Publications

Ben-Nissan, B, Choi, AH, Green, DW, Latella, BA, Chou, J & Bendavid, A 2011, 'Synthesis and Characterization of Hydroxyapatite Nanocoatings by Sol-Gel Method for Clinical Applications' in Sam Zhang (ed), Biological and Biomedical Coatings Handbook: Processing and Characterization, CRC Press, United States, pp. 37-79.
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Nanostructured materials are associated with a diversity of uses within the medical field, for instance, in drug-delivery systems, regenerative medicine, formation of surgical tools, medical devices, and diagnostic systems. It has long been established that porous bulk hydroxyapatite (HAp) cannot be used for load-bearing applications due to its unfavorable mechanical properties. As a result, HAp has been used instead as a coating in orthopedic surgery on metallic alloys, metals giving the support required. Of the metallic alloys used, titanium-based and cobalt chromium alloys are the preferred materials for these HAp coatings for orthopedic and maxillofacial implants (Figure 2.1).

Chen, H & Morris, MJ 2011, 'Overnutrition in Mothers and Appetite Regulators in Offspring' in Preedy, VR (ed), Handbook of Behavior, Food and Nutrition, Springer New York, pp. 1745-1757.
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Overconsumption of energy-rich food and a sedentary lifestyle make significant contributions to the development of obesity. Over the past several decades, the proportion of people who are overweight or obese has risen sharply. As obesity becomes a global epidemic, the rate of childhood obesity is also increasing. Epidemiological and experimental evidence suggests that programming of obesity may occur following overnutrition during early development. Indeed, intrauterine factors such as abnormal glucose and lipid levels, along with hormonal changes due to maternal obesity may also be important determinants of subsequent obesity risk, even more so than genetic factors, thus contributing to the increased incidence of obesity in children. This highlights the importance of understanding the underlying mechanisms to enable better prevention and to permit development of therapeutic strategies. Over the past 5 years, the focus of research on programming of brain appetite regulation has moved from studying the impact of maternal undernutrition to that of overnutrition, as more and more women around the world enter pregnancy either overweight or obese. The appetite circuits that regulate feeding are highly conserved across mammalian species. Animal models provide an opportunity to investigate the impact of in utero or early postnatal overnutrition while controlling genetic and environmental influences. Rat offspring from mothers rendered obese by access to ‘junk food’ are more likely to overeat and prefer ‘junk food’. They tend to develop very early (weaning age) onset lipid and glucose metabolic disorders, such as hyperlipidemia and glucose intolerance, and these last into adulthood. These offspring also manifest resistance to the anorexigenic effects of leptin. Studies in different species suggest that maternal obesity or consuming a lipid dense diet alter the key hypothalamic neuropeptides controlling food intake and energy homeostasis in offspring in utero, with aberra...

Chien, HY, Fok, S, Raviraj, V, Lee, J, Cole, L, Guy Lyons, J & Soon, L 2011, 'Matrix Scaffolds in Cancer Cell Biology; Physiological Representation and Nanoscale Characterisation' in Nanomedicine and Cancer, CRC Press, pp. 150-167.
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© 2012 by Taylor & Francis Group, LLC. All rights reserved. In vitro cultures such as 2-dimensional (D) cell culture, semi-3D, 3D, and in vivo mouse models represent sub-approximations to native conditions that had led to the development of successful translational applications. However, it is also becoming clear that not all in vivo situations are adequately represented and for a subset of patients, their disease conditions and corresponding therapeutic measures may not have been properly addressed. It is essential to match experimental approaches with in vivo environmental conditions for cellular studies. Some of these include the use of clustered cells called spheroids and single tumour cells embedded in matrices with differing densities and architecture. These configurations mimic, for example, desmoplastic tumours in breast cancers. Concomitantly, appropriate analytical tools that can accommodate samples in their native conditions and/or enable nanostructural studies are critical to evaluate the adherence of novel in vitro models to physiological conditions.

Deng, W, Jin, D & Goldys, EM 2011, 'METAL NANOSTRUCTURE-ENHANCED FLUORESCENCE AND ITS BIOLOGICAL APPLICATIONS' in Kane, D, Micolich, A & Rabeau, J (eds), Nanotechnology in Australia: Showcase of Early Career Research, Pan Stanford Publishing, USA, pp. 347-374.
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Over the last two decades, fluorescence-based detection has become one of the leading sensing technologies in biomedical, biological, and related sciences. Its sensitivity makes it possible to detect a single biomolecule through labelling with a suitable fluorophore. Two principal fluorophore properties, brightness and photostability, are fundamentally important to achieve a high level of sensitivity, and in many conventional fluorophores these often fall short of the requirements. Among the methods used to improve the sensitivity of fluorescence detection, the metal-enhanced fluorescence (MEF) technique has been recently actively developed. The MEF phenomenon occurs when an excited fluorophore is located in close proximity to metals, and it is particularly pronounced near noble metal nanostructures. Electrons in such metal nanostructures exhibit strong resonances often located in the visible part of the spectrum (also known as surface plasmon resonance). They can interact with proximal fluorophores, modifying their optical properties and producing increased quantum yield (fluorescence efficiency) and improved photostability. It has been experimentally demonstrated that the MEF technique can increase fluorescence intensity up to several hundreds times. This chapter provides an overview of MEF, covering its basic theory, synthesis of metal nanostructures, and biological applications based on MEF. We focus on silver nanostructures because their strong surface plasmon resonance in the visible matches the absorption and emission bands of most fluorophores. We discuss traditional planar MEF substrates as well as silver nanostructures deposited on micrometre-sized silica beads, generating a fluorescence enhancement of more than one order of magnitude. This achievement allowed us to demonstrate for the first time MEF immunoassays on silica beads by using high-throughput flow cytometry. Furthermore, we discovered that these silver nanostructure-coated silica beads are ab...

Field, C 2011, 'Towards adaptation measures in protecting mangroves from climate change' in Jenkins, AL (ed), Climate Change Adaptation: Ecology, Mitigation and Management, Nova Science Publishers, USA, pp. 65-85.
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A brief account of the nature of mangrove ecosystems is given. This shows that mangroves are generally resilient to climate change and are aggressive colonizers if suitable land is available. An examination of the current worldwide status of mangrove ecosystems and loss of area shows that the quantification of worldwide mangrove area needs improvement. There is an analysis of the response of mangroves to changes in climate: rise in sea level, rise in atmospheric carbon dioxide, rise in air and water temperature, ocean acidification and change in precipitation and storm frequency. A significant lack of information exists on some aspects of these responses. The literature proposes a range of adaptation strategies to prevent the loss of mangrove ecosystems. In the main, these are concerned with the effects of sea level rise and involve planting mangroves, preserving space for mangrove migration or preventing erosion. An examination of these strategies shows the need for extensive local knowledge. Adaptation and mitigation strategies will be useless without an intimate understanding, both spatially and temporally, of the local physical, chemical and biological structures. Such information is often ignored or not available. The management of adaptation strategies requires knowledge of population pressure as well as the effects of climate change. In the near future, the impact of population growth and development is more likely than climate change to impinge on mangrove ecosystems. © 2011 by Nova Science Publishers, Inc. All rights reserved.

Ford, MJ 2011, 'SIESTA: Properties and Applications' in Computational Methods for Large Systems, Wiley, pp. 367-395.
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In this chapter a number of these properties are discussed through examples relevant to nanoscience and technology. The SIESTA methodology in detail in Chapter 2; the present chapter is intended as an accompaniment. The first three examples illustrate the general capabilities of the SIESTA code for problems containing relatively small numbers of atoms and that are amenable to standard diagonalization to solve the self-consistent problem. The last example illustrates the divide-and-conquer linear-scaling capabilities to tackle problems containing large numbers of atoms. © 2011 John Wiley & Sons, Inc.

Gale, PA & Caltagirone, C 2011, 'Anion Sensors' in Chemosensors, Wiley, pp. 395-427.
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Godara, P & Milthorpe, B 2011, 'Surgical Adhesion and Its Prevention' in Ducheyne, P, Healy, KE, Hutmacher, DW, Grainger, DW & Kirkpatrick, CJ (eds), Comprehensive Biomaterials, Elsevier, USA, pp. 561-572.
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Adhesion of freely moving tissues and organs due to surgical injury and trauma can be a serious postoperative complication. High rates of incidence due to surgical intervention, especially associated with abdominal procedures, have been reported. This chapter gives an introduction to the formation of adhesions, with particular focus on peritoneum, urinary and reproductive (female) systems, tendon, ligament, joint, and pericardium. A number of techniques, treatments, and materials have been proposed for the prevention/reduction of adhesion formation. Of these, barrier methods are considered the only effective method currently available. An overview of biomaterials currently used as barriers for postsurgical tissue adhesion is presented. Current clinical practice utilizes solid membranes/mechanical barriers, spray-on, and gel and liquid barriers. These barriers can be either resorbable, nonresorbable, or a combination of both. Complications of barrier films are examined, and design criteria for barrier membranes are presented. Adhesion formation can be beneficial in particular circumstances, such as for anchoring implants, and these uses are commented upon. Much advancement has been made in this area, thanks to the increasing knowledge and understanding regarding the events that control adhesion formation, but there is still a long way to go before an optimum solution to this problem is found.

Huete, A & Glenn, EP 2011, 'Recent advances in remote sensing of ecosystem structure and function' in Weng, Q (ed), Advances in Environmental Remote Sensing: Sensors, Algorithms, and Applications, CRC Press, Taylor and Francis Group, Boca Raton, Florida USA, pp. 291-319.
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Earth-observing remote sensing technologies are becoming widely adopted within the resource management, ecosystem sciences, and sustainable development communities. Satellite data offer unprecedented capabilities to capture the spatial and temporal detail of ecosystem properties at regional to global scales, and remote sensing tools are now employed in characterising ecosystem structure and biologic properties and in monitoring ecosystem health, seasonal dynamics and functional processes.

Huete, A, Didan, K, van Leeuwen, W, Miura, T & Glenn, E 2011, 'MODIS vegetation indices' in Ramachandran, B, Justice, CO & Abrams, M (eds), Remote Sensing and Digital Image Processing, Springer, New York, pp. 579-602.
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Assessments of vegetation condition, cover, change, and processes are major components of global change research prograrns, and are topics of considerable societal relevance. Spectral vegetation indices are among the most widely used satellite data products, which provide key measurements for climate, hydrologic, and biogeochemical studies; phenology, land cover, and land cover change detection; natural resource management and sustainable development.

Huete, A, Solano-Barajas, R, Glenn, EP & Restrepo Coupe, N 2011, 'Monitoreo de propiedades y procesos ecosistamicos con indices de vegetacion MODIS' in Jean-Francois Mas (ed), Aplicaciones del sensorMODIS para el monitoreo del territorio, Secretaria de Medio Ambiente, Mexico, pp. 195-230.
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En este capítulo revisamos los importantes avances y las aplicaciones en el uso de índices de vegetación (IV) de MODIS como herramientas para el análisis y monitoreo de propiedades y procesos ecosistémicos, incluyendo aquellos relacionados con la fotosíntesis y la transpiración del dosel. Presentamos las características básicas de los productos IV-MODIS estándar, incluidas las series de tiempo, las medidas cualitativas, el método de composición y las incertidumbres presentes en las series de datos. Discutimos construcciones alternativas de las series de datos temporales de IV, incluyendo aquellos de la recepción directa de datos. Los perfiles de los IV interanuales y estacionales son presentados y analizados en varios sitios de cobertura terrestre en México y los IV MODIS son comparados con mediciones temporales de productividad bruta y evapotranspiración de ecosistemas realizadas con torres de medición de flujo en La Paz, Baja California Sur. Se muestra que los IV-MODIS son herramientas de inestimable valor en el estudio temporal de las dinámicas de los ecosistemas.

Huete, AR & Glenn, EP 2011, 'Remote Sensing Image Classification' in Advances in Environmental Remote Sensing, CRC Press, pp. 219-240.
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Jin, D, Yuan, J & Piper, J 2011, 'LONG-LIFETIME LUMINESCENT NANOBIOPROBES FOR ADVANCED CYTOMETRY BIOSENSING' in Kane, D, Micolich, A & Rabeau, J (eds), Nanotechnology in Australia: Showcase of Early Career Research, Pan Stanford Publishing, USA, pp. 317-344.
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In biological discovery and disease diagnosis, there are increasing demands for rapid detection of trace amounts of cells, organisms, and molecules. one of the most popular methods is labelling the target analytes with fluorescent bioprobes, thus making the targets spectrally distinguishable. However, conventional molecular bioprobes are weak, photobleaching, and often not sufficient to suppress autofluorescence backgrounds by spectral discrimination, since many naturally occurring substances are autofluorescent under ultraviolet (uV) or visible-wavelength excitation. This represents a typical biosensing problem of detecting a needle in a haystack. Here we show long-lifetime luminescent silica nanoparticles as bioprobes to provide excellent opportunities in suppression of autofluorescence backgrounds in the temporal domain. This is due to the exceptionally long lifetime from lanthanide bioprobes in the order of several hundred microseconds, in contrast to the few-nanosecond-lifetime autofluorescence backgrounds. using a covalent-binding nanoencapsulation technique, the as-prepared ~40 nm monodisperse silica nanoparticle effectively protects thousands of lanthanide complex dyes against the quenching environment. This results in both remarkable signal amplification and enhanced photostability. Due to the large difference in the lifetime, the microsecond-lived signal luminescence can be detected in a background-free condition against the nanosecond-lived autofluorescence using time-gated detection. Furthermore, the effective simultaneous confinement of multiple lanthanide-element dyes within nanoparticles also provides opportunities to produce multiplexing bioprobes. In this chapter, we showcase our successfully engineered microsecond-lifetime nanobioprobes for immunobioassays of human prostate-specific antigen (PSA) and bioimaging applications of an environmental pathogen Giardia lamblia. Our achievements include a radical extension of the excitation wavelength fro...

Marsh, J, Gloeckl, S, Tyndall, J & Huston, WM 2011, 'The role of HtrA as a chaperone and protease in bacterial pathogenesis' in Berhardt, LV (ed), Advances in Medicine and Biology, Nova Biomedical, Hauppage, New York, pp. 87-121.
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HtrA (High Temperature Requirement A) is a critical stress response protease and chaperone for many bacteria. HtrA is a multitasking protein which can degrade unfolded proteins, conduct specific proteolysis of some substrates for correct assembly, interact with substrates to ensure correct folding, assembly or localisation, and chaperone unfolded proteins. These functions are critical for the virulence of a number of bacterial pathogens, in some cases not simply due to the broad activities of HtrA in protection against the protein stress conditions which occur during virulence. But also due to the role of HtrA in either specific proteolysis or assembly of key protein substrates which function directly in virulence. Remarkably, these activities are all conducted without any requirement for ATP. The biochemical mechanism of HtrA relies both on the chymotryptic serine protease active site as well as the presence of two PDZ (protein binding) domains. The mechanism is a unique combination of activation by substrate motifs to alter the confirmation of the active site, and assembly into a multimeric complex which has enhanced degradation and may also act as a protective cage for proteins which are not degraded. The role of this protease in the pathogenesis of a number of bacteria and the details of its distinctive biochemical activation and assembly mechanisms are discussed in this chapter.

Mazard, S, Ostrowski, M, Garczarek, L & Scanlan, DJ 2011, 'A Targeted Metagenomic Approach to Determine the “Population Genome” of Marine Synechococcus' in Handbook of Molecular Microbial Ecology II, Wiley, pp. 301-307.
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Monahan, LG, D'Elia, M & Harry, L 2011, 'Mining bacterial cell division for new antibacterial drugs' in Miller, AA & Miller, PF (eds), Emerging Trends in Antibacterial Discovery: Answering the Call to Arms, Caister Academic Press, United Kingdom, pp. 35-75.
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As bacterial antibiotic resistance continues to exhaust our supply of effective antibiotics, a global public health disaster appears likely. Poor financial investment in antibiotic research has exacerbated the situation. A call to arms raised by several prestigious scientific organisations a few years ago rallied the scientific community, and now the scope of antibacterial research has broadened considerably. Multi-disciplinary approaches have yielded a wealth of new data on areas ranging from the identification of novel antibacterial targets to the use of biological agents for antibacterial therapy.

Murrihy, RC 2011, 'Social Competency CBT-Based Group Training for Youth in Alternative School Settings' in Clinical Handbook of Assessing and Treating Conduct Problems in Youth, Springer New York, pp. 295-332.
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This volume serves as a one-stop reference for all professionals who seek a solid grounding in theory as well as those who need access to evidence-based assessment and therapies for conduct problems.

Murrihy, RC, Ollendick, TH & Kidman, AD 2011, 'Epilogue: Future Directions in Research and Practice' in Clinical Handbook of Assessing and Treating Conduct Problems in Youth, Springer New York, pp. 517-530.
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Platen, E 2011, 'A benchmark approach to investing and pricing' in MacLean, LC, Thorp, EO & Ziemba, WT (eds), The Kelly Capital Growth Investment Criterion: Theory and Practice, World Scientific Publishing, USA, pp. 409-426.
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This paper introduces a general market modeling framework, the benchmark appma.chl which assumes the existence of the nume!'raire portfolio. This is the strictly positive portfolio that when used as benchmMk makes all benchmarked non-negati.ve portfolios sllperma.rtinga!es, that is intuitively speaking downward trending or trendless. It can be shQ'Wn to equal the Kelly portfolio, which tna.-'jmiz. es expected logarithmk utility. In several Wa.ys, the KeUy or numeraire portfolio is the 'bestll performing portfolio and cannot be outperformed systematically by any other non-negative portfolio. Its use in pricing as nttmeroire leads directly to the real world pricing formula) which employs the real world probability when calculating conditional expectations. In a large regular financial market, the Kelly portfolio is shawn to be approxima.ted by well·divcnrified portfolios.

Polgar, G & Lim, R 2011, 'Mudskippers: Human use, ecotoxicology and biomonitoring of mangrove and other soft bottom intertidal ecosystems' in Mangroves: Ecology, Biology and Taxonomy, Nova, USA, pp. 51-86.
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Mudskippers (Gobiidae: Oxudercinae) are air-breathing gobies, which are widely distributed throughout the West African coast and the Indo-Pacific region. They are closely linked to mangrove and adjacent soft bottom peri-tidal ecosystems. Some species are amongst the best adapted fishes to an amphibious lifestyle. All mudskippers are benthic burrowers in anoxic sediments, and since tidal mudflats are efficient sediment traps, and sinks for nutrients and other chemical compounds, they are constantly in contact with several types of pollutants produced by industrial, agricultural and domestic activities. Due to their natural abundance, considerable resistance to highly polluted conditions, and their benthic habits, mudskippers are frequently used in aquatic ecotoxicological studies. For the same reasons, mudskippers also frequently occur in urbanised or semi-natural coastal areas. Since several species are widely consumed throughout their whole geographical range, these same characteristics also facilitate their aquaculture in several countries, such as Bangladesh, Thailand, Philippines, China, Taiwan and Japan. Even when not directly used, mudskippers are often abundant and are important prey items for many intertidal transient species (marine visitors), and several species of shorebirds. Therefore, there is potential for bioaccumulation of toxicants wherever mudskippers and pollution co-occur. This chapter reviews the ecotoxicology of mudskippers, and their potential for use as biomonitors to better manage coastal swamp ecosystems. The diverse sympatric assemblages of mudskipper species allow for spatially differentiated ecotoxicological investigations along the whole intertidal zone, since adults are often territorial and/or sedentary, and show species-specific patterns of habitat differentiation. A case study is also proposed where this approach could be adopted to address potential health-risk issues in a local population who are regular consumers of mudskipper...

Reimers, JR 2011, 'Preface: Choosing the Right Method for Your Problem' in Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, Wiley, pp. xvii-xxii.
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Thenkabail, P, Lyon, J & Huete, A 2011, 'Advances in Hyperspectral Remote Sensing of Vegetation and Agricultural Croplands' in Thenkabail, PS, Lyon, JG & Huete, A (eds), Hyperspectral Remote Sensing of Vegetation, CRC Press, USA, pp. 3-36.
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Thenkabail, P, Lyon, J & Huete, A 2011, 'Hyperspectral Remote Sensing of Vegetation and Agricultural Crops' in Hyperspectral Remote Sensing of Vegetation, CRC Press, pp. 663-688.
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Thenkabail, P, Lyon, JG & Huete, A 2011, 'Hyperspectral remote sensing of vegetation and agricultural crops: Knowledge gain and knowledge gap after 40 years of research' in Thenkabail, PS, Lyon, JG & Huete, A (eds), Hyperspectral Remote Sensing of Vegetation, Taylor & Francis, USA, pp. 663-688.

Zhang, F, Lidbury, BA, Richardson, AM, Yates, BF, Gardiner, MG, Bridgeman, AJ, Schulte, J, Rodger, JC & Mate, KE 2011, 'Preface' in Zhang, F, Lidbury, BA, Richardson, AM, Yates, BF, Gardiner, MG, Bridgeman, AJ, Schulte, J, Rodger, JC & Mate, KE (eds), Sustainable Language Support Practises in Science Education, IGI Global, Hershey PA, USA, pp. 160-194.
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First year physics courses for non-physics majors are among the most difficult course to cope with for science and engineering students alike. Not only are students confronted with physics specific concepts and mathematics applied in unfamiliar environment, students also have to learn the specific lingo of physics and keep it separate from common language and language used in their own field of major. Anecdotally, we know that students have to master the language of their respective field of study in order to master the field. We investigated the link between language of physics used in our first year physics lectures, understanding of related physics concept, and student performance after a language focused intervention. We found that a language conscious approach in first year physics not only improved the performance of students of non-English background but also benefited the performance of students of native English speaking background.

Achterman, RR, Smith, AR, Oliver, BG & White, TC 2011, 'Sequenced dermatophyte strains: Growth rate, conidiation, drug susceptibilities, and virulence in an invertebrate model', Fungal Genetics and Biology, vol. 48, no. 3, pp. 335-341.
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Ahadi, K, Mahdavi, SM, Nemati, A & Kianinia, M 2011, 'Photoconductivity and diode effect in Bi rich multiferroic BiFeO3 thin films grown by pulsed-laser deposition', JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS, vol. 22, no. 7, pp. 815-820.
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Aharonovich, I, Castelletto, S, Johnson, BC, McCallum, JC & Prawer, S 2011, 'Engineering chromium-related single photon emitters in single crystal diamonds', NEW JOURNAL OF PHYSICS, vol. 13, p. 045015.
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Color centers in diamond, as single photon emitters, are leading candidates for future quantum devices due to their room temperature operation and photostability. The recently discovered chromium-related centers are particularly attractive because they possess narrow bandwidth emission and a very short lifetime. In this paper, we investigate the fabrication methodologies for engineering these centers in monolithic diamond. We show that the emitters can be successfully fabricated by ion implantation of chromium in conjunction with oxygen or sulfur. Furthermore, our results indicate that the background nitrogen concentration is an important parameter, which governs the probability of success in generating these centers.

Aharonovich, I, Castelletto, S, Simpson, DA, Su, C-H, Greentree, AD & Prawer, S 2011, 'Diamond-based single-photon emitters', REPORTS ON PROGRESS IN PHYSICS, vol. 74, no. 7.
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The exploitation of emerging quantum technologies requires efficient fabrication of key building blocks. Sources of single photons are extremely important across many applications as they can serve as vectors for quantum informationthereby allowing long-range (perhaps even global-scale) quantum states to be made and manipulated for tasks such as quantum communication or distributed quantum computation. At the single-emitter level, quantum sources also afford new possibilities in terms of nanoscopy and bio-marking. Color centers in diamond are prominent candidates to generate and manipulate quantum states of light, as they are a photostable solid-state source of single photons at room temperature. In this review, we discuss the state of the art of diamond-based single-photon emitters and highlight their fabrication methodologies. We present the experimental techniques used to characterize the quantum emitters and discuss their photophysical properties. We outline a number of applications including quantum key distribution, bio-marking and sub-diffraction imaging, where diamond-based single emitters are playing a crucial role. We conclude with a discussion of the main challenges and perspectives for employing diamond emitters in quantum information processing.

Aharonovich, I, Greentree, AD & Prawer, S 2011, 'Diamond photonics', NATURE PHOTONICS, vol. 5, no. 7, pp. 397-405.
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Diamond, a material marvelled for its strength, beauty and perfection, was first used to polish stone axes in Neolithic times. This most ancient of materials is now being touted by many as the ideal platform for quantum-age technologies. In this Review, we describe how the properties of diamond match the requirements of the `second quantum revolution. We also discuss recent progress in the development of diamond and particularly diamond colour centres for transforming quantum information science into practical quantum information technology.

Aharonovich, I, Niu, N, Rol, F, Russell, KJ, Woolf, A, El-Ella, HAR, Kappers, MJ, Oliver, RA & Hu, EL 2011, 'Controlled tuning of whispering gallery modes of GaN/InGaN microdisk cavities', APPLIED PHYSICS LETTERS, vol. 99, no. 11.
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Aitken, C, Berger, CEH, Buckleton, JS, Champod, C, Curran, J, Dawid, AP, Evett, IW, Gill, P, Gonzalez-Rodriguez, J, Jackson, G, Kloosterman, A, Lovelock, T, Lucy, D, Margot, P, McKenna, L, Meuwly, D, Neumann, C, Daeid, NN, Nordgaard, A, Puch-Solis, R, Rasmusson, B, Redmayne, M, Roberts, P, Robertson, B, Roux, C, Sjerps, MJ, Taroni, F, Tjin-A-Tsoi, T, Vignaux, GA, Willis, SM & Zadora, G 2011, 'Expressing evaluative opinions: A position statement', SCIENCE & JUSTICE, vol. 51, no. 1, pp. 1-2.
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Ajani, P, Ingleton, T, Pritchard, T & Armand, L 2011, 'Microalgal blooms in the coastal waters of New South Wales, Australia', Proceedings of the Linnean Society of New South Wales, vol. 133, pp. 15-31.
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We investigated the frequency and causative taxa of observed microalgal blooms in New South Wales (NSW) coastal waters from 2000 to 2009 and compared these to an earlier bloom inventory from 1990 to 1999. The majority of recurrent blooms are harmless water discolourations caused by Noctiluca scintillans and Trichodesmium erythraeum. The recent reporting period witnessed the first blooms of Astrionellopsis glacialis, Guinardia sp., Skeletonema sp., cf. Heterocapsa sp., Dinophysis caudata, Prorocentrum dentatum, Prorocentrum rhathymum, Fibrocapsa japonica, Gymnodinium catenatum, Oscillaroria sp., and Anabaena circinalis. The frequency of blooms appears to have increased over time with a shift in maximum bloom activity from January (1990 to 1999) to October (2000 to 2009). Peak bloom years correspond with El Niño episodes, the most significant being 1997 to 1998 and 2002 to 2003. No significant difference was found between the causative species or spatial distribution of dominant taxa over two decades. Differences were observed in bloom type in estuaries with more 'potentially harmful to marine organisms' blooms during 1990 to 1999 and more 'harmless' blooms during 2000 to 2009. More 'unidentified' blooms were reported during 2000 to 2009 compared to 1990 to 1999, for both marine and estuarine waters. We emphasize that although algal bloom reports are ad hoc in their nature, they can contribute valuable baseline information, which may suggest causative relationships for evaluating trends in phytoplankton ecology.

Algarin, JM, Freire, MJ, Lopez, MA, Lapine, M, Jakob, PM, Behr, VC & Marqués, R 2011, 'Analysis of the resolution of split-ring metamaterial lenses with application in parallel magnetic resonance imaging', Applied Physics Letters, vol. 98, no. 1, pp. 014105-014105.
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In this work, we experimentally determine the resolution of split-ring metamaterials lenses with emphasis in magnetic resonance imaging applications. Two small sources are used to determine the minimal resolution of the lens, which is compared with previous theoretical predictions. Taking into account this minimal resolution, a second experiment is designed in order to study the ability of a split-ring lens to improve the localization of the field produced by two closely spaced coils. This ability could find application in parallel magnetic resonance imaging, which take advantage of the distinct coil sensitivities in order to reduce the image acquisition time.

Allison, DB, Carroll, RJ, Divers, J & Redden, DT 2011, 'How to estimate the measurement error variance associated with ancestry proportion estimates', Statistics and Its Interface, vol. 4, no. 3, pp. 327-337.
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Allsop, DJ, Norberg, MM, Copeland, J, Fu, S & Budney, AJ 2011, 'The Cannabis Withdrawal Scale development: Patterns and predictors of cannabis withdrawal and distress', DRUG AND ALCOHOL DEPENDENCE, vol. 119, no. 1-2, pp. 123-129.
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Background Rates of treatment seeking for cannabis are increasing, and relapse is common. Management of cannabis withdrawal is an important intervention point. No psychometrically sound measure for cannabis withdrawal exists, and as a result treatment developments cannot be optimally targeted. The aim is to develop and test the psychometrics of the Cannabis Withdrawal Scale and use it to explore predictors of cannabis withdrawal. Methods A volunteer sample of 49 dependent cannabis users provided daily scores on the Cannabis Withdrawal Scale during a baseline week and 2 weeks of abstinence. Results Internal reliability (Cronbach's alpha = 0.91), testretest stability (average intra-class correlation = 0.95) and content validity analysis show that the Cannabis Withdrawal Scale has excellent psychometric properties. Nightmares and/or strange dreams was the most valid item (Wald ?2 = 105.6, P < 0.0001), but caused relatively little associated distress (Wald ?2 = 25.11, P = 0.03). Angry outbursts were considered intense (Wald ?2 = 73.69, P < 0.0001) and caused much associated distress (Wald ?2 = 45.54, P < 0.0001). Trouble getting to sleep was also an intense withdrawal symptom (Wald ?2 = 42.31, P < 0.0001) and caused significant associated distress (Wald ?2 = 47.76, P < 0.0001). Scores on the Severity of Dependence Scale predicted cannabis withdrawal. Conclusions The Cannabis Withdrawal Scale can be used as a diagnostic instrument in clinical and research settings where regular monitoring of withdrawal symptoms is required.

Ampawong, S, Combes, V, Hunt, NH, Radford, J, Chan-Ling, T, Pongponratn, E & Grau, GER 2011, 'Quantitation of brain edema and localisation of aquaporin 4 expression in relation to susceptibility to experimental cerebral malaria.', Int J Clin Exp Pathol, vol. 4, no. 6, pp. 566-574.
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The pathogenic mechanisms underlying the occurrence of cerebral malaria (CM) are still incompletely understood but, clearly, cerebral complications may result from concomitant microvessel obstruction and inflammation. The extent to which brain edema contributes to pathology has not been investigated. Using the model of P. berghei ANKA infection, we compared brain microvessel morphology of CM-susceptible and CM-resistant mice. By quantitative planimetry, we provide evidence that CM is characterized by enlarged perivascular spaces (PVS). We show a dramatic aquaporin 4 (AQP4) upregulation, selectively at the level of astrocytic foot processes, in both CM and non-CM disease, but significantly more pronounced in mice with malarial-induced neurological syndrome. This suggests that a threshold of AQP4 expression is needed to lead to neurovascular pathology, a view that is supported by significantly higher levels in mice with clinically overt CM. Numbers of intravascular leukocytes significantly correlated with both PVS enlargement and AQP4 overexpression. Thus, brain edema could be a contributing factor in CM pathogenesis and AQP4, specifically in its astrocytic location, a key molecule in this mechanism. Since experimental CM is associated with substantial brain edema, it models paediatric CM better than the adult syndrome and it is tempting to evaluate AQP4 in the former context. If AQP4 changes are confirmed in human CM, it may represent a novel target for therapeutic intervention.

Anderson, LO, Aragao, LEOC, Shimabukuro, YE, Almeida, S & Huete, A 2011, 'Fraction images for monitoring intra-annual phenology of different vegetation physiognomies in Amazonia', INTERNATIONAL JOURNAL OF REMOTE SENSING, vol. 32, no. 2, pp. 387-408.
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In this study we investigate the potential of fraction images derived from a linear spectral mixture model to detect vegetation phenology in Amazonia, and evaluate their relationships with the Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices. Time series of MODIS 250-m data over three contrasting land cover types in the Amazon were used in conjunction with rainfall data, a land cover map and a forest inventory survey to support the interpretation of our findings. Each vegetation physiognomy was characterized by a particular intra-annual variability detected by a combination of the fraction images. Both vegetation and shade fractions were important to evaluate the seasonality of the open tropical forest (OTF). The association of these results with forest inventory data and the literature suggests that Enhanced Vegetation Index (EVI) and vegetation fraction images are sensitive to structural changes in the canopy of OTF. In cerrado grassland (CG) the phenology was better characterized by combined soil and vegetation fractions. Soybean (SB) areas were characterized by the highest ranges in the vegetation and soil fraction images. Vegetation fraction and vegetation indices for the OTF showed a significant positive relationship with EVI but not with Normalized Difference Vegetation Index (NDVI). Significant relationships for vegetation fraction and vegetation indices were also found for the CG and soybean areas. In contrast to vegetation index approaches to monitoring phenology, fraction images provide additional information that allows a more comprehensive exploration of the spectral and structural changes in vegetation formations.

Anderson, R, Kjelleberg, S, McDougald, D & Jürgens, K 2011, 'Species-specific patterns in the vulnerability of ­carbon-starved bacteria to protist grazing', Aquatic Microbial Ecology, vol. 64, no. 2, pp. 105-116.
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Andreasen, J, Asatryan, AA, Botten, LC, Byrne, MA, Cao, H, Ge, L, Labonte, L, Sebbah, P, Stone, AD, Tuereci, HE & Vanneste, C 2011, 'Modes of random lasers', ADVANCES IN OPTICS AND PHOTONICS, vol. 3, no. 1, pp. 88-127.
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In conventional lasers, the optical cavity that confines the photons also determines essential characteristics of the lasing modes such as wavelength, emission pattern, directivity, and polarization. In random lasers, which do not have mirrors or a well-defined cavity, light is confined within the gain medium by means of multiple scattering. The sharp peaks in the emission spectra of semiconductor powders, first observed in 1999, has therefore lead to an intense debate about the nature of the lasing modes in these so-called lasers with resonant feedback. We review numerical and theoretical studies aimed at clarifying the nature of the lasing modes in disordered scattering systems with gain. The past decade has witnessed the emergence of the idea that even the low-Q resonances of such open systems could play a role similar to the cavity modes of a conventional laser and produce sharp lasing peaks. We focus here on the near-threshold single-mode lasing regime where nonlinear effects associated with gain saturation and mode competition can be neglected. We discuss in particular the link between random laser modes near threshold and the resonances or quasi-bound (QB) states of the passive system without gain. For random lasers in the localized (strong scattering) regime, QB states and threshold lasing modes were found to be nearly identical within the scattering medium.

