All rights reserved.

George, AM & Jones, PM 2013, 'An Asymmetric Post-Hydrolysis State of the ABC Transporter ATPase Dimer', PLoS ONE, vol. 8, no. 4, pp. e59854-e59854.
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ABC transporters are a superfamily of enzyme pumps that hydrolyse ATP in exchange for translocation of substrates across cellular membranes. Architecturally, ABC transporters are a dimer of transmembrane domains coupled to a dimer of nucleotide binding domains (NBDs): the NBD dimer contains two ATP-binding sites at the intersubunit interface. A current controversy is whether the protomers of the NBD dimer separate during ATP hydrolysis cycling, or remain in constant contact. In order to investigate the ABC ATPase catalytic mechanism, MD simulations using the recent structure of the ADP+Pi-bound MJ0796 isolated NBD dimer were performed. In three independent simulations of the ADP+Pi/apo state, comprising a total of .0.5 ms, significant opening of the apo (empty) active site was observed; occurring by way of intrasubunit rotations between the core and helical subdomains within both NBD monomers. In contrast, in three equivalent simulations of the ATP/apo state, the NBD dimer remained close to the crystal structure, and no opening of either active site occurred. The results thus showed allosteric coupling between the active sites, mediated by intrasubunit conformational changes. Opening of the apo site is exquisitely tuned to the nature of the ligand, and thus to the stage of the reaction cycle, in the opposite site. In addition to this, in also showing how one active site can open, sufficient to bind nucleotide, while the opposite site remains occluded and bound to the hydrolysis products ADP+Pi, the results are consistent with a Constant Contact Model. Conversely, they show how there may be no requirement for the NBD protomers to separate to complete the catalytic cycle.

Gerace, D, Ren, B, Hawthorne, WJ, Byrne, MR, Phillips, PM, O'Brien, BA, Nassif, N, Alexander, IE & Simpson, AM 2013, 'Pancreatic Transdifferentiation in Porcine Liver Following Lentiviral Delivery of Human Furin-Cleavable Insulin', TRANSPLANTATION PROCEEDINGS, vol. 45, no. 5, pp. 1869-1874.
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Type I diabetes mellitus (TID) results from the autoimmune destruction of the insulin-producing pancreatic β-cells. Gene therapy is one strategy being actively explored to cure TID by affording non-β-cells the ability to secrete insulin in response to physiologic stimuli. In previous studies, we used a novel surgical technique to express furin-cleavable human insulin (INS-FUR) in the livers of streptozotocin (STZ)-diabetic Wistar rats and nonobese diabetic (NOD) mice with the use of the HMD lentiviral vector. Normoglycemia was observed for 500 and 150 days, respectively (experimental end points). Additionally, some endocrine transdifferentiation of the liver, with storage of insulin in granules, and expression of some β-cell transcription factors (eg, Pdx1, Neurod1, Neurog3, Nkx2-2, Pax4) and pancreatic hormones in both studies. The aim of this study was to determine if this novel approach could induce liver to pancreatic transdifferentiation to reverse diabetes in pancreatectomized Westran pigs. Nine pigs were used in the study, however only one pig maintained normal fasting blood glucose levels for the period from 10 to 44 days (experimental end point). This animal was given 2.8 × 10 9 transducing units/kg of the lentiviral vector expressing INS-FUR. A normal intravenous glucose tolerance test was achieved at 30 days. Reverse-transcription polymerase chain reaction analysis of the liver tissue revealed expression of several β-cell transcription factors, including the key factors, Pdx-1 and Neurod1, pancreatic hormones, glucagon, and somatostatin; however, endogenous pig insulin was not expressed. Triple immunofluorescence showed extensive insulin expression, as was previously observed in our studies with rodents. Additionally, a small amount of glucagon and somatostatin protein expression was seen. Collectively, these data indicate that pancreatic transdifferentiation of the liver tissue had occurred. Our data suggest that this regimen may ultimately ...

Gladstone, W, Curley, B & Shokri, MR 2013, 'Environmental impacts of tourism in the Gulf and the Red Sea', Marine Pollution Bulletin, vol. 72, no. 2, pp. 375-388.
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The Gulf and Red Sea possess diverse coastal and marine environments that support rapidly expanding mass tourism. Despite the associated environmental risks, there is no analysis of the tourism-related literature or recent analysis of impacts. Environmental issues reported in 101 publications (25 from the Gulf, 76 from the Red Sea) include 61 purported impacts (27 from the Gulf, 45 from the Red Sea). Gulf literature includes quantitative studies (68% publications) and reviews (32%), and addresses mostly land reclamation and artificial habitats. Most Gulf studies come from Iran and UAE (64%). Red Sea literature includes quantitative studies (81%) and reviews (11%), with most studies occurring in Egypt (70%). The most published topics relate to coral breakage and its management. A full account of tourisms environmental impacts is constrained by limited tourism data, confounding of impacts with other coastal developments, lack of baseline information, shifting baselines, and fragmentation of research across disciplines.

Gleason, FH, van Ogtrop, F, Lilje, O & Larkum, AWD 2013, 'Ecological roles of zoosporic parasites in blue carbon ecosystems', Fungal Ecology, vol. 6, no. 5, pp. 319-327.
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Pathosystems describe the relationships between parasites, hosts and the environment. Generally these systems remain in a dynamic equilibrium over time. In this review we examine some of the evidence for the potential impacts of change in dynamic equilibrium in blue carbon ecosystems and the relationships to the amount of stored carbon. Blue carbon ecosystems are marine and estuarine ecosystems along the coasts. Virulent pathogens can be introduced into ecosystems along with non-native hosts. Alteration of environmental conditions, such as temperature, pH and salinity, may cause parasites to dominate the pathosystems resulting in significant decreases in productivity and population sizes of producer hosts and in changes in the overall species composition and function in these ecosystems. Such changes in blue carbon ecosystems may result in accelerated release of carbon dioxide back into the ocean and atmosphere, which could then drive further changes in the global climate. The resiliency of these ecosystems is not known. However, recent evidence suggests that significant proportions of blue carbon ecosystems have already disappeared.

Gloag, ES, Javed, MA, Wang, H, Gee, ML, Wade, SA, Turnbull, L & Whitchurch, CB 2013, 'Stigmergy', Communicative & Integrative Biology, vol. 6, no. 6, pp. e27331-e27331.
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Bacterial biofilms are complex multicellular communities that are often associated with the emergence of largescale patterns across the biofilm. How bacteria self-organize to form these structured communities is an area of active research. We have recently determined that the emergence of an intricate network of trails that forms during the twitching motility mediated expansion of Pseudomonas aeruginosa biofilms is attributed to an interconnected furrow system that is forged in the solidified nutrient media by aggregates of cells as they migrate across the media surface. This network acts as a means for self-organization of collective behavior during biofilm expansion as the cells following these vanguard aggregates were preferentially confined within the furrow network resulting in the formation of an intricate network of trails of cells. Here we further explore the process by which the intricate network of trails emerges. We have determined that the formation of the intricate network of furrows is associated with significant remodeling of the sub-stratum underlying the biofilm. The concept of stigmergy has been used to describe a variety of selforganization processes observed in higher organisms and abiotic systems that involve indirect communication via persistent cues in the environment left by individuals that influence the behavior of other individuals of the group at a later point in time. We propose that the concept of stigmergy can also be applied to describe self-organization of bacterial biofilms and can be included in the repertoire of systems used by bacteria to coordinate complex multicellular behaviors. © 2013 Landes Bioscience.

Gloag, ES, Turnbull, L, Huang, A, Vallotton, P, Wang, H, Nolan, LM, Mililli, L, Hunt, C, Lu, J, Osvath, SR, Monahan, LG, Cavaliere, R, Charles, IG, Wand, MP, Gee, ML, Prabhakar, R & Whitchurch, CB 2013, 'Self-organization of bacterial biofilms is facilitated by extracellular DNA', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 110, no. 28, pp. 11541-11546.
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Twitching motility-mediated biofilm expansion is a complex, multicellular behavior that enables the active colonization of surfaces by many species of bacteria. In this study we have explored the emergence of intricate network patterns of interconnected trails that form in actively expanding biofilms of Pseudomonas aeruginosa. We have used high-resolution, phase-contrast time-lapse microscopy and developed sophisticated computer vision algorithms to track and analyze individual cell movements during expansion of P. aeruginosa biofilms. We have also used atomic force microscopy to examine the topography of the substrate underneath the expanding biofilm. Our analyses reveal that at the leading edge of the biofilm, highly coherent groups of bacteria migrate across the surface of the semisolid media and in doing so create furrows along which following cells preferentially migrate. This leads to the emergence of a network of trails that guide mass transit toward the leading edges of the biofilm. We have also determined that extracellular DNA (eDNA) facilitates efficient traffic flow throughout the furrow network by maintaining coherent cell alignments, thereby avoiding traffic jams and ensuring an efficient supply of cells to the migrating front. Our analyses reveal that eDNA also coordinates the movements of cells in the leading edge vanguard rafts and is required for the assembly of cells into the 'bulldozer' aggregates that forge the interconnecting furrows. Our observations have revealed that large-scale self-organization of cells in actively expanding biofilms of P. aeruginosa occurs through construction of an intricate network of furrows that is facilitated by eDNA.

Gloeckl, S, Ong, VA, Patel, P, Tyndall, JDA, Timms, P, Beagley, KW, Allan, JA, Armitage, CW, Turnbull, L, Whitchurch, CB, Merdanovic, M, Ehrmann, M, Powers, JC, Oleksyszyn, J, Verdoes, M, Bogyo, M & Huston, WM 2013, 'Identification of a serine protease inhibitor which causes inclusion vacuole reduction and is lethal to Chlamydia trachomatis', MOLECULAR MICROBIOLOGY, vol. 89, no. 4, pp. 676-689.
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The mechanistic details of the pathogenesis of Chlamydia, an obligate intracellular pathogen of global importance, have eluded scientists due to the scarcity of traditional molecular genetic tools to investigate this organism. Here we report a chemical biology strategy that has uncovered the first essential protease for this organism. Identification and application of a unique CtHtrA inhibitor (JO146) to cultures of Chlamydia resulted in a complete loss of viable elementary body formation. JO146 treatment during the replicative phase of development resulted in a loss of Chlamydia cell morphology, diminishing inclusion size, and ultimate loss of inclusions from the host cells. This completely prevented the formation of viable Chlamydia elementary bodies. In addition to its effect on the human Chlamydia trachomatis strain, JO146 inhibited the viability of the mouse strain, Chlamydia muridarum, both in vitro and in vivo. Thus, we report a chemical biology approach to establish an essential role for ChlamydiaCtHtrA. The function of CtHtrA for Chlamydia appears to be essential for maintenance of cell morphology during replicative the phase and these findings provide proof of concept that proteases can be targeted for antimicrobial therapy for intracellular pathogens. © 2013 John Wiley & Sons Ltd.

Gobler, CJ, Lobanov, AV, Tang, Y-Z, Turanov, AA, Zhang, Y, Doblin, M, Taylor, GT, Sanudo-Wilhelmy, SA, Grigoriev, IV & Gladyshev, VN 2013, 'The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens', ISME JOURNAL, vol. 7, no. 7, pp. 1333-1343.
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The trace element selenium (Se) is required for the biosynthesis of selenocysteine (Sec), the 21st amino acid in the genetic code, but its role in the ecology of harmful algal blooms (HABs) is unknown. Here, we examined the role of Se in the biology and ecology of the harmful pelagophyte, Aureococcus anophagefferens, through cell culture, genomic analyses and ecosystem studies. This organism has the largest and the most diverse selenoproteome identified to date that consisted of at least 59 selenoproteins, including known eukaryotic selenoproteins, selenoproteins previously only detected in bacteria, and novel selenoproteins. The A. anophagefferens selenoproteome was dominated by the thioredoxin fold proteins and oxidoreductase functions were assigned to the majority of detected selenoproteins. Insertion of Sec in these proteins was supported by a unique Sec insertion sequence. Se was required for the growth of A. anophagefferens as cultures grew maximally at nanomolar Se concentrations. In a coastal ecosystem, dissolved Se concentrations were elevated before and after A. anophagefferens blooms, but were reduced by 495% during the peak of blooms to 0.05 nM. Consistent with this pattern, enrichment of seawater with selenite before and after a bloom did not affect the growth of A. anophagefferens, but enrichment during the peak of the bloom significantly increased population growth rates. These findings demonstrate that Se inventories, which can be anthropogenically enriched, can support proliferation of HABs, such as A. anophagefferens through its synthesis of a large arsenal of Se-dependent oxidoreductases that fine-tune cellular redox homeostasis.

Godecke, E, Armstrong, E, Bernhardt, J, Middleton, S, Rai, T, Holland, A, Cadilhac, DA, Whitworth, A, Rose, M, Ciccone, N & Hankey, GJ 2013, 'Very Early Rehabilitation in SpEech (VERSE): the development of an Australian randomised controlled trial of aphasia therapy after stroke', INTERNATIONAL JOURNAL OF STROKE, vol. 8, pp. 44-45.

Godecke, E, Rai, T, Ciccone, N, Armstrong, E, Granger, A & Hankey, GJ 2013, 'Amount of Therapy Matters in Very Early Aphasia Rehabilitation after Stroke: A Clinical Prognostic Model', SEMINARS IN SPEECH AND LANGUAGE, vol. 34, no. 3, pp. 129-141.
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Background and Aim The effects of very early aphasia therapy on recovery are equivocal. This article examines predictors of very early aphasia recovery through statistical modeling. Methods This study involved a secondary analysis of merged data from two randomized, single-blind trials conducted in Australian acute and subacute hospitals. Study 1 (n = 59) compared daily therapy to usual ward care for up to 4 weeks poststroke in patients with moderate to severe aphasia. Study 2 (n = 20) compared daily group therapy to daily individual therapy for 20 1-hour sessions over 5 weeks, in patients with mild to severe aphasia. The primary outcome measure was the Western Aphasia Battery Aphasia Quotient (AQ) at therapy completion. This analysis used regression modeling to examine the effects of age, baseline AQ and baseline modified Rankin Scale (mRS), average therapy amount, therapy intensity, and number of therapy sessions on aphasia recovery. Results Baseline AQ (p = 0.047), average therapy amount (p = 0.030), and baseline mRS (p = 0.043) were significant predictors in the final regression model, which explained 30% (p < 0.001) of variance in aphasia recovery. Conclusion The amount of very early aphasia therapy could significantly affect communication outcomes at 4 to 5 weeks poststroke. Further studies should include amount of therapy provided to enhance reliability of prognostic modeling in aphasia recovery. © 2013 by Thieme Medical Publishers, Inc.

Goerigk, L & Reimers, JR 2013, 'Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries', JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 9, no. 7, pp. 3240-3251.
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We demonstrate how quantum chemical Hartree-Fock (HF) or density functional theory (DFT) optimizations with small basis sets of peptide and water cluster structures are decisively improved if London-dispersion effects, the basis-set-superposition error (BSSE), and other basis-set incompleteness errors are addressed. We concentrate on three empirical corrections to these problems advanced by Grimme and co-workers that lead to computational strategies that are both accurate and efficient. Our analysis encompasses a reoptimized version of Hobza's P26 set of tripeptide structures, a new test set of conformers of cysteine dimers, and isomers of the water hexamer. These systems reflect features commonly found in protein crystal structures. In all cases, we recommend Grimme's DFT-D3 correction for London-dispersion. We recommend usage of large basis sets such as cc-pVTZ whenever possible to reduce any BSSE effects and, if this is not possible, to use Grimme's gCP correction to account for BSSE when small basis sets are used. We demonstrate that S-S and C-S bond lengths are very prone to basis-set incompleteness and that polarization functions should always be used on S atoms. At the double-ζ level, the PW6B95-D3-gCP DFT method combined with the SVP and 6-31G* basis sets yields accurate results. Alternatively, the HF-D3-gCP/SV method is recommended, with inclusion of polarization functions for S atoms only. Minimal basis sets offer an intriguing route to highly efficient calculations, but due to significant basis-set incompleteness effects, calculated bond lengths are seriously overestimated, making applications to large proteins very difficult, but we show that Grimme's newest HF-3c correction overcomes this problem and so makes this computational strategy very attractive. Our results provide a useful guideline for future applications to the optimization, quantum refinement, and dynamics of large proteins. © 2013 American Chemical Society.

Gogova, D, Petrov, PP, Buegler, M, Wagner, MR, Nenstiel, C, Callsen, G, Schmidbauer, M, Kucharski, R, Zajac, M, Dwilinski, R, Phillips, MR, Hoffmann, A & Fornari, R 2013, 'Structural and optical investigation of non-polar (1-100) GaN grown by the ammonothermal method', JOURNAL OF APPLIED PHYSICS, vol. 113, no. 20, pp. 203513-203513.
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We studied the structural and optical properties of state-of-the-art non-polar bulk GaN grown by the ammonothermal method. The investigated samples have an extremely low dislocation density (DD) of less than 5 × 104cm-2, which results in very narrow high-resolution x-ray rocking curves. The a and c lattice parameters of these stress-free GaN samples were precisely determined by using an x-ray diffraction technique based on the modified Bond method. The obtained values are compared to the lattice parameters of free-standing GaN from different methods and sources. The observed differences are discussed in terms of free-electron concentrations, point defects, and DD. Micro Raman spectroscopy revealed a very narrow phonon linewidth and negligible built-in strain in accordance with the high-resolution x-ray diffraction data. The optical transitions were investigated by cathodoluminescence measurements. The analysis of the experimental data clearly demonstrates the excellent crystalline perfection of ammonothermal GaN material and its potential for fabrication of non-polar substrates for homoepitaxial growth of GaN based device structures. © 2013 AIP Publishing LLC.

Goh, S, Zhang, Q, Zhang, J, McDougald, D, Krantz, WB, Liu, Y & Fane, AG 2013, 'Impact of a biofouling layer on the vapor pressure driving force and performance of a membrane distillation process', Journal of Membrane Science, vol. 438, pp. 140-152.
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Gonçalves, LFFF, Kanodarwala, FK, Stride, JA, Silva, CJR & Gomes, MJM 2013, 'One-pot synthesis of CdS nanoparticles exhibiting quantum size effect prepared within a sol–gel derived ureasilicate matrix', Optical Materials, vol. 36, no. 2, pp. 186-190.
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Gonçalves, LFFF, Silva, CJR, Kanodarwala, FK, Stride, JA, Pereira, MR & Gomes, MJM 2013, 'Synthesis and characterization of organic–inorganic hybrid materials prepared by sol–gel and containing ZnxCd1−xS nanoparticles prepared by a colloidal method', Journal of Luminescence, vol. 144, pp. 203-211.
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Gong, J, Luk, F, Jaiswal, R, George, AM, Grau, GER & Bebawy, M 2013, 'Microparticle drug sequestration provides a parallel pathway in the acquisition of cancer drug resistance', EUROPEAN JOURNAL OF PHARMACOLOGY, vol. 721, no. 1-3, pp. 116-125.
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Expanding on our previous findings demonstrating that microparticles (MPs) spread cancer multidrug resistance, we now show that MPs sequester drugs, reducing the free drug concentration available to cells. MPs were isolated from drug-sensitive and drug-resistant sub-clones of a human breast adenocarcinoma cell line and from human acute lymphoblastic leukemia cells. MPs were assessed for size, mitochondria, RNA and phospholipid content, P-glycoprotein (P-gp) expression and orientation and ATPase activity relative to drug sequestration capacity. Of the drug classes examined, MPs sequestered the anthracycline class to a significant degree. The degree of sequestration was likely due to the size of MPs and thus the amount of cargo they contain, to which the anthracyclines bind. Moreover, a proportion of the P-gp present on MPs was inside-out in orientation, enabling it to influx drugs rather than its typical efflux function. This was confirmed by surface immunofluorescence and by assessment of drug-stimulated ATPase activity following MP permeabilization. Thus we determined that breast cancer MPs carried a proportion of their P-gp oriented inside-out, providing active sequestration within the microvesicular compartment. These results demonstrate a capacity for MPs to sequester chemotherapeutic drugs, which has a predominantly active sequestration component for MPs derived from drug-resistant cells and a predominantly passive component for MPs derived from drug-sensitive cells. This reduction in available drug concentration has potential to contribute to a parallel pathway and complements that of the intercellular transfer of P-gp. These findings lend further support to the role of MPs in limiting the successful management of cancer.© 2013 Elsevier B.V. All rights reserved.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2013, 'A guide to in silico vaccine discovery for eukaryotic pathogens', BRIEFINGS IN BIOINFORMATICS, vol. 14, no. 6, pp. 753-774.
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In this article, a framework for an in silico pipeline is presented as a guide to high-throughput vaccine candidate discovery for eukaryotic pathogens, such as helminths and protozoa. Eukaryotic pathogens are mostly parasitic and cause some of the most damaging and difficult to treat diseases in humans and livestock. Consequently, these parasitic pathogens have a significant impact on economy and human health. The pipeline is based on the principle of reverse vaccinology and is constructed from freely available bioinformatics programs. There are several successful applications of reverse vaccinology to the discovery of subunit vaccines against prokaryotic pathogens but not yet against eukaryotic pathogens. The overriding aim of the pipeline, which focuses on eukaryotic pathogens, is to generate through computational processes of elimination and evidence gathering a ranked list of proteins based on a scoring system. These proteins are either surface components of the target pathogen or are secreted by the pathogen and are of a type known to be antigenic. No perfect predictive method is yet available; therefore, the highest-scoring proteins from the list require laboratory validation.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2013, 'A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms', BMC BIOINFORMATICS, vol. 14, no. 1, pp. 315-327.
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An in silico vaccine discovery pipeline for eukaryotic pathogens typically consists of several computational tools to predict protein characteristics. The aim of the in silico approach to discovering subunit vaccines is to use predicted characteristics to identify proteins which are worthy of laboratory investigation. A major challenge is that these predictions are inherent with hidden inaccuracies and contradictions. This study focuses on how to reduce the number of false candidates using machine learning algorithms rather than relying on expensive laboratory validation. Proteins from Toxoplasma gondii, Plasmodium sp., and Caenorhabditis elegans were used as training and test datasets.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2013, 'A review of the infection, genetics, and evolution of Neospora caninum: From the past to the present', INFECTION GENETICS AND EVOLUTION, vol. 13, no. 1, pp. 133-150.
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This paper is a review of current knowledge on Neospora caninum in the context of other apicomplexan parasites and with an emphasis on: life cycle, disease, epidemiology, immunity, control and treatment, evolution, genomes, and biological databases and web resources. N. caninum is an obligate, intracellular, coccidian, protozoan parasite of the phylum Apicomplexa. Infection can cause the clinical disease neosporosis, which most notably is associated with abortion in cattle. These abortions are a major root cause of economic loss to both the dairy and beef industries worldwide. N. caninum has been detected in every country in which a study has been specifically conducted to detect this parasite in cattle. The major mode of transmission in cattle is transplacental (or vertical) transmission and several elements of the N. caninum life cycle are yet to be studied in detail. The outcome of an infection is inextricably linked to the precise timing of the infection coupled with the status of the immune system of the dam and foetus. There is no community consensus as to whether it is the dams pro-inflammatory cytotoxic response to tachyzoites that kills the foetus or the tachyzoites themselves. From economic analysis the most cost-effective approach to control neosporosis is a vaccine. The perfect vaccine would protect against both infection and the clinical disease, and this implies a vaccine is needed that can induce a non-foetopathic cell mediated immunity response. Researchers are beginning to capitalise on the vast potential of -omics data (e.g. genomes, transcriptomes, and proteomes) to further our understanding of pathogens but especially to identify vaccine and drug targets. The recent publication of a genome for N. caninum offers vast opportunities in these areas.

Gorrie, CA, Larsen, LG & Waite, PME 2013, 'Age and gender differences in perceptions of traffic risk and safety for older pedestrians in metropolitan Sydney', JOURNAL OF THE AUSTRALASIAN COLLEGE OF ROAD SAFETY, vol. 24, no. 4, pp. 28-36.
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Older pedestrians are over represented in serious injury and fatality statistics compared to younger age groups and are considered to be at fault in over 72% of pedestrianmotor vehicle crashes. This study sought to investigate the perceptions of risk and safety in the local traffic environment as reported by older people in the course of everyday pedestrian journeys by asking them to complete a kerb-side survey. The majority of the older pedestrians interviewed (475 women: 265 men) considered that they engaged in safe pedestrian activity and that their own behaviour did not make them vulnerable road users. Perceptions of risk were predominantly associated with external factors such as motorist behaviour and traffic speed. Men tended to be more confident of their own abilities in traffic situations, reported less difficulty crossing roads and paid less attention to route selection than women. Increasing age (65 to 95 years) did not appear to change these perceptions. This is an important consideration for caregivers and medical practitioners when discussing road safety issues with older people, and a critical concern for professionals involved in the planning and implementation of traffic awareness and road safety campaigns for older people.

Grayson, TH, Chadha, PS, Bertrand, PP, Chen, H, Morris, MJ, Senadheera, S, Murphy, TV & Sandow, SL 2013, 'Increased caveolae density and caveolin-1 expression accompany impaired NO-mediated vasorelaxation in diet-induced obesity', Histochemistry and Cell Biology, vol. 139, no. 2, pp. 309-321.
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Diet-induced obesity induces changes in mechanisms that are essential for the regulation of normal artery function, and in particular the function of the vascular endothelium. Using a rodent model that reflects the characteristics of human dietary obesity, in the rat saphenous artery we have previously demonstrated that endothelium-dependent vasodilation shifts from an entirely nitric oxide (NO)-mediated mechanism to one involving upregulation of myoendothelial gap junctions and intermediate conductance calcium-activated potassium channel activity and expression. This study investigates the changes in NO-mediated mechanisms that accompany this shift. In saphenous arteries from controls fed a normal chow diet, acetylcholine-mediated endothelium-dependent vasodilation was blocked by NO synthase and soluble guanylyl cyclase inhibitors, but in equivalent arteries from obese animals sensitivity to these agents was reduced. The expression of endothelial NO synthase (eNOS) and caveolin-3 in rat saphenous arteries was unaffected by obesity, whilst that of caveolin-1 monomer and large oligomeric complexes of caveolins-1 and -2 were increased in membrane-enriched samples. The density of caveolae was increased at the membrane and cytoplasm of endothelial and smooth muscle cells of saphenous arteries from obese rats. Dissociation of eNOS from caveolin-1, as a prerequisite for activation of the enzyme, may be compromised and thereby impair NO-mediated vasodilation in the saphenous artery from diet-induced obese rats. Such altered signaling mechanisms in obesity-related vascular disease represent significant potential targets for therapeutic intervention. © 2012 Springer-Verlag.

Green, D, Padula, M, Santos, J, Chou, J, Milthorpe, B & Ben-Nissan, B 2013, 'A Therapeutic Potential for Marine Skeletal Proteins in Bone Regeneration', Marine Drugs, vol. 11, no. 12, pp. 1203-1220.
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A vital ingredient for engineering bone tissue, in the culture dish, is the use of recombinant matrix and growth proteins to help accelerate the growth of cultivated tissues into clinically acceptable quantities. The skeletal organic matrices of calcifying marine invertebrates are an untouched potential source of such growth inducing proteins. They have the advantage of being ready-made and retain the native state of the original protein. Striking evidence shows that skeleton building bone morphogenic protein-2/4 (BMP) and transforming growth factor beta (TGF-β) exist within various marine invertebrates such as, corals. Best practice mariculture and the latest innovations in long-term marine invertebrate cell cultivation can be implemented to ensure that these proteins are produced sustainably and supplied continuously. This also guarantees that coral reef habitats are not damaged during the collection of specimens. Potential proteins for bone repair, either extracted from the skeleton or derived from cultivated tissues, can be identified, evaluated and retrieved using chromatography, cell assays and proteomic methods. Due to the current evidence for bone matrix protein analogues in marine invertebrates, together with the methods established for their production and retrieval there is a genuine prospect that they can be used to regenerate living bone for potential clinical use. © 2013 by the authors; licensee MDPI.

Griekspoor, P, Colles, FM, McCarthy, ND, Hansbro, PM, Ashhurst‐Smith, C, Olsen, B, Hasselquist, D, Maiden, MCJ & Waldenström, J 2013, 'Marked host specificity and lack of phylogeographic population structure of Campylobacter jejuni in wild birds', Molecular Ecology, vol. 22, no. 5, pp. 1463-1472.
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AbstractZoonotic pathogens often infect several animal species, and gene flow among populations infecting different host species may affect the biological traits of the pathogen including host specificity, transmissibility and virulence. The bacterium Campylobacter jejuni is a widespread zoonotic multihost pathogen, which frequently causes gastroenteritis in humans. Poultry products are important transmission vehicles to humans, but the bacterium is common in other domestic and wild animals, particularly birds, which are a potential infection source. Population genetic studies of C. jejuni have mainly investigated isolates from humans and domestic animals, so to assess C. jejuni population structure more broadly and investigate host adaptation, 928 wild bird isolates from Europe and Australia were genotyped by multilocus sequencing and compared to the genotypes recovered from 1366 domestic animal and human isolates. Campylobacter jejuni populations from different wild bird species were distinct from each other and from those from domestic animals and humans, and the host species of wild bird was the major determinant of C. jejuni genotype, while geographic origin was of little importance. By comparison, C. jejuni differentiation was restricted between more phylogenetically diverse farm animals, indicating that domesticated animals may represent a novel niche for C. jejuni and thereby driving the evolution of those bacteria as they exploit this niche. Human disease is dominated by isolates from this novel domesticated animal niche.

Groszmann, M, Greaves, IK, Fujimoto, R, Peacock, WJ & Dennis, ES 2013, 'The role of epigenetics in hybrid vigour', TRENDS IN GENETICS, vol. 29, no. 12, pp. 684-690.
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Hybrid vigour, or heterosis, refers to the increased yield and biomass of hybrid offspring relative to the parents. Although this has been exploited in plants for agriculture and horticulture, the molecular and cellular mechanisms underlying hybrid vigour are largely unknown. Genetic analyses show that there are a large number of quantitative trait loci (QTLs) that contribute to the heterotic phenotype, indicating that it is a complex phenomenon. Gene expression in hybrids is regulated by the interactions of the two parental epigenetic systems and the underlying genomes. Increasing understanding of the interplay of small RNA (sRNA) molecules, DNA methylation, and histone marks provides new opportunities to define the basis of hybrid vigour and to understand why F1 heterosis is not passed on to subsequent generations. We discuss recent findings that suggest the existence of several pathways that alter DNA methylation patterns, which may lead to transcriptional changes resulting in the heterotic phenotype.

Guenther, PM, Kirkpatrick, SI, Krebs‐Smith, SM, Reedy, J, Buckman, DW, Dodd, KW & Carroll, RJ 2013, 'Evaluation of the Healthy Eating Index‐2010 (HEI‐2010)', The FASEB Journal, vol. 27, no. S1.
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The Healthy Eating Index, a measure of diet quality, was recently updated to reflect the 2010 Dietary Guidelines for Americans. To assess the validity and reliability of the HEI‐2010, 24‐hour dietary recall data from individuals aged 2 years and older (n=8262) from the 2003–2004 National Health and Nutrition Examination Survey were used to estimate usual HEI‐2010 scores and to assess whether the HEI‐2010 measures diet quality independently of energy intake, distinguishes between groups with known differences in diet quality, and has more than one underlying dimension. In addition to these population‐level assessments, exemplary menus expected to have high diet quality were scored with the HEI‐2010. Low correlations were observed between total and component scores with energy intake (|r|<0.21), demonstrating that the HEI‐2010 uncouples diet quality from quantity. Diet quality was lower among smokers (mean total HEI‐2010 score=45.7) compared to nonsmokers (53.3) (P<0.01), and exemplary menus received scores at or near the maximum levels, indicating construct validity. Cronbach's alpha was 0.68, supporting the reliability of the total score as an indicator of overall diet quality. Nonetheless, principal components analysis indicated multiple underlying factors, highlighting the importance of the component scores. Overall, the HEI‐2010 is a valid and reliable measure of diet quality. Support: NCI/CNPP.

Gul, S, Ahmed, S, Gul, H, Shad, KF, Zia-Ul-Haq, M & Badiu, D 2013, 'The antioxidant potential of Brassica rapa L. on glutathione peroxidase, superoxide dismutase enzymes and total antioxidant status', Romanian Review of Laboratory Medicine, vol. 21, no. 2.
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Gunawan, C, Sirimanoonphan, A, Teoh, WY, Marquis, CP & Amal, R 2013, 'Submicron and nano formulations of titanium dioxide and zinc oxide stimulate unique cellular toxicological responses in the green microalga Chlamydomonas reinhardtii', Journal of Hazardous Materials, vol. 260, pp. 984-992.
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The work investigates the eco-cytoxicity of submicron and nano TiO2 and ZnO, arising from the unique interactions of freshwater microalga Chlamydomonas reinhardtii to soluble and undissolved components of the metal oxides. In a freshwater medium, submicron and nano TiO2 exist as suspended aggregates with no-observable leaching. Submicron and nano ZnO undergo comparable concentration-dependent fractional leaching, and exist as dissolved zinc and aggregates of undissolved ZnO. Cellular internalisation of solid TiO2 stimulates cellular ROS generation as an early stress response. The cellular redox imbalance was observed for both submicron and nano TiO2 exposure, despite exhibiting benign effects on the alga proliferation (8-day EC50>100mgTiO2/L). Parallel exposure of C. reinhardtii to submicron and nano ZnO saw cellular uptake of both the leached zinc and solid ZnO and resulting in inhibition of the alga growth (8-day EC50≥0.01mgZnO/L). Despite the sensitivity, no zinc-induced cellular ROS generation was detected, even at 100mgZnO/L exposure. Taken together, the observations confront the generally accepted paradigm of cellular oxidative stress-mediated cytotoxicity of particles. The knowledge of speciation of particles and the corresponding stimulation of unique cellular responses and cytotoxicity is vital for assessment of the environmental implications of these materials. © 2013 Elsevier B.V.

Gunawan, C, Teoh, WY, Marquis, CP & Amal, R 2013, 'Induced Adaptation of Bacillus sp. to Antimicrobial Nanosilver', Small, vol. 9, no. 21, pp. 3554-3560.
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The natural ability of Bacillus sp. to adapt to nanosilver cytotoxicity upon prolonged exposure is reported for the first time. The combined adaptive effects of nanosilver resistance and enhanced growth are induced under various intensities of nanosilver-stimulated cellular oxidative stress, ranging from only minimal cellular redox imbalance to the lethal levels of cellular ROS stimulation. An important implication of the present work is that such adaptive effects lead to the ultimate domination of nanosilver-resistant Bacillus sp. in the microbiota, to which nanosilver cytotoxicity is continuously applied. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gunawan, C, Teoh, WY, Ricardo, Marquis, CP & Amal, R 2013, 'Zinc Oxide Nanoparticles Induce Cell Filamentation in Escherichia coli', Particle & Particle Systems Characterization, vol. 30, no. 4, pp. 375-380.
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Zinc oxide nanoparticles (ZnO NPs) induce morphological transformation of Escherichia coli from its native rod‐shape of ≈2–4 μm to filamentous cells of 20–40 μm in length. The transient response can only be observed at up to 3.5 h proliferation, beyond which the cytotoxic effect is neutralized and the rod‐shape is restored. The filamentation is part of the bacterium SOS response to the Trojan horse‐type internalization of undissolved ZnO solids. In the absence of ZnO solids, no cell filamentation can be observed from the leached soluble zinc fraction or dissolved zinc salt.

Gupta, V, Thakur, RS, Reddy, CRK & Jha, B 2013, 'Central metabolic processes of marine macrophytic algae revealed from NMR based metabolome analysis', RSC Advances, vol. 3, no. 19, pp. 7037-7037.
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Gupta, V, Trivedi, N, Kumar, M, Reddy, CRK & Jha, B 2013, 'Purification and characterization of exo-β-agarase from an endophytic marine bacterium and its catalytic potential in bioconversion of red algal cell wall polysaccharides into galactans', Biomass and Bioenergy, vol. 49, pp. 290-298.
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An extracellular exo-β-agarase was characterized from an endophytic bacterial strain Pseudomonas sp. isolated from the red alga Gracilaria dura. The enzyme was purified to homogeneity with a recovery of 28.2% and a purity fold of 8.33. The purified enzyme was composed of single polypeptide with a molecular mass of about 66 kDa. The enzyme exhibited a maximum activity of 81.74 U mL-1 and a specific activity of 615.5 U mg-1. The optimal pH and temperature for its maximum activity were 9.0 and 35 °C respectively. The enzyme stabilized its activity in alkaline pH 7-11 and high salt concentration up to 4 mol dm-3. The enzymatic hydrolyzed product of agar was characterized as neoagarobiose while the bacterium when incubated with G. dura biomass yielded galactose 20% on dry wt basis. The agarolytic ability of the former was further confirmed by release of protoplasts from G. dura tissue through digestion of cell wall polysaccharides. The bacterium investigated in this study could possibly be used for bioconversion of marine red algal polysaccharides into energy feedstock and the purified enzyme for preparation of compounds having pharmaceutical importance. © 2013 Elsevier Ltd.

Gustafsson, MSM, Baird, ME & Ralph, PJ 2013, 'The interchangeability of autotrophic and heterotrophic nitrogen sources in Scleractinian coral symbiotic relationships: A numerical study', ECOLOGICAL MODELLING, vol. 250, pp. 183-194.
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The success of corals in tropical oligotrophic waters depends largely on their symbiotic relationship with the dinoflagellate algae residing in their tissues. Understanding the dynamics of this symbiosis is essential to predict how corals respond to environmental stressors, such as changes in nutrients availability, water temperatures and irradiance. This study presents a numerical model of the symbiotic relationship between a heterotrophic coral (cnidarian) host and autotrophic symbiotic dinoflagellates, including the major metabolic and physical functions of the system, under non-bleaching conditions. The coral acquires nitrogen (N) through two processes, uptake of dissolved inorganic nitrogen (VH DIN) and heterotrophic feeding (ZN). Numerical experiments were used to highlight the importance of these different sources of N for coral survival and growth. The model was analyzed for four external nutrient supply scenarios, using combinations of two VH DIN rates (high and low) and two ZN rates (high and low), and for a range of light levels. The model outputs showed the importance of the algae symbionts to the coral host as a source of both N and C when the feeding rate was limited, with heterotrophic feeding providing only 14% of the N needed to sustain the host biomass for the low ZN + high VH DIN scenario. In contrast, with no light or low light, conditions under which the symbiont population dies, the host was able to survive if ZN was high. Living inside the host the symbiont population thrived as long as there was enough light, as well as, DIN and DIC in the host tissues, independent of whether N was supplied as ZN or VH DIN. Translocation and recycling of nutrient were two of the most important features of this model, emphasizing why it is essential to resolve host and symbiont in a coral model. The model highlights that the interchangeability of N sources, and the ability to exchange and recycle nutrients in the host-symbiont system, is the key to coral su...

Haav, K, Kadam, SA, Toom, L, Gale, PA, Busschaert, N, Wenzel, M, Hiscock, JR, Kirby, IL, Haljasorg, T, Lõkov, M & Leito, I 2013, 'Accurate Method To Quantify Binding in Supramolecular Chemistry', The Journal of Organic Chemistry, vol. 78, no. 16, pp. 7796-7808.
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Hall, JD, Xue, M, Ran, L & Leslie, LM 2013, 'High-Resolution Modeling of Typhoon Morakot (2009): Vortex Rossby Waves and Their Role in Extreme Precipitation over Taiwan', Journal of the Atmospheric Sciences, vol. 70, no. 1, pp. 163-186.
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Abstract A high-resolution nonhydrostatic numerical model, the Advanced Regional Prediction System (ARPS), was used to simulate Typhoon Morakot (2009) as it made landfall over Taiwan, producing record rainfall totals. In particular, the mesoscale structure of the typhoon was investigated, emphasizing its associated deep convection, the development of inner rainbands near the center, and the resultant intense rainfall over western Taiwan. Simulations at 15- and 3-km grid spacing revealed that, following the decay of the initial inner eyewall, a new, much larger eyewall developed as the typhoon made landfall over Taiwan. Relatively large-amplitude wave structures developed in the outer eyewall and are identified as vortex Rossby waves (VRWs), based on the wave characteristics and their similarity to VRWs identified in previous studies. Moderate to strong vertical shear over the typhoon system produced a persistent wavenumber-1 (WN1) asymmetric structure during the landfall period, with upward motion and deep convection in the downshear and downshear-left sides, consistent with earlier studies. This strong asymmetry masks the effects of WN1 VRWs. WN2 and WN3 VRWs apparently are associated with the development of deep convective bands in Morakot’s southwestern quadrant. This occurs as the waves move cyclonically into the downshear side of the cyclone. Although the typhoon track and topographic enhancement contribute most to the record-breaking rainfall totals, the location of the convective bands, and their interaction with the mountainous terrain of Taiwan, also affect the rainfall distribution. Quantitatively, the 3-km ARPS rainfall forecasts are superior to those obtained from coarser-resolution models.

Hamidian, M & Hall, RM 2013, 'ISAba1 targets a specific position upstream of the intrinsic ampC gene of Acinetobacter baumannii leading to cephalosporin resistance', Journal of Antimicrobial Chemotherapy, vol. 68, no. 11, pp. 2682-2683.
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Hamidian, M, Hancock, DP & Hall, RM 2013, 'Horizontal transfer of an ISAba125-activated ampC gene between Acinetobacter baumannii strains leading to cephalosporin resistance', Journal of Antimicrobial Chemotherapy, vol. 68, no. 1, pp. 244-245.
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Hansbro, PM & Knight, DA 2013, 'Are Lymphoid Follicles Important in the Pathogenesis of Chronic Obstructive Pulmonary Disease?', American Journal of Respiratory and Critical Care Medicine, vol. 188, no. 3, pp. 267-269.
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Hansbro, PM, Scott, GV, Essilfie, A-T, Kim, RY, Starkey, MR, Nguyen, DH, Allen, PD, Kaiko, GE, Yang, M, Horvat, JC & Foster, PS 2013, 'Th2 cytokine antagonists: potential treatments for severe asthma', Expert Opinion on Investigational Drugs, vol. 22, no. 1, pp. 49-69.
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Hansen, MJ, Chen, H, Jones, JE, Langenbach, SY, Vlahos, R, Gualano, RC, Morris, MJ & Anderson, GP 2013, 'The Lung Inflammation and Skeletal Muscle Wasting Induced by Subchronic Cigarette Smoke Exposure Are Not Altered by a High-Fat Diet in Mice', PLoS ONE, vol. 8, no. 11, pp. e80471-e80471.
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Obesity and cigarette smoking independently constitute major preventable causes of morbidity and mortality and obesity is known to worsen lung inflammation in asthma. Paradoxically, higher body mass index (BMI) is associated with reduced mortality in smoking induced COPD whereas low BMI increases mortality risk. To date, no study has investigated the effect of a dietary-induced obesity and cigarette smoke exposure on the lung inflammation and loss of skeletal muscle mass in mice. Male BALB/c mice were exposed to 4 cigarettes/day, 6 days/week for 7 weeks, or sham handled. Mice consumed either standard laboratory chow (3.5 kcal/g, 12% fat) or a high fat diet (HFD, 4.3 kcal/g, 32% fat). Mice exposed to cigarette smoke for 7 weeks had significantly more inflammatory cells in the BALF (P<0.05) and the mRNA expression of proinflammatory cytokines and chemokines was significantly increased (P<0.05); HFD had no effect on these parameters. Sham- and smoke-exposed mice consuming the HFD were significantly heavier than chow fed animals (12 and 13%, respectively; P<0.05). Conversely, chow and HFD fed mice exposed to cigarette smoke weighed 16 and 15% less, respectively, compared to sham animals (P<0.05). The skeletal muscles (soleus, tibialis anterior and gastrocnemius) of cigarette smoke-exposed mice weighed significantly less than sham-exposed mice (P<0.05) and the HFD had no protective effect. For the first time we report that cigarette smoke exposure significantly decreased insulin-like growth factor-1 (IGF-1) mRNA expression in the gastrocnemius and tibialis anterior and IGF-1 protein in the gastrocnemius (P<0.05). We have also shown that cigarette smoke exposure reduced circulating IGF-1 levels. IL-6 mRNA expression was significantly elevated in all three skeletal muscles of chow fed smoke-exposed mice (P<0.05). In conclusion, these findings suggest that a downregulation in local IGF-1 may be responsible for the loss of skeletal muscle mass following cigarett...

Harasti, D & Gladstone, W 2013, 'Does underwater flash photography affect the behaviour, movement and site persistence of seahorses?', Journal of Fish Biology, vol. 83, no. 5, pp. 1344-1353.
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The effect of flash photography on seahorse species has never been tested. An experiment was established to test the effect of flash photography and the handling of Hippocampus whitei, a medium‐sized seahorse species endemic to Australia, on their behavioural responses, movements and site persistence. A total of 24 H. whitei were utilized in the experiment with eight in each of the three treatments (flash photography, handling and control). The effect of underwater flash photography on H. whitei movements was not significant; however, the effect of handling H. whitei to take a photograph had a significant effect on their short‐term behavioural responses to the photographer. Kaplan–Meier log‐rank test revealed that there was no significant difference in site persistence of H. whitei from each of the three treatments and that flash photography had no long‐term effects on their site persistence. It is concluded that the use of flash photography by divers is a safe and viable technique with H. whitei, particularly if photographs can be used for individual identification purposes.

Harding, R, O'Reilly, M, Sozo, F, Hansbro, P, Horvat, J & Beckett, E 2013, 'Persistent effects of neonatal hyperoxia on bronchioles and lung function in adult mice: additional effects of concomitant growth restriction', Paediatric Respiratory Reviews, vol. 14, pp. S69-S69.
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Hare, D, Ayton, S, Bush, A & Lei, P 2013, 'A delicate balance: Iron metabolism and diseases of the brain', FRONTIERS IN AGING NEUROSCIENCE, vol. 5.
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Hare, DJ, Adlard, PA, Doble, PA & Finkelstein, DI 2013, 'Metallobiology of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine neurotoxicity', METALLOMICS, vol. 5, no. 2, pp. 91-109.
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1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a potent toxin used to selectively destroy dopaminergic neurons in the substantia nigra and induce parkinsonism. MPTP is metabolised to the 1-methyl-4-phenylpyridinium ion (MPP(+)) in glia, after which it enters the neuron via the dopamine transporter and results in elevated levels of oxidative stress. The mechanism through which MPP(+) causes cell death is thought to involve redox-active metals, particularly iron (Fe). This review will examine how cellular metal metabolism is altered following MPTP insult, and how this relates to metal dyshomeostasis in idiopathic Parkinson's disease. This includes both cell damage arising from increased metal concentration, and how metal-binding proteins respond to MPTP-induced neurotoxicity. Implications for using MPTP as a model for human Parkinson's disease will be discussed in terms of cell metallobiology.

Hare, DJ, Grubman, A, Ryan, TM, Lothian, A, Liddell, JR, Grimm, R, Matsuda, T, Doble, PA, Cherny, RA, Bush, AI, White, AR, Masters, CL & Roberts, BR 2013, 'Profiling the iron, copper and zinc content in primary neuron and astrocyte cultures by rapid online quantitative size exclusion chromatography-inductively coupled plasma-mass spectrometry', METALLOMICS, vol. 5, no. 12, pp. 1656-1662.
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Metals often determine the chemical reactivity of the proteins to which they are bound. Each cell in the body tightly maintains a unique metalloproteomic profile, mostly dependent on function. This paper describes an analytical online flow injection quan

Hare, DJ, Lear, J, Bishop, D, Beavis, A & Doble, PA 2013, 'Protocol for production of matrix-matched brain tissue standards for imaging by laser ablation-inductively coupled plasma-mass spectrometry', ANALYTICAL METHODS, vol. 5, no. 8, pp. 1915-1921.
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Calibration with matrix-matched standards remains the most practical means for producing quantitative images of trace metal distribution in tissue sections by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). A general guide for producing matrix-matched standards for assay of trace metals in brain tissue is presented. Cortical tissue was taken from pooled sheep brains and spiked with varying approximate concentrations of standard solutions of Co, Cu, Fe, Mg, Mn, Sr, Se and Zn. The tissue was homogenised and the total analyte amount accurately determined by solution nebulisation ICP-MS. The analytical figures of merit for LA-ICP-MS imaging were determined from these tissue standards cryosectioned at 30 μm. Repeated 8-point calibration curves were reproducibly linear, with correlation coefficients ranging from 0.9874 (Mg) to 0.9991 (Sr). Limits of analysis were suitable for quantifying most analytes in a sample mouse brain, with the exception of Co and Se. © 2013 The Royal Society of Chemistry.

He, R, Tang, B, Ton-That, C, Phillips, M & Tsuzuki, T 2013, 'Physical structure and optical properties of Co-doped ZnO nanoparticles prepared by co-precipitation', JOURNAL OF NANOPARTICLE RESEARCH, vol. 15, no. 11.
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Herbert, C, Siegle, JS, Shadie, AM, Nikolaysen, S, Garthwaite, L, Hansbro, NG, Foster, PS & Kumar, RK 2013, 'Development of asthmatic inflammation in mice following early-life exposure to ambient environmental particulates and chronic allergen challenge', Disease Models & Mechanisms, vol. 6, no. 2, pp. 479-488.
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Summary Childhood exposure to environmental particulates increases the risk of development of asthma. The underlying mechanisms might include oxidant injury to airway epithelial cells (AEC). We investigated the ability of ambient environmental particulates to contribute to sensitization via the airways, and thus to the pathogenesis of childhood asthma. To do so, we devised a novel model in which weanling BALB/c mice were exposed to both ambient particulate pollutants and ovalbumin for sensitization via the respiratory tract, followed by chronic inhalational challenge with a low mass concentration of the antigen. We also examined whether these particulates caused oxidant injury and activation of AEC in vitro. Furthermore, we assessed the potential benefit of minimizing oxidative stress to AEC through the period of sensitization and challenge by dietary intervention. We found that characteristic features of asthmatic inflammation developed only in animals that received particulates at the same time as respiratory sensitization, and were then chronically challenged with allergen. However, these animals did not develop airway hyper-responsiveness. Ambient particulates induced epithelial injury in vitro, with evidence of oxidative stress, and production of both pro-inflammatory cytokines and Th2-promoting cytokines such as IL-33. Treatment of AEC with an antioxidant in vitro inhibited the pro-inflammatory cytokine response to these particulates. Ambient particulates also induced pro-inflammatory cytokine expression following administration to weanling mice. However, early-life dietary supplementation with antioxidants did not prevent the development of an asthmatic inflammatory response in animals that were exposed to particulates, sensitized and challenged. We conclude that injury to airway epithelium by ambient environmental particulates in early life is capable of promoting the development of an asthmatic in...

Higginbotham, HF, Cox, RP, Sandanayake, S, Graystone, BA, Langford, SJ & Bell, TDM 2013, 'A fluorescent “2 in 1” proton sensor and polarity probe based on core substituted naphthalene diimide', Chemical Communications, vol. 49, no. 44, pp. 5061-5061.
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Hirota, JA, Im, H, Rahman, MM, Rumzhum, NN, Manetsch, M, Pascoe, CD, Bunge, K, Alkhouri, H, Oliver, BG & Ammit, AJ 2013, 'The Nucleotide-Binding Domain and Leucine-Rich Repeat Protein-3 Inflammasome Is Not Activated in Airway Smooth Muscle Upon Toll-Like Receptor-2 Ligation', AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, vol. 49, no. 4, pp. 517-524.
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Inflammasomes have emerged as playing key roles in inflammation and innate immunity. A growing body of evidence has suggested that the nucleotide-binding domain and leucine-rich repeat protein-3 (NLRP3) inflammasomeisimportant inchronic airwaydiseases suchas asthma and chronic obstructive pulmonary disease. Inflammasome activation results, in part, in pro-IL-1β processing and the secretion of the proinflammatory cytokine IL-1β. Because asthma exacerbations are associated with elevated concentrations of secreted IL-1β, we addressed whether the NLRP3 inflammasome is activated under in vitro conditions that mimic infectious exacerbations in asthma. Primary cultures of airway smoothmuscle (ASM) cells were treated with infectious stimuli (mimicked using the Toll-like receptor-2 agonist Pam3CSK4, a synthetic bacterial lipopeptide).Whereas Pam3CSK4 robustlyup-regulatedASMcytokineexpressionin response toTNF-αand significantly enhanced IL-1β mRNA expression, we were unable to detect IL-1β in the cell supernatants. Thus, IL-1β was not secreted and therefore was unable to act in an autocrine manner to promote the amplification of ASMinflammatory responses.Moreover, Toll-like receptor-2 ligation did not enhanceNLRP3 or caspase-1 expression in ASM cells, and NLRP3 and caspase-1 protein were not present in the ASM layer of tracheal sections from human donors. In conclusion, these data demonstrate that the enhanced synthetic function of ASM cells, induced by infectious exacerbations of airway inflammation, is NLRP3 inflammasome-independent and IL-1β-independent. Activation of the NLRP3 inflammasome by invading pathogens may prove cell type-specific in exacerbations of airway inflammation in asthma. Copyright © 2013 by the American Thoracic Society.

Hiscock, JR, Piana, F, Sambrook, MR, Wells, NJ, Clark, AJ, Vincent, JC, Busschaert, N, Brown, RCD & Gale, PA 2013, 'Detection of nerve agent via perturbation of supramolecular gel formation', Chemical Communications, vol. 49, no. 80, pp. 9119-9119.
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Hitchcock, JN & Mitrovic, SM 2013, 'Different resource limitation by carbon, nitrogen and phosphorus between base flow and high flow conditions for estuarine bacteria and phytoplankton', Estuarine, Coastal and Shelf Science, vol. 135, no. 1, pp. 106-115.
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Freshwater inflows can deliver substantial inputs of allochthonous organic carbon to estuaries. The role that allochthonous DOC has on structuring bacterial and phytoplankton communities is still not well understood. We performed a series of 1.25 L bioassay limitation experiments on the Bega and Clyde River estuaries in NSW, Australia, examining what resources limit bacteria and phytoplankton growth. We hypothesized that during base flow conditions bacteria would be carbon limited, and after high flow conditions they would be nutrient limited. A full factorial design was used with additions of carbon (glucose), nitrogen (KNO3) and phosphorus (KH2PO4). During the experiments that took place during base flow conditions bacteria were always primarily C-limited. After high flow conditions, bacteria were P-limited on the Clyde River, and remained C-limited on the Bega River. Phytoplankton growth was limited at all times in each estuary, tending toward N-limitation on the Bega River and P-limitation on the Clyde river. During high flow conditions on the Clyde River, when bacteria and phytoplankton were both primarily P-limited, it appeared that bacteria was able to outcompete phytoplankton for nutrients. These results suggest that freshwater inflows and allochthonous DOC maybe important in structuring estuarine microbial ecosystems and individual estuaries may behave differently in terms of their limiting resources.

Hocking, JS, Vodstrcil, LA, Huston, WM, Timms, P, Chen, MY, Worthington, K, McIver, R & Tabrizi, SN 2013, 'A cohort study of Chlamydia trachomatis treatment failure in women: a study protocol', BMC Infectious Diseases, vol. 13, no. 1.
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Holland-Moritz, HE, Bevans, DR, Lang, JM, Darling, AE, Eisen, JA & Coil, DA 2013, 'Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria )', Genome Announcements, vol. 1, no. 3, pp. 1-2.
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ABSTRACT Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains 3,317,267 bp in 11 scaffolds. This strain was isolated from a residential toilet as part of an undergraduate project to sequence reference genomes of microbes from the built environment.

Holt, SA, Le Brun, AP, Nelson, ARJ & Lakey, JH 2013, 'In situ study of the impact of acidic and neutral deposition pH on alkane phosphate film formation and stability on TiO2', RSC Advances, vol. 3, no. 8, pp. 2581-2581.
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Hong, Y, Burford, MA, Ralph, PJ, Udy, JW & Doblin, MA 2013, 'The cyanobacterium Cylindrospermopsis raciborskii is facilitated by copepod selective grazing', HARMFUL ALGAE, vol. 29, no. 1, pp. 14-21.
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Blooms of the toxin-producing cyanobacterium Cylindrospermopsis raciborskii occur in tropical and subtropical lakes during spring-summer but the mechanisms behind bloom formation are unclear. This study tests the hypothesis that C. raciborskii accumulations in freshwater systems are facilitated by selective copepod grazing. Prey selection was examined in a series of experiments with C. raciborskii and the green alga, Chlamydomonas reinhardtii, as well as within natural phytoplankton assemblages. Clearance rates of the copepod Boeckella sp. on a C. raciborskii diet were 24 times lower than that of a common cladoceran Ceriodaphnia sp. when both grazers had prey choice. More C. raciborskii was cleared by Boeckella sp. when in mixed natural phytoplankton assemblages, but the clearance rate declined when nutrient replete C. reinhardtii was added, demonstrating that when alternate high quality algae were present, so did C. raciborskii consumption. The clearance rates of Boeckella sp. on two toxic C. raciborskii strains were significantly lower than on a non-toxic strain, and on C. raciborskii with low cellular P content. When we tested the grazing preference of a copepod dominated mixed zooplankton community on C. raciborskii during the early bloom period, clearance rates were relatively low (0.050.20 ml individual-1 h-1), and decreased significantly as the proportion of C. raciborskii increased above 5%. These results suggest that C. raciborskii persistence could be promoted by copepods preferentially grazing on other algae, with significant loss of top-down control as C. raciborskii abundance increases.

Hoppenrath, M, Chomerat, N, Horiguchi, T, Schweikert, M, Nagahama, Y & Murray, S 2013, 'Taxonomy and phylogeny of the benthic Prorocentrum species (Dinophyceae)-A proposal and review', HARMFUL ALGAE, vol. 27, no. 1, pp. 1-28.
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Based on a literature review and new morphological and molecular phylogenetic data, a summary of all described benthic Prorocentrum species is presented. Short descriptions of the 29 species are provided including information and illustrations of platelet pattern. Increasing morphological data of the same taxon from different sites has revealed unexpected morphological variability. The variability of characters used for taxonomy is discussed. Many of these may be more variable than previously thought or phenotypically plastic. We conclude that the following features are constant within a species: (1) asymmetry or symmetry of the theca in combination with (2) the shape of the periflagellar area visible on the right thecal plate, (a) arc-shaped, (b) wide or simply V-shaped, (c) narrow and deep V-shaped, and (d) linear. At the same time, we are now beginning to understand that the cell shape of some species is more variable than thought and not in others. The stability of pore patterns is not known to date nor is it known whether the presence of a starch sheath is a reliable taxonomic character. The morphology of the periflagellar area might be a very useful character. The unstable terminology to describe similar or identical structures has made it difficult to interpret the literature on these features.

Horsington, J, Lynn, H, Turnbull, L, Cheng, D, Braet, F, Diefenbach, RJ, Whitchurch, CB, Karupiah, G & Newsome, TP 2013, 'A36-dependent Actin Filament Nucleation Promotes Release of Vaccinia Virus', PLOS PATHOGENS, vol. 9, no. 3, pp. e1003239-e1003239.
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Cell-to-cell transmission of vaccinia virus can be mediated by enveloped virions that remain attached to the outer surface of the cell or those released into the medium. During egress, the outer membrane of the double-enveloped virus fuses with the plasma membrane leaving extracellular virus attached to the cell surface via viral envelope proteins. Here we report that F-actin nucleation by the viral protein A36 promotes the disengagement of virus attachment and release of enveloped virus. Cells infected with the A36YdF virus, which has mutations at two critical tyrosine residues abrogating localised actin nucleation, displayed a 10-fold reduction in virus release. We examined A36YdF infected cells by transmission electron microscopy and observed that during release, virus appeared trapped in small invaginations at the plasma membrane. To further characterise the mechanism by which actin nucleation drives the dissociation of enveloped virus from the cell surface, we examined recombinant viruses by super-resolution microscopy. Fluorescently-tagged A36 was visualised at sub-viral resolution to image cell-virus attachment in mutant and parental backgrounds. We confirmed that A36YdF extracellular virus remained closely associated to the plasma membrane in small membrane pits. Virus-induced actin nucleation reduced the extent of association, thereby promoting the untethering of virus from the cell surface. Virus release can be enhanced via a point mutation in the luminal region of B5 (P189S), another virus envelope protein. We found that the B5P189S mutation led to reduced contact between extracellular virus and the host membrane during release, even in the absence of virus-induced actin nucleation. Our results posit that during release virus is tightly tethered to the host cell through interactions mediated by viral envelope proteins. Untethering of virus into the surrounding extracellular space requires these interactions be relieved, either through the for...

Hosta‐Rigau, L, Shimoni, O, Städler, B & Caruso, F 2013, 'Advanced Subcompartmentalized Microreactors: Polymer Hydrogel Carriers Encapsulating Polymer Capsules and Liposomes', Small, vol. 9, no. 21, pp. 3573-3583.
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AbstractThe design of compartmentalized carriers for advanced drug delivery systems or artificial cells and organelles is of interest for biomedical applications. Herein, a polymer carrier microreactor that contains two different classes of subcompartments, multilayered polymer capsules and liposomes, is presented. 50 nm‐diameter liposomes and 300 nm‐diameter polymer capsules are encapsulated into a larger polymer carrier capsule, demonstrating control over the spatial positioning of the subcompartments, which are either ‘membrane‐associated’ or 'free‐floating’ in the aqueous interior. Selective and spatially dependent degradation of the 300 nm‐diameter subcompartments (without destroying the structural integrity of the enzyme‐loaded liposomes) is also shown, by performing an encapsulated enzymatic reaction using the liposomal subcompartments. These findings cover several important aspects toward the development of engineered compartmentalized carrier vessels for the creation of artificial cell mimics or advanced therapeutic delivery systems.

Hovis, KM, Mojica, S, McDermott, JE, Pedersen, L, Simhi, C, Rank, RG, Myers, GSA, Ravel, J, Hsia, R-C & Bavoil, PM 2013, 'Genus-optimized strategy for the identification of chlamydial type III secretion substrates', Pathogens and Disease, vol. 69, no. 3, pp. 213-222.
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Howlett, C, Ferreira, J-A, Seini, M & Matthews, C 2013, 'Indigenising the Griffith School of Environment Curriculum: Where to From Here?', The Australian Journal of Indigenous Education, vol. 42, no. 1, pp. 68-74.
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This article presents a discussion on a study undertaken by academics within the Griffith School of Environment, Brisbane, Australia that sought to explore the potential of an Indigenised curriculum to attract and retain Indigenous students, and thereby facilitate greater participation of Indigenous students in science. The article highlights the need for staff to be both reflective and reflexive about the limitations their particular knowledge systems may impose on Indigenous ways of knowing and knowledge systems. The article also acknowledges the need for professional development opportunities for staff prior to any attempts towards Indigenisation of the curriculum.