Anuj, SN, Whiley, DM, Kidd, TJ, Ramsay, KA, Bell, SC, Syrmis, MW, Grimwood, K, Wainwright, CE, Nissen, MD & Sloots, TP 2011, 'Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis', Clinical Microbiology and Infection, vol. 17, no. 9, pp. 1403-1408.
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Background Chronic lung infection with the bacterium Pseudomonas aeruginosa is one of the hallmarks of cystic fibrosis (CF) and is associated with worsening lung function, increased hospitalisation and reduced life expectancy. A virulent clonal strain of P. aeruginosa (Australian epidemic strain I; AES-I) has been found to be widespread in CF patients in eastern Australia. Methods Suppression subtractive hybridization (SSH) was employed to identify genetic sequences that are present in the AES-I strain but absent from the sequenced reference strain PAO1. We used PCR to evaluate the distribution of several of the AES-I loci amongst a collection of 188 P. aeruginosa isolates which was comprised of 35 AES-I isolates (as determined by PFGE), 78 non-AES-I CF isolates including other epidemic CF strains as well as 69 P. aeruginosa isolates from other clinical and environmental sources. Results We have identified a unique AES-I genetic locus that is present in all 35 AES-I isolates tested and not present in any of the other 153 P. aeruginosa strains examined. We have used this unique AES-I locus to develop a diagnostic PCR and a real-time PCR assay to detect the presence of P. aeruginosa and AES-I in patient sputum samples.

Arora, M, Hare, D, Austin, C, Smith, DR & Doble, P 2011, 'Spatial distribution of manganese in enamel and coronal dentine of human primary teeth', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 409, no. 7, pp. 1315-1319.
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Emerging evidence indicates that excessive exposure to manganese (Mn) during the prenatal period and early childhood may result in neurodevelopmental deficits. However, accurate exposure biomarkers are not well established, limiting our understanding of exposureresponse relationships over these susceptible periods of development. Naturally shed deciduous teeth are potentially a useful biomarker of environmental exposure to Mn. However, the uptake and distribution of Mn in human teeth has not been studied in detail. Mn distribution was measured at high resolution (~20 ìm) in eight human primary teeth using laser ablationinductively coupled plasma-mass spectrometry. A bio-imaging methodology was applied to construct detailed elemental maps of three incisors, and bone meal (NIST SRM 1486) was used to validate the analyses. The distribution of Mn in enamel and coronal dentine showed a distinct and reproducible pattern. In enamel, the 55Mn:43Ca ratio was highest at the outer edge of enamel (range=0.57 to 4.74) for approximately 2040 ìm butwas substantially lower in deeper layers (range=0.005 to 0.013). The highest levels ofMnwere observed in dentine immediately adjacent the pulpal margin (55Mn:43Ca range=2.27 to 6.95). Importantly, a clearly demarcated high Mn zone was observed in dentine at the incisal end of the teeth. Using confocal laser scanning microscopy to visualize the neonatal line, this region was identified as being in the prenatally formed dentine. The high-resolution map of the spatial distribution of Mn in human primary teeth highlighted specific reproducible patterns of Mn distribution in enamel and coronal dentine.

Arora, S, Flower, O, Murray, NPS & Lee, BB 2011, 'Respiratory care of patients with cervical spinal cord injury: A review', Critical Care and Resuscitation, vol. 13, no. 3, pp. 64-73.
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Respiratory complications following cervical spinal cord injury are common and are the leading cause of morbidity and mortality after this type of injury. Impaired mechanics of ventilation, poor cough, increased secretions and bronchospasm predispose to atelectasis, pneumonia and exacerbations of respiratory failure. Prolonged mechanical ventilation and tracheostomy are often required. This review discusses the relevant pathophysiology, various ventilatory strategies and timing of tracheostomy, and examines the evidence surrounding physiotherapeutic and pharmacological treatment options.

Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2011, 'A self-assembling hexameric spheroid with variable degrees of hydration', Journal of Inclusion Phenomena and Macrocyclic Chemistry, vol. 71, no. 3-4, pp. 297-302.
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The V-shaped racemic compound 4,12-dinitro-6,7,14,15-tetrahydro-6,14- methanocycloocta[1,2-b:5,6-b']diquinoline 2 crystallises from solvents of differing water content as a centrosymmetric spheroidal hexamer in the form of a series of isostructural clusters (2) 6 •(water) x X-ray structures of these crystals in space group R3̄ show that they can exhibit an extent of hydration anywhere throughout the composition range x = 0 to 1. © 2011 Springer Science+Business Media B.V.

Asquith, KL, Horvat, JC, Kaiko, GE, Carey, AJ, Beagley, KW, Hansbro, PM & Foster, PS 2011, 'Interleukin-13 Promotes Susceptibility to Chlamydial Infection of the Respiratory and Genital Tracts', PLoS Pathogens, vol. 7, no. 5, pp. e1001339-e1001339.
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Au, PCK, Zhu, Q-H, Dennis, ES & Wang, M-B 2011, 'Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants', RNA BIOLOGY, vol. 8, no. 3, pp. 404-414.
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Recent advances in the field of RNA research have provided compelling evidence implicating long non-coding RNA molecules in many diverse and substantial biological processes that include transcriptional and post-transcriptional regulation of gene express

Austin, C, Fryer, F, Lear, J, Bishop, D, Hare, D, Rawling, T, Kirkup, L, McDonagh, A & Doble, P 2011, 'Factors affecting internal standard selection for quantitative elemental bio-imaging of soft tissues by LA-ICP-MS', JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY, vol. 26, no. 7, pp. 1494-1501.
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Element response variations under different laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) operating conditions were investigated to identify important factors for selecting an internal standard (IS) for quantitative elemental bi

Baghel, RS, Kumari, P, Bijo, AJ, Gupta, V, Reddy, CRK & Jha, B 2011, 'Genetic analysis and marker assisted identification of life phases of red alga Gracilaria corticata (J. Agardh)', Molecular Biology Reports, vol. 38, no. 6, pp. 4211-4218.
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Baird, ME, Suthers, IM, Griffin, DA, Hollings, B, Pattiaratchi, C, Everett, JD, Roughan, M, Oubelkheir, K & Doblin, M 2011, 'The effect of surface flooding on the physical-biogeochemical dynamics of a warm-core eddy off southeast Australia', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 58, no. 5, pp. 592-605.
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Warm core eddies (WCEs) formed from the East Australian Current (EAC) play an important role in the heat, mass and biogeochemical budgets of the western Tasman Sea. The development and separation of an EAC WCE during July-December 2008 was observed using remotely-sensed temperature, ocean colour and sea-level elevation, three Argo floats, a shipboard CTD, a shelf mooring array and a 15-day deployment of a Slocum glider.

Baleriola, C, Rawlinson, WD, Dore, GJ, Chaverot, S, Stelzer-Braid, S, Yoshihara, M, Crawford, D, Sievert, W, McCaughan, G, Weltman, M, Cheng, W, Rizkalla, B, Dubois, D, Thommes, J & Roberts, S 2011, 'Effect of Low-Level HCV Viraemia at Week 24 on HCV Treatment Response in Genotype 1 Patients', Antiviral Therapy, vol. 16, no. 2, pp. 173-180.
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Background We examined the detection of low-level viraemia at week 24 as a predictor of sustained virological response (SVR) and viral relapse/breakthrough, and the agreement between the Roche Cobas TaqMan™ HCV RNA assay (TaqMan) and Roche Cobas® Amplicor HCV qualitative assay (Amplicor; both Roche Molecular Diagnostics, Pleasanton, CA, USA) for detection of low-level viraemia. Methods A total of 871 treatment-naive HCV genotype 1 patients participating in an induction-dose pegylated interferon therapy study had virological responses assessed using TaqMan. A total of 151 patients with HCV RNA levels ≤500 IU/ml had samples tested in parallel using the Amplicor and TaqMan assays. Results SVR was significantly lower and relapse/breakthrough significantly higher in patients with low-level residual viraemia at week 24 compared with those who had undetectable viraemia: SVR was 72%, 29% and 14% ( P<0.0001) and relapse/breakthrough 28%, 71% and 86% ( P<0.0001) in patients with viraemia that was undetectable, detectable <15 IU/ml and detectable 15–<50 IU/ml, respectively, at week 24. The negative predictive value (NPV) for a week-24 virological response for SVR was 86%, 90% and 90% using Taq-Man cutoffs of undetectable, <15 IU/ml and <50 IU/ml, respectively. The percentage agreement between Amplicor and TaqMan was similarly high for TaqMan cutoffs of 50 IU/ml and 15 IU/ml, but lower for undetectable viraemia (83%, 83% and 70%, respectively). Conclusions These data emphasize the importance of achieving undetectable HCV RNA during pegylated interferon therapy to maximize SVR; however, the current 24-week stopping rule of undetectable HCV RNA appears too stringent when using sensitive PCR assays given the observed lower NPV for S...

Banik, GR, Barratt, JLN, Marriott, D, Harkness, J, Ellis, JT & Stark, D 2011, 'A case-controlled study of Dientamoeba fragilis infections in children', PARASITOLOGY, vol. 138, no. 7, pp. 819-823.
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Dientamoeba fragilis is a pathogenic protozoan parasite that is implicated as a cause of human diarrhoea. A case-controlled study was conducted to determine the clinical signs associated with D. fragilis infection in children presenting to a Sydney Hospital. Treatment options are also discussed. Stool specimens were collected from children aged 15 years or younger and analysed for the presence of D. fragilis. In total, 41 children were included in the study along with a control group. Laboratory diagnosis was performed by microscopy of permanently stained, fixed faecal smears and by real-time PCR. Gastrointestinal symptoms were present in 40/41 (98%) of these children with dientamoebiasis, with diarrhoea (71%) and abdominal pain (29%) the most common clinical signs. Chronic gastrointestinal symptoms were present in 2% of cases. The most common anti-microbial used for treatment was metronidazole (n=41), with complete resolution of symptoms and clearance of parasite occurring in 85% of cases. A treatment failure rate occurred in 15% of those treated with metronidazole. Follow-up treatment comprised of an additional course of metronidazole or iodoquinol was needed in order to achieve complete resolution of infection and symptoms in this group. This study demonstrates the pathogenic potential of D. fragilis in children and as such it is recommended that all laboratories must routinely test for this organism and treat if detected.

Barratt, JLN, Harkness, J, Marriott, D, Ellis, JT & Stark, D 2011, 'A review ofDientamoeba fragiliscarriage in humans: Several reasons why this organism should be considered in the diagnosis of gastrointestinal illness', Gut Microbes, vol. 2, no. 1, pp. 3-12.
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Dientamoeba fragilis is a protozoan that inhabits the human gut. It is approximately 100 years since Dientamoebas discovery and first description when it was described as a rare and harmless commensal. Since then it has struggled to gain recognition as a pathogen despite the evidence supporting its pathogenicity. Dientamoeba remains neglected, probably due to the misconceptions that it is uncommon and non-pathogenic. Usually, carriage of Dientamoeba is associated with symptoms such as abdominal pain and diarrhea. Moreover, antimicrobial therapy followed by resolution of symptoms coincides with the eradication of Dientamoeba. This manuscript reviews the scientific literature relating to Dientamoebas prevalence and pathogenicity. While much of the evidence supporting its pathogenicity is only circumstantial, it is apparent that most researchers agree that Dientamoeba is pathogenic. Therefore, in symptomatic patients who harbor Dientamoeba and no other pathogen, Dientamoeba should be considered as the etiological agent and treated as such.

Barratt, JLN, Harkness, J, Marriott, D, Ellis, JT & Stark, D 2011, 'The ambiguous life of Dientamoeba fragilis: the need to investigate current hypotheses on transmission', PARASITOLOGY, vol. 138, no. 5, pp. 557-572.
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Dientamoeba fragilis is an inhabitant of the human bowel and is associated with gastrointestinal illness. Despite its discovery over a century ago, the details of Dientamoebas life cycle are unclear and its mode of transmission is unknown. Several theories exist which attempt to explain how Dientamoeba may be transmitted. One theory suggests that animals are responsible for the transmission of Dientamoeba. However, reports of Dientamoeba in animals are sporadic and most are not supported by molecular evidence. Another theory suggests that Dientamoeba may be transmitted via the ova of a helminth. Given that the closest relative of Dientamoeba is transmitted via the ova of a helminth, this theory seems plausible. It has also been suggested that Dientamoeba could be transmitted directly between humans. This theory also seems plausible given that other relatives of Dientamoeba are transmitted in this way. Despite numerous investigations, Dientamoebas mode of transmission remains unknown. This review discusses the strengths and weaknesses of theories relating to Dientamoebas mode of transmission and, by doing so, indicates where gaps in current knowledge exist. Where information is lacking, suggestions are made as to how future research could improve our knowledge on the life cycle of Dientamoeba.

Barton, DA, Cole, L, Collings, DA, Liu, DYT, Smith, PMC, Day, DA & Overall, RL 2011, 'Cell-to-cell transport via the lumen of the endoplasmic reticulum', The Plant Journal, vol. 66, no. 5, pp. 806-817.
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Beaujouan, É, Brown, JJ & Ní Bhrolcháin, M 2011, 'Reweighting the General Household Survey 1979–2007', Population Trends, vol. 145, no. 1, pp. 119-145.
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We have calculated two new sets of weights applicable to the General Household Survey (GHS) from 1979 to 2007. One of these is for use with any general analysis of GHS topics and the second is designed for analyses of data collected in the Family Information section. The methods used follow closely those employed by ONS from 1996 onwards. The performance of the weights is assessed in estimating the Total Fertility Rate (TFR) from 1971-2007, an aggregate measure of fertility for which reliable figures are available at national level from vital registration statistics. Our weights improve the GHS estimates, reducing bias both in the TFR and in age-specific fertility rates.

Becue, A, Moret, S, Champod, C & Margot, P 2011, 'Use of stains to detect fingermarks', BIOTECHNIC & HISTOCHEMISTRY, vol. 86, no. 3, pp. 140-160.
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Beger, M, Babcock, R, Booth, DJ, Bucher, D, Condie, SA, Creese, B, Cvitanovic, C, Dalton, SJ, Harrison, P, Hoey, A, Jordan, A, Loder, J, Malcolm, H, Purcell, SW, Roelfsma, C, Sachs, P, Smith, SDA, Sommer, B, Stuart-Smith, R, Thomson, D, Wallace, CC, Zann, M & Pandolfi, JM 2011, 'Research challenges to improve the management and conservation of subtropical reefs to tackle climate change threats', Ecological Management & Restoration, vol. 12, no. 1, pp. e7-e10.
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This paper reports on a workshop conducted in Australia in 2010, entitled 'Management, Conservation, and Scientific Challenges on Subtropical Reefs under Climate Change'. The workshop brought together 26 experts actively involved in the science and management of subtropical reefs. Its primary aim was to identify the areas of research that need to be most urgently addressed to improve the decision-making framework for managers of subtropical reefs. The main findings of the workshop were a sustainable subtropical reefs declaration that highlights seven research priorities for subtropical reefs. These are to (i) conduct research and management activities across local government, state and bioregion borders; (ii) understand natural variability of environmental conditions; (iii) quantify socio-economic factors and ecosystem services; (iv) benchmark cross-realm connectivity; (v) know marine population connectivity; (vi) habitat mapping and ecological research; and (v) determine refugia. These findings are hoped to form a basis for focussing research efforts, leveraging funds and assisting managers with allocation of resources. © 2011 Ecological Society of Australia.

Beham, AW, Puellmann, K, Laird, R, Fuchs, T, Streich, R, Breysach, C, Raddatz, D, Oniga, S, Peccerella, T, Findeisen, P, Kzhyshkowska, J, Gratchev, A, Schweyer, S, Saunders, B, Wessels, JT, Möbius, W, Keane, J, Becker, H, Ganser, A, Neumaier, M & Kaminski, WE 2011, 'A TNF-Regulated Recombinatorial Macrophage Immune Receptor Implicated in Granuloma Formation in Tuberculosis', PLoS Pathogens, vol. 7, no. 11, pp. e1002375-e1002375.
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Behrendt, L, Larkum, AWD, Norman, A, Qvortrup, K, Chen, M, Ralph, P, Sorensen, SJ, Trampe, E & Kuehl, M 2011, 'Endolithic chlorophyll d-containing phototrophs', ISME JOURNAL, vol. 5, no. 6, pp. 1072-1076.
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Cyanobacteria in the genus Acaryochloris are the only known oxyphototrophs that have exchanged chlorophyll a (Chl a) with Chl d as their primary photopigment, facilitating oxygenic photosynthesis with near infrared (NIR) light. Yet their ecology and natural habitats are largely unknown. We used hyperspectral and variable chlorophyll fluorescence imaging, scanning electron microscopy, photopigment analysis and DNA sequencing to show that Acaryochloris-like cyanobacteria thrive underneath crustose coralline algae in a widespread endolithic habitat on coral reefs. This finding suggests an important role of Chl d-containing cyanobacteria in a range of hitherto unexplored endolithic habitats, where NIR light-driven oxygenic photosynthesis may be significant.

Bell, ME, Fender, RP, Swinbank, J, Miller-Jones, JCA, Law, CJ, Scheers, B, Spreeuw, H, Wise, MW, Stappers, BW, Wijers, RAMJ, Hessels, JWT & Masters, J 2011, 'An automated archival Very Large Array transients survey', Monthly Notices of the Royal Astronomical Society, vol. 415, no. 1, pp. 2-10.
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In this paper we present the results of a survey for radio transients using data obtained from the Very Large Array archive. We have reduced, using a pipeline procedure, 5037 observations of the most common pointings - i.e. the calibrator fields. These fields typically contain a relatively bright point source and are used to calibrate 'target' observations: they are therefore rarely imaged themselves. The observations used span a time range ~1984-2008 and consist of eight different pointings, three different frequencies (8.4, 4.8 and 1.4 GHz) and have a total observing time of 435 h. We have searched for transient and variable radio sources within these observations using components from the prototype LOFAR transient detection system. In this paper we present the methodology for reducing large volumes of Very Large Array data; and we also present a brief overview of the prototype LOFAR transient detection algorithms. No radio transients were detected in this survey, therefore we place an upper limit on the snapshot rate of GHz frequency transients >8.0 mJy toρ≤0.032 deg that have typical time-scales 4.3 to 45.3 d. We compare and contrast our upper limit with the snapshot rates - derived from either detections or non-detections of transient and variable radio sources - reported in the literature. When compared with the current LogN-LogSdistribution formed from previous surveys, we show that our upper limit is consistent with the observed population. Current and future radio transient surveys will hopefully further constrain these statistics, and potentially discover dominant transient source populations. In this paper we also briefly explore the current transient commissioning observations with LOFAR, and the impact they will make on the field. © 2011 The Authors Monthly Notices of the Royal Astronomical Society © 2011 RAS. -2

Bell, ME, Tzioumis, T, Uttley, P, Fender, RP, Arévalo, P, Breedt, E, McHardy, I, Calvelo, DE, Jamil, O & Körding, E 2011, 'X-ray and radio variability in the low-luminosity active galactic nucleus NGC 7213', Monthly Notices of the Royal Astronomical Society, vol. 411, no. 1, pp. 402-410.
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Ben-Dov, E, Siboni, N, Shapiro, OH, Arotsker, L & Kushmaro, A 2011, 'Substitution by Inosine at the 3 '-Ultimate and Penultimate Positions of 16S rRNA Gene Universal Primers', MICROBIAL ECOLOGY, vol. 61, no. 1, pp. 1-6.
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Berle, C, Cobbin, D, Smith, N & Zaslawski, C 2011, 'An Innovative Method to Accommodate Chinese Medicine Pattern Diagnosis within the Framework of Evidence-Based Medical Research', CHINESE JOURNAL OF INTEGRATIVE MEDICINE, vol. 17, no. 11, pp. 824-833.
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Pattern diagnosis is an integral aspect of Chinese medicine (CM). CM differentiates biomedical diseases into patterns, based upon the patients symptoms and signs. Pattern identification (PI) is used to diagnose, direct the treatment principle and determine the treatment protocol. Most CM research has used fixed formula treatments for Western-defined diseases with outcomes measured using objective biomedical markers. This article presents an innovative method used in a randomised controlled pilot study using acupuncture for participants with hepatitis C virus. Each participants CM patterns were identified and quantified at baseline which directed the treatment protocol for the treatment group. Data identified that while each participant expressed different patterns at baseline all participants displayed multiple patterns. Six patterns showed some expression by all 16 participants; Liver (Gan) yin vacuity expressing a group aggregate mean percentage of 47.2, binding depression of Liver qi 46.9, and Liver Kidney (Shen) yin vacuity 45.1. Further sub category gender grouping revealed that pattern ranking changed with gender; Liver yin vacuity (male 53.4%, female 51.93%), binding depression of Liver qi (male 50.0%, female 42.86%) and Liver Kidney yin vacuity (male 42.9%, female 47.96%). The quantification of CM patterns described in this article permitted statistical evaluation of presenting CM patterns. Although this methodology is in its infancy it may have potential use in the integration of PI with rigorous evidence based clinical research. Biomedical markers often do not relate to symptom/signs and therefore this innovative measure may offer an additional CM evaluation methodology and further CM PI understanding.

Bertrand, RL, Senadheera, S, Markus, I, Liu, L, Howitt, L, Chen, H, Murphy, TV, Sandow, SL & Bertrand, PP 2011, 'A Western Diet Increases Serotonin Availability in Rat Small Intestine', Endocrinology, vol. 152, no. 1, pp. 36-47.
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Abstract Diet-induced obesity is associated with changes in gastrointestinal function and induction of a mild inflammatory state. Serotonin (5-HT) containing enterochromaffin (EC) cells within the intestine respond to nutrients and are altered by inflammation. Thus, our aim was to characterize the uptake and release of 5-HT from EC cells of the rat ileum in a physiologically relevant model of diet-induced obesity. In chow-fed (CF) and Western diet–fed (WD) rats electrochemical methods were used to measure compression evoked (peak) and steady state (SS) 5-HT levels with fluoxetine used to block the serotonin reuptake transporter (SERT). The levels of mRNA for tryptophan hydroxylase 1 (TPH1) and SERT were determined by quantitative PCR, while EC cell numbers were determined immunohistochemically. In WD rats, the levels of 5-HT were significantly increased (SS: 19.2±3.7 μm; peak: 73.5±14.1 μm) compared with CF rats (SS: 12.3±1.8 μm; peak: 32.2±7.2 μm), while SERT-dependent uptake of 5-HT was reduced (peak WD: 108% of control versus peak CF: 212% control). In WD rats, there was a significant increase in TPH1 mRNA, a decrease in SERT mRNA and protein, and an increase in EC cells. In conclusion, our data show that foods typical of a Western diet are associated with an increased 5-HT availability in the rat ileum. Increased 5-HT availability is driven by the up-regulation of 5-HT synthesis genes, decreased re-uptake of 5-HT, and increased numbers and/or 5-HT content of EC cells which are likely to cause altered intestinal motility and sensation in vivo.

Bhatia, V, Thorogood, G, Dowd, A & Cortie, MB 2011, 'Thin Films of AuCuAl Shape Memory Alloy for Use in Plasmonic Nano-actuators', MRS Proceedings, vol. 1295, pp. 1-6.
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ABSTRACTWe describe the fabrication and structure of nanoscale thin films of β phase shape memory alloys with the nominal atomic stoichiometry Au7Cu5Al4 (corresponding to 5.8 wt% Al). These alloys possess properties that suggest they could be used in nanoscale actuators. The films described here are between 20 and 50 nm thick which is below the thickness at which some other shape memory alloys cease to transform. However, microstructural and X-ray studies confirm that the coatings still exhibit the displacive transformations that are a prerequisite for the shape memory effect.

Bhatia, VK, Kealley, CS, Prior, MJ & Cortie, MB 2011, 'Martensite destabilization in Au7Cu5Al4 shape-memory alloy', ACTA MATERIALIA, vol. 59, no. 5, pp. 2193-2200.
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Aging-induced changes in the austenite peak (A(P)) temperature of Au(7)Cu(5)Al(4) shape-memory alloy are investigated. Whereas heat treating the parent phase at temperatures >140 degrees C or aging the martensite for long times at room temperature both s

Boardman, AD, Grimalsky, VV, Kivshar, YS, Koshevaya, SV, Lapine, M, Litchinitser, NM, Malnev, VN, Noginov, M, Rapoport, YG & Shalaev, VM 2011, 'Active and tunable metamaterials', Laser & Photonics Reviews, vol. 5, no. 2, pp. 287-307.
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Bogema, DR, Scott, NE, Padula, MP, Tacchi, JL, Raymond, BBA, Jenkins, C, Cordwell, SJ, Minion, FC, Walker, MJ & Djordjevic, SP 2011, 'Sequence TTKF down arrow QE Defines the Site of Proteolytic Cleavage in Mhp683 Protein, a Novel Glycosaminoglycan and Cilium Adhesin of Mycoplasma hyopneumoniae', JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 286, no. 48, pp. 41217-41229.
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Mycoplasma hyopneumoniae colonizes the ciliated respiratory epithelium of swine, disrupting mucociliary function and inducing chronic inflammation. P97 and P102 family members are major surface proteins of M. hyopneumoniae and play key roles in colonizing cilia via interactions with glycosaminoglycans and mucin. The p102 paralog, mhp683, and homologs in strains from different geographic origins encode a 135-kDa pre-protein (P135) that is cleaved into three fragments identified here as P45683, P48683, and P50683. A peptide sequence (TTKF?QE) was identified surrounding both cleavage sites in Mhp683. N-terminal sequences of P48683 and P50683, determined by Edman degradation and mass spectrometry, confirmed cleavage after the phenylalanine residue. A similar proteolytic cleavage site was identified by mass spectrometry in another paralog of the P97/P102 family. Trypsin digestion and surface biotinylation studies showed that P45683, P48683, and P50683 reside on the M. hyopneumoniae cell surface. Binding assays of recombinant proteins F1683F5683, spanning Mhp683, showed saturable and dose-dependent binding to biotinylated heparin that was inhibited by unlabeled heparin, fucoidan, and mucin. F1683F5683 also bound porcine epithelial cilia, and antisera to F2683 and F5683 significantly inhibited cilium binding by M. hyopneumoniae cells. These data suggest that P45683, P48683, and P50683 each display cilium- and proteoglycan-binding sites. Mhp683 is the first characterized glycosaminoglycan-binding member of the P102 family.

Bokil, NJ, Totsika, M, Carey, AJ, Stacey, KJ, Hancock, V, Saunders, BM, Ravasi, T, Ulett, GC, Schembri, MA & Sweet, MJ 2011, 'Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages', Immunobiology, vol. 216, no. 11, pp. 1164-1171.
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Bond, DM, Dennis, ES & Finnegan, EJ 2011, 'The low temperature response pathways for cold acclimation and vernalization are independent', PLANT CELL AND ENVIRONMENT, vol. 34, no. 10, pp. 1737-1748.
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Vernalization is the promotion of flowering in response to the prolonged cold of winter. To survive sub-zero winter temperatures, plants must first acclimate to low, nonfreezing temperatures (cold acclimation). Induction of VERNALIZATION INSENSITIVE 3 (VIN3), the first gene in the vernalization pathway, is initiated within the same time frame as the induction of genes in the cold acclimation pathway raising the question of whether there are common elements in the signal transduction pathways that activate these two responses to cold.We show that none of the signalling components required for cold acclimation, including the `master regulator INDUCTION OF CBF EXPRESSION1 (ICE1) or HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 (HOS1), which has been described as a link between cold acclimation and vernalization, play a role in VIN3 induction.We also show that the hormone abscisic acid (ABA) does not modulate VIN3 induction, consistent with earlier reports that ABA signalling plays no role in the vernalization response. The cold acclimation pathway is activated at 12 °C, at which temperature there is no induction of VIN3 expression. Taken together, our data demonstrate that the responses to low temperatures leading to cold acclimation and vernalization are controlled by distinct signalling pathways.

Booth, DJ & Parkinson, K 2011, 'Pelagic larval duration is similar across 23A degrees of latitude for two species of butterflyfish (Chaetodontidae) in eastern Australia', CORAL REEFS, vol. 30, no. 4, pp. 1071-1075.
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Duration of the pelagic phase of benthic marine fishes has been related to dispersal distance, with longer pelagic larval duration (PLD) expected to result in greater dispersal potential. Here, we examine PLDs of 2 species of coral-reef butterflyfish (Chaetodon auriga and C. flavirostris) across latitudes (14°S37°S) along the Great Barrier Reef into south-eastern Australia; we predict that PLD will be higher for fish collected below the breeding latitudes of 24°S. For C. auriga, apart from significantly longer PLDs at Lord Howe Island and Jervis Bay (means of 54 and 52 days, respectively), all locations had similar PLDs (mean 41 days). For C. flavirostris, there was no significant location effect on PLD (mean 41.5 days); however, PLD at Lord Howe Island was 58 days with high variance precluding significance. Also, there was no significant variation in PLD among years for either species despite considerable variation in East Australian Current strength.

Booth, DJ, Bond, N & Macreadie, P 2011, 'Detecting range shifts among Australian fishes in response to climate change', MARINE AND FRESHWATER RESEARCH, vol. 62, no. 9, pp. 1027-1042.
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One of the most obvious and expected impacts of climate change is a shift in the distributional range of organisms, which could have considerable ecological and economic consequences. Australian waters are hotspots for climate-induced environmental changes; here, we review these potential changes and their apparent and potential implications for freshwater, estuarine and marine fish. Our meta-analysis detected <300 papers globally on 'fish' and 'range shifts', with similar to 7% being from Australia. Of the Australian papers, only one study exhibited definitive evidence of climate-induced range shifts, with most studies focussing instead on future predictions. There was little consensus in the literature regarding the definition of 'range', largely because of populations having distributions that fluctuate regularly. For example, many marine populations have broad dispersal of offspring (causing vagrancy). Similarly, in freshwater and estuarine systems, regular environmental changes (e. g. seasonal, ENSO cycles - not related to climate change) cause expansion and contraction of populations, which confounds efforts to detect range 'shifts'. We found that increases in water temperature, reduced freshwater flows and changes in ocean currents are likely to be the key drivers of climate-induced range shifts in Australian fishes. Although large-scale frequent and rigorous direct surveys of fishes across their entire distributional ranges, especially at range edges, will be essential to detect range shifts of fishes in response to climate change, we suggest careful co-opting of fisheries, museum and other regional databases as a potential, but imperfect alternative.

Bossers, LCAM, Roux, C, Bell, M & McDonagh, AM 2011, 'Methods for the enhancement of fingermarks in blood', Forensic Science International, vol. 210, no. 1-3, pp. 1-11.
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Fingermarks formed in or by blood often require specific development techniques. This review examines techniques and materials that may be used to enhance and record fingermarks deposited in blood or fingermarks generated by blood-contaminated papillary ridges. A large number of techniques are presented here and are discussed from a chemical as well as practical perspective. It is concluded that an optimized sequence of techniques targeting both latent (non-bloody) and bloody fingermarks must be applied to detect and enhance the maximum number of marks, and therefore optimize the information content from exhibits that may bear marks in blood.

Boyle, JR, Sparks, RS, Keijzers, GB, Crilly, JL, Lind, JF & Ryan, LM 2011, 'Prediction and surveillance of influenza epidemics', MEDICAL JOURNAL OF AUSTRALIA, vol. 194, no. 4, pp. S28-S33.

Brading, P, Warner, ME, Davey, P, Smith, DJ, Achterberg, EP & Suggett, DJ 2011, 'Differential effects of ocean acidification on growth and photosynthesis among phylotypes of Symbiodinium (Dinophyceae)', Limnology and Oceanography, vol. 56, no. 3, pp. 927-938.
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We investigated the effect of elevated partial pressure of CO2 (pCO(2)) on the photosynthesis and growth of four phylotypes (ITS2 types A1, A13, A2, and B1) from the genus Symbiodinium, a diverse dinoflagellate group that is important, both free-living a

Bradshaw, LN, Zhong, J, Bradbury, P, Mahmassani, M, Smith, JL, Ammit, AJ & O'Neill, GM 2011, 'Estradiol stabilizes the 105-kDa phospho-form of the adhesion docking protein NEDD9 and suppresses NEDD9-dependent cell spreading in breast cancer cells', Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol. 1813, no. 2, pp. 340-345.
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Bresin, M, Thiel, BL, Toth, M & Dunn, KA 2011, 'Focused electron beam-induced deposition at cryogenic temperatures', Journal of Materials Research, vol. 26, no. 3, pp. 357-364.
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Abstract

Brito, BP, Gardner, IA, Hietala, SK & Crossley, BM 2011, 'Variation inBluetongue virusreal-time reverse transcription polymerase chain reaction assay results in blood samples of sheep, cattle, and alpaca', Journal of Veterinary Diagnostic Investigation, vol. 23, no. 4, pp. 753-756.
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Bluetongue is a vector-borne viral disease that affects domestic and wild ruminants. The epidemiology of this disease has recently changed, with occurrence in new geographic areas. Various real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) assays are used to detect Bluetongue virus (BTV); however, the impact of biologic differences between New World camelids and domestic ruminant samples on PCR efficiency, for which the BTV real-time qRT-PCR was initially validated are unknown. New world camelids are known to have important biologic differences in whole blood composition, including hemoglobin concentration, which can alter PCR performance. In the present study, sheep, cattle, and alpaca blood were spiked with BTV serotypes 10, 11, 13, and 17 and analyzed in 10-fold dilutions by real-time qRT-PCR to determine if species affected nucleic acid recovery and assay performance. A separate experiment was performed using spiked alpaca blood subsequently diluted in 10-fold series in sheep blood to assess the influence of alpaca blood on performance efficiency of the BTV real-time qRT-PCR assay. Results showed that BTV-specific nucleic acid detection from alpaca blood was consistently 1–2 logs lower than from sheep and cattle blood, and results were similar for each of the 4 BTV serotypes analyzed.

Brito, BP, Perez, AM, Cosentino, B, Rodriguez, LL & König, GA 2011, 'Factors Associated With Within-Herd Transmission of Serotype A Foot-and-Mouth Disease Virus in Cattle, During the 2001 Outbreak in Argentina: A Protective Effect of Vaccination', Transboundary and Emerging Diseases, vol. 58, no. 5, pp. 387-393.
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Brown, J 2011, 'DISCUSSION ON THE PAPER BY STEELE', Australian & New Zealand Journal of Statistics, vol. 53, no. 1, pp. 23-24.
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Brown, J, Abbott, O & Smith, PA 2011, 'Design of the 2001 and 2011 Census Coverage Surveys for England and Wales', Journal of the Royal Statistical Society Series A: Statistics in Society, vol. 174, no. 4, pp. 881-906.
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Summary In many countries, a key component of measuring census coverage is a post-enumeration survey. In the 2001 censuses of the UK this was called the Census Coverage Survey. The paper reviews the design of the 2001 Census Coverage Survey and develops the design for the survey in 2011, taking advantage of the experience of 2001 and the data that were generated by the 2001 process. This leads to a proposed design that is less clustered than in 2001 and has an allocation that is more skewed towards areas where coverage in the 2011 census is expected to be lowest. The updated design balances optimal allocation against maintaining a sufficient sample across all areas.

Bryant, CE, Brown, RD, Yang, S, Suen, H, Aklilu, E, Favaloro, J, Hart, DNJ, Fromm, P, Woodland, N, Nassif, N, Iland, H, Gibson, J, Ho, PJ & Joshua, DE 2011, 'Ten Year Survivors of Multiple Myeloma Demonstrate a Differential Expression of Immunological Biomarkers Including a High Incidence of Cytotoxic T-Cell Clones Which Have Not Acquired Myeloma-Associated Anergy,', Blood, vol. 118, no. 21, pp. 3924-3924.
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Abstract Abstract 3924 Prior to the introduction of novel therapies for patients with multiple myeloma (MM) few patients survived for more than 10 years. Several reports have suggested that 10 year survival is associated with a younger age at diagnosis and the duration of exposure to effective agents. Although the number of patients surviving 10 years is increasing, there have been no significant reports of immunological biomarkers in these patients. This is especially true in those for whom the prolonged survival has occurred without novel drugs. Previous studies have shown that the presence of expanded peripheral blood CD8 T-cell clones in MM patients is associated with a better prognosis; raising the possibility that these T-cells, confirmed as clones by TCR sequencing, mediate an anti-tumor effect. However microarray gene set enrichment analysis and proliferation tracking studies demonstrated that these cells are in an anergic state. In addition, there is evidence that Tregs inhibit and Th17 cells enhance autologous immune response in malignancy and that an imbalance in MM may impair disease control. Slan-DCs are a subset of myeloid dendritic cells and are of interest in MM because of their ability to stimulate cytotoxic T-cell responses and reverse anergy in tumor infiltrating lymphocytes. We have investigated the immune mechanisms of disease control which may contribute to long-term survival by analyzing Tregs, Th17 cells, Slan-DCs and the incidence and relative degree of anergy of T-cell clones in all current >10 year survivors. Peripheral blood samples were analyzed for the presence of CD3+ T-cell receptor Vβ restricted T-cell clones (BetaMark Kit), the number of CD3+CD4+CD25h+CD127- Tregs, CD4+IL-17+ Th17 cells and CD16+CD14low M-DC8+ Slan-DCs. Proliferation of T-cells was analyzed using CFSE tracked 4 day cul...

Burke, C, Steinberg, P, Rusch, D, Kjelleberg, S & Thomas, T 2011, 'Bacterial community assembly based on functional genes rather than species', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 108, no. 34, pp. 14288-14293.
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The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be ï½speciesï½ (by means of rRNA taxonomy), but rather the more functional level of genes.

Burke, C, Thomas, T, Lewis, M, Steinberg, P & Kjelleberg, S 2011, 'Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis', ISME JOURNAL, vol. 5, no. 4, pp. 590-600.
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Green Ulvacean marine macroalgae are distributed worldwide in coastal tidal and subtidal ecosystems. As for many living surfaces in the marine environment, little is known concerning the epiphytic bacterial biofilm communities that inhabit algal surfaces. This study reports on the largest published libraries of near full-length 16S rRNA genes from a marine algal surface (5293 sequences from six samples) allowing for an in-depth assessment of the diversity and phylogenetic profile of the bacterial community on a green Ulvacean alga. Large 16S rRNA gene libraries of surrounding seawater were also used to determine the uniqueness of this bacterial community. The surface of Ulva australis is dominated by sequences of Alphaproteobacteria and the Bacteroidetes, especially within the Rhodobacteriaceae, Sphingomonadaceae, Flavobacteriaceae and Sapropiraceae families. Seawater libraries were also dominated by Alphaproteobacteria and Bacteroidetes sequences, but were shown to be clearly distinct from U. australis libraries through the clustering of sequences into operational taxonomic units and BrayCurtis similarity analysis. Almost no similarity was observed between these two environments at the species level, and only minor similarity was observed at levels of sequence clustering representing clades of bacteria within family and genus taxonomic groups. Variability between libraries of U. australis was relatively high, and a consistent sub-population of bacterial species was not detected. The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface.

Busschaert, N, Wenzel, M, Light, ME, Iglesias-Hernández, P, Pérez-Tomás, R & Gale, PA 2011, 'Structure–Activity Relationships in Tripodal Transmembrane Anion Transporters: The Effect of Fluorination', Journal of the American Chemical Society, vol. 133, no. 35, pp. 14136-14148.
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Callsen, G, Reparaz, JS, Wagner, MR, Kirste, R, Nenstiel, C, Hoffmann, A & Phillips, MR 2011, 'Phonon deformation potentials in wurtzite GaN and ZnO determined by uniaxial pressure dependent Raman measurements', APPLIED PHYSICS LETTERS, vol. 98, no. 6, pp. 1-3.
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We report the phonon deformation potentials of wurtzite GaN and ZnO for all zone center optical phonon modes determined by Raman measurements as a function of uniaxial pressure. Despite all the structural and optical similarities between these two materi

Callsen, G, Reparaz, JS, Wagner, MR, Vierck, A, Phillips, MR, Thomsen, C & Hoffmann, A 2011, 'Titanium-assisted growth of silica nanowires: from surface-matched to free-standing morphologies', NANOTECHNOLOGY, vol. 22, no. 40, pp. 1-6.
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We report on an oxide-assisted growth technique for silica nanowires which allows tuning the growth from surface-matched nanowires to free-standing morphologies based on growth control by Ti in the role of a catalyst and surfactant. Using an adjustable Ti concentration, we grew silica nanowires with lengths ranging from 100 nm up to several millimetres whose defect chemistry was analysed by electron microscopy tools, monochromatic cathodoluminescence imaging and time resolved photoluminescence spectroscopy. The knowledge of the luminescence properties and the related defect occurrence along with their spatial distribution is pivotal for advancing silica nanowire growth in order to realize successful device designs based on self-assembled Si/SiO(x) nanostructures. We demonstrate a core-shell structure of the grown nanowires with a highly luminescent 150 nm thick shell and outstandingly fast decaying dynamics (approximate to 1 ns) for glass-like materials. The conjunction of the observed efficient and stable luminescences with their attributed decaying behaviours suggests applications for silica nanowires such as active and passive optical interconnectors and white light phosphors. The identification of a time domain difference for the spectral regime from 2.3 to 3.3 eV, within the confined spatial dimensions of a single nanowire, is very promising for future, e. g. data transmission applications, employing silica nanowires which exhibit achievable compatibility with commonly applied silicon-based electronics. A qualitative growth model based on silica particle diffusion and Ti-assisted seed formation is developed for the various types of segregated silica nanowires which extends commonly assumed oxide-assisted growth mechanisms.

Cao, X, Chen, J, Wen, S, Peng, C, Shen, M & Shi, X 2011, 'Effect of surface charge of polyethyleneimine-modified multiwalled carbon nanotubes on the improvement of polymerase chain reaction', Nanoscale, vol. 3, no. 4, pp. 1741-1741.
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Carroll, RJ, Delaigle, A & Hall, P 2011, 'Testing and Estimating Shape-Constrained Nonparametric Density and Regression in the Presence of Measurement Error', Journal of the American Statistical Association, vol. 106, no. 493, pp. 191-202.
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Carroll, RJ, Lobach, I & Mallick, B 2011, 'Semiparametric Bayesian analysis of gene-environment interactions with error in measurement of environmental covariates and missing genetic data', Statistics and Its Interface, vol. 4, no. 3, pp. 305-315.
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Caruso, V, Chen, H & Morris, MJ 2011, 'Early Hypothalamic FTO Overexpression in Response to Maternal Obesity – Potential Contribution to Postweaning Hyperphagia', PLoS ONE, vol. 6, no. 9, pp. e25261-e25261.
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Background: Intrauterine and postnatal overnutrition program hyperphagia, adiposity and glucose intolerance in offspring. Single-nucleotide polymorphisms (SNPs) of the fat mass and obesity associated (FTO) gene have been linked to increased risk of obesity. FTO is highly expressed in hypothalamic regions critical for energy balance and hyperphagic phenotypes were linked with FTO SNPs. As nutrition during fetal development can influence the expression of genes involved in metabolic function, we investigated the impact of maternal obesity on FTO. Methods: Female Sprague Dawley rats were exposed to chow or high fat diet (HFD) for 5 weeks before mating, throughout gestation and lactation. On postnatal day 1 (PND1), some litters were adjusted to 3 pups (vs. 12 control) to induce postnatal overnutrition. At PND20, rats were weaned onto chow or HFD for 15 weeks. FTO mRNA expression in the hypothalamus and liver, as well as hepatic markers of lipid metabolism were measured. Results: At weaning, hypothalamic FTO mRNA expression was increased significantly in offspring of obese mothers and FTO was correlated with both visceral and epididymal fat mass (P<0.05); body weight approached significance (P = 0.07). Hepatic FTO and Fatty Acid Synthase mRNA expression were decreased by maternal obesity. At 18 weeks, FTO mRNA expression did not differ between groups; however body weight was significantly correlated with hypothalamic FTO. Postnatal HFD feeding significantly reduced hepatic Carnitine Palmitoyltransferase-1a but did not affect the expression of other hepatic markers investigated. FTO was not affected by chronic HFD feeding. Significance: Maternal obesity significantly impacted FTO expression in both hypothalamus and liver at weaning.

Cassar, J, Stuart, B, Dent, B, Notter, S, Forbes, S, O'Brien, C & Dadour, I 2011, 'A study of adipocere in soil collected from a field leaching study', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 43, no. 1, pp. 3-11.
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An investigation of a post-mortem product, adipocere, resulting from the decomposition of a pig carcass left on a soil surface is reported. The presence of this material should provide valuable information for forensic investigators: although a body may have been removed from a crime scene, decomposition products may remain in the soil below and the depth to which these are observed can provide insight into the problem of how long a body remained on the soil surface. Infrared spectroscopy and gas chromatographymass spectrometry were used in this study to identify the compounds associated with adipocere, which is comprised of particular fatty acids, in soil samples taken from different depths below the carcass. Both techniques demonstrate that adipocere may be detected in soil beneath a body and the depth to which it is detected is dependent upon the time since the body was deposited on the soil surface.

Cassar, N, DiFiore, PJ, Barnett, BA, Bender, ML, Bowie, AR, Tilbrook, B, Petrou, K, Westwood, KJ, Wright, SW & Lefevre, D 2011, 'The influence of iron and light on net community production in the Subantarctic and Polar Frontal Zones', BIOGEOSCIENCES, vol. 8, no. 2, pp. 227-237.
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The roles of iron and light in controlling biomass and primary productivity are clearly established in the Southern Ocean. However, their influence on net community production (NCP) and carbon export remains to be quantified. To improve our understanding

Castorina, A, Leggio, GM, Giunta, S, Magro, G, Scapagnini, G, Drago, F & D’Agata, V 2011, 'Neurofibromin and Amyloid Precursor Protein Expression in Dopamine D3 Receptor Knock-Out Mice Brains', Neurochemical Research, vol. 36, no. 3, pp. 426-434.
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Cave, GE & Fraser, WB 2011, 'The effect of yarn elasticity on the stability of the two‐for‐one twister balloon', Journal of the Textile Institute, vol. 102, no. 5, pp. 373-388.
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Cawood, PA, Leitch, EC, Merle, RE & Nemchin, AA 2011, 'Orogenesis without collision: Stabilizing the Terra Australis accretionary orogen, eastern Australia', GEOLOGICAL SOCIETY OF AMERICA BULLETIN, vol. 123, no. 11-12, pp. 2240-2255.
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The Neoproterozoic to end-Paleozoic Terra Australis orogen extended along the Gondwana margin of the paleo-Pacific Ocean, and it now provides a detailed record of orogenic activity and continental stabilization within an ongoing convergent, accretionary

Cawood, PA, Pisarevsky, SA & Leitch, EC 2011, 'Unraveling the New England orocline, east Gondwana accretionary margin', TECTONICS, vol. 30, no. 5, pp. 1-15.
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The New England orocline lies within the Eastern Australian segment of the Terra Australis accretionary orogen and developed during the late Paleozoic to early Mesozoic Gondwanide Orogeny (310-230 Ma) that extended along the Pacific margin of the Gondwana supercontinent. The orocline deformed a pre-Permian arc assemblage consisting of a western magmatic arc, an adjoining forearc basin and an eastern subduction complex. The orocline is doubly vergent with the southern and northern segments displaying counter-clockwise and clockwise rotation, respectively, and this has led to contrasting models of formation. We resolve these conflicting models with one that involves buckling of the arc system about a vertical axis during progressive northward translation of the southern segment of the arc system against the northern segment, which is pinned relative to cratonic Gondwana. Paleomagnetic data are consistent with this model and show that an alternative model involving southward motion of the northern segment relative to the southern segment and cratonic Gondwana is not permissible. The timing of the final stage of orocline formation (similar to 270-265 Ma) overlaps with a major gap in magmatic activity along this segment of the Gondwana margin, suggesting that northward motion and orocline formation were driven by a change from orthogonal to oblique convergence and coupling between the Gondwana and Pacific plates.

Chacón, JE, Duong, T & Wand, MP 2011, 'Asymptotics for general multivariate kernel density derivative estimators', Statistica Sinica, vol. 21, no. 2, pp. 807-807.
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We investigate kernel estimators of multivariate density derivative functions using general (or unconstrained) bandwidth matrix selectors. These density derivative estimators have been relatively less well researched than their density estimator analogues. A major obstacle for progress has been the intractability of the matrix analysis when treating higher order multivariate derivatives. With an alternative vectorization of these higher order derivatives, mathematical intractabilities are surmounted in an elegant and unified framework. The finite sample and asymptotic analysis of squared errors for density estimators are generalized to density derivative estimators. Moreover, we are able to exhibit a closed form expression for a normal scale bandwidth matrix for density derivative estimators. These normal scale bandwidths are employed in a numerical study to demonstrate the gain in performance of unconstrained selectors over their constrained counterparts.

Chadwick, S, Maynard, P, Kirkbride, P, Lennard, C, Spindler, X & Roux, C 2011, 'Use of Styryl 11 and STaR 11 for the Luminescence Enhancement of Cyanoacrylate-Developed Fingermarks in the Visible and Near-Infrared Regions', JOURNAL OF FORENSIC SCIENCES, vol. 56, no. 6, pp. 1505-1513.
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In current casework, most post-cyanoacrylate stains rely on luminescence emission in the visible region (400-700 nm). While traditional stains such as rhodamine 6G work well under most circumstances, some surfaces may generate background luminescence under the same conditions. Detection in the near-infrared region (NIR > 700 nm) has shown to be effective in minimizing the interferences from such surfaces. The laser dye styryl 11 generated strongly luminescent fingermarks when applied after cyanoacrylate fuming on all surfaces tested. When compared to rhodamine 6G, the dye was superior only when viewed in the NIR. Styryl 11 was subsequently combined with rhodamine 6G, and the mixed stain formulation (named StaR 11 by the authors) induced stronger luminescence compared with styryl 11 alone with an ability to visualize in both the visible and NIR regions. Reliable and consistent results were obtained when using either styryl 11 alone or the STaR 11 mixture. The enhancement achieved did not otherwise vary depending on the source of the fingermark secretions. With visualization possible in both the visible and NIR regions, the styryl 11/rhodamine 6G mixture showed significant potential as a post-cyanoacrylate stain.

Chan, DKY, O'Rourke, F, Shen, Q, Mak, JCS & Hung, WT 2011, 'Meta-analysis of the cardiovascular benefits of intensive lipid lowering with statins', ACTA NEUROLOGICA SCANDINAVICA, vol. 124, no. 3, pp. 188-195.
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Objective - To evaluate the efficacy of intensive lipid lowering with higher-dose statins. Methods - Meta-analysis of seven randomized controlled trials comprising 50,972 participants. Results - Mean follow-up was 3.1 years with mean age 63 years. Final

Chan, Y-W, Mohr, R, Millard, AD, Holmes, AB, Larkum, AW, Whitworth, AL, Mann, NH, Scanlan, DJ, Hess, WR & Clokie, MRJ 2011, 'Discovery of Cyanophage Genomes Which Contain Mitochondrial DNA Polymerase', Molecular Biology and Evolution, vol. 28, no. 8, pp. 2269-2274.
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Chapman, RP, Hiscock, JR, Gale, PA & Bryce, DL 2011, 'A solid-state ^35/37Cl NMR study of a chloride ion receptor and a GIPAW-DFT study of chlorine NMR interaction tensors in organic hydrochlorides', Canadian Journal of Chemistry, vol. 89, no. 7, pp. 822-834.
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The results of a 35/37Cl solid-state nuclear magnetic resonance (SSNMR) study of the 1-butyl-3-methylimidazolium chloride complex of meso-octamethylcalix[4]pyrrole (1) are reported. Line shapes obtained from magic-angle-spinning and stationary powder samples collected at 9.4 and 21.1 T are analyzed to provide the 35/37Cl quadrupolar tensor and chemical shift (CS) tensor and their relative orientation. The relatively high symmetry of the chloride ion coordination environment is manifested in the small value of the quadrupole coupling constant, CQ(35Cl) = 1.0 MHz. The isotropic chemical shift of 120 ppm (with respect to NaCl(s)) is at the upper edge of the typical range seen for organic hydrochlorides. Consideration of chemical shift anisotropy (span, Ω = 50 ppm) and non-coincidence of the quadrupolar and CS tensors were essential to properly simulate the experimental spectra. The utility of gauge-including projector-augmented wave density functional theory (GIPAW-DFT) calculations of chlorine quadrupolar and CS tensors in organic chlorides was explored by validation against available benchmark experimental data for solid amino acid hydrochlorides. The calculations are shown to systematically overestimate the value of the 35Cl quadrupole coupling constant. Additional calculations on various hydrated and solvated models of 1 are consistent with a structure in which solvent and water of hydration are absent.

Chen, H, Iglesias, MA, Caruso, V & Morris, MJ 2011, 'Maternal Cigarette Smoke Exposure Contributes to Glucose Intolerance and Decreased Brain Insulin Action in Mice Offspring Independent of Maternal Diet', PLoS ONE, vol. 6, no. 11, pp. e27260-e27260.
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Background: Maternal smoking leads to intrauterine undernutrition and is associated with low birthweight and higher risk of offspring obesity. Intrauterine smoke exposure (SE) may alter neuroendocrine mediators regulating energy homeostasis as chemicals in cigarette smoke can reach the fetus. Maternal high-fat diet (HFD) consumption causes fetal overnutrition; however, combined effects of HFD and SE are unknown. Thus we investigated the impact of combined maternal HFD and SE on adiposity and energy metabolism in offspring. Method: Female Balb/c mice had SE (2 cigarettes/day, 5 days/week) or were sham exposed for 5 weeks before mating. Half of each group was fed HFD (33% fat) versus chow as control. The same treatment continued throughout gestation and lactation. Female offspring were fed chow after weaning and sacrificed at 12 weeks. Results: Birthweights were similar across maternal groups. Faster growth was evident in pups from SE and/or HFD dams before weaning. At 12 weeks, offspring from HFD-fed dams were significantly heavier than those from chow-fed dams (chow-sham 17.6 +/- 0.3 g; chow-SE 17.8 +/- 0.2 g; HFD-sham 18.7 +/- 0.3 g; HFD-SE 18.8 +/- 0.4 g, P<0.05 maternal diet effect); fat mass was significantly greater in offspring from chow+SE, HFD+SE and HFD+sham dams. Both maternal HFD and SE affected brain lactate transport. Glucose intolerance and impaired brain response to insulin were observed in SE offspring, and this was aggravated by maternal HFD consumption. Conclusion: While maternal HFD led to increased body weight in offspring, maternal SE independently programmed adverse health outcomes in offspring. A smoke free environment and healthy diet during pregnancy is desirable to optimize offspring health.

Chen, JS, Liu, H, Qiao, SZ & Lou, XWD 2011, 'Carbon-supported ultra-thin anatase TiO2 nanosheets for fast reversible lithium storage', JOURNAL OF MATERIALS CHEMISTRY, vol. 21, no. 15, pp. 5687-5692.
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This work reports a two-step method to synthesize carbon-supported ultrathin anatase TiO2 nanosheets (C-TiO2 NSs). Three samples with distinct structures were prepared via the assembly of these unique C-TiO2 NSs, including solid TiO2 hierarchical spheres and their hollow counterparts, as well as randomly-oriented C-TiO2 NSs. Specifically, the organic additive (diethylenetriamine) serves as both the capping agent during the initial solvothermal synthesis that stabilizes the (001) facets of anatase TiO2 and also the carbon source during the subsequent carbonization process. When evaluated for electrochemical lithium storage, all three samples assembled from carbon-supported anatase TiO2 NSs exhibit high reversible capacities with superior cyclic capacity retention at a high current rate. This enhanced lithium storage performance could be attributed to the ultrathin NS structure allowing efficient Li+ ion diffusion, as well as the effective nanocarbon support granting better structural stability. These findings suggest that carbon-supported TiO2 NSs may be used as a promising anode material for high-power lithium-ion batteries.

Chen, PP-T, Downes, JE, Fernandes, AJ, Butcher, KSA, Wintrebert-Fouquet, M, Wuhrer, R & Phillips, MR 2011, 'Effects of crystallinity and chemical variation on apparent band-gap shift in polycrystalline indium nitride', THIN SOLID FILMS, vol. 519, no. 6, pp. 1831-1836.
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The nature of the apparent band-gap shift in polycrystalline indium nitride thin-films, grown by remote-plasma-enhanced chemical vapour deposition at 535 +/- 10 degrees C. has been investigated separately in relation to growth temperature dependent crystallinity and chemical variation. Substrates of sapphire and gallium nitride on sapphire were used to study the effect of a stress-reduced template on indium nitride crystallite quality and apparent band-gap. To mimic surface growth temperature variations two glass substrates of differing thickness and thermal conductivity were intentionally used for the same growth conditions. The samples were characterised using optical transmission, scanning electron microscope, X-ray diffraction, and high-resolution X-ray photoelectron spectroscopy. The results indicate that the apparent band-gap shift in polycrystalline narrow band-gap indium nitride thin-films is not primarily determined by the quality of indium nitride crystallites but rather it is associated with growth temperature dependent chemical variations in the films

Chen, PY, Poulton, CG, Asatryan, AA, Steel, MJ, Botten, LC, de Sterke, CM & McPhedran, RC 2011, 'Folded bands in metamaterial photonic crystals', NEW JOURNAL OF PHYSICS, vol. 13, pp. 1-18.
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The dispersion relation of periodic structures that include metamaterials or materials with large anomalous dispersion can give bands with infinite group velocity points. These bands do not span the entire first Brillouin zone but are instead localized in k-space. We show that these points arise when both positive and negative elements are present, with the group index rather than the refractive index being the controlling quantity. A rigorous condition and two approximations are derived, each showing that an appropriate weighted average of group index being zero leads to infinite group velocity points.

Chen, W, Lim, CED, Kang, H-J & Liu, J 2011, 'Chinese Herbal Medicines for the Treatment of Type A H1N1 Influenza: A Systematic Review of Randomized Controlled Trials', PLoS ONE, vol. 6, no. 12, pp. e28093-e28093.
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Chin, Y, Panduwinata, D, Sintic, M, Sum, TJ, Hush, NS, Crossley, MJ & Reimers, JR 2011, 'Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite', JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 2, no. 2, pp. 62-66.
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The atomic structures of the chains of an alkyl porphyrin (5, 10, 15, 20- tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for prophyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and of the many possible atomic structure modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.

Cho, Y, Kim, H, Turner, ND, Mann, JC, Wei, J, Taddeo, SS, Davidson, LA, Wang, N, Vannucci, M, Carroll, RJ, Chapkin, RS & Lupton, JR 2011, 'A Chemoprotective Fish Oil- and Pectin-Containing Diet Temporally Alters Gene Expression Profiles in Exfoliated Rat Colonocytes throughout Oncogenesis', The Journal of Nutrition, vol. 141, no. 6, pp. 1029-1035.
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Choi, JH, Ryan, LM, Cramer, DW, Hornstein, MD & Missmer, SA 2011, 'Effects of Caffeine Consumption by Women and Men on the Outcome of In Vitro Fertilization', Journal of Caffeine Research, vol. 1, no. 1, pp. 29-34.
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Objective

The objective of this study was to estimate the association between caffeine consumption and in vitro fertilization (IVF) outcomes.

Methods

A total of 2474 couples were prospectively enrolled prior to undergoing their first cycle of IVF, contributing a total of 4716 IVF cycles. Discrete survival analysis adjusting for observed confounders was applied to quantify the relation between caffeine consumption and livebirth. Secondary outcomes of interest were oocyte retrieval, peak estradiol level, implantation rate, and fertilization rate.

Results

Overall, caffeine consumption by women was not significantly associated with livebirth (p_trend=0.74). Compared with women who do not drink caffeine, the likelihood of livebirth was not significantly different for women who drank low (>0-800 mg/week; odds ratio [OR]=1.00, 95% confidence interval [CI])=0.83-1.21), moderate (>800-1400 mg/week; OR=0.89, 95% CI=0.71-1.12), or high levels of caffeine (>1400 mg/week; OR=1.07, 95% CI=0.85-1.34). Greater caffeine intake by women was associated with a significantly lower peak estradiol level (p_trend=0.03), but was not associated with the number of oocytes retrieved (p_trend=0.75), fertilization rate (p_trend=0.10), or implantation rate (p_trend=0.23). There was no significant association between caffeine intake by men and livebirth (p_trend=0.27), fertilization (p_trend=0.72), or implantation (p_trend=0.24). The individual effects of consumption of coffee, tea, or soda by women or men were not related to livebirth.

Conclusion

Caffeine consumption by women or men was not associated with IVF outcomes.

Chou, J, Ben‐Nissan, B, Green, DW, Valenzuela, SM & Kohan, L 2011, 'Targeting and Dissolution Characteristics of Bone Forming and Antibacterial Drugs by Harnessing the Structure of Microspherical Shells from Coral Beach Sand', Advanced Engineering Materials, vol. 13, no. 1-2, pp. 93-99.
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Pharmaceutical drugs for the treatment of metabolic bone diseases lead to a number of side effects due to the their uncontrollable dispersion throughout the body.([1]) Therefore, many groups directed their research to develop devices that are targeted to

Chowdhury, PR, Boucher, Y, Hassan, KA, Paulsen, IT, Stokes, HW & Labbate, M 2011, 'Genome Sequence of Vibrio rotiferianus Strain DAT722', JOURNAL OF BACTERIOLOGY, vol. 193, no. 13, pp. 3381-3382.
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Vibrio rotiferianus is a marine pathogen capable of causing disease in various aquatic organisms. We announce the genome sequence of V. rotiferianus DAT722, which has a large chromosomal integron containing 116 gene cassettes and is a model organism for studying the role of this system in vibrio evolution.

Chowdhury, PR, Ingold, A, Vanegas, N, Martinez, E, Merlino, J, Karina Merkier, A, Castro, M, Gonzalez Rocha, G, Borthagaray, G, Centron, D, Bello Toledo, H, Marquez, CM & Stokes, HW 2011, 'Dissemination of Multiple Drug Resistance Genes by Class 1 Integrons in Klebsiella pneumoniae Isolates from Four Countries: a Comparative Study', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 55, no. 7, pp. 3140-3149.
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A comparative genetic analysis of 42 clinical Klebsiella pneumoniae isolates, resistant to two or more antibiotics belonging to the broad-spectrum -lactam group, sourced from Sydney, Australia, and three South American countries is presented. The study focuses on the genetic contexts of class 1 integrons, mobilizable genetic elements best known for their role in the rapid evolution of antibiotic resistance among Gram-negative pathogens. It was found that the class 1 integrons in this cohort were located in a number of different genetic contexts with clear regional differences. In Sydney, IS26-associated Tn21-like transposons on IncL/M plasmids contribute greatly to the dispersal of integron-associated multiple-drug-resistant (MDR) loci. In contrast, in the South American countries, Tn1696-like transposons on an IncA/C plasmid(s) appeared to be disseminating a characteristic MDR region. A range of mobile genetic elements is clearly being recruited by clinically important mobile class 1 integrons, and these elements appear to be becoming more common with time. This in turn is driving the evolution of complex and laterally mobile MDR units and may further complicate antibiotic therapy.

Christensen, S, Irle, A & Novikov, A 2011, 'An Elementary Approach to Optimal Stopping Problems for AR(1) Sequences', Sequential Analysis, vol. 30, no. 1, pp. 79-93.
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Optimal stopping problems form a class of stochastic optimization problems that has a wide range of applications in sequential statistics and mathematical finance. Here we consider a general optimal stopping problem with discounting for autoregressive processes. Our strategy for a solution consists of two steps: First we give elementary conditions to ensure that an optimal stopping time is of threshold type. Then the resulting one-dimensional problem of finding the optimal threshold is to be solved explicitly. The second step is carried out for the case of exponentially distributed innovations.

Colella, M, Parkinson, A, Evans, T, Robertson, J & Roux, C 2011, 'The Effect of Ionizing Gamma Radiation on Natural and Synthetic Fibers and Its Implications for the Forensic Examination of Fiber Evidence', JOURNAL OF FORENSIC SCIENCES, vol. 56, no. 3, pp. 591-605.
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Circumstances of criminal activities involving radioactive materials may mean fiber evidence recovered from a crime scene could have been exposed to materials emitting ionizing radiation. The consequences of radiation exposed fibers on the result of the

Collingro, A, Tischler, P, Weinmaier, T, Penz, T, Heinz, E, Brunham, RC, Read, TD, Bavoil, PM, Sachse, K, Kahane, S, Friedman, MG, Rattei, T, Myers, GSA & Horn, M 2011, 'Unity in Variety--The Pan-Genome of the Chlamydiae', Molecular Biology and Evolution, vol. 28, no. 12, pp. 3253-3270.
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Cortie, MB & McDonagh, AM 2011, 'Synthesis and Optical Properties of Hybrid and Alloy Plasmonic Nanoparticles', CHEMICAL REVIEWS, vol. 111, no. 6, pp. 3713-3735.
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The plasmon resonances and other optical properties of elemental noble and alkali metal nanoparticles have generated enormous scienti?c interest. 1-11 There are numerous applications for plasmon-active nanoparticles, especially in areas such as biological microscopy, medicine, and sensors. 12-18 The various applications exploit some aspect of the plasmon resonance, which include particle-particle plasmon interactions, 19 the unusual coloring or dichroic e?ects in isolated particles, 20,21 light-induced plasmonic heating, 22 light scattering, 23 or twophoton phenomena. 24 Hybrid or multifunctional nanoparticles constructed from more than one component phase have also been attracting increasing interest due to their additional functionalities. 25-30 In this review, we consider speci?cally the optical properties of solid nanoparticles composed of more than one phase or compound. Alloyed nanoparticles (solid solutions or intermetallic compounds of the metallic elements) are also included because these intergrade with the two-phase hybrids

Cortie, MB, Kealley, CS, Bhatia, V, Thorogood, GJ, Elcombe, MM & Avdeev, M 2011, 'High temperature transformations of the Au7Cu5Al4 shape-memory alloy', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 509, no. 8, pp. 3502-3508.
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The beta-phase of Au(7)Cu(5)Al(4) undergoes a reversible shape-memory phase transformation, however there has been some uncertainty regarding the crystal structure or structures of the parent phase. Here we show that, under equilibrium conditions, the pa

Cortie, MB, Xiao, L, Erdei, L, Kealley, CS, Dowd, AR, Kimpton, JA & McDonagh, AM 2011, 'Thermal Stability of (KxNayH1-x-y)2Ti6O13 Nanofibers', EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, vol. 2011, no. 33, pp. 5087-5095.
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Potassium-rich titanate nanofibers were produced by digesting TiO2 in concentrated KOH solutions under hydrothermal conditions. The nanofibers were characterized by scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, and thermogravimetric analysis. A hexatitanate structure was assigned, in contrast to the trititanate structure usually resulting from NaOH treatment of TiO2. The potassium cations could be exchanged with others, such as sodium, hydrogen, and ammonium. The potassium-rich hexatitanate was found to be photocatalytic in its as-synthesized condition. The thermal stability of the fibers during calcination was followed in situ using X-ray diffraction and was found to be strongly dependent on the chemical composition. The potassium-rich titanate converted to anatase at only 480 °C, whereas the hydrogen- and ammonium-rich materials had to be heated to over 600 °C before conversion took place. Conversion was notably slowest in the ammonium-rich material. Surprisingly, the sodium-rich hexatitanate did not form anatase at temperatures up to 800 °C and instead recrystallized.

Courtenay, G, Gladstone, W, Scammell, M, Kidson, R & Wood, J 2011, 'The influence of estuarine water quality on cover of barnacles and Enteromorpha spp.', ENVIRONMENTAL MONITORING AND ASSESSMENT, vol. 175, no. 1-4, pp. 685-697.
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The influence of ambient water quality on the settlement of barnacles and the green alga Enteromorpha spp. to an artificial substratum in the estuaries of Sydney, Australia, was investigated to test the efficacy of both groups of organisms as indicators of changes in water quality due to urban stormwater runoff and/or sewage overflows. Wooden settlement panels were immersed for 4 months on 17 occasions between 1996 and 2005 at 11 locations known to vary in water-quality parameters (conductivity, total uncombined ammonia, oxidised nitrogen, total nitrogen, filterable phosphorus, total phosphorus, faecal coliforms and chlorophyll-a) and ambient meteorological conditions (total rainfall, maximum rainfall). Water-quality data were collected during the time that the settlement panels were deployed. Cover of barnacles was highly variable among locations (range 1.255.2%). Hierarchical partitioning found that chlorophyll-a, total phosphorus and total nitrogen had significant independent positive effects on barnacle cover. Together, these variables explained 26% of the variation in barnacle cover. Mean cover of Enteromorpha spp., however, did not vary significantly among locations suggesting that other potentially more important factors are influencing its settlement and growth. The results of this study suggest that barnacle cover is likely to be a useful indicator of some components of water quality.