Hu, H, Harmer, C, Anuj, S, Wainwright, CE, Manos, J, Cheney, J, Harbour, C, Zablotska, I, Turnbull, L, Whitchurch, CB, Grimwood, K, Rose, B & Investigators, ACFBALS 2013, 'Type 3 secretion system effector genotype and secretion phenotype of longitudinally collected Pseudomonas aeruginosa isolates from young children diagnosed with cystic fibrosis following newborn screening', CLINICAL MICROBIOLOGY AND INFECTION, vol. 19, no. 3, pp. 266-272.
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Studies of the type 3 secretion system (T3SS) in Pseudomonas aeruginosa isolates from chronically infected older children and adults with cystic fibrosis (CF) show a predominantly exoS+/exoU) (exoS+) genotype and loss of T3SS effector secretion over time. Relatively little is known about the role of the T3SS in the pathogenesis of early P. aeruginosa infection in the CF airway. In this longitudinal study, 168 P. aeruginosa isolates from 58 children diagnosed with CF following newborn screening and 47 isolates from homes of families with or without children with CF were genotyped by pulsed-field gel electrophoresis (PFGE) and T3SS genotype and phenotype determined using multiplex PCR and western blotting. Associations were sought between T3SS data and clinical variables and comparisons made between T3SS data of clinical and environmental PFGE genotypes. Seventy-seven of the 92 clinical strains were exoS+ (71% secretors (ExoS+)) and 15 were exoU+ (93% secretors (ExoU+)). Initial exoS+ strains were five times more likely to secrete ExoS than subsequent exoS+ strains at first isolation. The proportion of ExoS+ strains declined with increasing age at acquisition. No associations were found between T3SS characteristics and gender, site of isolation, exacerbation, a persistent strain or pulmonary outcomes. Fourteen of the 23 environmental strains were exoS+ (79% ExoS+) and nine were exoU+ (33% ExoU+). The exoU+ environmental strains were significantly less likely to secrete ExoU than clinical strains. This study provides new insight into the T3SS characteristics of P. aeruginosa isolated from the CF airway early in life.

Huang, X, Sun, B, Li, K, Chen, S & Wang, G 2013, 'Mesoporous graphene paper immobilised sulfur as a flexible electrode for lithium-sulfur batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 1, no. 43, pp. 13484-13489.
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Free-standing flexible mesoporous graphene-sulfur nanocomposite electrodes have been prepared by a sulfur vapor treatment approach. Amorphous sulfur homogeneously was distributed in the mesoporous architectures of porous graphene paper, in which sulfur was immobilized. The as-prepared mesoporous graphene-sulfur papers can be directly applied as electrodes in lithium-sulfur batteries without using a binder, conductive additives or an extra current collector. The conductive flexible porous graphene networks can effectively facilitate electron transfer and electrolyte diffusion. The free-standing sulfur-graphene nanocomposite electrodes achieved a high discharge capacity of 1393 mA h g^-1 with an enhanced cycling stability and good rate performance. © The Royal Society of Chemistry 2013.

Humphrys, MS, Creasy, T, Sun, Y, Shetty, AC, Chibucos, MC, Drabek, EF, Fraser, CM, Farooq, U, Sengamalay, N, Ott, S, Shou, H, Bavoil, PM, Mahurkar, A & Myers, GSA 2013, 'Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells', PLoS ONE, vol. 8, no. 12, pp. e80597-e80597.
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We developed an RNA-Seq-based method to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with intracellular bacteria. As proof of principle, this method was applied to Chlamydia trachomatis-infected epithelial cell monolayers in vitro, successfully obtaining transcriptomes of both C. trachomatis and the host cells at 1 and 24 hours post-infection. Chlamydiae are obligate intracellular bacterial pathogens that cause a range of mammalian diseases. In humans chlamydiae are responsible for the most common sexually transmitted bacterial infections and trachoma (infectious blindness). Disease arises by adverse host inflammatory reactions that induce tissue damage & scarring. However, little is known about the mechanisms underlying these outcomes. Chlamydia are genetically intractable as replication outside of the host cell is not yet possible and there are no practical tools for routine genetic manipulation, making genome-scale approaches critical. The early timeframe of infection is poorly understood and the host transcriptional response to chlamydial infection is not well defined. Our simultaneous RNA-Seq method was applied to a simplified in vitro model of chlamydial infection. We discovered a possible chlamydial strategy for early iron acquisition, putative immune dampening effects of chlamydial infection on the host cell, and present a hypothesis for Chlamydia-induced fibrotic scarring through runaway positive feedback loops. In general, simultaneous RNA-Seq helps to reveal the complex interplay between invading bacterial pathogens and their host mammalian cells and is immediately applicable to any bacteria/host cell interaction.

Hutchinson, AT, Malik, A, Berkahn, MB, Agostino, M, To, J, Tacchi, JL, Djordjevic, SP, Turnbull, L, Whitchurch, CB, Edmundson, AB, Jones, DR, Raison, RL & Ramsland, PA 2013, 'Formation of assemblies on cell membranes by secreted proteins: molecular studies of free lambda light chain aggregates found on the surface of myeloma cells', BIOCHEMICAL JOURNAL, vol. 454, no. 3, pp. 479-489.
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We have described the presence of cell-membrane-associated κFLCs (free immunoglobulin light chains) on the surface of myeloma cells. Notably, the anti-κFLC mAb (monoclonal antibody) MDX-1097 is being assessed in clinical trials as a therapy for κ light chain isotype multiple myeloma. Despite the clinical potential of anti-FLC mAbs, there have been limited studies on characterizing membrane-associated FLCs at a molecular level. Furthermore, it is not known whether λFLCs can associate with cell membranes of myeloma cells. In the present paper, we describe the presence of λFLCs on the surface of myeloma cells. We found that cell-surface-associated λFLCs are bound directly to the membrane and in an aggregated form. Subsequently, membrane interaction studies revealed that λFLCs interact with saturated zwitterionic lipids such as phosphatidylcholine and phosphatidylethanolamine, and using automated docking, we characterize a potential recognition site for these lipids. Atomic force microscopy confirmed that membrane-associated λFLCs are aggregated. Given the present findings, we propose a model whereby individual FLCs show modest affinity for zwitterionic lipids, with aggregation stabilizing the interaction due to multivalency. Notably, this is the first study to image FLCs bound to phospholipids and provides important insights into the possible mechanisms of membrane association by this unique myeloma surface antigen. © 2013 Biochemical Society.

Huyang, G, Canning, J, Petermann, I, Bishop, D, McDonagh, A & Crossley, MJ 2013, 'Room temperature sol-gel fabrication and functionalization for sensor applications', Photonic Sensors, vol. 3, no. 2, pp. 168-177.
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The structure and physical properties of a thin titania sol-gel layer prepared on silicon and silica surfaces were examined. Spectroscopic (FTIR, UV-VIS spectroscopy), refractive index (ellipsometry) and microscopic (light microscopy and SEM/EDS) tools were used to examine both chemical uniformity and physical uniformity of the sol-gel glass layers. The conditions for the fabrication of uniform layers were established, and room temperature dopant incorporation was examined. The absorption bands of porphyrin-containing titania sol-gel layers were characterized. By addition of a metal salt to the titania layer, it was possible to metallate the free-base porphyrin within and change the UV-VIS absorbance of the porphyrin, the basis of metal detection using porphyrins. The metalloporphyrins were detected by localized laser ablation inductive coupled mass spectroscopy (LA-ICP-MS), indicating fairly uniform distribution of metals across the titania surface.

Ibacache‐Quiroga, C, Ojeda, J, Espinoza‐Vergara, G, Olivero, P, Cuellar, M & Dinamarca, MA 2013, 'The hydrocarbon‐degrading marine bacterium Cobetia sp. strain MM1IDA2H‐1 produces a biosurfactant that interferes with quorum sensing of fish pathogens by signal hijacking', Microbial Biotechnology, vol. 6, no. 4, pp. 394-405.
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SummaryBiosurfactants are produced by hydrocarbon‐degrading marine bacteria in response to the presence of water‐insoluble hydrocarbons. This is believed to facilitate the uptake of hydrocarbons by bacteria. However, these diffusible amphiphilic surface‐active molecules are involved in several other biological functions such as microbial competition and intra‐ or inter‐species communication. We report the isolation and characterization of a marine bacterial strain identified as Cobetia sp. MM1IDA2H‐1, which can grow using the sulfur‐containing heterocyclic aromatic hydrocarbon dibenzothiophene (DBT). As with DBT, when the isolated strain is grown in the presence of a microbial competitor, it produces a biosurfactant. Because the obtained biosurfactant was formed by hydroxy fatty acids and extracellular lipidic structures were observed during bacterial growth, we investigated whether the biosurfactant at its critical micelle concentration can interfere with bacterial communication systems such as quorum sensing. We focused on Aeromonas salmonicida subsp. salmonicida, a fish pathogen whose virulence relies on quorum sensing signals. Using biosensors for quorum sensing based on Chromobacterium violaceum and Vibrio anguillarum, we showed that when the purified biosurfactant was mixed with N

Idrees, S & Ashfaq, UA 2013, 'RNAi: antiviral therapy against dengue virus', Asian Pacific Journal of Tropical Biomedicine, vol. 3, no. 3, pp. 232-236.
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Idrees, S & Ashfaq, UA 2013, 'Structural analysis and epitope prediction of HCV E1 protein isolated in Pakistan: an in-silico approach', Virology Journal, vol. 10, no. 1.
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Idrees, S, Ashfaq, UA & Idrees, N 2013, 'Development of global consensus sequence of HCV glycoproteins involved in viral entry', Theoretical Biology and Medical Modelling, vol. 10, no. 1.
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Idrees, S, Ashfaq, UA & Khaliq, S 2013, 'HCV Envelope protein 2 sequence comparison of Pakistani isolate and In-silico prediction of conserved epitopes for vaccine development', Journal of Translational Medicine, vol. 11, no. 1.
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Abstract Background HCV is causing hundreds of cases yearly in Pakistan and has become a threat for Pakistani population. HCV E2 protein is a transmembrane protein involved in viral attachment and thus can serve as an important target for vaccine development but because of its variability, vaccine development against it has become a challenge. Therefore, this study was designed to isolate the HCV E2 gene from Pakistani HCV infected patients of 3a genotype, to perform In-silico analysis of HCV E2 isolated in Pakistan and to analyze HCV E2 protein sequence in comparison with other E2 proteins belonging to 3a and 1a genotypes to find potential conserved B-cells and T-cell epitopes that can be important in designing novel inhibitory compounds and peptide vaccine against genotype 3a and 1a. Patients and methods Patients were selected on the basis of elevated serum ALT and AST levels at least for six months, histological examination, and detection of serum HCV RNA anti-HCV antibodies (3rd generation ELISA). RNA isolation, cDNA synthesis, amplification, cloning and sequencing was performed from 4 patient’s serum samples in order to get the HCV E2 sequence. HCV E2 protein of Pakistani origin was analyzed using various bioinformatics tools including sequence and structure tools. Results HCV E1 protein modeling was performed with I-TASSER online server and quality of the model was assessed with ramchandran plot and Z-score. A total of 3 B-cell and 3 T-cell epitopes were found to be highly conserved among HCV 3a and 1a genotype.

Im, H, Hirota, J, Rahman, M, Rumzhum, N, Manetsch, M, Pascoe, C, Oliver, B & Ammit, A 2013, 'The NLRP3 inflammasome is not activated in airway smooth muscle upon TLR2 ligation', EUROPEAN RESPIRATORY JOURNAL, vol. 42, no. S57, pp. 559-559.
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Inflammasomes have emerged as playing key roles in inflammation and innate immunity. A growing body of evidence has suggested that the nucleotide-binding domain and leucine-rich repeat protein 3 (NLRP3) inflammasome is important in chronic airway diseases such as asthma and COPD. Inflammasome activation results, in part, in pro-IL-1ß processing and secretion of the pro-inflammatory cytokine IL-1ß. Because asthma exacerbations are associated with elevated levels of secreted IL-1ß we addressed whether the NLRP3 inflammasome is activated under in vitro conditions that mimic infectious exacerbation in asthma. Primary cultures of airway smooth muscle (ASM) cells were treated with infectious stimuli (mimicked using the TLR2 agonist Pam3CSK4, a synthetic bacterial lipopeptide). While Pam3CSK4 robustly upregulated ASM cytokine expression in response to TNFa and significantly enhanced IL-1ß mRNA expression, we were unable to detect IL-1ß in the cell supernatants. Thus, IL-1ß was not secreted and therefore unable to act in an autocrine manner to promote amplification of ASM inflammatory responses. Moreover, TLR2 ligation did not enhance NLRP3 mRNA expression in ASM cells, nor was NLRP3 protein detected in the airway smooth muscle layer of tracheal sections from human donors. In conclusion, these data demonstrate that enhanced synthetic function of ASM cells, induced by infectious exacerbation of airway inflammation, is NLRP3 inflammasome and IL-1ß-independent. Activation of NLRP3 inflammasome by invading pathogens may prove cell-type specific in exacerbation of airway inflammation in asthma.

Irga, PJ, Torpy, FR & Burchett, MD 2013, 'Can hydroculture be used to enhance the performance of indoor plants for the removal of air pollutants?', ATMOSPHERIC ENVIRONMENT, vol. 77, no. 1, pp. 267-271.
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The indoor plant, Syngonium podophyllum, grown in both conventional potting mix and hydroculture, was investigated for its capacity to reduce two components of indoor air pollution; volatile organic compounds (VOCs) and CO2. It was found that, with a moderate increase in indoor light intensity, this species removed significant amounts of CO2 from test chambers, removing up to 61%±2.2 of 1000ppmv over a 40min period. It was also found that the hydroculture growth medium facilitated increased CO2 removal over potting mix. The VOC removing potential of hydroculture plants was also demonstrated. Whilst the rate of VOC (benzene) removal was slightly lower for hydroculture-grown plants than those grown in potting mix, both removed 25ppmv from the test chambers within 7 days. The effect of benzene on the community level physiological profiles of rhizospheric bacteria was also assessed. There was less variability in the carbon substrate utilisation profile of the bacterial community from the rhizosphere of hydroculture plants compared to potting mix, however the species present encompassed at least those involved with VOC removal. Overall, we propose that plants grown in hydroculture can simultaneously deplete CO2 and VOCs, and thus may have potential for improving indoor air quality. © 2013.

Islam, A, Labbate, M, Djordjevic, SP, Alam, M, Darling, A, Melvold, J, Holmes, AJ, Johura, FT, Cravioto, A, Charles, IG & Stokes, HW 2013, 'Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic', OPEN BIOLOGY, vol. 3, no. FEB, p. 120181.
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Of the 200+ serogroups of Vibrio cholerae, only O1 or O139 strains are reported to cause cholera, and mostly in endemic regions. Cholera outbreaks elsewhere are considered to be via importation of pathogenic strains. Using established animal models, we show that diverse V. cholerae strains indigenous to a nonendemic environment (Sydney, Australia), including non-O1/O139 serogroup strains, are able to both colonize the intestine and result in fluid accumulation despite lacking virulence factors believed to be important. Most strains lacked the type three secretion system considered a mediator of diarrhoea in non- O1/O13 V. cholerae. Multi-locus sequence typing (MLST) showed that the Sydney isolates did not form a single clade and were distinct from O1/O139 toxigenic strains. There was no correlation between genetic relatedness and the profile of virulence-associated factors. Current analyses of diseases mediated by V. cholerae focus on endemic regions, with only those strains that possess particular virulence factors considered pathogenic. Our data suggest that factors other than those previously well described are of potential importance in influencing disease outbreaks. © 2013 The Authors.

Jackson, F, Maynard, P, Cavanagh-Steer, K, Dusting, T & Roux, C 2013, 'A survey of glass found on the headwear and head hair of a random population vs. people working with glass', Forensic Science International, vol. 226, no. 1-3, pp. 125-131.
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This study investigated the prevalence of glass particles on the headwear and head hair of two different population groups; the general public who do not work with glass, and glaziers from OBrien® Glass Industries who work with glass and have regular contact with broken glass. The 232 samples collected from the head hair and headwear from the random population resulted in the recovery of 6 glass fragments in total on 6 individuals (i.e. one fragment each). All of these fragments were from head hair samples with no multiple fragments recovered. The two headwear samples that were taken revealed no fragments. These results were in contrast to the survey that was conducted on the head hair and headwear of 25 glaziers from OBrien®, in which 138 glass fragments were found in total on 24 of the 25 glaziers. The size and number of fragments found in each sample were also generally larger for the glaziers group. The results from this study indicate that the prevalence of glass on the head hair and head wear of the random population is very low in comparison to the head hair and headwear of those who have regular contact with breaking glass. The significance of this finding with respect to the interpretation of glass evidence is also discussed

Jennings, EM, Morris, JS, Carroll, RJ, Manyam, GC & Baladandayuthapani, V 2013, 'Bayesian methods for expression-based integration of various types of genomics data', EURASIP Journal on Bioinformatics and Systems Biology, vol. 2013, no. 1.
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Abstract We propose methods to integrate data across several genomic platforms using a hierarchical Bayesian analysis framework that incorporates the biological relationships among the platforms to identify genes whose expression is related to clinical outcomes in cancer. This integrated approach combines information across all platforms, leading to increased statistical power in finding these predictive genes, and further provides mechanistic information about the manner in which the gene affects the outcome. We demonstrate the advantages of the shrinkage estimation used by this approach through a simulation, and finally, we apply our method to a Glioblastoma Multiforme dataset and identify several genes potentially associated with the patients’ survival. We find 12 positive prognostic markers associated with nine genes and 13 negative prognostic markers associated with nine genes.

Jeong, S, Naidu, G, Vigneswaran, S, Ma, CH & Rice, SA 2013, 'A rapid bioluminescence-based test of assimilable organic carbon for seawater', Desalination, vol. 317, pp. 160-165.
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The accumulation of biological materials and bacteria on water purification membranes, termed biofouling, is associated with decreased membrane performance and increased cost of operation. One strategy to minimize biofouling is pretreatment of the influent water. In this regard, tools and indicators that can assess the influent water are required, enabling an optimum selection of pretreatment methods. One parameter directly linked to biofouling potential is the concentration of assimilable organic carbon (AOC) in the feed-water. High AOC levels are associated with increased growth potential of the microbial fouling community. This work focused on the development of a new method for rapid and accurate quantification of AOC concentration in seawater. The method is based on the quantification of the bioluminescence response of the marine bacterium Vibrio fischeri MJ-1. Compared to previous methods, this new V. fischeri method was rapid (within 1. h), sensitive (detection limit. = 0.1. μg-C glucose equivalents/L) and highly suitable for seawater samples. V. fischeri method was evaluated using real seawater samples. The results showed positive reproductive AOC values. The new V. fischeri AOC method developed has a highly promising potential to be practically adopted as a rapid indicator of AOC concentration and hence biofouling potential of influent marine water. © 2013 Elsevier B.V.

Jessop, TS, Letnic, M, Webb, JK & Dempster, T 2013, 'Adrenocortical stress responses influence an invasive vertebrate's fitness in an extreme environment', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 280, no. 1768, pp. 1-9.
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Continued range expansion into physiologically challenging environments requires invasive species to maintain adaptive phenotypic performance. The adrenocortical stress response, governed in part by glucocorticoid hormones, influences physiological and behavioural responses of vertebrates to environmental stressors. However, any adaptive role of this response in invasive populations that are expanding into extreme environments is currently unclear. We experimentally manipulated the adrenocortical stress response of invasive cane toads (Rhinella marina) to investigate its effect on phenotypic performance and fitness at the species' range front in the Tanami Desert, Australia. Here, toads are vulnerable to overheating and dehydration during the annual hot-dry season and display elevated plasma corticosterone levels indicative of severe environmental stress. By comparing unmanipulated control toads with toads whose adrenocortical stress response was manipulated to increase acute physiological stress responsiveness, we found that control toads had significantly reduced daily evaporative water loss and higher survival relative to the experimental animals. The adrenocortical stress response hence appears essential in facilitating complex phenotypic performance and setting fitness trajectories of individuals from invasive species during range expansion. © 2013 The Author(s) Published by the Royal Society. All rights reserved.

Johnson, AP, Mikac, KM & Wallman, JF 2013, 'Thermogenesis in decomposing carcasses', Forensic Science International, vol. 231, no. 1-3, pp. 271-277.
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Jones, K, Benson, S & Roux, C 2013, 'The forensic analysis of office paper using carbon isotope ratio mass spectrometry – Part 1: Understanding the background population and homogeneity of paper for the comparison and discrimination of samples', Forensic Science International, vol. 231, no. 1-3, pp. 354-363.
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Isotope Ratio Mass Spectrometry (IRMS) has been shown to be a useful tool in the comparison of materials that are chemically identical either through man-made production processes or for materials that have been naturally produced. Paper therefore, is an ideal material for this type of measurement given that it is manufactured from a naturally produced product that can be difficult to discriminate based on physical feature comparison alone. To determine whether carbon isotopes are useful for discriminating document papers, 125 samples from Australia and New Zealand were collected over a 24-month period. When measured, a range of 8 was observed. A homogeneity study was undertaken to examine the range of values expected from paper sources including single sheets, single reams and multiple reams from the same brand. These results can also be used to suggest how best to sample from these different sources. After characterizing the natural variation of the material, a range of 1 was defined for use as a benchmark for discrimination. Utilizing this threshold, 68% of the 125 collected samples (when paired against each other) could be discriminated using the carbon isotope abundances alone. Additionally, correlation was observed when measured values were plotted against their production region of origin.

Jones, K, Benson, S & Roux, C 2013, 'The forensic analysis of office paper using carbon isotope ratio mass spectrometry. Part 3: Characterizing the source materials and the effect of production and usage on the δ13C values of paper', Forensic Science International, vol. 233, no. 1-3, pp. 355-364.
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When undertaking any study of the isotope abundance values of a bulk material, consideration should be given to the source materials and how they are combined to reach the final product being measured. While it is demonstrative to measure and record the values of clean papers, such as the results published as part one of this series, the majority of forensic casework samples would have undergone some form of writing or printing process prior to examination. Understanding the effects of these processes on the d13C values of paper is essential for interpretation and comparison with clean samples, for example in cases where printed documents need to be compared to paper from an unprinted suspect ream. This study was undertaken so that the source materials, the effects of the production process and the effects of printing and forensic testing could be observed with respect to 80 gsm white office papers. Samples were taken sequentially from the paper production facility at the Australian Paper Mill (Maryvale, VIC). These samples ranged from raw wood chips through the pulping, whitening and refinement steps to the final formed and packed paper. Cellulose was extracted from each sample to observe both fractionation and mixing steps and their effect on the d13C values. Overall, the mixing steps were observed to have a larger effect on the isotopic values of the bulk materials than any potential fractionation. Printing of papers using toner and inkjet printing processes and forensic testing were observed to have little effect on d13C.

Jones, K, Benson, S & Roux, C 2013, 'The forensic analysis of office paper using carbon isotope ratio mass spectrometry—Part 2: Method development, validation and sample handling', Forensic Science International, vol. 231, no. 1-3, pp. 364-374.
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This paper describes the development and validation of a method for the analysis of office papers by measuring carbon isotopes using isotope ratio mass spectrometry (IRMS). The method development phase included testing protocols for storage, sample materials, set-up of the analytical run; and examining the effects of other paper examination procedures on IRMS results. A method validation was performed so that the Deltaplus XP IRMS instrument (Thermo Finnigan, Bremen, Germany) with Flash EA 1112 could be used to measure document paper samples for forensic casework. A validation protocol that would meet international standards for laboratory accreditation (international standard ISO 17025) was structured so that the instruments performance characteristics could be observed. All performance characteristics measured were found to be within an acceptable range and an expanded measurement uncertainty for the measurement of carbon isotopes in paper was calculated at 0.26, with a coverage factor of 2. This method was utilized in a large-scale study, published as part one of this series, that showed that IRMS of document papers is useful as a chemical comparison technique for 80 gsm white office papers

Jones, PM & George, AM 2013, 'Mechanism of the ABC transporter ATPase domains: catalytic models and the biochemical and biophysical record', Critical Reviews in Biochemistry and Molecular Biology, vol. 48, no. 1, pp. 39-50.
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ABC transporters comprise a large, diverse, and ubiquitous superfamily of membrane active transporters. Their core architecture is a dimer of dimers, comprising two transmembrane domains that bind substrate and form the channel, and two ATP-binding cassettes, which bind and hydrolyze ATP to energize the translocase function. The prevailing paradigm for the ABC transport mechanism is the Switch Model, in which the nucleotide binding domains are proposed to dimerise upon binding of two ATP molecules, and thence dissociate upon sequential hydrolysis of the ATP. This idea appears consistent with crystal structures of both isolated subunits and whole transporters, as well as with a significant body of biochemical data. Nonetheless, an alternative Constant Contact Model has been proposed, in which the nucleotide binding domains do not fully dissociate, and ATP hydrolysis occurs alternately at each of the two active sites. Here, we review the biochemical and biophysical data relating to the ABC catalytic mechanism, to show how they may be construed as consistent with a Constant Contact Model, and to assess to what extent they support the Switch Model.

Jones, PM, Curmi, PMG, Valenzuela, SM & George, AM 2013, 'Computational Analysis of the Soluble Form of the Intracellular Chloride Ion Channel Protein CLIC1', BioMed Research International, vol. 2013, pp. 1-14.
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The chloride intracellular channel (CLIC) family of proteins has the remarkable property of maintaining both a soluble form and an integral membrane form acting as an ion channel. The soluble form is structurally related to the glutathione-S-transferase family, and CLIC can covalently bind glutathione via an active site cysteine. We report approximately 0.6 μs of molecular dynamics simulations, encompassing the three possible ligand-bound states of CLIC1, using the structure of GSH-bound human CLIC1. Noncovalently bound GSH was rapidly released from the protein, whereas the covalently ligand-bound protein remained close to the starting structure over 0.25 μs of simulation. In the unliganded state, conformational changes in the vicinity of the glutathione-binding site resulted in reduced reactivity of the active site thiol. Elastic network analysis indicated that the changes in the unliganded state are intrinsic to the protein architecture and likely represent functional transitions. Overall, our results are consistent with a model of CLIC function in which covalent binding of glutathione does not occur spontaneously but requires interaction with another protein to stabilise the GSH binding site and/or transfer of the ligand. The results do not indicate how CLIC1 undergoes a radical conformational change to form a transmembrane chloride channel but further elucidate the mechanism by which CLICs are redox controlled.

Kabakova, IV, Pant, R, Choi, D-Y, Debbarma, S, Luther-Davies, B, Madden, SJ & Eggleton, BJ 2013, 'Narrow linewidth Brillouin laser based on chalcogenide photonic chip', OPTICS LETTERS, vol. 38, no. 17, pp. 3208-3211.
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We present the first demonstration of a narrow linewidth, waveguide-basedBrillouin laser which is enabled by large Brillouin gain of a chalcogenidechip. The waveguides are equipped with vertical tapers for low loss coupling.Due to optical feedback for the Stokes wave, the lasing threshold is reduced to360 mW, which is 5 times lower than the calculated single-pass Brillouinthreshold for the same waveguide. The slope efficiency of the laser is found tobe 30% and the linewidth of 100 kHz is measured using a self-heterodyne method.

Kaemper, W, Webb, JK, Crowther, MS, Greenlees, MJ & Shine, R 2013, 'Behaviour and survivorship of a dasyurid predator (Antechinus flavipes) in response to encounters with the toxic and invasive cane toad (Rhinella marina)', AUSTRALIAN MAMMALOGY, vol. 35, no. 2, pp. 136-143.
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Australia's biogeographical isolation has rendered many endemic species vulnerable to invaders. The recent spread of the cane toad (Rhinella marina) has caused serious population declines for some predatory reptile and mammal species. To determine a priori whether or not cane toad poisoning endangers native species, we can test the fates of predators in laboratory trials. We investigated whether an Australian marsupial whose range is increasingly being occupied by cane toads (the yellow-footed antechinus, Antechinus flavipes) is at risk of toad poisoning by testing (1)whether yellow-footed antechinuses approach or attack canetoads and, if so, whether they die as a result; and (2) ifthey survive, whether they then learn to avoid toads in subsequent encounters. We also investigated the effects of sympatry with toads on the feeding response. In all, 58% ofantechinuses from eastern New South Wales approached or attacked a toad (over 4 or 5 opportunities to do so, on successive nights), and none showed ill effects after doing so. Antechinuses that attacked (killed or ingested) toads rapidly learnt to avoid them. Antechinuses from toad-exposed populations ingested more toad flesh, but otherwise reacted in the same ways as did conspecifics from toad-free areas. Hence, the yellow-footed antechinus is unlikely to face population declines via toad poisoning. © 2013 Australian Mammal Society.

Karagiannidis, LE, Hiscock, JR & Gale, PA 2013, 'The influence of stereochemistry on anion binding and transport', Supramolecular Chemistry, vol. 25, no. 9-11, pp. 626-630.
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Kardaras, C & Platen, E 2013, 'MULTIPLICATIVE APPROXIMATION OF WEALTH PROCESSES INVOLVING NO-SHORT-SALES STRATEGIES VIA SIMPLE TRADING', MATHEMATICAL FINANCE, vol. 23, no. 3, pp. 579-590.
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A financial market model with general semimartingale asset-price processes and where agents can only trade using no-short-sales strategies is considered. We show that wealth processes using continuous trading can be approximated very closely by wealth processes using simple combinations of buy-and-hold trading. This approximation is based on controlling the proportions of wealth invested in the assets. As an application, the utility maximization problem is considered and it is shown that optimal expected utilities and wealth processes resulting from continuous trading can be approximated arbitrarily well by the use of simple combinations of buy-and-hold strategies.

Keast, VJ, Zwan, B, Supansomboon, S, Cortie, MB & Persson, POA 2013, 'AuAl2 and PtAl2 as potential plasmonic materials', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 577, no. 1, pp. 581-586.
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The dielectric functions of PtAl2, AuAl2 and hypothetical intermediate alloys of the two in the form of Aux- Pt1-xAl 2 were calculated from first principles using density functional theory (DFT) and the random phase approximation (RPA). From these, the reflectivity, electron energy-loss spectra (EELS) and small sphere extinction spectra are predicted. The experimental reflectivity and EELS were measured for PtAl2 and showed good agreement with the theoretical spectra. The yellow color of PtAl2 is associated with a bulk plasmon at 3 eV. We predict that the optical properties of hypothetical intermediate alloys would show a smooth evolution with composition. The details of this change can be understood by examination of the underlying density of states (DOS). The predicted small sphere extinction spectra and quality factors show a strong surface plasmon resonance for these materials, with PtAl2 having the optimum performance. The results indicate that these materials are good candidates for applications in plasmonics. © 2013 Elsevier B.V. All rights reserved.

Keglowich, L, Roth, M, Philippova, M, Resink, T, Tjin, G, Oliver, B, Lardinois, D, Dessus-Babus, S, Gosens, R, Hostettler Haack, K, Tamm, M & Borger, P 2013, 'Bronchial Smooth Muscle Cells of Asthmatics Promote Angiogenesis through Elevated Secretion of CXC-Chemokines (ENA-78, GRO-α, and IL-8)', PLoS ONE, vol. 8, no. 12, pp. e81494-e81494.
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Background: Airway wall remodelling is a key pathology of asthma. It includes thickening of the airway wall, hypertrophy and hyperplasia of bronchial smooth muscle cells (BSMC), as well as an increased vascularity of the sub-epithelial cell layer BSMC are known to be the effector cells of bronchoconstriction, but they are increasingly recognized as an important source of inflammatory mediators and angiogenic factors. Objective: To compare the angiogenic potential of BSMC of asthmatic and non-asthmatic patients and to identify asthma-specific angiogenic factors Methods: Primary BSMC were isolated from human airway tissue of asthmatic and non-asthmatic patients. Conditioned medium (CM) collected from BSMC isolates was tested for angiogenic capacity using the endothelial cell (EC)-spheroid in vitro angiogenesis assay. Angiogenic factors in CM were quantified using a human angiogenesis antibody array and enzyme linked immunosorbent assay. Results: Induction of sprout outgrowth from EC-spheroids by CM of BSMC obtained from asthma patients was increased compared with CM of control BSMC (twofold, p < 0.001). Levels of ENA-78, GRO-α and IL-8 were significantly elevated in CM of BSMC from asthma patients (p < 0.05 vs. non-asthmatic patients). SB 265610, a competitive antagonist of chemokine (CXC-motif) receptor 2 CXCR2), attenuated the increased sprout outgrowth induced by CM of asthma patient-derived BSMC. Conclusions: BSMC isolated from asthma patients exhibit increased angiogenic potential. This effect is mediated through the CXCR2 ligands (ENA78, GRO-α and IL-8) produced by BSMC Implications: CXCR2 ligands may play a decisive role in directing the neovascularization in the sub-epithelial cell layers of the lungs of asthma patients Counteracting the CXCR2 mediated neovascularization by pharmaceutical compounds may represent a novel strategy to reduce airway remodelling in asthma. © 2013 Keglowich et al.

Kelaher, BP, Van Den Broek, J, York, PH, Bishop, MJ & Booth, DJ 2013, 'Positive responses of a seagrass ecosystem to experimental nutrient enrichment', MARINE ECOLOGY PROGRESS SERIES, vol. 487, no. 1, pp. 15-25.
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Nutrient enrichment of coastal waters is widely recognized as a major driver of seagrass decline. Under conditions where seagrasses are nutrient-limited, however, moderately elevated nutrient loads can enhance seagrass biomass and increase above- and below-ground consumers that support higher order predators. To improve understanding of bottom-up processes in seagrass ecosystems, we conducted a manipulative field experiment to simultaneously evaluate the responses of primary producers (seagrass and epiphytes) and the epiphyte- and the sedimentbased components of seagrass food webs to moderate and high levels of waterborne nutrients. Fifteen 7 m 2 sites in Zostera muelleri meadows were assigned randomly to control, moderate or high nutrient treatments and were enriched with 0, 1800 g and 3600 g respectively of slow-release fertilizer in above-ground dispensers. The experiment ran for 9 mo (August 2006 to April 2007) and the fertilizer was replaced every 2 mo to ensure continuous enrichment. The biomass of primary producers (seagrasses Z. muelleri, Halophila ovalis and associated epiphytes) and the abundance of predators in the epiphyte- and the sediment-based components of the food web were greater in nutrient-enriched treatments than in controls. Epiphyte grazers, deposit feeders/detritivores, suspension feeders and benthic grazers did not respond significantly to the nutrient enrichment. In general, responses to nutrient enrichment were similar for medium and high nutrient treatments except that the biomass and surface area of seagrass was greater in high enrichment sites. These results demonstrate that Z. muelleri-dominated seagrass meadows in oligotrophic systems may be resilient to greater nutrient loads. Effective conservation strategies for Z. muelleri meadows should continue to consider interactions among nutrient enrichment and other key anthropogenic stressors, particularly non-nutrient pollutants in runoff and sewage discharge. © Inter-Research 2013.

Kendig, MD, Boakes, RA, Rooney, KB & Corbit, LH 2013, 'Chronic restricted access to 10% sucrose solution in adolescent and young adult rats impairs spatial memory and alters sensitivity to outcome devaluation', Physiology & Behavior, vol. 120, pp. 164-172.
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Kennard, JE, Hadden, JP, Marseglia, L, Aharonovich, I, Castelletto, S, Patton, BR, Politi, A, Matthews, JCF, Sinclair, AG, Gibson, BC, Prawer, S, Rarity, JG & O'Brien, JL 2013, 'On-Chip Manipulation of Single Photons from a Diamond Defect', PHYSICAL REVIEW LETTERS, vol. 111, no. 21.
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Operating reconfigurable quantum circuits with single photon sources is a key goal of photonic quantum information science and technology. We use an integrated waveguide device containing directional couplers and a reconfigurable thermal phase controller to manipulate single photons emitted from a chromium related color center in diamond. Observation of both a wavelike interference pattern and particlelike sub-Poissionian autocorrelation functions demonstrates coherent manipulation of single photons emitted from the chromium related center and verifies wave particle duality. © 2013 American Physical Society.

Khachadorian, S, Papagelis, K, Ogata, K, Hofmann, S, Phillips, MR & Thomsen, C 2013, 'Elastic Properties of Crystalline-Amorphous Core-Shell Silicon Nanowires', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 117, no. 8, pp. 4219-4226.
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The pressure behavior of Raman frequencies and line widths of crystalline core-amorphous shell silicon nanowires (SiNWs) with two different core-to-shell ratio thicknesses was studied at pressures up to 8 GPa. The obtained isothermal compressibility (bulk modulus) of SiNWs with a core-to-shell ratio of about 1.8 is ∼20% higher (lower) than reported values for bulk Si. For SiNWs with smaller core-to-shell ratios, a plastic deformation of the shell was observed together with a strain relaxation. A significant increase in the full width at half-maximum of the Raman LTO-peak due to phonon decay was used to determine the critical pressure at which LTO-phonons decay into LO + TA phonons. Our results reveal that this critical pressure in strained core-shell SiNWs (∼4 GPa) is different from the reported value for bulk Si (∼7 GPa), whereas no change is observed for relaxed core-shell SiNWs. © 2013 American Chemical Society.

Khaw, LT, Ball, HJ, Golenser, J, Combes, V, Grau, GE, Wheway, J, Mitchell, AJ & Hunt, NH 2013, 'Endothelial Cells Potentiate Interferon-γ Production in a Novel Tripartite Culture Model of Human Cerebral Malaria', PLoS ONE, vol. 8, no. 7, pp. e69521-e69521.
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We have established a novel in vitro co-culture system of human brain endothelial cells (HBEC), Plasmodium falciparum parasitised red blood cells (iRBC) and peripheral blood mononuclear cells (PBMC), in order to simulate the chief pathophysiological lesion in cerebral malaria (CM). This approach has revealed a previously unsuspected pro-inflammatory role of the endothelial cell through potentiating the production of interferon (IFN)-γ by PBMC and concurrent reduction of interleukin (IL)-10. The IFN-γ increased the expression of CXCL10 and intercellular adhesion molecule (ICAM)-1, both of which have been shown to be crucial in the pathogenesis of CM. There was a shift in the ratio of IL-10:IFN-γ protein from >1 to <1 in the presence of HBEC, associated with the pro-inflammatory process in this model. For this to occur, a direct contact between PBMC and HBEC, but not PBMC and iRBC, was necessary. These results support HBEC playing an active role in the pathogenesis of CM. Thus, if these findings reflect the pathogenesis of CM, inhibition of HBEC and PBMC interactions might reduce the occurrence, or improve the prognosis, of the condition. © 2013 Khaw et al.

Kim, JJY, Tan, Y, Xiao, L, Sun, Y-L & Qu, X 2013, 'Green Tea Polyphenol Epigallocatechin-3-Gallate Enhance Glycogen Synthesis and Inhibit Lipogenesis in Hepatocytes', BioMed Research International, vol. 2013, pp. 1-8.
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The beneficial effects of green tea polyphenols (GTP) against metabolic syndrome and type 2 diabetes by suppressing appetite and nutrient absorption have been well reported. However the direct effects and mechanisms of GTP on glucose and lipid metabolism remain to be elucidated. Since the liver is an important organ involved in glucose and lipid metabolism, we examined the effects and mechanisms of GTP on glycogen synthesis and lipogenesis in HepG2 cells. Concentrations of GTP containing 68% naturally occurring (−)-epigallocatechin-3-gallate (EGCG) were incubated in HepG2 cells with high glucose (30 mM) under 100 nM of insulin stimulation for 24 h. GTP enhanced glycogen synthesis in a dose-dependent manner. 10 μM of EGCG significantly increased glycogen synthesis by 2fold (P<0.05) compared with insulin alone. Western blotting revealed that phosphorylation of Ser9 glycogen synthase kinase 3βand Ser641 glycogen synthase was significantly increased in GTP-treated HepG2 cells compared with nontreated cells. 10 μM of EGCG also significantly inhibited lipogenesis (P<0.01). We further demonstrated that this mechanism involves enhanced expression of phosphorylated AMP-activated protein kinaseαand acetyl-CoA carboxylase in HepG2 cells. Our results showed that GTP is capable of enhancing insulin-mediated glucose and lipid metabolism by regulating enzymes involved in glycogen synthesis and lipogenesis.

Kim, SB, Paudel, KR & Kim, DW 2013, 'Preventive Effect of Traditional Korean Formulations on Intimal Thickening of Rat Carotid Artery Injured by Balloon Catheter', Korean Journal of Plant Resources, vol. 26, no. 6, pp. 678-685.
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Kimizuka, H, Fronzi, M & Ogata, S 2013, 'Effect of alloying elements on in-plane ordering and disordering of solute clusters in Mg-based long-period stacking ordered structures: A first-principles analysis', Scripta Materialia, vol. 69, no. 8, pp. 594-597.
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Kirby, IL, Pitak, MB, Wenzel, M, Wilson, C, Sparkes, HA, Coles, SJ & Gale, PA 2013, 'Systematic structural analysis of a series of anion receptor complexes', CrystEngComm, vol. 15, no. 44, pp. 9003-9003.
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Koilraj, P, Antonyraj, CA, Gupta, V, Reddy, CRK & Kannan, S 2013, 'Novel approach for selective phosphate removal using colloidal layered double hydroxide nanosheets and use of residue as fertilizer', Applied Clay Science, vol. 86, pp. 111-118.
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Kondaveeti, S, Chejara, DR & Siddhanta, AK 2013, 'A facile one-pot synthesis of a fluorescent agarose-O-naphthylacetyl adduct with slow release properties', Carbohydrate Polymers, vol. 98, no. 1, pp. 589-595.
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Kondaveeti, S, Prasad, K & Siddhanta, AK 2013, 'Functional modification of agarose: A facile synthesis of a fluorescent agarose-tryptophan based hydrogel', Carbohydrate Polymers, vol. 97, no. 1, pp. 165-171.
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Kopp, C, Pernice, M, Domart-Coulon, I, Djediat, C, Spangenberg, JE, Alexander, DTL, Hignette, M, Meziane, T & Meibom, A 2013, 'Highly Dynamic Cellular-Level Response of Symbiotic Coral to a Sudden Increase in Environmental Nitrogen', mBio, vol. 4, no. 3.
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ABSTRACT Metabolic interactions with endosymbiotic photosynthetic dinoflagellate Symbiodinium spp. are fundamental to reef-building corals (Scleractinia) thriving in nutrient-poor tropical seas. Yet, detailed understanding at the single-cell level of nutrient assimilation, translocation, and utilization within this fundamental symbiosis is lacking. Using pulse-chase 15 N labeling and quantitative ion microprobe isotopic imaging (NanoSIMS; nanoscale secondary-ion mass spectrometry), we visualized these dynamic processes in tissues of the symbiotic coral Pocillopora damicornis at the subcellular level. Assimilation of ammonium, nitrate, and aspartic acid resulted in rapid incorporation of nitrogen into uric acid crystals (after ~45 min), forming temporary N storage sites within the dinoflagellate endosymbionts. Subsequent intracellular remobilization of this metabolite was accompanied by translocation of nitrogenous compounds to the coral host, starting at ~6 h. Within the coral tissue, nitrogen is utilized in specific cellular compartments in all four epithelia, including mucus chambers, Golgi bodies, and vesicles in calicoblastic cells. Our study shows how nitrogen-limited symbiotic corals take advantage of sudden changes in nitrogen availability; this opens new perspectives for functional studies of nutrient storage and remobilization in microbial symbioses in changing reef environments. IMPORTANCE The methodology applied, combining transmission electron microscopy with nanoscale secondary-ion mass spectrometry (NanoSIMS) imaging of coral tissue labeled with stable isotope tracers, allows quantification and submicrometric localization of metabolic fluxes in an intact s...

Korbel, KL, Hancock, PJ, Serov, P, Lim, RP & Hose, GC 2013, 'Groundwater Ecosystems Vary with Land Use across a Mixed Agricultural Landscape', JOURNAL OF ENVIRONMENTAL QUALITY, vol. 42, no. 2, pp. 380-390.
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Changes in surface land use may threaten groundwater quality and ecosystem integrity, particularly in shallow aquifers where links between groundwater and surface activities are most intimate. In this study we examine the response of groundwater ecosystem to agricultural land uses in the shallow alluvial aquifer of the Gwydir River valley, New South Wales, Australia. We compared groundwater quality and microbial and stygofauna assemblages among sites under irrigated cropping, non-irrigated cropping and grazing land uses. Stygofauna abundance and richness was greatest at irrigated sites, with the composition of the assemblage suggestive of disturbance. Microbial assemblages and water quality also varied with land use. Our study demonstrates significant differences in the composition of groundwater ecosystems in areas with different surface land use, and highlights the utility of groundwater biota for biomonitoring, particularly in agricultural landscapes.

Korbel, KL, Lim, RP & Hose, GC 2013, 'An inter-catchment comparison of groundwater biota in the cotton-growing region of north-western New South Wales', CROP & PASTURE SCIENCE, vol. 64, no. 11-12, pp. 1195-1208.
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Groundwater is essential to crop production in many parts of the world, and the provision of clean groundwater is dependent on healthy groundwater ecosystems. To understand better the functioning of groundwater ecosystems, it is necessary to understand h

Kraemer, WE, Schrameyer, V, Hill, R, Ralph, PJ & Bischof, K 2013, 'PSII activity and pigment dynamics of Symbiodinium in two Indo-Pacific corals exposed to short-term high-light stress', MARINE BIOLOGY, vol. 160, no. 3, pp. 563-577.
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This study examined the capacity for photoprotection and repair of photo-inactivated photosystem II in the same Symbiodinium clade associated with two coexisting coral species during high-light stress in order to test for the modulation of the symbionts photobiological response by the coral host. After 4 days exposure to in situ irradiance, symbionts of the bleaching-sensitive Pocillopora damicornis showed rapid synthesis of photoprotective pigments (by 44 %) and strongly enhanced rates of xanthophyll cycling (by 446 %) while being insufficient to prevent photoinhibition (sustained loss in F v/F m at night) and loss of symbionts after 4 days. By contrast, Pavona decussata showed no significant changes in F v/F m, symbiont density or xanthophyll cycling. Given the association with the same Symbiodinium clade in both coral species, our findings suggest that symbionts in the two species examined may experience different in hospite light conditions as a result of different biometric properties of the coral host.

Krug, LA, Gherardi, DFM, Stech, JL, Leão, ZMAN, Kikuchi, RKP, Hruschka, ER & Suggett, DJ 2013, 'The construction of causal networks to estimate coral bleaching intensity', Environmental Modelling & Software, vol. 42, no. 1, pp. 157-167.
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Current metrics for predicting bleaching episodes, e.g. NOAA's Coral Reef Watch Program, do not seem to apply well to Brazil's marginal reefs located in Bahia state and alternative predictive approaches must be sought for effective long term management. Bleaching occurrences at Abrolhos have been observed since the 1990s but with a much lower frequency/extent than for other reef systems worldwide. We constructed a Bayesian Belief Network (BN) to back-predict the intensity of bleaching events and learn how local and regional scale forcing factors interact to enhance or alleviate coral bleaching specific to Abrolhos. Bleaching intensity data were collected for several reef sites across Bahia state coast (~12°-20°S; 37°-40°W) during the austral summer 1994-2005 and compared to environmental data: sea surface temperature (SST), diffuse light attenuation coefficient at 490 nm (K490), rain precipitation, wind velocities, and El Niño Southern Oscillation (ENSO) proxies. Conditional independence tests were calculated to produce four specialized BNs, each with specific factors that likely regulate bleaching intensity. All specialized BNs identified that a five-day accumulated SST proxy (SSTAc5d) was the exclusive parent node for coral bleaching producing a total predictive rate of 88% based on SSTAc5d state. When SSTAc5d was simulated as unknown, the Thermal-Eolic Resultant BN kept the total predictive rate of 88%. Our approach has produced initial means to predict beaching intensity at Abrolhos. However, the robustness of the model required for management purposes must be further (and regularly) operationally tested with new in situ and remote sensing data. © 2013 Elsevier Ltd.

Kumar, M, Reddy, CRK & Jha, B 2013, 'The ameliorating effect of Acadian marine plant extract against ionic liquids-induced oxidative stress and DNA damage in marine macroalga Ulva lactuca', Journal of Applied Phycology, vol. 25, no. 2, pp. 369-378.
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Ionic liquids (ILs) are generally considered as the green replacement for conventional volatile organic solvents. Nonetheless, their high solubility in water with proven toxic effects on aquatic biota has questioned their green credentials. In the present study, the detoxification potential of Acadian marine plant extract powder (AMPEP) prepared from the brown alga Ascophyllum nodosum was investigated against the 1-alkyl-3-methylimidazolium bromide [C12mim]Br ionic liquid-induced toxicity and oxidative stress in marine macroalga Ulva lactuca. The IL ([C12mim]Br) at LC50 (70 μM) exposure triggered the generation of reactive oxygen species (ROS) such as O2·-, H2O2 and OH· causing membrane and DNA damage together with inhibition of antioxidant systems in the alga. The supplementation of AMPEP (150 μg mL-1) to the culture medium significantly reduced the accumulation of ROS and lipid peroxidation together with the inhibition of lipoxygenase (LOX) activity specially LOX-2 and LOX-3 isoforms. This is for the first time wherein comet assay was performed to ascertain the protective role of AMPEP against DNA damage in algal tissue grown in medium supplemented with IL and AMPEP. The AMPEP showed protective role against DNA damage (5-45 % tail DNA) when compared to those of grown in IL alone (45-70 % tail DNA). Further, specific isomorphs of different antioxidant enzymes such as superoxide dismutase (Mn-SOD-1, ~150 kDa), ascorbate peroxidase (APX-4, ~55 kDa), glutathione peroxidase (GSH-Px-2, ~55 kDa) and glutathione reductase (GR-1, ~180 kDa) responded specifically to AMPEP supplementation. It is evident from these findings that AMPEP could possibly be used for circumventing the negative effects arising from ILs-induced toxicity in marine ecosystem. © 2012 Springer Science+Business Media B.V.

Kumar, P, Mehta, M, Satija, S & Garg, M 2013, 'Enzymatic in vitro Anti-diabetic Activity of Few Traditional Indian Medicinal Plants', Journal of Biological Sciences, vol. 13, no. 6, pp. 540-544.
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Controlling post-prandial hyperglycaemia through enzymatic inhibition of starch degradation is an effective therapeutic approach in the management of diabetes mellitus. To achieve this, twelve indigenous antidiabetic Indian medicinal plants such as Trigonella foenum-graecum, Ocimum sanctum, Aegle marmelos, Plantago ovata, Catharanthus roseus, Alium cepa, Azadirachta indica, Aloe vera, Magnifera indica, Terminalia chebula, Eugenia jambolana and Linum usitatisumum were subjected to sequential solvent extraction and thereafter, 48 fractions were screened for their a-amylase inhibitory potential at three dosage levels in vitro. Out of the 144 samples, Eugenia jambolana water extract showed maximum a-amylase inhibitory activity with IC50 value 1.33 mg mL-1 in comparison with standard drug acarbose (IC50 value 0.86 mg inL-1). Quantitative phytochemical analysis of the lead extract revealed the presence of phenolic content as 69.68 mg tannic acid equivalent g-1 while flavonoidal content as 57.39 mg rutin equivalent g-1. Present study indicated Eugenia jambolana as a potential a-amylase inhibitor in the management of diabetes. © 2013 Asian Network for Scientific Information.

Kutty, SK, Barraud, N, Pham, A, Iskander, G, Rice, SA, Black, DS & Kumar, N 2013, 'Design, Synthesis, and Evaluation of Fimbrolide–Nitric Oxide Donor Hybrids as Antimicrobial Agents', Journal of Medicinal Chemistry, vol. 56, no. 23, pp. 9517-9529.
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Kuzhiumparambil, U & Fu, S 2013, 'Effect of hydrogen peroxide oxidation systems on human urinary steroid profiles', ANALYTICAL METHODS, vol. 5, no. 17, pp. 4402-4408.
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In sports drug testing the steroid profile is the most versatile and informative screening tool for the detection of steroid abuse. Despite the introduction of observed urine collection procedures by the World Anti-Doping Agency (WADA), chemical manipulation of urine specimens by athletes to conceal drug use still occurs and poses an ongoing challenge for doping control laboratories worldwide. In vitro urine adulteration using highly oxidative chemicals have been reported several times in the past. In this study we report the effect of two oxidising agents, Fenton's reagent and peroxidase-peroxide system on the human urinary steroid profile. Varying concentrations of these oxidants were reacted with urine and the reactions monitored by gas chromatography-mass spectrometry. A significant decrease in the absolute concentrations of androsterone, etiocholanolone, 5α-androstane-3α, 17β-diol, 5β-androstane-3α,17β-diol and epitestosterone was observed with consequent alteration of the steroid profile ratios. Adulteration of urine sample with these oxidants can thus mask the abnormality in a steroidal profile following steroid abuse. Drug testing authorities should take into account the effects of these oxidizing adulterants while interpreting the steroid profile data for doping control purposes. © The Royal Society of Chemistry.

Kuzhiumparambil, U & Fu, S 2013, 'Effect of oxidizing adulterants on human urinary steroid profiles', STEROIDS, vol. 78, no. 2, pp. 288-296.
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Steroid profiling is the most versatile and informative technique adapted by doping control laboratories for detection of steroid abuse. The absolute concentrations and ratios of endogenous steroids including testosterone, epitestosterone, androsterone, etiocholanolone, 5α-androstane-3α, 17β-diol and 5β-androstane-3α,17β-diol constitute the significant characteristics of a steroid profile. In the present study we report the influence of various oxidizing adulterants on the steroid profile of human urine. Gas chromatography-mass spectrometry analysis was carried out to develop the steroid profile of human male and female urine. Oxidants potassium nitrite, sodium hypochlorite, potassium permanganate, cerium ammonium nitrate, sodium metaperiodate, pyridinium chlorochromate, potassium dichromate and potassium perchlorate were reacted with urine at various concentrations and conditions and the effect of these oxidants on the steroid profile were analyzed. Most of the oxidizing chemicals led to significant changes in endogenous steroid profile parameters which were considered stable under normal conditions. These oxidizing chemicals can cause serious problems regarding the interpretation of steroid profiles and have the potential to act as masking agents that can complicate or prevent the detection of the steroid abuse. © 2012 Elsevier Inc. All rights reserved.

Lambropoulos, NA, Reimers, JR, Crossley, MJ, Hush, NS & Silverbrook, K 2013, 'A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device', NANOTECHNOLOGY, vol. 24, no. 50.
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A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology. © 2013 IOP Publishing Ltd.

Langford, NK 2013, 'Errors in quantum tomography: diagnosing systematic versus statistical errors', New Journal of Physics, vol. 15, no. 3, pp. 035003-035003.
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Lapine, M, Krylova, AK, Belov, PA, Poulton, CG, McPhedran, RC & Kivshar, YS 2013, 'Broadband diamagnetism in anisotropic metamaterials', PHYSICAL REVIEW B, vol. 87, no. 2, pp. 1-7.
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We discuss the strategy for achieving the values of the effective magnetic permeability much smaller than unity by employing an appropriate arrangement of metamaterial elements ('meta-atoms'). We demonstrate that strong diamagnetism over a very wide frequency range can be realized in metamaterials by employing nonresonant elements with deeply subwavelength dimensions. We analyze the effect of the lattice parameters on the diamagnetic response and find that selecting an appropriate lattice type is crucial for optimal performance. Finally, we discuss the optimal characteristics required to obtain the lowest possible values of magnetic permeability and point out an efficient tuning possibility. © 2013 American Physical Society.

Latham, SL, Chaponnier, C, Dugina, V, Couraud, P, Grau, GER & Combes, V 2013, 'Cooperation between β‐ and γ‐cytoplasmic actins in the mechanical regulation of endothelial microparticle formation', The FASEB Journal, vol. 27, no. 2, pp. 672-683.
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Elevated endothelial microparticle (MP) levels are observed in numerous diseases, increasingly supporting roles as effectors and valuable markers of vascular dysfunction. While a contractile role for the actin cytoskeleton has been implicated in vesiculation, i.e., MP production, the precise interactions and mechanisms of its constituents, β-and α-cytoplasmic actins, is unknown. Human cerebral microvascular endothelial cells were stimulated with known agonists, and vesiculation development was monitored by scanning electron microscopy (SEM) and flow cytometry. These data in combination provide new insight into the kinetics, patterns of vesiculating cell recruitment, and degrees of response specific to stimuli. Reorganization of μ-and α-actins, F-actin, vinculin, and talin accompanied significant MP release. β-Actin redistribution into basal stress fibers following stimulation was associated with increased apically situated actin-rich particulate structures, which in turn directly correlated with electronlucent membrane protrusions observed by SEM. Y-27632 Rho-kinase inhibition abolished basal β-actin fiber formation, minimizing apically associated actinrich structures, significantly reducing membrane protrusions and MP release to near basal levels. Cytoskeletal protein expression and distribution varied between MPs and mother cells, as determined by Western blot. These data strongly suggest that β-actin plays an active facilitative role in agonist-induced protuberance formation, through mechanical interactions with newly described actin-rich structures. © FASEB.

Lau, N-SS, Gorrie, CA, Chia, JY, Bilston, LE & Clarke, EC 2013, 'Severity of Spinal Cord Injury in Adult and Infant Rats after Vertebral Dislocation Depends upon Displacement but not Speed', JOURNAL OF NEUROTRAUMA, vol. 30, no. 15, pp. 1361-1373.
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Spinal cord injury (SCI) is less common in children than in adults, but in children it is generally more severe. Spinal loading conditions (speed and displacement) are also thought to affect SCI severity, but the relationship between these parameters is not well understood. This study aimed to investigate the effects of vertebral speed and displacement on the severity of SCI in infants and adults using a rodent model of vertebral dislocation. Thoracolumbar vertebral dislocation was induced in anaesthetized infant rats (~30 g, 13-15 days postnatal, n=40) and adult rats (~250 g, n=57). The 12th thoracic vertebra was secured, whereas the first lumbar vertebra was dislocated laterally. Dislocation speed and magnitude were varied independently and scaled between adults and infants (Adults: 100-250mm/s, 4-10mm; Infants: 40-100mm/s, 1.6-4mm). At 5 h post-injury, rats were euthanized and spinal cords harvested. Spinal cord sections were stained to detect hemorrhage (hematoxylin and eosin) and axonal injury (β-amyloid precursor protein). For each millimeter increase in vertebral displacement, normalized hemorrhage volume increased by 1.9×10-3 mm3 (p=0.028) and normalized area of axonal injury increased by 2.2×10-1mm2 (p<0.001). Normalized hemorrhage volume was 3.3×10-3 mm3 greater for infants than for adults (p<0.001). Magnitude of dislocation was found to have a different effect on the normalized area of axonal injury in adults than in infants (p=0.003). Speed of dislocation was not found to have a significant effect on normalized hemorrhage volume (p=0.427) or normalized area of axonal injury (p=0.726) independent of displacement for the range of speeds tested. The findings of this study suggest that both age and amount of spinal motion are key factors in the severity of acute SCI. © Mary Ann Liebert, Inc.

Lawrence, FJ, de Sterke, CM, Botten, LC, McPhedran, RC & Dossou, KB 2013, 'Modeling photonic crystal interfaces and stacks: impedance-based approaches', ADVANCES IN OPTICS AND PHOTONICS, vol. 5, no. 4, pp. 385-455.
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In many research areas, the reflective properties of a bulk medium are characterized by its impedance or an impedance-like quantity. Such a quantity is essential for the efficient design of stacked structures such as antireflection coatings and thin-film filters. For 2D photonic crystals and metamaterials, the literature contains multiple definitions of impedance, not all of which are consistent. We review these proposed definitions, evaluate their regions of applicability, and numerically test their accuracy in a variety of salient photonic crystal examples. © 2013 Optical Society of America.

Lawrenz, E, Silsbe, G, Capuzzo, E, Ylöstalo, P, Forster, RM, Simis, SGH, Prášil, O, Kromkamp, JC, Hickman, AE, Moore, CM, Forget, M-H, Geider, RJ & Suggett, DJ 2013, 'Predicting the Electron Requirement for Carbon Fixation in Seas and Oceans', PLoS ONE, vol. 8, no. 3, pp. e58137-e58137.
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Marine phytoplankton account for about 50% of all global net primary productivity (NPP). Active fluorometry, mainly Fast Repetition Rate fluorometry (FRRf), has been advocated as means of providing high resolution estimates of NPP. However, not measuring CO2-fixation directly, FRRf instead provides photosynthetic quantum efficiency estimates from which electron transfer rates (ETR) and ultimately CO2-fixation rates can be derived. Consequently, conversions of ETRs to CO2-fixation requires knowledge of the electron requirement for carbon fixation (Φe,C, ETR/CO2 uptake rate) and its dependence on environmental gradients. Such knowledge is critical for large scale implementation of active fluorescence to better characterise CO2-uptake. Here we examine the variability of experimentally determined Φe,C values in relation to key environmental variables with the aim of developing new working algorithms for the calculation of Φe,C from environmental variables. Coincident FRRf and 14C-uptake and environmental data from 14 studies covering 12 marine regions were analysed via a meta-analytical, non-parametric, multivariate approach. Combining all studies, Φe,C varied between 1.15 and 54.2 mol e- (mol C)-1 with a mean of 10.9±6.91 mol e- mol C)-1. Although variability of Φe,C was related to environmental gradients at global scales, region-specific analyses provided far improved predictive capability. However, use of regional Φe,C algorithms requires objective means of defining regions of interest, which remains challenging. Considering individual studies and specific small-scale regions, temperature, nutrient and light availability were correlated with Φe,C albeit to varying degrees and depending on the study/region and the composition of the extant phytoplankton community. At the level of large biogeographic regions and distinct water masses, Φe,C was related to nutrient availability, chlorophyll, as well as temperature and/or salinity in most regions, while light...