Cummings, DO, Lee, RW, Simpson, SJ, Booth, DJ, Pile, AJ & Holmes, SP 2011, 'Resource partitioning amongst co-occurring decapods on wellheads from Australia's North–West shelf. An analysis of carbon and nitrogen stable isotopes', Journal of Experimental Marine Biology and Ecology, vol. 409, no. 1-2, pp. 186-193.
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On the North West shelf of Australia, assemblages of co-occurring decapods formed the dominant taxa that had colonised a series of petroleum wellheads. Stable isotope analysis was utilised to infer how eleven co-occurring decapods species partition troph

Darling, AE, Tritt, A, Eisen, JA & Facciotti, MT 2011, 'Mauve Assembly Metrics', BIOINFORMATICS, vol. 27, no. 19, pp. 2756-2757.
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High-throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to

Datta, A, Zhang, L, Nunn, J, Langford, NK, Feito, A, Plenio, MB & Walmsley, IA 2011, 'A compact entanglement distillery', Phys. Rev. Lett., vol. 108, no. 6, pp. 060502-060502.
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Large-scale quantum-correlated networks could transform technologies ranging from communications and cryptography to computation, metrology, and simulation of novel materials. Critical to achieving such quantum enhancements is distributing high-quality entanglement between distant nodes. This is made possible in the unavoidable presence of decoherence by entanglement distillation. However, current versions of this protocol are prohibitively costly in terms of resources. We introduce a new scheme for continuous-variable entanglement distillation that requires only linear temporal and constant physical or spatial resources, both of which are exponential improvements over existing protocols. Our scheme uses a fixed module - an entanglement distillery - comprising only four quantum memories of at most 50 % storage efficiency and allowing a feasible experimental implementation. Tangible quantum advantages are obtained by using non-ideal quantum memories outside their conventional role of storage. By creating, storing and processing information in the same physical space, the scheme establishes a potentially valuable technique for designing stable, scalable protocols across different quantum technologies.

Davidson, S, Kaiko, G, Loh, Z, Lalwani, A, Zhang, V, Spann, K, Foo, SY, Hansbro, N, Uematsu, S, Akira, S, Matthaei, KI, Rosenberg, HF, Foster, PS & Phipps, S 2011, 'Plasmacytoid Dendritic Cells Promote Host Defense against Acute Pneumovirus Infection via the TLR7–MyD88-Dependent Signaling Pathway', The Journal of Immunology, vol. 186, no. 10, pp. 5938-5948.
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Abstract Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in infants. In human infants, plasmacytoid dendritic cells (pDC) are recruited to the nasal compartment during infection and initiate host defense through the secretion of type I IFN, IL-12, and IL-6. However, RSV-infected pDC are refractory to TLR7-mediated activation. In this study, we used the rodent-specific pathogen, pneumonia virus of mice (PVM), to determine the contribution of pDC and TLR7 signaling to the development of the innate inflammatory and early adaptive immune response. In wild-type, but not TLR7- or MyD88-deficient mice, PVM inoculation led to a marked infiltration of pDC and increased expression of type I, II, and III IFNs. The delayed induction of IFNs in the absence of TLR7 or MyD88 was associated with a diminished innate inflammatory response and augmented virus recovery from lung tissue. In the absence of TLR7, PVM-specific CD8+ T cell cytokine production was abrogated. The adoptive transfer of TLR7-sufficient, but not TLR7-deficient pDC to TLR7 gene-deleted mice recapitulated the antiviral responses observed in wild-type mice and promoted virus clearance. In summary, TLR7-mediated signaling by pDC is required for appropriate innate responses to acute pneumovirus infection. It is conceivable that as-yet–unidentified defects in the TLR7 signaling pathway may be associated with elevated levels of RSV-associated morbidity and mortality among otherwise healthy human infants.

Davis, J, Short, K, Wuhrer, R, Phillips, M & Whittle, K 2011, 'Plasma Immersion Ion Implantation of Stainless Steel 316', Microscopy and Microanalysis, vol. 17, no. S2, pp. 1886-1887.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

De Silva, KSB, Xu, X, Gambhir, S, Wang, XL, Li, WX, Wallace, GG & Dou, SX 2011, 'Flux pinning mechanisms in graphene-doped MgB2 superconductors', SCRIPTA MATERIALIA, vol. 65, no. 7, pp. 634-637.
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De Silva, KSB, Xu, X, Li, WX, Zhang, Y, Rindfleisch, M & Tomsic, M 2011, 'Improving Superconducting Properties of MgB2 by Graphene Doping', IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY, vol. 21, no. 3, pp. 2686-2689.
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Deacon, RM, Wand, H, Stelzer-Braid, S, Treloar, C & Maher, L 2011, 'Improving surveillance for acute hepatitis C.', Commun Dis Intell Q Rep, vol. 35, no. 1, pp. 16-20.
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Understanding patterns of newly acquired hepatitis C virus (HCV) infection is fundamental to assessing the impact of prevention and treatment interventions. However, identifying newly acquired cases is difficult, usually requiring documented testing before and after exposure. As the proportion of cases identified as newly acquired by current New South Wales surveillance methodologies is significantly lower than that identified nationally, the impact on the identification of newly acquired cases of systematic reporting of past negative HCV test results from notifying laboratories was assessed. HCV notifications data for 2007 from two New South Wales laboratories were analysed. Cases with a negative HCV antibody test within the past 24 months were classified as newly acquired. These were linked to the NSW Department of Health (NSW Health)-identified cases to assess the effectiveness of accessing laboratory data. The laboratories accounted for approximately half of all new HCV notifications in 2007. Of the 2,206 newly diagnosed cases, 21 (1.0%) were newly acquired, 18 of which had not been identified under the current surveillance system, increasing the total number of newly acquired cases to 83 from 65. This increased the yield by 28% and increased the proportion of newly acquired cases from 65/4,192 (1.6%) to 83/4,196 (2.0%). Laboratory-identified cases were significantly more likely than NSW Health-identified cases to be aged 30 years or over. Combined with current reporting mechanisms, laboratory data on previous HCV test results have the potential to increase the number of newly acquired cases identified through the New South Wales surveillance system and to enhance the identification of cases among those aged 30 years or more.

Deng, W, Jin, D, Drozdowicz-Tomsia, K, Yuan, J, Wu, J & Goldys, EM 2011, 'Ultrabright Eu-Doped Plasmonic Ag@SiO2 Nanostructures: Time-gated Bioprobes with Single Particle Sensitivity and Negligible Background', Advanced Materials, vol. 23, no. 40, pp. 4649-4654.
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Deng, W, Sudheendra, L, Zhao, J, Fu, J, Jin, D, Kennedy, IM & Goldys, EM 2011, 'Upconversion in NaYF₄:Yb, Er nanoparticles amplified by metal nanostructures', Nanotechnology, vol. 22, no. 32, pp. 325604-325604.
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Deng, W, Ying, H, Helliwell, CA, Taylor, JM, Peacock, WJ & Dennis, ES 2011, 'FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 108, no. 16, pp. 6680-6685.
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FLOWERING LOCUS C (FLC) has a key role in the timing of the initiation of flowering in Arabidopsis. FLC binds and represses two genes that promote flowering, FT and SOC1. We show that FLC binds to many other genes, indicating that it has regulatory roles

Depamede, SN & Menz, I 2011, 'Phylogenetic Analysis and Protein Modeling of Plasmodium falciparum Aspartate Transcarbamoylase (ATCase)', Research Journal of Microbiology, vol. 6, no. 7, pp. 599-608.
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Deplazes, E, Jayatilaka, D & Corry, B 2011, 'Testing the use of molecular dynamics to simulate fluorophore motions and FRET', Physical Chemistry Chemical Physics, vol. 13, no. 23, pp. 11045-11045.
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Doblin, MA, Petrou, KL, Shelly, K, Westwood, K, van den Enden, R, Wright, S, Griffiths, B & Ralph, PJ 2011, 'Diel variation of chlorophyll-a fluorescence, phytoplankton pigments and productivity in the Sub-Antarctic and Polar Front Zones south of Tasmania, Australia', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 58, no. 21-22, pp. 2189-2199.
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Marine primary production is a fundamental measure of the oceanâs capacity to convert carbon dioxide to particulate organic carbon for the marine foodweb, and as such is an essential variable used in ecosystem and biogeochemical models to assess trophic dynamics and carbon cycling. The Sub-Antarctic Zone (SAZ) is a major sink for atmospheric carbon and exhibits large gradients in ocean conditions on both temporal and spatial scales. In this dynamic system, an understanding of small-scale temporal changes is critical for modelling primary production at larger scales. Thus, we investigated diel effects on maximum quantum yield of PSII (FV/FM), photosynthetic pigment pools and primary productivity in the western (Diel 1) and eastern SAZ region (Diel 3) south of Tasmania, Australia, and compared this to a station at the polar front (Diel 2). Phytoplankton in the eastern SAZ had the greatest diel response, with cells showing decreased FV/FM and increased biosynthesis and transformation of xanthophyll and other photoprotective pigments during the day, but only in the surface waters (0 and 10m). Diel responses diminished by 30 m. Cells in the western SAZ had similar responses across the depths sampled, increasing their FV/FM during the night and increasing their xanthophyll pigment content during the day. Phytoplankton at the polar front (Diel 2) showed intermediate diel-related variations in photophysiology, with xanthophyll conversion and increases in photoprotective pigments during the day but constant FV/FM.

Donnelly, S, Dalton, JP & Robinson, MW 2011, 'HOW PATHOGEN-DERIVED CYSTEINE PROTEASES MODULATE HOST IMMUNE RESPONSES', CYSTEINE PROTEASES OF PATHOGENIC ORGANISMS, vol. 712, pp. 192-207.
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In mammals, cysteine proteases are essential for the induction and development of both innate and adaptive immune responses. These proteases play a role in antigen-and pathogen-recognition and elimination, signal processing and cell homeostasis. Many pathogens also secrete cysteine proteases that often act on the same target proteins as the mammalian proteases and thereby can modulate host immunity from initial recognition to effector mechanisms. Pathogen-derived proteases range from nonspecific proteases that degrade multiple proteins involved in the immune response to enzymes that are very specific in their mode of action. Here, we overview current knowledge of pathogen-derived cysteine proteases that modulate immune responses by altering the normal function of key receptors or pathways in the mammalian immune system.

Dooley, AH, Hawkins, J & Ralston, D 2011, 'Families of type III0 ergodic transformations in distinct orbit equivalent classes', MONATSHEFTE FUR MATHEMATIK, vol. 164, no. 4, pp. 369-381.
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Dregan, A, Brown, J & Armstrong, D 2011, 'Do adult emotional and behavioural outcomes vary as a function of diverse childhood experiences of the public care system?', Psychological Medicine, vol. 41, no. 10, pp. 2213-2220.
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BackgroundLongitudinal data from the 1970 British Cohort Study were used to examine the long-term adult outcomes of those who, as children, were placed in public care.MethodMultivariate logistic estimation models were used to determine whether public care and placement patterns were associated with adult psychosocial outcomes. Seven emotional and behavioural outcomes measured at age 30 years were considered: depression, life dissatisfaction, self-efficacy, alcohol problems, smoking, drug abuse, and criminal convictions.ResultsThe analyses revealed a significant association between public care status and adult maladjustment on depression [odds ratio (OR) 1.74], life dissatisfaction (OR 1.45), low self-efficacy (OR 1.95), smoking (OR 1.70) and criminal convictions (OR 2.13).ConclusionsOverall, the present study findings suggest that there are enduring influences of a childhood admission to public care on emotional and behavioural adjustment from birth to adulthood. Some of the associations with childhood public care were relatively strong, particularly with respect to depression, self-efficacy and criminal convictions.

Dubey, S, Sumner, J, Pike, DA, Keogh, JS, Webb, JK & Shine, R 2011, 'Genetic Connectivity among Populations of an Endangered Snake Species from Southeastern Australia (Hoplocephalus bungaroides, Elapidae)', ECOLOGY AND EVOLUTION, vol. 1, no. 2, pp. 218-227.
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For endangered species that persist as apparently isolated populations within a previously more extensive range, the degree of genetic exchange between those populations is critical to conservation and management. A lack of gene flow can exacerbate impacts of threatening processes and delay or prevent colonization of sites after local extirpation. The broad-headed snake, Hoplocephalus bungaroides, is a small venomous species restricted to a handful of disjunct reserves near Sydney, Australia. Mark-recapture studies have indicated low vagility for this ambush predator, suggesting that gene flow also may be low. However, our analyses of 11 microsatellite loci from 163 snakes collected inMortonNational Park, from six sites within a 10-km diameter, suggest relatively high rates of gene flow among sites. Most populations exchange genes with each other, with one large population serving as a source area and smaller populations apparently acting as sinks. About half of the juvenile snakes, for which we could reliably infer parentage, were collected from populations other than those in which we collected their putative parents. As expected from the snakes reliance on rocky outcrops during cooler months of the year, most gene flow appears to be along sandstone plateaux rather than across the densely forested valleys that separate plateaux. The unexpectedly high rates of gene flow on a landscape scale are encouraging for future conservation of this endangered taxon. For example, wildlife managers could conserve broad-headed snakes by restoring habitats near extant source populations in areas predicted to be least affected by future climate change.

Duggin, IG, Dubarry, N & Bell, SD 2011, 'Replication termination and chromosome dimer resolution in the archaeon Sulfolobus solfataricus', EMBO JOURNAL, vol. 30, no. 1, pp. 145-153.
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Archaea of the genus Sulfolobus have a single-circular chromosome with three replication origins. All three origins fire in every cell in every cell cycle. Thus, three pairs of replication forks converge and terminate in each replication cycle. Here, we report 2D gel analyses of the replication fork fusion zones located between origins. These indicate that replication termination involves stochastic fork collision. In bacteria, replication termination is linked to chromosome dimer resolution, a process that requires the XerC and D recombinases, FtsK and the chromosomal dif site.

Dunlop, RA, Brunk, UT & Rodgers, KJ 2011, 'Proteins containing oxidized amino acids induce apoptosis in human monocytes', BIOCHEMICAL JOURNAL, vol. 435, pp. 207-216.
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Cellular deposits of oxidized and aggregated proteins are hallmarks of a variety of age-related disorders, but whether such proteins contribute to pathology is not well understood. We previously reported that oxidized proteins form lipofuscin/ceroid-like bodies with a lysosomal-type distribution and up-regulate the transcription and translation of proteolytic lysosomal enzymes in cultured J774 mouse macrophages. Given the recently identified role of lysosomes in the induction of apoptosis, we have extended our studies to explore a role for oxidized proteins in apoptosis. Oxidized proteins were biosynthetically generated in situ by substituting oxidized analogues for parent amino acids. Apoptosis was measured with Annexin-V/PI (propidium iodide), TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP nick-end labelling), MMP (mitochondrial membrane permeabilization), caspase activation and cytochrome c release, and related to lysosomal membrane permeabilization. Synthesized proteins containing the tyrosine oxidation product L-DOPA (L-3,4-dihydroxyphenylalanine) were more potent inducers of apoptosis than proteins containing the phenylalanine oxidation product o-tyrosine. Apoptosis was dependent upon incorporation of oxidized residues, as indicated by complete abrogation in cultures incubated with the non-incorporation control D-DOPA (D-3,4-dihydroxyphenylalanine) or when incorporation was competed out by parent amino acids. The findings of the present study suggest that certain oxidized proteins could play an active role in the progression of age-related disorders by contributing to LMP (lysosomal membrane permeabilization)-initiated apoptosis and may have important implications for the long-term use of L-DOPA as a therapeutic agent in Parkinson's disease

E.L. Temple, S & Hansbro, P 2011, 'New Insights into the Immune Response to Pneumococci', Current Respiratory Medicine Reviews, vol. 7, no. 4, pp. 257-261.
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Infection by Streptococcus pneumoniae (the pneumococcus) is associated with enormous morbidity and mortality worldwide and this bacterium remains the commonest cause of pneumonia, meningitis and otitis media. While immunity to pneumococcal disease has been widely accepted to depend mainly on the humoral arm of the immune system recent studies have shown a critical role for cellular immunity, specifically T lymphocytes (T cells), that is independent of antibody, in the prevention and clearance of pneumococcal infection. Here we review the evidence that supports the importance of T cells, specifically CD4+, CD8+ and regulatory T cells, in host responses to pneumococcal infection. © 2011 Bentham Science Publishers Ltd.

Earl, D, Bradnam, K, St. John, J, Darling, A, Lin, D, Fass, J, Yu, HOK, Buffalo, V, Zerbino, DR, Diekhans, M, Nguyen, N, Ariyaratne, PN, Sung, W-K, Ning, Z, Haimel, M, Simpson, JT, Fonseca, NA, Birol, İ, Docking, TR, Ho, IY, Rokhsar, DS, Chikhi, R, Lavenier, D, Chapuis, G, Naquin, D, Maillet, N, Schatz, MC, Kelley, DR, Phillippy, AM, Koren, S, Yang, S-P, Wu, W, Chou, W-C, Srivastava, A, Shaw, TI, Ruby, JG, Skewes-Cox, P, Betegon, M, Dimon, MT, Solovyev, V, Seledtsov, I, Kosarev, P, Vorobyev, D, Ramirez-Gonzalez, R, Leggett, R, MacLean, D, Xia, F, Luo, R, Li, Z, Xie, Y, Liu, B, Gnerre, S, MacCallum, I, Przybylski, D, Ribeiro, FJ, Yin, S, Sharpe, T, Hall, G, Kersey, PJ, Durbin, R, Jackman, SD, Chapman, JA, Huang, X, DeRisi, JL, Caccamo, M, Li, Y, Jaffe, DB, Green, RE, Haussler, D, Korf, I & Paten, B 2011, 'Assemblathon 1: A competitive assessment of de novo short read assembly methods', Genome Research, vol. 21, no. 12, pp. 2224-2241.
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Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.

Earp, A, Hanson, CE, Ralph, PJ, Brando, VE, Allen, S, Baird, M, Clementson, L, Daniel, P, Dekker, AG, Fearns, PRCS, Parslow, J, Strutton, PG, Thompson, PA, Underwood, M, Weeks, S & Doblin, MA 2011, 'Review of fluorescent standards for calibration of in situ fluorometers: Recommendations applied in coastal and ocean observing programs', OPTICS EXPRESS, vol. 19, no. 27, pp. 26768-26782.
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Fluorometers are widely used in ecosystem observing to monitor fluorescence signals from organic compounds, as well as to infer geophysical parameters such as chlorophyll or CDOM concentration, but measurements are susceptible to variation caused by biofouling, instrument design, sensor drift, operating environment, and calibration rigor. To collect high quality data, such sensors need frequent checking and regular calibration. In this study, a wide variety of both liquid and solid fluorescent materials were trialed to assess their suitability as reference standards for performance assessment of in situ fluorometers. Criteria used to evaluate the standards included the spectral excitation/emission responses of the materials relative to fluorescence sensors and to targeted ocean properties, the linearity of the fluorometerâs optical response with increasing concentration, stability and consistency, availability and ease of use, as well as cost. Findings are summarized as a series of recommended reference standards for sensors deployed on stationary and mobile platforms, to suit a variety of in situ coastal to ocean sensor configurations. Repeated determinations of chlorophyll scale factor using the recommended liquid standard, Fluorescein, achieved an accuracy of 2.5%. Repeated measurements with the recommended solid standard, Plexiglas Satinice® plum 4H01 DC (polymethylmethacrylate), over an 18 day period varied from the mean value by 1.0% for chlorophyll sensors and 3.3% for CDOM sensors.

Earp, AA & Smith, GB 2011, 'Evolution of plasmonic response in growing silver thin films with pre-percolation non-local conduction and emittance drop', JOURNAL OF PHYSICS D-APPLIED PHYSICS, vol. 44, no. 25, pp. 1-8.
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The optical response of growing silver thin films undergoes a transition dominated by three distinct plasmonic modes, two localized and one delocalized. Their admix as a function of added mass is analysed. The onset of the delocalized or Drude mode occurs before the sharp electrical percolation transition so optically the full insulator-metal transition is broadened. A scaling explanation supported by images shows Ag islands only have to link up over 200-300 nm to yield partial delocalization. The localized modes are (i) from silver nano-islands and (ii) a transitional anomalous mode, peaking near the dc critical percolation point, from islands surrounded by network. Growing silver within a multilayer oxide stack is compared with that on glass. The transition in thermal emittance matches that in the delocalized mode. Its broadening enables practical tuning of intermediate emittance by varying mass.

Earp, AA, Franklin, JB & Smith, GB 2011, 'Absorption tails and extinction in luminescent solar concentrators', SOLAR ENERGY MATERIALS AND SOLAR CELLS, vol. 95, no. 4, pp. 1157-1162.
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Non-ultraviolet (UV) photoexposure of luminescent solar concentrators (LSC's) can produce photoproducts that cause additional extinction at wavelengths somewhat longer than the main dye absorption peak. This photo-induced 'tails' extinction is deleterious to luminous output in collectors of useful lengths. An experimental method that enables the subdivision of tails extinction in an LSC into absorbed and scattered components is described. The relevant theory is outlined, and experimental results are presented for a polymethyl methacrylate (PMMA) LSC containing Lumogen F083 dye. For this sample, tails absorption increased significantly with outdoor exposure, while tails scattering remained constant. Further measurements indicate that LSC luminous output is around five times more sensitive to tails absorption than to fluorescence quenching. This work also indicates that merely checking for dye quenching, as is often done, can be a misleading indicator of long-term LSC output.

Edmonds, I & Smith, G 2011, 'Surface reflectance and conversion efficiency dependence of technologies for mitigating global warming', RENEWABLE ENERGY, vol. 36, no. 5, pp. 1343-1351.
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A means of assessing the relative impact of different renewable energy technologies on global warming has been developed. All power plants emit thermal energy to the atmosphere. Fossil fuel power plants also emit CO(2) which accumulates in the atmosphere

El-Assaad, F, Hempel, C, Combes, V, Mitchell, AJ, Ball, HJ, Kurtzhals, JAL, Hunt, NH, Mathys, J-M & Grau, GER 2011, 'Differential MicroRNA Expression in Experimental Cerebral and Noncerebral Malaria', Infection and Immunity, vol. 79, no. 6, pp. 2379-2384.
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ABSTRACTMicroRNAs (miRNAs) are posttranscriptional regulatory molecules that have been implicated in the regulation of immune responses, but their role in the immune response toPlasmodiuminfection is unknown. We studied the expression of selected miRNAs following infection of CBA mice withPlasmodium bergheiANKA (PbA), which causes cerebral malaria (CM), orPlasmodium bergheiK173 (PbK), which causes severe malaria but without cerebral complications, termed non-CM. The differential expression profiles of selected miRNAs (let-7i, miR-27a, miR-150, miR-126, miR-210, and miR-155) were analyzed in mouse brain and heart tissue by quantitative reverse transcription-PCR (qRT-PCR). We identified three miRNAs that were differentially expressed in the brain of PbA-infected CBA mice: let7i, miR-27a, and miR-150. In contrast, no miRNA changes were detected in the heart, an organ with no known pathology during acute malaria. To investigate the involvement of let-7i, miR-27a, and miR-150 in CM-resistant mice, we assessed the expression levels in gamma interferon knockout (IFN-γ−/−) mice on a C57BL/6 genetic background. The expression of let-7i, miR-27a, and miR-150 was unchanged in both wild-type (WT) and IFN-γ−/−mice following infection. Overexpression of these three miRNAs during PbA, but not PbK, infection in WT mice may be critical for the triggering of the neurological syndrome via regulation of their potential downstream targets. Our data suggest that in the CBA mouse at least, miRNA may have a regulatory rol...

Elder, M, Rechnitzer, A & Wong, T 2011, 'On the cogrowth of Thompson's group $F$', Groups - Complexity - Cryptology, vol. 4, no. 2, pp. 301-320.
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We investigate the cogrowth and distribution of geodesics in R. Thompson's group $F$.

Erken, M, Weitere, M, Kjelleberg, S & McDougald, D 2011, 'In situ grazing resistance of Vibrio cholerae in the marine environment', FEMS Microbiology Ecology, vol. 76, no. 3, pp. 504-512.
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Essilfie, A-T, Simpson, JL, Horvat, JC, Preston, JA, Dunkley, ML, Foster, PS, Gibson, PG & Hansbro, PM 2011, 'Haemophilus influenzae Infection Drives IL-17-Mediated Neutrophilic Allergic Airways Disease', PLoS Pathogens, vol. 7, no. 10, pp. e1002244-e1002244.
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Faes, C, Ormerod, JT & Wand, MP 2011, 'Variational Bayesian Inference for Parametric and Nonparametric Regression With Missing Data', Journal of the American Statistical Association, vol. 106, no. 495, pp. 959-971.
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Bayesian hierarchical models are attractive structures for conducting regression analyses when the data are subject to missingness. However, the requisite probability calculus is challenging and Monte Carlo methods typically are employed. We develop an alternative approach based on deterministic variational Bayes approximations. Both parametric and nonparametric regression are considered. Attention is restricted to the more challenging case of missing predictor data. We demonstrate that variational Bayes can achieve good accuracy, but with considerably less computational overhead. The main ramification is fast approximate Bayesian inference in parametric and nonparametric regression models with missing data.

Felix Wong, WS & Danforn Lim, CE 2011, 'Hormonal treatment for endometriosis associated pelvic pain.', Iran J Reprod Med, vol. 9, no. 3, pp. 163-170.
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BACKGROUND: Endometriosis is a common gynecological problem associated with chronic pelvic pain. OBJECTIVE: To evaluate the effectiveness of current hormonal treatments of endometriosis associated pain. MATERIALS AND METHODS: Randomized Controlled studies identified from databases of Medline and Cochrane Systemic Review groups were pooled. 7 RCTs were recruited for evaluation in this review. Data from these studies were pooled and meta-analysis was performed in three comparison groups: 1) Progestogen versus GnRHa; 2) Implanon versus Progestogen (injection); 3) Combined oral contraceptive pills versus placebo and progestogen. Response to treatment was measured as a reduction in pain score. Pain improvement was defined as improvement ≥1 at the end of treatment. RESULTS: There was no significant difference between treatment groups of progestogen and GnRHa (RR: 0.036; CI:-0.030-0.102) for relieving endometriosis associated pelvic pain. Long acting progestogen (Implanon) and Mirena are not inferior to GnRHa and depot medroxy progesterone acetate (DMPA) (RR: 0.006; CI:-0.142-0.162). Combined oral contraceptive pills demonstrated effective treatment of relieving endometriosis associated pelvic pain when compared with placebo groups (RR:0.321CI-0.066-0.707). Progestogen was more effective than combined oral contraceptive pills in controlling dysmenorrhea (RR:-0.160; CI:-0.386-0.066), however, progestogen is associated with more side effects like spotting and bloating than the combined contraceptive pills. CONCLUSION: Combined oral contraceptive pills (COCP), GnRHa and progestogens are equally effective in relieving endometriosis associated pelvic pain. COCP and progestogens are relatively cheap and more suitable for long-term use as compared to GnRHa. Long-term RCT of medicated contraceptive devices like Mirena and Implanon are required to evaluate their long-term effects on relieving the endometriosis associated pelvic pain.

Finn, TE, Wang, L, Smolilo, D, Smith, NA, White, R, Chaudhury, A, Dennis, ES & Wang, M-B 2011, 'Transgene Expression and Transgene-Induced Silencing in Diploid and Autotetraploid Arabidopsis', GENETICS, vol. 187, no. 2, pp. 409-U89.
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Previous studies have suggested that transgene expression in plants can be affected by ploidy. Here we show that three different transgenes, a reporter transgene, an antisense transgene, and a hairpin RNA (hpRNA) transgene, are all expressed at a lower level in autotetraploid (4n) than in diploid (2n) Arabidopsis. RNA silencing of two endogenous genes was induced by the antisense and hpRNA transgenes and this silencing is significantly less effective in 4n than in 2n Arabidopsis; furthermore, the reduced silencing in 4n Arabidopsis correlated with reduced accumulation of silencing-inducer RNAs. Methylation analysis both of independent 2n and 4n transgenic lines and of 2n and 4n progeny derived from the same 3n transgenic parent, indicated that transgenes are more methylated in 4n than 2n Arabidopsis. These results suggest that transgenes are transcriptionally repressed in the 4n background, resulting in expression levels lower than in the 2n background. Transgenes designed to silence endogenous genes express lower concentrations of silencing-inducer RNAs in 4n Arabidopsis plants, resulting in less effective silencing of target genes than in 2n Arabidopsis plants.

Finnegan, EJ, Bond, DM, Buzas, DM, Goodrich, J, Helliwell, CA, Tamada, Y, Yun, J-Y, Amasino, RM & Dennis, ES 2011, 'Polycomb proteins regulate the quantitative induction of VERNALIZATION INSENSITIVE 3 in response to low temperatures', PLANT JOURNAL, vol. 65, no. 3, pp. 382-391.
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Vernalization, the promotion of flowering in response to low temperatures, is one of the best characterized examples of epigenetic regulation in plants. The promotion of flowering is proportional to the duration of the cold period, but the mechanism by which plants measure time at low temperatures has been a long-standing mystery. We show that the quantitative induction of the first gene in the Arabidopsis vernalization pathway, VERNALIZATION INSENSITIVE 3 (VIN3), is regulated by the components of Polycomb Response Complex 2, which trimethylates histone H3 lysine 27 (H3K27me3). In differentiated animal cells, H3K27me3 is mostly associated with long-term gene repression, whereas, in pluripotent embyonic stem cells, many cell lineagespecific genes are inactive but exist in bivalent chromatin that carries both active (H3K4me3) and repressive (H3K27me3) marks on the same molecule. During differentiation, bivalent domains are generally resolved to an active or silent state. We found that H3K27me3 maintains VIN3 in a repressed state prior to cold exposure; this mark is not removed during VIN3 induction. Instead, active VIN3 is associated with bivalently marked chromatin. The continued presence of H3K27me3 ensures that induction of VIN3 is proportional to the duration of the cold, and that plants require prolonged cold to promote the transition to flowering. The observation that Polycomb proteins control VIN3 activity defines a new role for Polycomb proteins in regulating the rate of gene induction.

Fletcher, SM, Stark, D & Ellis, J 2011, 'Prevalence of gastrointestinal pathogens in Sub-Saharan Africa: systematic review and meta-analysis', Journal of Public Health in Africa, vol. 2, no. 2, pp. 30-30.
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A significant proportion of vulnerable people in sub-Saharan Africa (SSA) remain at risk for contracting diarrhoeal diseases due to the presence of many risk factors facilitating their transmission. A systematic review of published articles from the SSA region was done to determine the prevalence and types of diarrhoeal pathogens in circulation, based on a search of databases, including EBSCO host, PubMed, Scopus, Science Direct, Google scholar and Web of Science was done between September 2009 and December 2010.

Florance, D, Webb, JK, Dempster, T, Kearney, MR, Worthing, A & Letnic, M 2011, 'Excluding access to invasion hubs can contain the spread of an invasive vertebrate', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 278, no. 1720, pp. 2900-2908.
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Many biological invasions do not occur as a gradual expansion along a continuous front, but result from the expansion of satellite populations that become established at 'invasion hubs'. Although theoretical studies indicate that targeting control efforts at invasion hubs can effectively contain the spread of invasions, few studies have demonstrated this in practice. In arid landscapes worldwide, humans have increased the availability of surface water by creating artificial water points (AWPs) such as troughs and dams for livestock. By experimentally excluding invasive cane toads (Bufo marinus) from AWP, we show that AWP provide a resource subsidy for non-arid-adapted toads and serve as dry season refuges and thus invasion hubs for cane toads in arid Australia. Using data on the distribution of permanent water in arid Australia and the dispersal potential of toads, we predict that systematically excluding toads from AWP would reduce the area of arid Australia across which toads are predicted to disperse and colonize under average climatic conditions by 38 per cent from 2 242 000 to 1 385 000 km(2). Our study shows how human modification of hydrological regimes can create a network of invasion hubs that facilitates a biological invasion, and confirms that targeted control at invasion hubs can reduce landscape connectivity to contain the spread of an invasive vertebrate.

Forbes, SL, Wilson, MEA & Stuart, BH 2011, 'Examination of adipocere formation in a cold water environment', INTERNATIONAL JOURNAL OF LEGAL MEDICINE, vol. 125, no. 5, pp. 643-650.
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Adipocere is a late-stage postmortem decomposition product that forms from the lipids present in soft tissue. Its formation in aquatic environments is typically related to the presence of a moist, warm, anaerobic environment, and the effect of decomposer

Freedman, LS, Midthune, D, Carroll, RJ, Tasevska, N, Schatzkin, A, Mares, J, Tinker, L, Potischman, N & Kipnis, V 2011, 'Using Regression Calibration Equations That Combine Self-Reported Intake and Biomarker Measures to Obtain Unbiased Estimates and More Powerful Tests of Dietary Associations', American Journal of Epidemiology, vol. 174, no. 11, pp. 1238-1245.
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Fronzi, M, De Vita, A, Tateyama, Y & Traversa, E 2011, 'ZrO₂-CeO₂ Interface Properties: A First-Principle Investigation', ECS Meeting Abstracts, vol. MA2011-01, no. 12, pp. 772-772.
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Abstract not Available.

Fu, S, Molnar, A, Bowron, P, Lewis, J & Wang, H 2011, 'Reduction of temazepam to diazepam and lorazepam to delorazepam during enzymatic hydrolysis', ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 400, no. 1, pp. 153-164.
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It has been previously reported that treatment of urinary oxazepam by commercial ß-glucuronidase enzyme preparations, from Escherichia coli, Helix pomatia and Patella vulgata, results in production of nordiazepam (desmethyldiazepam) artefact. In this study, we report that this unusual reductive transformation also occurs in other benzodiazepines with a hydroxyl group at the C3 position such as temazepam and lorazepam. As determined by liquid chromatography-mass spectrometry analysis, all three enzyme preparations were found capable of converting urinary temazepam into diazepam following enzymatic incubation and subsequent liquidliquid extraction procedures. For example, when H. pomatia enzymes were used with incubation conditions of 18 h and 50 °C, the percentage conversion, although small, was significantapproximately 1% (0.591.54%) in both patient and spiked blank urines. Similarly, using H. pomatia enzyme under these incubation conditions, a reductive transformation of urinary lorazepam into delorazepam (chlordesmethyldiazepam) occurred. These findings have both clinical and forensic implications. Detection of diazepam or delorazepam in biological samples following enzyme treatment should be interpreted with care.