Lazenby, JJ, Griffin, PE, Kyd, J, Whitchurch, CB & Cooley, MA 2013, 'A Quadruple Knockout of lasIR and rhlIR of Pseudomonas aeruginosa PAO1 That Retains Wild-Type Twitching Motility Has Equivalent Infectivity and Persistence to PAO1 in a Mouse Model of Lung Infection', PLOS ONE, vol. 8, no. 4, pp. 1-10.
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It has been widely reported that quorum-sensing incapable strains of Pseudomonas aeruginosa are less virulent than wild type strains. However, quorum sensing mutants of P. aeruginosa have been shown to develop other spontaneous mutations under prolonged culture conditions, and one of the phenotypes of P. aeruginosa that is frequently affected by this phenomenon is type IV pili-dependent motility, referred to as twitching motility. As twitching motility has been reported to be important for adhesion and colonisation, we aimed to generate a quorum-sensing knockout for which the heritage was recorded and the virulence factor production in areas unrelated to quorum sensing was known to be intact. We created a lasIRrhlIR quadruple knockout in PAO1 using a published technique that allows for the deletion of antibiotic resistance cartridges following mutagenesis, to create an unmarked QS knockout of PAO1, thereby avoiding the need for use of antibiotics in culturing, which can have subtle effects on bacterial phenotype. We phenotyped this mutant demonstrating that it produced reduced levels of protease and elastase, barely detectable levels of pyoverdin and undetectable levels of the quorum sensing signal molecules N-3-oxododecanoly-L-homoserine lactone and N-butyryl homoserine lactone, but retained full twitching motility. We then used a mouse model of acute lung infection with P. aeruginosa to demonstrate that the lasIRrhlIR knockout strain showed equal persistence to wild type parental PAO1, induced equal or greater neutrophil infiltration to the lungs, and induced similar levels of expression of inflammatory cytokines in the lungs and similar antibody responses, both in terms of magnitude and isotype. Our results suggest, in contrast to previous reports, that lack of quorum sensing alone does not significantly affect the immunogenicity, infectiveness and persistence of P. aeruginosa in a mouse model of acute lung infection

Le Brun, AP, Clifton, LA, Halbert, CE, Lin, B, Meron, M, Holden, PJ, Lakey, JH & Holt, SA 2013, 'Structural Characterization of a Model Gram-Negative Bacterial Surface Using Lipopolysaccharides from Rough Strains of Escherichia coli', Biomacromolecules, vol. 14, no. 6, pp. 2014-2022.
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Lee, JC, Magyar, AP, Bracher, DO, Aharonovich, I & Hu, EL 2013, 'Fabrication of thin diamond membranes for photonic applications', DIAMOND AND RELATED MATERIALS, vol. 33, no. 1, pp. 45-48.
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High quality, thin diamond membranes containing nitrogen-vacancy centers provide critical advantages in the fabrication of diamond-based structures for a variety of applications, including wide field magnetometry, photonics and biosensing. In this work we describe, in detail, the generation of thin, optically-active diamond membranes by means of ion implantation and overgrowth. To establish the suitability of our method for photonic applications, photonic crystal cavities with quality factor of 1000 are fabricated.

Lee, KWK, Arumugam, K, Purbojati, RW, Tay, QXM, Williams, RBH, Kjelleberg, S & Rice, SA 2013, 'Draft Genome Sequence of Klebsiella pneumoniae Strain KP-1', Genome Announcements, vol. 1, no. 6.
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ABSTRACT Klebsiella pneumoniae is ubiquitous in the environment and is a member of a three-species biofilm model. We compared the genome sequence of an environmental isolate, K. pneumoniae strain KP-1, to those of two clinical strains (NTUH-K2044 and MGH 78578). KP-1 possesses strain-specific prophage sequences that distinguish it from the clinical strains.

Lee, SH, Bae, K-H, Kim, GO, Nam, MH, Choi, YB, Kwon, H-M, Ryu, Y & Soh, K-S 2013, 'Primo Vascular System in the Lymph Vessel from the Inguinal to the Axillary Nodes', Evidence-Based Complementary and Alternative Medicine, vol. 2013, no. Article ID 472704, pp. 1-6.
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The primo vascular system (PVS) in a lymph system was observed mostly in large caliber ducts around the caudal vena cava of rabbits, rats, and mice. This required a severe surgery with laparectomy and massive removal of fat tissues in the abdomen to expose the lymph vessel. In the current brief report, we presented a new method to evade these shortcomings by observing the PVS in a less large caliber duct in the skin, that is, the lymph vessel from the inguinal to the axillary nodes. The Alcian blue injection into the inguinal node revealed the desired primo vessel in the target lymph vessel. This opened a new perspective for the investigation of the lymphatic PVS without severe damage to subject animals and for monitoring of the PVS in a long period of time.

Lek, A, Evesson, FJ, Lemckert, FA, Redpath, GMI, Lueders, A-K, Turnbull, L, Whitchurch, CB, North, KN & Cooper, ST 2013, 'Calpains, Cleaved Mini-Dysferlin(C72), and L-Type Channels Underpin Calcium-Dependent Muscle Membrane Repair', JOURNAL OF NEUROSCIENCE, vol. 33, no. 12, pp. 5085-5094.
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Dysferlin is proposed as a key mediator of calcium-dependent muscle membrane repair, although its precise role has remained elusive. Dysferlin interacts with a new membrane repair protein, mitsugumin 53 (MG53), an E3 ubiquitin ligase that shows rapid recruitment to injury sites. Using a novel ballistics assay in primary human myotubes, we show it is not full-length dysferlin recruited to sites of membrane injury but an injury-specific calpain-cleavage product, mini-dysferlinc72. Mini-dysferlinc72-rich vesicles are rapidly recruited to injury sites and fuse with plasma membrane compartments decorated by MG53 in a process coordinated by L-type calcium channels. Collective interplay between activated calpains, dysferlin, and L-type channels explains how muscle cells sense a membrane injury and mount a specialized response in the unique local environment of a membrane injury. Mini-dysferlinc72 and MG53form an intricate lattice that intensely labels exposed phospholipids of injury sites, then infiltrates and stabilizes the membrane lesion during repair. Our results extend functional parallels between ferlins and synaptotagmins. Whereas otoferlin exists as long and short splice isoforms, dysferlin is subject to enzymatic cleavage releasing a synaptotagmin-like fragment with a specialized protein- or phospholipid-binding role for muscle membrane repair. © 2013 the authors.

Li, CCY, Eaton, SA, Young, PE, Lee, M, Shuttleworth, R, Humphreys, DT, Grau, GE, Combes, V, Bebawy, M, Gong, J, Brammah, S, Buckland, ME & Suter, CM 2013, 'Glioma microvesicles carry selectively packaged coding and non-coding RNAs which alter gene expression in recipient cells', RNA BIOLOGY, vol. 10, no. 8, pp. 1333-1344.
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Interactions between glioma cells and their local environment are critical determinants of brain tumor growth, infiltration and neovascularisation. Communication with host cells and stroma via microvesicles represents one pathway by which tumors can modify their surroundings to achieve a tumor-permissive environment. Here we have taken an unbiased approach to identifying RNAs in glioma-derived microvesicles, and explored their potential to regulate gene expression in recipient cells. We find that glioma microvesicles are predominantly of exosomal origin and contain complex populations of coding and noncoding RNAs in proportions that are distinct from those in the cells from which they are derived. Microvesicles show a relative depletion in microRNA compared with their cells of origin, and are enriched in unusual or novel noncoding RNAs, most of which have no known function. Short-term exposure of brain microvascular endothelial cells to glioma microvesicles results in many gene expression changes in the endothelial cells, most of which cannot be explained by direct delivery of transcripts. Our data suggest that the scope of potential actions of tumor-derived microvesicles is much broader and more complex than previously supposed, and highlight a number of new classes of small RNA that remain to be characterized. © 2013 Landes Bioscience.

Li, JJ, Tay, HL, Plank, M, Essilfie, A-T, Hansbro, PM, Foster, PS & Yang, M 2013, 'Activation of Olfactory Receptors on Mouse Pulmonary Macrophages Promotes Monocyte Chemotactic Protein-1 Production', PLoS ONE, vol. 8, no. 11, pp. e80148-e80148.
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Background: Emerging evidence suggests that non-olfactory tissues and cells can express olfactory receptors (ORs), however, the exact function of ectopic OR expression remains unknown. We have previously shown in mouse models that a unique cooperation between interferon-γ (IFN-γ) and lipopolysaccharide (LPS) drives the activation of pulmonary macrophages and leads to the induction of pathogenic responses in the respiratory tract. Further, through gene array studies, we have shown that activation of macrophages by these molecules results in the selective expression of a number of ORs. In this study, we validated the expression of these ORs in mouse airway and pulmonary macrophages in response to IFN-γ and LPS (γ/LPS) stimulation, and further explored the effect of odorant stimulation on macrophage function. Methodology/Principal Findings: OR expression in airway and pulmonary macrophages in response to IFN-γ, LPS or γ/LPS treatments was assessed by microarray and validated by q-PCR. OR expression (e.g. OR622) on macrophages was confirmed by visualization in immunofluoresence assays. Functional responses to odorants were assessed by quantifying inflammatory cytokine and chemokine expression using q-PCR and cell migration was assessed by a modified Boyden chamber migration assay. Our results demonstrate that eight ORs are expressed at basal levels in both airway and pulmonary macrophages, and that γ/LPS stimulation cooperatively increased this expression. Pulmonary macrophages exposed to the combined treatment of γ/LPS+octanal (an odorant) exhibited a 3-fold increase in MCP-1 protein production, compared to cells treated with γ/LPS alone. Supernatants from γ/LPS+octanal exposed macrophages also increased macrophage migration in vitro. Conclusions/Significance: Eight different ORs are expressed at basal levels in pulmonary macrophages and expression is upregulated by the synergistic action of γ/LPS. Octanal stimulation further increased MCP-1 production and...

Li, K, Wen, Larson, AC, Zhang, Z, Shen, Chen, Shi, X & Zhang 2013, 'Multifunctional dendrimer-based nanoparticles for in vivo MR/CT dual-modal molecular imaging of breast cancer', International Journal of Nanomedicine, vol. 8, pp. 2589-2589.
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Li, WX, Xu, X, De Silva, KSB, Xiang, FX & Dou, SX 2013, 'Graphene Micro-Substrate Induced High Electron-Phonon Coupling in MgB2', IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY, vol. 23, no. 3.
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Li, X-H, McGrath, KCY, Tran, VH, Li, Y-M, Duke, CC, Roufogalis, BD & Heather, AK 2013, 'Attenuation of Proinflammatory Responses byS-[6]-Gingerol via Inhibition of ROS/NF-Kappa B/COX2 Activation in HuH7 Cells', Evidence-Based Complementary and Alternative Medicine, vol. 2013, pp. 1-8.
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Introduction. Hepatic inflammation underlies the pathogenesis of chronic diseases such as insulin resistance and type 2 diabetes mellitus.S-[6]-Gingerol has been shown to have anti-inflammatory properties. Important inflammatory mediators of interleukins include nuclear factorκB (NFκB) and cyclooxygenase 2 (COX2). We now explore the mechanism of anti-inflammatory effects ofS-[6]-gingerol in liver cells.Methods. HuH7 cells were stimulated with IL1βto establish anin vitrohepatic inflammatory model.Results.S-[6]-Gingerol attenuated IL1β-induced inflammation and oxidative stress in HuH7 cells, as evidenced by decreasing mRNA levels of inflammatory factor IL6, IL8, and SAA1, suppression of ROS generation, and increasing mRNA levels of DHCR24. In addition,S-[6]-gingerol reduced IL1β-induced COX2 upregulation as well as NFκB activity. Similar to the protective effects ofS-[6]-gingerol, both NS-398 (a selective COX2 inhibitor) and PDTC (a selective NFκB inhibitor) suppressed mRNA levels of IL6, IL8, and SAA1. Importantly, PDTC attenuated IL1β-induced overexpression of COX2. Of particular note, the protective effect ofS-[6]-gingerol against the IL1β-induced inflammatory response was similar to that of BHT, an ROS scavenger.Conclusions. The findings of this study demonstrate thatS-[6]-gingerol protects HuH7 cells against IL1β-induced inflammatory insults through inhibition...

Li, X-H, McGrath, KCY, Tran, VH, Li, Y-M, Mandadi, S, Duke, CC, Heather, AK & Roufogalis, BD 2013, 'Identification of a Calcium Signalling Pathway ofS-[6]-Gingerol in HuH-7 Cells', Evidence-Based Complementary and Alternative Medicine, vol. 2013, pp. 1-7.
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Calcium signals in hepatocytes control cell growth, proliferation, and death. Members of the transient receptor potential (TRP) cation channel superfamily are candidate calcium influx channels. NFκB activation strictly depends on calcium influx and often induces antiapoptotic genes favouring cell survival. Previously, we reported thatS-[6]-gingerol is an efficacious agonist of the transient receptor potential cation channel subfamily V member 1 (TRPV1) in neurones. In this study, we tested the effect ofS-[6]-gingerol on HuH-7 cells using the Fluo-4 calcium assay, RT-qPCR, transient cell transfection, and luciferase measurements. We found thatS-[6]-gingerol induced a transient rise in[Ca2+]iin HuH-7 cells. The increase in[Ca2+]iinduced byS-[6]-gingerol was abolished by preincubation with EGTA and was also inhibited by the TRPV1 channel antagonist capsazepine. Expression of TRPV1 in HuH-7 cells was confirmed by mRNA analysis as well as a test for increase of

Li, Y, Wang, N & Carroll, RJ 2013, 'Selecting the Number of Principal Components in Functional Data', Journal of the American Statistical Association, vol. 108, no. 504, pp. 1284-1294.
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Functional principal component analysis (FPCA) has become the most widely used dimension reduction tool for functional data analysis. We consider functional data measured at random, subject-specific time points, contaminated with measurement error, allowing for both sparse and dense functional data, and propose novel information criteria to select the number of principal component in such data. We propose a Bayesian information criterion based on marginal modeling that can consistently select the number of principal components for both sparse and dense functional data. For dense functional data, we also develop an Akaike information criterion based on the expected Kullback-Leibler information under a Gaussian assumption. In connecting with the time series literature, we also consider a class of information criteria proposed for factor analysis of multivariate time series and show that they are still consistent for dense functional data, if a prescribed undersmoothing scheme is undertaken in the FPCA algorithm. We perform intensive simulation studies and show that the proposed information criteria vastly outperform existing methods for this type of data. Surprisingly, our empirical evidence shows that our information criteria proposed for dense functional data also perform well for sparse functional data. An empirical example using colon carcinogenesis data is also provided to illustrate the results. Supplementary materials for this article are available online. © 2013 American Statistical Association.

Liao, J, Yang, Z, Wu, H, Yan, D, Qiu, J, Song, Z, Yang, Y, Zhou, D & Yin, Z 2013, 'Enhancement of the up-conversion luminescence of Yb3+/Er3+ or Yb3+/Tm3+ co-doped NaYF4 nanoparticles by photonic crystals', Journal of Materials Chemistry C, vol. 1, no. 40, pp. 6541-6541.
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A new method for enhancing the upconversion (UC) emission of rare-earth doped nanoparticles is reported, in which Yb3+/Er3+ or Yb3+/Tm3+ co-doped NaYF4 nanoparticles are deposited on to the surface of photonic crystal (PC) films. The UC emission of the Yb3+/Er3+ or Yb3+/Tm3+ co-doped NaYF4 nanoparticles on the PC surface was notably enhanced when the UC emission bands of the Yb3+/Er3+ or Yb 3+/Tm3+ co-doped NaYF4 nanoparticles were within the range of the photonic band gap of the PCs, indicating that the PCs were efficient and selective reflection mirrors. The results show that PCs may have potential applications in UC optoelectronics and lighting devices. © 2013 The Royal Society of Chemistry.

Liao, X, Spiegelman, D & Carroll, RJ 2013, 'Regression Calibration Is Valid When Properly Applied', Epidemiology, vol. 24, no. 3, pp. 466-467.
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Liao, Y, Li, C-M, Chen, H, Wu, Q, Shan, Z & Han, X-Y 2013, 'Site-Directed Mutagenesis Improves the Thermostability and Catalytic Efficiency of Aspergillus niger N25 Phytase Mutated by I44E and T252R', Applied Biochemistry and Biotechnology, vol. 171, no. 4, pp. 900-915.
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Lim, CED & Cheng, NCL 2013, 'Acupuncture for allergic rhinitis: active and sham acupuncture both seem to work', Focus on Alternative and Complementary Therapies, vol. 18, no. 3, pp. 136-137.
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Lim, CED & Cheng, NCL 2013, 'Electroacupuncture for symptom improvement in benign prostatic hyperplasia', Focus on Alternative and Complementary Therapies, vol. 18, no. 4, pp. 199-200.
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Lim, CED, Ng, RWC & Xu, K 2013, 'Non-hormonal methods for induction of labour', Current Opinion in Obstetrics & Gynecology, vol. 25, no. 6, pp. 441-447.
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PURPOSE OF REVIEW: The percentage of induced live birth has more than doubled from the 1990s to 2008. Induction of labour can either be based on medical indications, or performed as an elective procedure. A large range of pharmacological and non-pharmacological modalities are available for the induction of labour and the optimal method for labour induction is unknown. This article is aimed to examine literature on non-hormonal methods for labour induction, published from January 2012 to May 2013. RECENT FINDINGS: Eleven studies were identified in our search and included into the review. Foley balloon catheter appears to be more cost-effective and commonly used non-hormonal technique for induction of labour, although further meta-analysis is required in this area. Currently, there is not enough evidence to support routine use in all women for labour induction among other methods including amniotomy, acupuncture, sexual intercourse, isosorbide mononitrate, hypnosis, castor oil and breast stimulation. The latest three studies suggest that amniotomy may increase need for oxytocin augmentation during labour induction. SUMMARY: Many non-hormonal methods for labour induction still require further evidence to support their use within the clinical setting. Balloon catheter seems to be a more widely accepted non-hormonal method that has been supported by various literatures. © 2013 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Lim, HY, Thiam, CH, Yeo, KP, Bisoendial, R, Hii, CS, McGrath, KCY, Tan, KW, Heather, A, Alexander, JSJ & Angeli, V 2013, 'Lymphatic Vessels Are Essential for the Removal of Cholesterol from Peripheral Tissues by SR-BI-Mediated Transport of HDL', Cell Metabolism, vol. 17, no. 5, pp. 671-684.
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Removal of cholesterol from peripheral tissues to the bloodstream via reverse cholesterol transport (RCT) is a process of major biological importance. Here we demonstrate that lymphatic drainage is required for RCT. We have previously shown that hypercholesterolemia in mice is associated with impaired lymphatic drainage and increased lipid accumulation in peripheral tissues. We now show that restoration of lymphatic drainage in these mice significantly improves cholesterol clearance. Conversely, obstruction of lymphatic vessels in wild-type mice significantly impairs RCT. Finally, we demonstrate using silencing RNA interference, neutralizing antibody, and transgenic mice that removal of cholesterol by lymphatic vessels is dependent on the uptake and transcytosis of HDL by scavenger receptor class B type I expressed on lymphatic endothelium. Collectively, this study challenges the current view that lymphatic endothelium is a passive exchange barrier for cholesterol transport and provides further evidence for its interplay with lipid biology in health and disease. © 2013 Elsevier Inc.

Limbri, H, Gunawan, C, Rosche, B & Scott, J 2013, 'Challenges to Developing Methane Biofiltration for Coal Mine Ventilation Air: A Review', Water, Air, & Soil Pollution, vol. 224, no. 6.
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Coal mine methane is a significant greenhouse gas source as well as a potential lost energy resource if not effectively used. In recent years, mine ventilation air (MVA) capture and use has become a key element of research and development due to comparatively larger methane emissions by MVA than other coal mine sources. Technologies have been evaluated to treat the low methane concentrations in MVA such as thermal-based technologies or processing by biofiltration. This review initially considers the techniques available for treating the low methane concentrations encountered in MVA, after which it focuses on developments in biofiltration systems. Biofiltration represents a simple, energy-efficient, and cheap alternative to oxidize methane from MVA. Major factors influencing biofilter performance along with knowledge gaps in relation to its application to MVA are identified and discussed. © 2013 Springer Science+Business Media Dordrecht.

Lin, G, Baraban, L, Han, L, Karnaushenko, D, Makarov, D, Cuniberti, G & Schmidt, OG 2013, 'Magnetoresistive Emulsion Analyzer', Scientific Reports, vol. 3, no. 1.
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Liu, B, Ray, A & Thomas, PS 2013, 'Investigation of autoclaved cement systems with reactive MgO and Al₂O₃-SiO₂ rich fired clay brick', Advances in Cement Research, vol. 25, no. 5, pp. 281-287.
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Portland cement (PC) is one of the world's most important building materials, as it is a fundamental component of concrete. However, the manufacture of PC is highly energy intensive and leads to the emission of carbon dioxide (CO2). One promising control measure is the use of industrial wastes and by-products as supplementary cementing materials (SCMs) in order to minimise PC consumption, thereby producing greener cement-based products. This study investigates mechanical properties and phase development of hydrothermally treated cement–ground quartz sand blends with the incorporation of fired clay-brick (CB) waste and reactive magnesia (MgO). The addition of CB waste in autoclaved PC–quartz mortar mixes showed that the alumina–silica rich CB waste was pozzolanic when the Al2O3 accelerated formation and increased crystallinity of Al substituted 1·1 nm tobermorite, resulting in the observed strength gain. Autoclaved mortar specimens incorporating reactive MgO showed a reduction in strength with increasing MgO addition. This was a result of dilution when the relative proportion of PC available for the formation of the strength contributing hydration products including tobermorite is decreased.

Liu, H, Xu, Y, Wen, S, Chen, Q, Zheng, L, Shen, M, Zhao, J, Zhang, G & Shi, X 2013, 'Targeted Tumor Computed Tomography Imaging Using Low‐Generation Dendrimer‐Stabilized Gold Nanoparticles', Chemistry – A European Journal, vol. 19, no. 20, pp. 6409-6416.
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AbstractWe report a facile approach to fabricating low‐generation poly(amidoamine) (PAMAM) dendrimer‐stabilized gold nanoparticles (Au DSNPs) functionalized with folic acid (FA) for in vitro and in vivo targeted computed tomography (CT) imaging of cancer cells. In this study, amine‐terminated generation 2 PAMAM dendrimers were employed as stabilizers to form Au DSNPs without additional reducing agents. The formed Au DSNPs with an Au core size of 5.5 nm were covalently modified with the targeting ligand FA, followed by acetylation of the remaining dendrimer terminal amines to endow the particles with targeting specificity and improved biocompatibility. Our characterization data show that the formed FA‐modified Au DSNPs are stable at different pH values (5—8) and temperatures (4–50 °C), as well as in different aqueous media. MTT assay data along with cell morphology observations reveal that the FA‐modified Au DSNPs are noncytotoxic in the particle concentration range of 0–3000 nM. X‐ray attenuation coefficient measurements show that the CT value of FA‐modified Au DSNPs is much higher than that of Omnipaque (a clinically used CT contrast agent) at the same concentration of the radiodense elements (Au or iodine). Importantly, the FA‐modified Au DSNPs are able to specifically target a model cancer cell line (KB cells, a human epithelial carcinoma cell line) over‐expressing FA receptors and they enable targeted CT imaging of the cancer cells in vitro and the xenografted tumor model in vivo after intravenous administration of the particles. With the simple synthesis approach, easy modification, good cytocompatibility, and high X‐ray attenuation coefficient, the FA‐modified low‐generation Au DSNPs could be used as promising contrast agents for targeted CT imaging of different tumors over‐expressing FA receptors.

Liu, H, Xu, Y, Wen, S, Zhu, J, Zheng, L, Shen, M, Zhao, J, Zhang, G & Shi, X 2013, 'Facile hydrothermal synthesis of low generation dendrimer-stabilized gold nanoparticles for in vivo computed tomography imaging applications', Polymer Chemistry, vol. 4, no. 6, pp. 1788-1788.
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Liu, M, Powell, DA, Shadrivov, IV, Lapine, M & Kivshar, YS 2013, 'Self-oscillations in nonlinear torsional metamaterials', New Journal of Physics, vol. 15, no. 7, pp. 073036-073036.
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Liu, M, Sun, Y, Powell, DA, Shadrivov, IV, Lapine, M, McPhedran, RC & Kivshar, YS 2013, 'Nonlinear response via intrinsic rotation in metamaterials', Physical Review B, vol. 87, no. 23.
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We propose and experimentally verify a way to achieve strong nonlinear coupling between the electromagnetic and elastic properties in metamaterials. This coupling is provided through a novel degree of freedom in metamaterial design: the internal rotation within structural elements. Our meta-atoms have high sensitivity to electromagnetic wave power, and the elastic and electromagnetic properties can be independently designed to optimize the response. We demonstrate a rich range of nonlinear phenomena including self-tuning and bistability, and provide a comprehensive experimental demonstration of the predicted effects. © 2013 American Physical Society.

Lloyd, A, Russell, M, Blanes, L, Doble, P & Roux, C 2013, 'Lab-on-a-chip screening of methamphetamine and pseudoephedrine in samples from clandestine laboratories', Forensic Science International, vol. 228, no. 1-3, pp. 8-14.
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The clandestine manufacture of methamphetamine in New Zealand predominantly involves the reduction of pseudoephedrine, extracted from pharmaceutical preparations, using hydrogen iodide. This method of illicit manufacture leaves a variety of materials at the scene that are a rich source of information. Efficient processing and preliminary identification of extraction and reaction mixtures, precursors and products is essential to minimise exposure to potential hazardous materials and to provide investigative and intelligence information. In this study, we employed a portable lab-on-a-chip instrument for the rapid and cost effective screening of methamphetamine, pseudoephedrine and ephedrine in a variety of sample types found in typical clandestine laboratory scenarios

Lord, MS, Tsoi, B, Gunawan, C, Teoh, WY, Amal, R & Whitelock, JM 2013, 'Anti-angiogenic activity of heparin functionalised cerium oxide nanoparticles', Biomaterials, vol. 34, no. 34, pp. 8808-8818.
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Lothian, A, Hare, DJ, Grimm, R, Ryan, TM, Masters, CL & Roberts, BR 2013, 'Metalloproteomics: principles, challenges, and applications to neurodegeneration', FRONTIERS IN AGING NEUROSCIENCE, vol. 5.
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Lu, J, Carter, DA, Turnbull, L, Rosendale, D, Hedderley, D, Stephens, J, Gannabathula, S, Steinhorn, G, Schlothauer, RC, Whitchurch, CB & Harry, EJ 2013, 'The Effect of New Zealand Kanuka, Manuka and Clover Honeys on Bacterial Growth Dynamics and Cellular Morphology Varies According to the Species', PLOS ONE, vol. 8, no. 2, pp. e55898-e55898.
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Treatment of chronic wounds is becoming increasingly difficult due to antibiotic resistance. Complex natural products with antimicrobial activity, such as honey, are now under the spotlight as alternative treatments to antibiotics. Several studies have shown honey to have broad-spectrum antibacterial activity at concentrations present in honey dressings, and resistance to honey has not been attainable in the laboratory. However not all honeys are the same and few studies have used honey that is well defined both in geographic and chemical terms. Here we have used a range of concentrations of clover honey and a suite of manuka and kanuka honeys from known geographical locations, and for which the floral source and concentration of methylglyoxal and hydrogen peroxide potential were defined, to determine their effect on growth and cellular morphology of four bacteria: Bacillus subtilis, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa. While the general trend in effectiveness of growth inhibition was manuka>manuka-kanuka blend>kanuka>clover, the honeys had varying and diverse effects on the growth and cellular morphology of each bacterium, and each organism had a unique response profile to these honeys. P. aeruginosa showed a markedly different pattern of growth inhibition to the other three organisms when treated with sub-inhibitory concentrations of honey, being equally sensitive to all honeys, including clover, and the least sensitive to honey overall. While hydrogen peroxide potential contributed to the antibacterial activity of the manuka and kanuka honeys, it was never essential for complete growth inhibition. Cell morphology analysis also showed a varied and diverse set of responses to the honeys that included cell length changes, cell lysis, and alterations to DNA appearance. These changes are likely to reflect the different regulatory circuits of the organisms that are activated by the stress of honey treatment. © 2013 Lu et al.

Lu, J, Paulsen, IT & Jin, D 2013, 'Application of Exonuclease III-Aided Target Recycling in Flow Cytometry: DNA Detection Sensitivity Enhanced by Orders of Magnitude', Analytical Chemistry, vol. 85, no. 17, pp. 8240-8245.
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DNA-functionalized microspheres in conjugation with flow cytometry detection are widely used for high-throughput nucleic acid assays. Although such assays are rapid and capable of simultaneous analysis of multiple nucleic acid analytes in a single test, the intrinsic limitation in sensitivity remains challenging. Here we report a simple, highly sensitive, and reproducible method based on Exonuclease III-aided target recycling technique applied for DNA quantification in flow cytometry. By loading a high density of Cy5-labeled probe DNA on microspheres (15 μm), we achieved hitherto unreported DNA detection limit of 3.2 pM in flow cytometry bead assay, enhancing the sensitivity by a factor of over 56.8 compared to the conventional direct hybridization bead assay. Furthermore, we evaluated multiplexing capability by simultaneous detections of two target DNAs with FAM and Cy5 reporter conjugated probes. Therefore, the novel Exonuclease III-amplified flow cytometry bead assay has great potential for the rapid, sensitive, and accurate detection and quantification of nucleic acids in clinical diagnosis and biomedical research. © 2013 American Chemical Society.

Luts, J & Wand, MP 2013, 'Variational inference for count response semiparametric regression', Bayesian Analysis, vol. 10, no. 4, pp. 991-1023.
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Fast variational approximate algorithms are developed for Bayesiansemiparametric regression when the response variable is a count, i.e. anon-negative integer. We treat both the Poisson and Negative Binomial familiesas models for the response variable. Our approach utilizes recently developedmethodology known as non-conjugate variational message passing. Forconcreteness, we focus on generalized additive mixed models, although ourvariational approximation approach extends to a wide class of semiparametricregression models such as those containing interactions and elaborate randomeffect structure.

Lutz, C, Erken, M, Noorian, P, Sun, S & McDougald, D 2013, 'Environmental reservoirs and mechanisms of persistence of Vibrio cholerae', Frontiers in Microbiology, vol. 4, no. DEC.
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It is now well accepted that Vibrio cholerae, the causative agent of the water-borne disease cholera, is acquired from environmental sources where it persists between outbreaks of the disease. Recent advances in molecular technology have demonstrated that this bacterium can be detected in areas where it has not previously been isolated, indicating a much broader, global distribution of this bacterium outside of endemic regions. The environmental persistence of V. cholerae in the aquatic environment can be attributed to multiple intra- and interspecific strategies such as responsive gene regulation and biofilm formation on biotic and abiotic surfaces, as well as interactions with a multitude of other organisms. This review will discuss some of the mechanisms that enable the persistence of this bacterium in the environment. In particular, we will discuss how V. cholerae can survive stressors such as starvation, temperature, and salinity fluctuations as well as how the organism persists under constant predation by heterotrophic protists. © 2013 Lutz, Erken, Noorian, Sun and McDougald.

Ma, X, Huete, A, Yu, Q, Coupe, NR, Davies, K, Broich, M, Ratana, P, Beringer, J, Hutley, LB, Cleverly, J, Boulain, N & Eamus, D 2013, 'Spatial patterns and temporal dynamics in savanna vegetation phenology across the North Australian Tropical Transect', REMOTE SENSING OF ENVIRONMENT, vol. 139, no. 1, pp. 97-115.
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The phenology of a landscape is a key parameter in climate and biogeochemical cycle models and its correct representation is central to the accurate simulation of carbon, water and energy exchange between the land surface and the atmosphere. Whereas biogeographic phenological patterns and shifts have received much attention in temperate ecosystems, much less is known about the phenology of savannas, despite their sensitivity to climate change and their coverage of approximately one eighth of the global land surface. Savannas are complex assemblages of multiple tree, shrub, and grass vegetation strata, each with variable phenological responses to seasonal climate and environmental variables. The objectives of this study were to investigate biogeographical and inter-annual patterns in savanna phenology along a 1100. km ecological rainfall gradient, known as North Australian Tropical Transect (NATT), encompassing humid coastal Eucalyptus forests and woodlands to xeric inland Acacia woodlands and shrublands. Key phenology transition dates (start, peak, end, and length of seasonal greening periods) were extracted from 13. years (2000-2012) of Moderate Resolution Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI) data using Singular Spectrum Analysis (SSA).Two distinct biogeographical patterns in phenology were observed, controlled by different climate systems. The northern (mesic) portion of the transect, from 12°S, to around 17.7°S, was influenced by the Inter-Tropical Convergence Zone (ITCZ) seasonal monsoon climate system, resulting in strong latitudinal shifts in phenology patterns, primarily associated with the functional response of the C4 grass layer. Both the start and end of the greening (enhanced vegetation activity) season occurred earlier in the northern tropical savannas and were progressively delayed towards the southern limit of the Eucalyptus-dominated savannas resulting in relatively stable length of greening periods. In contr...

Macha, IJ, Ozyegin, LS, Chou, J, Samur, R, Oktar, FN & Ben-Nissan, B 2013, 'An Alternative Synthesis Method for Di Calcium Phosphate (Monetite) Powders from Mediterranean Mussel (Mytilus galloprovincialis) Shells', JOURNAL OF THE AUSTRALIAN CERAMIC SOCIETY, vol. 49, no. 2, pp. 122-128.
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Marine species, such as corals, sea shells and nacres, attract special interest in bioceramics field for bone graft, bone cements and drug delivery applications. Most of the marine structures are made up of pure calcium carbonate (calcite or aragonite) with a very small amount of an organic matrix. In the past the most common way to transform these structures to hydroxyapatite was hydrothermal transformation method. This current work introduces a new approach for producing fine powders of calcium phosphates from Mediterranean mussel (Mytilus galloprovincialis) shells. A comparative study was carried out to investigate the differences of these powders under only hot plate heating and hot plate heating together with ultrasonic agitation while H3PO4 was added. The temperature of the hotplate was kept constant at 80 degrees C and then, H3PO4 was added drop wise into the solution for 2 hrs. The mixture was then placed into an oven at 100 degrees C for 24 hrs. They were further calcined at 800 degrees C for 3 hrs. XRD, FTIR. and ICP-MS were used to identify the structure and composition. It was found that the final powders were predominantly monetite, with some tricalcium phosphate as a secondary phase. This relatively simple and efficient method can be easily applied to produce calcium phosphate precursor powders for a range of biomedical applications.

Magyar, AP, Aharonovich, I, Baram, M & Hu, EL 2013, 'Photoluminescent SiC Tetrapods', NANO LETTERS, vol. 13, no. 3, pp. 1210-1215.
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Recently, significant research efforts have been made to develop complex nanostructures to provide more sophisticated control over the optical and electronic properties of nanomaterials. However, there are only a handful of semiconductors that allow control over their geometry via simple chemical processes. Herein, we present a molecularly seeded synthesis of a complex nanostructure, SiC tetrapods, and report on their structural and optical properties. The SiC tetrapods exhibit narrow line width photoluminescence at wavelengths spanning the visible to near-infrared spectral range. Synthesized from low-toxicity, earth abundant elements, these tetrapods are a compelling replacement for technologically important quantum optical materials that frequently require toxic metals such as Cd and Se. This previously unknown geometry of SiC nanostructures is a compelling platform for biolabeling, sensing, spintronics, and optoelectronics.

Mahendru, AA & Morris, E 2013, 'Cardiovascular disease in menopause: Does the obstetric history have any bearing?', Menopause International, vol. 19, no. 3, pp. 115-120.
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Cardiovascular disease remains a leading cause of morbidity and mortality in menopausal women in spite of the overall reduction in age-adjusted mortality from the disease in the last few years. It is now clear that mechanisms of cardiovascular disease in menopausal women are similar to men and rather than midlife acceleration of cardiovascular disease in women, the final impact of cardiovascular disease in later life may be a reflection of cardiovascular changes during reproductive years as a result of woman’s obstetric history. A decade after the Women’s Health Initiative trial, there is upcoming evidence to suggest that hormone replacement therapy in young recently menopausal women has a cardioprotective effect. Cardiovascular changes during normal pregnancy or pregnancy complications such as preeclampsia may affect a woman’s long-term cardiovascular health. Therefore, it is plausible that the cardioprotective benefit of hormone replacement therapy depends on occult pre-existing cardiovascular risks in women in relation to their previous obstetric history. In this review, we describe the cardiovascular changes during and after pregnancy in obstetric complications such as recurrent miscarriage, preeclampsia, intrauterine growth restriction, preterm labour and gestational diabetes; existing evidence regarding their association with cardiovascular disease later in life, and hypothesize possible mechanisms. Our aim is to improve the understanding and highlight the importance of including obstetric history in risk assessment in menopausal women and individualizing their risks before prescribing hormone replacement therapy. Future research in risk benefit assessment of hormone replacement therapy should also account for a woman’s background cardiovascular risk in the light of her obstetric history.

Malaei, F, Hesaraki, M, Saadati, M, Ahdi, AM, Sadraeian, M, Honari, H & Nazarian, S 2013, 'Immunogenicity of a new recombinant IpaC from Shigella dysenteriae type I in guinea pig as a vaccine candidate.', Iran J Immunol, vol. 10, no. 2, pp. 110-117.
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BACKGROUND: Recombinant vaccine technology is one of the most developed means in controlling infectious diseases. However, an effective vaccine against Shigella is still missing. OBJECTIVE: To evaluate recombinant IpaC protein of Shigella as a vaccine candidate. METHODS: In this study we cloned IpaC gene into an expression vector in prokaryotic system. The protein expression was evaluated by SDS-PAGE and Western-Blotting analysis. The recombinant protein was purified using Ni-NTA affinity chromatography. Guinea pigs were immunized with the recombinant protein and the level of immunogenicity was examined by ELISA and Western blotting of IpaC. Challenge test was done through the intraoculary injection of Shigella dysenteriae (6×108 CFU/eye) and after 48 hours was scored for keratoconjunctivitis. RESULTS: The results showed a remarkable level of immunogenicity in terms of antibody response and protection against keratoconjunctivitis in tested animals. The recombinant IpaC protein provided a protective system against Shigella dysenteriae type I during the challenge test. CONCLUSION: The results showed the potential of using recombinant IpaC in preparation of vaccine in perspective studies.

Manetsch, M, Rahman, MM, Patel, BS, Ramsay, EE, Rumzhum, NN, Alkhouri, H, Ge, Q & Ammit, AJ 2013, 'Long-Acting β2-Agonists Increase Fluticasone Propionate-Induced Mitogen-Activated Protein Kinase Phosphatase 1 (MKP-1) in Airway Smooth Muscle Cells', PLoS ONE, vol. 8, no. 3, pp. e59635-e59635.
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Mitogen-activated protein kinase phosphatase 1 (MKP-1) represses MAPK-driven signalling and plays an important anti-inflammatory role in asthma and airway remodelling. Although MKP-1 is corticosteroid-responsive and increased by cAMP-mediated signalling, the upregulation of this critical anti-inflammatory protein by long-acting β2-agonists and clinically-used corticosteroids has been incompletely examined to date. To address this, we investigated MKP-1 gene expression and protein upregulation induced by two long-acting β2-agonists (salmeterol and formoterol), alone or in combination with the corticosteroid fluticasone propionate (abbreviated as fluticasone) in primary human airway smooth muscle (ASM) cells in vitro. β2-agonists increased MKP-1 protein in a rapid but transient manner, while fluticasone induced sustained upregulation. Together, long-acting β2-agonists increased fluticasone-induced MKP-1 and modulated ASM synthetic function (measured by interleukin 6 (IL-6) and interleukin 8 (IL-8) secretion). As IL-6 expression (like MKP-1) is cAMP/adenylate cyclase-mediated, the long-acting β2-agonist formoterol increased IL-6 mRNA expression and secretion. Nevertheless, when added in combination with fluticasone, β2-agonists significantly repressed IL-6 secretion induced by tumour necrosis factor α (TNFα). Conversely, as IL-8 is not cAMP-responsive, β2-agonists significantly inhibited TNFα-induced IL-8 in combination with fluticasone, where fluticasone alone was without repressive effect. In summary, long-acting β2-agonists increase fluticasone-induced MKP-1 in ASM cells and repress synthetic function of this immunomodulatory airway cell type.

Manos, J, Hu, H, Rose, BR, Wainwright, CE, Zablotska, IB, Cheney, J, Turnbull, L, Whitchurch, CB, Grimwood, K, Harmer, C, Anuj, SN, Harbour, C & Grp, ACFBALS 2013, 'Virulence factor expression patterns in Pseudomonas aeruginosa strains from infants with cystic fibrosis', EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES, vol. 32, no. 12, pp. 1583-1592.
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Pseudomonas aeruginosa is the leading cause of morbidity and mortality in cystic fibrosis (CF). This study examines the role of organism-specific factors in the pathogenesis of very early P. aeruginosa infection in the CF airway. A total of 168 longitudinally collected P. aeruginosa isolates from children diagnosed with CF following newborn screening were genotyped by pulsed-field gel electrophoresis (PFGE) and phenotyped for 13 virulence factors. Ninety-two strains were identified. Associations between virulence factors and gender, exacerbation, persistence, timing of infection and infection site were assessed using multivariate regression analysis. Persistent strains showed significantly lower pyoverdine, rhamnolipid, haemolysin, total protease, and swimming and twitching motility than strains eradicated by aggressive antibiotic treatments. Initial strains had higher levels of virulence factors, and significantly higher phospholipase C, than subsequent genotypically different strains at initial isolation. Strains from males had significantly lower pyoverdine and swimming motility than females. Colony size was significantly smaller in strains isolated during exacerbation than those isolated during non-exacerbation periods. All virulence factors were higher and swimming motility significantly higher in strains from bronchoalveolar lavage (BAL) and oropharyngeal sites than BAL alone. Using unadjusted regression modelling, age at initial infection and age at isolation of a strain showed U-shaped profiles for most virulence factors. Among subsequent strains, longer time since initial infection meant lower levels of most virulence factors. This study provides new insight into virulence factors underpinning impaired airway clearance seen in CF infants, despite aggressive antibiotic therapy. This information will be important in the development of new strategies to reduce the impact of P. aeruginosa in CF. © 2013 Springer-Verlag Berlin Heidelberg.

Mansour, H, McColm, JR, Cole, L, Weible, M, Korlimbinis, A & Chan-Ling, T 2013, 'Connexin 30 Expression and Frequency of Connexin Heterogeneity in Astrocyte Gap Junction Plaques Increase with Age in the Rat Retina', PLoS ONE, vol. 8, no. 3, pp. e57038-e57038.
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Marcon, F, Purtell, L, Santos, J, Hains, PG, Escoubas, P, Graudins, A & Nicholson, GM 2013, 'Characterization of monomeric and multimeric snake neurotoxins and other bioactive proteins from the venom of the lethal Australian common copperhead (Austrelaps superbus)', BIOCHEMICAL PHARMACOLOGY, vol. 85, no. 10, pp. 1555-1573.
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Envenomation by Australian copperheads results mainly in muscle paralysis largely attributed to the presence of postsynaptic a-neurotoxins. However, poorly reversible neurotoxic effects suggest that these venoms may contain snake presynaptic phospholipase A2 neurotoxins (SPANs) that irreversibly inhibit neurotransmitter release. Using size-exclusion liquid chromatography, the present study isolated the first multimeric SPAN complex from the venom of the Australian common copperhead, Austrelaps superbus. The multimeric SPAN P-elapitoxin-As1a (P-EPTX-As1a) along with two novel monomeric SPANs and a new postsynaptic a-neurotoxin were then pharmacologically characterized using the chick biventer cervicis nerve-muscle preparation. All SPANs inhibited nerve-evoked twitch contractions at the neuromuscular junction without inhibiting contractile responses to cholinergic agonists or KCl. These actions are consistent with a prejunctional action to inhibit neurotransmitter release, without direct myotoxicity. Furthermore, the multimeric P-EPTX-As1a caused tetanic `fade in muscle tension under high frequency nerve stimulation, and produced a triphasic alteration to neurotransmitter release. These actions have been previously noted with other multimeric SPAN complexes such as taipoxin. Moreover, the neurotoxic a-subunit of P-EPTX-As1a shows high homology to taipoxin a-chain. Several other coagulopathic and myotoxic high mass proteins including a class PIII snake venom metalloproteinase, C- type lectin, L-amino acid oxidase, acetylcholinesterase and phospholipase B were also identified that may contribute to the overall toxicity of A. superbus venom. In conclusion, clinicians should be aware that early antivenom intervention might be necessary to prevent the onset of irreversible presynaptic neurotoxicity caused by multimeric and monomeric SPANs and that A. superbus venom is potentially capable of producing coagulopathic and myotoxic effects.

Mariotto, I, Thenkabail, PS, Huete, A, Slonecker, ET & Platonov, A 2013, 'Hyperspectral versus multispectral crop-productivity modeling and type discrimination for the HyspIRI mission', REMOTE SENSING OF ENVIRONMENT, vol. 139, no. 1, pp. 291-305.
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Precise monitoring of agricultural crop biomass and yield quantities is critical for crop production management and prediction. The goal of this study was to compare hyperspectral narrowband (HNB) versus multispectral broadband (MBB) reflectance data in studying irrigated cropland characteristics of five leading world crops (cotton, wheat, maize, rice, and alfalfa) with the objectives of: 1. Modeling crop productivity, and 2. Discriminating crop types. HNB data were obtained from Hyperion hyperspectral imager and field ASD spectroradiometer, and MBB data were obtained from five broadband sensors: Landsat-7 Enhanced Thematic Mapper Plus (ETM+), Advanced Land Imager (ALI), Indian Remote Sensing (IRS), IKONOS, and QuickBird. A large collection of field spectral and biophysical variables were gathered for the 5 crops in Central Asia throughout the growing seasons of 2006 and 2007. Overall, the HNB and hyperspectral vegetation index (HVI) crop biophysical models explained about 25% greater variability when compared with corresponding MBB models. Typically, 3 to 7 HNBs, in multiple linear regression models of a given crop variable, explained more than 93% of variability in crop models. The evaluation of λ1 (400-2500nm) versus λ2 (400-2500nm) plots of various crop biophysical variables showed that the best two-band normalized difference HVIs involved HNBs centered at: (i) 742nm and 1175nm (HVI742-1175), (ii) 1296nm and 1054nm (HVI1296-1054), (iii) 1225nm and 697nm (HVI1225-697), and (iv) 702nm and 1104nm (HVI702-1104). Among the most frequently occurring HNBs in various crop biophysical models, 74% were located in the 1051-2331nm spectral range, followed by 10% in the moisture sensitive 970nm, 6% in the red and red-edge (630-752nm), and the remaining 10% distributed between blue (400-500nm), green (501-600nm), and NIR (760-900nm).Discriminant models, used for discriminating 3 or 4 or 5 crop types, showed significantly higher accuracies when using HNBs (>. 90%)...

Markin, DM, Solntsev, AS & Sukhorukov, AA 2013, 'Generation of orbital-angular-momentum-entangled biphotons in triangular quadratic waveguide arrays', Physical Review A, vol. 87, no. 6.
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Marsh, J, Lott, W, Tyndall, J & Huston, W 2013, 'Proteolytic activation of Chlamydia trachomatis HTRA is mediated by PDZ1 domain interactions with protease domain loops L3 and LC and beta strand β5', Cellular and Molecular Biology Letters, vol. 18, no. 4, pp. 522-537.
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AbstractChlamydia trachomatis is a bacterial pathogen responsible for one of the most prevalent sexually transmitted infections worldwide. Its unique development cycle has limited our understanding of its pathogenic mechanisms. However, CtHtrA has recently been identified as a potential C. trachomatis virulence factor. CtHtrA is a tightly regulated quality control protein with a monomeric structural unit comprised of a chymotrypsin-like protease domain and two PDZ domains. Activation of proteolytic activity relies on the C-terminus of the substrate allosterically binding to the PDZ1 domain, which triggers subsequent conformational change and oligomerization of the protein into 24-mers enabling proteolysis. This activation is mediated by a cascade of precise structural arrangements, but the specific CtHtrA residues and structural elements required to facilitate activation are unknown. Using in vitro analysis guided by homology modeling, we show that the mutation of residues Arg362 and Arg224, predicted to disrupt the interaction between the CtHtrA PDZ1 domain and loop L3, and between loop L3 and loop LD, respectively, are critical for the activation of proteolytic activity. We also demonstrate that mutation to residues Arg299 and Lys160, predicted to disrupt PDZ1 domain interactions with protease loop LC and strand β5, are also able to influence proteolysis, implying their involvement in the CtHtrA mechanism of activation. This is the first investigation of protease loop LC and strand β5 with respect to their potential interactions with the PDZ1 domain. Given their high level of conservation in bacterial HtrA, these structural elements may be equally significant in the activation mechanism of DegP and other HtrA family members.

Martin, AA, Phillips, MR & Toth, M 2013, 'Dynamic Surface Site Activation: A Rate Limiting Process in Electron Beam Induced Etching', ACS APPLIED MATERIALS & INTERFACES, vol. 5, no. 16, pp. 8002-8007.
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We report a new mechanism that limits the rate of electron beam induced etching (EBIE). Typically, the etch rate is assumed to scale directly with the precursor adsorbate dissociation rate. Here, we show that this is a special case, and that the rate can instead be limited by the concentration of active sites at the surface. Novel etch kinetics are expected if surface sites are activated during EBIE, and observed experimentally using the electron sensitive material ultra nanocrystalline diamond (UNCD). In practice, etch kinetics are of interest because they affect resolution, throughput, proximity effects, and the topography of nanostructures and nanostructured devices fabricated by EBIE. © 2013 American Chemical Society.

Martinez, JG, Bohn, KM, Carroll, RJ & Morris, JS 2013, 'A Study of Mexican Free-Tailed Bat Chirp Syllables: Bayesian Functional Mixed Models for Nonstationary Acoustic Time Series', Journal of the American Statistical Association, vol. 108, no. 502, pp. 514-526.
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We describe a new approach to analyze chirp syllables of free-tailed bats from two regions of Texas in which they are predominant: Austin and College Station. Our goal is to characterize any systematic regional differences in the mating chirps and assess whether individual bats have signature chirps. The data are analyzed by modeling spectrograms of the chirps as responses in a Bayesian functional mixed model. Given the variable chirp lengths, we compute the spectrograms on a relative time scale interpretable as the relative chirp position, using a variable window overlap based on chirp length. We use two-dimensional wavelet transforms to capture correlation within the spectrogram in our modeling and obtain adaptive regularization of the estimates and inference for the regions-specific spectrograms. Our model includes random effect spectrograms at the bat level to account for correlation among chirps from the same bat and to assess relative variability in chirp spectrograms within and between bats. The modeling of spectrograms using functional mixed models is a general approach for the analysis of replicated nonstationary time series, such as our acoustical signals, to relate aspects of the signals to various predictors, while accounting for between-signal structure. This can be done on raw spectrograms when all signals are of the same length and can be done using spectrograms defined on a relative time scale for signals of variable length in settings where the idea of defining correspondence across signals based on relative position is sensible. Supplementary materials for this article are available online. © 2013 American Statistical Association.

McClements, L, Yakkundi, A, Papaspyropoulos, A, Harrison, H, Ablett, MP, Jithesh, PV, McKeen, HD, Bennett, R, Donley, C, Kissenpfennig, A, McIntosh, S, McCarthy, HO, O'Neill, E, Clarke, RB & Robson, T 2013, 'Targeting Treatment-Resistant Breast Cancer Stem Cells with FKBPL and Its Peptide Derivative, AD-01, via the CD44 Pathway', Clinical Cancer Research, vol. 19, no. 14, pp. 3881-3893.
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AbstractPurpose: FK506-binding protein like (FKBPL) and its peptide derivative, AD-01, have already shown tumor growth inhibition and CD44-dependent antiangiogenic activity. Here, we explore the ability of AD-01 to target CD44-positive breast cancer stem cells (BCSC).Experimental Design: Mammosphere assays and flow cytometry were used to analyze the effect of FKBPL overexpression/knockdown and AD-01 treatment ± other anticancer agents on BCSCs using breast cancer cell lines (MCF-7/MDA-231/ZR-75), primary patient samples, and xenografts. Delays in tumor initiation were evaluated in vivo. The anti–stem cell mechanisms were determined using clonogenic assays, quantitative PCR (qPCR), and immunofluorescence.Results: AD-01 treatment was highly effective at inhibiting the BCSC population by reducing mammosphere-forming efficiency and ESA+/CD44+/CD24− or aldehyde dehydrogenase (ALDH)+ cell subpopulations in vitro and tumor initiation in vivo. The ability of AD-01 to inhibit the self-renewal capacity of BCSCs was confirmed; mammospheres were completely eradicated by the third generation. The mechanism seems to be due to AD-01–mediated BCSC differentiation shown by a significant decrease in the number of holoclones and an associated increase in meroclones/paraclones; the stem cell markers, Nanog, Oct4, and Sox2, were also significantly reduced. Furthermore, we showed additive inhibitory effects when AD-01 was combined with the Notch inhibitor, DAPT. AD-01 was also able to abrogate a chemo- and radiotherapy-induced enrichment in BCSCs. Finally, FKBPL knockdown led to an increase in Nanog/Oct4/Sox2 and an increase in BCSCs, highlighting a role for endogenous FKBPL in stem cell signaling.Conclusions: AD-01 has dual antiangiogenic and anti-BCSC activity, which will be advantageous as this agent enters clinical trial. Clin Cancer Res; 19(14); 3881–93. ©2013 AACR.

McGinley, MP, Suggett, DJ & Warner, ME 2013, 'Transcript patterns of chloroplast‐encoded genes in cultured Symbiodinium spp. (Dinophyceae): testing the influence of a light shift and diel periodicity', Journal of Phycology, vol. 49, no. 4, pp. 709-718.
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Microalgae possess numerous cellular mechanisms specifically employed for acclimating the photosynthetic pathways to changes in the physical environment. Despite the importance of coral‐dinoflagellate symbioses, little focus has been given as to how the symbiotic algae (Symbiodinium spp.) regulate the expression of their photosynthetic genes. This study used real‐time PCR to investigate the transcript abundance of the plastid‐encoded genes, psbA (encoding the D1 protein of photosystem II) and psaA (encoding the P700 protein in photosystem I), within the cultured Symbiodinium ITS‐2 (internal transcribed spacer region) types A20 and A13. Transcript abundance was monitored during a low to high‐light shift, as well as over a full diel light cycle. In addition, psaA was characterized in three isolates (A20, A13, and D4‐5) and noted as another example of a dinoflagellate plastid gene encoded on a minicircle. In general, the overall incongruence of transcript patterns for both psbA and psaA between the Symbiodinium isolates and other models of transcriptionally controlled chloroplast gene expression (e.g., Pisum sativum [pea], Sinapis alba [mustard seedling], and Syne...

McNevin, D, Santos, C, Gómez-Tato, A, Álvarez-Dios, J, de Cal, MC, Daniel, R, Phillips, C & Lareu, MV 2013, 'An assessment of Bayesian and multinomial logistic regression classification systems to analyse admixed individuals', Forensic Science International: Genetics Supplement Series, vol. 4, no. 1, pp. e63-e64.
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Multinomial logistic regression (MLR) has been applied to the prediction of hair and eye colour. Here we apply it to the prediction of biogeographical ancestry (BGA) in a test set of 1092 admixed and non-admixed genotypes from the 1000 Genomes Project using a training set of 571 non-admixed genotypes from the HGDP CEPH cell line panel. Predicted BGAs are consistent with those of Structure, a naïve Bayesian classifier. © 2013.

Meakin, G & Jamieson, A 2013, 'DNA transfer: Review and implications for casework', Forensic Science International: Genetics, vol. 7, no. 4, pp. 434-443.
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Medek, D, Vicendese, D, Jaggard, A, Campbell, B, Johnston, F, Godwin, I, Huete, A, Green, B, Newnham, R, Bowman, D, Newbigin, E, Erbas, B, Beggs, P, Haberle, S & Davies, J 2013, 'REGIONAL AND SEASONAL VARIATION IN AIRBORNE GRASS POLLEN LEVELS BETWEEN CITIES OF AUSTRALIA AND NEW ZEALAND', INTERNAL MEDICINE JOURNAL, vol. 43, pp. 7-7.

Mehta, B, Daniel, R & McNevin, D 2013, 'High resolution melting (HRM) of forensically informative SNPs', Forensic Science International: Genetics Supplement Series, vol. 4, no. 1, pp. e376-e377.
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© 2014 Elsevier Ireland Ltd The SNaPshot® assay is commonly used for forensic SNP analysis. However, it is a multi-step process with potential post-PCR contamination risk. The single tube high resolution melting (HRM) temperature real-time PCR method is an alternative, eliminating the post-PCR tube transfer of SNaPshot®. Eight individual DNA samples were genotyped at the six IrisPlex SNP loci using both the IrisPlex published primer set and a set of custom designed HRM primers. The performance of MeltDoctor™ (Life Technologies®) and SensiFast™ (Bioline®) HRM mastermixes was examined on the ViiA™ 7 Real Time PCR platform for 10 ng and 1 ng DNA template amounts. The resultant genotypes were compared with those derived from SNaPshot®. This preliminary study demonstrates HRM potentially offers a fast and flexible alternative to SNaPshot® for small numbers of SNP loci without the associated contamination risk from post-PCR processes.

Mehta, M, Satija, S, Nanda, A & Garg, M 2013, 'Nanotechnologies for Boswellic Acids', American Journal of Drug Discovery and Development, vol. 4, no. 1, pp. 1-11.
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Boswellic Acids (BAs) are the main ingredients of Boswellia serrata (Family: Burseraceae) gum resin extract for the treatment of a variety of inflammatory diseases besides acting as both internal and external stimulant, expectorant, diuretic and stomachic. Despite its multipurpose benefits, BAs have low oral bioavailability especially 11-keto-β-boswellic acid (KBA) and 3-acetyl-11-keto-β-boswellic acid (AKBA), (the most therapeutically potential BAs) because these BAs are lipophilic in nature and not solubilises into the intestinal fluid thus limiting its systemic availability. For decades, many attempts have been made to compensate for these disadvantages, with the development of improved delivery platforms as the feasible approaches. The past ten years has witnessed the encouraging progress in the use of nano scale drug delivery systems on BAs such as loading BAs into liposomes, solid lipid nanoparticles as well as the latest reported technologies such as niosomes, phytosomes and nanomicelles etc. This review summarizes the recent works on the design and development of nanoscale delivery systems of BAs, with the goal of harnessing the true difficulties of this multifunctional agent in the clinical arena. © 2014 Academic Journals Inc.

Meiklejohn, KA, Wallman, JF & Dowton, M 2013, 'DNA Barcoding Identifies all Immature Life Stages of a Forensically Important Flesh Fly (Diptera: Sarcophagidae)', Journal of Forensic Sciences, vol. 58, no. 1, pp. 184-187.
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AbstractCarrion‐breeding insects, such as flesh flies (Diptera: Sarcophagidae), can be used as evidence in forensic investigations. Despite their considerable forensic potential, their use has been limited because morphological species identification, at any life stage, is very challenging. This study investigated whether DNA could be extracted and cytochrome oxidase subunit I (COI) barcode sequences obtained for molecular identification of each immature life stage of the forensically important Australian flesh fly, Sarcophaga (Sarcorohdendorfia) impatiens (Walker). Genomic DNA extracts were prepared from all larval instars and puparia. Amplification of the barcoding region was successful from all extracts, but puparia amplicons were weak. All sequences were identified as S. impatiens with 99.95% confidence using the Barcoding of Life Database (BOLD). Importantly, crop removal was necessary to eliminate PCR inhibition for specimens from late second and early third instars. Similar results are expected for immatures of other carrion‐breeding species, enhancing the use of evidence from immature flies in forensic investigations.

Mengoni, A, Focardi, A, Bacci, G & Ugolini, A 2013, 'High genetic diversity and variability of bacterial communities associated with the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda)', Estuarine, Coastal and Shelf Science, vol. 131, pp. 75-82.
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Menictas, M & Wand, MP 2013, 'Variational inference for marginal longitudinal semiparametric regression', Stat, vol. 2, no. 1, pp. 61-71.
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We derive a variational inference procedure for approximate Bayesian inference in marginal longitudinal semiparametric regression. Fitting and inference is much faster than existing Markov chain Monte Carlo approaches. Numerical studies indicate that the new methodology is very accurate for the class of models under consideration. Copyright © 2013 John Wiley & Sons Ltd

Merson, TD, Castelletto, S, Aharonovich, I, Turbic, A, Kilpatrick, TJ & Turnley, AM 2013, 'Nanodiamonds with silicon vacancy defects for nontoxic photostable fluorescent labeling of neural precursor cells', OPTICS LETTERS, vol. 38, no. 20, pp. 4170-4173.
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Nanodiamonds (NDs) containing silicon vacancy (SiV) defects were evaluated as a potential biomarker for the labeling and fluorescent imaging of neural precursor cells (NPCs). SiV-containing NDs were synthesized using chemical vapor deposition and silicon ion implantation. Spectrally, SiV-containing NDs exhibited extremely stable fluorescence and narrow bandwidth emission with an excellent signal to noise ratio exceeding that of NDs containing nitrogen-vacancy centers. NPCs labeled with NDs exhibited normal cell viability and proliferative properties consistent with biocompatibility. We conclude that SiV-containing NDs are a promising biomedical research tool for cellular labeling and optical imaging in stem cell research. © 2013 Optical Society of America.

Metcalf, BJ, Thomas-Peter, N, Spring, JB, Kundys, D, Broome, MA, Humphreys, PC, Jin, X-M, Barbieri, M, Steven Kolthammer, W, Gates, JC, Smith, BJ, Langford, NK, Smith, PGR & Walmsley, IA 2013, 'Multiphoton quantum interference in a multiport integrated photonic device', Nature Communications, vol. 4, no. 1.
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Mitchell, JG, Seuront, L, Doubell, MJ, Losic, D, Voelcker, NH, Seymour, J & Lal, R 2013, 'The Role of Diatom Nanostructures in Biasing Diffusion to Improve Uptake in a Patchy Nutrient Environment', PLoS ONE, vol. 8, no. 5, pp. e59548-e59548.
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Background Diatoms are important single-celled autotrophs that dominate most lit aquatic environments and are distinguished by surficial frustules with intricate designs of unknown function. Principal Findings We show that some frustule designs constrain diffusion to positively alter nutrient uptake. In nutrient gradients of 4 to 160 times over <5 cm, the screened-chambered morphology of Coscincodiscus sp. biases the nutrient diffusion towards the cell by at least 3.8 times the diffusion to the seawater. In contrast, the open-chambers of Thalassiosira eccentrica produce at least a 1.3 times diffusion advantage to the membrane over Coscincodiscus sp. when nutrients are homogeneous. Significance Diffusion constraint explains the success of particular diatom species at given times and the overall success of diatoms. The results help answer the unresolved question of how adjacent microplankton compete. Furthermore, diffusion constraint by supramembrane nanostructures to alter molecular diffusion suggests that microbes compete via supramembrane topology, a competitive mechanism not considered by the standard smooth-surface equations used for nutrient uptake nor in microbial ecology and cell physiology.

Miura, T, Turner, JP & Huete, AR 2013, 'Spectral Compatibility of the NDVI Across VIIRS, MODIS, and AVHRR: An Analysis of Atmospheric Effects Using EO-1 Hyperion', IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING, vol. 51, no. 3, pp. 1349-1359.
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We evaluated the cross-sensor compatibilities of the normalized difference vegetation index (NDVI) across the Visible/Infrared Imager/Radiometer Suite (VIIRS), Moderate Resolution Imaging Spectroradiometer (MODIS), and the National Oceanic and Atmospheric Administration (NOAA)-14 and NOAA-19 Advanced Very High Resolution Radiometer (AVHRR) (AVHRR/2 and AVHRR/3) bandpasses using a global set of Earth Observing One Hyperion hyperspectral data. Five levels of atmospheric correction were simulated to examine the impact of the atmosphere on intersensor NDVI compatibility. These were the uncorrected 'top-of-atmosphere'; Rayleigh (RAY); Rayleigh and ozone (RO); Rayleigh, ozone, and water vapor (ROW); and total atmosphere-corrected 'top-of-canopy (TOC)' reflectances. Among all possible sensor pairs examined, the highest compatibility was observed for VIIRS versus MODIS. Cross-sensor NDVI relationships between the two sensor bandpasses remained nearly the same throughout all levels of atmospheric correction. AVHRR/3-versus-AVHRR/2 NDVI relationships changed very little and also showed an equivalent level of compatibility to VIIRS versus MODIS across all levels of atmospheric correction although they were subject to systematic differences. Intersensor NDVI compatibilities of VIIRS and MODIS to AVHRR/2 and to AVHRR/3 were lower due primarily to the differential sensitivities of these sensors' near-infrared bands to the atmospheric water vapor effects. Comparisons of cross-sensor NDVI compatibilities where operational atmospheric correction schemes were assumed for each of the sensors suggest the need of VIIRS TOC NDVI for long-term continuity with MODIS and AVHRR, which is not currently produced as part of the standard VIIRS Vegetation Index Environmental Data Record. © 2012 IEEE.

Moezzi, A, Cortie, M & McDonagh, AM 2013, 'Formation of Zinc Hydroxide Nitrate by H+-Catalyzed Dissolution-Precipitation', EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, vol. 8, no. 8, pp. 1326-1335.
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The formation of zinc hydroxide nitrate, Zn5(OH)8(NO3)2·2H2O, by reaction between zinc oxide and aqueous zinc nitrate solution was examined. Scanning electron microscopy, X-ray diffraction and thermogravimetric analysis were used to analyze the conversion of nanoscale ZnO particles into much larger crystals of the hydroxide nitrate. The rate of the reaction displayed sigmoidal behavior with the maximum conversion rate at ca. 75 min. The reaction stoichiometry involves a 1:1 ZnO/Zn(NO3)2 molar ratio. The data indicate that an amorphous zinc-containing intermediate phase is formed during the transition, and that the zinc hydroxide nitrate crystals nucleate and grow from this phase. The crystals of zinc hydroxide nitrate are several µm in size, but are formed from zinc oxide crystals of only a few hundred nanometers in size, indicating that mass transfer in the aqueous phase plays an important role. We propose that H+-catalyzed dissolution/precipitation is the key process in the mechanism of the reaction. The zinc hydroxide nitrate is stable to about 110 °C, but decomposes above that temperature to a series of less hydrated phases, with associated loss of mass, until zinc oxide is formed at about 190 °C. The solubility product, Ksp, of Zn5(OH)8(NO3)2·2H2O in water was measured by two independent techniques and found to be in the range of 7.48.5?×?1011

Moezzi, A, Cortie, MB & McDonagh, AM 2013, 'Zinc hydroxide sulphate and its transformation to crystalline zinc oxide', DALTON TRANSACTIONS, vol. 42, no. 40, pp. 14432-14437.
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The thermal transformation of zinc hydroxide sulphate hydrate to zinc oxide has been examined using synchrotron X-ray diffraction, thermogravimetric analysis, scanning electron microscopy, and surface area measurements. By collecting X-ray diffraction da

Moezzi, A, Cortie, MB, Shimmon, R & McDonagh, AM 2013, 'On the Reactivity of Zinc Hydroxide Acetate Dihydrate in Ethanol', EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, vol. 2013, no. 29, pp. 5133-5137.
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Zinc hydroxide acetate dihydrate, Zn-5(OH)(8)(CH3CO2)(2)2H(2)O, reacts in ethanol at room temperature to yield a mixture of zinc oxide and anhydrous zinc acetate. The process is driven by dehydration of the starting salt. Dehydration of Zn-5(OH)(8)(CH3CO

Moezzi, A, McDonagh, A, Dowd, A & Cortie, M 2013, 'Zinc Hydroxyacetate and Its Transformation to Nanocrystalline Zinc Oxide', INORGANIC CHEMISTRY, vol. 52, no. 1, pp. 95-102.
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The synthesis of nanocrystalline ZnO by thermal decomposition of zinc hydroxyacetate, Zn-5(OH)(8)(CH3CO2)(2)center dot nH(2)O, was investigated. The decomposition process was examined using X-ray diffraction, thermogravimetric analysis, mass spectrometry

Monahan, LG & Harry, EJ 2013, 'Identifying how bacterial cells find their middle: a new perspective', MOLECULAR MICROBIOLOGY, vol. 87, no. 2, pp. 231-234.
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Bacterial cell division begins with the polymerization of the FtsZ protein to form a Z ring at the division site. This ring subsequently recruits the division machinery to allow cytokinesis. How the Z ring is positioned correctly remains a challenging question in biology and our knowledge in this area has been restricted to a few model species. Spatial regulation of division in these bacteria has been considered to be negatively controlled, with Z rings assembling in the area of least inhibition: the cell centre. An article in this issue of Molecular Microbiology reports the discovery of a new protein in Myxococcus xanthus, called PomZ (Positioning at midcell of FtsZ), that is required for the efficient recruitment of the Z ring to the division site. PomZ is a member of the Mrp/Min family of P loop ATPases that includes a diverse range of proteins involved in spatial regulation in bacteria. PomZ is the first positive regulator of Z ring positioning to be identified in vegetatively growing bacterial cells. Positive spatial regulation of division has previously been observed during sporulation in Streptomyces coelicolor and has been suggested to occur in Bacillus subtilis. Perhaps this will emerge as a common theme in the future. © 2012 Blackwell Publishing Ltd.

Mondal, AK, Su, D, Wang, Y, Chen, S & Wang, G 2013, 'Hydrothermal Synthesis of Nickel Oxide Nanosheets for Lithium-Ion Batteries and Supercapacitors with Excellent Performance', CHEMISTRY-AN ASIAN JOURNAL, vol. 8, no. 11, pp. 2828-2832.
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Nickel oxide nanosheets have been successfully synthesized by a facile ethylene glycol mediated hydrothermal method. The morphology and crystal structure of the nickel oxide nanosheets were characterized by X-ray diffraction, field-emission SEM, and TEM. When applied as electrode materials for lithium-ion batteries and supercapacitors, nickel oxide nanosheets exhibited a high, reversible lithium storage capacity of 1193 mA h g-1 at a current density of 500 mA g-1, an enhanced rate capability, and good cycling stability. Nickel oxide nanosheets also demonstrated a superior specific capacitance of 999 F g-1 at a current density of 20 A g-1 in supercapacitors. Between the sheets: NiO nanosheets were synthesized by a facile ethylene glycol mediated hydrothermal method (see picture). The NiO nanosheets exhibited a high, reversible lithium storage capacity of 1193 mA h g-1 at a current density of 500 mA g-1 for lithium-ion batteries and a superior specific capacitance of 999 F g-1 at a current density of 20 A g-1 in supercapacitors. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mondal, D, Sharma, M, Mukesh, C, Gupta, V & Prasad, K 2013, 'Improved solubility of DNA in recyclable and reusable bio-based deep eutectic solvents with long-term structural and chemical stability', Chemical Communications, vol. 49, no. 83, pp. 9606-9606.
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Monteiro, AT, Fava, F, Goncalves, J, Huete, A, Gusmeroli, F, Parolo, G, Spano, D & Bocchi, S 2013, 'Landscape context determinants to plant diversity in the permanent meadows of Southern European Alps', BIODIVERSITY AND CONSERVATION, vol. 22, no. 4, pp. 937-958.
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In the Southern Alps, the role of landscape context on meadows plant diversity was evaluated using a multi-model information theoretic approach and five competing hypotheses of landscape context factors: habitat quality (H1), matrix quality (H2), habitat change (H3), matrix quality change (H4) and topography-environmental conditions (H5)- measured at three spatial scales (125, 250 and 500 m). Shannon diversity index and species richness represented plant diversity obtained in 34 plots (100 m2 size). Landscape context affected plant diversity measures differently. Matrix quality change at larger scale (500 m) was the most supported hypothesis explaining Shannon diversity index, while species richness responded mostly to topography-environmental conditions in the immediate surroundings (125 m). No effects of present-day habitat and matrix quality (H1 and H2) were found. Matrix quality change affected positively Shannon diversity index through an effect of landscape neighbourhood context on farming management practices. Due to the importance of exposure and inclination of slopes, topography-environmental conditions influenced species richness mostly through energy-driven processes and farming management strategies. In terms of scale, matrix quality change was the strongest hypothesis explaining Shannon diversity index at all scales, while the underlying process affecting species richness changed with scale (H5 or H3). Overall, landscape context explained only 25-28 % of the variation in plant diversity, suggesting that landscape management may support biodiversity conservation when comprised in a global strategy including farming practices. In the study area, change in landscape diversity may be a good indicator for Shannon diversity index and south-eastern facing meadows should be preserved. © 2013 Springer Science+Business Media Dordrecht.

Morales, PK, Yunusa, IAM, Lugg, G, Li, Z, Gribben, P & Eamus, D 2013, 'Belowground eco-restoration of a suburban waste-storage landscape: Earthworm dynamics in grassland and in a succession of woody vegetation covers', LANDSCAPE AND URBAN PLANNING, vol. 120, no. 1, pp. 16-24.
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Restoration of belowground ecology is seldom a priority in designing revegetation strategies for disturbed landscapes. We determined earthworm abundance and diversity in a 16-year old grass sward (grassland), a 6-year old (Plantation-04) and a 4-year old (Plantation-06) plantation, both of mixed woody species, on a reclaimed waste disposal site, and in nearby remnant woodland, in suburban Sydney, Australia. While no catches were made in autumn, more earthworms were found in spring (21±8.6m-2) than in winter (10.2±5.9m-2) or summer (14.4±5.5m-2). Earthworm abundance in spring was in the order grassland≈Plantation-04 (35.2m-2)>woodland (12.8m-2)>Plantation-06 (0.8m-2). None of the revegetated covers had restored earthworm diversity to levels found in the woodland. Exotic species, mostly Microscolex dubius, dominated in the four vegetation covers at any time; the only two native species (Heteroporodrilus sp. and Megascoleceides sp.) found were in the woodland. We also assessed how quality of the evolving soils from the three revegetated covers, compared with that from the woodland, impacted viability of common exotic earthworm species. Both weight gain and cocoon production by the exotic earthworms were higher in the soil from Plantation-04 than in soils from the other vegetation covers, including the woodland; the two variables were positively correlated with the pH and mineral nutrient content (as indicated by electrical conductivity that was in turn correlated with clay content) of the soil. Age of vegetation rather than its composition explained differences in the level of earthworm recovery observed. © 2013.

Morelato, M, Beavis, A, Kirkbride, P & Roux, C 2013, 'Forensic applications of desorption electrospray ionisation mass spectrometry (DESI-MS)', FORENSIC SCIENCE INTERNATIONAL, vol. 226, no. 1-3, pp. 10-21.
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Desorption electrospray ionisation mass spectrometry (DESI-MS) is an emerging analytical technique that enables in situ mass spectrometric analysis of specimens under ambient conditions. It has been successfully applied to a large range of forensically relevant materials. This review assesses and highlights forensic applications of DESI-MS including the analysis and detection of illicit drugs, explosives, chemical warfare agents, inks and documents, fingermarks, gunshot residues and drugs of abuse in urine and plasma specimens. The minimal specimen preparation required for analysis and the sensitivity of detection achieved offer great advantages, especially in the field of forensic science. © 2013.

Morelato, M, Beavis, A, Tahtouh, M, Ribaux, O, Kirkbride, P & Roux, C 2013, 'The use of forensic case data in intelligence-led policing: The example of drug profiling', FORENSIC SCIENCE INTERNATIONAL, vol. 226, no. 1-3, pp. 1-9.
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To date, forensic science has predominantly focused on generating evidence for judicial proceedings. While many recognise its broader and important contribution to the initial stages of the forensic process, resources do not seem to be employed efficiently. It is often discovered retrospectively that necessary information was previously available in a database or within existing files. Such information could have been proactively used in order to solve a particular case, a number of linked cases or better understand the criminal activity as a whole. This article reviews this broader contribution of forensic science, with a particular emphasis on drug intelligence at the Australian Federal Police (AFP) in Australia. Using the AFP as a model organisation, an overview of the current situation and the contribution of physical and chemical profiling are first discussed. The situation in Europe, and in particular in Switzerland, is also presented. It is argued that a change of attitude towards a more intelligence-led perspective is required in forensic science in general, and in drug profiling in particular. © 2013 Elsevier Ireland Ltd.

Mueller, P, Alber, DG, Turnbull, L, Schlothauer, RC, Carter, DA, Whitchurch, CB & Harry, EJ 2013, 'Synergism between Medihoney and Rifampicin against Methicillin-Resistant Staphylococcus aureus (MRSA)', PLOS ONE, vol. 8, no. 2, pp. e57679-e57679.
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Skin and chronic wound infections caused by highly antibiotic resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) are an increasing and urgent health problem worldwide, particularly with sharp increases in obesity and diabetes. New Zealand manuka honey has potent broad-spectrum antimicrobial activity, has been shown to inhibit the growth of MRSA strains, and bacteria resistant to this honey have not been obtainable in the laboratory. Combinational treatment of chronic wounds with manuka honey and common antibiotics may offer a wide range of advantages including synergistic enhancement of the antibacterial activity, reduction of the effective dose of the antibiotic, and reduction of the risk of antibiotic resistance. The aim of this study was to investigate the effect of Medihoney in combination with the widely used antibiotic rifampicin on S. aureus. Using checkerboard microdilution assays, time-kill curve experiments and agar diffusion assays, we show a synergism between Medihoney and rifampicin against MRSA and clinical isolates of S. aureus. Furthermore, the Medihoney/rifampicin combination stopped the appearance of rifampicin-resistant S. aureus in vitro. Methylglyoxal (MGO), believed to be the major antibacterial compound in manuka honey, did not act synergistically with rifampicin and is therefore not the sole factor responsible for the synergistic effect of manuka honey with rifampicin. Our findings support the idea that a combination of honey and antibiotics may be an effective new antimicrobial therapy for chronic wound infections. © 2013 Müller et al.

Munasinghe, VS, Vella, NGF, Ellis, JT, Windsor, PA & Stark, D 2013, 'Cyst formation and faecal-oral transmission of Dientamoeba fragilis - the missing link in the life cycle of an emerging pathogen', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 43, no. 11, pp. 879-883.
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Dientamoeba fragilis is a protozoan parasite emerging as a cause of diarrhoea and irritable-bowel-like gastrointestinal disease in humans with a propensity for establishing long-term, chronic infections in humans. Although Dientamoeba was discovered over a century ago its life cycle and mode of transmission is not known. No cyst stage has been described and no animal models are presently available for the study of this parasite. Here we describe the establishment of an animal model using laboratory rodents, the fulfilling of Kochs postulates, and the discovery of a new cyst stage in the life cycle of D. fragilis. Our demonstration of long-term parasite carriage by rodents and prolonged shedding of cysts, together with elevated levels of calprotectin in the stool, confirms the capacity of this organism to cause disease and indicates dientamoebiasis should be considered in the differential diagnosis of gastrointestinal diseases such as Inflammatory Bowel Syndrome (IBS). Finally, we suggest that the cyst stage described here is the vehicle that mediates faecaloral transmission of D. fragilis between hosts.

Naderi, N, Hashim, MR, Rouhi, J & Mahmodi, H 2013, 'Enhanced optical and electrical stability of thermally carbonized porous silicon', Materials Science in Semiconductor Processing, vol. 16, no. 2, pp. 542-546.
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Naidu, G, Jeong, S, Vigneswaran, S & Rice, SA 2013, 'Microbial activity in biofilter used as a pretreatment for seawater desalination', Desalination, vol. 309, pp. 254-260.
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Biofilters as a pretreatment process in seawater desalination can reduce biofoulants through adsorption and biodegradation. In this study, the performance of granular activated carbon (GAC) biofilter with three different filtration velocities was studied in terms of dissolved organic carbon (DOC) removal. This apart, the microbial activities in the biofilters were measured in terms of concentration of active biomass (adenosine tri-phosphate; ATP) and total cell count. Biofouling potential in biofilter effluents were assessed in terms of transparent exopolymer particles (TEP) and assimilable organic carbon (AOC) concentration. AOC was carried out using a new rapid bioluminescence method. Upon reaching mature stage, the GAC biofilters achieved high DOC removal efficiency of more than 60%, especially the low molecular weight organics. This organic removal was mostly attributed to active biomass on the GAC media. In addition, GAC biofilters led to significant reduction of the AOC and TEP concentration amounting to only 0.6. ±0.2. μg-C glucose/L and 5.3 ± 1.1. μg-C/L, respectively in effluents. Thus, GAC biofilter is an effective pretreatment in reducing biofouling potential. © 2012 Elsevier B.V.

Nielsen, DA, Schramm, A, Nielsen, LP & Revsbech, NP 2013, 'Seasonal Methane Oxidation Potential in Manure Crusts', Applied and Environmental Microbiology, vol. 79, no. 1, pp. 407-410.
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ABSTRACT Organic crusts on liquid manure storage tanks harbor ammonia- and nitrite-resistant methane oxidizers and may significantly reduce methane emissions. Methane oxidation potential (0.6 mol CH 4 m −2 day −1 ) peaked during fall and winter, after 4 months of crust development. Consequences for methane mitigation potential of crusts are discussed.

Nikeghbali, A & Platen, E 2013, 'A reading guide for last passage times with financial applications in view', FINANCE AND STOCHASTICS, vol. 17, no. 3, pp. 615-640.
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In this survey on last passage times, we propose a new viewpoint which provides a unified approach to many different results which appear in the mathematical finance literature and in the theory of stochastic processes. In particular, we are able to improve the assumptions under which some well-known results are usually stated. Moreover we give some new and detailed calculations for the computation of the distribution of some large classes of last passage times. We have kept in this survey only the aspects of the theory which we expect potentially to be relevant for financial applications.

Noginov, M, Lapine, M, Podolskiy, V & Kivshar, Y 2013, 'Focus issue: hyperbolic metamaterials', Optics Express, vol. 21, no. 12, pp. 14895-14895.
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This special issue presents a cross-section of recent progress in the rapidly developing area of optics of hyperbolic metamaterials. © 2013 Optical Society of America.

Novikov, A & Kordzakhia, N 2013, 'Pitman Estimators: An Asymptotic Variance Revisited', Theory of Probability & Its Applications, vol. 57, no. 3, pp. 521-529.
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We provide an analytic expression for the variance of ratio of integral functionals of fractional Brownian motion which arises as an asymptotic variance of Pitman estimators for a location parameter of independent identically distributed observations. The expression is obtained in terms of derivatives of a logarithmic moment of the integral functional of limit likelihood ratio process (LLRP). In the particular case when the LLRP is a geometric Brownian motion, we show that the established expression leads to the known representation of the asymptotic variance of Pitman estimator in terms of Riemann zeta-function. © by SIAM.

Novikov, A & Shiryaev, A 2013, 'Remarks on moment inequalities and identities for martingales', Statistics & Probability Letters, vol. 83, no. 4, pp. 1260-1261.
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We present some comments on moment inequalities and identities for martingales in the context of the paper of Langovoy (2011). © 2013 Elsevier B.V.

Nuchtavorn, N, Smejkal, P, Breadmore, MC, Guijt, RM, Doble, P, Bek, F, Foret, F, Suntornsuk, L & Macka, M 2013, 'Exploring chip-capillary electrophoresis-laser-induced fluorescence field-deployable platform flexibility: Separations of fluorescent dyes by chip-based non-aqueous capillary electrophoresis', Journal of Chromatography A, vol. 1286, no. 1, pp. 216-221.
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Microfluidic chip electrophoresis (chip-CE) is a separation method that is compatible with portable and on-site analysis, however, only few commercial chip-CE systems with laser-induced fluorescence (LIF) and light emitting diode (LED) fluorescence detection are available. They are established for several application tailored methods limited to specific biopolymers (DNA, RNA and proteins), and correspondingly the range of their applications has been limited. In this work we address the lack of commercially available research-type flexible chip-CE platforms by exploring the limits of using an application-tailored system equipped with chips and methods designed for DNA separations as a generic chip-CE platform this is a very significant issue that has not been widely studied. In the investigated Agilent Bioanalyzer chip-CE system, the fixed components are the Agilent chips and the detection (LIF at 635 nm and LEDIF at 470 nm), while the chemistry (electrolyte) and the programming of all the high voltages are flexible. Using standard DNA chips, we show that a generic CE function of the system is easily possible and we demonstrate an extension of the applicability to non-aqueous CE (NACE). We studied the chip compatibility with organic solvents (i.e. MeOH, ACN, DMF and DMSO) and demonstrated the chip compatibility with DMSO as a non-volatile and non-hazardous solvent with satisfactory stability of migration times over 50 h. The generic CE capability is illustrated with separations of fluorescent basic blue dyes methylene blue (MB), toluidine blue (TB), nile blue (NB) and brilliant cresyl blue (BC).

Nunn, J, Langford, NK, Kolthammer, WS, Champion, TFM, Sprague, MR, Michelberger, PS, Jin, X-M, England, DG & Walmsley, IA 2013, 'Enhancing Multiphoton Rates with Quantum Memories', Physical Review Letters, vol. 110, no. 13.
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Obata, K, Miura, T, Yoshioka, H & Huete, AR 2013, 'Derivation of a MODIS-compatible enhanced vegetation index from visible infrared imaging radiometer suite spectral reflectances using vegetation isoline equations', JOURNAL OF APPLIED REMOTE SENSING, vol. 7, no. 1.
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We developed a unique methodology that spectrally translates the enhanced vegetation index (EVI) across sensors for data continuity based on vegetation isoline equations and derived a moderate resolution imaging spectroradiometer (MODIS)-compatible EVI for the visible/infrared imager/radiometer suite (VIIRS) sensor. The derived equation had four coefficients that were a function of soil, canopy, and atmosphere, e.g., soil line slope, leaf area index (LAI), and aerosol optical thickness (AOT). The PROSAIL canopy reflectance and 6S atmospheric models were employed to numerically characterize the MODIS-compatible VIIRS EVI. MODIS-compatible VIIRS EVI values only differed from those of MODIS EVI by, at most, 0.002 EVI units, whereas VIIRS and MODIS EVI values differed by 0.018 EVI units. The derived coefficients were sensitive mainly to LAI and AOT for the full-and a partial-covered canopy, respectively. The MODIS-compatible EVI resulted in a reasonable level of accuracy when the coefficients were fixed at values found via optimization for model-simulated and actual sensor data (83 and 41% reduction in the root mean square error, respectively), demonstrating the potential practical utility of the derived equation. The developed methodology can be used to obtain a spectrally compatible EVI for any pair of sensors in the data continuity context. © The Authors.

O'Brien, CJ, Peloquin, JA, Vogt, M, Heinle, M, Gruber, N, Ajani, P, Andruleit, H, Arístegui, J, Beaufort, L, Estrada, M, Karentz, D, Kopczyńska, E, Lee, R, Poulton, AJ, Pritchard, T & Widdicombe, C 2013, 'Global marine plankton functional type biomass distributions: coccolithophores', Earth System Science Data, vol. 5, no. 2, pp. 259-276.
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Abstract. Coccolithophores are calcifying marine phytoplankton of the class Prymnesiophyceae. They are considered to play an import role in the global carbon cycle through the production and export of organic carbon and calcite. We have compiled observations of global coccolithophore abundance from several existing databases as well as individual contributions of published and unpublished datasets. We make conservative estimates of carbon biomass using standardised conversion methods and provide estimates of uncertainty associated with these values. The quality-controlled database contains 57 321 individual observations at various taxonomic levels. This corresponds to 11 503 observations of total coccolithophore abundance and biomass. The data span a time period of 1929–2008, with observations from all ocean basins and all seasons, and at depths ranging from the surface to 500 m. Highest biomass values are reported in the North Atlantic, with a maximum of 127.2 μg C L−1. Lower values are reported for the Pacific (maximum of 20.0 μg C L−1) and Indian Ocean (up to 45.2 μg C L−1). Maximum biomass values show peaks around 60° N and between 40 and 20° S, with declines towards both the equator and the poles. Biomass estimates between the equator and 40° N are below 5 μg C L−1. Biomass values show a clear seasonal cycle in the Northern Hemisphere, reaching a maximum in the summer months (June–July). In the Southern Hemisphere the seasonal cycle is less evident, possibly due to a greater proportion of low-latitude data. The original and gridded datasets can be downloaded from Pangaea (doi:10.1594/PANGAEA.785092).

O'Carroll, SJ, Gorrie, CA, Velamoor, S, Green, CR & Nicholson, LFB 2013, 'Connexin43 mimetic peptide is neuroprotective and improves function following spinal cord injury', NEUROSCIENCE RESEARCH, vol. 75, no. 3, pp. 256-267.
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Connexin43 (Cx43) is a gap junction protein up-regulated after spinal cord injury and is involved in the on-going spread of secondary tissue damage. To test whether a connexin43 mimetic peptide (Peptide5) reduces inflammation and tissue damage and improves function in an in vivo model of spinal cord injury, rats were subjected to a 10 g, 12.5 mm weight drop injury at the vertebral level T10 using a MASCIS impactor. Vehicle or connexin43 mimetic peptide was delivered directly to the lesion via intrathecal catheter and osmotic mini-pump for up to 24 h after injury. Treatment with Peptide5 led to significant improvements in hindlimb function as assessed using the BassoBeattieBresnahan scale. Peptide5 caused a reduction in Cx43 protein, increased Cx43 phosphorylation and decreased levels of TNF-a and IL-1ß as assessed by Western blotting. Immunohistochemistry of tissue sections 5 weeks after injury showed reductions in astrocytosis and activated microglia as well as an increase in motor neuron survival. These results show that administration of a connexin mimetic peptide reduces secondary tissue damage after spinal cord injury by reducing gliosis and cytokine release and indicate the clinical potential for mimetic peptides in the treatment of spinal cord patients.

Oktar, FN, Agathopoulos, S, Ozyegin, LS, Turner, IG, Gunduz, O, Demirkol, N, Brück, S, Ben-Nissan, B, Samur, R, Kayali, ES & Aktas, C 2013, 'Nano-Bioceramic Production via Mechano-Chemical Conversion (Ultrasonication)', Key Engineering Materials, vol. 529-530, no. 1, pp. 609-614.
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The production of nano-calcium phosphate powders, such as HA (hydroxyapatite), from synthetic chemicals can be expensive and time consuming. The skeleton or shells of sea creatures (e.g. sea urchins, shells, corals) could be an alternative source of materials to produce very fine and even nano-structured calcium phosphate biomaterial powders. Ηydrothermal conversion under very high pressures or methods such as hot-plating (chemical) or ultrasonication (mechano-chemical), have been proposed to transform naturally derived CaCO3, e.g. aragonite, into apatite based materials. The aim of the present work was to prepare inexpensive nano-sized HA and TCP bioceramics powders from a local sea snail shells as a possible raw material for HA/TCP bioceramics. Empty shells of a local sea snail (Nassarius hinia reticulatus) from Marmara Sea, Turkey were collected from a beach near Istanbul. The collected shells were ground to a particle size <75µm. Thermal analyses (DTA/TGA) were performed to determine the exact CaCO3 content and thermal behavior. The raw powder was suspended in an aqueous media which was placed in an ultrasonic bath. The temperature was set at 80°C for 15min. Then, an equivalent (to CaO content) amount of H3PO4 was added drop by drop very gently into the solution. The reaction continued for 8h, following which the liquid component was evaporated off in an incubator at 100°C for 24h. The dried sediment was collected and heat treated at two different temperatures, 400 and 800°C. The morphology of the powders produced was examined using SEM. The crystalline phases were indentified using X-ray analysis. X-ray diffractograms indicated the presence of two calcium phosphate phases, namely HA and whitlockite. SEM observations showed that the powder produced comprised nano-sized particles. FTIR results also indicated the presence of HA and...

Ong, VA, Marsh, JW, Lawrence, A, Allan, JA, Timms, P & Huston, WM 2013, 'The protease inhibitor JO146 demonstrates a critical role for CtHtrA for Chlamydia trachomatis reversion from penicillin persistence', FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, vol. 3, no. DEC.
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The Chlamydia trachomatis serine protease HtrA (CtHtrA) has recently been demonstrated to be essential during the replicative phase of the chlamydial developmental cycle. A chemical inhibition strategy (serine protease inhibitor JO146) was used to demonstrate this essential role and it was found that the chlamydial inclusions diminish in size and are lost from the cell after CtHtrA inhibition without formation of viable elementary bodies. The inhibitor (JO146) was used in this study to investigate the role of CtHtrA for penicillin persistence and heat stress conditions for Chlamydia trachomatis. JO146 addition during penicillin persistence resulted in only minor reductions (~1 log) in the final viable infectious yield after persistent Chlamydia were reverted from persistence. However, JO146 treatment during the reversion and recovery from penicillin persistence was completely lethal for Chlamydia trachomatis. JO146 was completely lethal when added either during heat stress conditions, or during the recovery from heat stress conditions. These data together indicate that CtHtrA has essential roles during some stress environments (heat shock), recovery from stress environments (heat shock and penicillin persistence), as well as the previously characterized essential role during the replicative phase of the chlamydial developmental cycle. Thus, CtHtrA is an essential protease with both replicative phase and stress condition functions for Chlamydia trachomatis. © 2013 Ong, Marsh, Lawrence, Allan, Timms and Huston.

Orr, RJS, Stuken, A, Murray, SA & Jakobsen, KS 2013, 'Evolution and Distribution of Saxitoxin Biosynthesis in Dinoflagellates', MARINE DRUGS, vol. 11, no. 8, pp. 2814-2828.
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Numerous species of marine dinoflagellates synthesize the potent environmental neurotoxic alkaloid, saxitoxin, the agent of the human illness, paralytic shellfish poisoning. In addition, certain freshwater species of cyanobacteria also synthesize the same toxic compound, with the biosynthetic pathway and genes responsible being recently reported. Three theories have been postulated to explain the origin of saxitoxin in dinoflagellates: The production of saxitoxin by co-cultured bacteria rather than the dinoflagellates themselves, convergent evolution within both dinoflagellates and bacteria and horizontal gene transfer between dinoflagellates and bacteria. The discovery of cyanobacterial saxitoxin homologs in dinoflagellates has enabled us for the first time to evaluate these theories. Here, we review the distribution of saxitoxin within the dinoflagellates and our knowledge of its genetic basis to determine the likely evolutionary origins of this potent neurotoxin

Orr, RJS, Stuken, A, Murray, SA & Jakobsen, KS 2013, 'Evolutionary Acquisition and Loss of Saxitoxin Biosynthesis in Dinoflagellates: the Second 'Core' Gene, sxtG', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 79, no. 7, pp. 2128-2136.
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Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that sxtA originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize sxtG, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire sxtG transcripts from Alexandrium fundyense CCMP1719 and Alexandrium minutum CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial sxtG transcript fragments were amplified from four additional Alexandrium species and Gymnodinium catenatum. The phylogenetic inference of dinoflagellate sxtG, congruent with sxtA, revealed a bacterial origin. However, it is not known if sxtG was acquired independently of sxtA. Amplification and sequencing of the corresponding genomic sxtG region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike sxtA, sxtG was also amplified from Alexandrium species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus Alexandrium or G. catenatum. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with sxtA for some descendant species.

Pant, R, Li, E, Poulton, CG, Choi, D-Y, Madden, S, Luther-Davies, B & Eggleton, BJ 2013, 'Observation of Brillouin dynamic grating in a photonic chip', Optics Letters, vol. 38, no. 3, pp. 305-305.
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We report demonstration of a Brillouin dynamic grating (BDG) in a photonic chip. A BDG was characterized in a 6.5 cm long chalcogenide (As 2S3) rib waveguide using CW pumps in x polarization and read using a CW probe in y polarization. The measured reflectivity, on-off ratio, and 3 dB bandwidth (f3dB) for the BDG were 0.4%, ∼28 dB, and ∼6 GHz, respectively. © 2013 Optical Society of America.

Parker, L, Ross, P, O'Connor, W, Pörtner, H, Scanes, E & Wright, J 2013, 'Predicting the Response of Molluscs to the Impact of Ocean Acidification', Biology, vol. 2, no. 2, pp. 651-692.
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Elevations in atmospheric carbon dioxide (CO2 are anticipated to acidify oceans because of fundamental changes in ocean chemistry created by CO2 absorption from the atmosphere. Over the next century, these elevated concentrations of atmospheric CO2 are expected to result in a reduction of the surface ocean waters from 8.1 to 7.7 units as well as a reduction in carbonate ion (CO32- concentration. The potential impact that this change in ocean chemistry will have on marine and estuarine organisms and ecosystems is a growing concern for scientists worldwide. While species-specific responses to ocean acidification are widespread across a number of marine taxa, molluscs are one animal phylum with many species which are particularly vulnerable across a number of life-history stages. Molluscs make up the second largest animal phylum on earth with 30,000 species and are a major producer of CaCO3. Molluscs also provide essential ecosystem services including habitat structure and food for benthic organisms (i.e., mussel and oyster beds, purification of water through filtration and are economically valuable. Even sub lethal impacts on molluscs due to climate changed oceans will have serious consequences for global protein sources and marine ecosystems. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Petrou, K, Jimenez-Denness, I, Chartrand, K, McCormack, C, Rasheed, M & Ralph, PJ 2013, 'Seasonal heterogeneity in the photophysiological response to air exposure in two tropical intertidal seagrass species', MARINE ECOLOGY PROGRESS SERIES, vol. 482, pp. 93-106.
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Photosynthesis, chlorophyll a fluorescence, leaf bio-optical properties and pigments were measured in 2 tropical intertidal seagrass species, Zostera muelleri ssp. capricorni and Halophila ovalis before, during and after air-exposure over a tidal cycle. Data were collected across 4 seasons (October and January-growing seasons; May and July-senescent seasons) to determine seasonal dynamics in physiological responses to air exposure. Both species showed clear light-dependent responses with a decline in photosynthetic efficiency and increased photoprotection during periods of combined maximum daily irradiance and air exposure for all seasons. In Z. muelleri ssp. capricorni there was a negative correlation between air-exposed effective quan - tum yield and light intensity, suggesting exposure was driving this decline. Conversely, sensitivity (decline in effective quantum yield of photosystem II) to increased irradiance dominated the response in H. ovalis, with no change in the magnitude of this response between air-exposed and submerged blades. The response to air exposure observed in Z. muelleri ssp. capricorni showed seasonal variation, with a greater decline in photosynthesis during the spring (October). Tidal exposure did not provide intertidal seagrasses a 'window' of photosynthetic respite (increase in photosynthesis) from high natural or anthropogenic turbidity. However, the periods immediately prior to and after exposure were important for providing an optimum period for net photosynthetic gain. © Inter-Research 2013.

Pham, AQN, Kelly, T & Fu, S 2013, 'Urine adulteration: can bleach be used to mask MDMA use?', ANALYTICAL METHODS, vol. 5, no. 16, pp. 3948-3955.
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Concerns regarding specimen integrity have long been a major issue of urine drug testing due to acts of urine adulteration. At a high concentration, in vitro urine adulteration using sodium hypochlorite (bleach) produced false-negative results for 3,4-methylenedioxymethamphetamine (MDMA) in CEDIA immunoassay screening with strong negative readings. However, these strong negative readings may act as a warning sign for further investigation of the sample where the detection of a unique marker in the form of N-chloroMDMA will suggest urine adulteration via bleach. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) identi?ed N-chloroMDMA is a major product formed between hypochlorite and MDMA in urine. N-ChloroMDMA was found stable at 4 C for at least 10 h, but decomposed over time at room temperature (20 C) with MDMA being identified as one of its main decomposition products

Pham, TH, Ormerod, JT & Wand, MP 2013, 'Mean field variational Bayesian inference for nonparametric regression with measurement error', Computational Statistics & Data Analysis, vol. 68, no. 1, pp. 375-387.
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A fast mean field variational Bayes (MFVB) approach to nonparametric regression when the predictors are subject to classical measurement error is investigated. It is shown that the use of such technology to the measurement error setting achieves reasonable accuracy. In tandem with the methodological development, a customized Markov chain Monte Carlo method is developed to facilitate the evaluation of accuracy of the MFVB method. © 2013 Published by Elsevier B.V. All rights reserved.

Philp, M, Shimmon, R, Stojanovska, N, Tahtouh, M & Fu, S 2013, 'Development and validation of a presumptive colour spot test method for the detection of piperazine analogues in seized illicit materials', ANALYTICAL METHODS, vol. 5, no. 20, pp. 5402-5410.
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The increasingly large quantities of potentially illicit samples received for confirmatory analysis highlights the importance and demand for preliminary testing procedures that are simple, rapid, selective, inexpensive and able to be used in the field. C

Phyu, YL, Palmer, CG, Warne, MSJ, Dowse, R, Mueller, S, Chapman, J, Hose, GC & Lim, RP 2013, 'Assessing the Chronic Toxicity of Atrazine, Permethrin, and Chlorothalonil to the Cladoceran Ceriodaphnia cf. dubia in Laboratory and Natural River Water', ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY, vol. 64, no. 3, pp. 419-426.
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The majority of ecotoxicological data are generated from standard laboratory-based experiments with organisms exposed in nonflowing systems using highly purified water, which contains very low amounts of dissolved organic matter and suspended particulates. However, such experimental conditions are not ecologically relevant. Thus, there is a need to develop more realistic approaches to determining toxicity, including both lethal and sublethal effects. This research provides information on the effect of natural water constituents, such as suspended particulates and dissolved organic matter, in river water (RW) on the chronic toxicity (7-day reproductive impairment) of the pesticides atrazine, chlorothalonil, and permethrin to the freshwater cladoceran Ceriodaphnia cf. dubia. Standard bioassays were conducted under standard laboratory and more environmentally realistic conditions (using RW). The 7-day IC25 (reproduction impairment) values of atrazine, chlorothalonil, and permethrin to C. cf. dubia ranged from 862.4 to >1000, 51.3 to 66.4, and 0.19 to 0.23 µg/L, respectively. Using the Globally Harmonized System of Classification and Labelling of Chemicals, atrazine is classified as moderately to highly toxic, whereas permethrin and chlorothalonil were both highly toxic. The presence of dissolved organic matter and suspended particles in natural RW did not significantly (p > 0.05) change the toxicity of any of the pesticides to C. cf. dubia compared with that tested in laboratory water (LW). For the tested pesticides, toxicity testing in LW provided an adequate estimate of the hazard posed.

Platen, E & Shi, L 2013, 'On the numerical stability of simulation methods for SDEs under multiplicative noise in finance', QUANTITATIVE FINANCE, vol. 13, no. 2, pp. 183-194.
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When simulating discrete-time approximations of solutions of stochastic differential equations (SDEs), in particular martingales, numerical stability is clearly more important than some higher order of convergence. Discrete-time approximations of solutions of SDEs with multiplicative noise, similar to the BlackScholes model, are widely used in simulation in finance. The stability criterion presented in this paper is designed to handle both scenario simulation and Monte Carlo simulation, i.e. both strong and weak approximations. Methods are identified that have the potential to overcome some of the numerical instabilities experienced when using the explicit Euler scheme. This is of particular importance in finance, where martingale dynamics arise frequently and the diffusion coefficients are often multiplicative. Stability regions for a range of schemes are visualized and analysed to provide a methodology for a better understanding of the numerical stability issues that arise from time to time in practice. The result being that schemes that have implicitness in the approximations of both the drift and the diffusion terms exhibit the largest stability regions. Most importantly, it is shown that by refining the time step size one can leave a stability region and may face numerical instabilities, which is not what one is used to experiencing in deterministic numerical analysis.

Potgieter, AB, Lawson, K & Huete, AR 2013, 'Determining crop acreage estimates for specific winter crops using shape attributes from sequential MODIS imagery', INTERNATIONAL JOURNAL OF APPLIED EARTH OBSERVATION AND GEOINFORMATION, vol. 23, no. 1, pp. 254-263.
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There are increasing societal and plant industry demands for more accurate, objective and near realtime crop production information to meet both economic and food security concerns. The advent of the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite platform has augmented the capability of satellite-based applications to monitor large agricultural areas at acceptable pixel scale, cost and accuracy. Fitting parametric profiles to growing season vegetation index time series reduces the volume of data and provides simple quantitative parameters that relates to crop phenology (sowing date, flowering). In this study, we modelled various Gaussian profiles to time sequential MODIS enhanced vegetation index (EVI) images over winter crops in Queensland, Australia. Three simple Gaussian models were evaluated in their effectiveness to identify and classify various winter crop types and coverage at both pixel and regional scales across Queensland's main agricultural areas. Equal to or greater than 93% classification accuracies were obtained in determining crop acreage estimates at pixel scale for each of the Gaussian modelled approaches. Significant high to moderate correlations (log-linear transformation) were also obtained for determining total winter crop (R2 = 0.93) areas as well as specific crop acreage for wheat (R2 = 0.86) and barley (R2 = 0.83). Conversely, it was much more difficult to predict chickpea acreage (R2 ≤ 0.26), mainly due to very large uncertainties in survey data. The quantitative approach utilised here further had additional benefits of characterising crop phenology in terms of length of growing season and providing regression diagnostics of how well the fitted profiles matched the EVI time series. The Gaussian curve models utilised here are novel in application and therefore will enhance the use and adoption of remote sensing technologies in targeted agricultural application. With innate simplicity and accuracies comparable to ...

Poulos, DE, Harasti, D, Gallen, C & Booth, DJ 2013, 'Biodiversity value of a geographically restricted soft coral species within a temperate estuary', AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS, vol. 23, no. 6, pp. 838-849.
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A threatened and uncommon soft coral species, Dendronephthya australis found in large abundance in Port Stephens, within the Port Stephens-Great Lakes Marine Park (PSGLMP), New South Wales, Australia, was hypothesized to be an important habitat for many marine fishes and invertebrates, but is currently under threat from boat anchors, fishing debris entanglement and sand inundation. Surveys were undertaken to assess the biodiversity associated with the soft coral habitat and its adjacent habitats (sponge, seagrass and unvegetated sand), using a combination of Underwater Visual Census (UVC) and Baited Remote Underwater Video System (BRUVS) techniques. In total, 77 fish species and 21 invertebrate species utilized the D. australis habitat, and multivariate fish assemblages associated with soft corals were significantly different to those associated with nearby sponges, seagrass and sand habitats. Species richness of fishes and invertebrates were significantly higher in soft coral and sponge habitats than seagrass. The D. australis habitat was found to be of high importance to juvenile snapper (Pagrus auratus: Sparidae), a species of recreational and commercial fishery importance, which occurred in highest abundance within D. australis, and were significantly smaller in size within the soft coral habitat than the adjacent sponge habitat. Evidently, this rare soft coral habitat supports an extensive marine assemblage, potentially providing a valuable source of food and shelter for fishes and invertebrates, and given it is threatened by human-induced impacts, its protection should be a priority. © 2013 John Wiley & Sons, Ltd.

Poulton, CG, Pant, R & Eggleton, BJ 2013, 'Acoustic confinement and Stimulated Brillouin Scattering in integrated optical waveguides', Journal of the Optical Society of America B: Optical Physics, vol. 30, no. 10, pp. 2657-2664.
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We examine the effect of acoustic mode confinement on Stimulated BrillouinScattering in optical waveguides that consist of a guiding core embedded in asolid substrate. We find that SBS can arise due to coupling to acoustic modesin three different regimes. First, the acoustic modes may be guided by totalinternal reflection; in this case the SBS gain depends directly on the degreeof confinement of the acoustic mode in the core, which is in turn determined bythe acoustic V-parameter. Second, the acoustic modes may be leaky, but maynevertheless have a sufficiently long lifetime to have a large effect on theSBS gain; the lifetime of acoustic modes in this regime depends not only on thecontrast in acoustic properties between the core and the cladding, but is alsohighly dependent on the waveguide dimensions. Finally SBS may occur due tocoupling to free modes, which exist even in the absence of acousticconfinement; we find that the cumulative effect of coupling to thesenon-confined modes results in significant SBS gain. We show how the differentacoustic properties of core and cladding lead to these different regimes, anddiscuss the feasibility of SBS experiments using different material systems.

Pravadali, S, Bassanese, DN, Conlan, XA, Francis, PS, Smith, ZM, Terry, JM & Shalliker, RA 2013, 'Comprehensive sample analysis using high performance liquid chromatography with multi-detection', Analytica Chimica Acta, vol. 803, pp. 188-193.
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Price, HL, Teasdale, PR & Jolley, DF 2013, 'An evaluation of ferrihydrite- and Metsorb™-DGT techniques for measuring oxyanion species (As, Se, V, P): Effective capacity, competition and diffusion coefficients', Analytica Chimica Acta, vol. 803, pp. 56-65.
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Price-Rees, SJ, Webb, JK & Shine, R 2013, 'Reducing the impact of a toxic invader by inducing taste aversion in an imperilled native reptile predator', ANIMAL CONSERVATION, vol. 16, no. 4, pp. 386-394.
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It is virtually impossible to eradicate invasive organisms once they have spread widely, and even low densities of invaders may have devastating impacts. We need to explore alternative management options that accept the inevitability of encounters between alien and native taxa, but reduce the negative consequences of those encounters. Conditioned taste aversion (CTA) is one approach that offers promise in this respect. The spread of the invasive cane toad Rhinella marina across northern Australia is devastating populations of predators such as the blue-tongued skink Tiliqua scincoides intermedia. Predators unable to tolerate the toads' powerful bufadienolide chemical defences are likely to die if they ingest a toad. We trained field-caught skinks to avoid eating cane toad flesh, by offering them toad sausages laced with a nausea-inducing chemical (lithium chloride). These individuals (and controls) were then released and radio-tracked as toads arrived at our study site in north-western Australia. Skinks that regurgitated after consuming the toad sausage survived after release, whereas most untrained animals were fatally poisoned by toad ingestion. Even if we cannot eradicate invasive cane toads, we can ameliorate their ecological impact by CTA training of vulnerable predators. © 2012 The Zoological Society of London.

Pugh, JD, Twigg, DE, Martin, TL & Rai, T 2013, 'Western Australia facing critical losses in its midwifery workforce: A survey of midwives' intentions', MIDWIFERY, vol. 29, no. 5, pp. 497-505.
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Objective: the ongoing attrition of the midwifery workforce frustrates future workforce planning and the provision of maternity services in Western Australia. This project determined factors contributing to the intention of the midwives to move jobs and/or leave the profession. Design: a cross-sectional survey approach was taken for this descriptive research utilising a self-administered questionnaire developed by the Nursing and Midwifery Office, Department of Health, Western Australia. Setting: public and private health sectors in Western Australia, April-May 2010. Participants: 1,600 midwives employed in the public and private health sectors throughout Western Australia were invited to participate: 712 responded (44.5%), one-fifth of the state's registered midwives. Findings: most midwives worked part-time in a clinical role in public hospitals. Almost half intended moving jobs within 5 years and/or leaving midwifery. Excluding midwives of retirement age, the most common reasons for intending to move jobs were family commitments, working conditions and role dissatisfaction. Those intending to leave midwifery cited work-life balance, career change and family commitments. Midwives thought addressing the following issues would improve midwifery retention: flexible work arrangements, remuneration, staffing and caseload, workplace culture, professional development and models of care. Key conclusions: retaining the midwifery workforce requires attention to workforce practices particularly flexible work arrangements and workloads; models of care to strengthen midwives' relationships with clients and colleagues; and accessible professional development. Implications for practice: a review of workplace practices at unit and institution levels is urgently required in Western Australia so that midwives can achieve work-life balance and practice to the full extent of their professional role. These changes are necessary to forestall premature retirement of skilled...

Pushpamalar, V, Langford, SJ, Ahmad, M, Hashim, K & Lim, YY 2013, 'Absorption characterization of Ca²⁺, Na⁺, and K⁺ on irradiation crosslinked carboxymethyl sago pulp hydrogel', Journal of Applied Polymer Science, vol. 128, no. 3, pp. 1828-1833.
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AbstractHydrogel of carboxymethyl sago pulp (CMSP) of various degree of substitution (DS) was prepared by electron beam irradiation of various radiation doses. The CMSP hydrogels were subjected to swelling in different ionic strength solutions of KCl, NaCl, and CaCl2. The CMSP hydrogels, due to its polyelectrolyte nature, were found to be highly sensitive to ionic strength of the medium. All the CMSP hydrogels showed the absorption of K+ and Ca2+ increases with the increase in the concentrations of the respective cation solutions. The cation absorption also decreases with DS and % gel fraction (%GF) of the CMSP hydrogels. Subjecting the CMSP hydrogels in NaCl results in deswelling and releases Na+ to swelling medium where the Na+ release increases with the increase of DS and %GF. The sorption capacity depends on the extent of crosslinking and decreases with the increase in the extent of crosslinking. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

Pushpamalar, V, Langford, SJ, Ahmad, M, Hashim, K & Lim, YY 2013, 'Preparation of carboxymethyl sago pulp hydrogel from sago waste by electron beam irradiation and swelling behavior in water and various pH media', Journal of Applied Polymer Science, vol. 128, no. 1, pp. 451-459.
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AbstractSolutions of carboxymethyl sago pulp (CMSP) of various degree of substitution were irradiated with electron beam of various radiation doses. The gelation dose (Dg) and po/qo ratio (po is degradation density, qo is crosslinking density) is dependent on CMSP concentration and degree of substitution. In the range of concentrations of 10% to 80% (w/v) CMSP with degree of substitutions of 0.4, 0.6, and 0.8, the po/qo ratio decreases with increasing %CMSP showing that crosslinking processes are dominating and increasing the gel network of the CMSP hydrogel. The fourier transform infrared spectra of CMSP hydrogels of degree of substitutions of 0.4, 0.6, and 0.8 with percentage of gel fractions 25, 35, and ≥ 40 show differences in the intensity of the absorption bands at 1020–1100, 1326, and 1422 cm−1 with different degree of substitutions and percentage of gel fraction (%GF) that correspond to different extents of chain scission and crosslinking. The swelling behavior in water shows that CMSP hydrogels could absorb 3500–5300% of water by 1 g of CMSP hydrogel. The ability to absorb water increases with the decrease of degree of substitution and %GF of the CMSP hydrogels. It is also observed that the optimum pH for swelling CMSP hydrogel is at pH 7. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2013

Radchik, A, Skryabin, I, Maisano, J, Novikov, A & Gazarian, T 2013, 'Ensuring long term investment for large scale solar power stations: Hedging instruments for green power', SOLAR ENERGY, vol. 98, no. Part B, pp. 167-179.
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There is a general consensus that solar power is one of the cleanest energy technologies available. Nevertheless, investment in large-scale Solar Power Generators (SPGs) is largely impeded by the intermittent nature of solar power. Since the electricity market has a critical responsibility to maintain the reliability of energy supply, the SPG can be registered only as the market semi-scheduled generator (AEMC, 2011). This option excludes the advantages of providing baseload supply, which in turn impedes efficient market contracting for SPGs. The existing approach relies on energy storage or co-generation facilities to be built at the same connection point as the SPG to compensate for output shortages when there is insufficient sunlight. The co-located facilities require significant additional investment in infrastructure. This paper proposes a market based financial approach that does not require an additional construction effort. The approach financially links solar or other intermittent power generation with a gas-fired station through a set of tailored swap-type instruments.

Rahman, MA, Hasegawa, H, Rahman, MM, Maki, T & Lim, RP 2013, 'Effect of Iron (Fe2+) Concentration in Soil on Arsenic Uptake in Rice Plant (Oryza sativa L.) when Grown with Arsenate [As(V)] and Dimethylarsinate (DMA)', Water, Air, & Soil Pollution, vol. 224, no. 7.
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Raina, J-B, Tapiolas, DM, Forêt, S, Lutz, A, Abrego, D, Ceh, J, Seneca, FO, Clode, PL, Bourne, DG, Willis, BL & Motti, CA 2013, 'DMSP biosynthesis by an animal and its role in coral thermal stress response', Nature, vol. 502, no. 7473, pp. 677-680.
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Globally, reef-building corals are the most prolific producers of dimethylsulphoniopropionate (DMSP)1,2, a central molecule in the marine sulphur cycle and precursor of the climate-active gas dimethylsulphide3,4. At present, DMSP production by corals is attributed entirely to their algal endosymbiont, Symbiodinium2. Combining chemical, genomic and molecular approaches, we show that coral juveniles produce DMSP in the absence of algal symbionts. DMSP levels increased up to 54% over time in newly settled coral juveniles lacking algal endosymbionts, and further increases, up to 76%, were recorded when juveniles were subjected to thermal stress. We uncovered coral orthologues of two algal genes recently identified in DMSP biosynthesis, strongly indicating that corals possess the enzymatic machinery necessary for DMSP production. Our results overturn the paradigm that photosynthetic organisms are the sole biological source of DMSP, and highlight the double jeopardy represented by worldwide declining coral cover, as the potential to alleviate thermal stress through coral-produced DMSP declines correspondingly.

Rajia, S, Chen, H & Morris, MJ 2013, 'Voluntary post weaning exercise restores metabolic homeostasis in offspring of obese rats', Nutrition, Metabolism and Cardiovascular Diseases, vol. 23, no. 6, pp. 574-581.
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Aim Physical exercise reduces obesity, insulin resistance and dyslipidemia. We previously found that maternal obesity alters central appetite circuits and contributes to increased adiposity, glucose intolerance and metabolic disease in offspring. Here we hypothesized that voluntary exercise would ameliorate the adverse metabolic effects of maternal obesity on offspring. Methods and Results SpragueDawley females fed chow (C) or high-fat diet HFD (H) were mated. Female offspring from C dams were weaned onto chow (CC); those from H dams recieved chow (HC) or HFD (HH). Half of each group was provided with running wheels (CCEX, HCEX, HHEX; n = 1012). Maternal obesity increased body weight (12%), adiposity, plasma lipids and induced glucose intolerance (HC vs CC; P < 0.05). These were exaggerated by postweaning HFD (HH vs HC; P < 0.01), showed doubled energy intake, a 37% increase in body weight, insulin resistance and glucose intolerance (HH vs HC; P < 0.01). Exercise reduced fat mass, plasma lipids, HOMA and fasting glucose in HCEX (vs HC; P < 0.05) and HHEX (vs HH; P < 0.01). Values in HCEX were indistinguishable from CC, however in HHEX these metabolic parameters remained higher than the sedentary HC and CC rats (P < 0.01). mRNA expression of hypothalamic pro-opiomelanocortin, and adipose tumour necrosis factor a and 11ß-hydroxysteroid dehydrogenase type 1 were reduced by exercise in HHEX (vs HH; P < 0.05).

Raman, H, Raman, R, Eckermann, P, Coombes, N, Manoli, S, Zou, X, Edwards, D, Meng, J, Prangnell, R, Stiller, J, Batley, J, Luckett, D, Wratten, N & Dennis, E 2013, 'Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)', THEORETICAL AND APPLIED GENETICS, vol. 126, no. 1, pp. 119-132.
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Ramsey, DM, Islam, MA, Turnbull, L, Davis, RA, Whitchurch, CB & McAlpine, SR 2013, 'Psammaplysin F: A unique inhibitor of bacterial chromosomal partitioning', BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, vol. 23, no. 17, pp. 4862-4866.
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Described is the antibiotic activity of a marine natural product. Psammaplysin F (1) inhibited the growth of four Gram-positive strains by >80% at 50 μM, and the amine at position C-20 is responsible for the observed antibacterial activity. When tested against two strains of methicillin resistant Staphylococcus aureus (MRSA), the minimum inhibitory concentrations (MICs) for psammaplysin F (40-80 μM) were similar to the structurally-related alkaloid psammaplysin H (2). Psammaplysin F (1) increased membrane permeability by two to four-fold compared to psammaplysin H (2) or control-treated bacteria, respectively. Unlike psammaplysin H (2), we show that psammaplysin F (1) inhibits equal partitioning of DNA into each daughter cell, suggesting that this natural product is a unique prokaryotic cell division inhibitor. © 2013 Elsevier Ltd. All rights reserved.

Rapa, RA, Shimmon, R, Djordjevic, SP, Stokes, HW & Labbate, M 2013, 'Deletion of Integron-Associated Gene Cassettes Impact on the Surface Properties of Vibrio rotiferianus DAT722', PLOS ONE, vol. 8, no. 3.
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Rathner, JA, van Reyk, D & Crane, JW 2013, 'Editorial-volume 21, numbers 2 & 3', International Journal of Innovation in Science and Mathematics Education, vol. 21, no. 2.

Raven, JA, Beardall, J, Larkum, AWD & Sánchez-Baracaldo, P 2013, 'Interactions of photosynthesis with genome size and function', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 368, no. 1622, pp. 20120264-20120264.
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Photolithotrophs are divided between those that use water as their electron donor (Cyanobacteria and the photosynthetic eukaryotes) and those that use a different electron donor (the anoxygenic photolithotrophs, all of them Bacteria). Photolithotrophs with the most reduced genomes have more genes than do the corresponding chemoorganotrophs, and the fastest-growing photolithotrophs have significantly lower specific growth rates than the fastest-growing chemoorganotrophs. Slower growth results from diversion of resources into the photosynthetic apparatus, which accounts for about half of the cell protein. There are inherent dangers in (especially oxygenic) photosynthesis, including the formation of reactive oxygen species (ROS) and blue light sensitivity of the water spitting apparatus. The extent to which photolithotrophs incur greater DNA damage and repair, and faster protein turnover with increased rRNA requirement, needs further investigation. A related source of environmental damage is ultraviolet B (UVB) radiation (280–320 nm), whose flux at the Earth's surface decreased as oxygen (and ozone) increased in the atmosphere. This oxygenation led to the requirements of defence against ROS, and decreasing availability to organisms of combined (non-dinitrogen) nitrogen and ferrous iron, and (indirectly) phosphorus, in the oxygenated biosphere. Differential codon usage in the genome and, especially, the proteome can lead to economies in the use of potentially growth-limiting elements

Raymond, BBA, Tacchi, JL, Jarocki, VM, Minion, FC, Padula, MP & Djordjevic, SP 2013, 'P159 from Mycoplasma hyopneumoniae Binds Porcine Cilia and Heparin and Is Cleaved in a Manner Akin to Ectodomain Shedding', Journal of Proteome Research, vol. 12, no. 12, pp. 5891-5903.
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Mycoplasma hyopneumoniae colonizes the ciliated epithelial lining of the upper respiratory tract of swine and results in chronic infection. Previously, we have observed that members of P97 and P102 paralog families of cilium adhesins undergo endoproteolytic processing on the surface of M. hyopneumoniae. We show that P159 (MHJ-0494), an epithelial cell adhesin unrelated to P97 and P102 paralog families, is a cilium adhesin that undergoes dominant cleavage events at S/T-X-F↓X-D/E-like motifs located at positions 233F↓Q234 and 981F↓Q982, generating P27, P110, and P52. An unrelated cleavage site 738L-K- V↓G-A-A743 in P110 shows sequence identity with a cleavage site (L-N-V↓A-V-S) identified in the P97 paralog, Mhp385, and generates 76 (P76) and 35 kDa (P35) fragments. LC-MS/MS analysis of biotinylated surface proteins identified six peptides with a biotin moiety on their N-terminus indicating novel, low abundance neo-N-termini. LC-MS/MS of proteins separated by 2D-PAGE, 2D immunoblotting using monospecific antiserum raised against recombinant fragments spanning P159 (F1P159-F4P159), and proteins that bound to heparin-agarose were all used to map P159 cleavage fragments. P159 is the first cilium adhesin not belonging to the P97/P102 paralog families and is extensively processed in a manner akin to ectodomain shedding in eukaryotes. © 2013 American Chemical Society.

Razakandrainibe, R, Combes, V, Grau, GE & Jambou, R 2013, 'Crossing the wall: The opening of endothelial cell junctions during infectious diseases', The International Journal of Biochemistry & Cell Biology, vol. 45, no. 7, pp. 1165-1173.
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Vascular endothelial cells (ECs) form a barrier that plays a crucial role in the health and integrity of tissues by regulating the passage of molecules, liquids and immune cells. Dysfunctions or disruption of this barrier leads to edema, inflammation, and associated pathologies. During infection, ECs control transmigration of cells by a complex system of molecules. However pathogens can hijack this pathway to invade ECs and/or tissues. They can also trigger the opening of intercellular junction, apoptosis of ECs or activation of the immune system, which in turn lead to the destruction of the endothelial wall and subsequent edema. Activation of immune cells by pathogens can also enhance the destruction of EC and edema. The review summarizes the state-of-the-art knowledge on the key steps of the complex interactions between the endothelial wall, pathogens, and the immune system that lead to the opening of junctions and/or destruction of the wall, enhancing pathology. A better understanding of these points will allow the development of adjunctive treatments to be used in combination with therapies targeting pathogens, with the aim of protecting the wall and improving the recovery of patients with severe infectious diseases. © 2013 Elsevier Ltd.

Reichel, MP, Alejandra Ayanegui-Alcerreca, M, Gondim, LFP & Ellis, JT 2013, 'What is the global economic impact of Neospora caninum in cattle - The billion dollar question', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 43, no. 2, pp. 133-142.
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Neospora caninum is regarded as one of the most important infectious causes of abortions in cattle worldwide, yet the global economic impact of the infection has not been established. A systematic review of the economic impact of N. caninum infections/abortions was conducted, searching PubMed with the terms 'cattle' and '. Neospora'. This yielded 769 publications and the abstracts were screened for economically relevant information (e.g. abortion prevalence and risk, serological prevalence). Further analysis was restricted to countries with at least five relevant publications. In total, 99 studies (12.9%) from 10 countries contained data from the beef industry (25 papers (25.3%)) and 72 papers (72.8%) from the dairy industry (with the remaining two papers (2.0%) describing general abortion statistics). The total annual cost of N. caninum infections/abortions was estimated to range from a median US -1.1 million in the New Zealand beef industry to an estimated median total of US -546.3 million impact per annum in the US dairy population. The estimate for the total median N. caninum-related losses exceeded US -1.298 billion per annum, ranging as high as US -2.380 billion. Nearly two-thirds of the losses were incurred by the dairy industry (US -842.9 million). Annual losses on individual dairy farms were estimated to reach a median of US -1,600.00, while on beef farms these costs amounted to just US -150.00. Pregnant cows and heifers were estimated to incur, on average, a loss due to N. caninum of less than US -20.00 for dairy and less than US -5.00 for beef. These loss estimates, however, rose to ∼US -110.00 and US -40.00, respectively, for N. caninum-infected pregnant dairy and beef cows. This estimate of global losses due to N. caninum, with the identification of clear target markets (countries, as well as cattle industries), should provide an incentive to develop treatment options and/or vaccines. © 2012 Australian Society for Parasitology Inc.