Fujimoto, R, Sasaki, T, Kudoh, H, Taylor, JM, Kakutani, T & Dennis, ES 2011, 'Epigenetic variation in the FWA gene within the genus Arabidopsis', PLANT JOURNAL, vol. 66, no. 5, pp. 831-843.
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fwa is a late flowering epi-mutant in Arabidopsis thaliana. FWA is silenced by DNA methylation in vegetative tissue but is demethylated in the central cell of the female ovule and continues to be expressed in the endosperm from the maternal copy. FWA is stably silenced in A. thaliana, but in related Arabidopsis species, FWA expression and DNA methylation levels vary in vegetative tissue. In this study, we show that variation in FWA expression in field isolates having identical DNA sequences is associated with changes in DNA methylation and may change over time. Vegetative FWA expression is correlated with decreased methylation at non-CG sites in the region upstream of the transcription start site in species related to A. thaliana and we conclude that methylation of this region is critical for FWA silencing in these species. In A. thaliana, FWA expression is affected by methylation in regions both upstream and downstream of the transcription start site. Ectopic A. thaliana FWA expression causes a late flowering phenotype, but over-expression of Arabidopsis lyrata FWA does not. In A. thaliana, stable silencing of FWA to prevent late flowering may have evolved through the selection of large tandem repeats and spread of the critical methylated region to include these repeats.

Fujimoto, R, Taylor, JM, Sasaki, T, Kawanabe, T & Dennis, ES 2011, 'Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis', PLANT MOLECULAR BIOLOGY, vol. 77, no. 4-5, pp. 419-431.
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The merging of two different genomes occurs during the formation of amphidiploids, and the merged regulatory networks have the potential to generate a new gene expression pattern. We examined the genome-wide gene expression of two newly synthesized amphidiploids between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera. 1,137 (4.7%) and 1,316 (5.4%) of probesets showed differential gene expression in A. thaliana-A. halleri and A. thaliana-A. lyrata hybrids respectively, compared to the mid parent value and of these, 489 were in common. Genes that differed in expression between the parental lines tended to have an expression level in both hybrids differing from the mid parent value. In contrast to protein coding genes, there is little differential expression of transposons. Genes in the categories of chloroplast-targeted and response to stress were overrepresented in the non-additively expressed genes in both amphidiploids. As these genes have the potential to contribute directly to the plant phenotype, we suggest that rapid changes of gene expression in amphidiploids might be important for producing greater biomass.

Fung, TC, Grimwood, K, Shimmon, R, Spindler, X, Maynard, P, Lennard, C & Roux, C 2011, 'Investigation of hydrogen cyanide generation from the cyanoacrylate fuming process used for latent fingermark detection', FORENSIC SCIENCE INTERNATIONAL, vol. 212, no. 1-3, pp. 143-149.
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Cyanoacrylate fuming is one of the most common techniques employed for the detection of latent fingermarks on non-porous surfaces such as plastic and glass. The technique is generally applied by exposing items of interest to the vapours generated by heating a suitable quantity of commercial cyanoacrylate adhesive. In this study, the potential for highly toxic hydrogen cyanide (HCN) to be generated from the overheating of cyanoacrylate was investigated. Two commercial cyanoacrylate adhesives and two quantitative methods for the determination of HCN were employed: (i) the sodium picrate method; and (ii) the picrateresorcinol method. 13C nuclear magnetic resonance (NMR) analysis was used to confirm the presence of cyanide. In addition, the thermal decomposition of cyanoacrylate was studied using simultaneous thermogravimetric and differential thermal analysis (TGADTA). It was determined that detectable and quantifiable amounts of HCN were generated from the thermal decomposition of cyanoacrylate monomer and polymer at temperatures as low as 200 8C. Using an optimised picrateresorcinol method, it was shown that around 10 mg of HCN could be generated from the heating of 1 g of cyanoacrylate monomer at 200 8C. For one of the adhesives tested, this increased to above 100 mg of HCN when 1 g of cyanoacrylate monomer was heated at 280 8C. Recommendations are provided that, if followed, should ensure that the cyanoacrylate fuming process can be safely applied with minimal risk to the operator.

Gale, PA 2011, 'ChemInform Abstract: Anion Receptor Chemistry', ChemInform, vol. 42, no. 12, pp. no-no.
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Gale, PA 2011, 'From Anion Receptors to Transporters', Accounts of Chemical Research, vol. 44, no. 3, pp. 216-226.
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Gale, PA, Sessler, JL & Steed, JW 2011, 'Supramolecular Chemistry—Introducing the latest web themed issue', Chemical Communications, vol. 47, no. 21, pp. 5931-5931.
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Gentle, AR, Aguilar, JLC & Smith, GB 2011, 'Optimized cool roofs: Integrating albedo and thermal emittance with R-value', SOLAR ENERGY MATERIALS AND SOLAR CELLS, vol. 95, no. 12, pp. 3207-3215.
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For cool roofs the combined effect of the three parameters that define heat gain and loss from a roof, namely solar albedo a, thermal emittance E, and sub-roof R-value, must be considered. An accurate contribution of night sky cooling, and hence humidity and total down-welling atmospheric radiation is needed. A systematic analysis of the contribution of a roof to average cooling load per day and to peak load reductions is presented for a temperate climate zone over 6 cooling months using an hour-by-hour analysis. Eighteen 3-parameter sets (a,E,R) demonstrate the over-riding importance of a high a, while sensitivity to R-value and E drops away as albedo rises. Up-front cost per unit reductions in peak demand or average energy use per day always rises strongly as R rises unless albedo is low. A moderate R similar to 1.63 is superior to high R unless a roof is dark, or winter heating demand is high. We indicate briefly why the roof typically does not present a dominant influence on average winter heating needs in most temperate zones, enhancing the benefits of cool roofs.

George, AM & Jones, PM 2011, 'Type II ABC Permeases: Are They Really So Different?', Structure, vol. 19, no. 11, pp. 1540-1542.
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ATP binding-cassette (ABC) transporters couple ATP hydrolysis to vectorial movement of substrates across cell membranes. Of ancient origin and ubiquitous occurrence, they have been adapted to traffic a vast array of compounds, performing roles such as nutrient import and removal of toxins, antigen presentation, hormone release, signal reception, channel gating, and many others (Higgins, 1992; Jones and George. 2004). Their central roles in many physiological process has brought ABC transporters to the forefront in biomedical research in diverse areas including multidrug resistance in cancers and human genetic disorders, such as cystic fibrosis.

Gerrits, T, Thomas-Peter, N, Gates, JC, Lita, AE, Metcalf, BJ, Calkins, B, Tomlin, NA, Fox, AE, Linares, AL, Spring, JB, Langford, NK, Mirin, RP, Smith, PGR, Walmsley, IA & Nam, SW 2011, 'On-chip, photon-number-resolving, telecommunication-band detectors for scalable photonic information processing', Physical Review A, vol. 84, no. 6.
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Gervásio, OL, Phillips, WD, Cole, L & Allen, DG 2011, 'Caveolae respond to cell stretch and contribute to stretch-induced signaling', Journal of Cell Science, vol. 124, no. 21, pp. 3581-3590.
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Caveolae are invaginations of the plasma membrane that are formed by caveolins. Caveolar membranes are also enriched in cholesterol, glycosphingolipids and signaling enzymes such as Src kinase. Here we investigate the effect of cell stretch upon caveolar dynamics and signaling. Transfection of C2 myoblasts with caveolin-3–YFP led to the formation of caveolae-like membrane pits 50–100 nm in diameter. Glycosphingolipids became immobilized and tightly packed together within caveolin-rich regions of the plasma membrane. Fluorescence resonance energy transfer (FRET) was used to assess the degree of glycosphingolipid packing. Myoblasts were subjected to a brief (1 minute) stretch on an elastic substratum. Stretch caused a reduction in glycosphingolipid FRET, consistent with a reversible unfolding of caveolar pits in response to membrane tension. Cells expressing caveolin-3–YFP also displayed an enhanced stretch-induced activation of Src kinase, as assessed by immunofluorescence. Repeated stretches resulted in the trafficking and remodeling of caveolin-3-rich membrane domains and accelerated turnover of membrane glycosphingolipids. The stretch-induced unfolding of caveolae, activation of Src and redistribution of caveolin and glycosphingolipids might reflect mechanisms of the cellular adaptation to mechanical stresses.

Glenn, EP, Doody, TM, Guerschman, JP, Huete, AR, King, EA, McVicar, TR, Van Dijk, AIJM, Van Niel, TG, Yebra, M & Zhang, Y 2011, 'Actual evapotranspiration estimation by ground and remote sensing methods: the Australian experience', HYDROLOGICAL PROCESSES, vol. 25, no. 26, pp. 4103-4116.
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On average, Australia is a dry continent with many competing uses for water. Hence, there is an urgent need to know actual evapotranspiration (ETa) patterns across wide areas of agricultural and natural ecosystems, as opposed to just point measurements of ETa. The Australian Government has tasked the science agencies with operationally developing monthly and annual estimates of ETa and other hydrological variables, and with forecasting water availability over periods of days to decades, as part of its national water assessment programme. To meet these needs, Australian researchers have become leaders in developing large-area methods for estimating ETa at regional and continental scales. Ground methods include meteorological models, eddy covariance towers, sap flow sensors and catchment water balance models. Remote sensing methods use thermal infrared, mid infrared and/or vegetation indices usually combined with meteorological data to estimate ETa. Ground and remote sensing ETa estimates are assimilated into the Australian Water Resource Assessment, which issues annual estimates of the state of the continental water balance for policy and planning purposes. The best ETa models are estimated to have an error or uncertainty of 10% to 20% in Australia. Developments in Australian ETa research over the past 20?years are reviewed, and sources of error and uncertainty in current methods and models are discussed.

Goldsmith, J, Wand, MP & Crainiceanu, C 2011, 'Functional regression via variational Bayes', Electronic Journal of Statistics, vol. 5, no. none, pp. 572-602.
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We introduce variational Bayes methods for fast approximate inference in functional regression analysis. Both the standard cross-sectional and the increasingly common longitudinal settings are treated. The methodology allows Bayesian functional regression analyses to be conducted without the computational overhead of Monte Carlo methods. Confidence intervals of the model parameters are obtained both using the approximate variational approach and nonparametric resampling of clusters. The latter approach is possible because our variational Bayes functional regression approach is computationally efficient. A simulation study indicates that variational Bayes is highly accurate in estimating the parameters of interest and in approximating the Markov chain Monte Carlo-sampled joint posterior distribution of the model parameters. The methods apply generally, but are motivated by a longitudinal neuroimaging study of multiple sclerosis patients. Code used in simulations is made available as a web-supplement.

Gracanin, M, Lam, MA, Morgan, PE, Rodgers, KJ, Hawkins, CL & Davies, MJ 2011, 'Amino acid, peptide, and protein hydroperoxides and their decomposition products modify the activity of the 26S proteasome', FREE RADICAL BIOLOGY AND MEDICINE, vol. 50, no. 2, pp. 389-399.
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Proteins are major biological targets for oxidative damage within cells because of their high abundance and rapid rates of reaction with radicals and singlet oxygen. These reactions generate high yields of hydroperoxides. The turnover of both native and modified/damaged proteins is critical for maintaining cell homeostasis, with this occurring via the proteasomal and endosomallysosomal systems; the former is of particular importance for intracellular proteins. In this study we have examined whether oxidation products generated on amino acids, peptides, and proteins modulate 26S proteasome activity. We show that oxidation products, and particularly protein hydroperoxides, are efficient inhibitors of the 26S proteasome tryptic and chymotryptic activities, with this depending, at least in part, on the presence of hydroperoxide groups. Removal of these species by reduction significantly reduces proteasome inhibition. This loss of activity is accompanied by a loss of thiol residues, but an absence of radical formation, consistent with molecular, rather than radical, reactions being responsible for proteasome inhibition. Aldehydes also seem to play a role in the inhibition of chymotryptic activity, with this prevented by treatment with NaBH4, which reduces these groups. Inhibition occurred at hydroperoxide concentrations of = 1 µM for oxidized amino acids and peptides and = 10 µM for oxidized proteins, compared with ca. 100 µM for H2O2, indicating that H2O2 is a much less effective inhibitor. These data indicate that the formation of oxidized proteins within cells may modulate cell function by interfering with the turnover of native proteins and the clearance of modified materials.

Grage, SL, Keleshian, AM, Turdzeladze, T, Battle, AR, Tay, WC, May, RP, Holt, SA, Contera, SA, Haertlein, M, Moulin, M, Pal, P, Rohde, PR, Forsyth, VT, Watts, A, Huang, KC, Ulrich, AS & Martinac, B 2011, 'Bilayer-Mediated Clustering and Functional Interaction of MscL Channels', Biophysical Journal, vol. 100, no. 5, pp. 1252-1260.
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Graham, PL, Ryan, LM & Luszcz, MA 2011, 'Joint modelling of survival and cognitive decline in the Australian Longitudinal Study of Ageing', JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS, vol. 60, no. 2, pp. 221-238.
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The paper describes the use of a longitudinal tobit model to characterize cognitive decline over a 13-year period in a cohort of 2087 elderly Australians. Use of a tobit formulation allows for the so-called `ceiling effect wherein many subjects achieve perfect test scores. A Bayesian hierarchical joint model is presented that allows for random subject-specific intercepts and slopes, as well as for informative dropout. Results suggest several potential areas of intervention. For example, there is a clear doseresponse effect of exercise whereby increasing levels of exercise are associated with higher cognitive scores.

Grinblat-Huse, V, Drabek, EF, Creasy, HH, Daugherty, SC, Jones, KM, Santana-Cruz, I, Tallon, LJ, Read, TD, Hatch, TP, Bavoil, P & Myers, GSA 2011, 'Genome Sequences of the Zoonotic Pathogens Chlamydia psittaci 6BC and Cal10', JOURNAL OF BACTERIOLOGY, vol. 193, no. 15, pp. 4039-4040.
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Groszmann, M, Greaves, IK, Albert, N, Fujimoto, R, Helliwell, CA, Dennis, ES & Peacock, WJ 2011, 'Epigenetics in plants-vernalisation and hybrid vigour', BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, vol. 1809, no. 8, pp. 427-437.
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In this review we have analysed two major biological systems involving epigenetic control of gene activity. In the ?rst system we demonstrate the interplay between genetic and epigenetic controls over the transcriptional activity of FLC, a major repressor of ?owering in Arabidopsis. FLC is down-regulated by low temperature treatment (vernalisation) releasing the repressor effect on ?owering. We discuss the mechanisms of the reduced transcription and the memory of the vernalisation treatment through vegetative development. We also discuss the resetting of the repressed activity level of the FLC gene, following vernalisation, to the default high activity level and show it occurs during both male and female gametogenesis but with different timing in each. In the second part of the review discussed the complex multigenic system which is responsible for the patterns of gene activity which bring about hybrid vigour in crosses between genetically similar but epigenetically distinct parents. The epigenetic systems that we have identi?ed as contributing to the heterotic phenotype are the 24nt siRNAs and their effects on RNA dependent DNA methylation (RdDM) at the target loci leading to changed expression levels. We conclude that it is likely that epigenetic controls are involved in expression systems in many aspects of plant development and plant function.

Groszmann, M, Greaves, IK, Albertyn, ZI, Scofield, GN, Peacock, WJ & Dennis, ES 2011, 'Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 108, no. 6, pp. 2617-2622.
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Intraspecific hybrids between the Arabidopsis thaliana accessions C24 and Landsberg erecta have strong heterosis. The reciprocal hybrids show a decreased level of 24-nt small RNA (sRNA) relative to the parents with the decrease greatest for those loci wh

Gu, BJ, Saunders, BM, Petrou, S & Wiley, JS 2011, 'P2X7 Is a Scavenger Receptor for Apoptotic Cells in the Absence of Its Ligand, Extracellular ATP', The Journal of Immunology, vol. 187, no. 5, pp. 2365-2375.
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Abstract Phagocytosis of apoptotic cells is essential during development and tissue remodeling. Our previous study has shown that the P2X7 receptor regulates phagocytosis of nonopsonized particles and bacteria. In this study, we demonstrate that P2X7 also mediates phagocytosis of apoptotic lymphocytes and neuronal cells by human monocyte-derived macrophages under serum-free conditions. ATP inhibited this process to a similar extent as observed with cytochalasin D. P2X7-transfected HEK-293 cells acquired the ability to phagocytose apoptotic lymphocytes. Injection of apoptotic thymocytes into the peritoneal cavity of wild-type mice resulted in their phagocytosis by macrophages, but injection of ATP prior to thymocytes markedly decreased this uptake. In contrast, ATP failed to inhibit phagocytosis of apoptotic thymocytes in vivo by P2X7-deficient peritoneal macrophages. The surface expression of P2X7 on phagocytes increased significantly during phagocytosis of either beads or apoptotic cells. A peptide screen library containing 24 biotin-conjugated peptides mimicking the extracellular domain of P2X7 was used to evaluate the binding profile to beads, bacteria, and apoptotic cells. One peptide showed binding to all particles and cell membrane lipids. Three other cysteine-containing peptides uniquely bound the surface of apoptotic cells but not viable cells, whereas substitution of alanine for cysteine abolished peptide binding. Several thiol-reactive compounds including N-acetyl-L-cysteine abolished phagocytosis of apoptotic SH-SY5Y cells by macrophages. These data suggest that the P2X7 receptor in its unactivated state acts like a scavenger receptor, and its extracellular disulphide bonds play an important role in direct recognition and engulfment of apoptotic cells.

Gunawan, C, Teoh, WY, Marquis, CP & Amal, R 2011, 'Cytotoxic Origin of Copper(II) Oxide Nanoparticles: Comparative Studies with Micron-Sized Particles, Leachate, and Metal Salts', ACS Nano, vol. 5, no. 9, pp. 7214-7225.
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Guo, Z & Platen, E 2011, 'The Small and Large Time Implied Volatilities in the Minimal Market Model', International Journal of Theoretical and Applied Finance, vol. 15, no. 08, pp. 1-23.
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This paper derives explicit formulas for both the small and large time limits of the implied volatility in the minimal market model. It is shown that interest rates do impact on the implied volatility in the long run even though they are negligible in the short time limit.

Gupta, V, Baghel, RS, Kumar, M, Kumari, P, Mantri, VA, Reddy, CRK & Jha, B 2011, 'Growth and agarose characteristics of isomorphic gametophyte (male and female) and sporophyte of Gracilaria dura and their marker assisted selection', Aquaculture, vol. 318, no. 3-4, pp. 389-396.
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Gupta, V, Kumar, M, Brahmbhatt, H, Reddy, CRK, Seth, A & Jha, B 2011, 'Simultaneous determination of different endogenetic plant growth regulators in common green seaweeds using dispersive liquid–liquid microextraction method', Plant Physiology and Biochemistry, vol. 49, no. 11, pp. 1259-1263.
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Gupta, V, Kumar, M, Kumari, P, Reddy, CRK & Jha, B 2011, 'Optimization of protoplast yields from the red algae Gracilaria dura (C. Agardh) J. Agardh and G. verrucosa (Huds.) Papenfuss', Journal of Applied Phycology, vol. 23, no. 2, pp. 209-218.
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Gutman, N, Botten, LC, Sukhorukov, AA & de Sterke, CM 2011, 'Degenerate band edges in optical fiber with multiple grating: efficient coupling to slow light', OPTICS LETTERS, vol. 36, no. 16, pp. 3257-3259.
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Degenerate band edges (DBEs) of a photonic bandgap have the form (omega - omega(D)) proportional to k(2m) for integers m > 1, with omega(D) the frequency at the band edge. We show theoretically that DBEs lead to efficient coupling into slow-light modes without a transition region, and that the field strength in the slow mode can far exceed that in the incoming medium. A method is proposed to create a DBE of arbitrary order m by coupling m optical modes with multiple superimposed gratings. The enhanced coupling near a DBE occurs because of the presence of one or more evanescent modes, which are absent at conventional quadratic band edges. We furthermore show that the coupling can be increased or suppressed by varying the number of excited evanescent waves.

Hall, P, Ormerod, JT & Wand, MP 2011, 'Theory of Gaussian variational approximation for a Poisson mixed model', Statistica Sinica, vol. 21, no. 1, pp. 369-389.
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Likelihood-based inference for the parameters of generalized linear mixed models is hindered by the presence of intractable integrals. Gaussian variational approximation provides a fast and effective means of approximate inference. We provide some theory for this type of approximation for a simple Poisson mixed model. In particular, we establish consistency at rate m -1/2 +n-1, where m is the number of groups and n is the number of repeated measurements.

Hamidian, M & Hall, RM 2011, 'AbaR4 replaces AbaR3 in a carbapenem-resistant Acinetobacter baumannii isolate belonging to global clone 1 from an Australian hospital', Journal of Antimicrobial Chemotherapy, vol. 66, no. 11, pp. 2484-2491.
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Hamidian, M, Sanaei, M, Azimi-Rad, M, Tajbakhsh, M, Dabiri, H & Zali, M-R 2011, 'fla-typing, RAPD analysis, isolation rate and antimicrobial resistance profile of Campylobacter jejuni and Campylobacter coli of human origin collected from hospitals in Tehran, Iran', Annals of Microbiology, vol. 61, no. 2, pp. 315-321.
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Hamidian, M, Sanaei, M, Bolfion, M, Dabiri, H, Zali, M-R & Walther-Rasmussen, J 2011, 'Prevalence of putative virulence markers inCampylobacter jejuniandCampylobacter coliisolated from hospitalized children, raw chicken, and raw beef in Tehran, Iran', Canadian Journal of Microbiology, vol. 57, no. 2, pp. 143-148.
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The incidence of the virulence-associated genes cdtA, cdtB, cdtC, cadF, dnaJ, racR, and pldA has been investigated in Campylobacter jejuni and Campylobacter coli collected from raw chicken and beef from retailers in Tehran, Iran, and from hospitalized children (age, ≤14 years) suffering from diarrhea. Campylobacter spp. were collectively identified by morphological and biochemical methods. Campylobacter jejuni and C. coli were discriminated from other Campylobacter spp. by amplification of a specific conserved fragment of the 16S rRNA gene. The distinction between C. jejuni and C. coli was subsequently made by molecular determination of the presence of the hipO gene in C. jejuni or the ask gene in C. coli. Fragments of the studied virulence-associated genes, cdtA, cdtB, cdtC, cadF, racR, dnaJ, and pldA, were amplified by PCR and subjected to horizontal gel electrophoresis. A total of 71 isolates of C. jejuni and 24 isolates of C. coli from meat were analyzed, while the numbers of isolates from the hospitalized children were 28 and 9, respectively. The unequal distribution of C. jejuni and C. coli in the samples has also been reported in other studies. Statistical analyses by the use of the two-tailed Fisher’s exact test of the occurrence of the virulence genes in the isolates of different origins showed that the occurrence of the dnaJ gene was consistently significantly higher in all C. jejuni isolates than in C. coli. The occurrence of the other virulence markers did not differ significantly between species in the majority of the isolates. The PCR results also showed that the occurrence of the virulence markers in the analyzed isolates was much lower than in other studies, which may be caused by a divergent genomic pool of our isolates in comparison with others.

Hamidian, M, Tajbakhsh, M, Tohidpour, A, Rahbar, M, Zali, MR & Walther-Rasmussen, J 2011, 'Detection of novel gyrA mutations in nalidixic acid-resistant isolates of Salmonella enterica from patients with diarrhoea', International Journal of Antimicrobial Agents, vol. 37, no. 4, pp. 360-364.
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Hansbro, PM, Kaiko, GE & Foster, PS 2011, 'Cytokine/anti‐cytokine therapy – novel treatments for asthma?', British Journal of Pharmacology, vol. 163, no. 1, pp. 81-95.
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Asthma is a chronic inflammatory disease of the airways and there are no preventions or cures. Inflammatory cells through the secretion of cytokines and pro‐inflammatory molecules are thought to play a critical role in pathogenesis. Type 2 CD4+ lymphocytes (Th2 cells) and their cytokines predominate in mild to moderate allergic asthma, whereas severe steroid‐resistant asthma has more of a mixed Th2/Th1 phenotype with a Th17 component. Other immune cells, particularly neutrophils, macrophages and dendritic cells, as well structural cells such as epithelial and airway smooth muscle cells also produce disease‐associated cytokines in asthma. Increased levels of these immune cells and cytokines have been identified in clinical samples and their potential role in disease demonstrated in studies using mouse models of asthma. Clinical trials with inhibitors of cytokines such as interleukin (IL)‐4, ‐5 and tumour necrosis factor‐α have had success in some studies but not others. This may reflect the design of the clinical trials, including treatments regimes and the patient population included in these studies. IL‐13, ‐9 and granulocyte‐macrophage colony‐stimulating factor are currently being evaluated in clinical trials or preclinically and the outcome of these studies is eagerly awaited. Roles for IL‐25, ‐33, thymic stromal lymphopoietin, interferon‐γ, IL‐17 and ‐27 in the regulation of asthma are just emerging, identifying new ways to treat inflammation. Careful interpretation of results from mouse studies will inform the development and application of therapeutic approaches for asthma. The most effective approaches may be combination therapies that suppress multiple cytokines and a range of redundant and disconnected pathways that separately contribute to asthma pathogenesis. Astute application of these approaches may eventually lead to the development of effective asthma therapeutics. Here we review the current state of knowledge in the fi...

Hare, D, Austin, C, Doble, P & Arora, M 2011, 'Elemental bio-imaging of trace elements in teeth using laser ablation-inductively coupled plasma-mass spectrometry', JOURNAL OF DENTISTRY, vol. 39, no. 5, pp. 397-403.
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Objectives: In this study we present the application of a novel laboratory method that employs laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to construct two-dimensional maps of trace elements in teeth. Methods: Teeth were secti

Hart, JE, Garshick, E, Dockery, DW, Smith, TJ, Ryan, L & Laden, F 2011, 'Long-Term Ambient Multipollutant Exposures and Mortality', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, vol. 183, no. 1, pp. 73-78.
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Rationale: Population-based studies have demonstrated associations between ambient air pollution exposures and mortality, but few have been able to adjust for occupational exposures. Additionally, two studies have observed higher risks in individuals with occupational dust, gas, or fume exposure. Objectives: We examined the association of ambient residential exposure to particulate matter less than 10 mm in diameter (PM10), particulate matter less than 2.5 mm in diameter (PM2.5), NO2, SO2, and mortality in 53,814 men in the U.S. trucking industry. Methods: Exposures for PM10, NO2, and SO2 at each residential address were assigned using models combining spatial smoothing and geographic covariates. PM2.5 exposures in 2000 were assigned from the nearest available monitor. Single and multipollutant Cox proportional hazard models were used to examine the association of an interquartile range (IQR) change (6 mg/m3 for PM10, 4 mg/m3 for PM2.5, 4ppb for SO2, and 8ppb for NO2) and the risk of all-cause and cause-specific mortality. Measurements and Main Results: An IQR change in ambient residential exposures to PM10 was associated with a 4.3% (95% confidence interval [CI], 1.17.7%) increased risk of all-cause mortality. The increase for an IQR change in SO2 was 6.9% (95% CI, 2.311.6%), for NO2 was8.2%(95%CI, 4.512.1%), andforPM2.5 was3.9%(95%CI, 1.06.9%). Elevated associations with cause-specific mortality (lung cancer, cardiovascular and respiratory disease) were observed for PM2.5, SO2, and NO2, but not PM10. None of the pollutants were confounded by occupational exposures. In multipollutant models, overall, the associations were attenuated, most strongly forPM10. In sensitivity analyses excluding long-haul drivers, who spend days away from home, larger hazard ratios were observed. Conclusions: In this population of men, residential ambient air pollution exposures were associated with mortality.

Hassler, CS, Djajadikarta, JR, Doblin, MA, Everett, JD & Thompson, PA 2011, 'Characterisation of water masses and phytoplankton nutrient limitation in the East Australian Current separation zone during spring 2008', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 58, no. 5, pp. 664-677.
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This study focuses on the comparison of oceanic and coastal cold-core eddies with inner-shelf and East Australian Current (EAC) waters at the time of the spring bloom (October 2008).

Haynes, CJE & Gale, PA 2011, 'Transmembrane anion transport by synthetic systems', Chemical Communications, vol. 47, no. 29, pp. 8203-8203.
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Hazlewood, LC, Wood, LG, Hansbro, PM & Foster, PS 2011, 'Dietary lycopene supplementation suppresses Th2 responses and lung eosinophilia in a mouse model of allergic asthma', The Journal of Nutritional Biochemistry, vol. 22, no. 1, pp. 95-100.
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He, L, Onaizi, SA, Dimitrijev-Dwyer, M, Malcolm, AS, Shen, H-H, Dong, C, Holt, SA, Thomas, RK & Middelberg, APJ 2011, 'Comparison of positional surfactant isomers for displacement of rubisco protein from the air–water interface', Journal of Colloid and Interface Science, vol. 360, no. 2, pp. 617-622.
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Heine, KB, Clegg, JK, Heine, A, Gloe, K, Gloe, K, Henle, T, Bernhard, G, Cai, Z-L, Reimers, JR, Lindoy, LF, Lach, J & Kersting, B 2011, 'Complexation, Computational, Magnetic, and Structural Studies of the Maillard Reaction Product Isomaltol Including Investigation of an Uncommon pi Interaction with Copper(II)', INORGANIC CHEMISTRY, vol. 50, no. 4, pp. 1498-1505.
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Helliwell, CA, Robertson, M, Finnegan, EJ, Buzas, DM & Dennis, ES 2011, 'Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts', PLOS ONE, vol. 6, no. 6.
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The repression of Arabidopsis FLC expression by vernalization (extended cold) has become a model for understanding polycomb-associated epigenetic regulation in plants. Antisense and sense non-coding RNAs have been respectively implicated in initiation an

Hempel, C, Combes, V, Hunt, NH, Kurtzhals, JAL & Grau, GER 2011, 'CNS Hypoxia Is More Pronounced in Murine Cerebral than Noncerebral Malaria and Is Reversed by Erythropoietin', The American Journal of Pathology, vol. 179, no. 4, pp. 1939-1950.
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Henderson, MR, Gibson, BC, Ebendorff-Heidepriem, H, Kuan, K, Afshar V., S, Orwa, JO, Aharonovich, I, Tomljenovic-Hanic, S, Greentree, AD, Prawer, S & Monro, TM 2011, 'Hybrid Materials: Diamond in Tellurite Glass: a New Medium for Quantum Information (Adv. Mater. 25/2011)', Advanced Materials, vol. 23, no. 25, pp. 2772-2772.
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Henderson, MR, Gibson, BC, Ebendorff-Heidepriem, H, Kuan, K, Afshar, SV, Orwa, JO, Aharonovich, I, Tomljenovic-Hanic, S, Greentree, AD, Prawer, S & Monro, TM 2011, 'Diamond in Tellurite Glass: a New Medium for Quantum Information', ADVANCED MATERIALS, vol. 23, no. 25, pp. 2806-+.
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Nitrogen-vacancy (NV) centers in diamond exhibit unique quantum properties. On page 2806, Matthew R. Henderson and co-workers describe integrated diamond nanocrystals containing NV centers with an optical medium, tellurite soft glass. The inside cover image shows an example of a confocal scan of an optical fiber drawn from this material, detecting the photoluminescence from NV centers, with a conceptual image of a scan in progress.

Hill, F, Kim, CF, Gorrie, CA & Moalem-Taylor, G 2011, 'Interleukin-17 deficiency improves locomotor recovery and tissue sparing after spinal cord contusion injury in mice', NEUROSCIENCE LETTERS, vol. 487, no. 3, pp. 363-367.
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Following the initial impact, spinal cord injury (SCI) triggers a number of inflammatory responses which can exacerbate tissue damage in the cord and impair functional recovery. The involvement of several pro-inflammatory cytokines in the secondary degenerative mechanisms of SCI has been well established, although the role of interleukin-17 (IL-17) remains unclear. In the present study, we used IL-17 knockout (KO) and C57BL/6J wildtype (WT) mice to investigate the effects of IL-17 deficiency on locomotor recovery, lesion size, glial activation and inflammatory cell response following spinal cord contusion injury. Our results show that compared to WT mice, IL-17 KO mice had a significantly smaller lesion size, corresponding with significantly improved locomotor functional recovery following SCI. At 6 weeks after injury, recruitment of B cells, dendritic cells and neutrophils was significantly lower in IL-17 KO than WT mice, however there was no difference in the presence of activated microglia and reactive astrocytes, in the injured spinal cord. These findings suggest that IL-17 is a mediator of secondary degeneration, which contributes to neuroinflammation and hinders functional recovery, though its actions do not affect glial activation following SCI.

Hill, R, Brown, CM, DeZeeuw, K, Campbell, DA & Ralph, PJ 2011, 'Increased rate of D1 repair in coral symbionts during bleaching is insufficient to counter accelerated photo-inactivation', LIMNOLOGY AND OCEANOGRAPHY, vol. 56, no. 1, pp. 139-146.
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We dissect the primary photo-inactivation and the counteracting metabolic repair rates in fragments of the scleractinian coral, Pocillopora damicornis, subjected to a combined stress of a shift to elevated temperature (from 26 degrees C to 32 degrees C) and increased light (from 200 mu mol photons m(-2) s(-1) to 400 mmol photons m(-2) s(-1)) to induce bleaching. During the bleaching treatment the dinoflagellate symbionts showed a 5.5-fold acceleration in their photosystem II (PSII) repair rate constant, demonstrating that they maintain strong metabolic capacity to clear and replace photo-damaged D1 protein at the elevated temperature and light conditions. Nevertheless, the symbionts concurrently suffered a seven-fold increase in the rate constant for PSII photo-inactivation. This rapid photo-inactivation exceeded the PSII repair capacity, therefore tipping the symbionts, and by implication the symbiosis, into net photo-inhibition. Increased photo-inactivation in hospite, rather than an inhibition of PSII repair, is the principle trigger for net photo-inhibition under bleaching conditions.