Reid, AL, Millward, M, Pearce, R, Lee, M, Frank, MH, Ireland, A, Monshizadeh, L, Rai, T, Heenan, P, Medic, S, Kumarasinghe, P & Ziman, M 2013, 'Markers of circulating tumour cells in the peripheral blood of patients with melanoma correlate with disease recurrence and progression', BRITISH JOURNAL OF DERMATOLOGY, vol. 168, no. 1, pp. 85-92.
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Background Multimarker quantitative real-time polymerase chain reaction (qRT-PCR) represents an effective method for detecting circulating tumour cells in the peripheral blood of patients with melanoma. Objectives To investigate whether the phenotype of circulating melanoma cells represents a useful indicator of disease stage, recurrence and treatment efficacy. Methods Peripheral blood was collected from 230 patients with melanoma and 152 healthy controls over a period of 3 years and 9 months. Clinical data and blood samples were collected from patients with primary melanoma (early stages, 0-II, n = 154) and metastatic melanoma (late stages, III-IV, n = 76). Each specimen was examined by qRT-PCR analysis for the expression of five markers: MLANA, ABCB5, TGFβ2, PAX3d and MCAM. Results In total, 212 of the patients with melanoma (92%) expressed markers in their peripheral blood. Two markers, MLANA and ABCB5, had the greatest prognostic value, and were identified as statistically significant among patients who experienced disease recurrence within our study period, being expressed in 45% (MLANA) and 49% (ABCB5) of patients with recurrence (P = 0·001 and P = 0·031, respectively). For patients administered nonsurgical treatments, MCAM expression correlated with poor treatment outcome. Conclusions Circulating tumour cells were detectable at all stages of disease and long after surgical treatment, even when patients were considered disease free. Specifically, expression of ABCB5 and MLANA had significant prognostic value in inferring disease recurrence, while MCAM expression was associated with poor patient outcome after treatment, confirming multimarker qRT-PCR as a potential technique for monitoring disease status. See also the Commentary by Sullivan © 2012 The Authors. BJD © 2012 British Association of Dermatologists.

Reid, BL, Briggs, SB, Karagiannidis, LE, Muzzioli, S, Raiteri, P, Light, ME, Stagni, S, Brulatti, P, Gale, PA, Ogden, MI & Massi, M 2013, 'Blue emitting C2-symmetrical dibenzothiazolyl substituted pyrrole, furan and thiophene', Journal of Materials Chemistry C, vol. 1, no. 11, pp. 2209-2209.
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Reimers, JR, Cai, Z-L, Kobayashi, R, Raetsep, M, Freiberg, A & Krausz, E 2013, 'Assignment of the Q-Bands of the Chlorophylls: Coherence Loss via Q(x) - Q(y) Mixing', SCIENTIFIC REPORTS, vol. 3, pp. 1-8.
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We provide a new and definitive spectral assignment for the absorption, emission, high-resolution fluorescence excitation, linear dichroism, and/or magnetic circular dichroism spectra of 32 chlorophyllides in various environments. This encompases all data used to justify previous assignments and provides a simple interpretation of unexplained complex decoherence phenomena associated with Q x → Q y relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Q x (S 2) and Q y (S 1), strong vibronic coupling inseparably mixes these states in chlorophyll-a. This spreads x-polarized absorption intensity over the entire Q-band system to influence all exciton-transport, relaxation and coherence properties of chlorophyll-based photosystems. The fraction of the total absorption intensity attributed to Q x ranges between 7% and 33%, depending on chlorophyllide and coordination, and is between 10% and 25% for chlorophyll-a. CAM-B3LYP density-functional-theory calculations of the band origins, relative intensities, vibrational Huang-Rhys factors, and vibronic coupling strengths fully support this new assignment.

Rembach, A, Hare, DJ, Lind, M, Fowler, CJ, Cherny, RA, McLean, C, Bush, AI, Masters, CL & Roberts, BR 2013, 'Decreased Copper in Alzheimer’s Disease Brain Is Predominantly in the Soluble Extractable Fraction', International Journal of Alzheimer's Disease, vol. 2013, pp. 1-7.
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Alzheimer’s disease (AD) is the leading cause of dementia and represents a significant burden on the global economy and society. The role of transition metals, in particular copper (Cu), in AD has become of significant interest due to the dyshomeostasis of these essential elements, which can impart profound effects on cell viability and neuronal function. We tested the hypothesis that there is a systemic perturbation in Cu compartmentalization in AD, within the brain as well as in the periphery, specifically within erythrocytes. Our results showed that the previously reported decrease in Cu within the human frontal cortex was confined to the soluble (P<0.05) and total homogenate (P<0.05) fractions. No differences were observed in Cu concentration in erythrocytes. Our data indicate that there is a brain specific alteration in Cu levels in AD localized to the soluble extracted material, which is not reflected in erythrocytes. Further studies using metalloproteomics approaches will be able to elucidate the metabolic mechanism(s) that results in the decreased brain Cu levels during the progression of AD.

Ren, B, O'Brien, BA, Byrne, MR, Ch'ng, E, Gatt, PN, Swan, MA, Nassif, NT, Wei, MQ, Gijsbers, R, Debyser, Z & Simpson, AM 2013, 'Long‐term reversal of diabetes in non‐obese diabetic mice by liver‐directed gene therapy', The Journal of Gene Medicine, vol. 15, no. 1, pp. 28-41.
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AbstractBackgroundType 1 diabetes (T1D) results from an autoimmune attack against the insulin‐producing β‐cells of the pancreas. The present study aimed to reverse T1D by gene therapy.MethodsWe used a novel surgical technique, which involves isolating the liver from the circulation before the delivery of a lentiviral vector carrying furin‐cleavable human insulin (INS‐FUR) or empty vector to the livers of diabetic non‐obese diabetic mice (NOD). This was compared with the direct injection of the vector into the portal circulation. Mice were monitored for body weight and blood glucose. Intravenous glucose tolerance tests were performed. Expression of insulin and pancreatic transcription factors was determined by the reverse transcriptase‐polymerase chain reaction and immunohistochemistry and immunoelectron microscopy was used to localise insulin.ResultsUsing the novel surgical technique, we achieved long‐term transduction (42% efficiency) of hepatocytes, restored normoglycaemia for 150 days (experimental endpoint) and re‐established normal glucose tolerance. We showed the expression of β‐cell transcription factors, murine insulin, glucagon and somatostatin, and hepatic storage of insulin in granules. The expression of hepatic markers, C/EBP‐β, G6PC, AAT and GLUI was down‐regulated in INS‐FUR‐treated livers. Liver function tests remained normal, with no evidence of intrahepatic inflammation or autoimmune destruction of the insulin‐secreting liver tissue. By comparison, direct injection of INS‐FUR reduced blood glucose levels, and no pancreatic transdifferentiation or normal glucose tolerance was observed.Conclusions

Ren, D, Leslie, LM & Lynch, MJ 2013, 'Antarctic ice sheet mass loss estimates using Modified Antarctic Mapping Mission surface flow observations', Journal of Geophysical Research: Atmospheres, vol. 118, no. 5, pp. 2119-2135.
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The long residence time of ice and the relatively gentle slopes of the Antarctica Ice Sheet make basal sliding a unique positive feedback mechanism in enhancing ice discharge along preferred routes. The highly organized ice stream channels extending to the interior from the lower reach of the outlets are a manifestation of the role of basal granular material in enhancing the ice flow. In this study, constraining the model‐simulated year 2000 ice flow fields with surface velocities obtained from InSAR measurements permits retrieval of the basal sliding parameters. Forward integrations of the ice model driven by atmospheric and oceanic parameters from coupled general circulation models under different emission scenarios provide a range of estimates of total ice mass loss during the 21st century. The total mass loss rate has a small intermodel and interscenario spread, rising from approximately −160 km3/yr at present to approximately −220 km3/yr by 2100. The accelerated mass loss rate of the Antarctica Ice Sheet in a warming climate is due primarily to a dynamic response in the form of an increase in ice flow speed. Ice shelves contribute to this feedback through a reduced buttressing effect due to more frequent systematic, tabular calving events. For example, by 2100 the Ross Ice Shelf is projected to shed ~40 km3 during each systematic tabular calving. After the frontal section's attrition, the remaining shelf will rebound. Consequently, the submerged cross‐sectional area will reduce, as will the buttressing stress. Longitudinal differential warming of ocean temperature contributes to tabular calving. Because of the prevalence of fringe ice shelves, oceanic effects likely will play a very important role in the future mass balance of the Antarctica Ice Sheet, under a possible future warming climate.

Ren, D, Leslie, LM & Lynch, MJ 2013, 'Verification of model simulated mass balance, flow fields and tabular calving events of the Antarctic ice sheet against remotely sensed observations', Climate Dynamics, vol. 40, no. 11-12, pp. 2617-2636.
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Richman, MB & Leslie, LM 2013, 'Classification of Changes in Extreme Heat Over Southeastern Australia', Procedia Computer Science, vol. 20, pp. 148-155.
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Riglar, DT, Rogers, KL, Hanssen, E, Turnbull, L, Bullen, HE, Charnaud, SC, Przyborski, J, Gilson, PR, Whitchurch, CB, Crabb, BS, Baum, J & Cowman, AF 2013, 'Spatial association with PTEX complexes defines regions for effector export into Plasmodium falciparum-infected erythrocytes', NATURE COMMUNICATIONS, vol. 4.
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Export of proteins into the infected erythrocyte is critical for malaria parasite survival. The majority of effector proteins are thought to export via a proteinaceous translocon, resident in the parasitophorous vacuole membrane surrounding the parasite. Identification of the Plasmodium translocon of exported proteins and its biochemical association with exported proteins suggests it performs this role. Direct evidence for this, however, is lacking. Here using viable purified Plasmodium falciparum merozoites and three-dimensional structured illumination microscopy, we investigate remodelling events immediately following parasite invasion.We show that multiple complexes of the Plasmodium translocon of exported proteins localize together in foci that dynamically change in clustering behaviour. Furthermore, we provide conclusive evidence of spatial association between exported proteins and exported protein 2, a core component of the Plasmodium translocon of exported proteins, during native conditions and upon generation of translocation intermediates. These data provide the most direct cellular evidence to date that protein export occurs at regions of the parasitophorous vacuole membrane housing the Plasmodium translocon of exported proteins complex. © 2013 Macmillan Publishers Limited.

Rinke, C, Schwientek, P, Sczyrba, A, Ivanova, NN, Anderson, IJ, Cheng, J-F, Darling, A, Malfatti, S, Swan, BK, Gies, EA, Dodsworth, JA, Hedlund, BP, Tsiamis, G, Sievert, SM, Liu, W-T, Eisen, JA, Hallam, SJ, Kyrpides, NC, Stepanauskas, R, Rubin, EM, Hugenholtz, P & Woyke, T 2013, 'Insights into the phylogeny and coding potential of microbial dark matter', Nature, vol. 499, no. 7459, pp. 431-437.
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Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet. © 2013 Macmillan Publishers Limited. All rights reserved.

Roberts, T, Stark, D, Harkness, J & Ellis, J 2013, 'Subtype distribution of Blastocystis isolates from a variety of animals from New South Wales, Australia', VETERINARY PARASITOLOGY, vol. 196, no. 1-2, pp. 85-89.
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A total of 438 stool samples from 38 different species of animal from seven different locations were studied for the presence of Blastocystis. PCR analysis was completed on all samples and DNA sequence data from the rDNA were submitted to subtype allocation. There was a total of 80 (18%) sequences from 18 species, and nine different subtypes were identified - ST1, ST2, ST3, ST4, ST5, ST7, ST11, ST12 and ST13. This is the first report of Blastocystis from the eastern grey kangaroo, red kangaroo, wallaroo, snow leopard and ostrich. This study highlights the need for further investigation into the genetic diversity of Blastocystis which could help show the zoonotic potential of Blastocystis. © 2013 Elsevier B.V.

Roberts, T, Stark, D, Harkness, J & Ellis, J 2013, 'Subtype distribution of Blastocystis isolates identified in a Sydney population and pathogenic potential of Blastocystis', EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES, vol. 32, no. 3, pp. 335-343.
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Blastocystis is one of the most common enteric parasites present in humans. There is still much uncertainty about the pathogenic potential of this parasite, and it was suggested that its pathogenicity could be subtype-related. This report aimed to study 98 Blastocystis isolates found in human stool specimens to identify the subtypes present and carry out phylogenetic analysis on these isolates. This study also aimed to show the relationship between subtype and symptoms. Five-hundred and thirteen stool samples were submitted to five different diagnostic techniques for the detection of Blastocystis. Polymerase chain reaction (PCR)-positive samples were then sequenced and the small subunit (SSU) rDNA sequences were aligned and submitted to phylogenetic analysis. Ninety-eight samples were positive by any of the diagnostic methods for Blastocystis and 96 were positive by PCR. There were seven different subtypes (1, 2, 3, 4, 6, 7 and 8) identified by PCR and sequencing. This is the first large-scale study to examine the occurrence of Blastocystis in Australia. This study reports the high incidence of subtype 3 (44 %) in this population and discusses the emerging idea of subtype-dependent pathogenicity

Robinson, MW, Buchtmann, KA, Jenkins, C, Tacchi, JL, Raymond, BBA, To, J, Chowdhury, PR, Woolley, LK, Labbate, M, Turnbull, L, Whitchurch, CB, Padula, MP & Djordjevic, SP 2013, 'MHJ_0125 is an M42 glutamyl aminopeptidase that moonlights as a multifunctional adhesin on the surface of Mycoplasma hyopneumoniae', OPEN BIOLOGY, vol. 3, no. APR.
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Bacterial aminopeptidases play important roles in pathogenesis by providing a source of amino acids from exogenous proteins, destroying host immunological effector peptides and executing posttranslational modification of bacterial and host proteins. We show that MHJ-0125 from the swine respiratory pathogen Mycoplasma hyopneumoniae represents a new member of the M42 class of bacterial aminopeptidases. Despite lacking a recognizable signal sequence, MHJ-0125 is detectable on the cell surface by fluorescence microscopy and LC-MS/MS of (i) biotinylated surface proteins captured by avidin chromatography and (ii) peptides released by mild trypsin shaving. Furthermore, surface-associated glutamyl aminopeptidase activity was detected by incubation of live M. hyopneumoniae cells with the diagnostic substrate H-Glu-AMC. MHJ-0125 moonlights as a multifunctional adhesin, binding to both heparin and plasminogen. Native proteomics and comparative modelling studies suggest MHJ-0125 forms a dodecameric, homopolymeric structure and provide insight into the positions of key residues that are predicted to interact with heparin and plasminogen. MHJ-0125 is the first aminopeptidase shown to both bind plasminogen and facilitate its activation by tissue plasminogen activator. Plasmin cleaves host extracellular matrix proteins and activates matrix metalloproteases, generating peptide substrates for MHJ-0125 and a source of amino acids for growth of M. hyopneumoniae. This unique interaction represents a new paradigm in microbial pathogenesis. © 2013 The Authors.

Robinson, MW, Dalton, JP, O'Brien, BA & Donnelly, S 2013, 'Fasciola hepatica: The therapeutic potential of a worm secretome', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 43, no. 3-4, pp. 283-291.
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The success of helminth parasites is partly related to their ability to modulate host immune responses towards an anti-inflammatory/regulatory phenotype. This ability resides with the molecules contained in the secretome of various helminths that have been shown to interact with host immune cells and influence their function. Consequently, there exists a unique opportunity to exploit these molecules for the prophylactic and therapeutic treatment of human pro- and auto-inflammatory disorders (for example septic shock, transplant rejection and autoimmune disease). In this review, we describe the mechanisms used by the trematode parasite, Fasciola hepatica, to modulate the immune responses of its host and discuss the potent immune-modulatory effects of three individual molecules within the secretome; namely cathepsin L1, peroxiredoxin and helminth defence molecule. With a focus on the requirements from industry, we discuss the strategies by which these molecules may be clinically developed to control human immune responses in a way that is conducive to the prevention of immune-mediated diseases. © 2012.

Robinson, MW, Donnelly, S & Dalton, JP 2013, 'Helminth defence molecules-immunomodulators designed by parasites!', FRONTIERS IN MICROBIOLOGY, vol. 4, no. OCT.
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Robotham, B, Lastman, KA, Langford, SJ & Ghiggino, KP 2013, 'Ultrafast electron transfer in a porphyrin-amino naphthalene diimide dyad', Journal of Photochemistry and Photobiology A: Chemistry, vol. 251, pp. 167-174.
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Rong, Y, Wu, W, Ni, X, Kuang, T, Jin, D, Wang, D & Lou, W 2013, 'Lactate dehydrogenase A is overexpressed in pancreatic cancer and promotes the growth of pancreatic cancer cells', Tumor Biology, vol. 34, no. 3, pp. 1523-1530.
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Roseblade, A, Luk, F, Rawling, T, Ung, A, Grau, GER & Bebawy, M 2013, 'Cell-Derived Microparticles: New Targets in the Therapeutic Management of Disease', JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES, vol. 16, no. 2, pp. 238-253.
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Intercellular communication is essential to maintain vital physiological activities and to regulate the organisms phenotype. There are a number of ways in which cells communicate with one another. This can occur via autocrine signaling, endocrine signaling or by the transfer of molecular mediators across gap junctions. More recently communication via microvesicular shedding has gained important recognition as a significant pathway by which cells can coordinate the spread and dominance of selective traits within a population. Through this communication apparatus, cells can now acquire and secure a survival advantage, particularly in the context of malignant disease. This review aims to highlight some of the functions and implications of microparticles in physiology of various disease states, and present a novel therapeutic strategy through the regulation of microparticle production.

Roudnew, B, Lavery, TJ, Seymour, JR, Smith, RJ & Mitchell, JG 2013, 'Spatially varying complexity of bacterial and virus-like particle communities within an aquifer system', AQUATIC MICROBIAL ECOLOGY, vol. 68, no. 3, pp. 259-266.
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Hydrological and geological heterogeneity in the subsurface can isolate groundwater bodies in an aquifer system and create hydrologically distinct aquifers overlying each other with varying amounts of water exchange and unknown amounts of biological exchange. The heterogeneous nature of these subsurface waters likely drives changes in groundwater microbiological parameters. In the present study, flow cytometry was used to examine the abundance and cytometrically defined subpopulation structure of bacteria and virus-like particles (VLPs) in 3 distinct, vertically stratified aquifer layers consisting of an unconfined aquifer, a confining layer and a confined aquifer. Despite total microbial abundances remaining constant, the composition of bacterial and VLP communities varied among the aquifer layers. Cytometrically defined subpopulations were defined by nucleic acid content and size and ranged from 1 bacterial and VLP subpopulation in the unconfined aquifer to 4 bacterial and 3 VLP subpopulations in the confined aquifer. This variability in the subpopulation assemblages is likely driven by a combination of hydrological heterogeneity and biological interactions. The results presented here indicate complexity in microbial communities in discrete aquifer layers that may be overlooked when reporting general abundances. Groundwater bacteria and VLPs appear to be a sensitive indicator of the biological dynamics of aquifer systems and may be used to identify heterogeneous water bodies and help distinguish individual aquifer layers in an aquifer system.

Rowe, CC, Bourgeat, P, Ellis, KA, Brown, B, Lim, YY, Mulligan, R, Jones, G, Maruff, P, Woodward, M, Price, R, Robins, P, Tochon‐Danguy, H, O'Keefe, G, Pike, KE, Yates, P, Szoeke, C, Salvado, O, Macaulay, SL, O'Meara, T, Head, R, Cobiac, L, Savage, G, Martins, R, Masters, CL, Ames, D & Villemagne, VL 2013, 'Predicting Alzheimer disease with β‐amyloid imaging: Results from the Australian imaging, biomarkers, and lifestyle study of ageing', Annals of Neurology, vol. 74, no. 6, pp. 905-913.
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ObjectiveBiomarkers for Alzheimer disease (AD) can detect the disease pathology in asymptomatic subjects and individuals with mild cognitive impairment (MCI), but their cognitive prognosis remains uncertain. We aimed to determine the prognostic value of β‐amyloid imaging, alone and in combination with memory performance, hippocampal atrophy, and apolipoprotein E ε4 status in nondemented, older individuals.MethodsA total of 183 healthy individuals (age = 72.0 ± 7.26 years) and 87 participants with MCI (age = 73.7 ± 8.27) in the Australian Imaging, Biomarkers, and Lifestyle study of ageing were studied. Clinical reclassification was performed after 3 years, blind to biomarker findings. β‐Amyloid imaging was considered positive if the 11C‐Pittsburgh compound B cortical to reference ratio was ≥1.5.ResultsThirteen percent of healthy persons progressed (15 to MCI, 8 to dementia), and 59% of the MCI cohort progressed to probable AD. Multivariate analysis showed β‐amyloid imaging as the single variable most strongly associated with progression. Of combinations, subtle memory impairment (Z score = −0.5 to −1.5) with a positive amyloid scan was most strongly associated with progression in healthy individuals (odds ratio [OR] = 16, 95% confidence interval [CI] = 3.7–68; positive predictive value [PPV] = 50%, 95% CI = 19–81; negative predictive value [NPV] = 94%, 95% CI = 88–98). Almost all amnestic MCI subjects (Z score ≤ −1.5) with a positive amyloid scan developed AD (OR = ∞; PPV = 86%, 95% CI = 72–95; NPV = 100%, 95% CI = 80–100). Hippocampal atrophy and ε4 status did not add further predictive value.InterpretationSubtle memory impairment with a positive β‐amy...

Ryu, HS, Park, JW, Park, J, Ahn, J-P, Kim, K-W, Ahn, J-H, Nam, T-H, Wang, G & Ahn, H-J 2013, 'High capacity cathode materials for Li–S batteries', J. Mater. Chem. A, vol. 1, no. 5, pp. 1573-1578.
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To enhance the stability of sulfur cathode for a high energy lithium-sulfur battery, sulfur-activated carbon (S-AC) composite was prepared by encapsulating sulfur into micropores of activated carbon using a solution-based processing technique. In the analysis using the prepared specimen of S-AC composite by the focused ion beam (FIB) technique, the elemental sulfur exists in a highly dispersed state inside the micropores of activated carbon, which has a large surface area and a narrow pore distribution. The S-AC composite was characterized through X-ray powder diffraction (XRD), transmission electron microscopy (TEM), Brunauer-Emmett-Teller (BET) method, selected area electron diffraction (SAED), energy dispersive X-ray spectrometry (EDX), Fourier transform infrared spectroscopy (FT-IR), thermogravimetry analysis (TGA), and field emission scanning electron microscopy (FESEM). A lithium-sulfur cell using the S-AC composite has a high first discharge capacity over 800 mA h g -1 S even at a high current density such as 2C (3200 mA g -1 S) and has good cycleability around 500 mA h g-1 S discharge capacity at the 50th cycle at the same current density. © 2013 The Royal Society of Chemistry.

Sackett, O, Petrou, K, Reedy, B, De Grazia, A, Hill, R, Doblin, M, Beardall, J, Ralph, P & Heraud, P 2013, 'Phenotypic Plasticity of Southern Ocean Diatoms: Key to Success in the Sea Ice Habitat?', PLOS ONE, vol. 8, no. 11.
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Diatoms are the primary source of nutrition and energy for the Southern Ocean ecosystem. Microalgae, including diatoms, synthesise biological macromolecules such as lipids, proteins and carbohydrates for growth, reproduction and acclimation to prevailing environmental conditions. Here we show that three key species of Southern Ocean diatom (Fragilariopsis cylindrus, Chaetoceros simplex and Pseudo-nitzschia subcurvata) exhibited phenotypic plasticity in response to salinity and temperature regimes experienced during the seasonal formation and decay of sea ice. The degree of phenotypic plasticity, in terms of changes in macromolecular composition, was highly species-specific and consistent with each species' known distribution and abundance throughout sea ice, meltwater and pelagic habitats, suggesting that phenotypic plasticity may have been selected for by the extreme variability of the polar marine environment. We argue that changes in diatom macromolecular composition and shifts in species dominance in response to a changing climate have the potential to alter nutrient and energy fluxes throughout the Southern Ocean ecosystem. © 2013 Sackett et al.

Sadraeian, M, Ghoshoon, MB, Mohkam, M, Karimi, Z, Rasoul-Amini, S & Ghasemi, Y 2013, 'Modification in media composition to obtain secretory production of STxB-based vaccines using Escherichia coli', Virologica Sinica, vol. 28, no. 1, pp. 43-48.
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Sadraeian, M, Khoshnood Mansoorkhani, MJ, Mohkam, M, Rasoul-Amini, S, Hesaraki, M & Ghasemi, Y 2013, 'Prevention and Inhibition of TC-1 Cell Growth in Tumor Bearing Mice by HPV16 E7 Protein in Fusion with Shiga Toxin B-Subunit from shigella dysenteriae.', Cell J, vol. 15, no. 2, pp. 176-181.
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OBJECTIVE: For immunotherapy of human papillomavirus (HPV) -16-associated cervical cancers the E7 protein is considered a prime candidate. However it is a poor inducer of cytotoxic T-cell response, when being used as a singular antigen in protein vaccination. Hence, in this study we focused on the utilization of a vaccine delivery system for prevention or treatment of cervical cancer. MATERIALS AND METHODS: In this experimental study, we designed and evaluated a novel fusion protein comprising HPV16 E7 antigen fused to Shiga toxin B-subunit (STxB) as both an antigen vector and an adjuvant. Then we designed two preventive and therapeutic tumor models to investigate the prevention and inhibition of TC-1 cell growth in female C57BL/6 mice, respectively. In each model, mice were immunized with the recombinant protein of E7-STxB or E7 without any adjuvant. RESULTS: We demonstrated that prophylactic immunization of E7-STxB protected mice against TC-1 cells. Also in the therapeutic model, E7-STxB inhibited TC-1 tumor growth inlungs. The results were significant when compared with the immunization of E7 singularly. CONCLUSION: We concluded that immunization with the E7-STxB protein without any adjuvant could generate anti-tumor effect in mice challenged with TC-1 cells.This research verifies the clinical applications and the future prospects of developing HPV16 E7 therapeutic vaccines fused to immunoadjuvants.

Sadraeian, M, Rasoul-Amini, S, Mansoorkhani, MJK, Mohkam, M, Ghoshoon, MB & Ghasemi, Y 2013, 'Induction of Antitumor Immunity Against Cervical Cancer by Protein HPV-16 E7 in Fusion With Ricin B Chain in Tumor-Bearing Mice', International Journal of Gynecologic Cancer, vol. 23, no. 5, pp. 809-814.
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ObjectiveIn immunotherapy of HPV-16–associated cervical cancers, the E7 protein is considered as a prime candidate. However, it is a poor inducer of a cytotoxic T-cell response when used as a singular antigen in protein vaccination. Therefore, to design effective cancer vaccines, the best tumor antigens should be combined with the most effective immunogens or drug delivery tools to achieve positive clinical results. In this study, we fused HPV-16 E7 with the lectin subunit of ricin toxin (RTB) from castor plant as a vaccine adjuvant/carrier.Materials and MethodsAfter reaching the soluble form of the recombinant protein, we designed 2 preventive and inhibition tumor models for investigation of the prevention and rejection of TC-1 cell growth in female C57BL/6 mice, respectively. In each model, mice were immunized with the recombinant protein of E7-RTB or E7 without any adjuvant.ResultsWe demonstrated that prophylactic immunization of E7-RTB protected mice against challenge from TC-1 cells. Also in the therapeutic model, E7-RTB could inhibit TC-1 tumor growth in the lung. The results were significant compared with the immunization of E7 singularly.ConclusionsWe concluded that immunization with E7-RTB protein without any adjuvant could generate antitumor effects in mice challenged with TC-1 cells. This research verifies the clinical applications and the future prospects for development of HPV-16 E7 therapeutic vaccines fused to immunoadjuvants.

Sampson, JN, Chatterjee, N, Carroll, RJ & Muller, S 2013, 'Controlling the local false discovery rate in the adaptive Lasso', Biostatistics, vol. 14, no. 4, pp. 653-666.
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The Lasso shrinkage procedure achieved its popularity, in part, by its tendency to shrink estimated coefficients to zero, and its ability to serve as a variable selection procedure. Using data-adaptive weights, the adaptive Lasso modified the original procedure to increase the penalty terms for those variables estimated to be less important by ordinary least squares. Although this modified procedure attained the oracle properties, the resulting models tend to include a large number of 'false positives' in practice. Here, we adapt the concept of local false discovery rates (lFDRs) so that it applies to the sequence, λn, of smoothing parameters for the adaptive Lasso.We define the lFDR for a given λn to be the probability that the variable added to the model by decreasing λn to λn - δ is not associated with the outcome, where δ is a small value. We derive the relationship between the lFDR and λn, show lFDR =1 for traditional smoothing parameters, and show how to select λn so as to achieve a desired lFDR.We compare the smoothing parameters chosen to achieve a specified lFDR and those chosen to achieve the oracle properties, as well as their resulting estimates for model coefficients, with both simulation and an example from a genetic study of prostate specific antigen. © The Author 2013. Published by Oxford University Press. All rights reserved.

Sánchez-Bayo, F, Hyne, RV, Kibria, G & Doble, P 2013, 'Calibration and Field Application of Chemcatcher® Passive Samplers for Detecting Amitrole Residues in Agricultural Drain Waters', Bulletin of Environmental Contamination and Toxicology, vol. 90, no. 6, pp. 635-639.
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A passive sampler device suitable for monitoring of residues of the hydrophilic ionic herbicide amitrole in irrigation waterways was developed. Uptake of amitrole on styrenedivinylbenzene-reverse phase sulfonated Empore disks was linear and proportional to its water concentration over the range of 110 µg/L with a sampling rate of 23.1 mL/day under laboratory flow-through conditions. Performance of the sampler was evaluated by deployment in an agricultural irrigation drain for 10 days. The amount of amitrole adsorbed by the passive samplers compared well with the cumulative mean water concentrations calculated from daily spot samplings of the drain water.

SCHLIEP, M, CAVIGLIASSO, G, QUINNELL, RG, STRANGER, R & LARKUM, AWD 2013, 'Formyl group modification of chlorophyll a: a major evolutionary mechanism in oxygenic photosynthesis', Plant, Cell & Environment, vol. 36, no. 3, pp. 521-527.
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ABSTRACTWe discuss recent advances in chlorophyll research in the context of chlorophyll evolution and conclude that some derivations of the formyl side chain arrangement of the porphyrin ring from that of the Chl a macrocycle can extend the photosynthetic active radiation (PAR) of these molecules, for example, Chl d and Chl f absorb light in the near‐infrared region, up to ∼750 nm. Derivations such as this confer a selective advantage in particular niches and may, therefore, be beneficial for photosynthetic organisms thriving in light environments with particular light signatures, such as red‐ and near‐far‐red light‐enriched niches. Modelling of formyl side chain substitutions of Chl a revealed yet unidentified but theoretically possible Chls with a distinct shift of light absorption properties when compared to Chl a.

Scott, ML, Whiting, MJ, Webb, JK & Shine, R 2013, 'Chemosensory discrimination of social cues mediates space use in snakes, Cryptophis nigrescens (Elapidae)', ANIMAL BEHAVIOUR, vol. 85, no. 6, pp. 1493-1500.
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Snakes have traditionally been viewed as solitary, asocial animals whose habitat use is driven by temperature, prey and predators. However, recent studies suggest that snake spatial ecology may also be socially mediated. We examined the influence of conspecific chemical cues on refuge selection in a small nocturnal snake (the small-eyed snake) that engages in male contest competition. Females preferred refuges containing scent cues from conspecifics (of either sex) rather than scentless refuges. Males preferred female-scented rather than male-scented refuges, and preferred the scent of larger (and hence, more fecund) females than smaller females. Males spent more time in refuges containing the scent of smaller rather than larger males, but males that lost a contest did not avoid the refuge scented by the winner and therefore did not show evidence of the winner-loser effect. Females preferred refuges scented by larger males. Small-eyed snakes can distinguish conspecific sex and body size using chemical cues, and they use these cues to select alternative refuge sites. We suggest that social factors play a significant role in driving snake spatial distribution patterns in the wild and that snakes may exhibit more complex social systems than has generally been believed. © 2013 The Association for the Study of Animal Behaviour.

Scuderi, S, D’Amico, AG, Castorina, A, Imbesi, R, Carnazza, ML & D’Agata, V 2013, 'Ameliorative effect of PACAP and VIP against increased permeability in a model of outer blood retinal barrier dysfunction', Peptides, vol. 39, pp. 119-124.
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Segele, ZT, Leslie, LM & Lamb, PJ 2013, 'Weather Research and Forecasting Model simulations of extended warm-season heavy precipitation episode over the US Southern Great Plains: data assimilation and microphysics sensitivity experiments', Tellus A: Dynamic Meteorology and Oceanography, vol. 65, no. 1, pp. 19599-19599.
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Serban, N, Staicu, A-M & Carroll, RJ 2013, 'Multilevel Cross-Dependent Binary Longitudinal Data', Biometrics, vol. 69, no. 4, pp. 903-913.
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Summary We provide insights into new methodology for the analysis of multilevel binary data observed longitudinally, when the repeated longitudinal measurements are correlated. The proposed model is logistic functional regression conditioned on three latent processes describing the within- and between-variability, and describing the cross-dependence of the repeated longitudinal measurements. We estimate the model components without employing mixed-effects modeling but assuming an approximation to the logistic link function. The primary objectives of this article are to highlight the challenges in the estimation of the model components, to compare two approximations to the logistic regression function, linear and exponential, and to discuss their advantages and limitations. The linear approximation is computationally efficient whereas the exponential approximation applies for rare events functional data. Our methods are inspired by and applied to a scientific experiment on spectral backscatter from long range infrared light detection and ranging (LIDAR) data. The models are general and relevant to many new binary functional data sets, with or without dependence between repeated functional measurements.

Sergeyev, A, Geiss, R, Solntsev, AS, Steinbrück, A, Schrempel, F, Kley, E-B, Pertsch, T & Grange, R 2013, 'Second-harmonic generation in lithium niobate nanowires for local fluorescence excitation', Optics Express, vol. 21, no. 16, pp. 19012-19012.
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Shabannia, R, Abu Hassan, H, Mahmodi, H, Naderi, N & Abd, HR 2013, 'ZnO nanorod ultraviolet photodetector on porous silicon substrate', Semiconductor Science and Technology, vol. 28, no. 11, pp. 115007-115007.
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Shanmuganatham, K, Feeroz, MM, Jones-Engel, L, Smith, GJD, Fourment, M, Walker, D, McClenaghan, L, Alam, SMR, Hasan, MK, Seiler, P, Franks, J, Danner, A, Barman, S, McKenzie, P, Krauss, S, Webby, RJ & Webster, RG 2013, 'Antigenic and Molecular Characterization of Avian Influenza A(H9N2) Viruses, Bangladesh', Emerging Infectious Diseases, vol. 19, no. 9, pp. 1393-1402.
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Shimoni, O, Yan, Y, Wang, Y & Caruso, F 2013, 'Shape-Dependent Cellular Processing of Polyelectrolyte Capsules', ACS Nano, vol. 7, no. 1, pp. 522-530.
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Particle shape is emerging as a key design parameter for tailoring the interactions between particles and cells. Herein, we report the preparation of rod-shaped layer-by-layer (LbL)-assembled polymer hydrogel capsules with tunable aspect ratios (ARs). By templating spherical and rodlike silica particles, disulfide-stabilized poly(methacrylic acid) hydrogel capsules (PMA HCs) with different ARs (from 1 to 4) are generated. The influence of capsule AR on cellular internalization and intracellular fate was quantitatively investigated by flow cytometry, imaging flow cytometry, and fluorescence deconvolution microscopy. These experiments reveal that the cellular internalization kinetics of PMA HCs are dependent on the AR, with spherical capsules being internalized more rapidly and to a greater extent compared with rod-shaped capsules. In contrast, the capsules with different ARs are colocalized with the lysosomal marker LAMP1, suggesting that the lysosomal compartmentalization is independent of shape for these soft polymer capsules. © 2012 American Chemical Society.

Shokri, MR & Gladstone, W 2013, 'Integrating Vulnerability Into Estuarine Conservation Planning: Does the Data Treatment Method Matter?', ESTUARIES AND COASTS, vol. 36, no. 4, pp. 866-880.
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Protected areas will more efficiently protect biodiversity if threats to the persistence of populations are addressed. Seagrass meadows are globally regarded as critical habitats because of their ecosystem services, human use values, and their diminishing extent. While selecting priority areas for conservation of seagrass meadows is largely aimed at maximizing the protection of their biodiversity, little attention is paid to consider simultaneously the representation of biodiversity and the minimization of threats. This study developed and tested an approach for integrating vulnerability of seagrass meadows to anthropogenic disturbance with the selection of estuarine-protected areas. Vulnerability was measured by data on different land use types in subcatchments. Conservation value was measured by irreplaceability, diversity indices, and rarity of macroinvertebrate species in seagrass meadows. Vulnerability was incorporated into conservation planning by plotting grid cell scores for conservation value versus their scores for vulnerability. The results showed that the performance of the model for the integration of vulnerability into estuarine conservation planning was sensitive to the data treatment. The vulnerability of seagrass meadows and accordingly the arrangement of priority areas for conservation and management attention may change if more information is incorporated into the measurement of vulnerability.

Shokri, MR & Gladstone, W 2013, 'Limitations of habitats as biodiversity surrogates for conservation planning in estuaries', ENVIRONMENTAL MONITORING AND ASSESSMENT, vol. 185, no. 4, pp. 3477-3492.
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Increasing pressures on global biodiversity and lack of data on the number and abundance of species have motivated conservation planners and researchers to use more readily available information as proxies or surrogates for biodiversity. "Habitat" is one of the most frequently used surrogates but its assumed value in marine conservation planning is not often tested. The present study developed and tested three alternative habitat classification schemes of increasing complexity for a large estuary in south-east Australia and tested their effectiveness in predicting spatial variation in macroinvertebrate biodiversity and selecting estuarine protected areas to represent species. The three habitat classification schemes were: (1) broad-scale habitats (e.g., mangroves and seagrass), (2) subdivision of each broad-scale habitat by a suite of environmental variables that varied significantly throughout the estuary, and (3) subdivision of each broad-scale habitat by the subset of environmental variables that best explained spatial variation in macroinvertebrate biodiversity. Macroinvertebrate assemblages differed significantly among the habitats in each classification scheme. For each classification scheme, habitat richness was significantly correlated with species richness, total density of macroinvertebrates, assemblage dissimilarity, and summed irreplaceability. However, in a reserve selection process designed to represent examples of each habitat, no habitat classification scheme represented species significantly better than a random selection of sites. Habitat classification schemes may represent variation in estuarine biodiversity; however, the results of this study suggest they are inefficient in designing representative networks of estuarine protected areas.

Siddhanta, AK, Kumar, S, Mehta, GK, Chhatbar, MU, Oza, MD, Sanandiya, ND, Chejara, DR, Godiya, CB & Kondaveeti, S 2013, 'Cellulose Contents of Some Abundant Indian Seaweed Species', Natural Product Communications, vol. 8, no. 4, pp. 1934578X1300800-1934578X1300800.
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Crude cellulose as well as α- and β-celluloses were estimated in thirty-four seaweed species of fifteen orders of Chlorophyta, Phaeophyta and Rhodophyta of Indian waters. The greatest yields of crude cellulose and α-cellulose were obtained from Chaetomorpha aerea (approx. 20.0% and 18.5%, respectively), and of β-cellulose (approx. 3.1%) from Caulerpa imbricata. The lowest crude cellulose, and α-and β-contents were recorded for the calcareous red alga Liagora indica (approx. 0.90%, 0.70% and 0.10%, respectively). There was little variation in cellulose content among the brown algae, while wide variations in the yields were found in the green and red algae. The present work contributes to the repertoire of 67 Indian seaweed species studied to now for their cellulose contents in our laboratory. The combined studies highlight that Chaetomorpha aerea, Acrosiphonia orientalis, Caulerpa taxifolia, Sargassum tenerrimum, Hydroclathrus clathratus and Gelidiella acerosa possess relatively high (>10%) cellulose contents, which could be of potential utility.

Simpson, AM, Ren, B, O'Brien, BA & Nassif, NT 2013, 'Response to the letter to the editor by M. Elsner et al: “Comment on Binhai Ren et al (2013;15:28–41). Long term reversal of diabetes in non‐obese diabetic mice by liver‐directed gene therapy”', The Journal of Gene Medicine, vol. 15, no. 8-9, pp. 309-310.
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Simpson, JL, McDonald, VM, Baines, KJ, Oreo, KM, Wang, F, Hansbro, PM & Gibson, PG 2013, 'Influence of Age, Past Smoking, and Disease Severity on TLR2, Neutrophilic Inflammation, and MMP-9 Levels in COPD', Mediators of Inflammation, vol. 2013, pp. 1-13.
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Chronic obstructive pulmonary disease (COPD) is a common and serious respiratory disease, particularly in older individuals, characterised by fixed airway obstruction and persistent airway neutrophilia. The mechanisms that lead to these features are not well established. We investigated the contribution of age, prior smoking, and fixed airflow obstruction on sputum neutrophils, TLR2 expression, and markers of neutrophilic inflammation. Induced sputum from adults with COPD (n = 69) and healthy controls (n = 51) was examined. A sputum portion was dispersed, total, differential cell count and viability recorded, and supernatant assayed for CXCL8, matrix metalloproteinase- (MMP-) 9, neutrophil elastase, and soluble TLR2. Peripheral blood cells (n = 7) were stimulated and TLR2 activation examined. TLR2 levels were increased with ageing, while sputum neutrophils and total sputum MMP-9 levels increased with age, previous smoking, and COPD. In multivariate regression, TLR2 gene expression and MMP-9 levels were significant independent contributors to the proportion of sputum neutrophils after adjustment for age, prior smoking, and the presence of airflow obstruction. TLR2 stimulation led to enhanced release of MMP-9 from peripheral blood granulocytes. TLR2 stimulation activates neutrophils for MMP-9 release. Efforts to understand the mechanisms of TLR2 signalling and subsequent MMP-9 production in COPD may assist in understanding neutrophilic inflammation in COPD. © 2013 Jodie L. Simpson et al.

Sinutok, S, Hill, R, Doblin, MA & Ralph, PJ 2013, 'Diurnal photosynthetic response of the motile symbiotic benthic foraminiferan Marginopora vertebralis', MARINE ECOLOGY PROGRESS SERIES, vol. 478, pp. 127-138.
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Movement of the symbiont-bearing foraminiferan Marginopora vertebralis and photo physiological response to diurnal fluctuations in irradiance were investigated in field and laboratory experiments. The abundance of M. vertebralis from both light-exposed and sheltered habitats was determined 5 times during the day, from pre-dawn to post-dusk. M. vertebralis abundance was significantly higher in sheltered compared to exposed habitats at midday under high irradiance, and this movement enabled the algal symbionts to avoid excessive photoinhibition. The diurnal changes in photosynthetic efficiency were not consistent with the typical midday solar maximum downregulation of photosystem II observed in other photoautotrophs and was likely due to the negatively phototactic capacity of the foraminifera. To confirm the light-dependent movement of foraminifera, individuals in exposed and sheltered habitats were exposed to the photosynthetic inhibitor 3-(3,4-dichlorophenyl)-1, 1-dimethylurea (DCMU) in the laboratory. The lack of movement in DCMU-exposed specimens confirmed light-dependent movement and subsequent disruption of signalling between the host foraminiferan and the algal symbionts. Analysis of chlorophyll and xanthophyll pigments, as well as symbiont density, indicated that under high irradiance, foraminiferal symbionts have the capacity to reduce light stress by activating photoprotective mechanisms. The negatively phototactic behaviour prevented chlorophyll degradation, symbiont loss and bleaching, suggesting that it is the primary mechanism for controlling light exposure in these foraminifera. This behaviour provides a competitive advantage over other sessile organisms in avoiding photoinhibition and bleaching by moving away from over-saturating irradiance, towards less damaging light fields. © Inter-Research 2013.

Slobozhanyuk, AP, Lapine, M, Powell, DA, Shadrivov, IV, Kivshar, YS, McPhedran, RC & Belov, PA 2013, 'Flexible Helices for Nonlinear Metamaterials', ADVANCED MATERIALS, vol. 25, no. 25, pp. 3409-3412.
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The successful fabrication and experimental verification of a novel metamaterial based on flexible metallic helices is reported. The helices undergo compression under the influence of incident radiation, demonstrating a nonlinear chiral electromagnetic response, associated with the power-dependent change in the helix pitch. This design is promising for application to power-dependent polarization rotation of propagating waves. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Smith, GB, Golestan, D & Gentle, AR 2013, 'The insulator to correlated metal phase transition in molybdenum oxides', APPLIED PHYSICS LETTERS, vol. 103, no. 5.
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Smith, RJ, Jeffries, TC, Roudnew, B, Seymour, JR, Fitch, AJ, Simons, KL, Speck, PG, Newton, K, Brown, MH & Mitchell, JG 2013, 'Confined aquifers as viral reservoirs', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 5, no. 5, pp. 725-730.
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Knowledge about viral diversity and abundance in deep groundwater reserves is limited. We found that the viral community inhabiting a deep confined aquifer in South Australia was more similar to reclaimed water communities than to the viral communities in the overlying unconfined aquifer community. This similarity was driven by high relative occurrence of the single-stranded DNA viral groups Circoviridae, Geminiviridae and Microviridae, which include many known plant and animal pathogens. These groups were present in a 1500-year-old water situated 80?m below the surface, which suggests the potential for long-term survival and spread of potentially pathogenic viruses in deep, confined groundwater. Obtaining a broader understanding of potentially pathogenic viral communities within aquifers is particularly important given the ability of viruses to spread within groundwater ecosystems.

Sobinoff, AP, Beckett, EL, Jarnicki, AG, Sutherland, JM, McCluskey, A, Hansbro, PM & McLaughlin, EA 2013, 'Scrambled and fried: Cigarette smoke exposure causes antral follicle destruction and oocyte dysfunction through oxidative stress', Toxicology and Applied Pharmacology, vol. 271, no. 2, pp. 156-167.
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Somaweera, R, Shine, R, Webb, J, Dempster, T & Letnic, M 2013, 'Why does vulnerability to toxic invasive cane toads vary among populations of Australian freshwater crocodiles?', Animal Conservation, vol. 16, no. 1, pp. 86-96.
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AbstractThe ecological impact of an invasive species can be heterogeneous through space and time. One such case in Australia involves native freshwater crocodiles Crocodylus johnstoni, which are highly sensitive to invasive cane toads Rhinella marina in some areas, whereas other populations experience little or no mortality from ingestion of the toxic toads. We studied the impact of toad invasion on three crocodile populations: one crashed, one showed a minor decrease and one appeared unaffected. We tested three hypotheses for the cause of this spatial variation in impact: differences among populations in toad–crocodile encounter rates (proximity of toads to crocodiles during spotlight surveys), differences in crocodile feeding responses (trials of prey preference in the laboratory) and differences in crocodile physiology (reduction of swim speed after receiving a dose of toad toxin). We found little divergence among populations in any of these traits: crocodiles from the three populations all encountered cane toads in the wild, and exhibited similar feeding responses and toxin tolerances. Thus, we cannot confidently identify causation for the impact heterogeneity. Reliance on alternative food resources and an ability to rapidly learn taste aversion may have allowed crocodiles to deal with toad arrival in Lake Argyle and the Daly River. Future work could usefully evaluate potential explanations for the failure of these adaptive mechanisms in ...

Song, EJ, Gordon-Thomson, C, Cole, L, Stern, H, Halliday, GM, Damian, DL, Reeve, VE & Mason, RS 2013, '1α,25-Dihydroxyvitamin D3 reduces several types of UV-induced DNA damage and contributes to photoprotection', The Journal of Steroid Biochemistry and Molecular Biology, vol. 136, pp. 131-138.
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Sonuga-Barke, EJS, Cartwright, KL, Thompson, MJ, Brown, J, Bitsakou, P, Daley, D, Gramzow, RH, Psychogiou, L & Simonoff, E 2013, 'Family Characteristics, Expressed Emotion, and Attention-Deficit/Hyperactivity Disorder', Journal of the American Academy of Child & Adolescent Psychiatry, vol. 52, no. 5, pp. 547-548.e2.
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Speer, MS 2013, 'Dust storm frequency and impact over Eastern Australia determined by state of Pacific climate system', Weather and Climate Extremes, vol. 2, pp. 16-21.
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Dust storms resulting from synoptic-scale mid-latitude frontal systems affect inland, eastern Australia, predominantly through spring and summer but extend to the east coast only rarely when strong, frontal westerly winds crossing the continent are sustained over the coast. Here it is shown that extreme westerly wind dust events are anomalous to the more pervasive southerly winds that have shaped the sand dunes over inland eastern Australia. It is also shown that while antecedent dry conditions are very important, higher SON and DJF dust storm frequencies from 1957 to the mid-1970s occurred due to both anomalously strong, southerly winds existing on the western side of a cyclonic anomaly adjacent to the east Australian coast, which resulted from the state of the Pacific climate system, and an anticyclonic anomaly at the top of the Great Australian Bight. A change in BoM observing practice, after 1973, is unlikely to be the major cause of changes in total dust frequency from the mid-1970s. Rather, extreme rainfall years are more likely to have been a major contributing factor to the large decreases in dust occurrence from 1973 to 1976, in addition to the other La Niña periods of 2000/01 to 2010/11. Synoptic-scale frontal systems in the westerlies that result in the transport of dust remained low in frequency throughout the whole period from 1957 to 2011. However, those dust storms in the westerlies that do reach the east coast, although infrequent, tend to occur during El Niño-dominated years. On the other hand, they occur during both negative and positive phases of the southern annular mode (SAM). This ambiguity with the SAM phase is consistent with the fact that the mid-latitude westerlies and associated frontal systems are usually at their most equatorward position in Australian longitudes in late winter/spring regardless of the SAM phase. This suggests little change is likely in the frequency of westerly induced dust storms in late winter/spring over central/e...

Spring, JB, Metcalf, BJ, Humphreys, PC, Kolthammer, WS, Jin, X-M, Barbieri, M, Datta, A, Thomas-Peter, N, Langford, NK, Kundys, D, Gates, JC, Smith, BJ, Smith, PGR & Walmsley, IA 2013, 'Boson Sampling on a Photonic Chip', Science, vol. 339, no. 6121, pp. 798-801.
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Computing Power of Quantum Mechanics There is much interest in developing quantum computers in order to perform certain tasks much faster than, or that are intractable for, a classical computer. A general quantum computer, however, requires the fabrication and operation a number of quantum logic devices (see the Perspective by Franson ). Broome et al. (p. 794 , published online 20 December) and Spring et al. (p. 798 , published online 20 December) describe experiments in which single photons and quantum interference were used to perform a calculation (the permanent of a matrix) that is very difficult on a classical computer. Similar to random walks, quantum walks on a graph describe the movement of a walker on a set of predetermined paths; instead of flipping a coin to decide which way to go at each point, a quantum walker can take several paths at once. Childs

Spring, JB, Salter, PS, Metcalf, BJ, Humphreys, PC, Moore, M, Thomas-Peter, N, Barbieri, M, Jin, X-M, Langford, NK, Kolthammer, WS, Booth, MJ & Walmsley, IA 2013, 'On-chip low loss heralded source of pure single photons', Optics Express, vol. 21, no. 11, pp. 13522-13522.
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Stansfield, SH, Patel, P, Debattista, J, Armitage, CW, Cunningham, K, Timms, P, Allan, J, Mittal, A & Huston, WM 2013, 'Proof of concept: A bioinformatic and serological screening method for identifying new peptide antigens for Chlamydia trachomatis related sequelae in women', Results in Immunology, vol. 3, pp. 33-39.
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This study aimed to identify new peptide antigens from Chlamydia (C.) trachomatis in a proof of concept approach which could be used to develop an epitope-based serological diagnostic for C. trachomatis related infertility in women. A bioinformatics analysis was conducted examining several immunodominant proteins from C. trachomatis to identify predicted immunoglobulin epitopes unique to C. trachomatis. A peptide array of these epitopes was screened against participant sera. The participants (all female) were categorized into the following cohorts based on their infection and gynecological history; acute (single treated infection with C. trachomatis), multiple (more than one C. trachomatis infection, all treated), sequelae (PID or tubal infertility with a history of C. trachomatis infection), and infertile (no history of C. trachomatis infection and no detected tubal damage). The bioinformatics strategy identified several promising epitopes. Participants who reacted positively in the peptide 11 ELISA were found to have an increased likelihood of being in the sequelae cohort compared to the infertile cohort with an odds ratio of 16.3 (95% c.i. 1.65-160), with 95% specificity and 46% sensitivity (0.19-0.74). The peptide 11 ELISA has the potential to be further developed as a screening tool for use during the early IVF work up and provides proof of concept that there may be further peptide antigens which could be identified using bioinformatics and screening approaches. © 2013 The Authors.

Starkey, MR, Essilfie, AT, Horvat, JC, Kim, RY, Nguyen, DH, Beagley, KW, Mattes, J, Foster, PS & Hansbro, PM 2013, 'Constitutive production of IL-13 promotes early-life Chlamydia respiratory infection and allergic airway disease', Mucosal Immunology, vol. 6, no. 3, pp. 569-579.
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Starkey, MR, Jarnicki, AG, Essilfie, A-T, Gellatly, SL, Kim, RY, Brown, AC, Foster, PS, Horvat, JC & Hansbro, PM 2013, 'Murine models of infectious exacerbations of airway inflammation', Current Opinion in Pharmacology, vol. 13, no. 3, pp. 337-344.
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STARKEY, MR, NGUYEN, DH, KIM, RY, NAIR, PM, BROWN, AC, ESSIFIE, A-T, HORVAT, JC & HANSBRO, PM 2013, 'Programming of the Lung in Early Life by Bacterial Infections Predisposes to Chronic Respiratory Disease', Clinical Obstetrics & Gynecology, vol. 56, no. 3, pp. 566-576.
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Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, McPhedran, RC & de Sterke, CM 2013, 'Absorption enhancing proximity effects in aperiodic nanowire arrays', OPTICS EXPRESS, vol. 21, no. 22, pp. A964-A969.
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Aperiodic Nanowire (NW) arrays have higher absorption than equivalent periodic arrays, making them of interest for photovoltaic applications. An inevitable property of aperiodic arrays is the clustering of some NWs into closer proximity than in the equivalent periodic array. We focus on the modes of such clusters and show that the reduced symmetry associated with cluster formation allows external coupling into modes which are dark in periodic arrays, thus increasing absorption. To exploit such modes fully, arrays must include tightly clustered NWs that are unlikely to arise from fabrication variations but must be created intentionally. © 2013 Optical Society of America.

Su, D & Wang, G 2013, 'Single-Crystalline Bilayered V₂O₅ Nanobelts for High-Capacity Sodium-Ion Batteries', ACS Nano, vol. 7, no. 12, pp. 11218-11226.
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Single-crystalline bilayered vanadium oxide nanobelts were synthesized by a simple solvothermal method. FESEM and AFM analyses identified the nanobelt morphology of the as-prepared vanadium oxide with a rectangular cross-section and a thickness of approximately 50 nm. XRD and TEM characterizations revealed the presence of a large (001) interlayer spacing (∼11.53 Å), which can accommodate Na-ion insertion and extraction. When applied as cathode materials in Na-ion batteries, vanadium oxide nanobelts exhibited a high capacity of 231.4 mA h g-1 at a current density of 80 mA g-1. This corresponds to the theoretical capacity to form Na2V 2O5 on Na-ion insertion. Vanadium oxide nanobelts also demonstrated an excellent high-rate performance and a satisfactory cyclability. These superior electrochemical performances could be ascribed to the unique bilayered vanadium oxide nanobelts with dominantly exposed {100} crystal planes, which provide large interlayer spacing for facile Na-ion insertion/extraction. Single-crystalline bilayered vanadium oxide nanobelts could be promising cathode materials for high-performance Na-ion batteries. © 2013 American Chemical Society.

Su, D, Ahn, H-J & Wang, G 2013, 'Hydrothermal synthesis of alpha-MnO2 and beta-MnO2 nanorods as high capacity cathode materials for sodium ion batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 1, no. 15, pp. 4845-4850.
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Two types of MnO2 polymorphs, α-MnO2 and β-MnO2 nanorods, have been synthesized by a hydrothermal method. Their crystallographic phases, morphologies, and crystal structures were characterized by XRD, FESEM and TEM analysis. Different exposed crystal planes have been identified by TEM. The electrochemical properties of α-MnO 2 and β-MnO2 nanorods as cathode materials in Na-ion batteries were evaluated by galvanostatic charge/discharge testing. Both α-MnO2 and β-MnO2 nanorods achieved high initial sodium ion storage capacities of 278 mA h g-1 and 298 mA h g-1, respectively. β-MnO2 nanorods exhibited a better electrochemical performance such as good rate capability and cyclability than that of α-MnO2 nanorods, which could be ascribed to a more compact tunnel structure of β-MnO2 nanorods. Furthermore, the one-dimensional architecture of nanorods could also contribute to facile sodium ion diffusion in the charge and discharge process. © The Royal Society of Chemistry 2013.

Su, D, Ahn, H-J & Wang, G 2013, 'One-dimensional magnetite Fe3O4 nanowires as electrode material for Li-ion batteries with improved electrochemical performance', Journal of Power Sources, vol. 244, no. 1, pp. 742-746.
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One-dimensional magnetite (3O4) nanowires were synthesized by the low temperature hydrothermal method. The as-prepared 3O4 nanowires were systematically characterized by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy. X-ray diffraction and transmission electron microscopy have confirmed the cubic structure of 3O4 nanowires with a space group of Fd3m. Electrochemical properties of 3O4 nanowires were tested as anodes in lithium-ion cells by cyclic voltammetry and galvanostatic charge/discharge. 3O4 nanowires exhibited an excellent reversible lithium storage capacity and a satisfactory cycling performance. © 2012 Elsevier B.V. All rights reserved.

Su, D, Ahn, H-J & Wang, G 2013, 'SnO2@graphene nanocomposites as anode materials for Na-ion batteries with superior electrochemical performance', Chemical Communications, vol. 49, no. 30, pp. 3131-3131.
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An in situ hydrothermal synthesis approach has been developed to prepare SnO2@graphene nanocomposites. The nanocomposites exhibited a high reversible sodium storage capacity of above 700 mA h g-1 and excellent cyclability for Na-ion batteries. In particular, they also demonstrated a good high rate capability for reversible sodium storage. © 2013 The Royal Society of Chemistry.

Su, D, Ahn, H-J & Wang, G 2013, 'β-MnO2 nanorods with exposed tunnel structures as high-performance cathode materials for sodium-ion batteries', NPG Asia Materials, vol. 5, no. 11, pp. e70-e70.
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Sodium-ion batteries are being considered as a promising system for stationary energy storage and conversion, owing to the natural abundance of sodium. It is important to develop new cathode and anode materials with high capacities for sodium-ion batteries. Herein, we report the synthesis of β-MnO2 nanorods with exposed tunnel structures by a hydrothermal method. The as-prepared β-MnO2 nanorods have exposed {111} crystal planes with a high density of (1 × 1) tunnels, which leads to facile sodium ion (Na-ion) insertion and extraction. When applied as cathode materials in sodium-ion batteries, β-MnO2 nanorods exhibited good electrochemical performance with a high initial Na-ion storage capacity of 350 mAh g-1. β-MnO2 nanorods also demonstrated a satisfactory high-rate capability as cathode materials for sodium-ion batteries.

Su, D, Fu, H, Jiang, X & Wang, G 2013, 'ZnO nanocrystals with a high percentage of exposed reactive facets for enhanced gas sensing performance', Sensors and Actuators B: Chemical, vol. 186, pp. 286-292.
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Zinc oxide single crystals with a high percentage of exposed {4 2̄ 2̄ 3̄} reactive facet were prepared by a facile hydrothermal route. X-ray diffraction, field emission scanning electron microscopy, and high resolution transmission microscopy confirmed the faceted single crystal structure. Through the density functional theory (DFT) calculations, it is validated that the {4 2̄ 2̄ 3̄} surface of ZnO crystals has high surface energy. When used as a sensing material in gas sensors, ZnO crystals with dominating exposed {4 2̄ 2̄ 3̄} planes exhibited a superior sensitivity toward toxic and flammable gases. © 2013 Elsevier B.V.

Su, D, Kim, H-S, Kim, W-S & Wang, G 2013, 'A study of PtxCoy alloy nanoparticles as cathode catalysts for lithium-air batteries with improved catalytic activity', Journal of Power Sources, vol. 244, pp. 488-493.
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A series of PtxCoy (x:y = 4, 2, 1, and 0.5) alloy nanoparticles deposited on Vulcan XC-72 carbon was prepared through a chemical reduction method. The structures and morphologies of the as-prepared nanoparticles were characterized by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy, which revealed the formation of Pt-Co alloys during the co-reduction process. PtxCo y alloy nanoparticles were applied as catalysts in lithium-air batteries. Through electrochemical testing, we found that the Pt based alloy nanocatalysts significantly increased the specific capacity of lithium-air batteries and the increase of Co content in PtxCoy alloy nanoparticles further enhanced the catalytic activity. This result illustrated that PtxCoy alloy nanoparticles could be used as an efficient catalyst material for lithium-air batteries with the feature of much reduced cost, but drastically increased catalytic activity. © 2012 Elsevier B.V. All rights reserved.

Su, D, Wang, C, Ahn, H & Wang, G 2013, 'Octahedral tin dioxide nanocrystals as high capacity anode materials for Na-ion batteries', Physical Chemistry Chemical Physics, vol. 15, no. 30, pp. 12543-12543.
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Single crystalline SnO2 nanocrystals (∼60 nm in size) with a uniform octahedral shape were synthesised using a hydrothermal method. Their phase and morphology were characterized by XRD and FESEM observation. TEM and HRTEM analyses identified that SnO2 octahedral nanocrystals grow along the [001] direction, consisting of dominantly exposed {221} high energy facets. When applied as anode materials for Na-ion batteries, SnO2 nanocrystals exhibited high reversible sodium storage capacity and excellent cyclability (432 mA h g-1 after 100 cycles). In particular, SnO 2 nanocrystals also demonstrated a good high rate performance. Ex situ TEM analysis revealed the reaction mechanism of SnO2 nanocrystals for reversible Na ion storage. It was found that Na ions first insert into SnO2 crystals at the high voltage plateau (from 3 V to ∼0.8 V), and that the exposed (1 × 1) tunnel-structure could facilitate the initial insertion of Na ions. Subsequently, Na ions react with SnO2 to form NaxSn alloys and Na2O in the low voltage range (from ∼0.8 V to 0.01 V). The superior cyclability of SnO 2 nanocrystals could be mainly ascribed to the reversible Na-Sn alloying and de-alloying reactions. Furthermore, the reduced Na2O 'matrix' may help retard the aggregation of tin nanocrystals, leading to an enhanced electrochemical performance. This journal is © the Owner Societies 2013.

Su, D, Wang, C, Ahn, H & Wang, G 2013, 'Single Crystalline Na_0.7MnO₂ Nanoplates as Cathode Materials for Sodium‐Ion Batteries with Enhanced Performance', Chemistry – A European Journal, vol. 19, no. 33, pp. 10884-10889.
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AbstractSingle crystalline rhombus‐shaped Na0.7MnO2 nanoplates have been synthesized by a hydrothermal method. TEM and HRTEM analyses revealed that the Na0.7MnO2 single crystals predominantly exposed their (100) crystal plane, which is active for Na+‐ion insertion and extraction. When applied as cathode materials for sodium‐ion batteries, Na0.7MnO2 nanoplates exhibited a high reversible capacity of 163 mA h g−1, a satisfactory cyclability, and a high rate performance. The enhanced electrochemical performance could be ascribed to the predominantly exposed active (100) facet, which could facilitate fast Na+‐ion insertion/extraction during the discharge and charge process.

Su, DW, Liu, H, Ahn, HJ & Wang, GX 2013, 'Synthesis of Highly Ordered Mesoporous Co3O4 for Gas Sensing', JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, vol. 13, no. 5, pp. 3354-3359.
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Highly ordered mesoporous Co3O4 nanostructures were prepared using SBA-15 silica as hard templates. The mesoporous structures were characterized by X-ray diffraction, high resolution transmission electron microscopy, and N2 adsorption/desorption isotherm analysis. The results demonstrated that the as-prepared mesoporous Co3O4 has an ordered P6mm symmetric mesoporous structure. The optical absorption properties of the mesoporous Co3O4 were investigated by UV-Vis spectroscopy and the results indicate that the mesoporous Co 3O4 materials are semiconducting with direct band gaps of 2, 1.385 and 0.38 eV. The gas-sensing performance of the mesoporous Co 3O4 was tested towards a series of typical solvents. They demonstrated a good sensing performance towards these vapour with rapid response and high sensitivity at low operating temperature. Copyright © 2013 American Scientific Publishers.

Suggett, DJ, Dong, LF, Lawson, T, Lawrenz, E, Torres, L & Smith, DJ 2013, 'Light availability determines susceptibility of reef building corals to ocean acidification', Coral Reefs, vol. 32, no. 2, pp. 327-337.
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Elevated seawater pCO2, and in turn ocean acidification (OA), is now widely acknowledged to reduce calcification and growth of reef building corals. As with other environmental factors (e. g., temperature and nutrients), light availability fundamentally regulates calcification and is predicted to change for future reef environments alongside elevated pCO2 via altered physical processes (e. g., sea level rise and turbidity); however, any potential role of light in regulating the OA-induced reduction of calcification is still unknown. We employed a multifactorial growth experiment to determine how light intensity and pCO2 together modify calcification for model coral species from two key genera, Acropora horrida and Porites cylindrica, occupying similar ecological niches but with different physiologies. We show that elevated pCO2 (OA)-induced losses of calcification in the light (GL) but not darkness (GD) were greatest under low-light growth conditions, in particular for A. horrida. High-light growth conditions therefore dampened the impact of OA upon GL but not GD. Gross photosynthesis (PG) responded in a reciprocal manner to GL suggesting OA-relieved pCO2 limitation of PG under high-light growth conditions to effectively enhance GL. A multivariate analysis of past OA experiments was used to evaluate whether our test species responses were more widely applicable across their respective genera. Indeed, the light intensity for growth was identified as a significant factor influencing the OA-induced decline of calcification for species of Acropora but not Porites. Whereas low-light conditions can provide a refuge for hard corals from thermal and light stress, our study suggests that lower light availability will potentially increase the susceptibility of key coral species to OA. © 2012 Springer-Verlag Berlin Heidelberg.

Sukhorukov, AA, Solntsev, AS & Sipe, JE 2013, 'Classical simulation of squeezed light in optical waveguide arrays', Physical Review A, vol. 87, no. 5.
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Sun, B, Munroe, P & Wang, G 2013, 'Ruthenium nanocrystals as cathode catalysts for lithium-oxygen batteries with a superior performance', SCIENTIFIC REPORTS, vol. 3.
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The key factor to improve the electrochemical performance of Li-O 2 batteries is to find effective cathode catalysts to promote the oxygen reduction and oxygen evolution reactions. Herein, we report the synthesis of an effective cathode catalyst of ruthenium nanocrystals supported on carbon black substrate by a surfactant assisting method. The as-prepared ruthenium nanocrystals exhibited an excellent catalytic activity as cathodes in Li-O 2 batteries with a high reversible capacity of about 9,800 mAh g -1, a low charge-discharge over-potential (about 0.37 V), and an outstanding cycle performance up to 150 cycles (with a curtaining capacity of 1,000 mAh g-1). The electrochemical testing shows that ruthenium nanocrystals can significantly reduce the charge potential comparing to carbon black catalysts, which demonstrated that ruthenium based nanomaterials could be effective cathode catalysts for high performance lithium-O2 batteries.

Sun, B, Wang, Y, Wang, B, Kim, H-S, Kim, W-S & Wang, G 2013, 'Porous LiFePO4/C Microspheres as High-Power Cathode Materials for Lithium Ion Batteries', JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, vol. 13, no. 5, pp. 3655-3659.
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Porous LiFePO4/C microspheres were synthesized by a novel hydrothermal reaction combined with high-temperature calcinations. The morphology of the prepared material was investigated by fieldemission scanning electron microscopy. Porous microspheres with diameters around 1-3 μm were obtained, which consisting of primary LiFePO4 nanoparticles. The electrochemical performances of the as-prepared LiFePO4 microspheres were evaluated by cyclic voltammetry, electrochemical impedance spectroscopy and galvanostatic charge-discharge cycling. The carbon coated LiFePO4 microspheres showed lower polarization, higher rate capability, and better cycling stability than that of pristine LiFePO4 microspheres, indicating the potential application as the cathode material for high-power lithium ion batteries. Copyright © 2013 American Scientific Publishers.

Sun, B, Zhang, J, Munroe, P, Ahn, H-J & Wang, G 2013, 'Hierarchical NiCo2O4 nanorods as an efficient cathode catalyst for rechargeable non-aqueous Li-O-2 batteries', ELECTROCHEMISTRY COMMUNICATIONS, vol. 31, pp. 88-91.
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NiCo2O4 nanorods were synthesized by a hydrothermal method followed by low temperature calcination. FESEM and TEM analyses confirmed that the as-prepared materials consist of a hierarchical nanorod structure. When applied as cathode catalysts in rechargeable Li-O2 batteries, NiCo2O4 nanorods exhibited a superior catalytic activity, including low charge over-potential, high discharge capacity and high-rate capability. © 2013 Elsevier B.V.

Sun, S, Kjelleberg, S & McDougald, D 2013, 'Relative Contributions of Vibrio Polysaccharide and Quorum Sensing to the Resistance of Vibrio cholerae to Predation by Heterotrophic Protists', PLoS ONE, vol. 8, no. 2, pp. e56338-e56338.
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Tan, SY-Y, Chua, S-L, Chen, Y, Rice, SA, Kjelleberg, S, Nielsen, TE, Yang, L & Givskov, M 2013, 'Identification of Five Structurally Unrelated Quorum-Sensing Inhibitors of Pseudomonas aeruginosa from a Natural-Derivative Database', Antimicrobial Agents and Chemotherapy, vol. 57, no. 11, pp. 5629-5641.
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ABSTRACT Bacteria communicate by means of small signal molecules in a process termed quorum sensing (QS). QS enables bacteria to organize their activities at the population level, including the coordinated secretion of virulence factors. Certain small-molecule compounds, known as quorum-sensing inhibitors (QSIs), have been shown to effectively block QS and subsequently attenuate the virulence of Pseudomonas aeruginosa , as well as increasing its susceptibility to both antibiotics and the immune system. In this study, a structure-based virtual screening (SB-VS) approach was used for the discovery of novel QSI candidates. Three-dimensional structures of 3,040 natural compounds and their derivatives were obtained, after which molecular docking was performed using the QS receptor LasR as a target. Based on docking scores and molecular masses, 22 compounds were purchased to determine their efficacies as quorum-sensing inhibitors. Using a live reporter assay for quorum sensing, 5 compounds were found to be able to inhibit QS-regulated gene expression in P. aeruginosa in a dose-dependent manner. The most promising compound, G1, was evaluated by isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis, and it was found to significantly affect the abundance of 46 proteins (19 were upregulated; 27 were downregulated) in P. aeruginosa PAO1. It specifically reduced the expression of several quorum-sensing-regulated virul...

Tan, X, Alrashdan, YA, Alkhouri, H, Oliver, BGG, Armour, CL & Hughes, JM 2013, 'Airway smooth muscle CXCR3 ligand production: regulation by JAK-STAT1 and intracellular Ca2+', AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY, vol. 304, no. 11, pp. L790-L802.
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In asthma, airway smooth muscle (ASM) chemokine (C-X-C motif) receptor 3 (CXCR3) ligand production may attract mast cells or T lymphocytes to the ASM, where they can modulate ASM functions. In ASM cells (ASMCs) from people with or without asthma, we aimed to investigate JAK-STAT1, JNK, and Ca2+ involvement in chemokine (C-X-C motif) ligand (CXCL)10 and CXCL11 production stimulated by interferon-γ, IL-1β, and TNF-α combined (cytomix). Confluent, growth-arrested ASMC were treated with inhibitors for pan-JAK (pyridone-6), JAK2 (AG-490), JNK (SP-600125), or the sarco(endo)plasmic reticulum Ca2+ATPase (SERCA) pump (thapsigargin), Ca2+ chelator (BAPTA-AM), or vehicle before and during cytomix stimulation for up to 24 h. Signaling protein activation as well as CXCL10/CXCL11 mRNA and protein production were examined using immunoblot analysis, real-time PCR, and ELISA, respectively. Cytomix-induced STAT1 activation was lower and CXCR3 ligand mRNA production was more sensitive to pyridone-6 and AG-490 in asthmatic than nonasthmatic ASMCs, but CXCL10/CXCL11 release was inhibited by the same proportion. Neither agent caused additional inhibition of release when used in combination with the JNK inhibitor SP-600125. Conversely, p65 NF-κB activation was higher in asthmatic than nonasthmatic ASMCs. BAPTA-AM abolished early CXCL10/CXCL11 mRNA production, whereas thapsigargin reduced it in asthmatic cells and inhibited CXCL10/CXCL11 release by both ASMC types. Despite these inhibitory effects, neither Ca2+ agent affected early activation of STAT1, JNK, or p65 NF-κB. In conclusion, intracellular Ca2+ regulated CXCL10/CXCL11 production but not early activation of the signaling molecules involved. In asthma, reduced ASM STAT1-JNK activation, increased NF-κB activation, and altered Ca2+ handling may contribute to rapid CXCR3 ligand production and enhanced inflammatory cell recruitment. © 2013 the American Physiological Society.

Tan, Y, Lao, W, Xiao, L, Wang, Z, Xiao, W, Kamal, MA, Seale, JP & Qu, X 2013, 'Managing the Combination of Nonalcoholic Fatty Liver Disease and Metabolic Syndrome with Chinese Herbal Extracts in High-Fat-Diet Fed Rats', Evidence-Based Complementary and Alternative Medicine, vol. 2013, no. 1, pp. 1-10.
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Nonalcoholic fatty liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome (MetS). The aim of the study was to evaluate the effects of Chinese herbal extracts fromSalvia miltiorrhizaandGardenia jasminoides(SGE) on the combination of NAFLD and MetS induced by a high-fat diet (HFD) in rats. After 6 weeks of HFD feeding, rats (n=10each group) were treated with saline, rosiglitazone (RSG), and SGE for 4 weeks. HFD rats were obese, hyperinsulinemic, hyperlipidemic and increased hepatic enzymes with the histological images of NAFLD. Treatment with SGE significantly reduced serum triglycerides (TG), nonesterified fatty acids and enhanced insulin sensitivity, and ameliorated the elevated serum hepatic enzymes compared with HFD-saline group. SGE treatment also attenuated hepatic TG by 18.5% (P<0.05). Histological stains showed SGE decreased lipids droplets in hepatocytes (P<0.05) and normalized macrovesicular steatosis in HFD rats. Significant reduction of TNF-αand IL6 in adipose tissue was detected in SGE treated rats. The anti-inflammatory action may be, at least in part, the mechanism of SGE on MetS associated with NAFLD. This study discovered that SGE is capable of managing metabolic and histological abnormalities of NAFLD and MetS. SGE may be an optimal treatment for the combination of NAFLD and MetS.

Tapiolas, DM, Raina, J-B, Lutz, A, Willis, BL & Motti, CA 2013, 'Direct measurement of dimethylsulfoniopropionate (DMSP) in reef-building corals using quantitative nuclear magnetic resonance (qNMR) spectroscopy', Journal of Experimental Marine Biology and Ecology, vol. 443, pp. 85-89.
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Reef building corals are among the largest producers of dimethylsulfoniopropionate (DMSP), a sulfur molecule synthesized by their endosymbiotic dinoflagellates in the genus Symbiodinium. DMSP is potentially involved in important physiological and ecological processes in corals, but investigating the functional role of this molecule requires rapid and accurate quantification techniques. Here we introduce a simple method enabling direct quantification of DMSP and one of its breakdown products acrylate using quantitative nuclear magnetic resonance (qNMR) spectroscopy. The method was tested on a range of coral genera and presents a number of advantages over currently used quantification techniques, including simultaneous and direct quantification of multiple molecules from the same extract, and rapid processing with high reproducibility enabling analyses of large numbers of samples in short time periods. The method was successfully applied to environmental samples and provides the first baseline information on diel variation of DMSP and acrylate concentrations in the coral Acropora millepora.

Taudte, RV, Beavis, A, Wilson-Wilde, L, Roux, C, Doble, P & Blanes, L 2013, 'A portable explosive detector based on fluorescence quenching of pyrene deposited on coloured wax-printed mu PADs', LAB ON A CHIP, vol. 13, no. 21, pp. 4164-4172.
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A new technique for the detection of explosives has been developed based on fluorescence quenching of pyrene on paper-based analytical devices (µPADs). Wax barriers were generated (150 °C, 5 min) using ten different colours. Magenta was found as the most suitable wax colour for the generation of the hydrophobic barriers with a nominal width of 120 µm resulting in fully functioning hydrophobic barriers. One microliter of 0.5 mg mL-1 pyrene dissolved in an 80:20 methanolwater solution was deposited on the hydrophobic circle (5 mm diameter) to produce the active microchip device. Under ultra-violet (UV) illumination, ten different organic explosives were detected using the µPAD, with limits of detection ranging from 100600 ppm. A prototype of a portable battery operated instrument using a 3 W power UV light-emitting-diode (LED) (365 nm) and a photodiode sensor was also built and evaluated for the successful automatic detection of explosives and potential application for field-based screening.

Tekwe, CD, Lei, J, Yao, K, Rezaei, R, Li, X, Dahanayaka, S, Carroll, RJ, Meininger, CJ, Bazer, FW & Wu, G 2013, 'Oral administration of interferon tau enhances oxidation of energy substrates and reduces adiposity in Zucker diabetic fatty rats', BioFactors, vol. 39, no. 5, pp. 552-563.
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AbstractMale Zucker diabetic fatty (ZDF) rats were used to study effects of oral administration of interferon tau (IFNT) in reducing obesity. Eighteen ZDF rats (28 days of age) were assigned randomly to receive 0, 4, or 8 μg IFNT/kg body weight (BW) per day (n = 6/group) for 8 weeks. Water consumption was measured every two days. Food intake and BW were recorded weekly. Energy expenditure in 4‐, 6‐, 8‐, and 10‐week‐old rats was determined using indirect calorimetry. Starting at 7 weeks of age, urinary glucose, and ketone bodies were tested daily. Rates of glucose and oleate oxidation in liver, brown adipose tissue, and abdominal adipose tissue, as well as leucine catabolism in skeletal muscle, and lipolysis in white and brown adipose tissues were greater for rats treated with 8 μg IFNT/kg BW/day in comparison with control rats. Treatment with 8 μg IFNT/kg BW/day increased heat production, reduced BW gain and adiposity, ameliorated fatty liver syndrome, delayed the onset of diabetes, and decreased concentrations of glucose, free fatty acids, triacylglycerol, cholesterol, and branched‐chain amino acids in plasma, compared with control rats. Oral administration of 8 µg IFNT/kg BW/day ameliorated oxidative stress in skeletal muscle, liver, and adipose tissue, as indicated by decreased ratios of oxidized glutathione to reduced glutathione and increased concentrations of tetrahydrobiopterin. These results indicate that IFNT stimulates oxidation of energy substrates and reduces obesity in ZDF rats and may have broad important implications for preventing and treating obesity‐related diseases in mammals. © 2013 BioFactors 39(5):552–563, 2013

Thivierge, K, Cotton, S, Schaefer, DA, Riggs, MW, To, J, Lund, ME, Robinson, MW, Dalton, JP & Donnelly, SM 2013, 'Cathelicidin-like Helminth Defence Molecules (HDMs): Absence of Cytotoxic, Anti-microbial and Anti-protozoan Activities Imply a Specific Adaptation to Immune Modulation', PLOS NEGLECTED TROPICAL DISEASES, vol. 7, no. 7, pp. 1-14.
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Host defence peptides (HDPs) are expressed throughout the animal and plant kingdoms. They have multifunctional roles in the defence against infectious agents of mammals, possessing both bactericidal and immune-modulatory activities. We have identified a novel family of molecules secreted by helminth parasites (helminth defence molecules; HDMs) that exhibit similar structural and biochemical characteristics to the HDPs. Here, we have analyzed the functional activities of four HDMs derived from Schistosoma mansoni and Fasciola hepatica and compared them to human, mouse, bovine and sheep HDPs. Unlike the mammalian HDPs the helminth-derived HDMs show no antimicrobial activity and are non-cytotoxic to mammalian cells (macrophages and red blood cells). However, both the mammalian- and helminth-derived peptides suppress the activation of macrophages by microbial stimuli and alter the response of B cells to cytokine stimulation. Therefore, we hypothesise that HDMs represent a novel family of HDPs that evolved to regulate the immune responses of their mammalian hosts by retaining potent immune modulatory properties without causing deleterious cytotoxic effects. © 2013 Thivierge et al.

Thorburn, AN, Brown, AC, Nair, PM, Chevalier, N, Foster, PS, Gibson, PG & Hansbro, PM 2013, 'Pneumococcal Components Induce Regulatory T Cells That Attenuate the Development of Allergic Airways Disease by Deviating and Suppressing the Immune Response to Allergen', The Journal of Immunology, vol. 191, no. 8, pp. 4112-4120.
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Abstract The induction of regulatory T cells (Tregs) to suppress aberrant inflammation and immunity has potential as a therapeutic strategy for asthma. Recently, we identified key immunoregulatory components of Streptococcus pneumoniae, type 3 polysaccharide and pneumolysoid (T+P), which suppress allergic airways disease (AAD) in mouse models of asthma. To elucidate the mechanisms of suppression, we have now performed a thorough examination of the role of Tregs. BALB/c mice were sensitized to OVA (day 0) i.p. and challenged intranasal (12–15 d later) to induce AAD. T+P was administered intratracheally at the time of sensitization in three doses (0, 12, and 24 h). T+P treatment induced an early (36 h–4 d) expansion of Tregs in the mediastinal lymph nodes, and later (12–16 d) increases in these cells in the lungs, compared with untreated allergic controls. Anti-CD25 treatment showed that Treg-priming events involving CD25, CCR7, IL-2, and TGF-β were required for the suppression of AAD. During AAD, T+P-induced Tregs in the lungs displayed a highly suppressive phenotype and had an increased functional capacity. T+P also blocked the induction of IL-6 to prevent the Th17 response, attenuated the expression of the costimulatory molecule CD86 on myeloid dendritic cells (DCs), and reduced the number of DCs carrying OVA in the lung and mediastinal lymph nodes. Therefore, bacterial components (T+P) drive the differentiation of highly suppressive Tregs, which suppress the Th2 response, prevent the Th17 response and disable the DC response resulting in the effective suppression of AAD.

Ting, SRS, Whitelock, JM, Tomic, R, Gunawan, C, Teoh, WY, Amal, R & Lord, MS 2013, 'Cellular uptake and activity of heparin functionalised cerium oxide nanoparticles in monocytes', Biomaterials, vol. 34, no. 17, pp. 4377-4386.
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Cerium oxide nanoparticles (nanoceria) are effective in scavenging intracellular reactive oxygen species (ROS). In this study nanoceria synthesized by flame spray pyrolysis (dXRD ¼ 12 nm) were functionalised with heparin via an organosilane linker, 3-aminopropyltriethoxysilane. Nanoceria were functionalised with approximately 130 heparin molecules per nanoparticle as determined by thermo gravimetric analysis. Heparin functionalised nanoceria were more effectively internalised by the human monocyte cell line, U937, and U937 cells that had been activated with phorbol 12 myristate 13-acetate (PMA) than bare nanoceria. The heparin functionalised nanoceria were also more effective in scavenging ROS than nanoceria in both activated and unactivated U937 cells. Heparin coupled nanoceria were found to be biologically active due to their ability to bind fibroblast growth factor 2 and signal through FGF receptor 1. Additionally, the heparin-coupled nanoceria, once internalised by the cells, were found to be degraded by 48 h. Together these data demonstrated that heparin enhanced the biological properties of nanoceria in terms of cellular uptake and ROS scavenging, while the nanoceria themselves were more effective at delivering heparin intracellularly than exposing cells to heparin in solution.

Ton-That, C, Nguyen, T-P & Dan, Y 2013, 'Enhanced photoluminescence of polyfluorene by incorporation of Al-doped ZnO nanoparticles', THIN SOLID FILMS, vol. 538, pp. 85-88.
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Photoluminescent and structural properties of nanocomposite films consisting of green-emitting polyfluorene (PF) and Al-doped ZnO (AZO) nanoparticles were investigated. Topographical analysis shows that AZO nanoparticles can be homogeneously dispersed in PF films with less than 10 wt.% AZO. Photoluminescence of the composite films was investigated under wavelength selective excitation of AZO. Photoexcitation with laser energy below the AZO bandgap produces a slight increase in the PF emission intensity with increasing AZO concentration, accompanied by a spectral blueshift. These effects are attributed to separation of polymer chains and twisting of the PF backbone as revealed by Raman spectroscopy. On the other hand, photoexcitation above the AZO bandgap shows a remarkable enhancement, with the intensity at 5-10 wt.% AZO being three times greater than that of pure PF. The luminescence enhancement is attributed to the efficient transfer of energy from AZO nanoparticles to PF. © 2013 Elsevier B.V. All rights reserved.

Tooze, JA, Troiano, RP, Carroll, RJ, Moshfegh, AJ & Freedman, LS 2013, 'A Measurement Error Model for Physical Activity Level as Measured by a Questionnaire With Application to the 1999-2006 NHANES Questionnaire', American Journal of Epidemiology, vol. 177, no. 11, pp. 1199-1208.
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Systematic investigations into the structure of measurement error of physical activity questionnaires are lacking. We propose a measurement error model for a physical activity questionnaire that uses physical activity level (the ratio of total energy expenditure to basal energy expenditure) to relate questionnaire-based reports of physical activity level to true physical activity levels. The 1999-2006 National Health and Nutrition Examination Survey physical activity questionnaire was administered to 433 participants aged 40-69 years in the Observing Protein and Energy Nutrition (OPEN) Study (Maryland, 1999-2000). Valid estimates of participants' total energy expenditure were also available from doubly labeled water, and basal energy expenditure was estimated from an equation; the ratio of those measures estimated true physical activity level ('truth'). We present a measurement error model that accommodates the mixture of errors that arise from assuming a classical measurement error model for doubly labeled water and a Berkson error model for the equation used to estimate basal energy expenditure. The method was then applied to the OPEN Study. Correlations between the questionnaire-based physical activity level and truth were modest (r = 0.32-0.41); attenuation factors (0.43-0.73) indicate that the use of questionnaire-based physical activity level would lead to attenuated estimates of effect size. Results suggest that sample sizes for estimating relationships between physical activity level and disease should be inflated, and that regression calibration can be used to provide measurement error-adjusted estimates of relationships between physical activity and disease. © 2013 Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health 2013.

Torpy, FR, Irga, PJ, Brennan, J & Burchett, MD 2013, 'Do indoor plants contribute to the aeromycota in city buildings?', AEROBIOLOGIA, vol. 29, no. 3, pp. 321-331.
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Many studies have focused on the sources of fungal contamination in indoor spaces. Pathogenic fungi have been detected in the potting mix of indoor plants; however, it is unclear if plants in indoor work spaces make qualitative or quantitative contributions to the aeromycota within buildings. The current work represents a field study to determine, under realistic office conditions, whether indoor plants make a contribution to the airborne aeromycota. Fifty-five offices, within two buildings in Sydney's central business district, were studied over two seasonal periods: autumn and spring. We found that indoor plant presence made no significant difference to either indoor mould spore counts or their species composition. No seasonal differences occurred between autumn and spring samples. Indoor spore loads were significantly lower than outdoor levels, demonstrating the efficiency of the heating, ventilation and air conditioning systems in the buildings sampled. Neither the number of plants nor the species of plant used had an influence on spore loads; however, variations of those two variables offer potential for further studies. We conclude that conservative numbers of indoor plants make no substantial contribution to building occupants exposure to fungi. © 2012 Springer Science+Business Media Dordrecht.

Torpy, FR, Irga, PJ, Moldovan, D, Tarran, J & Burchett, MD 2013, 'Characterization and Biostimulation of benzene biodegradation in the potting-mix of indoor plants', Journal of Applied Horticulture, vol. 15, no. 1, pp. 10-15.
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Over 900 volatile organic compounds (VOCs) have been detected in indoor air, where they cause acute and chronic health problems to building occupants. Potted-plants can significantly reduce VOC levels in indoor air, the root-zone bacteria of the potting mix effecting most of the VOC biodegradation. In this study, a baseline community level physiological profile (CLPP) was established for the potting mix bacteria of the indoor plant species, Spathiphyllum wallisii 'Petite', using Biolog EcoPlates, to provide information on the functional abilities of this community. Changes in the CLPP resulting from benzene exposure were then determined and following the identification of the carbon sources associated with changes in the CLPP, biostimulant solutions were formulated and applied to fresh potted-plant specimens. Biostimulation of benzene removal was observed, with increases in removal rates of about 15%, providing proof-of-concept for the biostimulation of this process. The findings further elucidate the mechanisms of bacterial activity associated with removal of indoor airborne benzene, and could be applied to increase VOC biodegradation rates, augmenting the uses of indoor plants in improving building environmental quality.

Torpy, FR, Irga, PJ, Moldovan, D, Tarran, J & Burchett, MD 2013, 'Characterization and biostimulation of benzene biodegradation in the potting-mix of indoor plants', Journal of Applied Horticulture, vol. 15, no. 01, pp. 10-15.
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Trivedi, N, Gupta, V, Reddy, CRK & Jha, B 2013, 'Detection of ionic liquid stable cellulase produced by the marine bacterium Pseudoalteromonas sp. isolated from brown alga Sargassum polycystum C. Agardh', Bioresource Technology, vol. 132, pp. 313-319.
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Trivedi, N, Gupta, V, Reddy, CRK & Jha, B 2013, 'Enzymatic hydrolysis and production of bioethanol from common macrophytic green alga Ulva fasciata Delile', Bioresource Technology, vol. 150, pp. 106-112.
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Umsumarng, S, Pintha, K, Pitchakarn, P, Sastraruji, K, Sastraruji, T, Ung, AT, Jatisatienr, A, Pyne, SG & Limtrakul, P 2013, 'Inhibition of P-Glycoprotein Mediated Multidrug Resistance by Stemofoline Derivatives', CHEMICAL & PHARMACEUTICAL BULLETIN, vol. 61, no. 4, pp. 399-404.
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Resistance to chemotherapy in cancer patients has been correlated to the overexpression of the ATP-binding cassette (ABC) drug transporters including P-glycoprotein (P-gp) that actively efflux chemotherapeutic drugs from cancer cells. We examined the mutidrug resistance reversing property of stemofoline derivatives in drug-resistance human cervical carcinoma (KB-V1) and human leukemic (K562/Adr) cell lines that overexpress P-gp. Didehydrostemofoline and eleven of its derivatives were synthesized and the cytotoxicity and their effect on doxorubicin, vinblastine and paclitaxel sensitivity in drug resistant (KB-V1 and K562/Adr) and drug sensitive (KB-3-1 and K562) cell lines by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay were determined. We found that three out of the twelve stemofoline derivatives including OH-A1, NH-B6 and NH-D6 showed commitment efficiency to increase sensitivity to doxorubicin, vinblastine and paclitaxel in KB-V1 cells and increase sensitivity to doxorubicin, and paclitaxel in K562/Adr cells whereas the effects have not been seen in their parental sensitive cancer cell lines (KB-3-1 and K562). These results indicate that stemofoline derivatives reversed P-gp-mediated multidrug resistance in vitro, and thus could be developed as effective. chemosensitizers to treat multidrug-resistant cancers. The molecular mechanism of modulation of P-gp would be further determined.

Ung, AT, Pyne, SG, Bischoff, F, Lesage, ASJ, Skelton, BW & White, AH 2013, 'Synthesis and inhibitory activities at mGluRs of 3-alkylated and N-alkylated cyclopentyl-glutamate analogues', TETRAHEDRON, vol. 69, no. 12, pp. 2577-2587.
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The conformationally restricted glutamate analogues, 3-alkyl-1-amino-2-cyclopentene-1,3-dicarboxylates and N-alkylated analogues have been prepared in a regioselective and diastereoselective manner. From the biological studies of the 3-alkylated analogue

Valenzuela, SM, Alkhamici, H, Brown, LJ, Almond, OC, Goodchild, SC, Carne, S, Curmi, PMG, Holt, SA & Cornell, BA 2013, 'Regulation of the Membrane Insertion and Conductance Activity of the Metamorphic Chloride Intracellular Channel Protein CLIC1 by Cholesterol', PLOS ONE, vol. 8, no. 2, pp. 1-8.
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The Chloride Intracellular ion channel protein CLIC1 has the ability to spontaneously insert into lipid membranes from a soluble, globular state. The precise mechanism of how this occurs and what regulates this insertion is still largely unknown, although factors such as pH and redox environment are known contributors. In the current study, we demonstrate that the presence and concentration of cholesterol in the membrane regulates the spontaneous insertion of CLIC1 into the membrane as well as its ion channel activity. The study employed pressure versus area change measurements of Langmuir lipid monolayer films; and impedance spectroscopy measurements using tethered bilayer membranes to monitor membrane conductance during and following the addition of CLIC1 protein. The observed cholesterol dependent behaviour of CLIC1 is highly reminiscent of the cholesterol-dependent-cytolysin family of bacterial pore-forming proteins, suggesting common regulatory mechanisms for spontaneous protein insertion into the membrane bilayer. © 2013 Valenzuela et al.

Van Ly, D, De Pedro, M, James, P, Morgan, L, Black, JL, Burgess, JK & Oliver, BGG 2013, 'Inhibition of phosphodiesterase 4 modulates cytokine induction from toll like receptor activated, but not rhinovirus infected, primary human airway smooth muscle', RESPIRATORY RESEARCH, vol. 14, no. 1.
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Background: Virus-induced exacerbations of Chronic Obstructive Pulmonary Disease (COPD) are a significant health burden and occur even in those receiving the best current therapies. Rhinovirus (RV) infections are responsible for half of all COPD exacerbations. The mechanism by which exacerbations occur remains undefined, however it is likely to be due to virus-induced inflammation. Given that phophodiesterase 4 (PDE4) inhibitors have an anti-inflammatory effect in patients with COPD they present a potential therapy prior to, and during, these exacerbations.Methods: In the present study we investigated whether the PDE4 inhibitor piclamilast (10-6 M) could alter RV or viral mimetic (5 μg/mL of imiquimod or poly I:C) induced inflammation and RV replication in primary human airway smooth muscle cells (ASMC) and bronchial epithelial cells (HBEC). The mediators IL-6, IL-8, prostaglandin E2 and cAMP production were assayed by ELISA and RV replication was assayed by viral titration.Results: We found that in ASMCs the TLR3 agonist poly I:C induced IL-8 release was reduced while induced IL-6 release by the TLR7/8 agonist imiquimod was further increased by the presence of piclamilast. However, in RV infected ASMCs, virus replication and induced mediator release were unaltered by piclamilast, as was also found in HBECs. The novel findings of this study reveal that although PDE inhibitors may not influence RV-induced cytokine production in ASMCs and replication in either ASMCs or HBECs, they have the capacity to be anti-inflammatory during TLR activation by modulating the induction of these chemotactic cytokines.Conclusion: By extrapolating our in vitro findings to exacerbations of COPD in vivo this suggests that PDE4 inhibitors may have beneficial anti-inflammatory properties when patients are infected with bacteria or viruses other than RV. © 2013 Van Ly et al.; licensee BioMed Central Ltd.

Van Ly, D, Faiz, A, Jenkins, C, Crossett, B, Black, JL, McParland, B, Burgess, JK & Oliver, BGG 2013, 'Characterising the Mechanism of Airway Smooth Muscle β2 Adrenoceptor Desensitization by Rhinovirus Infected Bronchial Epithelial Cells', PLoS ONE, vol. 8, no. 2, pp. e56058-e56058.
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Rhinovirus (RV) infections account for approximately two thirds of all virus-induced asthma exacerbations and often result in an impaired response to beta 2 agonist therapy. Using an in vitro model of RV infection, we investigated the mechanisms underlyi

Veasey, SC, Lear, J, Zhu, Y, Grinspan, JB, Hare, DJ, Wang, S, Bunch, D, Doble, PA & Robinson, SR 2013, 'Long-Term Intermittent Hypoxia Elevates Cobalt Levels in the Brain and Injures White Matter in Adult Mice', SLEEP, vol. 36, no. 10, pp. 1471-1481.
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Study Objectives: Exposure to the variable oxygenation patterns in obstructive sleep apnea (OSA) causes oxidative stress within the brain. We hypothesized that this stress is associated with increased levels of redox-active metals and white matter injury. Design: Participants were randomly allocated to a control or experimental group (single independent variable). Setting: University animal house. Participants: Adult male C57BL/6J mice. Interventions: To model OSA, mice were exposed to long-term intermittent hypoxia (LTIH) for 10 hours/day for 8 weeks or sham intermittent hypoxia (SIH).

Venturini, C, Hassan, KA, Roy Chowdhury, P, Paulsen, IT, Walker, MJ & Djordjevic, SP 2013, 'Sequences of Two Related Multiple Antibiotic Resistance Virulence Plasmids Sharing a Unique IS26-Related Molecular Signature Isolated from Different Escherichia coli Pathotypes from Different Hosts', PLoS ONE, vol. 8, no. 11, pp. e78862-e78862.
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Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant to multiple antibiotics. Here we describe two plasmids, pO26-CRL 125 (125 kb) from a human O26:H- EHEC, and pO111-CRL115 (115kb) from a bovine O111 aEPEC, that impart resistance to ampicillin, kanamycin, neomycin, streptomycin, sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1 integrons with an identical IS26-mediated deletion in their 3′-conserved segment. Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are essentially identical except for a 9.7 kb fragment, present in the backbone of pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment encodes IncI-associated genes involved in plasmid stability during conjugation, a putative transposase gene and three imperfect repeats. Contiguous sequence identical to regions within these pO26-CRL125 imperfect repeats was identified in pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be mobile. Sequences shared between the plasmids include a complete IncZ replicon, a unique toxin/antitoxin system, IncI stability and maintenance genes, a novel putative serine protease autotransporter, and an IncI1 transfer system including a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to trimethoprim, and 24 bp of the 3′-conserved segment followed by Tn6026, which encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721, encoding resistance to tetracycline, via a region containing the IncP-1α oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons, indicates that homologous recombination events played a key role in the formation of this complex antibiotic res...

Vijaykrishna, D, Deng, Y-M, Su, YCF, Fourment, M, Iannello, P, Arzey, GG, Hansbro, PM, Arzey, KE, Kirkland, PD, Warner, S, O'Riley, K, Barr, IG, Smith, GJD & Hurt, AC 2013, 'The Recent Establishment of North American H10 Lineage Influenza Viruses in Australian Wild Waterfowl and the Evolution of Australian Avian Influenza Viruses', Journal of Virology, vol. 87, no. 18, pp. 10182-10189.
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ABSTRACT Influenza A H10N7 virus with a hemagglutinin gene of North American origin was detected in Australian chickens and poultry abattoir workers in New South Wales, Australia, in 2010 and in chickens in Queensland, Australia, on a mixed chicken and domestic duck farm in 2012. We investigated their genomic origins by sequencing full and partial genomes of H10 viruses isolated from wild aquatic birds and poultry in Australia and analyzed them with all available avian influenza virus sequences from Oceania and representative viruses from North America and Eurasia. Our analysis showed that the H10N7 viruses isolated from poultry were similar to those that have been circulating since 2009 in Australian aquatic birds and that their initial transmission into Australia occurred during 2007 and 2008. The H10 viruses that appear to have developed endemicity in Australian wild aquatic birds were derived from several viruses circulating in waterfowl along various flyways. Their hemagglutinin gene was derived from aquatic birds in the western states of the United States, whereas the neuraminidase was closely related to that from viruses previously detected in waterfowl in Japan. The remaining genes were derived from Eurasian avian influenza virus lineages. Our analysis of virological data spanning 40 years in Oceania indicates that the long-term evolutionary dynamics of avian influenza viruses in Australia may be determined by climatic changes. The introduction and long-term persistence of avian influenza virus lineages were observed during periods with increased rainfall, whereas bottlenecks and extinction were observed during phases of widespread decreases in rainfall. These results extend our understanding of factors affecting the dynamics of avian influenza and provide important considerations for surveillance and disease control strategies.

Voyer, M, Dreher, T, Gladstone, W & Goodall, H 2013, 'Who cares wins: The role of local news and news sources in influencing community responses to marine protected areas', OCEAN & COASTAL MANAGEMENT, vol. 85, no. A, pp. 29-38.
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Mass media is a key tool by which environmental interventions, such as Marine Protected Areas (MPAs) are communicated to the public. The way in which local news outlets present and explain MPAs to local communities is likely to be influential in determining how they respond to the proposal. In particular the tendency of news media to focus on areas of conflict and dispute ensures ideology and politics play a central role in reporting of MPA proposals, often simplifying debate into an `us versus them or `fishers versus conservationists ideological conflict. This can lead to the outright rejection of an MPA or undermine acceptance of the park within local communities. The media coverage of two marine parks in NSW, Australia was compared to determine the way in which news presented the parks to each community and how this may have influenced public acceptance of the parks. In particular the study examined the role ideology and politics played in the news coverage of each park by investigating the way in which the news was framed and the positions of key media spokespeople. Media coverage of the Batemans Marine Park appears to have been highly politicised and heavily influenced by the strong convictions of a small handful of prominent spokespeople. By way of contrast media coverage of the Port Stephens Great Lakes Marine Park was more nuanced and drew from a wide range of sources. This research provides insight into how areas of conflict could be reframed as opportunities that enhance MPA planning exercises and highlights how ideology can help shape community sentiment. Acknowledging the role of ideology in contested areas such as these allows for the development of strategies that can accommodate as well as moderate its influence. These strategies may include the incorporation of `bottom up approaches into MPA planning, the promotion and support of a range of voices within the community, and seeking out and building upon common ground and shared values.

Wagner, MR, Callsen, G, Reparaz, JS, Kirste, R, Hoffmann, A, Rodina, AV, Schleife, A, Bechstedt, F & Phillips, MR 2013, 'Effects of strain on the valence band structure and exciton-polariton energies in ZnO', PHYSICAL REVIEW B, vol. 88, no. 23.
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The uniaxial stress dependence of the band structure and the exciton-polariton transitions in wurtzite ZnO is thoroughly studied using modern first-principles calculations based on the HSE+G0W0 approach, k·p modeling using the deformation potential framework, and polarized photoluminescence measurements. The ordering of the valence bands [A(Γ7), B(Γ9), C(Γ7)] is found to be robust even for high uniaxial and biaxial strains. Theoretical results for the uniaxial pressure coefficients and splitting rates of the A, B, and C valence bands and their optical transitions are obtained including the effects of the spin-orbit interaction. The excitonic deformation potentials are derived and the stress rates for hydrostatic pressure are determined based on the results for uniaxial and biaxial stress. In addition, the theory for the stress dependence of the exchange interaction and longitudinal-transversal splitting of the exciton polaritons is developed using the basic exciton functions of the quasicubic approximation and taking the interaction between all exciton states into account. It is shown that the consideration of these effects is crucial for an accurate description of the stress dependence of the optical spectra in ZnO. The theoretical results are compared to polarized photoluminescence measurements of different ZnO substrates as function of uniaxial pressure and experimental values reported in the literature demonstrating an excellent agreement with the computed pressure coefficients. © 2013 American Physical Society.

Walters, SB, Kieckbusch, J, Nagalingam, G, Swain, A, Latham, SL, Grau, GER, Britton, WJ, Combes, V & Saunders, BM 2013, 'Microparticles from Mycobacteria-Infected Macrophages Promote Inflammation and Cellular Migration', The Journal of Immunology, vol. 190, no. 2, pp. 669-677.
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AbstractMycobacterium tuberculosis infection is characterized by a strong inflammatory response whereby a few infected macrophages within the granuloma induce sustained cellular accumulation. The mechanisms coordinating this response are poorly characterized. We hypothesized that microparticles (MPs), which are submicron, plasma membrane-derived vesicles released by cells under both physiological and pathological conditions, are involved in this process. Aerosol infection of mice with M. tuberculosis increased CD45+ MPs in the blood after 4 wk of infection, and in vitro infection of human and murine macrophages with mycobacteria enhanced MP release. MPs derived from mycobacteria-infected macrophages were proinflammatory, and when injected into uninfected mice they induced significant neutrophil, macrophage, and dendritic cell recruitment to the injection site. When incubated with naive macrophages, these MPs enhanced proinflammatory cytokine and chemokine release, and they aided in the disruption of the integrity of a respiratory epithelial cell monolayer, providing a mechanism for the egress of cells to the site of M. tuberculosis infection in the lung. In addition, MPs colocalized with the endocytic recycling marker Rab11a within macrophages, and this association increased when the MPs were isolated from mycobacteria-infected cells. M. tuberculosis–derived MPs also carried mycobacterial Ag and were able to activate M. tuberculosis–specific CD4+ T cells in vivo and in vitro in a dendritic cell–dependent manner. Collectively, these data identify an unrecognized role for MPs in host response against M. tuberculosis by promoting inflammation, intercellular communication, and cell migration.

Wang, B, Wang, Y, Sun, B, Munroe, P & Wang, G 2013, 'Coral-like V2O5 nanowhiskers as high-capacity cathode materials for lithium-ion batteries', RSC ADVANCES, vol. 3, no. 15, pp. 5069-5075.
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Coral-like V2O5 nanowhiskers were prepared by a direct electrolytic synthesis method. The as-prepared V2O5 nanowhiskers are approximately 1 μm in length and 50-60 nm in width, which was confirmed by scanning electron microscopy and transmission electron microscopy analysis. When applied as cathode materials in lithium-ion batteries and combined with an ionic liquid electrolyte, the V2O5 nanowhiskers exhibited an initial capacity of 461 mAh g-1, which is a significant enhancement compared to commercial V2O5 powders. The high rate performance of the V2O5 nanowhiskers was further improved at an elevated working temperature of 50 °C. The V2O5 nanowhiskers demonstrated a high specific capacity and an excellent high-rate performance at elevated temperatures. © 2013 The Royal Society of Chemistry.

Wang, G, Norton, AS, Pokharel, D, Song, Y & Hill, RA 2013, 'KDEL peptide gold nanoconstructs: promising nanoplatforms for drug delivery', Nanomedicine: Nanotechnology, Biology and Medicine, vol. 9, no. 3, pp. 366-374.
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Wang, JJJ, Choy, STB & Chan, JSK 2013, 'Modelling stochastic volatility using generalizedtdistribution', Journal of Statistical Computation and Simulation, vol. 83, no. 2, pp. 340-354.
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In modelling financial return time series and time-varying volatility, the Gaussian and the Student-t distributions are widely used in stochastic volatility (SV) models. However, other distributions such as the Laplace distribution and generalized error distribution (GED) are also common in SV modelling. Therefore, this paper proposes the use of the generalized t (GT) distribution whose special cases are the Gaussian distribution, Student-t distribution, Laplace distribution and GED. Since the GT distribution is a member of the scale mixture of uniform (SMU) family of distribution, we handle the GT distribution via its SMU representation. We show this SMU form can substantially simplify the Gibbs sampler for Bayesian simulation-based computation and can provide a mean of identifying outliers. In an empirical study, we adopt a GT-SV model to fit the daily return of the exchange rate of Australian dollar to three other currencies and use the exchange rate to US dollar as a covariate. Model implementation relies on Bayesian Markov chain Monte Carlo algorithms using the WinBUGS package. © 2013 Copyright Taylor and Francis Group, LLC.

Wang, S, Wu, Y, Guo, R, Huang, Y, Wen, S, Shen, M, Wang, J & Shi, X 2013, 'Laponite Nanodisks as an Efficient Platform for Doxorubicin Delivery to Cancer Cells', Langmuir, vol. 29, no. 16, pp. 5030-5036.
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Wang, Y, Sharma, N, Su, D, Bishop, D, Ahn, H & Wang, G 2013, 'High capacity spherical Li[Li0.24Mn0.55Co0.14Ni0.07]O2 cathode material for lithium ion batteries', Solid State Ionics, vol. 233, pp. 12-19.
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Li[Li0.24Mn0.55Co0.14Ni 0.07]O2 cathode materials with controlled spherical morphology and particle size in the range of 5-10 μm were synthesized by a modified co-precipitation method. The crystal structure of Li[Li 0.24Mn0.55Co0.14Ni0.07]O 2 was investigated by Rietveld analysis of structural models using X-ray and neutron powder diffraction data, indicating the presence of Li 2MnO3 in the final product. Li[Li0.24Mn 0.55Co0.14Ni0.07]O2 shows low initial irreversible capacity loss (47.2 mAh/g), high reversible capacity (264.6 mAh/g), good capacity retention (90.4% over 50 cycles) and satisfactory rate capability when used as the cathode material in lithium ion batteries. X-ray photoelectron spectroscopy analysis of the pristine, charged and discharged electrodes of Li[Li0.24Mn0.55Co0.14Ni 0.07]O2 reveals that the Mn4 +/Mn3 + redox couple participates in the delithiation/lithiation process. Overall, the improved electrochemical performance of the Li[Li0.24Mn 0.55Co0.14Ni0.07]O2 electrode can be ascribed to the controlled and specially designed morphology and the composition of the sample that is produced by the co-precipitation method. © 2012 Elsevier B.V.

Wang, Y, Su, D & Wang, G 2013, 'The Effect of Carbon Coating on the Electrochemical Performance of Nanosized Li2FeSiO4 Cathode Materials', ACTA PHYSICA POLONICA A, vol. 123, no. 2, pp. 279-282.
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Carbon-coated Li2FeSiO4/C cathode materials have been synthesized through a modified ball-milling pro- cess. The physical characterizations of Li2FeSiO4 were conducted by using X-ray powder diffraction, field-emission scanning electron microscopy and transmission electron microscopy techniques. Field-emission scanning electron microscopy and transmission electron microscopy images revealed that Li2FeSiO4/C consists of nanosized parti- cles coated with an amorphous carbon layer. The electrochemical performances of Li2FeSiO4/C cathode materials were evaluated through fully assembled lithium batteries via cyclic voltammetry, charge/discharge test and electro- chemical impedance spectroscopy. The Li2FeSiO4/C cathode materials showed a much improved electrochemical performance in terms of higher specific capacity, better cycling performance and less charge transfer resistance than that of the pristine Li2FeSiO4.

Wang, Y, Su, D, Wang, C & Wang, G 2013, 'SnO2@MWCNT nanocomposite as a high capacity anode material for sodium-ion batteries', Electrochemistry Communications, vol. 29, pp. 8-11.
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We report the synthesis and characterization of SnO2@multiwalled carbon nanotubes (MWCNTs) nanocomposite as a high capacity anode material for sodium-ion battery. SnO2@MWCNT nanocomposite was synthesized by a solvothermal method. SEM and TEM analyses show the uniform distribution of SnO2 nanoparticles on carbon nanotubes. When applied as anode materials in Na-ion batteries, SnO2@MWCNT nanocomposite exhibited a high sodium storage capacity of 839 mAh g- 1 in the first cycle. SnO2@MWCNT nanocomposite also demonstrated much better cycling performance than that of bare SnO2 nanoparticles and bare MWCNTs. Furthermore, the nanocomposite electrode also showed a good cyclability and an enhanced Coulombic efficiency on cycling. © 2013 Elsevier B.V.

Watts, AL, Singh, N, Poulton, CG, Magi, EC, Kabakova, IV, Hudson, DD & Eggleton, BJ 2013, 'Photoinduced axial quantization in chalcogenide microfiber resonators', Journal of the Optical Society of America B, vol. 30, no. 12, pp. 3249-3249.
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We investigate axial quantization in chalcogenide (As2S3) whispering gallery mode microfiber resonators. A microcavity is fabricated using a positive photoinduced index perturbation in the microfiber, and the modes are excited through evanescent field coupling with a tapered silica fiber. We show that the modes of the unperturbed fiber split into ladders of modes due to the confinement along the axial direction of the fiber. The axial quantization of the modes is reproduced with a combination of numerical models. Due to the high nonlinearity and photosensitive properties of chalcogenide glasses, microcavities in these materials offer unique potential in nonlinear optics and sensing applications. © 2013 Optical Society of America.

Weber, FH, Jackson, JA, Sobecki, B, Choromanski, L, Olsen, M, Meinert, T, Frank, R, Reichel, MP & Ellis, JT 2013, 'On the Efficacy and Safety of Vaccination with Live Tachyzoites of Neospora caninum for Prevention of Neospora-Associated Fetal Loss in Cattle', CLINICAL AND VACCINE IMMUNOLOGY, vol. 20, no. 1, pp. 99-105.
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Infection of cattle with Neospora caninum may result in abortion or the birth of a congenitally infected calf. Vaccination with live N. caninum protects against experimental infection of cattle and mice, and the naturally attenuated Nc-Nowra strain of N. caninum is of particular interest as a potential vaccine candidate. Vaccination of heifers prior to breeding with live Nc-Nowra tachyzoites by either the subcutaneous or the intravenous route reduced the rate of abortion and the presence of the parasite in calves as determined by PCR and serology after infection of cows with a virulent isolate. Protected fractions were 55.6% to 85.2% depending on the route of vaccination and growth conditions of the vaccine strain, with cryopreserved Nc-Nowra tachyzoites being less effective, with a 25.9% protected fraction. Vaccination appeared to reduce the rate of pregnancy after artificial insemination in some groups compared to nonvaccinated, nonchallenged controls. One animal that was vaccinated but not challenged experienced an abortion, but Nc-Nowra could not be detected in any of the cows in this group or their progeny. This study confirms that live vaccination can be an effective method of preventing neosporosis in cattle and yet highlights the technical hurdle of preservation of live parasites that must be overcome for a vaccine to be commercially successful.

Wei, J, Carroll, RJ, Müller, UU, Keilegom, IV & Chatterjee, N 2013, 'Robust Estimation for Homoscedastic Regression in the Secondary Analysis of Case–Control Data', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 75, no. 1, pp. 185-206.
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SummaryPrimary analysis of case–control studies focuses on the relationship between disease D and a set of covariates of interest (Y, X). A secondary application of the case–control study, which is often invoked in modern genetic epidemiologic association studies, is to investigate the interrelationship between the covariates themselves. The task is complicated owing to the case–control sampling, where the regression of Y on X is different from what it is in the population. Previous work has assumed a parametric distribution for Y given X and derived semiparametric efficient estimation and inference without any distributional assumptions about X. We take up the issue of estimation of a regression function when Y given X follows a homoscedastic regression model, but otherwise the distribution of Y is unspecified. The semiparametric efficient approaches can be used to construct semiparametric efficient estimates, but they suffer from a lack of robustness to the assumed model for Y given X. We take an entirely different approach. We show how to estimate the regression parameters consistently even if the assumed model for Y given X is incorrect, and thus the estimates are model robust. For this we make the assumption that the disease rate is known or well estimated. The assumption can be dropped when the disease is rare, which is typically so for most case–control studies, and the estimation algorithm simplifies. Simulations and empirical examples are used to illustrate the approach.

Wen, S, Li, K, Cai, H, Chen, Q, Shen, M, Huang, Y, Peng, C, Hou, W, Zhu, M, Zhang, G & Shi, X 2013, 'Multifunctional dendrimer-entrapped gold nanoparticles for dual mode CT/MR imaging applications', Biomaterials, vol. 34, no. 5, pp. 1570-1580.
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Wen, S, Liu, H, Cai, H, Shen, M & Shi, X 2013, 'Targeted and pH‐Responsive Delivery of Doxorubicin to Cancer Cells Using Multifunctional Dendrimer‐Modified Multi‐Walled Carbon Nanotubes', Advanced Healthcare Materials, vol. 2, no. 9, pp. 1267-1276.
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AbstractWe report the use of multifunctional dendrimer‐modified multi‐walled carbon nanotubes (MWCNTs) for targeted and pH‐responsive delivery of doxorubicin (DOX) into cancer cells. In this study, amine‐terminated generation 5 poly(amidoamine) (PAMAM) dendrimers modified with fluorescein isothiocyanate (FI) and folic acid (FA) were covalently linked to acid‐treated MWCNTs, followed by acetylation of the remaining dendrimer terminal amines to neutralize the positive surface potential. The formed multifunctional MWCNTs (MWCNT/G5.NHAc‐FI‐FA) were characterized via different techniques. Then, the MWCNT/G5.NHAc‐FI‐FA was used to load DOX for targeted and pH‐responsive delivery to cancer cells overexpressing high‐affinity folic acid receptors (FAR). We showed that the MWCNT/G5.NHAc‐FI‐FA enabled a high drug payload and encapsulation efficiency both up to 97.8% and the formed DOX/MWCNT/G5.NHAc‐FI‐FA complexes displayed a pH‐responsive release property with fast DOX release under acidic environment and slow release at physiological pH conditions. Importantly, the DOX/MWCNT/G5.NHAc‐FI‐FA complexes displayed effective therapeutic efficacy, similar to that of free DOX, and were able to target to cancer cells overexpressing high‐affinity FAR and effectively inhibit the growth of the cancer cells. The synthesized multifunctional dendrimer‐modified MWCNTs may be used as a targeted and pH‐responsive delivery system for targeting therapy of different types of cancer cells.

Wen, S, Zheng, F, Shen, M & Shi, X 2013, 'Surface modification and PEGylation of branched polyethyleneimine for improved biocompatibility', Journal of Applied Polymer Science, vol. 128, no. 6, pp. 3807-3813.
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AbstractIn this article, we report the surface modification of branched polyethyleneimine (PEI) for improved biocompatibility. PEIs with different surface functionalities were synthesized via covalent modification of the PEI amines, including neutralized PEI modified with acetic anhydride, negatively charged PEI modified with succinic anhydride, hydroxylated PEI modified with glycidol, and PEI–poly(ethylene glycol) (PEG) conjugates modified with both PEG and acetic anhydride. The modified PEI derivatives were characterized with 1H‐NMR, Fourier transform infrared spectroscopy, and ζ‐potential measurements. An in vitro cytotoxicity assay of mouse fibroblasts revealed that the biocompatibility of PEI was significantly improved after these modifications. The neutral and negatively charged PEIs were nontoxic at concentrations up to 200 μg/mL, whereas the pristine PEI was toxic to cells at concentrations as low as 10 μg/mL. The successfully modified PEIs with different surface charges and functionalities may provide a range of opportunities for various biomedical applications. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

Wen, S, Zheng, F, Shen, M & Shi, X 2013, 'Synthesis of polyethyleneimine-stabilized gold nanoparticles for colorimetric sensing of heparin', Colloids and Surfaces A: Physicochemical and Engineering Aspects, vol. 419, pp. 80-86.
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Wheway, J, Obeid, S, Couraud, P-O, Combes, V & Grau, GER 2013, 'Correction: The Brain Microvascular Endothelium Supports T Cell Proliferation and Has Potential for Alloantigen Presentation', PLoS ONE, vol. 8, no. 4.
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Wheway, J, Obeid, S, Couraud, P-O, Combes, V & Grau, GER 2013, 'The Brain Microvascular Endothelium Supports T Cell Proliferation and Has Potential for Alloantigen Presentation', PLoS ONE, vol. 8, no. 1, pp. e52586-e52586.
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Endothelial cells (EC) form the inner lining of blood vessels and are positioned between circulating lymphocytes and tissues. Hypotheses have formed that EC may act as antigen presenting cells based on the intimate interactions with T cells, which are seen in diseases like multiple sclerosis, cerebral malaria (CM) and viral neuropathologies. Here, we investigated how human brain microvascular EC (HBEC) interact with and support the proliferation of T cells. We found HBEC to express MHC II, CD40 and ICOSL, key molecules for antigen presentation and co-stimulation and to take up fluorescently labeled antigens via macropinocytosis. In co-cultures, we showed that HBEC support and promote the proliferation of CD4+ and CD8+ T cells, which both are key in CM pathogenesis, particularly following T cell receptor activation and co-stimulation. Our findings provide novel evidence that HBEC can trigger T cell activation, thereby providing a novel mechanism for neuroimmunological complications of infectious diseases. © 2013 Wheway et al.

Whitley, R, Taylor, D, Macinnis-Ng, C, Zeppel, M, Yunusa, I, O'Grady, A, Froend, R, Medlyn, B & Eamus, D 2013, 'Developing an empirical model of canopy water flux describing the common response of transpiration to solar radiation and VPD across five contrasting woodlands and forests', HYDROLOGICAL PROCESSES, vol. 27, no. 8, pp. 1133-1146.
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A modified Jarvis-Stewart model of canopy transpiration (Ec) was tested over five ecosystems differing in climate, soil type and species composition. The aims of this study were to investigate the model's applicability over multiple ecosystems; to determine whether the number of model parameters could be reduced by assuming that site-specific responses of Ec to solar radiation, vapour pressure deficit and soil moisture content vary little between sites; and to examine convergence of behaviour of canopy water-use across multiple sites. This was accomplished by the following: (i) calibrating the model for each site to determine a set of site-specific (SS) parameters, and (ii) calibrating the model for all sites simultaneously to determine a set of combined sites (CS) parameters. The performance of both models was compared with measured Ec data and a statistical benchmark using an artificial neural network (ANN). Both the CS and SS models performed well, explaining hourly and daily variation in Ec. The SS model produced slightly better model statistics [R2=0.75-0.91; model efficiency (ME)=0.53-0.81; root mean square error (RMSE)=0.0015-0.0280mm h-1] than the CS model (R2=0.68-0.87; ME=0.45-0.72; RMSE=0.0023-0.0164mm h-1). Both were highly comparable with the ANN (R2=0.77-0.90; ME=0.58-0.80; RMSE=0.0007-0.0122mm h-1). These results indicate that the response of canopy water-use to abiotic drivers displayed significant convergence across sites, but the absolute magnitude of Ec was site specific. Period totals estimated with the modified Jarvis-Stewart model provided close approximations of observed totals, demonstrating the effectiveness of this model as a tool aiding water resource management. Analysis of the measured diel patterns of water use revealed significant nocturnal transpiration (9-18% of total water use by the canopy), but no Jarvis-Stewart formulations are able to capture this because of the dependence of water-use on solar radiation, which is z...

Whitney, M & Ryan, L 2013, 'Uncertainty due to low-dose extrapolation: modified BMD methodology for epidemiological data', ENVIRONMETRICS, vol. 24, no. 5, pp. 289-297.
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Traditional environmental risk assessment methodologies, including benchmark dose (BMD) estimation, were originally developed to be used with animal toxicology data. We discuss some problems that can occur when toxicology-based methods are applied to hum

Whitney, M, Ryan, L & Walkowiak, J 2013, 'On the Use of Bayesian Model Averaging for Covariate Selection in Epidemiological Modeling', Journal of Statistical Theory and Practice, vol. 7, no. 2, pp. 233-247.
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Bayesian model averaging (BMA) is a powerful technique to address model selection uncertainty and recent computational advances have led to a proliferation of usage. BMA methods are of particular interest in environmental health risk assessment because of the high degree of uncertainty that typically arises in that context. In this article, we review a variety of approaches to conducting BMA and compare four implementations in a setting where there are a number of potential predictors. We then use these four methods to calculate risk assessment measures that account for the uncertainty involved in modeling environmental exposures. These methods are used to reexamine data from a study conducted by Walkowiak et al. (2001) to investigate the effects of maternal polychlorinated biphenyl exposure on cognitive development in early childhood. This case study reveals that different strategies for implementing BMA can yield varying risk assessment results. We conclude with some practical recommendations. © 2013 Copyright Grace Scientific Publishing, LLC.

Willenborg, C & Stelzer-Braid, S 2013, 'Sneezing leads to wheezing: microorganisms important in asthma', Microbiology Australia, vol. 34, no. 3, pp. 125-125.
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Wilson, CH, Indarto, D, Doucet, A, Pogson, LD, Pitman, MR, McNicholas, K, Menz, RI, Overall, CM & Abbott, CA 2013, 'Identifying Natural Substrates for Dipeptidyl Peptidases 8 and 9 Using Terminal Amine Isotopic Labeling of Substrates (TAILS) Reveals in Vivo Roles in Cellular Homeostasis and Energy Metabolism', Journal of Biological Chemistry, vol. 288, no. 20, pp. 13936-13949.
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Winful, HG, Kabakova, IV & Eggleton, BJ 2013, 'Model for distributed feedback Brillouin lasers', Optics Express, vol. 21, no. 13, pp. 16191-16191.
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Wong, FWS & Lim, DCE 2013, 'Factors influencing the choice of hysterectomy approach for the management of fibroid uterus', Gynecology and Minimally Invasive Therapy, vol. 2, no. 2, pp. 61-64.
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Aim: The aim of this study was to identify factors influencing the choice between different approaches in hysterectomy for uterine fibroids. Methods: A cross-sectional study was conducted involving 285 women who had undergone hysterectomy for uterine fibroids at the Liverpool Hospital, New South Wales, Australia. Results: This study shows that several factors influenced the choice of hysterectomy approach. First, concomitant adnexal surgery increased the likelihood of undergoing an abdominal hysterectomy rather than either a vaginal or a laparoscopic hysterectomy by 10- and fivefold (both p<0.01), respectively. Second, women with a larger uterus (>280g) had a 20 (. p<0.05) and 10 (. p<0.01) times greater chance of undergoing an abdominal hysterectomy than either a vaginal or a laparoscopic hysterectomy, respectively. Third, gynecologic endoscopists were more likely to perform laparoscopic hysterectomy than gynecologic generalists (. p<0.001). Conclusion: Certain clinical parameters determine the choice of hysterectomy approach. Surgeons' expertise also has significant influence over the choice between laparoscopic and traditional approaches for hysterectomy. © 2013.