Hisano, M, Connolly, SR & Robbins, WD 2011, 'Population Growth Rates of Reef Sharks with and without Fishing on the Great Barrier Reef: Robust Estimation with Multiple Models', PLoS ONE, vol. 6, no. 9, pp. e25028-e25028.
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Hoeksema, BW & Matthews, JL 2011, 'Contrasting bleaching patterns in mushroom coral assemblages at Koh Tao, Gulf of Thailand', Coral Reefs, vol. 30, no. 1, pp. 95-95.
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Hoile, R, Banos, C, Colella, M & Roux, C 2011, 'Bioterrorism: The effects of biological decontamination on the recovery of electronic evidence', FORENSIC SCIENCE INTERNATIONAL, vol. 209, no. 1-3, pp. 143-148.
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The investigation of a bioterrorism event will ultimately lead to the collection of vital data from electronic devices such as computers and mobile phones. This project sought to determine the use of gamma irradiation and formaldehyde gas as effective biological decontaminants, and the effect of these methods on the recovery of electronic evidence. Electronic items were contaminated with viable spores and then exposed to both decontaminants. Log values for each matrix were calculated with flash drives recording the highest value of 566 Gy for gamma irradiation and a maximum of 50 min exposure to formaldehyde saw the effective destruction of spores. The results indicate that recovery of data varied based on the decontaminant selected, formaldehyde gas giving the most promising results, with electronic data recovered after the required exposure time. Gamma irradiation proved damaging to electronic circuitry at levels required to render the items safe. The implications to computer intelligence and forensics will be discussed based on the outcomes of these findings.

Holt, S, Cordente, AG, Williams, SJ, Capone, DL, Jitjaroen, W, Menz, IR, Curtin, C & Anderson, PA 2011, 'Engineering Saccharomyces cerevisiae To Release 3-Mercaptohexan-1-ol during Fermentation through Overexpression of an S. cerevisiae Gene, STR3 , for Improvement of Wine Aroma', Applied and Environmental Microbiology, vol. 77, no. 11, pp. 3626-3632.
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ABSTRACT Sulfur-containing aroma compounds are key contributors to the flavor of a diverse range of foods and beverages. The tropical fruit characters of Vitis vinifera L. cv. Sauvignon blanc wines are attributed to the presence of the aromatic thiols 3-mercaptohexan-1-ol (3MH), 3-mercaptohexan-1-ol-acetate, and 4-mercapto-4-methylpentan-2-one (4MMP). These volatile thiols are found in small amounts in grape juice and are formed from nonvolatile cysteinylated precursors during fermentation. In this study, we overexpressed a Saccharomyces cerevisiae gene, STR3 , which led to an increase in 3MH release during fermentation of a V. vinifera L. cv. Sauvignon blanc juice. Characterization of the enzymatic properties of Str3p confirmed it to be a pyridoxal-5′-phosphate-dependent cystathionine β-lyase, and we demonstrated that this enzyme was able to cleave the cysteinylated precursors of 3MH and 4MMP to release the free thiols. These data provide direct evidence for a yeast enzyme able to release aromatic thiols in vitro that can be applied in the development of self-cloned yeast to enhance wine flavor.

Houck, MM, Robertson, J, Found, B, Kobus, H, Lewis, S, Raymond, M, Reedy, P, Ross, A, Roux, C & Vining, R 2011, 'A Round Table Discussion on Forensic Science in Australia', Forensic Science Policy & Management: An International Journal, vol. 2, no. 1, pp. 44-54.
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Hsu, AC-Y, Barr, I, Hansbro, PM & Wark, PA 2011, 'Human Influenza Is More Effective than Avian Influenza at Antiviral Suppression in Airway Cells', American Journal of Respiratory Cell and Molecular Biology, vol. 44, no. 6, pp. 906-913.
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Huston, WM, Gloeckl, S, de Boer, L, Beagley, KW & Timms, P 2011, 'Apoptosis is Induced in Chlamydia trachomatis-infected HEp-2 Cells by the Addition of a Combination Innate Immune Activation Compounds and the Inhibitor Wedelolactone', American Journal of Reproductive Immunology, vol. 65, no. 5, pp. 460-465.
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Huston, WM, Tyndall, JDA, Lott, WB, Stansfield, SH & Timms, P 2011, 'Unique Residues Involved in Activation of the Multitasking Protease/Chaperone HtrA from Chlamydia trachomatis', PLoS ONE, vol. 6, no. 9, pp. e24547-e24547.
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Hutchinson, AT, Alexova, R, Bockhorni, V, Ramsland, PA, Jones, DR, Jennings, CV, Broady, K, Edmundson, AB & Raison, RL 2011, 'Characterization of a unique conformational epitope on free immunoglobulin kappa light chains that is recognized by an antibody with therapeutic potential', MOLECULAR IMMUNOLOGY, vol. 48, no. 9-10, pp. 1245-1252.
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The murine mAb, K-1-21, recognizes a conformational epitope expressed on free Ig kappa light chains (FkLCs) and also on cell membrane-associated FkLCs found on kappa myeloma cells. This has led to the development of a chimeric version of K-1-21, MDX-1097, which is being assessed in a Phase II clinical trial for the treatment of multiple myeloma. The epitope recognized by K-1-21 is of particular interest, especially in the context that it is not expressed on heavy chain-associated light chains such as in an intact Ig molecule. Using epitope excision techniques we have localized the K-1-21 epitope to a region spanning residues 104-110 of FkLC. This short strand of residues links the variable and constant domains, and is a flexible region that adopts different conformations in FkLC and heavy chain-associated light chain. We tested this region using site-directed mutations and found that the reactivity of K-1-21 for FkLC was markedly reduced. Finally, we applied in silico molecular docking to generate a model that satisfied the experimental data. Given the clinical potential of the Ag, this study may aid the development of next generation compounds that target the membrane form of FkLC expressed on the surface of myeloma plasma cells.

Hwang, FJ & Lin, BMT 2011, 'Coupled-task scheduling on a single machine subject to a fixed-job-sequence', COMPUTERS & INDUSTRIAL ENGINEERING, vol. 60, no. 4, pp. 690-698.
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This paper investigates single-machine coupled-task scheduling where each job has two tasks separated by an exact delay. The objective of this study is to schedule the tasks to minimize the makespan subject to a given job sequence. We introduce several intriguing properties of the fixed-job-sequence problem under study. While the complexity status of the studied problem remains open, an O(n2) algorithm is proposed to construct a feasible schedule attaining the minimum makespan for a given permutation of 2n tasks abiding by the fixed-job-sequence constraint. We investigate several polynomially solvable cases of the fixed-job-sequence problem and present a complexity graph of the problem.

Idzik, KR, Cywinski, PJ, Cranfield, CG, Mohr, GJ & Beckert, R 2011, 'Molecular Recognition of the Antiretroviral Drug Abacavir: Towards the Development of a Novel Carbazole-Based Fluorosensor', JOURNAL OF FLUORESCENCE, vol. 21, no. 3, pp. 1195-1204.
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Due to their optical and electro-conductive attributes, carbazole derivatives are interesting materials for a large range of biosensor applications. In this study, we present the synthesis routes and fluorescence evaluation of newly designed carbazole fluorosensors that, by modification with uracil, have a special affinity for antiretroviral drugs via either WatsonCrick or Hoogsteen base pairing. To an N-octylcarbazole-uracil compound, four different groups were attached, namely thiophene, furane, ethylenedioxythiophene, and another uracil; yielding four different derivatives. Photophysical properties of these newly obtained derivatives are described, as are their interactions with the reverse transcriptase inhibitors such as abacavir, zidovudine, lamivudine and didanosine. The influence of each analyte on biosensor fluorescence was assessed on the basis of the SternVolmer equation and represented by SternVolmer constants. Consequently we have demonstrated that these structures based on carbazole, with a uracil group, may be successfully incorporated into alternative carbazole derivatives to form biosensors for the molecular recognition of antiretroviral drugs.

Ip, KH, Stuart, B, Ray, A & Thomas, P 2011, 'ESEM-EDS Investigation of the Weathering of a Heritage Sydney Sandstone', Microscopy and Microanalysis, vol. 17, no. 2, pp. 292-295.
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AbstractThe degradation of Sydney sandstone used to build the heritage St Mary's Cathedral in Sydney, Australia, has been investigated using environmental scanning electron microscopy combined with energy dispersive X-ray spectroscopy. This technique provided the structural details of the cementing clay and an elemental characterization the sandstone. The observed differences in the elemental composition of the unweathered and weathered sandstones were associated with changes to the clay microstructure upon weathering. The results support the substitution theory that Fe3+ replaces Al3+ in the kaolinite clay component upon weathering. An examination of the impurities present prior to a nonstructural iron removal treatment revealed the presence of minerals that may provide a source of the elements responsible for the substitution process.

Ip, KH, Stuart, BH, Thomas, PS & Ray, A 2011, 'Characterisation of poly(vinyl alcohol)-montmorillonite composites with higher clay contents', POLYMER TESTING, vol. 30, no. 7, pp. 732-736.
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Polymer composites comprised of poly(vinyl alcohol) and montmorillonite with higher clay loadings have been prepared and characterised. The extent of intercalation in the composites was examined over a range of compositions using scanning electron microscopy energy dispersive spectroscopy and x-ray diffraction. The incorporation of an acidification step followed by washing the clay results in a homogenous polymer-clay film. The source of montmorillonite was found to have an effect on the morphology of the clay in the resulting composite. Montmorillonite was obtained from two sources and different clay structures within the polymer clay composites were identified in each case, indicating that the choice of clay is an important consideration when producing poly(vinyl alcohol) montmorillonite composites with higher clay content.

Jain, P 2011, 'Antibacterial and antioxidant activities of local seeded banana fruits', African Journal of Pharmacy and Pharmacology, vol. 5, no. 11, pp. 1398-1403.
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Jambou, R, El-Assaad, F, Combes, V & Grau, GE 2011, 'In vitro culture of Plasmodium berghei-ANKA maintains infectivity of mouse erythrocytes inducing cerebral malaria', Malaria Journal, vol. 10, no. 1.
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James, M, Nelson, A, Holt, SA, Saerbeck, T, Hamilton, WA & Klose, F 2011, 'The multipurpose time-of-flight neutron reflectometer “Platypus” at Australia's OPAL reactor', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, vol. 632, no. 1, pp. 112-123.
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Jamieson, A, Bader, S, Meakin, G & Mullen, C 2011, 'Two-, three-, and four-person mixtures in forensic casework: difficulties and questions', Croatian Medical Journal, vol. 52, no. 5, pp. 653-654.
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Jamting, AK, Cullen, J, Coleman, VA, Lawn, M, Herrmann, J, Miles, J & Ford, MJ 2011, 'Systematic study of bimodal suspensions of latex nanoparticles using dynamic light scattering', ADVANCED POWDER TECHNOLOGY, vol. 22, no. 2, pp. 290-293.
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Determining the size of nanoparticles accurately, quickly and easily is becoming more and more important as the use of such particles increases. One of the common techniques for measuring the size of particles in suspension is dynamic light scattering (D

Jeffries, TC, Seymour, JR, Gilbert, JA, Dinsdale, EA, Newton, K, Leterme, SSC, Roudnew, B, Smith, RJ, Seuront, L & Mitchell, JG 2011, 'Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats', PLOS ONE, vol. 6, no. 9, pp. 1-9.
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Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.

Jennings, PC, Cox, GC, Monahan, LG & Harry, EJ 2011, 'Super-resolution imaging of the bacterial cytokinetic protein FtsZ', MICRON, vol. 42, no. 4, pp. 336-341.
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The idea of a bacterial cytoskeleton arose just 10 years ago with the identification of the cell division protein, FtsZ, as a tubulin homolog. Fts,Z plays a pivotal role in bacterial division, and is present in virtually all prokaryotes and in some eukaryotic organelles. The earliest stage of bacterial cell division is the assembly of FtsZ into a Z ring at the -division site, which subsequently constricts during cytokinesis. FtsZ also assembles into dynamic helical structures along the bacterial ceil, which are thought to act as precursors to the Z fing via a cell-cycle-mediated FtsZ polymer remodelling. The fine structures of the FtsZ helix and ring are unknown but crucial for identifying the molecular details of Z ring assembly and its regulation. We now reveal, using STED microscopy that the FtsZ helical structure in cells of the gram positive bacterium, Bacillus subtilis, is a highly irregular and discontinuous helix of FtsZ; very different to the smooth cable-like appearance observed by conventional fluorescence optics. STED also identifies a novel FtsZ helical structure of smaJ!er pitch that is invisible to standard optical methods, identifying a possible third intermediate in the pathway to Z ring assembly, which commits bacterial cells to divide.

Jennings, PC, Merriman, JA, Beckett, EL, Hansbro, PM & Jones, KT 2011, 'Increased zona pellucida thickness and meiotic spindle disruption in oocytes from cigarette smoking mice', Human Reproduction, vol. 26, no. 4, pp. 878-884.
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Jimenez, IM, Kuhl, M, Larkum, AWD & Ralph, PJ 2011, 'Effects of flow and colony morphology on the thermal boundary layer of corals', JOURNAL OF THE ROYAL SOCIETY INTERFACE, vol. 8, no. 65, pp. 1785-1795.
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The thermal microenvironment of corals and the thermal effects of changing flow and radiation are critical to understanding heat-induced coral bleaching, a stress response resulting from the destruction of the symbiosis between corals and their photosynt

Jin, D 2011, 'Background-free Cytometry Using Rare Earth Complex Bioprobes', Methods in Cell Biology, vol. 102, pp. 479-513.
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In the analytical fields of microbiology, disease diagnosis, and antibioterrorism, there are increasing demands for rapid yet inexpensive quantification of rare cells. This has proven to be challenging by the conventional spectral discrimination of using traditional fluorescent probes, since the strong autofluorescence from background cells or particles overlaps spectrally with the probe fluorescence. This is particularly true when the target cell occurs at very low frequency (one in more than 100,000 background cells) representing a needle-in-a-haystack problem. This chapter describes a low-cost solution to overcome this problem by employing a novel detection technology, namely the use of rare-earth (lanthanide) complex bioprobes with luminescence lifetimes in the hundreds of microseconds. Due to this long persistence in lifetime, microsecond duration luminescence can be detected under conditions where fluorescent backgrounds would overwhelm the emission of conventional fluorochromes. The nanosecond duration autofluorescence associated with cells can be suppressed by time-gated detection, allowing detection of long lifetime lanthanide-based bioprobes with minimal background interference. This technology is applicable to a broad range of detection technologies in both cytometry and imaging. In this chapter, we highlight a typical application in the monitoring of the rare microbial pathogens Cryptosporidium parvum and Giardia lamblia against the complex background of concentrated drinking water. We also describe recent nanotechnological developments in the production of rare-earth nanoparticle bioprobes required for this technology. Other applications of rare-earth bioprobes and time-gated flow cytometry will also be discussed.

Jin, D 2011, 'Demonstration of true‐color high‐contrast microorganism imaging for terbium bioprobes', Cytometry Part A, vol. 79A, no. 5, pp. 392-397.
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AbstractLanthanide bioprobes offer a number of novel advantages for advanced cytometry, including the microsecond luminescence lifetime, sharp spectral emission, and large stokes shift. However, to date, only the europium‐based bioprobes have been broadly studied for time‐gated luminescence cell imaging, though a wide range of efficient terbium bioprobes have been synthesized and some of them are commercially available. We analyze that the bottleneck problem was due to the lack of an efficient microscope with pulsed excitation at wavelengths of 300–330 nm. We investigate a recently available 315 nm ultraviolet (UV) light emitting diode to excite an epifluorescence microscope. Substituting a commercial UV objective (40×), the 315 nm light efficiently delivered the excitation light onto the uncovered specimen. A novel pinhole‐assisted optical chopper unit was attached behind the eyepiece for direct lifetime‐gating to permit visual inspection of background‐free images. We demonstrate the use of a commercial terbium complex for high‐contrast imaging of an environmental pathogenic microorganism, Cryptosporidium parvum. As a result of effective autofluorescence suppression by a factor of 61.85 in the time domain, we achieved an enhanced signal‐to‐background ratio of 14.43. This type of time‐gating optics is easily adaptable to the use of routine epifluorescence microscopes, which provides an opportunity for high‐contrast imaging using multiplexed lanthanide bioprobes. © 2011 International Society for Advancement of Cytometry

Jin, D & Piper, JA 2011, 'Time-Gated Luminescence Microscopy Allowing Direct Visual Inspection of Lanthanide-Stained Microorganisms in Background-Free Condition', Analytical Chemistry, vol. 83, no. 6, pp. 2294-2300.
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Jones, PM & George, AM 2011, 'Molecular-Dynamics Simulations of the ATP/apo State of a Multidrug ATP-Binding Cassette Transporter Provide a Structural and Mechanistic Basis for the Asymmetric Occluded State', Biophysical Journal, vol. 100, no. 12, pp. 3025-3034.
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ATP-binding cassette transporters use the energy of ATP hydrolysis to transport substrates across cellular membranes. They have two transmembrane domains and two cytosolic nucleotide-binding domains.Biochemical studies have characterized an occluded state of the transporter in which nucleotide is tenaciously bound in one active site, whereas the opposite active site is empty or binds nucleotide loosely. Here, we report molecular-dynamics simulations of the bacterial multidrug ATP-binding cassette transporter Sav1866. In two simulations of the ATP/apo state, the empty site opened substantially by way of rotation of the nucleotide-binding domain (NBD) core subdomain, whereas the ATP-bound site remained occluded and intact. We correlate our findings with elastic network and molecular-dynamics simulation analyses of the 5av1866 NBD monomer, and with existing experimental data, to argue that the observed transition is physiological, and that the final structure observed in the ATP/apo simulations corresponds to the tight/loose state of the NBD dimer characterized experimentally..

Jones, PM, Robinson, MW, Dalton, JP & George, AM 2011, 'The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations', PLoS ONE, vol. 6, no. 12, pp. e28589-e28589.
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Malaria caused by several species of Plasmodium is major parasitic disease of humans, causing 1-3 million deaths worldwide annually. The widespread resistance of the human parasite to current drug therapies is of major concern making the identification of new drug targets urgent. While the parasite grows and multiplies inside the host erythrocyte it degrades the host cell hemoglobin and utilizes the released amino acids to synthesize its own proteins. The P. falciparum malarial M1 alanyl-aminopeptidase (PfA-M1) is an enzyme involved in the terminal stages of hemoglobin digestion and the generation of an amino acid pool within the parasite. The enzyme has been validated as a potential drug target since inhibitors of the enzyme block parasite growth in vitro and in vivo. In order to gain further understanding of this enzyme, molecular dynamics simulations using data from a recent crystal structure of PfA-M1 were performed. The results elucidate the pentahedral coordination of the catalytic Zn in these metallo-proteases and provide new insights into the roles of this cation and important active site residues in ligand binding and in the hydrolysis of the peptide bond. Based on the data, we propose a two-step catalytic mechanism, in which the conformation of the active site is altered between the Michaelis complex and the transition state. In addition, the simulations identify global changes in the protein in which conformational transitions in the catalytic domain are transmitted at the opening of the N-terminal 8 angstrom-long channel and at the opening of the 30 angstrom-long C-terminal internal chamber that facilitates entry of peptides to the active site and exit of released amino acids. The possible implications of these global changes with regard to enzyme function are discussed.

Julian, RD, Kelty, SF, Roux, C, Woodman, P, Robertson, J, Davey, A, Hayes, R, Margot, P, Ross, A, Sibly, H & White, R 2011, 'What is the value of forensic science? An overview of the effectiveness of forensic science in the Australian criminal justice system project', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 43, no. 4, pp. 217-229.
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Forensic science is increasingly relied upon by law enforcement to assist in solving crime and gaining convictions, and by the judicial system in the adjudication of specific criminal cases. However, the value of forensic science relative to the work involved and the outcome of cases has yet to be established in the Australian context. Previous research in this area has mainly focused on the science and technology, rather than examining how people can use forensic services/science to the best possible advantage to produce appropriate justice outcomes. This five-year project entails an investigation into the effectiveness of forensic science in police investigations and court trials. It aims to identify when, where and how forensic science can add value to criminal investigations, court trials and justice outcomes while ensuring the efficient use of available resources initially in the Victorian and the ACT criminal justice systems and ultimately across Australia and New Zealand. This paper provides an overview of the rationale and aims of the research project and discusses current work-in-progress.

Kabakova, IV, Grobnic, D, Mihailov, S, Mägi, EC, de Sterke, CM & Eggleton, BJ 2011, 'Bragg grating-based optical switching in a bismuth-oxide fiber with strong χ^(3)-nonlinearity', Optics Express, vol. 19, no. 7, pp. 5868-5868.
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Kan, DJ, Asatryan, AA, Poulton, CG, Dossou, KB & Botten, LC 2011, 'Modeling waveguides in photonic woodpiles using the fictitious source superposition method', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, vol. 28, no. 4, pp. 746-755.
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We extend the fictitious source superposition method in order to model linear defects in photonic woodpiles, and we use the method to model a waveguide that is created by changing either the radius or refractive index of a single rod of an infinite woodpile composed of chalcogenide glass cylinders. In one instance, a nearly constant dispersion was observed over a sizable kx interval, where kx is the Bloch vector in the waveguiding direction, making this a compelling geometry for slow-light waveguides. The principal advantage of the method is that it does not rely on a supercell, thus avoiding what is possibly the greatest source of inefficiency present in most of the other methods that are used for modeling these structures. Instead, the method proceeds by placing an artificial source inside each rod of the defect layer and then subsequently taking an appropriate field superposition to remove all but one of these sources. The remaining source can then be used to mimic the fields that would be produced by a defect rod.

Kan, DJ, Botten, LC, Poulton, CG, Asatryan, AA & Dossou, KB 2011, 'Semianalytical formulations for the surface modes of photonic woodpiles', PHYSICAL REVIEW A, vol. 84, no. 4, pp. 1-14.
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We have developed semianalytical methods that allow us to perform a comprehensive analysis of the surface modes of photonic woodpiles. The surface modes of both finite and semi-infinite woodpiles are characterized using transfer matrix and plane-wave matrix formulations, and, in the case of finite structures, we give a general analytical description of the "double-interface" modes, which propagate simultaneously along the top and bottom surfaces. We show that if the number of layers is even, then such modes will only exist for specific directions of the Brillouin zone. However, if the number of layers is odd, then every surface mode is a double-interface mode, and, in this case, the direction of propagation plays an important role in determining the coupling strength between the two surfaces: for certain directions, the coupling is negligible even when the number of layers is small. The dispersion curves of two different double-interface modes can anticross or be interwoven, depending on the symmetry of the modes. We also describe the conditions under which coupled surface modes will exist when two woodpiles are used to create a Fabry-Perot cavity.

Karagiannidis, LE, Gale, PA, Light, ME, Massi, M & Ogden, MI 2011, 'Further insight into the coordination of 2,5-dicarbothioamidopyrroles: the case of Cu and Co complexes', Dalton Transactions, vol. 40, no. 45, pp. 12097-12097.
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Kardaras, C & Platen, E 2011, 'On the semimartingale property of discounted asset-price processes', STOCHASTIC PROCESSES AND THEIR APPLICATIONS, vol. 121, no. 11, pp. 2678-2691.
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A financial market model where agents trade using realistic combinations of simple (i.e., finite combinations of buy-and-hold) no-short-sales strategies is considered. Minimal assumptions are made on the discounted asset-price process . in particular, the semimartingale property is not assumed. Via a natural market viability assumption, namely, absence of arbitrage of the first kind, we establish that discounted asset-prices have to be semimartingales. Our main result can also be regarded as reminiscent of the Fundamental Theorem of Asset Pricing.

Keast, VJ, Birt, K, Koch, CT, Supansomboon, S & Cortie, MB 2011, 'The role of plasmons and interband transitions in the color of AuAl2, AuIn2, and AuGa2', APPLIED PHYSICS LETTERS, vol. 99, no. 11.
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Kelehear, C, Webb, JK, Hagman, M & Shine, R 2011, 'INTERACTIONS BETWEEN INFECTIVE HELMINTH LARVAE AND THEIR ANURAN HOSTS', HERPETOLOGICA, vol. 67, no. 4, pp. 378-385.
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Detailed observations on interactions between parasites and prospective hosts during the infection process can clarify (1) the routes by which parasites enter the host and (2) the ability of prospective hosts to detect, avoid, or resist potential parasites. Such information can clarify determinants of host vulnerability. Infective larvae of the nematode Rhabdias pseudosphaerocephala entered the bodies of their anuran host the Cane Toad (Rhinella marina, formerly Bufo marinus) primarily through the orbit (i.e., by crawling over the surface of the toad's eye) rather than by burrowing through the skin (believed to be the usual route of infection for rhabditid parasites). In our experimental infections, metamorph Cane Toads detected infective R. pseudosphaerocephala larvae but did not avoid them, nor did they manage to restrict rates of infective larvae penetration by using behavioral means (the toads kicked at infective larvae but failed to dislodge them). Rhabdias pseudosphaerocephala cause damage to their toad host during the process of host entry and throughout the ensuing infection. Despite the high cost of infection and the low cost of avoidance, metamorph Cane Toads seem to lack effective parasite avoidance strategies.

Kendall, E, Sunderland, N, Barnett, L, Nalder, G & Matthews, C 2011, 'Beyond the Rhetoric of Participatory Research in Indigenous Communities', Qualitative Health Research, vol. 21, no. 12, pp. 1719-1728.
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Evidence-based approaches to health care have been difficult to achieve in Indigenous populations across the world, a situation which has contributed to the significant health disparities found in this group. One reason for the inadequacy of evidence-based health interventions is that empirical knowledge tends to be organized around professional disciplines that are grounded in Western ways of knowing. In this article we describe events that have led to more appropriate research methods in Australia, and the resulting changes in the research community. The principles that have guided Australian research policy development might not yet be fully matured, but the improvements we have experienced over the last several decades have gone a long way toward acknowledging the significant disparities that affect Indigenous people and the role of researchers in addressing this issue.

Kerrison, P, Hall-Spencer, JM, Suggett, DJ, Hepburn, LJ & Steinke, M 2011, 'Assessment of pH variability at a coastal CO2 vent for ocean acidification studies', Estuarine, Coastal and Shelf Science, vol. 94, no. 2, pp. 129-137.
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Marine environments with naturally high CO2 concentrations have become important research sites for studying the impacts of future ocean acidification on biological processes. We conducted high temporal resolution pH and temperature measurements in and around a shallow (2.5-3 m) CO2 vent site off Ischia, Italy in May and June 2008. Loggers were deployed at five stations to monitor water at both the surface and benthos. Our reference station, 500 m from the CO2 vent, had no noticeable vent influence. It had a naturally high and stable benthic pH (mean 8.16, inter-quartile range (IQ): 8.14-8.18) fluctuating with diel periodicity, presumably driven by community photosynthesis and respiration. A principal component analysis (PCA) revealed that the pH of this station was well constrained by meteorological parameters. In contrast, a station positioned within the vent zone, had a low and very variable benthic mean pH of 7.11 (IQ: 6.91-7.62) with large pH fluctuations not well constrained by a PCA. Any stations positioned within 20 m of the main vent zone had lowered pH, but suffered from abnormally large pH fluctuations making them unsuitable representatives to predict future changes to a shallow coastal environment. Between these extremes, we identified a benthic area with a lower pH of 7.84 (IQ: 7.83-7.88) that retained many of the characteristics of the reference station such as a natural diel pH periodicity and low variability. Our results indicate that a range of pH environments maybe commonplace near CO2 vents due to their characteristic acidification of benthic water over a wide area. Such environments could become invaluable natural laboratories for ocean acidification research, closely mimicking future CO2 conditions in a natural setting

Khan, N-UH, Pandya, N, Maity, NC, Kumar, M, Patel, RM, Kureshy, RI, Abdi, SHR, Mishra, S, Das, S & Bajaj, HC 2011, 'Influence of chirality of V(V) Schiff base complexes on DNA, BSA binding and cleavage activity', European Journal of Medicinal Chemistry, vol. 46, no. 10, pp. 5074-5085.
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Kianinia, M, Ahadi, K & Nemati, A 2011, 'Investigation of dark and light conductivities in calcium doped bismuth ferrite thin films', MATERIALS LETTERS, vol. 65, no. 19-20, pp. 3086-3088.
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Kim, N-K, Lee, D-H, Seo, H-S, Sun, S-H, Oh, Y-L, Kim, J-E, Yoon, I-H, Seo, E-S, Shim, G-S & Zaslawski, C 2011, 'Hwangryunhaedoktang in adult patients with Atopic Dermatitis: a randomised, double-blind, placebo-controlled, two-centre trial - study protocol', BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE, vol. 11, no. 68, pp. 1-8.
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Background: Atopic Dermatitis is a chronic relapsing eczematous skin disease with increasing prevalence and rising costs. It has a clear impact on a patient's quality of life. Many patients are worried about the use of usual care techniques, such as cort

King, JS, Jenkins, DJ, Ellis, JT, Fleming, P, Windsor, PA & Slapeta, J 2011, 'Implications of wild dog ecology on the sylvatic and domestic life cycle of Neospora caninum in Australia', VETERINARY JOURNAL, vol. 188, no. 1, pp. 24-33.
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Neospora caninum is transmitted either transplacentally or horizontally by ingestion of tissue cysts present in tissues or oocysts shed by dogs. Neosporosis is a significant disease, causing cattle abortion at 5 7 months of pregnancy. Infected cows may remain infective for life transmitting the infection in several consecutive or non-consecutive pregnancies. A great deal is known about the epidemiology of neosporosis, although only limited information is available on the main routes of horizontal transmission. In Australia, the presence of the dingo as the top-order predator suggests a potential sylvatic route of transmission between dingoes and as yet unknown native wildlife in addition to the domestic route via dogs with access to infected tissue on farms. This review article critically evaluates the overlap between the domestic and sylvatic routes, taking into account canine ecology, and summarises current understanding of the transmission of N. caninum to provide a foundation for epidemiologists, farmers and conservation biologists dealing with neosporosis and wild dog control programs.

King, JS, McAllan, B, Spielman, DS, Lindsay, SA, Hurkova-Hofmannova, L, Hartigan, A, Al-Qassab, SE, Ellis, JT & Slapeta, J 2011, 'Extensive production of Neospora caninum tissue cysts in a carnivorous marsupial succumbing to experimental neosporosis', VETERINARY RESEARCH, vol. 42, no. 1, pp. 75-84.
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Experimental infections of Sminthopsis crassicaudata, the fat-tailed dunnart, a carnivorous marsupial widely distributed throughout the arid and semi-arid zones of Australia, show that this species can act as an intermediate host for Neospora caninum. In contrast to existing models that develop relatively few N. caninum tissue cysts, dunnarts offer a new animal model in which active neosporosis is dominated by tissue cyst production. The results provide evidence for a sylvatic life cycle of N. caninum in Australia between marsupials and wild dogs. It establishes the foundation for an investigation of the impact and costs of neosporosis to wildlife.

Kosakovsky Pond, SL, Murrell, B, Fourment, M, Frost, SDW, Delport, W & Scheffler, K 2011, 'A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection', Molecular Biology and Evolution, vol. 28, no. 11, pp. 3033-3043.
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Krimmer, DI & Oliver, BGG 2011, 'What can in vitro models of COPD tell us?', Pulmonary Pharmacology & Therapeutics, vol. 24, no. 5, pp. 471-477.
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Chronic obstructive pulmonary disease (COPD) is a progressive lung disease characterised by chronic bronchitis, largely irreversible remodelling of the small airways, and emphysematous destruction of the alveoli. COPD is projected to be the third leading cause of death worldwide by 2020. COPD often results from prolonged exposure to irritants such as cigarette smoke or inhaled particulates. Current pharmacotherapies for COPD are unable to reverse the pathological changes of this disease, and this is partially due to a limited understanding of the intricate mechanisms by which chronic exposure lead to the different pathological components of COPD. This review examines how the mechanisms that underlie various components of COPD can be modelled in vitro, specifically using cigarette smoke extract with cells cultured from primary human lung tissue, and how the effectiveness of current and novel pharmacotherapies on successfully attenuating these pathological changes can also be examined in vitro.

Krimmer, DI, Burgess, JK, Black, JL & Oliver, BG 2011, 'Exposure To Biomass Smoke Extract Enhances Fibronectin Release From Human Lung Fibroblasts', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, vol. 183, no. 12.
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COPD induced following biomass smoke exposure has been reported to be associated with a more fibrotic phenotype than cigarette smoke induced COPD. This study aimed to investigate if biomass smoke induced extracellular matrix (ECM) protein production from

Kukush, A, Shklyar, S, Masiuk, S, Likhtarov, I, Kovgan, L, Carroll, RJ & Bouville, A 2011, 'Methods for estimation of radiation risk in epidemiological studies accounting for classical and Berkson errors in doses.', Int J Biostat, vol. 7, no. 1, p. 15.
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With a binary response Y, the dose-response model under consideration is logistic in flavor with pr(Y=1 | D) = R (1+R)(-1), R = λ(0) + EAR D, where λ(0) is the baseline incidence rate and EAR is the excess absolute risk per gray. The calculated thyroid dose of a person i is expressed as Dimes=fiQi(mes)/Mi(mes). Here, Qi(mes) is the measured content of radioiodine in the thyroid gland of person i at time t(mes), Mi(mes) is the estimate of the thyroid mass, and f(i) is the normalizing multiplier. The Q(i) and M(i) are measured with multiplicative errors Vi(Q) and ViM, so that Qi(mes)=Qi(tr)Vi(Q) (this is classical measurement error model) and Mi(tr)=Mi(mes)Vi(M) (this is Berkson measurement error model). Here, Qi(tr) is the true content of radioactivity in the thyroid gland, and Mi(tr) is the true value of the thyroid mass. The error in f(i) is much smaller than the errors in ( Qi(mes), Mi(mes)) and ignored in the analysis. By means of Parametric Full Maximum Likelihood and Regression Calibration (under the assumption that the data set of true doses has lognormal distribution), Nonparametric Full Maximum Likelihood, Nonparametric Regression Calibration, and by properly tuned SIMEX method we study the influence of measurement errors in thyroid dose on the estimates of λ(0) and EAR. The simulation study is presented based on a real sample from the epidemiological studies. The doses were reconstructed in the framework of the Ukrainian-American project on the investigation of Post-Chernobyl thyroid cancers in Ukraine, and the underlying subpolulation was artificially enlarged in order to increase the statistical power. The true risk parameters were given by the values to earlier epidemiological studies, and then the binary response was simulated according to the dose-response model.