Wong, KKY, Rockman, S, Ong, C, Bull, R, Stelzer‐Braid, S & Rawlinson, W 2013, 'Comparison of influenza virus replication fidelity in vitro using selection pressure with monoclonal antibodies', Journal of Medical Virology, vol. 85, no. 6, pp. 1090-1094.
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AbstractThe replication fidelity of reassortant A/Fujian/411/02(H3N2)‐like influenza viruses was assessed by in vitro detection of escape mutants developing under selective pressure from monoclonal antibodies. The results showed A/Wyoming/3/03(H3N2) possessed lower fidelity relative to the A/California/7/04(H3N2) and A/Wisconsin/57/05(H3N2) viruses through the emergence of mutant viruses carrying H156Q hemagglutinin mutation which allows antibody escape. Using the neutralization assay to compare the fidelity of reassortant pandemic A/California/7/09(H1N1) viruses, the pandemic virus was shown to possess relative higher fidelity compared to A/Wyoming/3/03. This higher fidelity may contribute to the lack of major antigenic changes in the pandemic virus since the emergence in 2009. J. Med. Virol. 85: 1090–1094, 2013. © 2013 Wiley Periodicals, Inc.

Woo, JKK, McElroy, K, Rice, SA, Kirov, SM, Thomas, T & Kjelleberg, S 2013, 'Draft Genome Sequence of the Chronic, Nonclonal Cystic Fibrosis Isolate Pseudomonas aeruginosa Strain 18A', Genome Announcements, vol. 1, no. 2.
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ABSTRACT Pseudomonas aeruginosa strain 18A is a clinical, nonclonal isolate retrieved from the sputum of a chronically infected cystic fibrosis patient. The genome of 18A was sequenced for comparison with environmental and clinical isolates to identify genes that might facilitate its persistence during infection.

Wood, M, Maynard, P, Spindler, X, Roux, C & Lennard, C 2013, 'Selective targeting of fingermarks using immunogenic techniques', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 45, no. 2, pp. 211-226.
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Latent fingermark detection remains one of the most commonly utilised forensic practices when dealing with scenes of crime or related items. Although many options are available to detect and visualise these marks, the quest for techniques with greater sensitivity and selectivity continues. This has led to many improvements in detection methods and also numerous new techniques being developed. However, these have largely only led to incremental advancements despite the desire for transformational improvements. The use of immunology in the detection of latent fingermarks is an area that has been investigated more recently as a possible proposal to provide these transformational improvements, specifically to overcome sensitivity and selectivity issues currently seen with existing methods. This paper reviews the attempts to harness the detection capabilities of immunology and utilise them in the field of latent fingermark detection. Results achieved to date have highlighted many advantages and possibilities in detection and visualisation of latent marks, including the possibility of gaining intelligence from the marks themselves. This paper also presents a brief introduction to the use of aptamers as the next logical step in immunogenic techniques for investigation. © 2013 Copyright Taylor and Francis Group, LLC.

Woodcock, S & Bush, S 2013, 'Slipping between the cracks? Maximising the effectiveness of prerequisite paths in UTS Maths degrees', ANZIAM Journal, vol. 54, pp. 297-297.
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© Austral. Mathematical Soc. 2014. As with almost all degree programs at major Australian universities, the courses offered by the School of Mathematical Sciences at the University of Technology, Sydney consist of a number of individual subjects which together form several prerequisite paths. That is, certain subjects must be successfully completed by students before they may enrol in more advanced subjects in the same broad academic area. This attempts to ensure that those entering later subjects have the sufficient prior knowledge to succeed in their enrolled subjects. While this model is largely successful, it does have one potential 'loophole'. The minimum mark to pass a subject is 50%, meaning that students can potentially complete a prerequisite subject and advance through their course while demonstrating understanding of only half of the prior material. The implications of applying this pass criterion are generally poorly understood and little quantitative work has been undertaken to assess its efficiency and effectiveness. Here, we present quantitative analyses of recent (2008-2013) subject results and discuss a number of possible concerns and issues that these highlight. Furthermore, we draw conclusions and propose several future initiatives which are being used to inform future practice within the school, both in terms of subject development and assessment and also in providing targeted additional support to students whose prior subject performances suggest they may be at risk of future failure.

Woodcock, S, Besemer, K, Battin, TJ, Curtis, TP & Sloan, WT 2013, 'Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms', ENVIRONMENTAL MICROBIOLOGY, vol. 15, no. 4, pp. 1216-1225.
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The spatial distribution of microbial taxa is determined primarily by physical and chemical environments and by dispersal. In a homogeneous landscape with limited dispersal, the similarity in abundance of taxa in samples declines with separation distance. We present a one-dimensional model for the spatial autocorrelation in abundances arising from immigration from some remote community and dispersal between environmentally similar landscape patches. Spatial correlation in taxa abundances were calculated from biofilms from the beds of two flumes which differed only in their bedform profiles; one flat and the other a periodic sawtooth shape. The hydraulic regime is approximately uniform over the flat bed, whereas the sawtooth induces fast flow over the peaks and recirculation in the troughs. On the flat bed, the correlation decline between samples was reproduced by a model using one biologically reasonable parameter. A decline was apparent in the other flume; however, a better fit was achieved when dispersal was not assumed constant everywhere. However, analysis of finer-resolution data for the heterogeneous flume suggested even this model did not adequately capture the community's complexity. We conclude that hydrodynamics are a strong driver of taxa-abundance patterns in stream biofilms. However, local adaptability must also be considered to build up a complete mechanistic model. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Woolley, LK, Fell, SA, Djordjevic, SP, Eamens, GJ & Jenkins, C 2013, 'Plasmin activity in the porcine airways is enhanced during experimental infection with Mycoplasma hyopneumoniae, is positively correlated with proinflammatory cytokine levels and is ameliorated by vaccination', Veterinary Microbiology, vol. 164, no. 1-2, pp. 60-66.
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In Mycoplasma hyopneumoniae (Mhp) infection of swine, the host immune response is considered a major driver of lung pathology; however the underlying inflammatory mechanisms are not well understood. The serine protease plasmin is being increasingly recognised as a significant player in inflammatory processes. Here we compare plasmin activity in tracheobronchial lavage fluid (TBLF) from pigs experimentally challenged with Mhp that were either unvaccinated (n = 10), or vaccinated with the commercial vaccine Suvaxyn® M.hyo (n = 10). TBLF collected immediately prior to challenge and at 21 d and 35 d post-challenge was also assayed for levels of proinflammatory cytokines (TNF-a, IL-1ß and IL-6), and for bacterial load (by qPCR). Clinical signs, pathology, cytokine analyses and qPCR all indicated that vaccinated pigs had significantly reduced disease relative to unvaccinated animals. Plasmin activity increased significantly in TBLF collected at 21 d post-challenge compared to pre-challenge TBLF in unvaccinated (P < 0.01), but not vaccinated animals (P > 0.05). A significant correlation was observed between bacterial load and plasmin activity in the 21 d (r = 0.66; P < 0.01) and the 35 d post-challenge samples, (r = 0.62; P < 0.01). Plasmin activity was also significantly correlated with levels of TNF-a, IL-1ß and IL-6 at 21 d (r = 0.78, P < 0.0001; r = 0.77, P < 0.0001; r = 0.64, P < 0.005) and with TNF-a and IL-1ß at 35 d post-challenge (r = 0.77, P < 0.0001; r = 0.74, P < 0.0005). Our results indicate that plasminogen is activated to plasmin in the respiratory tract of pigs as part of the host inflammatory response to Mhp infection and that this effect is ameliorated by vaccination.

Wu, WC, Yao, XZ, Jin, DY, Wang, DS, Lou, WH & Qin, XY 2013, 'Clinical strategies for differentiating autoimmune pancreatitis from pancreatic malignancy to avoid unnecessary surgical resection', Journal of Digestive Diseases, vol. 14, no. 9, pp. 500-508.
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ObjectiveThe study aimed to determine a practical strategy for differentiating between autoimmune pancreatitis (AIP) and pancreatic malignancy in order to avoid unnecessary surgical resection.MethodsAltogether, 19 patients with AIP or other pancreatic diseases underwent routine examinations including liver function test and carbohydrate antigen 19‐9, computed tomography and/or magnetic resonance imaging. Serum immunoglobulin G (IgG) and/or IgG4 was determined in patients with clinically suspected or pathologically proven AIP. Patients with suspected AIP either received diagnostic steroid therapy or laparotomy (if malignant tumors could not be excluded). Surgery was not performed in patients with a definite diagnosis of AIP by fast intraoperative frozen biopsy. Those with confirmed AIP received steroid treatment.ResultsIn total, 15 cases were finally confirmed as AIP with eight diagnosed preoperatively, five confirmed by surgical pathology (preoperatively misdiagnosed) and two by intraoperative biopsy. Of these 15 patients with AIP and one without AIP, 14 had...

Xia, YC, Redhu, NS, Moir, LM, Koziol-White, C, Ammit, AJ, Al-Alwan, L, Camoretti-Mercado, B & Clifford, RL 2013, 'Pro-inflammatory and immunomodulatory functions of airway smooth muscle: Emerging concepts', Pulmonary Pharmacology & Therapeutics, vol. 26, no. 1, pp. 64-74.
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Xiang, FX, Wang, XL, Xun, X, De Silva, KSB, Wang, YX & Dou, SX 2013, 'Evidence for transformation from delta T-c to delta l pinning in MgB2 by graphene oxide doping with improved low and high field J(c) and pinning potential', APPLIED PHYSICS LETTERS, vol. 102, no. 15.
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Xiao, L, Bhadbhade, M & Baker, AT 2013, 'catena-Poly[[copper(I)-l-2,6-bis[4- (pyridin-2-yl)thiazol-2-yl]pyridine] hexafluoridophosphate acetonitrile monosolvate] from single-crystal synchrotron data', Acta Crystallographica Section E: Structure Reports Online, vol. 69, no. 4, pp. 1-11.
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The title complex, {[Cu(C21H13N5S 2)]PF6·CH3CN}n, was formed immediately on adding together a methanol solution containing copper(I) ions and a methanol solution of 2,6-bis[4-(pyridin-2-yl)thiazol-2-yl]pyridine. Crystallographic studies of the complex re

Xiao, T, Hou, W, Cao, X, Wen, S, Shen, M & Shi, X 2013, 'Dendrimer-entrapped gold nanoparticles modified with folic acid for targeted gene delivery applications', Biomaterials Science, vol. 1, no. 11, pp. 1172-1172.
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Xiao, T, Wen, S, Wang, H, Liu, H, Shen, M, Zhao, J, Zhang, G & Shi, X 2013, 'Facile synthesis of acetylated dendrimer-entrapped gold nanoparticles with enhanced gold loading for CT imaging applications', Journal of Materials Chemistry B, vol. 1, no. 21, pp. 2773-2773.
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Xie, H, Liu, Y, Jin, D, Santangelo, PJ & Xi, P 2013, 'Analytical description of high-aperture STED resolution with 0–2π vortex phase modulation', Journal of the Optical Society of America A, vol. 30, no. 8, pp. 1640-1640.
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Stimulated emission depletion (STED) can achieve optical superresolution, with the optical diffraction limit broken by the suppression on the periphery of the fluorescent focal spot. Previously, it is generally experimentally accepted that there exists an inverse square root relationship with the STED power and the resolution, but with arbitrary coefficients in expression. In this paper, we have removed the arbitrary coefficients by exploring the relationship between the STED power and the achievable resolution from vector optical theory for the widely used 0-2π vortex phase modulation. Electromagnetic fields of the focal region of a high numerical aperture objective are calculated and approximated into polynomials of radius in the focal plane, and analytical expression of resolution as a function of the STED intensity has been derived. As a result, the resolution can be estimated directly from the measurement of the saturation power of the dye and the STED power applied in the region of high STED power. © 2013 Optical Society of America.

Xu, B, Jin, D, Lou, W & Wang, D 2013, 'Lipocalin‐2 is Associated With a Good Prognosis and Reversing Epithelial‐to‐Mesenchymal Transition in Pancreatic Cancer', World Journal of Surgery, vol. 37, no. 8, pp. 1892-1900.
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AbstractBackgroundLipocalin‐2 is a multifaceted modulator in cancer progression. Its clinical significance is not clear in pancreatic cancer. The purpose of this study was to investigate whether lipocalin‐2 is associated with good prognosis by reversing epithelial‐to‐mesenchymal transition (EMT) in pancreatic cancer.MethodsLipocalin‐2, E‐cadherin, or vimentin expression was detected in 60 pancreatic adenocarcinoma specimens. Correlations between lipocalin‐2 expression and EMT, the clinicopathologic characteristics, and prognosis were investigated. Whether pancreatic cancer cells’ migration and invasion (some characteristics of EMT) were affected by lipocalin‐2 was also explored.ResultsHigh lipocalin‐2 expression was significantly associated with a good prognosis in pancreatic cancer (p < 0.05). Overexpression of lipocalin‐2 correlated with a lower extent of EMT (p < 0.05), increased E‐cadherin expression (p < 0.05), decreased vimentin expression (p < 0.05), and reduced cancer cell migration and invasion in pancreatic cancer.ConclusionsLipocalin‐2 may be considered an epithelial inducer, which may reverse EMT and predict a good prognosis in pancreatic cancer.

Xun, X, Cao, J, Mallick, B, Maity, A & Carroll, RJ 2013, 'Parameter Estimation of Partial Differential Equation Models', Journal of the American Statistical Association, vol. 108, no. 503, pp. 1009-1020.
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Partial differential equation (PDE) models are commonly used to model complex dynamic systems in applied sciences such as biology and finance. The forms of these PDE models are usually proposed by experts based on their prior knowledge and understanding of the dynamic system. Parameters in PDE models often have interesting scientific interpretations, but their values are often unknown and need to be estimated from the measurements of the dynamic system in the presence of measurement errors. Most PDEs used in practice have no analytic solutions, and can only be solved with numerical methods. Currently, methods for estimating PDE parameters require repeatedly solving PDEs numerically under thousands of candidate parameter values, and thus the computational load is high. In this article, we propose two methods to estimate parameters in PDE models: a parameter cascading method and a Bayesian approach. In both methods, the underlying dynamic process modeled with the PDE model is represented via basis function expansion. For the parameter cascading method, we develop two nested levels of optimization to estimate the PDE parameters. For the Bayesian method, we develop a joint model for data and the PDE and develop a novel hierarchical model allowing us to employ Markov chain Monte Carlo (MCMC) techniques to make posterior inference. Simulation studies show that the Bayesian method and parameter cascading method are comparable, and both outperform other available methods in terms of estimation accuracy. The two methods are demonstrated by estimating parameters in a PDE model from long-range infrared light detection and ranging data. Supplementary materials for this article are available online. © 2013 American Statistical Association.

Yakkundi, A, McCallum, L, O’Kane, A, Dyer, H, Worthington, J, McKeen, HD, McClements, L, Elliott, C, McCarthy, HO, Hirst, DG & Robson, T 2013, 'The Anti-Migratory Effects of FKBPL and Its Peptide Derivative, AD-01: Regulation of CD44 and the Cytoskeletal Pathway', PLoS ONE, vol. 8, no. 2, pp. e55075-e55075.
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FK506 binding protein-like (FKBPL) and its peptide derivatives exert potent anti-angiogenic activity in vitro and in vivo and control tumour growth in xenograft models, when administered exogenously. However, the role of endogenous FKBPL in angiogenesis is not well characterised. Here we investigated the molecular effects of the endogenous protein and its peptide derivative, AD-01, leading to their anti-migratory activity. Inhibition of secreted FKBPL using a blocking antibody or siRNA-mediated knockdown of FKBPL accelerated the migration of human microvascular endothelial cells (HMEC-1). Furthermore, MDA-MB-231 tumour cells stably overexpressing FKBPL inhibited tumour vascular development in vivo suggesting that FKBPL secreted from tumour cells could inhibit angiogenesis. Whilst FKBPL and AD-01 target CD44, the nature of this interaction is not known and here we have further interrogated this aspect. We have demonstrated that FKBPL and AD-01 bind to the CD44 receptor and inhibit tumour cell migration in a CD44 dependant manner; CD44 knockdown abrogated AD-01 binding as well as its anti-migratory activity. Interestingly, FKBPL overexpression and knockdown or treatment with AD-01, regulated CD44 expression, suggesting a co-regulatory pathway for these two proteins. Downstream of CD44, alterations in the actin cytoskeleton, indicated by intense cortical actin staining and a lack of cell spreading and communication were observed following treatment with AD-01, explaining the anti-migratory phenotype. Concomitantly, AD-01 inhibited Rac-1 activity, up-regulated RhoA and the actin binding proteins, profilin and vinculin. Thus the anti-angiogenic protein, FKBPL, and AD-01, offer a promising and alternative approach for targeting both CD44 positive tumours and vasculature networks. © 2013 Yakkundi et al.

Yang, K, Xiang, J, Bao, G, Dang, Q & Bai, X 2013, 'Synthesis of Highly Substituted 4H-Pyrido[1,2-a]pyrimidines via a One-Pot Three-Component Condensation Reaction', ACS Combinatorial Science, vol. 15, no. 9, pp. 519-524.
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Yang, Z, Liao, J, Lai, S, Wu, H, Fan, Z, Qiu, J, Song, Z, Yang, Y & Zhou, D 2013, 'Energy transfer and photoluminescence properties in Bi<SUP>3+</SUP> and Eu<SUP>3+</SUP> co-doped ZnGa<SUB>2</SUB>O<SUB>4</SUB>', Materials Express, vol. 3, no. 4, pp. 350-354.
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Ye, Z, Suggett, DJ, Robakowski, P & Kang, H 2013, 'A mechanistic model for the photosynthesis–light response based on the photosynthetic electron transport of photosystem II in C₃ and C₄ species', New Phytologist, vol. 199, no. 1, pp. 110-120.
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SummaryA new mechanistic model of the photosynthesis–light response is developed based on photosynthetic electron transport via photosystem II (PSII) to specifically describe light‐harvesting characteristics and associated biophysical parameters of photosynthetic pigment molecules. This model parameterizes ‘core’ characteristics not only of the light response but also of difficult to measure physical parameters of photosynthetic pigment molecules in plants.Application of the model to two C3 and two C4 species grown under the same conditions demonstrated that the model reproduced extremely well (r2 > 0.992) the light response trends of both electron transport and CO2 uptake.In all cases, the effective absorption cross‐section of photosynthetic pigment molecules decreased with increasing light intensity, demonstrating novel operation of a key mechanism for plants to avoid high light damage.In parameterizing these previously difficult to measure characteristics of light harvesting in higher plants, the model provides a new means to understand the mechanistic processes underpinning variability of CO2 uptake, for example, photosynthetic down‐regulation or reversible photoinhibition induced by high light and photoprotection. However, an important next step is validating this parameterization, possibly through application to less structurally complex ...

Ye, Z-P, Robakowski, P & Suggett, DJ 2013, 'A mechanistic model for the light response of photosynthetic electron transport rate based on light harvesting properties of photosynthetic pigment molecules', Planta, vol. 237, no. 3, pp. 837-847.
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Models describing the light response of photosynthetic electron transport rate (ETR) are routinely used to determine how light absorption influences energy, reducing power and yields of primary productivity; however, no single model is currently able to provide insight into the fundamental processes that implicitly govern the variability of light absorption. Here we present development and application of a new mechanistic model of ETR for photosystem II based on the light harvesting (absorption and transfer to the core 'reaction centres') characteristics of photosynthetic pigment molecules. Within this model a series of equations are used to describe novel biophysical and biochemical characteristics of photosynthetic pigment molecules and in turn light harvesting; specifically, the eigen-absorption cross-section and the minimum average lifetime of photosynthetic pigment molecules in the excited state, which describe the ability of light absorption of photosynthetic pigment molecules and retention time of excitons in the excited state but are difficult to be measured directly. We applied this model to a series of previously collected fluorescence data and demonstrated that our model described well the light response curves of ETR, regardless of whether dynamic down-regulation of PSII occurs, for a range of photosynthetic organisms (Abies alba, Picea abies, Pinus mugo and Emiliania huxleyi). Inherent estimated parameters (e. g. maximum ETR and the saturation irradiance) by our model are in very close agreement with the measured data. Overall, our mechanistic model potentially provides novel insights into the regulation of ETR by light harvesting properties as well as dynamical down-regulation of PSII. © 2012 Springer-Verlag Berlin Heidelberg.

Yebra, M, Van Dijk, A, Leuning, R, Huete, A & Guerschman, JP 2013, 'Evaluation of optical remote sensing to estimate actual evapotranspiration and canopy conductance', REMOTE SENSING OF ENVIRONMENT, vol. 129, pp. 250-261.
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We compared estimates of actual evapotranspiration (ET) produced with six different vegetation measures derived from the MODerate resolution Imaging Spectroradiometer (MODIS) and three contrasting estimation approaches using measurements from eddy covariance flux towers at 16 FLUXNET sites located over six different land cover types. The aim was to assess optimal approaches in using optical remote sensing to estimate ET. The first two approaches directly regressed various MODIS vegetation indices (VIs) and products such as leaf area index (LAI) and fraction of photosynthetically active radiation (fPAR) with ET and evaporative fraction (EF). In the third approach, the Penman-Monteith (PM) equation was inverted to obtain surface conductance (Gs), for dry plant canopies. The Gs values were then regressed against the MODIS data products and used to parameterize the PM equation for retrievals of ET. Jack-Knife cross-validation was used to evaluate the various regression models against observed ET. The PM-Gs approach provided the lowest root mean square error (RMSE), and highest determination coefficients (R2) across all sites, with an average RMSE=38Wm-2 and R2=0.72. Direct regressions of observed ET against the VIs resulted in an average RMSE=60Wm-2 and R2=0.22, while the EF regressions an average RMSE=42Wm-2 and R2=0.64. The MODIS LAI and fPAR product produced the poorest estimates of ET (RMSE>44Wm-2 and R2<0.6); while the VIs each performed best for some of the land cover types. The enhanced vegetation index (EVI) produced the best ET estimates for evergreen needleleaf forest (RMSE=28.4Wm-2, R2=0.66). The normalized difference vegetation index (NDVI) best estimated ET in grassland (RMSE=23.8Wm-2 and R2=0.68), cropland (RMSE=29.2Wm-2 and R2=0.86) and woody savannas (RMSE=25.4Wm-2 and R2=0.82), while the VI-based crop coefficient (Kc) yielded the best estimates for evergreen and deciduous broadleaf forests (RMSE=27Wm-2 and R2=0.7 in both cases). Using the e...

Yeganeh, B, Xia, C, Movassagh, H, Koziol-White, C, Chang, Y, Al-Alwan, L, Bourke, JE & Oliver, BGG 2013, 'Emerging mediators of airway smooth muscle dysfunction in asthma', Pulmonary Pharmacology & Therapeutics, vol. 26, no. 1, pp. 105-111.
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Phenotypic changes in airway smooth muscle are integral to the pathophysiological changes that constitute asthma - namely inflammation, airway wall remodelling and bronchial hyperresponsiveness. In vitro and in vivo studies have shown that the proliferative, secretory and contractile functions of airway smooth muscle are dysfunctional in asthma. These functions can be modulated by various mediators whose levels are altered in asthma, derived from inflammatory cells or produced by airway smooth muscle itself. In this review, we describe the emerging roles of the CXC chemokines (GROs, IP-10), Th17-derived cytokines (IL-17, IL-22) and semaphorins, as well as the influence of viral infection on airway smooth muscle function, with a view to identifying new opportunities for therapeutic intervention in asthma. © 2012.

Yepuri, NR, Barraud, N, Mohammadi, NS, Kardak, BG, Kjelleberg, S, Rice, SA & Kelso, MJ 2013, 'Synthesis of cephalosporin-3′-diazeniumdiolates: biofilm dispersing NO-donor prodrugs activated by β-lactamase', Chemical Communications, vol. 49, no. 42, pp. 4791-4791.
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Use of biofilm dispersing NO-donor compounds in combinationwith antibiotics has emerged as a promising new strategy fortreating drug-resistant bacterial biofilm infections.This paper detailsthe synthesis and preliminary evaluation of six cephalosporin-30-diazeniumdiolates as biofilm-targeted NO-donor prodrugs. Eachof the compounds is shown to selectively release NO followingreaction with the bacteria-specific enzymeb-lactamas and totrigger dispersion ofPseudomonas aeruginosa biofilmsin vitro.

York, PH, Gruber, RK, Hill, R, Ralph, PJ, Booth, DJ & Macreadie, PI 2013, 'Physiological and Morphological Responses of the Temperate Seagrass Zostera muelleri to Multiple Stressors: Investigating the Interactive Effects of Light and Temperature', PLOS ONE, vol. 8, no. 10.
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Understanding how multiple environmental stressors interact to affect seagrass health (measured as morphological and physiological responses) is important for responding to global declines in seagrass populations. We investigated the interactive effects of temperature stress (24, 27, 30 and 32°C) and shading stress (75, 50, 25 and 0% shade treatments) on the seagrass Zostera muelleri over a 3-month period in laboratory mesocosms. Z. muelleri is widely distributed throughout the temperate and tropical waters of south and east coasts of Australia, and is regarded as a regionally significant species. Optimal growth was observed at 27°C, whereas rapid loss of living shoots and leaf mass occurred at 32°C. We found no difference in the concentration of photosynthetic pigments among temperature treatments by the end of the experiment; however, up-regulation of photoprotective pigments was observed at 30°C. Greater levels of shade resulting in high photochemical efficiencies, while elevated irradiance suppressed effective quantum yield (ΔF/FM'). Chlorophyll fluorescence fast induction curves (FIC) revealed that the J step amplitude was significantly higher in the 0% shade treatment after 8 weeks, indicating a closure of PSII reaction centres, which likely contributed to the decline in ΔF/FM' and photoinhibition under higher irradiance. Effective quantum yield of PSII (ΔF/FM') declined steadily in 32°C treatments, indicating thermal damage. Higher temperatures (30°C) resulted in reduced above-ground biomass ratio and smaller leaves, while reduced light led to a reduction in leaf and shoot density, above-ground biomass ratio, shoot biomass and an increase in leaf senescence. Surprisingly, light and temperature had few interactive effects on seagrass health, even though these two stressors had strong effects on seagrass health when tested in isolation. In summary, these results demonstrate that populations of Z. muelleri in south-eastern Australia are sensitive to...

Yuan, X, Wen, S, Shen, M & Shi, X 2013, 'Dendrimer-stabilized silver nanoparticles enable efficient colorimetric sensing of mercury ions in aqueous solution', Analytical Methods, vol. 5, no. 20, pp. 5486-5486.
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Yunusa, IAM, Manoharan, V, Harris, R, Lawrie, R, Pal, Y, Quiton, JT, Bell, R & Eamus, D 2013, 'Differential growth and yield by canola (Brassica napus L.) and wheat (Triticum aestivum L.) arising from alterations in chemical properties of sandy soils due to additions of fly ash', JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, vol. 93, no. 5, pp. 995-1002.
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Background There is a need for field trials on testing agronomic potential of coal fly ash to engender routine use of this technology. Two field trials were undertaken with alkaline and acidic fly ashes supplied at between 3 and 6 Mg ha1 to acidic soils and sown to wheat and canola at Richmond (Eastern Australia) and to wheat only at Merredin (Western Australia). Results Ash addition marginally (P< 0.10) raised the pH in the top soil layers at both sites. The exceptionally dry season at both sites constrained yields and thwarted any likelihood of gaining yield benefits from ash-induced improvements in soil conditions. Yield improvements due to ash addition were absent at Merredin and only marginal at Richmond, where no elevated accumulation of B, Mo, Se, P or S in either the straw or seeds of wheat was observed; canola increased accumulation of Mo and Se in its shoot with acidic fly ash, but it was well below phyto toxic levels. Simulations of wheat using APSIM at Richmond over a 100-year period (19092008) predicted yield increases in 52% of years with addition of ash at 3.0 Mg ha1 compared with 24% of years with addition of ash at 6.0 Mg ha1. The simulated yield increases did not exceed 40% over the control with addition of 6 Mg ha1 ash, but was between 40% and 50% with an addition rate of 3 Mg ha1. Conclusion We found no evidence of phytotoxicity in either crop in this unusually dry year and there is still a need for further field assessment in years with favourable rainfall to enable development of clear recommendations on fly ash rates for optimum yield benefits

Zaslawski, C 2013, 'Editorial', Australian Journal of Acupuncture and Chinese Medicine, vol. 8, no. 1, p. 1.

Zhang, J, Sun, B, Ahn, H-J, Wang, C & Wang, G 2013, 'Conducting polymer-doped polyprrrole as an effective cathode catalyst for Li-O-2 batteries', MATERIALS RESEARCH BULLETIN, vol. 48, no. 12, pp. 4979-4983.
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Polypyrrole conducting polymers with different dopants have been synthesized and applied as the cathode catalyst in Li-O2 batteries. Polypyrrole polymers exhibited an effective catalytic activity towards oxygen reduction in lithium oxygen batteries. It was discovered that dopant significantly influenced the electrochemical performance of polypyrrole. The polypyrrole doped with Cl- demonstrated higher capacity and more stable cyclability than that doped with ClO4-. Polypyrrole conducting polymers also exhibited higher capacity and better cycling performance than that of carbon black catalysts. © 2013 Elsevier Ltd. All rights reserved.

Zhang, L, McKay, A & Jin, D 2013, 'High-throughput 3-dimensional time-resolved spectroscopy: simultaneous characterisation of luminescence properties in spectral and temporal domains', RSC Advances, vol. 3, no. 23, pp. 8670-8670.
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Lanthanide luminescence is presented in full spectral and temporal detail by challenging the limits of low-light sensing and high-speed data acquisition. A robust system is demonstrated, capable of constructing high-resolution time-resolved spectra with high throughput processing. This work holds real value in advancing characterisation capability to decode interesting insights within lanthanide materials. © The Royal Society of Chemistry 2013.

Zhang, Y, Moran, MS, Nearing, MA, Campos, GEP, Huete, AR, Buda, AR, Bosch, DD, Gunter, SA, Kitchen, SG, McNab, WH, Morgan, JA, McClaran, MP, Montoya, DS, Peters, DPC & Starks, PJ 2013, 'Extreme precipitation patterns and reductions of terrestrial ecosystem production across biomes', JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, vol. 118, no. 1, pp. 148-157.
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Precipitation regimes are predicted to shift to more extreme patterns that are characterized by more heavy rainfall events and longer dry intervals, yet their ecological impacts on vegetation production remain uncertain across biomes in natural climatic conditions. This in situ study investigated the effects of these climatic conditions on aboveground net primary production (ANPP) by combining a greenness index from satellite measurements and climatic records during 2000-2009 from 11 long-term experimental sites in multiple biomes and climates. Results showed that extreme precipitation patterns decreased the sensitivity of ANPP to total annual precipitation (PT) at the regional and decadal scales, leading to decreased rain use efficiency (RUE; by 20% on average) across biomes. Relative decreases in ANPP were greatest for arid grassland (16%) and Mediterranean forest (20%) and less for mesic grassland and temperate forest (3%). The cooccurrence of heavy rainfall events and longer dry intervals caused greater water stress conditions that resulted in reduced vegetation production. A new generalized model was developed using a function of both PT and an index of precipitation extremes and improved predictions of the sensitivity of ANPP to changes in precipitation patterns. Our results suggest that extreme precipitation patterns have substantially negative effects on vegetation production across biomes and are as important as P T. With predictions of more extreme weather events, forecasts of ecosystem production should consider these nonlinear responses to altered extreme precipitation patterns associated with climate change. Key Points Extreme rainfall events reduced the sensitivity of ANPP to total annual rainfallCo-occurrence of intense rainfall and longer dry interval reduced greater ANPPA new model improved predictions of ANPP by accounting for extreme patterns ©2012. American Geophysical Union. All Rights Reserved.

Zhang, Y, Wang, C, Yao, F, Zhu, X, Qu, Q, Hu, X & Wang, G 2013, 'Determination of alkylamine carbonate nonionic–anion oil displacement agent in oil-field water using HPLC after derivatization with 4-methoxybenzenesulfonyl fluoride', Anal. Methods, vol. 5, no. 3, pp. 729-734.
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In this study, a method for the determination of alkylamine carbonate (AAC) nonionic-anion oil displacement agent in oil-field water was developed for the first time, involving pre-column derivatization using a novel labeling agent and HPLC with diode-array detection. The derivatization and chromatographic separation conditions were investigated thoroughly. The analyte was labeled with 4-methoxybenzenesulfonyl fluoride at 50 °C for 20 min. When the method was applied in the determination of C18A5C (an AAC oil displacement agent containing eighteen alkyl and five amino groups) a linear calibration curve was obtained from 1.0 to 100.0 μg mL^-1 with a correlation coefficient of more than 0.999 and a detection limit of 0.05 μg mL^-1. In the determination of real oil-field water samples, the recovery range of C18A5C was 91.8% to 96.2%, and the intra-day and inter-day relative standard deviations were 2.9-3.5% and 3.8-4.3%, respectively. The experimental results demonstrate that this method, with its merits of simplicity in pretreatment, rapidity in derivatization, and stability of the derivatives, can be employed in the analysis of C18A5C and has potential application in the detection of other oil displacement surfactants containing amino groups. It is of great significance to develop a fast, easy-to-operate, sensitive and reliable method for environmental impact assessment. © The Royal Society of Chemistry 2013.

Zhao, C, Liu, C, Zhao, J, Xia, J, Yu, Q & Eamus, D 2013, 'Zooplankton in highly regulated rivers: Changing with water environment', ECOLOGICAL ENGINEERING, vol. 58, no. 1, pp. 323-334.
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The Huai River Basin (HRB) of China is well-known globally for the extent of severe human activities (e.g., waste disposal and water project construction) which have resulted in severe water pollution and subsequently degraded water ecosystem quality in recent decades. However, influence of water pollution on water ecosystems has not yet been fully realized due to lack of water ecosystem data. In food webs of freshwater ecosystems, zooplankton occupy a critical position but they are highly susceptible to pollutants and temperature which in turn impact the community structure and biodiversity of zooplankton to a great extent. This paper aimed to assess impact of water chemistry variation on zooplankton through ecological-niche models and spatial heterogeneity of zooplankton along with water chemistry in the HRB. We investigated the impacts of nine dominant water chemistry indicators on zooplankton distribution and composition via ecological niche models based on water chemistry status and zooplankton communities at 71 typical sites of the HRB. A fuzzy clustering method (FCM) was employed to help study the impact characteristics and the spatial heterogeneity. Results indicate that across the nine water chemistry indicators, changes in water temperature has minimal impact on the zooplankton community of the Huai River while small variation in ammonianitrogen exerts significant stress on the community; with respect to water temperature and total phosphorous zooplankton species in the HRB are coexisting with little competition; as to spatial heterogeneity of zooplankton communities, communities in the southwest and southeast mountainous regions may adapt well to habitat variations, while those in the middle and northeast areas have a weak adaptability to habitat changes.

Zhao, J, Jin, D, Schartner, EP, Lu, Y, Liu, Y, Zvyagin, AV, Zhang, L, Dawes, JM, Xi, P, Piper, JA, Goldys, EM & Monro, TM 2013, 'Single-nanocrystal sensitivity achieved by enhanced upconversion luminescence', Nature Nanotechnology, vol. 8, no. 10, pp. 729-734.
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Upconversion nanocrystals convert infrared radiation to visible luminescence, and are promising for applications in biodetection1-3, bioimaging4-7, solar cells8-10 and three-dimensional display technologies8,9,11. Although the design of suitable nanocrystals has improved the performance of upconversion nanocrystals10,12-14, their emission brightness is limited by the low doping concentration of activator ions needed to avoid the luminescence quenching that occurs at high concentrations15,16. Here, we demonstrate that high excitation irradiance can alleviate concentration quenching in upconversion luminescence when combined with higher activator concentration, which can be increased from 0.5 mol% to 8 mol% Tm31 in NaYF4. This leads to significantly enhanced luminescence signals, by up to a factor of 70. By using such bright nanocrystals, we demonstrate remote tracking of a single nanocrystal with a microstructured optical-fibre dip sensor. This represents a sensitivity improvement of three orders of magnitude over benchmark nanocrystals such as quantum dots17. © 2013 Macmillan Publishers Limited. All rights reserved.

Zhao, J, Lu, Z, Yin, Y, McRae, C, Piper, JA, Dawes, JM, Jin, D & Goldys, EM 2013, 'Upconversion luminescence with tunable lifetime in NaYF₄:Yb,Er nanocrystals: role of nanocrystal size', Nanoscale, vol. 5, no. 3, pp. 944-952.
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Despite recent achievements to reduce surface quenching in NaYF 4:Yb,Er nanocrystals, a complete understanding of how the nanocrystal size affects the brightness of upconversion luminescence is still incomplete. Here we investigated upconversion luminescence of Yb,Er-doped nanocrystals in a broad range of sizes from 6 nm to 45 nm (cubic or hexagonal phases), displaying an increasing red-to-green luminescence intensity ratio and reduced luminescence lifetimes with decreasing size. By analyzing the upconversion process with a set of rate equations, we found that their asymptotic analytic solutions explain lower decay rates of red compared to green upconversion luminescence. Furthermore, we quantified the effect of the surface on luminescence lifetime in a model where nanocrystal emitters are divided between the near-surface and inside regions of each nanocrystal. We clarify the influence of the four nonradiative recombination mechanisms (intrinsic phonon modes, vibration energy of surface ligands, solvent-mediated quenching, and surface defects) on the decay rates for different-size nanocrystals, and find that the defect density dominates decay rates for small (below 15 nm) nanocrystals. Our results indicate that a defect-reduction strategy is a key step in producing small upconversion nanocrystals with increased brightness for a variety of bioimaging and biosensing applications. © 2013 The Royal Society of Chemistry.

Zheng, F, Wang, S, Wen, S, Shen, M, Zhu, M & Shi, X 2013, 'Characterization and antibacterial activity of amoxicillin-loaded electrospun nano-hydroxyapatite/poly(lactic-co-glycolic acid) composite nanofibers', Biomaterials, vol. 34, no. 4, pp. 1402-1412.
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Zhou, J, Deng, J, Zhu, H, Chen, X, Teng, Y, Jia, H, Xu, S & Qiu, J 2013, 'Up-conversion luminescence in LaF3:Ho3+via two-wavelength excitation for use in solar cells', Journal of Materials Chemistry C, vol. 1, no. 48, pp. 8023-8023.
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An efficient broadband excited near-infrared to visible up-conversion is observed in LaF3:Ho3+ as the result of a two-wavelength excitation. The visible up-conversion emission intensity is greatly enhanced upon simultaneous excitation at 970 nm and 1150 nm, due to an energy transfer up-conversion mechanism. Multi-wavelength excitation based on the ground-state absorption, excited-state absorption, and phonon-coupled absorption of rare-earth ions results in an efficient broadband excited up-conversion emission, which may provide a new approach to fully harvest NIR solar energy and has potential application in solar cells.

Zhou, J, Shirahata, N, Sun, H-T, Ghosh, B, Ogawara, M, Teng, Y, Zhou, S, Chu, RGS, Fujii, M & Qiu, J 2013, 'Efficient Dual-Modal NIR-to-NIR Emission of Rare Earth Ions Co-doped Nanocrystals for Biological Fluorescence Imaging', JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 4, no. 3, pp. 402-408.
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A novel approach has been developed for the realization of efficient near-infrared to near-infrared (NIR-to-NIR) upconversion and down-shifting emission in nanophosphors. The efficient dual-modal NIR-to-NIR emission is realized in a β-NaGdF4/Nd3+@NaGdF4/Tm3+–Yb3+ core–shell nanocrystal by careful control of the identity and concentration of the doped rare earth (RE) ion species and by manipulation of the spatial distributions of these RE ions. The photoluminescence results reveal that the emission efficiency increases at least 2-fold when comparing the materials synthesized in this study with those synthesized through traditional approaches. Hence, these core–shell structured nanocrystals with novel excitation and emission behaviors enable us to obtain tissue fluorescence imaging by detecting the upconverted and down-shifted photoluminescence from Tm3+ and Nd3+ ions, respectively. The reported approach thus provides a new route for the realization of high-yield emission from RE ion doped nanocrystals, which could prove to be useful for the design of optical materials containing other optically active centers.

Zhu, J, Yu, J, Wang, P, Yu, Q & Eamus, D 2013, 'Distribution patterns of groundwater-dependent vegetation species diversity and their relationship to groundwater attributes in northwestern China', ECOHYDROLOGY, vol. 6, no. 2, pp. 191-200.
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The study of the patterns of plant species diversity and the factors influencing these patterns is the basis of ecology and is also fundamental to conservation biology. Groundwater-dependent vegetation (GDV) must have access to groundwater to maintain their growth and function, and this is especially common in arid and semi-arid regions, including north-western China. In this paper, plant species diversity and groundwater attributes (composition and depth) were investigated in 31 plots in the Ejina Delta in north-western China to determine whether groundwater attributes influenced patterns species diversity in GDV. Detrended canonical correspondence analyses and generalised additive models were performed to analyse the data. A total of 29 plant species were recorded in the 31 plots; perennial herbs with deep roots had an advantage over all other groups, and GDV species diversity was primarily affected by groundwater depth (GWD), salinity (SAL) and total dissolved solids (TDS), HCO3, Ca2+, pH, and SO42. The herb layer species diversity and total species diversity reached their maximum in similar, moderate environmental conditions. The diversity of the tree species was influenced by SAL and TDS and was maximal at large values of GWD and low values of SAL and TDS. The diversity of shrub species was affected by Ca2+ and Mg2+ and was maximal low GWD and high SAL and TDS. Patrick's and ShannonWiener's index of the total community diversity presented a bimodal pattern along gradients of GWD and SAL, whilst Simpson's and Pielou's index showed a partially unimodal pattern. On the basis of field investigation and the analysis of field data, we concluded that the perfect combination of GWD and SAL for GDV species diversity is 2m and 1 center dot 8gl1, respectively. The appropriate combination range is 25m and 1 center dot 84 center dot 2gl1, and the critical combination for the damaged GDV species diversity is 5m and 4 center dot 2gl1.

Zhu, L, Ton-That, C & Phillips, MR 2013, 'Nitrogen incorporation in ZnO nanowires using N2O dopant gas', MATERIALS LETTERS, vol. 99, no. 1, pp. 42-45.
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Aligned nitrogen-doped ZnO nanowires were grown by chemical vapour deposition using Au catalyst. N incorporation was achieved through the introduction of N2O gas as a dopant source and confirmed by Raman spectroscopy, which reveals additional N-related modes at 275, 580 and 642 cm-1. The nanowires have a hexagonal faceted shape and are predominantly grown along the [001] direction. The nanowire morphology is unaffected by N incorporation. The luminescence peak at 3.24 eV was monitored as a function of N2O content. Intensity analysis of this band reveals that it can be partly attributed to donor-acceptor pair (DAP) emission originating from the N doping. © 2013 Elsevier B.V. All rights reserved.

Zhu, Q-H, Stephen, S, Kazan, K, Jin, G, Fan, L, Taylor, J, Dennis, ES, Helliwell, CA & Wang, M-B 2013, 'Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq', GENE, vol. 512, no. 2, pp. 259-266.
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We analyzed analyzed the dynamic defense transcriptome responsive to Fusarium oxysporum infection in Arabidopsis using a strand-specific RNA-sequencing approach. Following infection, 177 and 571 genes were up-regulated, 30 and 125 genes were down-regulat

Zinder, Y, Memar, J & Singh, G 2013, 'Discrete optimization with polynomially detectable boundaries and restricted level sets', JOURNAL OF COMBINATORIAL OPTIMIZATION, vol. 25, no. 2, pp. 308-325.
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The paper describes an optimization procedure for a class of discrete optimization problems which is defined by certain properties of the boundary of the feasible region and level sets of the objective function. It is shown that these properties are possessed, for example, by various scheduling problems, including a number of well known NP-hard problems which play an important role in scheduling theory. For one of these problems the presented optimization procedure is compared with a version of the branch-and-bound algorithm by means of computational experiments. © 2012 Springer Science+Business Media, LLC.

Zou, LE, Kabakova, IV, Mägi, EC, Li, E, Florea, C, Aggarwal, ID, Shaw, B, Sanghera, JS & Eggleton, BJ 2013, 'Efficient inscription of Bragg gratings in As_2S_3 fibers using near bandgap light', Optics Letters, vol. 38, no. 19, pp. 3850-3850.
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Aguilar, JLC, Smith, GB, Gentle, AR & Chen, D 1970, 'Optimum integration of albedo, sub-roof R-value, and phase change material for cool roofs', Proceedings of BS 2013: 13th Conference of the International Building Performance Simulation Association, International Conference of the International Building Performance Simulation Association, International Building Performance Simulation Association (IBPSA), Chambery, France, pp. 1315-1321.
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A cool roof aims to reduce total seasonal cooling loads and peak summer loads. It is often rated just in terms of its solar reflectance Rsol (or albedo), with some impact of infrared emittance considered. However the sensitivity of cooling loads to Rsolvaries as the R-value of sub-roof insulation changes. Knowing joint impacts led to better integrated energy savings design with R-value chosen on the basis of Rsol and local climate. This study extends previous work (Gentle et al., 2011) (Smith et al., 2012) (Aguilar et al., 2012) by considering the impact of phase change materials (PCM) within a roofing module on energy savings. The aim is to show how building simulation helps pinpoint the optimum combination. Copyright © 2011 by IPAC'11/EPS-AG.

Ajani, P 1970, 'Algal Blooms: the good, the bad and the downright toxic!', Diverse Depths: Sea Beneath the Shallows Forum, Sydney Coastal Council Group.
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Invited Oral presentation

Ajani, P, Armand, L, Murray, S, Brett, S & Hallegraeff, G 1970, 'Morphological, molecular and toxicological characterization of the diatom genus Pseudo-nitzschia in south eastern Australian coastal waters', 9th International Conference on Molluscan Shellfish Safety 2013, International Conference on Molluscan Shellfish Safety, Sydney 2013. Morphological, molecular and toxicological characterization of the diatom genus Pseudo-nitzschia in south eastern Australian coastal waters. P, Sydney, Australia.
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Oral Presentation, Runner Up Best Student Presentation (Oral Presentation - Runner Up Best Student Presentation),

Baldeaux, J & Platen, E 1970, 'Computing Functionals of Square Root and Wishart Processes Under the Benchmark Approach via Exact Simulation', Monte Carlo and Quasi Monte Carlo Methods 2012, Springer Proceedings in Mathematics and Statistics, International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing, Springer Berlin Heidelberg, Sydney, Australia, pp. 3-22.
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The aim of the paper is to show how Wishart processes can be used flexibly in financial modeling. We explain how functionals, resulting from the benchmark approach to finance, can be accurately computed via exact simulation methods. We employ Lie symmetry methods to identify explicit transition densities and explicitly computable functionals. We illustrate the proposed methods via finance problems formulated under the benchmark approach. This approach allows us to exploit conveniently the analytical tractability of the considered diffusion processes.

Berle, C, Zaslawski, C, Cobbin, D, Meier, P, Walsh, S & Cheah, SL 1970, 'The effect of acupuncture treatment compared to sham laser for lateral elbow pain: a randomised controlled pilot study', Australian Journal of Acupunture and Chinese Medicine, WFAS World Federation of Acupuncture Societies, Australian Acupuncture and chinese Medicine Association, Sydney, pp. 25-32.
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Background: Lateral elbow pain is a common painful musculoskeletal condition affecting approximately 1–3% of the population. Methods: A randomised participant-blinded controlled pilot study was undertaken to determine whether acupuncture could relieve pain and improve function for this condition. Twenty participants were randomly allocated to either a standardised acupuncture protocol (n= 11) or sham laser (n= 9) over ten sessions. Outcome measures were PPT test, McGill/Melzac pain, DASH and VAS pain questionnaires. Participants were evaluated at baseline, on completion of treatment (week five) and one month later. Results: There was no significant difference between the groups at baseline for any outcome parameter. There were no significant changes found at completion or one month follow-up for the PPT and VAS measures. There were significant improvements for the acupuncture group for the McGill questionnaire at week five for the affective (p= 0.01) and miscellaneous (p= 0.02) sections; week nine total score (p< 0.03), affective (p= 0.01) and miscellaneous (p= 0.01) sections; the DASH at week five for work (p= 0.02) and sport (p= 0.01) modules and week nine general (p < 0.04), work (p= 0.01) and sport (p= 0.006) modules. There were no significant changes for any outcome measure for the control group. There was no significant difference found between the two groups for blinding efficacy (expectancy/credibility scale) and experience of deqiat baseline or on completion. Conclusion: Results indicate that acupuncture may be helpful in alleviating pain and improving arm functionality, but small participant numbers preclude any definitive conclusions, a larger sufficiently powered study is required.

Bonnie, F, Arnold, MD, Smith, GB & Gentle, AR 1970, 'Modes of interaction between nanostructured metal and a conducting mirror as a function of separation and incident polarization', NANOSTRUCTURED THIN FILMS VI, Nanostructured Thin Films, SPIE, San Diego. USA, pp. 1-10.
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The optical resonances that occur in nanostructured metal layers are modulated in thin film stacks if the nanostructured layer is separated from a reflecting conducting layer by various thicknesses of thin dielectric. We have measured and modeled the optical response of interacting silver layers, with alumina spacer thickness ranging from a few nm to 50 nm, for s- and p-polarized incident light, and a range of incident angles. Standard thin film models, including standard effective medium models for the nanostructured layer, will break down for spacer thickness below a critical threshold. For example, with polarisation in the film plane and some nano-islands, it may occur at around 10 nm depending on spacer refractive index. Of particular interest here are novel effects observed with the onset of percolation in the nanolayer. Hot spot effects can be modified by nearby mirrors. Other modes to consider include (a) a two-particle mode involving a particle and its mirror image (b) A Fano resonance from hybridisation of localized and de-localised plasmon modes (c) a Babinet's core-(partial) shell particle with metal core-dielectric shell in metal (d) spacing dependent phase modulation (e) the impact of field gradients induced by the mirror at the nano-layer. © 2013 Copyright SPIE.

Brennan, SE, Tran, N, Clayton, A, McGowan, EM, Cozzi, PJ & Martiniello-Wilks, R 1970, 'PROSTATE CANCER EXOSOMES OFFERING NOVEL CIRCULATING BIOMARKERS FOR EARLY CANCER DIAGNOSIS AND PROGNOSIS', JOURNAL OF GENE MEDICINE, 8th Meeting of the Australasian-Gene-Therapy-Society, WILEY-BLACKWELL, Univ Technol, Sydney, AUSTRALIA, pp. 331-332.

Bretherton, L, Lawson, T, Moore, CM, Poulton, A, Geider, R & Suggett, D 1970, 'LIGHT AVAILABILITY AFFECTS THE OCEAN ACIDIFCATION RESPONSE IN COCCOLITHOPHORES', PHYCOLOGIA, INT PHYCOLOGICAL SOC, pp. 13-13.

Burgess, J, Jaffar, J, Unger, S, Keller, M, Corte, T, Wolters, P, Richeldi, L, Cerri, S, Argraves, WS, Black, J & Oliver, B 1970, 'Fibulin-1 is a novel biomarker of disease severity in pulmonary fibrosis', EUROPEAN RESPIRATORY JOURNAL, EUROPEAN RESPIRATORY SOC JOURNALS LTD.

Buttner, TFS, Kabakova, IV, Hudson, DD & Eggleton, BJ 1970, 'Picosecond pulse burst generation using cascaded Stimulated Brillouin Scattering in a chalcogenide As<inf>2</inf>Se<inf>3</inf> fiber cavity', 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, IEEE.
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Stimulated Brillouin Scattering (SBS) is an inelastic scattering process that has been exploited for applications ranging from tunable delay, microwave generation to sensing and lasers. The recent demonstration [1] of a frequency comb laser based on cascaded SBS in silica fiber has renewed interest in using SBS to generate ultra-high frequency picosecond pulses [2]. In [1] a broad SBS frequency comb is generated in a long (e.g. kilometres) ring cavity using an erbium doped fiber amplifier (EDFA) as gain medium. © 2013 IEEE.

Büttner, TFS, Kabakova, IV, Hudson, DD & Eggleton, BJ 1970, 'Picosecond pulse burst generation using cascaded Stimulated Brillouin Scattering in a chalcogenide As2Se3 fiber cavity', Optics InfoBase Conference Papers.

Canning, J, Ma, M, Gibson, B, Huyang, G, Beavis, A, Bishop, D, Cook, K, McDonagh, A, Shi, J, Shi, D, Peng, G-D & Crossley, M 1970, 'The nanostructure of silica microfibers fabricated by microfluidic self-assembly', FOURTH ASIA PACIFIC OPTICAL SENSORS CONFERENCE, Asia Pacific Optical Sensors Conference (APOS), SPIE.
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The porous properties of self-assembled waveguides made up of nanoparticles are characterised. Atomic force microscopy (AFM) reveals predominantly hcp or fcc packing suggesting a remarkably well ordered and distributed porous structure. N2 adsorption studies estimate a surface area SA ∼ 101 m2/g, a total interstitial volume Vi ∼ 1.7 mL/g and a pore size distribution of r ∼ (2 - 6) nm. This distribution is in excellent agreement with the idealised values for identically sized particles obtained for the octahedral and tetrahedral pores of the hcp and fcc lattices, estimated to lie within and rtet ∼ (2.2 - 3.3) nm and roct ∼ (4.2 - 6.2) nm for particles varying in size over 20 to 30 nm. Optical transmission based percolation studies reveal rapid penetration of Rhodamine dye ( < 5 s) with very little percolation of larger molecules such as ZnTPP observed under similar loading conditions. In the latter case, laser ablation was used to determine the transport of hydrated Zn2+ to be D ∼ 3 x 10-4 nm2s-1. By comparison, ZnTPP was not able to percolate into the wire over the time of exposure, t = 10 mins, effectively demonstrating the self-assembled structure acting as a molecular sieve. We discuss the potential of such structures more broadly and conclude that the controllable distribution of such nano-chambers offers the possibility of amplifying, or up-scaling, an otherwise local interaction or nanoreactions to make detection and diagnostics much simpler; it als o opens up a new approach to material engineering making new composites with periodic nanoscale variability. These and other unique aspects of these structures are embodied in an overall concept of lab-in-wire, or similar self-assembled structures, extending our previous concept of lab-in-fibre from the micro domain into the nano domain. © 2013 SPIE.

Castelletto, S, Johnson, BC, Aharonovich, I & Parker, A 1970, 'FLUORESCENT EMISSION IN DIFFERENT SILICON CARBIDE POLYTYPES', MICRO/NANO MATERIALS, DEVICES, AND SYSTEMS, Conference on Micro/Nano Materials, Devices, and Systems, SPIE, Australia.
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Silicon carbide (SiC) is a widely used material in several industrial applications such as high power electronics, light emitting diodes, and in research application such as photo-voltaic and quantum technologies. As nanoparticles it can be synthetised in many sizes and different polytypes from 200 nm down to 1 nm. In the form of quantum dots they are used as optical biomarkers, and their emission, occurring from the blue to the orange spectral region, is based on quantum confinement effect. In this work we report on emission in the red and near infrared in different SiC polytypes, specifically in 4H, 6H and 3C. In 4H SiC the red visible emission yielded non classical light attributed to an intrinsic defect, identified as a carbon-antisite vacancy pair. Similar spectral emission was observed in 3C SiC bulk and nanoparticles, also yielding very bright single photon emission. Emission in the far red has been observed in homogeneous hetero-structure in SiC tetrapods. © 2013 Copyright SPIE.

Chavez, AA, Gorman, C, Erken, M, Mcdougald, D, Steinberg, PD & Nishiguchi, MK 1970, 'Predation response of Vibrio fischeri biofilms to protozoan bacteriovores', INTEGRATIVE AND COMPARATIVE BIOLOGY, Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), OXFORD UNIV PRESS INC, San Francisco, CA, pp. E34-E34.

Chen, L, Ge, Q, Black, J, Burgess, J & Oliver, B 1970, 'Cigarette smoke extract and TGF-beta(1) induce distinctive expression of extracellular matrix protein genes in human airway smooth muscle cells', EUROPEAN RESPIRATORY JOURNAL, EUROPEAN RESPIRATORY SOC JOURNALS LTD.

Chen, L, Ge, Q, Black, JL, Burgess, JK & Oliver, BG 1970, 'Difference Between Matrix And Soluble Fibulin-1 In Airway Smooth Muscle Cells', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Chen, L, Ge, Q, Black, JL, Burgess, JK & Oliver, BGG 1970, 'DIFFERENCES BETWEEN DEPOSITED AND SOLUBLE FIBULIN-1 IN AIRWAY SMOOTH MUSCLE CELLS', RESPIROLOGY, WILEY-BLACKWELL, pp. 47-47.

Chen, L, Ge, Q, Faiz, A, Black, JL, Burgess, JK & Oliver, BG 1970, 'Cigarette Smoke Extract And Tgf-beta 1 Induce Distinctive Expression Of Extracellular Matrix And Adhesion Molecule Genes In COPD And Non-COPD Airway Smooth Muscle Cells', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Colvin, EK, Fuller, E, Cheng, J, Gill, A, Marsh, DJ & Howell, VM 1970, 'Abstract 330: Utilization of Sleeping Beauty mutagenesis for the identification of potential driver genes of ovarian cancer.', Cancer Research, Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC, American Association for Cancer Research (AACR), pp. 330-330.
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Abstract Background: The goal of this project is to increase our understanding of the molecular aetiology of ovarian cancer by developing a mouse model of this tumor. Inherited mutation of BRCA1 is the best known risk factor for the most common subtype of ovarian cancer, i.e. serous epithelial ovarian cancer (SEOC); however, loss of Brca1 alone is insufficient for SEOC development in the mouse. Somatic mutation of TP53 is the most common molecular change in SEOC, but does not result in SEOC in the mouse, either alone or in combination with loss of Brca1. These findings suggest that additional currently unknown genetic factors are required for ovarian carcinogenesis. We hypothesized that random mutagenesis would activate these genetic factors and utilized Sleeping Beauty (SB) insertional mutagenesis to initiate ovarian tumors in mice that we have sequenced to determine potential genetic drivers of these tumors. Methods: Breeding colonies of the following genetically engineered mice were established and cross bred: homozygous floxed SB (STOCK Rosa26-LsL-D-SB11;T2/Onc2,TG6113), homozygous floxed Brca1 knock-out (C57BL/6.Brca1tm2Brn) and Tp53 mutant (C57BL/6-Trp53tm1Tyj/J). CRE recombinase packaged into an adenoviral vector (AdCreM2, MicroBix Biosystems Inc, CA) was surgically injected under the ovarian bursal membrane of mature female mice to delete Brca1 and activate SB mutagenesis in the ovarian surface epithelium. Mice were monitored and sacrificed at ethically defined endpoints or a maximum of 15 months post-surgery. Tumors were assessed for SB transposase activity by immunohistochemical staining. DNA was extracted from paraffin embedded sections of ovarian tumors and underwent high-throughput sequencing for T2/Onc2 insertion sites (Illumina, University of Iowa). Results: Ovarian tumors were observed at low penetrance starting at 30 weeks pos...

Colvin, EK, Fuller, E, Cheng, J, Gill, A, Marsh, DJ & Howell, VM 1970, 'Abstract A10: A mutagenesis screen identifies tumor suppressors and kinases as potential driver genes of ovarian cancer', Clinical Cancer Research, Abstracts: AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; September 18-21, 2013; Miami, FL, American Association for Cancer Research (AACR), pp. A10-A10.
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Abstract Background: The goal of this project is to increase our understanding of the molecular aetiology of ovarian cancer by utilizing Sleeping Beauty (SB) insertional mutagenesis. Methods: Breeding colonies of the following genetically engineered mice were established and cross bred: homozygous floxed SB (STOCK Rosa26-LsL-D-SB11;T2/Onc2,TG6113), homozygous floxed Brca1 knock-out (C57BL/6.Brca1tm2Brn) and Tp53 mutant (C57BL/6-Trp53tm1Tyj/J). CRE recombinase packaged into an adenoviral vector (AdCreM2, MicroBix Biosystems Inc, CA) was surgically injected under the ovarian bursal membrane of mature female mice to delete Brca1 and activate SB mutagenesis in the ovarian surface epithelium. Mice were monitored and sacrificed at ethically defined endpoints or a maximum of 15 months post-surgery. Tumors were assessed for SB transposase activity by immunohistochemical staining. DNA was extracted from paraffin embedded sections of ovarian tumors and underwent high-throughput sequencing for T2/Onc2 insertion sites (Illumina, University of Iowa). Genes with insertion sites were interrogated against SEOC data from The Cancer Genome Atlas (TCGA) to identify genes also altered in the human malignancy. Functional annotation clustering was performed using DAVID (Database for Annotation, Visualization and Integrated Discovery, v6.7). Results: Ovarian tumors were observed at low penetrance starting at 30 weeks post-surgery in SBflox/+Tp53mut/+ mice (6%, 3/48) and SBflox/+Brca1flox/flox p53mut/+ mice (8%, 4/50). No ovarian tumors were observed in SBflox/+Brca1flox/flox mice (n=38) or in SBflox/+Brca1flox/+ mice (n=26). Sequencing of the insertion sites identified a number of genes of which 67 were altered in 10 - 30% of cases in the TCGA SEOC dataset (N = 316). This gene-set was enriched for kinases (P = 0.003, False discovery rate (FDR) = 3%) including Fgfr2,...

Cranfield, CG, Cornell, B, Grage, SL, Duckworth, P, Carne, S, Ulrich, AS & Martinac, B 1970, 'Characterization of Antimicrobial Peptide Insertion in Tethered Bilayer Lipid Membranes by Pulse Amperometry and Linear Sweep Voltammetry Methods', BIOPHYSICAL JOURNAL, 57th Annual Meeting of the Biophysical-Society, CELL PRESS, Philadelphia, PA, pp. 600A-600A.
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Dawes, JM, Zhao, J, Lu, Z, Yin, Y, Zhang, L, McKay, A, McRae, C, Piper, J, Jin, D & Goldys, EM 1970, 'Characterisation of Upconversion Nanoparticles for Imaging', Asia Communications and Photonics Conference 2013, Asia Communications and Photonics Conference, OSA.
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Devlin, M, Debose, J, Ajani, P & Brodie, J 1970, 'Chlorophyll biomass and phytoplankton community measures in flood plumes increasing the evidence base between degraded water quality and Crown of Thorns', Australian Marine Science Association Conference, Gold Coast, QLD, Australia.
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Oral Presentation

Donovan, C, Faiz, A, Oliver, BG, Black, JL, McParland, BE, Burgess, JK & Bourke, JE 1970, 'Black widow spider toxin, alpha-latrotoxin, contracts large and small airways in different species', EUROPEAN RESPIRATORY JOURNAL, EUROPEAN RESPIRATORY SOC JOURNALS LTD.