Kumar, M, Gupta, V, Kumari, P, Reddy, CRK & Jha, B 2011, 'Assessment of nutrient composition and antioxidant potential of Caulerpaceae seaweeds', Journal of Food Composition and Analysis, vol. 24, no. 2, pp. 270-278.
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Abstract The proximate nutrient composition, mineral contents, enzymatic and non-enzymatic antioxidant potential of three Caulerpa species were investigated. All three species were high in ash (24.20–33.70%) and carbohydrate content (37.23–48.95%) on dry weight basis (DW). The lipid content ranged between 2.64 and 3.06% DW. The mineral contents varied marginally among the species but were in the order of Na > K > Ca > Mg. The Na/K ratio among the species varied from 1.80 to 2.55 and was lowest in C. scalpelliformis. A 10 g DW of Caulerpa powder contains 11–21% Fe, 52–60% Ca and 35–43% Mg, which is higher than the recommended daily allowance (RDA), compared with non-seafood. The percentage sum of PUFAs (C18:2, C18:3, C20:4 and C20:5) in total fatty acids was highest in both C. scalpelliformis (39.25%) and C. veravelensis (36.73%) while it was the lowest in C. racemosa (24.50%). The n−6/n−3 ratio among the species varied from 1.44 to 7.72 and remained within the prescribed WHO standards (<10). Further, the higher enzymatic dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) and non-enzymatic antioxidant potential of Caulerpa species found in the present study confirm their usefulness in terms of nutrients and antioxidants.

Kumar, M, Gupta, V, Trivedi, N, Kumari, P, Bijo, AJ, Reddy, CRK & Jha, B 2011, 'Desiccation induced oxidative stress and its biochemical responses in intertidal red alga Gracilaria corticata (Gracilariales, Rhodophyta)', Environmental and Experimental Botany, vol. 72, no. 2, pp. 194-201.
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Kumar, M, Kumari, P, Trivedi, N, Shukla, MK, Gupta, V, Reddy, CRK & Jha, B 2011, 'Minerals, PUFAs and antioxidant properties of some tropical seaweeds from Saurashtra coast of India', Journal of Applied Phycology, vol. 23, no. 5, pp. 797-810.
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Abstract Twenty-two tropical seaweeds from the Rhodophyta, Phaeophyta and Chlorophyta were examined for their possible use as nutritional supplements. All seaweeds contained balanced Na/K and C/N ratio and high amounts of macroelements (Na, K, Ca, and Mg) as compared to the terrestrial vegetables. Among the microelements, Fe was the highest followed by Zn, Mn, Cu and other trace elements. Fatty acid distribution showed high level of n-6 and n-3 polyunsaturated fatty acids (PUFAs), and their ratios were within the WHO prescribed limits. The higher ratios of PUFA/SFA (>0.4) are in agreement with the recommendations of nutritional guidelines. Most of the species, especially the Chlorophyta and Phaeophyta, had permissible intake values of unsaturation, atherogenic and thrombogenic indexes comparable to milk-based products. Principal component analysis demonstrated a correlation between total phenolic content, total antioxidant activity, DPPH, and O 2 •− radical scavenging activity, suggesting polyphenols as the chief contributor to the antioxidant activity in seaweeds. These results indicate that these seaweeds could be a potential source of natural antioxidants, minerals and high-quality PUFAs and may be efficiently used as ingredients in functional foods.

Kumar, M, Trivedi, N, Reddy, CRK & Jha, B 2011, 'Toxic Effects of Imidazolium Ionic Liquids on the Green Seaweed Ulva lactuca: Oxidative Stress and DNA Damage', Chemical Research in Toxicology, vol. 24, no. 11, pp. 1882-1890.
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Kuo, C, Lim, S, King, NJC, Bartlett, NW, Walton, RP, Zhu, J, Glanville, N, Aniscenko, J, Johnston, SL, Burgess, JK, Black, JL & Oliver, BG 2011, 'Rhinovirus infection induces expression of airway remodelling factors in vitro and in vivo', RESPIROLOGY, vol. 16, no. 2, pp. 367-377.
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Background and objective: A hallmark of asthma is airway remodelling, which includes increased deposition of extracellular matrix (ECM) protein. Viral infections may promote the development of asthma and are the most common causes of asthma exacerbations

Kuo, C, Lim, S, King, NJC, Johnston, SL, Burgess, JK, Black, JL & Oliver, BG 2011, 'Rhinovirus infection induces extracellular matrix protein deposition in asthmatic and nonasthmatic airway smooth muscle cells', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 300, no. 6, pp. L951-L957.
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Airway remodeling, which includes increases in the extracellular matrix (ECM), is a characteristic feature of asthma and is correlated to disease severity. Rhinovirus (RV) infections are associated with increased risk of asthma development in young children and are the most common cause of asthma exacerbations. We examined whether viral infections can increase ECM deposition and whether this increased ECM modulates cell proliferation and migration. RV infection of nonasthmatic airway smooth muscle (ASM) cells significantly increased the deposition of fibronectin (40% increase, n = 12) and perlecan (80% increase, n = 14), while infection of asthmatic ASM cells significantly increased fibronectin (75% increase, n = 9) and collagen IV (15% increase, n = 9). We then treated the ASM cells with the Toll-like receptor (TLR) agonists polyinosinic:polycytidylic acid, imiquimod, and pure RV RNA and were able to show that the mechanism through which RV induced ECM deposition was via the activation of TLR3 and TLR7/8. Finally, we assessed whether the virus-induced ECM was bioactive by measuring the amount of migration and proliferation of virus-naive cells that seeded onto the ECM. Basically, ECM from asthmatic ASM cells induced twofold greater migration of virus-naive ASM cells than ECM from nonasthmatic ASM cells, and these rates of migration were further increased on RV-modulated ECM. Increased migration on the RV-modulated ECM was not due to increased cell proliferation, as RV-modulated ECM decreased the proliferation of virus-naive cells. Our results suggest that viruses may contribute to airway remodeling through increased ECM deposition, which in turn may contribute to increased ASM mass via increased cell migration.

Labbate, M, Boucher, Y, Chowdhury, PR & Stokes, HW 2011, 'Integration of a laterally acquired gene into a cell network important for growth in a strain of Vibrio rotiferianus', BMC Microbiology, vol. 11, no. 1, p. 253.
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Abstract Background Lateral Gene Transfer (LGT) is a major contributor to bacterial evolution and up to 25% of a bacterium's genome may have been acquired by this process over evolutionary periods of time. Successful LGT requires both the physical transfer of DNA and its successful incorporation into the host cell. One system that contributes to this latter step by site-specific recombination is the integron. Integrons are found in many diverse bacterial Genera and is a genetic system ubiquitous in vibrios that captures mobile DNA at a dedicated site. The presence of integron-associated genes, contained within units of mobile DNA called gene cassettes makes up a substantial component of the vibrio genome (1-3%). Little is known about the role of this system since the vast majority of genes in vibrio arrays are highly novel and functions cannot be ascribed. It is generally regarded that strain-specific mobile genes cannot be readily integrated into the cellular machinery since any perturbation of core metabolism is likely to result in a loss of fitness. Results In this study, at least one mobile gene contained within the Vibrio rotiferianus strain DAT722, but lacking close relatives elsewhere, is shown to greatly reduce host fitness when deleted and tested in growth assays. The precise role of the mobile gene product is unknown but impacts on the regulation of outermembrane porins. This demonstrates that strain specific laterally acquired mobile DNA can be integrated rapidly into bacterial networks such that it becomes advantageous for survival and adaptation in changing environments. Conclusions Mobile genes that are high...

Lapine, M, Shadrivov, IV, Powell, DA & Kivshar, YS 2011, 'Metamaterials with conformational nonlinearity', SCIENTIFIC REPORTS, vol. 1.
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Lapkiewicz, R, Li, P, Schaeff, C, Langford, NK, Ramelow, S, Wieśniak, M & Zeilinger, A 2011, 'Experimental non-classicality of an indivisible quantum system', Nature, vol. 474, no. 7352, pp. 490-493.
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Large, A, Brown, JJ, Abbott, O & Taylor, A 2011, 'Estimating and Correcting for Over-count in the 2011 Census', Survey Methodology Bulletin, vol. 69, pp. 35-49.
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This paper decscribes the proposed methodology for estimating and adjusting for over-count if it is found to be a significant issue in the 2011 Census. An approach to estimate over-count is developed, together with some indication of the sampling approach to be used. This estimated over-count is then used to develop an adjustment to the undercount estimation for the Census. This provides an adjustment of the Census estimates for undercount that is 'net' of estimated over-count. A simulation study is presented in order to verify the methodology and provide evidence to justify the implementation for the 2011 Census.

Larkum, AWD, Salih, A & Kuehl, M 2011, 'Rapid Mass Movement of Chloroplasts during Segment Formation of the Calcifying Siphonalean Green Alga, Halimeda macroloba', PLOS ONE, vol. 6, no. 7, pp. 1-9.
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Background: The calcifying siphonalean green alga, Halimeda macroloba is abundant on coral reefs and is important in the production of calcium carbonate sediments. The process by which new green segments are formed over-night is revealed here for the first time. Methodology/Principal Findings: Growth of new segments was visualised by epifluorescence and confocal microscopy and by pulse amplitude modulation (PAM) fluorimetry. Apical colourless proto-segments were initiated on day 1, and formed a loose network of non-calcified, non-septate filaments, containing no chloroplasts. Rapid greening was initiated at dusk by i) the mass movement of chloroplasts into these filaments from the parent segment and ii) the growth of new filaments containing chloroplasts. Greening was usually complete in 3-5 h and certainly before dawn on day 2 when the first signs of calcification were apparent. Mass chloroplast movement took place at a rate of 0.65 mm/s. Photosynthetic yield and rate remained low for a period of 1 to several hours, indicating that the chloroplasts were made de novo. Use of the inhibitors colchicine and cytochalasin d indicated that the movement process is dependent on both microtubules and microfilaments. Significance: This unusual process involves the mass movement of chloroplasts at a high rate into new segments during the night and rapid calcification on the following day and may be an adaptation to minimise the impact of herbivorous activity.

Lawrence, FJ, Botten, LC, Dossou, KB, McPhedran, RC & de Sterke, CM 2011, 'Erratum: Photonic-crystal surface modes found from impedances [Phys. Rev. A82, 053840 (2010)]', Physical Review A, vol. 83, no. 2.
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Lay, WCL, Zhang, Q, Zhang, J, McDougald, D, Tang, C, Wang, R, Liu, Y & Fane, AG 2011, 'Study of integration of forward osmosis and biological process: Membrane performance under elevated salt environment', Desalination, vol. 283, pp. 123-130.
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Le Brun, AP, Holt, SA, Shah, DSH, Majkrzak, CF & Lakey, JH 2011, 'The structural orientation of antibody layers bound to engineered biosensor surfaces', Biomaterials, vol. 32, no. 12, pp. 3303-3311.
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Le Brun, AP, Shah, DSH, Athey, D, Holt, SA & Lakey, JH 2011, 'Self-Assembly of Protein Monolayers Engineered for Improved Monoclonal Immunoglobulin G Binding', International Journal of Molecular Sciences, vol. 12, no. 8, pp. 5157-5167.
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Lee, KC, Sprague, MR, Sussman, BJ, Nunn, J, Langford, NK, Jin, X-M, Champion, T, Michelberger, P, Reim, KF, England, D, Jaksch, D & Walmsley, IA 2011, 'Entangling Macroscopic Diamonds at Room Temperature', Science, vol. 334, no. 6060, pp. 1253-1256.
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Optical pulses are used to quantum mechanically entangle two diamonds several centimeters apart.

Leigh, A, Zwieniecki, MA, Rockwell, FE, Boyce, CK, Nicotra, AB & Holbrook, NM 2011, 'Structural and hydraulic correlates of heterophylly in Ginkgo biloba', New Phytologist, vol. 189, no. 2, pp. 459-470.
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Summary This study investigates the functional significance of heterophylly in Ginkgo biloba, where leaves borne on short shoots are ontogenetically distinct from those on long shoots. Short shoots are compact, with minimal internodal elongation; their leaves are supplied with water through mature branches. Long shoots extend the canopy and have significant internodal elongation; their expanding leaves receive water from a shoot that is itself maturing. ⢠Morphology, stomatal traits, hydraulic architecture, Huber values, water transport efficiency, in situ gas exchange and laboratory-based steady-state hydraulic conductance were examined for each leaf type. ⢠Both structure and physiology differed markedly between the two leaf types. Short-shoot leaves were thinner and had higher vein density, lower stomatal pore index, smaller bundle sheath extensions and lower hydraulic conductance than long-shoot leaves. Long shoots had lower xylem area : leaf area ratios than short shoots during leaf expansion, but this ratio was reversed at shoot maturity. Longshoot leaves had higher rates of photosynthesis, stomatal conductance and transpiration than short-shoot leaves. ⢠We propose that structural differences between the two G. biloba leaf types reflect greater hydraulic limitation of long-shoot leaves during expansion. In turn, differences in physiological performance of short- and long-shoot leaves correspond to their distinct ontogeny and architecture.

Lem, LLC, Ton-That, C & Phillips, MR 2011, 'Distribution of visible luminescence centers in hydrogen-doped ZnO', JOURNAL OF MATERIALS RESEARCH, vol. 26, no. 23, pp. 2912-2915.
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ZnO crystals have been investigated by scanning cathodoluminescence microscopy and spectroscopy at 80 K following hydrogen incorporation by plasma exposure. The intensity of the ZnO near-band-edge ( NBE) emission is greatly enhanced while the defect-related green emission is quenched following plasma treatment. These effects are attributed to the passivation of zinc vacancies by hydrogen. The green and yellow intensities and their intensity ratios to the NBE vary with excitation depth for both undoped and H-doped ZnO crystals. The intensities of the green and yellow emissions exhibit sublinear dependencies on electron beam excitation density while the NBE intensity increases linearly with the excitation density. These saturation effects with increasing excitation density must be taken into account when assessing defects in ZnO by luminescence characterization.

Liang, D, Finnegan, EJ, Dennis, ES, Waterhouse, PM & Wang, M-B 2011, 'Mobile silencing in plants: what is the signal and what defines the target', Frontiers in Biology, vol. 6, no. 2, pp. 140-146.
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RNA-mediated silencing in plants can spread from cell to cell and over a long distance, and such mobile silencing has been extensively studied in the past decade. However, major questions remain as to what is the exact nature of the mobile silencing signals, how the components of the RNA-directed DNA methylation pathway are involved, and why systemic spread of silencing has only been observed for transgenes but not endogenous genes. In this review, we provide an overview of the current knowledge on mobile gene silencing in plants and present a model where systemic silencing involves long nuclear RNA transcripts that serve as a template to amplify primary siRNA signals. © Higher Education Press and Springer-Verlag Berlin Heidelberg 2011.

Liew, ATF, Theis, T, Jensen, SO, Garcia-Lara, J, Foster, SJ, Firth, N, Lewis, PJ & Harry, EJ 2011, 'A simple plasmid-based system that allows rapid generation of tightly controlled gene expression in Staphylococcus aureus', Microbiology, vol. 157, no. 3, pp. 666-676.
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We have established a plasmid-based system that enables tightly controlled gene expression and the generation of GFP fusion proteins in Staphylococcus aureus simply and rapidly. This system takes advantage of an Escherichia coli–S. aureus shuttle vector that contains the replication region of the S. aureus theta-mode multiresistance plasmid pSK41, and is therefore a stable low-copy-number plasmid in the latter organism. This vector also contains a multiple cloning site downstream of the IPTG-inducible Pspac promoter for insertion of the gene of interest. Production of encoded proteins can be stringently regulated in an IPTG-dependent manner by introducing a pE194-based plasmid, pGL485, carrying a constitutively expressed lacI gene. Using GFP fusions to two essential proteins of S. aureus, FtsZ and NusA, we showed that our plasmid allowed tightly controlled gene expression and accurate localization of fusion proteins with no detrimental effect on cells at low inducer concentrations. At higher IPTG concentrations, we obtained sixfold overproduction of protein compared with wild-type levels, with FtsZ–GFP-expressing cells showing lysis and delocalized fluorescence, while NusA–GFP showed only delocalized fluorescence. These results show that our system is capable of titratable induction of gene expression for localization or overexpression studies.

Lim, D & Zaslawski, C 2011, 'Non-specific effects of acupuncture: genuine or placebo?', Focus on Alternative and Complementary Therapies, vol. 16, no. 3, pp. 221-222.
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Lim, DC, Chen, W, Cheng, LN, Xue, CC, Wong, FW, O'Sullivan, AJ & Liu, JP 2011, 'Acupuncture for polycystic ovarian syndrome.', Cochrane Database Syst Rev, no. 8, p. CD007689.
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BACKGROUND: Polycystic ovarian syndrome (PCOS) is characterised by the clinical signs of oligo-amenorrhoea (infrequent or very light menstruation), infertility (failure to conceive), and hirsutism (excessive hair growth). Whilst Aleem 1987 revealed the presence of beta-endorphin in the follicular fluid of both normal and polycystic ovaries, Petraglia 1987 demonstrated that the beta-endorphin levels in ovarian follicular fluid of otherwise healthy women who were undergoing ovulation were much higher than the levels measured in plasma. Given that acupuncture has an impact on beta-endorphin production, which may affect gonadotropin-releasing hormone (GnRH) secretion, it is postulated that acupuncture may have a role in ovulation induction and fertility. OBJECTIVES: To assess the efficacy and safety of acupuncture treatment for women with polycystic ovarian syndrome (PCOS). SEARCH STRATEGY: Relevant studies were identified from the Menstrual Disorders and Subfertility Group Specialised Register, Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library), Ovid MEDLINE® In-Process and other non-indexed citations, Ovid MEDLINE® Daily and Ovid MEDLINE(R), EMBASE, PsycINFO, AMED, Chinese National Knowledge Infrastructure (CNKI) (including the Chinese journal full-text database (CJFD)), Chinese BioMedical Literature Database (CBM), VIP database for Chinese Technical Periodicals, China's important Conference Papers Database, and the China dissertation database. SELECTION CRITERIA: Truly randomised controlled trials (RCTs) that studied the efficacy of acupuncture treatment for infertility in women with PCOS. We excluded quasi- or pseudo-RCTs. DATA COLLECTION AND ANALYSIS: We aimed to extract data independently by three authors using a piloted data extraction form. Data on study characteristics including methods, participants, interventions, and outcomes would be extracted. Crossover trials were not included unless there were first-phase data provided. No...

Lin, BMT & Hwang, FJ 2011, 'Total completion time minimization in a 2-stage differentiation flowshop with fixed sequences per job type', INFORMATION PROCESSING LETTERS, vol. 111, no. 5, pp. 208-212.
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This paper addresses the total completion time minimization in a two-stage differentiation flowshop where the sequences of jobs per type are predetermined. The two-stage differentiation flowshop consists of a stage-1 common machine and m stage-2 parallel dedicated machines. The goal is to determine an optimal interleaved processing sequence of all jobs at the first stage. We propose an View the MathML source dynamic programming algorithm, where nk is the number of type-k jobs. The running time is polynomial when m is constant.

Lin, WH, Martin, JL, Marsh, DJ, Jack, MM & Baxter, RC 2011, 'Involvement of Insulin-like Growth Factor-binding Protein-3 in the Effects of Histone Deacetylase Inhibitor MS-275 in Hepatoma Cells', Journal of Biological Chemistry, vol. 286, no. 34, pp. 29540-29547.
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Lin, ZW, Li, YJ, Zhu, JG, Wang, XL, Dou, SX, Guo, YG, Lei, G, Wang, Y, Philips, M, Cortie, M, Li, YC, Choi, K-Y & Shi, X 2011, 'Visualization of vortex motion in FeAs-based BaFe(1.9)Ni(0.1)As(2) single crystal by means of magneto-optical imaging (vol 109, 07E142, 2011)', JOURNAL OF APPLIED PHYSICS, vol. 109, no. 10.
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Lin, ZW, Li, YJ, Zhu, JG, Wang, XL, Dou, SX, Guo, YG, Lei, G, Wang, Y, Philips, M, Cortie, M, Li, YC, Choi, K-Y & Shi, X 2011, 'Visualization of vortex motion in FeAs-based BaFe1.9Ni0.1As2 single crystal by means of magneto-optical imaging', JOURNAL OF APPLIED PHYSICS, vol. 109, no. 7, pp. 0-0.
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Superconductivity has been found in newly discovered iron-based compounds. This paper studies the motion of magnetic vortices in BaFe(1.9)Ni(0.1)As(2) single crystal by means of the magneto-optical imaging technique. A series of magneto-optical images re

Ling, ZL, Combes, V, Grau, GE & King, NJC 2011, 'Microparticles as Immune Regulators in Infectious Disease ? An Opinion', Frontiers in Immunology, vol. 2.
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Liu, H, Wang, G, Liu, J, Qiao, S & Ahn, H 2011, 'Highly ordered mesoporous NiO anode material for lithium ion batteries with an excellent electrochemical performance', JOURNAL OF MATERIALS CHEMISTRY, vol. 21, no. 9, pp. 3046-3052.
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In this work, we have synthesized highly ordered mesoporous NiO materials by a nanocasting method using mesoporous silica KIT-6 as the hard templates. Mesoporous NiO particles were characterized by small angle X-ray diffraction (XRD), nitrogen adsorption/desorption, and transmission electron microscopy (TEM). The results demonstrated that the as-prepared mesoporous NiO had an ordered Ia3d symmetric mesostructure, with a high surface area of 96 m(2)/g. Mesoporous NiO materials were tested as an anode material for lithium ion batteries, exhibiting much lower activation energy (20.75 kJ mol(-1)) compared to the bulk NiO (45.02 kJ mol(-1)). We found that the mesoporous NiO electrode has higher lithium intercalation kinetics than its bulk counterpart. The specific capacity of mesoporous NiO after 50 cycles was maintained 680 mAh/g at 0.1 C, which was much higher than that of the commercial bulk NiO (188 mAh/g). Furthermore, at a high rate of 2C, the discharge capacity of mesoporous NiO was as high as 515 mAh/g, demonstrating the potential to be used for high power lithium ion batteries.

Liu, J, Qiao, SZ, Liu, H, Chen, J, Orpe, A, Zhao, D & Max Lu, GQ 2011, 'Extension of The Stober Method to the Preparation of Monodisperse Resorcinol-Formaldehyde Resin Polymer and Carbon Spheres', ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, vol. 50, no. 26, pp. 5947-5951.
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Sphere we go: Monodisperse resorcinol formaldehyde (RF) resin polymer spheres with finely tunable particle size ranging from 200 to 1000 nm (see pictures) are prepared by an extension of the Stöber method. Pyrolysis of the RF spheres at 600°C under N 2 atmosphere yields uniform carbon spheres with a volume shrinkage of 19%.

Lloyd, A, Blanes, L, Beavis, A, Roux, C & Doble, P 2011, 'A rapid method for the in-field analysis of amphetamines employing the Agilent Bioanalyzer', ANALYTICAL METHODS, vol. 3, no. 7, pp. 1535-1539.
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This paper reports the first analysis of small molecules on the Agilent bio-analyser. The Bioanalyzer is a commercial lab-on-a-chip instrument designed for the analysis of DNA and proteins. We demonstrate that the instrument is suitable for analyses beyo

Lockrey, MN & Phillips, MR 2011, 'Characterisation of the optical properties of InGaN MQW structures using a combined SEM and CL spectral mapping system', Journal of Semiconductors, vol. 32, no. 1, pp. 012001-012001.
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We demonstrate the ability of a combined scanning electron microscope and cathodoluminescence (CL) spectral mapping system to provide important spatially resolved information. The degree of inhomogeneity in spectral output across a multi-quantum well sample is measured using the SEM-CL system as well as measuring the efficiency roll-off with increasing carrier concentration. The effects of low energy electron beam modification on the InGaN/GaN multi quantum wells have also been characterized.

Loreto, C, Musumeci, G, Castorina, A, Loreto, C & Martinez, G 2011, 'Degenerative disc disease of herniated intervertebral discs is associated with extracellular matrix remodeling, vimentin-positive cells and cell death', Annals of Anatomy - Anatomischer Anzeiger, vol. 193, no. 2, pp. 156-162.
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Lu, Y, Jin, D, Leif, RC, Deng, W, Piper, JA, Yuan, J, Duan, Y & Huo, Y 2011, 'Automated detection of rare‐event pathogens through time‐gated luminescence scanning microscopy', Cytometry Part A, vol. 79A, no. 5, pp. 349-355.
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AbstractMany microorganisms have a very low threshold (<10 cells) to trigger infectious diseases, and, in these cases, it is important to determine the absolute cell count in a low‐cost and speedy fashion. Fluorescent microscopy is a routine method; however, one fundamental problem has been associated with the existence in the sample of large numbers of nontarget particles, which are naturally autofluorescent, thereby obscuring the visibility of target organisms. This severely affects both direct visual inspection and the automated microscopy based on computer pattern recognition. We report a novel strategy of time‐gated luminescent scanning for accurate counting of rare‐event cells, which exploits the large difference in luminescence lifetimes between the lanthanide biolabels, >100 μs, and the autofluorescence backgrounds, <0.1 μs, to render background autofluorescence invisible to the detector. Rather than having to resort to sophisticated imaging analysis, the background‐free feature allows a single‐element photomultiplier to locate rare‐event cells, so that requirements for data storage and analysis are minimized to the level of image confirmation only at the final step. We have evaluated this concept in a prototype instrument using a 2D scanning stage and applied it to rare‐event Giardia detection labeled by a europium complex. For a slide area of 225 mm2, the time‐gated scanning method easily reduced the original 40,000 adjacent elements (0.075 mm × 0.075 mm) down to a few “elements of interest” containing the Giardia cysts. We achieved an averaged signal‐to‐background ratio of 41.2 (minimum ratio of 12.1). Such high contrasts ensured the accurate mapping of all the potential Giardia cysts free of false positives or negatives. This was confirmed by the automatic retrieving and time‐gated luminescence bioimaging of t...

Luan, F, Magi, E, Gong, T, Kabakova, I & Eggleton, BJ 2011, 'Photoinduced whispering gallery mode microcavity resonator in a chalcogenide microfiber', Optics Letters, vol. 36, no. 24, pp. 4761-4761.
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Ma, R, Bullock, E, Maynard, P, Reedy, B, Shimmon, R, Lennard, C, Roux, C & McDonagh, A 2011, 'Fingermark detection on non-porous and semi-porous surfaces using NaYF4:Er,Yb up-converter particles', FORENSIC SCIENCE INTERNATIONAL, vol. 207, no. 1-3, pp. 145-149.
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This article describes the first use of an anti-Stokes material, or up-converter, for the development of latent fingermarks on a range of non-porous surfaces. Anti-Stokes materials can absorb long-wavelength light and emit light at a shorter wavelength. This property is unusual in both natural and artificial materials and so fingermark detection techniques based on anti-Stokes luminescence are potentially sensitive and selective. Latent fingermarks on luminescent and non-luminescent substrates, including Australian polymer banknotes (a well-known `difficult surface), were developed with sodium yttrium tetrafluoride doped with erbium and ytterbium (NaYF4:Er,Yb) by dry powder, wet powder, and cyanoacrylate staining techniques. This study illustrates the potential of up-converter phosphors for the detection of latent fingermarks.

Ma, Y, Hart, JD & Carroll, RJ 2011, 'Density Estimation in Several Populations With Uncertain Population Membership', Journal of the American Statistical Association, vol. 106, no. 495, pp. 1180-1192.
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Ma, Y, Hart, JD, Janicki, R & Carroll, RJ 2011, 'Local and Omnibus Goodness-of-Fit Tests in Classical Measurement Error Models', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 73, no. 1, pp. 81-98.
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Summary We consider functional measurement error models, i.e. models where covariates are measured with error and yet no distributional assumptions are made about the mismeasured variable. We propose and study a score-type local test and an orthogonal series-based, omnibus goodness-of-fit test in this context, where no likelihood function is available or calculated—i.e. all the tests are proposed in the semiparametric model framework. We demonstrate that our tests have optimality properties and computational advantages that are similar to those of the classical score tests in the parametric model framework. The test procedures are applicable to several semiparametric extensions of measurement error models, including when the measurement error distribution is estimated non-parametrically as well as for generalized partially linear models. The performance of the local score-type and omnibus goodness-of-fit tests is demonstrated through simulation studies and analysis of a nutrition data set.

Ma, Z, Ji, H, Tan, D, Dong, G, Teng, Y, Zhou, J, Guan, M, Qiu, J & Zhang, M 2011, 'Large-scale preparation of strawberry-like, AgNP-doped SiO₂microspheres using the electrospraying method', Nanotechnology, vol. 22, no. 30, pp. 305307-305307.
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In this paper, we report on a novel strategy for the preparation of silver nanoparticle-doped SiO2 microspheres (Ag-SMSs) with an interesting strawberry-like morphology using a simple and efficient electrospraying method. SEM (scanning electron microscopy), TEM (transmission electron microscopy), XRD (x-ray diffraction), EDS (energy-dispersive spectroscopy) and UV–vis spectra (ultraviolet–visible spectra) were applied to investigate the morphology, structure, composition and optical properties of the hybrid microspheres, and E. coli (Escherichia coli) was used as a model microbe to evaluate their antibacterial ability. The results showed that the Ag-SMSs were environmentally stable and washing resistant. The Ag-SMSs exhibited effective inhibition against proliferation of E. coli, and their antibacterial ability could be well preserved for a long time. The environmental stability, washing resistance, efficient antibacterial ability and simple but productive preparation method endowed the Ag-SMSs with great potential for practical biomedical applications.

Ma, Z, Ji, H, Tan, D, Teng, Y, Dong, G, Zhou, J, Qiu, J & Zhang, M 2011, 'Silver nanoparticles decorated, flexible SiO2 nanofibers with long-term antibacterial effect as reusable wound cover', Colloids and Surfaces A: Physicochemical and Engineering Aspects, vol. 387, no. 1-3, pp. 57-64.
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As wound cover, electrospinning-derived organic polymer nanofibers usually cannot bear calcinations to remove contaminants from wound for regeneration of their functionality, thus are not reusable. In this investigation, we make an exploration of inorganic SiO2 nanofibers as reusable wound cover. SiO2 nanofibers here are fabricated with the sol–gel technique and the electrospinning method. Silver nanoparticles (Ag NPs) are grafted on fiber surface through post treatment to endow this material with antibacterial effect. Our results demonstrate the SiO2 nanofibers are very soft and flexible. They can be conveniently patterned into nonwoven film (the required shape of wound cover). The Ag NPs grafted SiO2 nanofibers can efficiently inhibit the proliferation of Escherichia coli with a long-term antibacterial effect. More importantly, this inorganic antibacterial wound cover can be renewed through calcinations without lost of its flexibility and antibacterial effect. Consequently, the Ag NPs grafted SiO2 nanofibers in this investigation are very suitable to be applied as reusable wound cover.

Ma, Z, Ji, H, Teng, Y, Dong, G, Tan, D, Guan, M, Zhou, J, Xie, J, Qiu, J & Zhang, M 2011, 'Engineering and optimisation of medically multi-functional mesoporous SiO2 fibers as effective wound dressing material', Journal of Materials Chemistry, vol. 21, no. 26, pp. 9595-9595.
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In this paper, we propose a novel strategy for the preparation of flexible mesoporous SiO2 fibers containing silver nanoparticles (Ag-cSiO2@mSiO2) as an effective wound dressing. The Ag-cSiO2@mSiO2 was core–shell structured, composed of a condensed electrospun SiO2 nanofiber doped with Ag NPs (silver nanoparticles) and a mesoporous SiO2 shell. Due to a high specific surface area and large pore volume, the Ag-cSiO2@mSiO2 can substantially absorb exudates, the absorption capacity for water and SBF (simulated body fluid) reached 267 wt% and 254 wt% of the sample, respectively. Additionally, the mesopores can also act as hosts for the accommodation of drugs. The Loading capacity of IBU (ibuprofen) reached up to 18 wt% of the sample, and its release was relatively fast, more than 85% of the drug was released within 12 h. The condensed core of the SiO2 nanofiber not only endowed the sample with a high flexibility, but also slowly released silver to possess a sustained antibiotic effect. Considering its effective exudate-absorption ability, dual drug-release profiles (fast release of IBU and sustained release of silver), together with its chemical and physical stability, biocompatibility and high flexibility, Ag-cSiO2@mSiO2 could be a promising wound dressing material.

Ma, Z, Ji, H, Teng, Y, Dong, G, Zhou, J, Tan, D & Qiu, J 2011, 'Engineering and optimization of nano- and mesoporous silica fibers using sol–gel and electrospinning techniques for sorption of heavy metal ions', Journal of Colloid and Interface Science, vol. 358, no. 2, pp. 547-553.
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In this paper, we report on a novel design strategy of an efficient sorbent for removal of trace contaminants from water. This kind of sorbent is composed of a nonporous core of SiO2 nanofiber and a mesoporous shell (denoted as nSiO2@mSiO2 (“n” means “nonporous” and “m” means “mesoporous”)). The nSiO2@mSiO2 fiber possesses a continuously long fibrous shape and mesoporous micromorphology, thus, showing both high sorption capacity and separability. The flexible nonporous SiO2 nanofiber was prepared with electrospinning first, followed by covering a mesoporous SiO2 shell based on a modified Stöber method using CTAB (cetyltrimethylammonium bromide) as the directing agent for formation of the mesopores. Also, functional thiol groups were grafted on the nSiO2@mSiO2 to enhance its performance. With a large specific surface area and long fibrous morphology, the nSiO2@mSiO2 fiber and its thiol-functionalized counterpart exhibit impressive performance on removal of Pb2+ and Cd2+ from water. Furthermore, the flexible texture and fibrous morphology of the nSiO2@mSiO2 fiber also made the removal of metal ions and the separation process more convenient and efficient, implying that the nSiO2@mSiO2 fiber could have great potential for industrial applications.

Macreadie, PI, Bishop, MJ & Booth, DJ 2011, 'Implications of climate change for macrophytic rafts and their hitchhikers', MARINE ECOLOGY PROGRESS SERIES, vol. 443, pp. 285-292.
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Most models predicting changes to species distributions under future climate scenarios ignore dispersal processes, despite their importance in determining community structure in both terrestrial and aquatic systems ('supply-side ecology'). In the marine environment, facilitation of long-distance dispersal of coastal organisms by macrophytic rafts may be severely modified by climate impacts on raft supply, quality, and persistence, and on transport processes. Increasing storminess in the coastal zone, higher water temperatures, and changes in water circulation represent some of the key mechanisms that will directly affect rafts, while increases in herbivore metabolism due to higher water temperatures are likely to indirectly reduce raft longevity through raft consumption. Accurate predictions of climate impacts on coastal biodiversity will be contingent on resolution of factors influencing rafting so that this and other dispersal mechanisms can be incorporated into species distribution models.