Dunlop, RA, Cox, PA, Banack, SA & Rodgers, KJ 1970, 'The non-protein amino acid BMAA is misincorporated into human proteins in place of L-serine causing protein misfolding and aggregation.', PLoS One, MND Australia Research Meeting, United States, p. e75376.
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Mechanisms of protein misfolding are of increasing interest in the aetiology of neurodegenerative diseases characterized by protein aggregation and tangles including Amyotrophic Lateral Sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), Lewy Body Dementia (LBD), and Progressive Supranuclear Palsy (PSP). Some forms of neurodegenerative illness are associated with mutations in genes which control assembly of disease related proteins. For example, the mouse sticky mutation sti, which results in undetected mischarging of tRNA(Ala) with serine resulting in the substitution of serine for alanine in proteins causes cerebellar Purkinje cell loss and ataxia in laboratory animals. Replacement of serine 422 with glutamic acid in tau increases the propensity of tau aggregation associated with neurodegeneration. However, the possibility that environmental factors can trigger abnormal folding in proteins remains relatively unexplored. We here report that a non-protein amino acid, β-N-methylamino-L-alanine (BMAA), can be misincorporated in place of L-serine into human proteins. We also report that this misincorporation can be inhibited by L-serine. Misincorporation of BMAA into human neuroproteins may shed light on putative associations between human exposure to BMAA produced by cyanobacteria and an increased incidence of ALS.

Eggleton, BJ, Poulton, CG, Marpaung, D, Morrison, B, Kabakova, IV, Choi, D-Y, Madden, SJ, Luther-Davies, B & Pant, R 1970, 'On-chip stimulated Brillouin scattering and its applications', SPIE Proceedings, SPIE NanoScience + Engineering, SPIE, San Diego, California, United States.
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We review recent demonstration of stimulated Brillouin scattering in a chalcogenide photonic chip and its application to optical and microwave signal processing tasks. The interaction between light and sound via stimulated Brillouin scattering (SBS) was exploited in chalcogenide photonic circuits to achieve on-chip SBS slow and fast light, microwave photonic filters, and dynamic gratings using travelling-wave geometry. Using a ring-resonator geometry, photonic-chip based Brillouin laser was demonstrated. © 2013 SPIE.

Eilenberger, F, Kabakova, I, Martin De Sterke, C, Eggleton, BJ & Pertsch, T 1970, 'Cavity optical pulse extraction: A novel, ultrashort light source based on nonlinearly seeded hawking radiation', Optics InfoBase Conference Papers.
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We show that light trapped in a linear cavity can be efficiently released into an ultrashort coherent pulse, using a non-resonant trigger pulse. We derive a simplified analytic description of the process and confirm its complex behavior by numerical simulation. This 'Cavity Optical Pulse Extraction' (COPE) process is shown to be analogous to classical Hawking radiation emitted from an optical event horizon with extremely high Hawking temperature. Nonlinear Optics Technical Digest. © OSA 2013.

Eilenberger, F, Kabakova, I, Martin de Sterke, C, Eggleton, BJ & Pertsch, T 1970, 'Cavity Optical Pulse Extraction: a novel, ultrashort light source based on nonlinearly seeded Hawking radiation', Nonlinear Optics, Nonlinear Optics, OSA.
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Faiz, A, Donovan, C, Halayko, AJ, Detillieux, K, Ward, JPT, Lee, T, Oliver, BG, Black, JL, McParland, B, Bourke, JE & Burgess, JK 1970, 'Abnormal Expression Of Latrophilin's Contributes To Increased Airway Smooth Muscle Mass And Contraction In Asthmatic Airways', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Faiz, A, Oliver, BGG, Black, JL & Burgess, JK 1970, 'ABNORMAL EXPRESSION OF LATROPHILINS IN ASTHMATIC AIRWAYS CONTRIBUTES TO INCREASED AIRWAY SMOOTH MUSCLE MASS', RESPIROLOGY, WILEY-BLACKWELL, pp. 23-23.

Faiz, A, Oliver, BGG, Black, JL & Burgess, JK 1970, 'CCL20 PRODUCTION BY AIRWAY SMOOTH MUSCLE CELLS CONTRIBUTES TO MUCUS HYPERSCRETION AND INCREASE MUSCLE MASS IN ASTHMATIC AIRWAYS', RESPIROLOGY, WILEY-BLACKWELL, pp. 47-47.

Franklin, JB, Smith, GB & Earp, AE 1970, 'A critical hurdle to widespread use of polymer based luminescent solar concentrators', RELIABILITY OF PHOTOVOLTAIC CELLS, MODULES, COMPONENTS, AND SYSTEMS VI, Reliability of Photovoltaic Cells, Modules, Components, and Systems, SPIE, San Diego, USA, pp. 1-9.
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Luminescent solar concentrators have been studied and improved for over 30 years. Of all moderate gain solar concentrator systems they are fundamentally the most attractive from a range of geometric and optical perspectives for many solar cell materials, for daylighting via light guides, and for some bio-applications. Of most significance is their étendue advantages over mirror and lens systems in terms of best dealing with the diffuse component and varying beam directions of solar radiation. Despite this and some attempted commercial ventures they have yet to achieve their potential. This paper addresses what is for the dominant class of such concentrators, those involving fluorophore doped polymers, especially PMMA, a core residual problem. Their long-term stability outdoors is insufficient. This is not due to UV effects and dye quenching, which can be controlled, but to fast local photo-thermal interactions between the activated dye molecules and the host material. Production of char like nanoscale absorbers may result. These absorb over a broad-band and though very dilute lower output transport efficiency in practical sizes. Data which led to this conclusion is presented, plus possible solutions. Other improvements in LSC polymer technology only have practical value if this core problem is first mitigated. © 2013 SPIE.

Gao, F, Pant, R, Li, E, Poulton, CG, Choi, DY, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'On-chip high sensitivity laser frequency sensing with brillouin mutually-modulated cross-gain modulation', CLEO: Science and Innovations, CLEO_SI 2013.
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We report the first demonstration of a photonic-chip based laser frequency sensor using Brillouin mutually-modulated cross-gain modulation (MMXGM) in a 7cm long chalcogenide waveguide. A large sensitivity (9.45mrad/kHz) of the modulation phase shift was demonstrated. © OSA 2013.

Ge, Q, Jaffar, J, Chen, L, Black, JL, Burgess, JK & Oliver, B 1970, 'THE ROLE OF FIBULIN-1 PEPTIDES IN LUNG FIBROBLAST ASSOCIATED REMODELLING AND INFLAMMATION', RESPIROLOGY, WILEY-BLACKWELL, pp. 47-47.

Ge, Q, Jaffar, J, Chen, L, Black, JL, Burgess, JK & Oliver, BG 1970, 'Identification Of The Active Region Of Fibulin1 In Remodelling And Inflammation In Lung Fibroblasts', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Gerace, D, Ren, B, Hawthorne, WJ, Byrne, MR, Phillips, P, O'Brien, BA, Nassif, N, Alexander, IE & Simpson, AM 1970, 'REVERSAL OF DIABETES IN A PORCINE MODEL FOLLOWING LIVER-DIRECTED GENE THERAPY', JOURNAL OF GENE MEDICINE, 8th Meeting of the Australasian-Gene-Therapy-Society, WILEY-BLACKWELL, Univ Technol, Sydney, AUSTRALIA, pp. 326-326.

Godecke, E, Armstrong, E, Bernhardt, J, Middleton, S, Rai, T, Holland, A, Cadilhac, D, Hankey, G, Whitworth, A, Rose, M & Ciccone, N 1970, 'An RCT of aphasia therapy after stroke', British Aphasiology Symposium, Manchester, UK.

Grafe, M, Solntsev, AS, Keil, R, Tunnermann, A, Nolte, S, Sukhorukov, AA, Kivshar, YS & Szameit, A 1970, 'Photon pair generation in quadratic waveguide arrays: A classical optical simulation', 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, IEEE, Munich, GERMANY.
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Grahn, T, Watkins, H, Joss, DT, Page, RD, Carroll, RJ, Dewald, A, Greenlees, PT, Hackstein, M, Herzberg, R-D, Jakobsson, U, Jones, PM, Julin, R, Juutinen, S, Ketelhut, S, Köll, T, Krücken, R, Labiche, M, Leino, M, Lumley, N, Maierbeck, P, Nyman, M, Nieminen, P, O'Donnell, D, Ollier, J, Pakarinen, J, Peura, P, Pissulla, T, Rahkila, P, Revill, JP, Rother, W, Ruotsalainen, P, Rigby, SV, Sarén, J, Sapple, PJ, Scheck, M, Scholey, C, Simpson, J, Sorri, J, Uusitalo, J & Venhart, M 1970, 'Transition probability studies in¹⁷⁵Au', Journal of Physics: Conference Series, International Conference on Nucleus-Nucleus Collisions (NN), IOP Publishing, San Antonio, Texas, USA, pp. 012047-012047.
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Transition probabilities have been measured between the low-lying yrast states in 175Au by employing the recoil distance Doppler-shift method combined with the selective recoil-decay tagging technique. Reduced transition probabilities and magnitudes of transition quadrupole moments have been extracted from measured lifetimes allowing dramatic changes in nuclear structure within a low excitation-energy range to probed. The transition quadrupole moment data are discussed in terms of available systematics as a function of atomic number and aligned angular momentum.

Green, DW, Padula, M, Santos, J, Chou, J, Milthorpe, B & Ben-Nissan, B 1970, 'A new role for marine skeletal proteins in regenerative orthopaedics', BIOCERAMICS 24, Bioceramics, Scientific.net, Fukuoka, Japan, pp. 654-659.
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Use of ready-made marine skeletons is one of the simplest possible remedies to major problems hindering the future development of regenerative orthopaedics- such as, providing a richness of framework designs and now a potentially rich, accessible source

Groen, L, Beames, SY, Coupland, MP, Stanley, J & Bush, S 1970, 'Are science students ready for university mathematics?', Proceedings of the Australian Conference of Science and Mathematics Education (2013), ACSME 2013, University of Sydney, The Australian National University, Canberra.

Habib, R, McGowan, E, Larsen, SR & Martiniello-Wilks, R 1970, 'CHARACTERISATION OF A PRIMITIVE BONE MARROW DERIVED MESENCHYMAL STEM CELL SUBPOPULATION SHOWING IMPROVED PROSTATE CANCER TROPISM', JOURNAL OF GENE MEDICINE, 8th Meeting of the Australasian-Gene-Therapy-Society, WILEY-BLACKWELL, Univ Technol, Sydney, AUSTRALIA, pp. 333-333.

Hansbro, P, Beckett, E, Stevens, R, Jarnicki, A, Kim, R, Hanish, I, Hansbro, N, Deane, A, Keely, S, Horvat, J, Yang, M, Oliver, B, van Rooijen, N, Inman, M, Adachi, R, Soberman, R, Hamadi, S, Wark, P & Foster, P 1970, 'A short-term model of COPD identifies a role for mast cell tryptase', JOURNAL OF IMMUNOLOGY, 100th Annual Meeting of the American-Association-of-Immunologists, AMER ASSOC IMMUNOLOGISTS, Honolulu, HI.

Hansbro, P, Beckett, E, Stevens, R, Jarnicki, A, Kim, R, Hanish, I, Hansbro, N, Deane, A, Keely, S, Horvat, J, Yang, M, Oliver, B, van Rooijen, N, Inman, M, Adachi, R, Soberman, R, Hamadi, S, Wark, P & Foster, P 1970, 'A short-term model of COPD identifies a role for mast cell tryptase (P3242)', The Journal of Immunology, The American Association of Immunologists, pp. 136.3-136.3.
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Abstract Cigarette smoke-induced chronic obstructive pulmonary disease (COPD) is a life-threatening inflammatory disorder of the lung. The development of effective therapies for COPD has been hampered by the lack of an animal model that mimics the human disease in a short time-frame.We have created a mouse model of cigarette smoke-induced COPD that develops the hallmark features of the human condition in a short amount of time. Tightly controlled amounts of cigarette smoke were delivered to the airways of mice, and the development of the pathological features of COPD were assessed. The roles of macrophages and mast cell (MC) tryptase in pathogenesis were evaluated using depletion and in vitro studies and MC protease-6 deficient mice. After 8 weeks of smoke exposure, wild-type mice developed chronic inflammation, mucus hypersecretion, airway remodeling, emphysema, and reduced lung function. These characteristic features of COPD were glucocorticoid-resistant and did not spontaneously resolve. Systemic effects on skeletal muscle and the heart, and increased susceptibility to respiratory infections also were observed. We demonstrate here that macrophages and tryptase-expressing MCs were required for the development of COPD. Recombinant MC tryptase induced pro-inflammatory responses from cultured macrophages. This model can be used to better understand multiple aspects of COPD pathogenesis.

Hansbro, P, Horvat, J, Essilfie, A-T, Kim, R, Mayall, J, Starkey, M & Foster, P 1970, 'Macrolides suppress key features of experimental steroid-sensitive and steroid-resistant asthma (P6229)', The Journal of Immunology, 100th Annual Meeting of the American-Association-of-Immunologists, The American Association of Immunologists, Honolulu, HI, pp. 62.13-62.13.
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Abstract Steroid-resistant asthma is an important clinical problem and effective therapies are urgently required. Macrolides have been shown to be efficacious in treating steroid-resistant forms of asthma. However, how these immunomodulatory antibiotics induce their effects is not known. Using mouse models of Chlamydia and Haemophilus lung infection and ovalbumin-induced allergic airway disease (AAD) we have previously shown that both infections induce airways hyperresponsiveness (AHR) and neutrophilic inflammation in AAD that is resistant to steroid treatment. In the current study the effects of clarithromycin versus amoxicillin on immune responses in Th2-associated, steroid-sensitive eosinophilic and infection-induced, Th1/Th17-associated, steroid-resistant neutrophilic AAD was assessed. We show that clarithromycin, but not amoxicillin, treatment reduces AHR and inflammation in both steroid-sensitive and steroid-resistant AAD. Suppression of these features of disease was associated with a reduction in a number of Th1, Th2 and Th17-associated immune factors. Significantly, clarithromycin treatment reduced Th2-associated factors in steroid-sensitive AAD and Th1/Th17-associated factors in infection-induced, steroid-resistant AAD. These findings suggest that macrolide treatment can have broad anti-inflammatory effects on immune responses in the asthmatic lung and that the specific immune responses that are suppressed may be dependent on the responses that predominate during disease.

Hansbro, PM, Horvat, JC, Essilfie, A-T, Kim, RY, Mayall, J, Starkey, MR, Beckett, EL & Foster, PS 1970, 'Immunomodulatory Effects Of Macrolide Treatment On Experimental Models Of Steroid-Sensitive And Steroid-Resistant Asthma', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Hatoum, D, Martiniello-Wilks, R, Nassif, N, Yagoub, D & McGowan, EM 1970, 'THE MISNOMER OF ACTIVATING P14ARF-P53 FOR BREAST CANCER THERAPY', JOURNAL OF GENE MEDICINE, 8th Meeting of the Australasian-Gene-Therapy-Society, WILEY, Univ Technol, Sydney, AUSTRALIA, pp. 333-334.

Herbert, C, Siegle, JS, Shadie, AM, Nikolaysen, S, Garthwaite, L, Hansbro, NG, Foster, PS & Kumar, RK 1970, 'EARLY LIFE EXPOSURE TO ENVIRONMENTAL PARTICULATES PREDISPOSES TO DEVELOPMENT OF ASTHMATIC INFLAMMATION', RESPIROLOGY, WILEY-BLACKWELL, pp. 39-39.

Hocking, J, Kong, F, Vodstrcil, L, Guy, R, Chen, M, Fairley, C, Bradshaw, C & Tabrizi, S 1970, 'O02.6 Azithromycin Versus Doxycycline For the Treatment of Genital Chlamydia Infection - a Meta-Analysis of Randomised Controlled Trials', Sexually Transmitted Infections, BMJ, pp. A30.1-A30.
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Horvat, JC, Essilfie, A-T, Kim, RY, Mayall, JR, Starkey, MR, Beckett, EL, Foster, PS & Hansbro, PM 1970, 'MACROLIDES SUPPRESS KEY FEATURES OF EXPERIMENTAL STEROID-SENSITIVE AND STEROID-RESISTANT ASTHMA', RESPIROLOGY, WILEY-BLACKWELL, pp. 40-40.

Howes, JM, Stuart, BH & Ralph, PJ 1970, 'Assessing metabolic variation of endosymbiotic and cultured Symbiodinium microadriaticum using synchrotron imaging FTIR spectroscopy', 7th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator-Based Sources Abstracts, 7th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator-Based Sources.

Howes, M, Stuart, BH & Ralph, PJ 1970, 'MACROMOLECULAR COMPOSITION VARIES SIGNIFICANTLY BETWEEN GENETIC CLADES OF SYMBIODINIUM MICROADRIATICUM', PHYCOLOGIA, 10th International Phycological Congress, pp. 46-47.

Hughes, JM, Wai-Shing, M, Krimmer, D, Oliver, BGG, Armour, CL & Alkhouri, H 1970, 'DIFFERENTIAL RESPONSES OF CENTRAL AND PERIPHERAL LUNG FIBROBLASTS TO ACTIVATED MAST CELL PRODUCTS', RESPIROLOGY, WILEY-BLACKWELL, pp. 41-41.

Jaffar, J, Jin, GT, Unger, S, Black, JL, Oliver, BG & Burgess, JK 1970, 'THE EXTRACELLULAR MATRIX PROTEIN FIBULIN-1 IS INCREASED IN PATIENTS WITH IPF', RESPIROLOGY, WILEY-BLACKWELL, pp. 27-27.

Jaffar, J, Unger, S, Corte, T, Wolters, PJ, Richeldi, L, Cerri, S, Argraves, W, Oliver, BG, Black, JL & Burgess, JK 1970, 'Levels Of Fibulin-1 In The Lung And Serum Are Increased In Fibrotic Interstitial Lung Disease', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Kabakova, IV, Büttner, TFS & Eggleton, BJ 1970, 'Frequency Combs Formed via Stimulated Brillouin Scattering in Chalcogenide', Workshop on Specialty Optical Fibers and their Applications, Workshop on Specialty Optical Fibers and their Applications, OSA.
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Kabakova, IV, Büttner, TFS & Eggleton, BJ 1970, 'Frequency combs formed via stimulated brillouin scattering in chalcogenide', Optics InfoBase Conference Papers.
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We exploit the strong Brillouin gain of chalcogenide glasses to generate frequency combs in a centimeter scale fiber devices. These can be applied to generation of ultra-high frequency picosecond pulse trains or complex reflection filters. © OSA 2013.

Kabakova, IV, Pant, R, Luther-Davies, B, Choi, D-Y, Madden, SJ, Eggleton, BJ & Debbarma, S 1970, 'Narrow linewidth Brillouin laser based on chalcogenide chip', 39th European Conference and Exhibition on Optical Communication (ECOC 2013), 39th European Conference and Exhibition on Optical Communication (ECOC 2013), Institution of Engineering and Technology, pp. 411-413.
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We demonstrate a narrow linewidth Brillouin ring-cavity laser based on chalcogenide photonic chip. The gain medium is a 7 cm-long As2S 3 waveguide with a cross-section of 4μm x 850nm and the Brillouin gain coefficient of 0.7 10-9 m/W. The waveguides are equipped with vertical tapers so that the coupling loss is reduced. The lasing threshold is approximately PL=360 mW, almost 5 times lower than the calculated single-pass threshold P0=1.73 W in the same waveguide. The slope efficiency is found to be 30% and the linewidth of 100 kHz is measured using a self-heterodyne method.

Kidman, AD, Murrihy, R, Perry, Y, Dedousis-Wallace, A, Ellis, D & Varlow, M 1970, 'The development of a specialized CBT for early psychosis: Translation to a user friendly manual', 7th World Congress of Behavioural and Cognitive Therapies, Lima, Peru.

Kim, RY, Horvat, JC, Starkey, MR, Essilfie, A, Foster, PS & Hansbro, PM 1970, 'Inhibition Of Early-Life Chlamydia Lung Infection-Induced Micrornas Prevents Infection-Induced Lung Pathologies In Later Life', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Klement, M, Šafránek, D, Děd, T, Pejznoch, A, Nedbal, L, Steuer, R, Červený, J & Müller, S 1970, 'A Comprehensive Web-based Platform For Domain-Specific Biological Models', Electronic Notes in Theoretical Computer Science, Elsevier BV, pp. 61-67.
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A Comprehensive Modeling Platform, that is, a general framework for public sharing, annotation, and visualization of domain-specific biological models, is presented. For a selected organism, the framework is instantiated as a web-based application which allows to capture several aspects of biological models represented as biochemical reaction networks or ordinary differential equations. The key feature of the instantiation for a given organism relies on mapping kinetic models to a precise textual and a schematic graphical representation of the related biological knowledge, thereby supporting the systems biological view of the modeled organism. Besides model repository and annotation, the platform includes basic model analysis features such as simulation and static analysis. © 2013 Elsevier B.V.

Krylova, AK, Lapine, M, Poulton, CG, McPhedran, RC, Kivshar, YS, Belov, PA & IEEE 1970, 'Tailoring lattice parameters for broadband artificial diamagnetism', 2013 7TH INTERNATIONAL CONGRESS ON ADVANCED ELECTROMAGNETIC MATERIALS IN MICROWAVES AND OPTICS (METAMATERIALS 2013), International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS), IEEE, Talence, France, pp. 34-36.
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We report a strategy to achieve the values of the effective magnetic permeability close to zero by using anisotropic metamaterial made of dense arrays of conductive loops. We present an extensive parametric analysis of the role of lattice parameters and symmetry, and also of the geometry of the loops. The magnitudes of the real part of the permeability reach 0.05 and are observed in a very broad frequency span, accompanied with negligible dissipation. Importantly, our analysis is applicable in a wide range of absolute sizes, being appropriate up to the THz range. Finally, we assess the dielectric properties of the optimal diamagnetic meta-materials, providing a complete picture of its interaction with the electromagnetic waves. © 2013 IEEE.

Lapine, M 1970, 'Mechanical nonlinearities in electromagnetic metamaterials', 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics, METAMATERIALS 2013, 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS 2013), IEEE, Talence, France, pp. 352-354.
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We review our recent achievements in the development of metamaterials with mechanical nonlinearity. The novel nonlinearity types are achieved by enabling new degrees of freedom in metamaterial design, which allow a dynamic changes in the geometry of 'meta-atoms' or in the lattice structure. We present the outcomes of magnetoelastic, conformational, rotational and optical nonlinear feedback, and predict unusual phenomena to be observed in such metamaterials. © 2013 IEEE.

Lawrenz, E, Huete-Ortega, M, Suggett, DJ & Geider, RJ 1970, 'ASSESSING THE RELATIONSHIPS BETWEEN ELECTRON TRANSFER AND CARBON FIXATION IN NITROGEN LIMITED MARINE PHYTOPLANKTON', PHYCOLOGIA, INT PHYCOLOGICAL SOC, pp. 59-59.

Liu, M, Powell, DA, Shadrivov, IV, Lapine, M & Kivshar, YS 1970, 'Dynamic optical activity and self-oscillation in torsional metamaterials', 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics, METAMATERIALS 2013, 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS 2013), IEEE, Talence, France, pp. 359-360.
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We study the nonlinear dynamic properties of coupled torsional meta-molecules. We find that this structure may exhibit self-oscillation behaviour, and we analyse two different mechanisms leading to this effect. Contrary to many previously studied optomechanical systems, self-oscillations of torsional meta-molecules can be extremely robust against mechanical damping and they can be manipulated by the polarisation of electromagnetic waves. We also study the dynamic nonlinear optical activity arising in the system and its active control. © 2013 IEEE.

Liu, M, Powell, DA, Shadrivov, IV, Lapine, M & Kivshar, YS 1970, 'Dynamic Optical Activity and Self-oscillation in Torsional Metamaterials', 2013 7TH INTERNATIONAL CONGRESS ON ADVANCED ELECTROMAGNETIC MATERIALS IN MICROWAVES AND OPTICS (METAMATERIALS 2013), 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS), IEEE, Bordeaux, FRANCE, pp. 358-360.

Liu, M, Sun, Y, Powell, DA, Shadrivov, IV, Lapine, M, McPhedran, RC & Kivshar, YS 1970, 'Twists and shifts make nonlinear metamaterials', 2013 Conference on Lasers and Electro-Optics Europe and International Quantum Electronics Conference, CLEO/Europe-IQEC 2013, 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, IEEE, Munich, Germany.
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Recent studies have demonstrated that it is possible to modify the properties of metamaterials by electromagnetic waves via inducing mechanical deformations of samples and therefore changing material properties. As an example, optical rotation of chiral particles was demonstrated [1], and a rich variety of nonlinear behaviour was achieved with magneto-elastic metamaterials [2]. The range of possible effects achievable in this way promises to be richer than in the prominent area of optomechanics, because the greater flexibility in metamaterial design overcomes the limits of available material functionalities, and offers wider possibilities for optimisation. At the same time, the implementation of magnetoelastic metamaterials [2] remains challenging and in some cases, such as the conformational nonlinearity in resonant spirals, remains inaccessible for optics. The reason for this is that the magnetic forces, employed in the initial designs, are relatively weak, so such materials require either high power or extremely small elastic restoring forces, which poses a considerable manufacturing challenge. We recall, however, that earlier research on structurally tunable metamaterials [3] indicated that near-field interaction may significantly improve the tunability range and leads to various effects associated with near-field coupling. © 2013 IEEE.

Lu, Y, Lu, J, Piper, JA, Xi, P & Jin, D 1970, 'Orthogonal scanning automated microscopy (OSAM) speeds up time-gated luminescence detection', Bio-Optics: Design and Application, BODA 2013.
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We report a versatile platform of orthogonal scanning automated microscopy (OSAM) cooperated with time-gated detection technique. Featuring rapid processing and background-free detection, it offers ultra-high sensitivity to spot rare-event cells and quantitate low-expression surface molecules. Optics in the Life Sciences Congress Technical Digest © 2013 The Optical Society (OSA).

Lu, Y, Lu, J, Piper, JA, Xi, P & Jin, D 1970, 'Orthogonal scanning automated microscopy speeds up time-gated luminescence detection', Optical Trapping Applications, OTA 2013.
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We report a versatile platform of orthogonal scanning automated microscopy (OSAM) cooperated with time-gated detection technique. Featuring rapid processing and background-free detection, it offers ultra-high sensitivity to spot rare-event cells and quantitate low-expression surface molecules. © 2013 The Optical Society (OSA).

Lu, Y, Lu, J, Piper, JA, Xi, P & Jin, D 1970, 'Orthogonal Scanning Automated Microscopy Speeds Up Time-Gated Luminescence Detection', Optics in the Life Sciences, Bio-Optics: Design and Application, OSA.
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We report a versatile platform of orthogonal scanning automated microscopy (OSAM) cooperated with time-gated detection technique. Featuring rapid processing and background-free detection, it offers ultra-high sensitivity to spot rare-event cells and quantitate low-expression surface molecules. ©2013 The Optical Society (OSA).

Marsh, DJ, deFazio, A, Clarkson, A, Kennedy, C, Gard, GG & Gill, AJ 1970, 'Abstract A29: Loss of histone H2B monoubiquitination in ovarian cancer – new therapeutic targeting opportunities based on chromatin relaxation', Clinical Cancer Research, Abstracts: AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; September 18-21, 2013; Miami, FL, American Association for Cancer Research (AACR), pp. A29-A29.
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Abstract Post-translational modifications of histones are involved in diverse functions, including gene transcription and the DNA damage response. Targeting elements of the DNA damage response pathway is of increasing interest for the treatment of epithelial ovarian cancer (EOC). Monoubiquitination of histone H2B at lysine 120 (H2Bub1) is present at the coding region of highly expressed genes such as the gene encoding p21, CDKN1A, under conditions of DNA damage. Addition of this histone mark relies on the E3 ubiquitin ligase ring finger protein complex RNF20-RNF40 that we, and others, have previously shown interacts with members of the PAF1 complex necessary for RNA polymerase II-based transcriptional elongation. At 8.5 kDa, ubiquitin constitutes a bulky addition likely sufficient to interfere with condensed chromatin fibres, leading to a more open fibre conformation with greater accessibility for transcription factors and DNA repair proteins. H2Bub1 has been described as a master switch for mammalian gene regulation, with roles in histone cross-talk. Furthermore, H2Bub1 has recently been linked to the cellular DNA damage response, with the protein kinase ATM phosphorylating RNF20-RNF40 to induce H2Bub1 at sites of double strand breaks, leading to a more open chromatin structure for optimal repair. Global H2Bub1 loss has been reported in breast, colon, lung and parathyroid tumors1, and in some of these tumor types has been associated with advancing stage. We have undertaken immunohistochemical analyses of global H2Bub1 and total histone H2B using tissue microarrays of EOC sourced from the Australian Ovarian Cancer Study and the Gynaecological Oncology Biobank at Westmead. Expression of total histone H2B was high and consistent across all tumors, whereas over 70% of tumors showed total loss of global H2Bub1. Contrary to reports that global H2Bub1 levels decreased with advanced stage in breast cancer, we did...

McKemmish, LK, Reimers, JR, McKenzie, RH, Marks, AE & Hush, NS 1970, 'Electron transfer, biological phonon condensates, and the 'Quantum Consciousness' hypothesis', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 245th National Spring Meeting of the American-Chemical-Society (ACS), AMER CHEMICAL SOC, New Orleans, LA.

Memar, J, Singh, G & Zinder, Y 1970, 'Scheduling Partially Ordered UET Tasks on Dedicated Machines', IFAC Proceedings Volumes, IFAC Conference on Manufacturing Modelling, Management, and Control, Elsevier BV, Saint Petersburg, Russia, pp. 1672-1677.
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The paper is concerned with scheduling partially ordered unit execution time tasks on dedicated machines. The considered scheduling model is important in control of different systems, in particular computer systems. The presented algorithm is an alternative to the conventional branch-and-bound method. In contrast to the branch-and-bound method with its single search tree, corresponding to partitioning of the feasible region, the presented method involves a sequence of search trees each associated with a certain portion of the domain of the objective function. The branching is based on a generalisation of the Garey-Johnson due date modification. The performance of the presented algorithm is compared by means of computational experiments with a version of the branch-and-bound algorithm. © IFAC.

Metcalf, BJ, Thomas-Peter, N, Spring, JB, Humphreys, PC, Langford, NK, Kolthammer, WS, Barbieri, M, Jin, X-M, Smith, B, Walmsley, IA, Gates, JC, Kundys, D & Smith, PGR 1970, 'On-chip quantum teleportation', 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, 2013 Conference on Lasers & Electro-Optics Europe & International Quantum Electronics Conference CLEO EUROPE/IQEC, IEEE.
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Integrated quantum optics provides great promise for enabling photonic experiments to reach new regimes of complexity. Chip-based fabrication enables sophisticated networks involving multiple interfering pathways in a compact and stable physical architecture. In a recent work [1] we demonstrated an advance in the complexity of these integrated devices by showing the first quantum interference of three separate input photons. Such complexity allows the demonstration of three qubit protocols never before realised on-chip. Here, we report the first results showing quantum teleportation on an integrated photonic circuit. Quantum teleportation provides the mechanism for quantum relay schemes and is an important constituent in linear optical quantum computing. Whilst demonstrations to date have relied upon complex and fragile bulk optical systems, being able to teleport quantum states on a compact and stable integrated architecture will be a critical step towards scalable realisations of these schemes. © 2013 IEEE.

Mohanty, M, Ooi, WT & Atrey, PK 1970, 'Scale me, crop me, knowme not: Supporting scaling and cropping in secret image sharing', 2013 IEEE International Conference on Multimedia and Expo (ICME), 2013 IEEE International Conference on Multimedia and Expo (ICME), IEEE.
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Secret image sharing is a method for distributing a secret image amongst n data stores, each storing a shadow image of the secret, such that the original secret image can be recovered only if any k out of the n shares is available. Existing secret image sharing schemes, however, do not support scaling and cropping operations on the shadow image, which are useful for zooming on large images. In this paper, we propose an image sharing scheme that allows the user to retrieve a scaled or cropped version of the secret image by operating directly on the shadow images, therefore reducing the amount of data sent from the data stores to the user. Results and analyses show that our scheme is highly secure, requires low computational cost, and supports a large number of scale factors with arbitrary crop. © 2013 IEEE.

Mohanty, M, Ooi, WT & Atrey, PK 1970, 'Secure Cloud-Based Volume Ray-Casting', 2013 IEEE 5th International Conference on Cloud Computing Technology and Science, 2013 IEEE 5th International Conference on Cloud Computing Technology and Science (CloudCom), IEEE, Bristol, ENGLAND, pp. 531-538.
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Moir, L, Ng, HY, Oliver, B, Burgess, J, Krymskaya, V & Black, J 1970, 'Combination therapy may be beneficial for the treatment of lymphangioleiomyomatosis', EUROPEAN RESPIRATORY JOURNAL, EUROPEAN RESPIRATORY SOC JOURNALS LTD.

Murrihy, R, Kidman, AD, Ellis, D, Fitzgerald, D & Dedousis-Wallace, A 1970, 'Help seeking in adolescents: Have new government mental health initiatives in Australia improved treatment access and response for this critically underserviced population?', 7th World Congress of Behavioural and Cognitive Therapies, Lima, Peru.

Ng, H, Oliver, BG, Burgess, JK, Krymskaya, VP, Black, JL & Moir, LM 1970, 'Enhanced Migration Of Tsc2-Null Mouse Embryonic Fibroblasts Is Inhibited By Doxycycline Through A Rhoa-Gtpase Dependant Pathway', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Ng, HY, Oliver, BGG, Burgess, JK, Krymskaya, VP, Black, JL & Moir, LM 1970, 'DOXYCYCLINE INHIBITS RHOA-GTPASE ACTIVITY IN MOUSE EMBRYONIC FIBROBLASTS', RESPIROLOGY, WILEY-BLACKWELL, pp. 49-49.

Nickel, F, Gottlob, DM, Krug, IP, Doganay, H, Cramm, S, Kaiser, AM, Lin, G, Makarov, D, Schmidt, OG & Schneider, CM 1970, 'Time-resolved magnetic imaging in an aberration-corrected, energy-filtered photoemission electron microscope', Ultramicroscopy, 8th International Workshop on Low Energy Electron Microscopy and Photoemission Electron Microscopy (LEEM/PEEM), Elsevier BV, Hong Kong, PEOPLES R CHINA, pp. 54-62.
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Nield, BS, Martiniello-Wilks, R, Guzowski, R, Simpson, A & Nassif, N 1970, 'First use of Re:view – a tool to combine assessment tasks, marking criteria and graduate attributes', Australian Conference on Science and Mathematics Education, Canberra, ACT.

Nunn, J, Langford, NK, Kolthammer, WS, Champion, TFM, Sprague, MR, Michelberger, PS, Jin, X-M, England, DG & Walmsley, IA 1970, 'Towards scalable photonics via quantum storage', SPIE Proceedings, SPIE OPTO, SPIE.
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Single photons are a vital resource for optical quantum information processing. efficient and deterministic single photon sources do not yet exist, however. To date, experimental demonstrations of quantum processing primitives have been implemented using non-deterministic sources combined with heralding and/or postselection. Unfortunately, even for eight photons, the data rates are already so low as to make most experiments impracticable. It is well known that quantum memories, capable of storing photons until they are needed, are a potential solution to this 'scaling catastrophe'. Here, we analyze two protocols for generating multiphoton states using quantum memories, showing how the production rates can be enhanced by many orders of magnitude. We identify the time-bandwidth product as a key figure of merit in this connection. © 2013 SPIE.

Pant, R, Byrnes, A, Li, E, Choi, DY, Poulton, CG, Fan, S, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'Photonic chip based tunable and dynamically reconfigurable microwave photonic filter using stimulated brillouin scattering', Bragg Gratings, Photosensitivity, and Poling in Glass Waveguides, BGPP 2012.
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We report the first demonstration of on-chip tunable narrowband microwave photonic filter with shape reconfiguration. Stimulated Brillouin scattering is exploited in a chalcogenide chip to demonstrate a microwave filter with 3dB bandwidth ~23MHz over 2-12GHz. © OSA 2012.

Pant, R, Li, E, Poulton, CG, Choi, D-Y, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'Brillouin dynamic grating on a photonic chip', CLEO: 2013, CLEO: Science and Innovations, OSA, San Jose, California United States.
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We demonstrate an on-chip dynamic grating using stimulated Brillouin scattering in a 6.5cm long chalcogenide waveguide. The measured grating reflectivity is comparable to that measured in tens-of-meter long fiber and the On-Off ratio is ~28dB. © OSA 2013.

Parker, GK, Holt, SA & Hope, GA 1970, 'Characterisation of the Deposition of n-octanohydroxamate on Copper Surfaces', ECS Transactions, Symposium on Electrodeposition General Session - Fundamentals and New Materials - Dieter M. Kolb Memorial Symposium, The Electrochemical Society, Honolulu, HI, pp. 23-33.
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The interaction of the flotation reagent, n-octanohydroxamate, with a copper electrode was investigated using cyclic voltammetry, contact angles, surface-enhanced Raman scattering, neutron reflectometry and X-ray reflectometry. The data demonstrated that hydroxamate did not undergo underpotential chemisorption. A hydrophobic non-passivating multilayer of copper n-octanohydroximate formed in the CuII stability region that was more stable than the oxide formed in the absence of hydroxamate. In the CuI and Cu0 stability regions the interface contained more than 50% water and the hydroxamate moiety was present in the keto tautomeric form.

Rasaiah, BA, Malthus, TJ, Bellman, C, Chisholm, L, Gamon, J, Hueni, A, Huete, A, Jones, SD, Ong, C, Phinn, S, Roelfsema, C, Suarez, L, Townsend, P, Trevithick, R, Wyatt, M & IEEE 1970, 'APPROACHES TO ESTABLISHING A METADATA STANDARD FOR FIELD SPECTROSCOPY DATASETS', 2013 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM (IGARSS), IEEE International Geoscience and Remote Sensing Symposium, IEEE, VIC, Australia, pp. 4523-4525.
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There is an urgent need within the international remote sensing community to establish a metadata standard for field spectroscopy that ensures high quality, interoperable metadata sets that can be archived and shared efficiently within Earth observation data sharing systems. Careful examination of all stages of metadata collection and analysis can inform a robust standard that is applicable to a range of field campaigns. This paper presents approaches towards a standard that encompasses in situ metadata collection and initiatives towards sharing metadata within intelligent archiving systems. © 2013 IEEE.

Rehaume, L, Mondot, S, de Carcer, DA, Velasco, J, Benham, H, Hasnain, S, Bowman, J, Ruutu, M, Hansbro, P, McGuckin, M, Morrison, M & Thomas, R 1970, 'Host Genetic Background Disrupts The Relationship Between Microbiota and Gut Mucosal Tolerance Leading To Spondyloarthritis and Ileitis After a Dectin-1 Trigger.', ARTHRITIS AND RHEUMATISM, 77th Annual Meeting of the American-College-of-Rheumatology / 48th Annual Meeting of the Association-of-Rheumatology-Health-Professionals, WILEY-BLACKWELL, San Diego, CA, pp. S1152-S1152.

Reimers, JR 1970, 'Computational strategies for tackling complex electron-transfer related problems in biology and nanotechnology: Applications to natural photosynthesis and artificial solar-energy harvesting', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 245th National Spring Meeting of the American-Chemical-Society (ACS), AMER CHEMICAL SOC, New Orleans, LA.

Saerbeck, T, Cortie, DL, Brück, S, Bertinshaw, J, Holt, SA, Nelson, A, James, M, Lee, WT & Klose, F 1970, 'Time-of-Flight Polarized Neutron Reflectometry on PLATYPUS: Status and Future Developments', Physics Procedia, 9th International Conference on Polarised Neutrons in Condensed Matter Investigations (PNCMI), Elsevier BV, Paris, FRANCE, pp. 213-217.
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Schartner, EP, Jin, D, Zhao, J & Monro, TM 1970, 'Sensitive detection of NaYF₄: Yb/Tm nanoparticles using suspended core microstructured optical fibers', Colloidal Nanocrystals for Biomedical Applications VIII, SPIE BiOS, SPIE, San Francisco, California, United States.
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Rare-earth doped upconversion nanocrystals are emerging as the next-generation luminescent biomaterials. Here we load NaYF4: Yb/Er and NaYF4: Yb/Tm upconversion nanocrystals into a soft-glass suspended-core optical fiber dip sensor, allowing sensitive measurements and power-dependent characterizations to be performed. This, in combination with negligible background autofluorescence from the glass fiber when using infrared excitation has provided a significant improvement in terms of sensitivity over what has previously been demonstrated using an optical fiber dip sensor. For detection we employ suspended-core optical fibers, which have found extensive use in sensing applications. These combine the high evanescent overlap comparable to that of a nanowire, with the robust handling characteristics and long interaction length of a conventional fiber. The fiber sensor platform allows measurements to be performed using minimal sample volumes (<20 nL) while still maintaining the sensitivity of the platform. © 2013 Copyright SPIE.

Slobozhanyuk, AP, Belov, PA, Lapine, M, McPhedran, RC, Powell, DA, Shadrivov, IV & Kivshar, YS 1970, 'Novel nonlinear chiral metamaterials', IEEE Antennas and Propagation Society, AP-S International Symposium (Digest), 2013 IEEE International Symposium on Antennas and Propagation & USNC/URSI National Radio Science Meeting, IEEE, Orlando, FL, USA, pp. 488-489.
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We report on a novel metamaterial design based on multi-turn spiral resonators which strongly enhance nonlinear coupling between electromagnetic and mechanical response. The robust fabrication procedures allowed to produce a large number of resonators, suitable for assembling large metamaterials arrays. We experimentally demonstrate a remarkable self-tuning of the electromagnetic resonance, achieved via power-dependent mechanical reconfiguration, dominating over thermal effects. The corresponding compression of the spirals provides a nonlinear chiral response. © 2013 IEEE.

Slobozhanyuk, AP, Kapitanova, PV, Filonov, DS, Belov, PA, Shadrivov, IV, Powell, DA, Kivshar, YS & Lapine, M 1970, 'Photosensitive SRR-metamaterials', 2013 IEEE Antennas and Propagation Society International Symposium (APSURSI), 2013 IEEE International Symposium on Antennas and Propagation & USNC/URSI National Radio Science Meeting, IEEE, Orlando, FL, USA, pp. 1190-1191.
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We report a novel approach to design metamaterials with sign-varying nonlinear response. The metamaterial is build up with split-ring resonators loaded by photodiodes and varactor diodes. A non-monotonic frequency shift of the resonance frequency depending on incident microwave power is demonstrated. We show how the nonlinear response of such metamaterials can be directly controlled by light. © 2013 IEEE.

Slobozhanyuk, AP, Kapitanova, PV, Shadrivov, IV, Filonov, DS, Powell, DA, Belov, PA, Lapine, M & Kivshar, YS 1970, 'Light coupling in microwave metamaterials', 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics, 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS 2013), IEEE, Talence, France, pp. 190-192.
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We report our recent achievements in tuning metamaterials with light. We introduce a novel approach to design metamaterials with sign-varying nonlinear response. For this purpose, we use split-ring resonators loaded by photodiodes and varactor diodes. A non-monotonic frequency shift of the resonance frequency depending on incident microwave power is demonstrated. Finally, we show how the nonlinear response of photosensitive metamaterials can be directly controlled by light coupling. © 2013 IEEE.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, McPhedran, RC, de Sterke, CM & IEEE 1970, 'Positional Disorder in Nanowire Array Photovoltaics', 2013 IEEE 39TH PHOTOVOLTAIC SPECIALISTS CONFERENCE (PVSC), IEEE Photovoltaic Specialists Conference, IEEE, Tampa, FL, USA, pp. 322-325.
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Nanowire arrays are the focus of considerable research for incorporation into next generation solar cells. For these structures to be economically viable they must be designed to achieve high efficiencies in the presence of fabrication variations. Here we report on a systematic study of arrays of clustered nanowires, which reveals how the underlying physics of absorption enhancement in nanowire arrays is altered by the introduction of positional disorder. We find that positional disorder in fact enhances absorption efficiency over the majority of the parameter space due to the formation of additional modes in the structure and subsequently broadened absorption peaks. © 2013 IEEE.

Sukhorukov, AA, Solntsev, AS, Kruk, SS, Neshev, DN & Kivshar, YS 1970, 'Coupled-mode theory for nonlinear plasmonic structures and metamaterials', 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics, 2013 7th International Congress on Advanced Electromagnetic Materials in Microwaves and Optics (METAMATERIALS 2013), IEEE, Bordeaux, FRANCE, pp. 241-243.
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Suurbach, JH, McGowan, EM, Simpson, AM & Martiniello-Wilks, R 1970, 'STEM CELL-BASED DELIVERY OF SUICIDE GENE YCDUPRT THERAPY TO PROSTATE CANCER', JOURNAL OF GENE MEDICINE, 8th Meeting of the Australasian-Gene-Therapy-Society, WILEY-BLACKWELL, Univ Technol, Sydney, AUSTRALIA, pp. 323-323.

Tay, H, Kaiko, G, Hansbro, P & Foster, P 1970, 'The role of miRNA in regulating bacterial clearance (P1273)', The Journal of Immunology, 100th Annual Meeting of the American-Association-of-Immunologists, The American Association of Immunologists, Honolulu, HI, pp. 56.19-56.19.
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Abstract RATIONALE MicroRNAs (miRNAs) are small non-coding RNA that can bind to multiple target mRNA to repress protein production. While the expressions of specific miRNAs are known to be dysregulated in multiple human diseases, the role of miRNAs in regulating bacterial infection is unclear. Our aim is to investigate the roles of miRNA in regulating these processes. METHODS BALB/c mice were challenged with low doses of NTHi. Lung miRNAs that were differentially expressed were identified by microarray. miRNA inhibitors (antagomirs) were used to knockdown miRNA expression to investigate the roles of miRNA in bacterial clearance in vitro and in vivo. RESULTS Upon NTHi infection, 20 miRNAs were up-regulated while 52 were down-regulated by &gt; 2.5 fold. Interestingly, knockdown of a specific miRNA in vitro decreased bacterial load and increased phagocytosis by macrophages and neutrophils. Similarly, transfer of macrophages or neutrophils deficient in miRNA into naïve recipient mice leads to enhance clearance of the bacteria in vivo. This enhance clearance is independent of cellular infiltration. Inhibiting miRNA may play a protective role by enhancing the function of innate immune cells during bacterial infection. CONCLUSION Our study suggests that miRNA may play important roles in regulating the innate immune response to bacterial infection.

Van Reyk, DM & Ang, K 1970, 'Is H+ the symbol for acid? Provision of learning support in foundation-level chemistry for Bachelor of Nursing students enrolled in bioscience subjects', International First Year in Higher Education (FYHE) 16th Conference, First Year in Higher Education Centre, Wellington.
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Despite the value given to the teaching of bioscience as a central component of undergraduate nursing education, it has been accepted that nursing students often find bioscience subjects some of the most difficult to both master and perform well in. This nuts and bolts paper explores a practical approach undertaken to give first year students, commencing their anatomy and physiology unit, the opportunity to self-assess their existing knowledge of chemistry. We then evaluated the outcomes of a providing a wiki of student-sourced web pages on chemistry that students could use to address any knowledge gaps or revise aspects of basic chemistry. We found that students were open to using online resources provided they saw the relevance, were aware of them and had time and access to tools. Additionally, results also indicated that encouragement from teaching staff may drive the usage of self-directed online resources.

Vodstrcil, LA, Rupasinghe, T, Tull, D, Worthington, K, Chen, MY, Huston, WM, Fairley, CK, McConville, M, Tabrizi, SN & Hocking, JS 1970, 'P2.082 Post-Treatment Detection of Azithromycin in High-Vaginal Swabs Using Liquid Chromatography and Tandem Mass Spectrometry (LC-MS/MS)', Sexually Transmitted Infections, BMJ, pp. A113.1-A113.
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Walker, S & Zinder, Y 1970, 'The Solvable Cases of a Scheduling Algorithm', ALGORITHMS AND COMPUTATION, International Symposium on Algorithms and Computation, Springer, Hong Kong, PEOPLES R CHINA, pp. 229-239.
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When considering the NP-hard problem of scheduling precedence constrained tasks with preemptions on identical parallel machines with the goal of minimising the maximum lateness, approximation algorithms are commonly studied. It is desirable to characterise in some way the circumstances under which a given algorithm will provide an optimal solution. This paper considers a well-known scheduling algorithm called the Brucker-Garey-Johnson Algorithm, known to produce optimal schedules whenever the precedence constraints are in the form of in-trees. A new class of partial orders is presented and it is proved not only that the Brucker-Garey-Johnson Algorithm will solve every problem instance constrained by a partial order from that class but also that no larger class has this property.

Wang, J, Grzebieta, R, Walter, S & Olivier, J 1970, 'An evaluation of the methods used to assess the effectiveness of mandatory bicycle helmet legislation in New Zealand', Australasian College of RoadSafety Conference, Adelaide.

Wang, J, Olivier, J, Grzebieta, R & Walter, S 1970, 'On The Use of Empirical Bayes for ComparativeInterrupted Time Series with an Application toMandatory Helmet Legislation', Road Safety Research, Policing and Education Conference, Road Safety Research, Policing and Education Conference, Brisbane.

Wang, J, Olivier, J, Grzebieta, R & Walter, S 1970, 'Statistical errors in anti-helmet arguments', 2013 Australasian College of Road Safety Conference – “A Safe System: The Road Safety Discussion”, Australasian College of Road Safety Conference, Australasian College of Road Safety, Adelaide, Australia.

Wang, J, Walter, S, Grzebieta, R & Olivier, J 1970, 'A Comparison of Statistical Methods in Interrupted Time Series Analysis to Estimate an Intervention Effect', 2013 Australasian Road Safety Research, Policing and Education Conference, Australasian Road Safety Research, Policing and Education Conference, Australasian College of Road Safety, Brisbane.
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Since the introduction of mandatory helmet legislation (MHL) in Australia, debate on the effect of MHL on cyclist head injuries has been ongoing. The debate sometimes revolves around the statistical methodology used to assess intervention effectiveness. Supporters of rescinding the MHL thereby encouraging cyclists to ride without helmets, regularly dismiss statistical evaluations as being flawed for various reasons. In a more general context, researchers want to estimate whether and how a policy intervention changed an outcome of interest. Quasi-experimental interrupted time series (ITS) is the most appropriate design to evaluate the longitudinal effects of policy interventions and segmented regression analysis is often used as a powerful statistical method for ITS. Recent research has employed a log-linear regression model for the hospital admission counts of head and limb injuries from New South Wales, Australia, from a 36 month period centred at the time of legislation. Estimation of the model was done using a frequentist approach. In this paper, we re-analyse this data using empirical Bayes and full Bayesian methods, since the use of these methods has become popular in road safety studies. In particular, we show how a full Bayesian method can be readily implemented in WinBUGS software. We discuss the advantages and disadvantages of each method and describe and compare the different estimation methods in terms of parameter estimates. The results show that all three estimation methods give consistent conclusions regarding the positive effect of compulsory helmet wearing on cyclist head injuries in New South Wales.

Watson, CJ, Coupe, NR, Huete, AR & IEEE 1970, 'HYPERSPECTRAL ASSESMENTS OF CONDITION AND SPECIES COMPOSITION OF AUSTRALIAN GRASSLANDS', 2013 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM (IGARSS), IEEE International Geoscience and Remote Sensing Symposium, IEEE, Melbourne, VIC, Australia, pp. 2770-2773.
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Temperate grasslands in Australia show dynamic responses to climate, which renders them difficult to study using conventional remote sensing tools. However, the need to adequately describe native grassland variables is critical in maintaining ecological and agricultural values. We used a spectroradiometer to measure leaf-and canopy-level spectra from grassland plots in a controlled environment and compared results to fractional cover and species type. We found that the target species, Themeda australis and Poa labillardierei were separable at canopy and leaf level for both healthy and senescent foliage. In particular, we found differences in the 470-510 nm and 660-700 nm spectral regions. Comparison of narrow band vegetation indices for different combinations of photosynthetic and non-photosynthetic material showed strong relationships across a range of fractional cover values which was co-linear for both species. This method demonstrates the potential for remote sensing to identify Australian grasslands of different quality and composition. © 2013 IEEE.

Watts, AL, Singh, N, Poulton, CG, Magi, E, Kabakova, IV, Hudson, D & Eggleton, BJ 1970, 'Characterization of axial quantization in WGM chalcogenide microfiber resonators', Optics InfoBase Conference Papers.
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We experimentally and numerically characterize the axial quantization in whispering gallery mode (WGM) microfiber resonators exploiting a positive photoinduced index perturbation. Experimental results are in good agreement with numerical calculations. © OSA 2013.

Watts, AL, Singh, N, Poulton, CG, Magi, E, Kabakova, IV, Hudson, D & Eggleton, BJ 1970, 'Characterization of axial quantization in WGM chalcogenide microfiber resonators', Frontiers in Optics 2013, Frontiers in Optics, OSA.
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We experimentally and numerically characterize the axial quantization in whispering gallery mode (WGM) microfiber resonators exploiting a positive photoinduced index perturbation. Experimental results are in good agreement with numerical calculations. © OSA 2013.

Wen, S, Liu, H, Cai, H, Shen, M & Shi, X 1970, 'Targeted and pH-responsive delivery of doxorubicin to cancer cells using mutifunctional dendrimer-modified multi-walled carbon nanotubes', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 245th National Spring Meeting of the American-Chemical-Society (ACS), AMER CHEMICAL SOC, New Orleans, LA.

Xi, P, Xie, H, Liu, Y & Jin, D 1970, 'Stimulated emission depletion point spread function generation with vector solution', Nanophotonics, Nanoelectronics and Nanosensor, N3 2013.
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The excitation and depletion point spread functions of stimulated emission depletion optical microscopy have been derived, based on the vectorial diffraction theory. The performance of STED with high numerical aperture objective can be simulated with this method. © OSA 2013.

Xie, H, Ding, Y, Liu, Y, Zhang, L, Jin, D, Santangelo, PJ, Ren, Q & Xi, P 1970, 'STED3D: point spread function simulation for high numerical aperture objective and resolution evaluation', Optics in the Life Sciences, Bio-Optics: Design and Application, OSA.
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We developed STED3D to accelerate the calculation of point spread function with vector diffraction theory. Electromagnetic fields for both excitation and vortex modulated depletion beams can be simulated, to yield the resolution of STED nanoscopy.©Optics in the Life Sciences Congress Technical Digest.

Xie, H, Ding, Y, Liu, Y, Zhang, L, Jin, D, Santangelo, PJ, Ren, Q & Xi, P 1970, 'STED3D: Point spread function simulation for high numerical aperture objective and resolution evaluation', Bio-Optics: Design and Application, BODA 2013.
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We developed STED3D to accelerate the calculation of point spread function with vector diffraction theory. Electromagnetic fields for both excitation and vortex modulated depletion beams can be simulated, to yield the resolution of STED nanoscopy. Optics in the Life Sciences Congress Technical Digest © 2013 The Optical Society (OSA).

Xie, H, Ding, Y, Liu, Y, Zhang, L, Jin, D, Santangelo, PJ, Ren, Q & Xi, P 1970, 'Sted3D: Point spread function simulation for high numerical aperture objective and resolution evaluation', Optical Trapping Applications, OTA 2013.
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We developed STED3D to accelerate the calculation of point spread function with vector diffraction theory. Electromagnetic fields for both excitation and vortex modulated depletion beams can be simulated, to yield the resolution of STED nanoscopy. © 2013 The Optical Society (OSA).

Yu, Z, Kabakova, IV, Fonjallaz, PY, Tarasenko, O, Margulis, W & De Sterke, CM 1970, 'Dynamic frequency tuning in a fiber grating cavity', Bragg Gratings, Photosensitivity, and Poling in Glass Waveguides, BGPP 2012.
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Dynamic frequency tuning of trapped light in a phase-shifted fiber grating cavity is demonstrated by high-voltage electrical pulses. Y-polarization light is found to be sensitive to refractive index changes caused by a transverse pressure-wave. © 2012 OCA.

Yu, Z, Rugeland, P, Kabakova, IV, Fonjallaz, PY, Tarasenko, O, De Sterke, CM & Margulis, W 1970, 'Dynamic wavelength switching in a fiber grating cavity', CLEO: Science and Innovations, CLEO_SI 2013.
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Dynamic wavelength switching of a phase-shifted fiber grating cavity with electrical pulses is studied experimentally and numerically. Simulations accurately describe observations. The effect of acoustic oscillations and fiber Bragg grating cavity refilling explains the results. © 2013 Optical Society of America.

Yu, Z, Rugeland, P, Kabakova, IV, Fonjallaz, P-Y, Tarasenko, O, de Sterke, CM & Margulis, W 1970, 'Dynamic Wavelength Switching in a Fiber Grating Cavity', CLEO: 2013, CLEO: Science and Innovations, OSA, San Jose, CA.
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Zhao, J, Lu, Z, Yin, Y, Zhang, L, McKay, A, McRae, C, Piper, JA, Jin, D, Goldys, EM & Dawes, JM 1970, 'Characterisation of Upconversion Nanoparticles for Imaging', Asia Communications and Photonics Conference 2013, Asia Communications and Photonics Conference, OSA, Beijing, China.
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By controlling the size of Yb,Er, doped upconversion nanoparticles, we obtain varying emission lifetimes and emission ratios of green and red light, which we explain by modelling of excited state decay mechanisms. © OSA 2013.

Zheng, F, Wang, S, Wen, S, Shen, M & Shi, X 1970, 'Amoxicillin-loaded electrospun nano-hydroxyapatite/poly(lactic-co-glycolic acid) composite nanofibers: Preparation, characterization and antibacterial activity', Journal of Controlled Release, Elsevier BV, pp. e30-e31.
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Devlin, M, Debose, J, Ajani, PA & Brodie, J TropWATER 2013, Chapter 8: Analysis of phytoplankton community structure in flood events in the Great Barrier Reef, Assessment of the relative risk of water quality to ecosystems of the Great Barrier Reef: Supporting Studies. A report to the Department of the Environment and Heritage Protection, Queensland Government, Brisbane, no. 13/30, Townsville, Australia.

Pettitt, A, Rai, T, Alexander, S, Carstens, J, Gamachchi, A, Hall, J & Stebila, D 2013, Disclosure-Protected Regression Coefficients with Linked Micro-Data, pp. 1-3, Brisbane.

Rai, T 2013, Data Analysis of Cobalt and Chromium Ion Levels in Arthroplasty Patients, no. 2013001271, pp. 1-38, Sydney.

Rai, T 2013, Factors influencing the success of vaginal birth after a caesarean section, no. 2013001375, pp. 1-21, Sydney.

Rai, T 2013, Report on the 2013 Library Materials Availability Survey, pp. 1-8, Sydney.

Rai, T 2013, The Statistical Methodology Used to Assess the Effect of Limestone Addition to General Purpose Cement, no. 2013001253, pp. 1-17, Sydney.

Rai, T, Pettitt, A & Hall, J 2013, Disclosure Risks Associated With Statistical Modelling of Linked Data, pp. 1-18, Brisbane.

Ralph, PJ & Sinutok, S AccessUTS Pty Limited 2013, Vallisneria and submerged macrophyte management in Penrith Lakes, Sydney.

Ralph, PJ, Skilbeck, G & Sinutok, S AccessUTS Pty Limited 2013, Vallisneria and submerged macrophyte management in the Penrith Lakes Scheme, Sydney.

Waterhouse, J TropWATER 2013, Assessment of the relative risk ofdegraded water quality to ecosystems ofthe Great Barrier Reef:Supporting Studies, no. 13/30.

Baldeaux, J & Platen, E 2013, 'Liability Driven Investments under a Benchmark Based Approach'.
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In this paper, we present an alternative approach as a suitable framework under which liability driven investments can be valued and hedged. This benchmark approach values both assets and liabilities consistently under the real world probability measure using the best performing portfolio, the growth optimal portfolio, as benchmark and numeraire. The benchmark approach identifies the investment strategy which is replicating a given claim at minimal cost. Should the liability under consideration be subject to nonhedgeable risk, e.g. mortality risk, benchmarked risk minimization identifies with its real world pricing formula the investment strategy which minimizes in a practical sense the price of a given claim and minimizes the benchmarked profit and loss from hedging. The application of the approach will be demonstrated for pensions. A least expensive pension scheme will be described that allows one in a fair and transparent manner to hedge in the least expensive way with minimal risk the post retirement payments for its members.

Fergusson, K & Platen, E 2013, 'Real World Pricing of Long Term Cash-Linked Annuities and Equity-Linked Annuities with Cash-Linked Guarantees'.
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This paper proposes a paradigm shift in the valuation of long term cash-linked annuities and equity-linked annuities with cash-linked guarantees, away from classical no-arbitrage pricing towards pricing under the real world probability measure. In contrast to risk neutral pricing, which is a form of relative pricing, the long term average excess return of the equity market comes into play. Instead of the savings account, the numeraire portfolio is employed as the fundamental unit of value in the analysis. The num eraire portfolio is the strictly positive, tradable portfolio that when used as benchmark makes all benchmarked nonnegative portfolios supermartingales. Intuitively, benchmarked portfolios are in the mean downward trending or trendless. The benchmarked real world price of a benchmarked contingent claim equals its real world conditional expectation. This yields the minimal possible price for its hedgeable part and minimizes the variance for its hedge error. Classical actuarial and risk neutral pricing emerge as special cases of the proposed real world pricing. In long term liability and asset valuation, the proposed real world pricing can lead to significantly lower prices than suggested by classical approaches. The existence of an equivalent risk neutral probability measure is not required.

Sarkar, A, Pati, D, Mallick, BK & Carroll, RJ 2013, 'Adaptive Posterior Convergence Rates in Bayesian Density Deconvolution with Supersmooth Errors'.
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Bayesian density deconvolution using nonparametric prior distributions is auseful alternative to the frequentist kernel based deconvolution estimators dueto its potentially wide range of applicability, straightforward uncertaintyquantification and generalizability to more sophisticated models. This articleis the first substantive effort to theoretically quantify the behavior of theposterior in this recent line of research. In particular, assuming a knownsupersmooth error density, a Dirichlet process mixture of Normals on the truedensity leads to a posterior convergence rate same as the minimax rate $(\logn)^{-\eta/\beta}$ adaptively over the smoothness $\eta$ of an appropriateH\'{o}lder space of densities, where $\beta$ is the degree of smoothness of theerror distribution. Our main contribution is achieving adaptive minimax rateswith respect to the $L_p$ norm for $2 \leq p \leq \infty$ under mild regularityconditions on the true density. En route, we develop tight concentration boundsfor a class of kernel based deconvolution estimators which might be ofindependent interest.

Xie, H, Liu, Y, Jin, D & Xi, P 2013, 'Analytical description of high-aperture STED resolution with 0-2$π$ vortex phase modulation'.