Macreadie, PI, Fowler, AM & Booth, DJ 2011, 'Rigs-to-reefs: will the deep sea benefit from artificial habitat?', FRONTIERS IN ECOLOGY AND THE ENVIRONMENT, vol. 9, no. 8, pp. 455-461.
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As a peak in the global number of offshore oil rigs requiring decommissioning approaches, there is growing pressure for the implementation of a rigs-to-reefs program in the deep sea, whereby obsolete rigs are converted into artificial reefs. Such decommissioned rigs could enhance biological productivity, improve ecological connectivity, and facilitate conservation/restoration of deep-sea benthos (eg cold-water corals) by restricting access to fishing trawlers. Preliminary evidence indicates that decommissioned rigs in shallower waters can also help rebuild declining fish stocks. Conversely, potential negative impacts include physical damage to existing benthic habitats within the drop zone, undesired changes in marine food webs, facilitation of the spread of invasive species, and release of contaminants as rigs corrode. We discuss key areas for future research and suggest alternatives to offset or minimize negative impacts. Overall, a rigs-to-reefs program may be a valid option for deep-sea benthic conservation.

Madin, EMP, Madin, JS & Booth, DJ 2011, 'Landscape of fear visible from space', SCIENTIFIC REPORTS, vol. 1, no. art14, pp. 1-4.
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By linking ecological theory with freely-available Google Earth satellite imagery, landscape-scale footprints of behavioural interactions between predators and prey can be observed remotely. A Google Earth image survey of the lagoon habitat at Heron Island within Australia's Great Barrier Reef revealed distinct halo patterns within algal beds surrounding patch reefs. Ground truth surveys confirmed that, as predicted, algal canopy height increases with distance from reef edges. A grazing assay subsequently demonstrated that herbivore grazing was responsible for this pattern. In conjunction with recent behavioural ecology studies, these findings demonstrate that herbivores' collective antipredator behavioural patterns can shape vegetation distributions on a scale clearly visible from space. By using sequential Google Earth images of specific locations over time, this technique could potentially allow rapid, inexpensive remote monitoring of cascading, indirect effects of predator removals (e.g., fishing; hunting) and/or recovery and reintroductions (e.g., marine or terrestrial reserves) nearly anywhere on earth.

Magyar, AP, Lee, JC, Limarga, AM, Aharonovich, I, Rol, F, Clarke, DR, Huang, M & Hu, EL 2011, 'Fabrication of thin, luminescent, single-crystal diamond membranes', APPLIED PHYSICS LETTERS, vol. 99, no. 8.
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Mai, K, Smith, NC, Feng, Z-P, Katrib, M, Slapeta, J, Slapetova, I, Wallach, MG, Luxford, C, Davies, MJ, Zhang, X, Norton, RS & Belli, SI 2011, 'Peroxidase catalysed cross-Linking of an intrinsically unstructured protein via dityrosine bonds in the oocyst wall of the apicomplexan parasite, Eimeria maxima', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 41, no. 11, pp. 1157-1164.
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Apicomplexan parasites such as Eimeria maxima possess a resilient oocyst wall that protects them upon excretion in host faeces and in the outside world, allowing them to survive between hosts. The wall is formed from the contents of specialised organelles - wall-forming bodies - found in macrogametes of the parasites. The presence of dityrosine in the oocyst wall suggests that peroxidase-catalysed dityrosine cross-linking of tyrosine-rich proteins from wall-forming bodies forms a matrix that is a crucial component of oocyst walls. Bioinformatic analyses showed that one of these tyrosine-rich proteins, EmGAM56, is an intrinsically unstructured protein, dominated by random coil (52-70%), with some alpha-helix (28-43%) but a relatively low percentage of beta-sheet (1-11%); this was confirmed by nuclear magnetic resonance and circular dichroism. Furthermore, the structural integrity of EmGAM56 under extreme temperatures and pH indicated its disordered nature. The intrinsic lack of structure in EmGAM56 could facilitate its incorporation into the oocyst wall in two ways: first, intrinsically unstructured proteins are highly susceptible to proteolysis, explaining the several differently-sized oocyst wall proteins derived from EmGAM56; and, second, its flexibility could facilitate cross-linking between these tyrosine-rich derivatives. An in vitro cross-linking assay was developed using a recombinant 42 kDa truncation of EmGAM56. Peroxides, in combination with plant or fungal peroxidases, catalysed the rapid formation of dityrosine cross-linked polymers of the truncated EmGAM56, as determined by western blotting and HPLC, confirming this protein's propensity to form dityrosine bonds.

Marcos, Seymour, JR, Luhar, M, Durham, WM, Mitchell, JG, Macke, A & Stocker, R 2011, 'Microbial alignment in flow changes ocean light climate', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 108, no. 10, pp. 3860-3864.
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The growth of microbial cultures in the laboratory often is assessed informally with a quick flick of the wrist: dense suspensions of microorganisms produce translucent

Marques, R, Jelinek, L, Freire, MJ, Baena, JD & Lapine, M 2011, 'Bulk Metamaterials Made of Resonant Rings', Proceedings of the IEEE, vol. 99, no. 10, pp. 1660-1668.
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Marsh, DJ & Gimm, O 2011, 'Multiple Endocrine Neoplasia: Types 1 and 2', Advances in Oto-Rhino-Laryngology, vol. 70, pp. 84-90.
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Multiple endocrine neoplasia type 1 (MEN 1) and type 2 (MEN 2) are autosomal-dominantly inherited syndromes where highly penetrant germline mutations predispose patients to the development of tumours in hormone-secreting cells. In the case of MEN 1, loss-of-function germline mutations in the tumour suppressor gene MEN1 increase the risk of developing pituitary, parathyroid and pancreatic islet tumours, and less commonly thymic carcinoids, lipomas and benign adrenocortical tumours. In the case of MEN 2, gain-of-function germline mutations clustered in specific codons of the RET proto-oncogene increase the risk of developing medullary thyroid carcinoma (MTC), phaeochromocytoma and parathyroid tumours. Offering RET testing is best practice for the clinical management of patients at-risk of MEN 2, and MEN 2 has become a classic model for the integration of molecular medicine into patient care. Prophylactic thyroidectomy in an asymptomatic RET mutation carrier to address the risk of developing MTC can prevent or cure this malignancy. No similar preventative strategies can be employed to prevent or cure MEN 1-associated tumours. Genetic testing for MEN 1 is therefore both more complex due to a general lack of mutational hotspots, and the benefit to patients is less straight forward. While a number of genotype-phenotype correlations exist in MEN 2, providing further rationale for performing genetic testing in this condition, these correlations are absent in MEN 1. This review summarises our current knowledge of these two syndromes with emphasis on those aspects with specific relevance to the otorhinolaryngologist. Copyright © 2011 S. Karger AG, Basel.

Marsh, J, Kollipara, A, Timms, P & Polkinghorne, A 2011, 'Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)', BMC Microbiology, vol. 11, no. 1.
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Abstract Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a 'true' phylogenetic signal. OmpA and incA were of ...

Martin, LJ & Murray, BR 2011, 'A comparison of short-term marking methods for small frogs using a model species, the striped marsh frog (Limnodynastes peronii)', HERPETOLOGICAL JOURNAL, vol. 21, no. 4, pp. 271-273.
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We compared three methods of marking individual small frogs for identification in short-term studies (several days) using a model species, Limnodynastes peronii (the striped marsh frog). We performed a manipulative experiment under laboratory conditions to compare retention times of gentian violet, mercurochrome and powdered fluorescent pigment. Gentian violet produced the most durable marks with retention times between two and four days. Mercurochrome was retained for at least one day by all treated frogs. Fluorescent pigment was either not retained at all or for one day at most, which suggests that this marking method may not be reliable for short-term studies where identification is required. No adverse reactions to any of the marking methods were detected in our study. Our findings indicate that gentian violet represents a promising alternative as a minimally invasive marking technique for studies of small frogs requiring only shortterm retention of identification marks.

Martin, LJ & Murray, BR 2011, 'A predictive framework and review of the ecological impacts of exotic plant invasions on reptiles and amphibians', BIOLOGICAL REVIEWS, vol. 86, no. 2, pp. 407-419.
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The invasive spread of exotic plants in native vegetation can pose serious threats to native faunal assemblages. This is of particular concern for reptiles and amphibians because they form a significant component of the worldâs vertebrate fauna, play a pivotal role in ecosystem functioning and are often neglected in biodiversity research. A framework to predict how exotic plant invasion will affect reptile and amphibian assemblages is imperative for conservation, management and the identification of research priorities. Here, we present a new predictive framework that integrates three mechanistic models. These models are based on exotic plant invasion altering: (1) habitat structure; (2) herbivory and predator-prey interactions; (3) the reproductive success of reptile and amphibian species and assemblages. We present a series of testable predictions from these models that arise from the interplay over time among three exotic plant traits (growth form, area of coverage, taxonomic distinctiveness) and six traits of reptiles and amphibians (body size, lifespan, home range size, habitat specialisation, diet, reproductive strategy). A literature review provided robust empirical evidence of exotic plant impacts on reptiles and amphibians from each of the three model mechanisms. Evidence relating to the role of body size and diet was less clear-cut, indicating the need for further research. The literature provided limited empirical support for many of the other model predictions. This was not, however, because findings contradicted our model predictions but because research in this area is sparse. In particular, the small number of studies specifically examining the effects of exotic plants on amphibians highlights the pressing need for quantitative research in this area. There is enormous scope for detailed empirical investigation of interactions between exotic plants and reptile and amphibian species and assemblages.

Martinez, JG, Carroll, RJ, Müller, S, Sampson, JN & Chatterjee, N 2011, 'Empirical Performance of Cross-Validation With Oracle Methods in a Genomics Context', The American Statistician, vol. 65, no. 4, pp. 223-228.
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McElroy, K, Luciani, F, Hui, J, Rice, S & Thomas, T 2011, 'Bacteriophage evolution drives Pseudomonas aeruginosa PAO1 biofilm diversification', BMC Bioinformatics, vol. 12, no. S11.
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McGowan, EM, Alling, N, Jackson, EA, Yagoub, D, Haass, NK, Allen, JD & Martinello-Wilks, R 2011, 'Evaluation of Cell Cycle Arrest in Estrogen Responsive MCF-7 Breast Cancer Cells: Pitfalls of the MTS Assay', PLoS ONE, vol. 6, no. 6, pp. e20623-e20623.
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Endocrine resistance is a major problem with anti-estrogen treatments and how to overcome resistance is a major concern in the clinic. Reliable measurement of cell viability, proliferation, growth inhibition and death is important in screening for drug t

McKemmish, LK, McKenzie, RH, Hush, NS & Reimers, JR 2011, 'Quantum entanglement between electronic and vibrational degrees of freedom in molecules', JOURNAL OF CHEMICAL PHYSICS, vol. 135, no. 24.
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We consider the quantum entanglement of the electronic and vibrational degrees of freedom in molecules with tendencies towards double welled potentials. In these bipartite systems, the von Neumann entropy of the reduced density matrix is used to quantify the electron-vibration entanglement for the lowest two vibronic wavefunctions obtained from a model Hamiltonian based on coupled harmonic diabatic potential-energy surfaces. Significant entanglement is found only in the region in which the ground vibronic state contains a density profile that is bimodal (i.e., contains two separate local maxima). However, in this region two distinct types of density and entanglement profiles are found: one type arises purely from the degeneracy of energy levels in the two potential wells and is destroyed by slight asymmetry, while the other arises through strong interactions between the diabatic levels of each well and is relatively insensitive to asymmetry. These two distinct types are termed fragile degeneracy-induced entanglement and persistent entanglement, respectively. Six classic molecular systems describable by two diabatic states are considered: ammonia, benzene, BNB, pyridine excited triplet states, the Creutz-Taube ion, and the radical cation of the "special pair" of chlorophylls involved in photosynthesis. These chemically diverse systems are all treated using the same general formalism and the nature of the entanglement that they embody is elucidated.

McNevin, D, Bate, A, Daniel, R & Walsh, SJ 2011, 'A preliminary mitochondrial DNA SNP genotyping assay for inferring genealogy', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 43, no. 1, pp. 39-51.
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McPhedran, RC, Botten, LC, Williamson, DJ & Nicorovici, N-AP 2011, 'The Riemann hypothesis and the zero distribution of angular lattice sums', PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, vol. 467, no. 2133, pp. 2462-2478.
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We give analytical results pertaining to the distributions of zeros of a class of sums which involve complex powers of the distance to points in a two-dimensional square lattice and trigonometric functions of their angle. Let C(0, 1; s) denote the produc

McQuillan, JA, Mitchell, AJ, Ho, YF, Combes, V, Ball, HJ, Golenser, J, Grau, GE & Hunt, NH 2011, 'Coincident parasite and CD8 T cell sequestration is required for development of experimental cerebral malaria', International Journal for Parasitology, vol. 41, no. 2, pp. 155-163.
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Mehta, M, Satija, S & Kalsi, V 2011, 'Invitro antioxidant evaluation of Psidium guajava stem extracts', International Journal of Drug Development and Research, vol. 3, no. 2, pp. 352-355.
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Dried powdered stem of Psidium guajava was successively extracted with acetone, methanol and water respectively and subjected to antioxidant activity. Methanolic and aqueous extracts were used for the evaluation of antioxidant activity. The activity was determined at ambient temperature by means of a DPPH(1,1-diphenyl-2-picrylhydrazyl) spectrophotometrically with detection scheme at 520 nm. The activity was evaluated by the decrease in absorbance as the result of DPPH colour change from purple to yellow. The higher the sample concentration used, the stronger was the free radical- scavenging effect. The results obtained showed that methanol extract has almost same antioxidant activity as of ascorbic acid while aqueous extract showed less antioxidant activity. This study revealed that guava stem extracts comprise effective potential source of natural antioxidants which might be helpful in preventing the progress of various oxidative stresses. © 2010 IJDDR.

Mehta, M, Satija, S & Kalsi, V 2011, 'Invitro antioxidant evaluation of Psidium guajava strem extracts', International Journal of Drug Development and Research, vol. 3, no. 3, pp. 213-216.
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Dried powdered stem of Psidium guajava was successively extracted with acetone, methanol and water respectively and subjected to antioxidant activity. Methanolic and aqueous extracts was used for the evaluation of antioxidant activity. The activity was determined at ambient temperature by means of a 2,2-diphenyl1-1-picrylhydryzyl (DPPH) spectrophotometrically with detection scheme at 520 nm. The activity was evaluated by the decrease in absorbance as the result of DPPH colour change from purple to yellow. The higher the sample concentration used, the stronger was the free radical-scavenging effect. The results obtained showed that methanol extract has almost same antioxidant activity as of ascorbic acid while aqueous extract showed less antioxidant activity. This study revealed that guava stem extracts comprise effective potential source of natural antioxidants which might be helpful in preventing the progress of various oxidative stresses. © 2010 IJDDR.

Meiklejohn, KA, Wallman, JF & Dowton, M 2011, 'DNA-based identification of forensically important Australian Sarcophagidae (Diptera)', International Journal of Legal Medicine, vol. 125, no. 1, pp. 27-32.
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Mella-Flores, D, Mazard, S, Humily, F, Partensky, F, Mahé, F, Bariat, L, Courties, C, Marie, D, Ras, J, Mauriac, R, Jeanthon, C, Bendif, EM, Ostrowski, M, Scanlan, DJ & Garczarek, L 2011, 'Is the distribution of &lt;i&gt;Prochlorococcus&lt;/i&gt; and &lt;i&gt;Synechococcus&lt;/i&gt; ecotypes in the Mediterranean Sea affected by global warming?', Biogeosciences Discussions, vol. 8, no. 3, pp. 4281-4330.
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Abstract. Biological communities populating the Mediterranean Sea, which is situated at the northern boundary of the subtropics, are often claimed to be particularly affected by global warming. This is indicated, for instance, by the introduction of (sub)tropical species of fish or invertebrates that can displace local species. This raises the question of whether microbial communities are similarly affected, especially in the Levantine basin where sea surface temperatures have risen in recent years. In this paper, the genetic diversity of the two most abundant members of the phytoplankton community, the picocyanobacteria Prochlorococcus and Synechococcus, was examined on a transect from the South coast of France to Cyprus in the summer of 2008 (BOUM cruise). Diversity was studied using dot blot hybridization with clade-specific 16S rRNA oligonucleotide probes and clone libraries of the 16S–23S ribosomal DNA Internal Transcribed Spacer (ITS) region. Data were compared with those obtained during the PROSOPE cruise held almost a decade earlier, with a focus on the abundance of clades that may constitute bioindicators of warm waters. During both cruises, the dominant Prochlorococcus clade in the upper mixed layer at all stations was HLI, a clade typical of temperate waters, whereas the HLII clade, the dominant group in (sub)tropical waters, was only present at very low concentrations. The Synechococcus community was dominated by clades I, III and IV in the northwestern waters of the Gulf of Lions and by clade III and groups genetically related to clades WPC1 and VI in the rest of the Mediterranean Sea. In contrast, only a few sequences of clade II, a group typical of warm waters, were observed. These data indicate that local cyanobacterial populations have not yet been displaced by their (sub)tropical counterparts. This is discussed in the context of the low phosphorus concentrations found in surface waters in the eastern Mediterranean basin, as this may cons...

Mella-Flores, D, Mazard, S, Humily, F, Partensky, F, Mahé, F, Bariat, L, Courties, C, Marie, D, Ras, J, Mauriac, R, Jeanthon, C, Mahdi Bendif, E, Ostrowski, M, Scanlan, DJ & Garczarek, L 2011, 'Is the distribution of &lt;i&gt;Prochlorococcus&lt;/i&gt; and &lt;i&gt;Synechococcus&lt;/i&gt; ecotypes in the Mediterranean Sea affected by global warming?', Biogeosciences, vol. 8, no. 9, pp. 2785-2804.
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Abstract. Biological communities populating the Mediterranean Sea, which is situated at the northern boundary of the subtropics, are often claimed to be particularly affected by global warming. This is indicated, for instance, by the introduction of (sub)tropical species of fish or invertebrates that can displace local species. This raises the question of whether microbial communities are similarly affected, especially in the Levantine basin where sea surface temperatures have significantly risen over the last 25 years (0.50 ± 0.11 °C in average per decade, P < 0.01). In this paper, the genetic diversity of the two most abundant members of the phytoplankton community, the picocyanobacteria Prochlorococcus and Synechococcus, was examined during two cruises through both eastern and western Mediterranean Sea basins held in September 1999 (PROSOPE cruise) and in June–July 2008 (BOUM cruise). Diversity was studied using dot blot hybridization with clade-specific 16S rRNA oligonucleotide probes and/or clone libraries of the 16S-23S ribosomal DNA Internal Transcribed Spacer (ITS) region, with a focus on the abundance of clades that may constitute bioindicators of warm waters. During both cruises, the dominant Prochlorococcus clade in the upper mixed layer at all stations was HLI, a clade typical of temperate waters, whereas the HLII clade, the dominant group in (sub)tropical waters, was only present at very low concentrations. The Synechococcus community was dominated by clades I, III and IV in the northwestern waters of the Gulf of Lions and by clade III and groups genetically related to clades WPC1 and VI in the rest of the Mediterranean Sea. In contrast, only a few sequences of clade II, a group typical of warm waters, were observed. These data indicate that local cyanobacterial populations have not yet been displaced by their (sub)tropical counterparts.

Midthune, D, Schatzkin, A, Subar, AF, Thompson, FE, Freedman, LS, Carroll, RJ, Shumakovich, MA & Kipnis, V 2011, 'Validating an FFQ for intake of episodically consumed foods: application to the National Institutes of Health–AARP Diet and Health Study', Public Health Nutrition, vol. 14, no. 7, pp. 1212-1221.
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AbstractObjectiveTo develop a method to validate an FFQ for reported intake of episodically consumed foods when the reference instrument measures short-term intake, and to apply the method in a large prospective cohort.DesignThe FFQ was evaluated in a sub-study of cohort participants who, in addition to the questionnaire, were asked to complete two non-consecutive 24 h dietary recalls (24HR). FFQ-reported intakes of twenty-nine food groups were analysed using a two-part measurement error model that allows for non-consumption on a given day, using 24HR as a reference instrument under the assumption that 24HR is unbiased for true intake at the individual level.SettingThe National Institutes of Health–AARP Diet and Health Study, a cohort of 567 169 participants living in the USA and aged 50–71 years at baseline in 1995.SubjectsA sub-study of the cohort consisting of 2055 participants.ResultsEstimated correlations of true and FFQ-reported energy-adjusted intakes were 0·5 or greater for most of the twenty-nine food groups evaluated, and estimated attenuation factors (a measure of bias in estimated diet–disease associations) were 0·4 or greater for most food groups.ConclusionsThe proposed methodology extends the class of foods and nutrients for which an FFQ can be evaluated in studies with short-term reference in...

Miller, CM, Boulter, NR, Fuller, SJ, Zakrzewski, AM, Lees, MP, Saunders, BM, Wiley, JS & Smith, NC 2011, 'The Role of the P2X7 Receptor in Infectious Diseases', PLoS Pathogens, vol. 7, no. 11, pp. e1002212-e1002212.
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Missmer, SA, Pearson, KR, Ryan, LM, Meeker, JD, Cramer, DW & Hauser, R 2011, 'Analysis of Multiple-cycle Data From Couples Undergoing In Vitro Fertilization Methodologic Issues and Statistical Approaches', EPIDEMIOLOGY, vol. 22, no. 4, pp. 497-504.
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The number of in vitro fertilization (IVF) cycles in the United States increased from fewer than 46,000 in 1995 to more than 120,000 in 2005. IVF and other assisted reproductive technology (ART) data are routinely collected and used to identify outcome predictors. However, researchers do not always make full use of the data due to their complexity. Design approaches have included restriction to first-cycle attempts only, which reduces power and identifies effects only of those factors associated with initial success. Many statistical techniques have been used or proposed for analysis of IVF data, ranging from simple t tests to sophisticated models designed specifically for IVF. We applied several of these methods to data from a prospective cohort of 2687 couples undergoing ART from 1994 through 2003. Results across methods are compared and the appropriateness of the various methods is discussed with the intent to illustrate methodologic validity. We observed a remarkable similarity of coefficient estimates across models. However, each method for dealing with multiple cycle data relies on assumptions that may or may not be expected to hold in a given IVF study. The robustness and reported magnitude of effect for individual predictors of IVF success may be inflated or attenuated due to violation of statistical assumptions, and should always be critically interpreted. Given that risk factors associated with IVF success may also advance our understanding of the physiologic processes underlying conception, implantation, and gestation, the application of valid methods to these complex data is critical.

Mitrovic, SM, Hardwick, L & Dorani, F 2011, 'Use of flow management to mitigate cyanobacterial blooms in the Lower Darling River, Australia', JOURNAL OF PLANKTON RESEARCH, vol. 33, no. 2, pp. 229-241.
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The growth of planktonic cyanobacteria in a weir pool on the Lower Darling River, Australia, downstream of the major regulated Menindee Lake system was examined. Blooms of the saxitoxin producing freshwater cyanobacterium Anabaena circinalis occurred for two summers out of four studied. Large cell numbers of other cyanobacteria including Aphanizomenon, Planktolyngbya and Merismopedia also occurred during the same summer periods as the Anabaena blooms. The growth events also coincided with periods of improved light climate. Flow releases from the regulated Menindee Lakes System were assessed for their ability to either suppress bloom development or to mitigate pre-existing blooms over this period.

Moezzi, A, Cortie, M & McDonagh, A 2011, 'Aqueous pathways for the formation of zinc oxide nanoparticles', DALTON TRANSACTIONS, vol. 40, no. 18, pp. 4871-4878.
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We examine the effect of reactant concentrations, temperatures and feeding methods on the morphology of ZnO formed when reacting solutions of ZnSO4 and NaOH. The catalytic effect of hydroxide in excess relative to the stoichiometric ratio is considered. It is shown that, having fixed other reaction conditions, the end-products, particle structures and size strongly depend on the mole ratio of the precursors. The presence of zinc salt hydroxide species was confirmed at sub-stoichiometric ratios in slightly acidic conditions. At the stoichiometric ratio both zinc hydroxide and zinc oxide are formed, while only zinc oxide forms in an excess of hydroxide. The method of feeding the reactants into the reaction vessel also has a strong influence on the end-product properties, as does the reaction temperature. By control of these parameters the specific surface area could be varied from 10 to 33 m2 g-1, the particle shape could be varied from equiaxed, through to star-like and needle-like, and the particle size may be varied from 50 to over 300 nm.

Moheimani, F, Tan, JTM, Brown, BE, Heather, AK, van Reyk, DM & Davies, MJ 2011, 'Effect of Exposure of Human Monocyte-Derived Macrophages to High, versus Normal, Glucose on Subsequent Lipid Accumulation from Glycated and Acetylated Low-Density Lipoproteins', EXPERIMENTAL DIABETES RESEARCH, vol. 2011, no. 851280, pp. 1-10.
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This is the second paper from Dr Moheimani's PhD thesis of which David van Reyk was a co-supervisor in his role as Visiting HRI Fellow. It examines the mechanisms that promote and accelerate the development and progression of atherosclerosis in people with diabetes

Moir, LM, Ng, HY, Poniris, MH, Santa, T, Burgess, JK, Oliver, BGG, Krymskaya, VP & Black, JL 2011, 'Doxycycline inhibits matrix metalloproteinase-2 secretion from TSC2-null mouse embryonic fibroblasts and lymphangioleiomyomatosis cells', British Journal of Pharmacology, vol. 164, no. 1, pp. 83-92.
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BACKGROUND AND PURPOSE Lymphangioleiomyomatosis (LAM) is characterized by the abnormal growth of smooth muscle-like cells (LAM cells) and cystic destruction of the lung parenchyma. LAM cell-derived matrix metalloproteinases (MMPs) are thought to play a prominent role in the tissue destruction. The aim of this study was to determine whether doxycycline, a known MMP inhibitor, can inhibit LAM cell proliferation or mitochondrial function and/or modulate MMPs and their tissue inhibitors (TIMPs). EXPERIMENTAL APPROACH Wild-type and tuberous sclerosis complex-2 (TSC2)-null mouse embryonic fibroblasts (MEFs) were cultured in DMEM containing 10% fetal bovine serum (FBS). Human LAM cells were derived from the lungs of LAM patients and airway smooth muscle cells from control subjects. Cells were stimulated with FBS with or without doxycycline for up to 9 days. Proliferation was assessed by manual cell counts and MTT assay, MMP production by zymography and ELISA, and TIMP production using ELISA. KEY RESULTS Doxycycline did not change FBS-induced proliferation in MEFs or human cells. However, doxycycline did reduce metabolic activity of both wild-type and TSC2-null MEFs and LAM cells, but had no effect on control cells. Furthermore, doxycycline reduced MMP-2 from MEFs and decreased active-MMP-2 from LAM cells but had no effect on TIMP-1 and TIMP-2 from human LAM cells. CONCLUSIONS AND IMPLICATIONS Doxycycline decreased MMP levels and cell metabolic activity, which raises the possibility of therapeutic efficacy in LAM.

Moir, LM, Trian, T, Ge, Q, Shepherd, PR, Burgess, JK, Oliver, BGG & Black, JL 2011, 'Phosphatidylinositol 3-Kinase Isoform-Specific Effects in Airway Mesenchymal Cell Function', Journal of Pharmacology and Experimental Therapeutics, vol. 337, no. 2, pp. 557-566.
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The phosphatidylinositol 3-kinase (PI3K) signal transduction pathway is implicated in the airway remodeling associated with asthma. The class IA PI3K isoforms are known to be activated by growth factors and cytokines. Because this pathway is a possible s

Mojica, S, Huot Creasy, H, Daugherty, S, Read, TD, Kim, T, Kaltenboeck, B, Bavoil, P & Myers, GSA 2011, 'Genome Sequence of the Obligate Intracellular Animal Pathogen Chlamydia pecorum E58', Journal of Bacteriology, vol. 193, no. 14, pp. 3690-3690.
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Moore, SJ, Fisher, MG, Yano, M, Tong, CC & Gale, PA 2011, 'A synergistic approach to anion antiport', Dalton Transactions, vol. 40, no. 45, pp. 12017-12017.
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Mora, C, Aburto-Oropeza, O, Ayala Bocos, A, Ayotte, PM, Banks, S, Bauman, AG, Beger, M, Bessudo, S, Booth, DJ, Brokovich, E, Brooks, A, Chabanet, P, Cinner, JE, Cortes, J, Cruz-Motta, JJ, Cupul Magana, A, DeMartini, EE, Edgar, GJ, Feary, DA, Ferse, SCA, Friedlander, AM, Gaston, KJ, Gough, C, Graham, NAJ, Green, A, Guzman, H, Hardt, M, Kulbicki, M, Letourneur, Y, Lopez Perez, A, Loreau, M, Loya, Y, Martinez, C, Mascarenas-Osorio, I, Morove, T, Nadon, M-O, Nakamura, Y, Paredes, G, Polunin, NVC, Pratchett, MS, Bonilla, HR, Rivera, F, Sala, E, Sandin, SA, Soler, G, Stuart-Smith, R, Tessier, E, Tittensor, DP, Tupper, M, Usseglio, P, Vigliola, L, Wantiez, L, Williams, I, Wilson, SK & Zapata, FA 2011, 'Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes', PLOS BIOLOGY, vol. 9, no. 4, pp. 1-9.
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Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a nonsaturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the worlds coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas.

Morton, JK & Gladstone, W 2011, 'Spatial, temporal and ontogenetic variation in the association of fishes (family Labridae) with rocky-reef habitats', MARINE AND FRESHWATER RESEARCH, vol. 62, no. 7, pp. 870-884.
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Habitat variability is an important factor structuring fish assemblages of rocky reefs in temperate Australia. Accepting the generality of this model requires that habitat-related variation is consistent through time, across multiple spatial scales, and applies to all life-history stages. We used repeated underwater visual surveys at multiple spatial scales over a 22-month period to test whether three distinct rocky-reef habitats had different wrasse assemblages and whether these assemblages were subject to spatial, temporal and ontogenetic variability. Overall, the strongest and most consistent habitat association was with sponge gardens, which had the most distinct assemblage, and the greatest species richness and density of individuals. Habitat associations in fringe and barrens were less consistent. A substantial increase in the abundance of small individuals, coinciding with warmer sea temperatures, contributed to temporal fluctuations in the density of wrasses. Overall, habitats were not strongly partitioned among larger individuals of the most abundant species, suggesting that adults are largely habitat generalists whereas small, recruiting individuals showed greater habitat specialisation. The present study emphasises the importance of incorporating spatial, temporal and ontogenetic variability into surveys of fish assemblages to understand more fully the dynamics of temperate rocky-reef systems

Moxon, JV, Padula, MP, Clancy, P, Emeto, TI, Herbert, BR, Norman, PE & Golledge, J 2011, 'Proteomic analysis of intra-arterial thrombus secretions reveals a negative association of clusterin and thrombospondin-1 with abdominal aortic aneurysm', ATHEROSCLEROSIS, vol. 219, no. 2, pp. 432-439.
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Objective: Abdominal aortic aneurysm (AAA) is usually accompanied by the formation of a large volume of intra-luminal thrombus (ILT). ILT-derived proteins have been suggested as circulating markers for AAA. We conducted a proteomic study screening whole

Mueller, T, Aharonovich, I, Lombez, L, Alaverdyan, Y, Vamivakas, AN, Castelletto, S, Jelezko, F, Wrachtrup, J, Prawer, S & Atatuere, M 2011, 'Wide-range electrical tunability of single-photon emission from chromium-based colour centres in diamond', NEW JOURNAL OF PHYSICS, vol. 13.
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We demonstrate electrical control of the single-photon emission spectrum from chromium-based colour centres implanted in monolithic diamond. Under an external electric field, the tunability range is typically three orders of magnitude larger than the radiative linewidth and at least one order of magnitude larger than the observed linewidth. The electric and magnetic field dependence of luminescence gives indications of the inherent symmetry, and we propose Cr-X or X-Cr-Y-type non-centrosymmetric atomic configurations as the most probable candidates for these centres.

Murray, SA, Mihali, TK & Neilan, BA 2011, 'Extraordinary Conservation, Gene Loss, and Positive Selection in the Evolution of an Ancient Neurotoxin', MOLECULAR BIOLOGY AND EVOLUTION, vol. 28, no. 3, pp. 1173-1182.
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The recent determination of the genetic basis for the biosynthesis of the neurotoxin, saxitoxin, produced by cyanobacteria, has revealed a highly complex sequence of reactions, involving over 30 biosynthetic steps encoded by up to 26 genes clustered at o

Murray, SA, Wiese, M, Stuken, A, Brett, S, Kellmann, R, Hallegraeff, G & Neilan, BA 2011, 'sxtA-Based Quantitative Molecular Assay To Identify Saxitoxin-Producing Harmful Algal Blooms in Marine Waters', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 77, no. 19, pp. 7050-7057.
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The recent identification of genes involved in the production of the potent neurotoxin and keystone metabolite saxitoxin (STX) in marine eukaryotic phytoplankton has allowed us for the first time to develop molecular genetic methods to investigate the ch

Nagahama, Y, Murray, S, Tomaru, A & Fukuyo, Y 2011, 'SPECIES BOUNDARIES IN THE TOXIC DINOFLAGELLATE PROROCENTRUM LIMA (DINOPHYCEAE, PROROCENTRALES), BASED ON MORPHOLOGICAL AND PHYLOGENETIC CHARACTERS', JOURNAL OF PHYCOLOGY, vol. 47, no. 1, pp. 178-189.
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Wild and cultured specimens of Prorocentrum lima (Ehrenb.) F. Stein from 26 widely different areas in 13 countries were examined in order to determine consistent characters for delimiting species boundaries in this taxon. The morphological characters val

Nagy, G, Posselt, D, Kovacs, L, Holm, JK, Szabo, M, Ughy, B, Rosta, L, Peters, J, Timmins, P & Garab, G 2011, 'Reversible membrane reorganizations during photosynthesis in vivo: revealed by small-angle neutron scattering', BIOCHEMICAL JOURNAL, vol. 436, pp. 225-230.
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In the present study, we determined characteristic repeat distances of the photosynthetic membranes in living cyanobacterial and eukaryotic algal cells, and in intact thylakoid membranes isolated from higher plants with time-resolved small-angle neutron scattering. This non-invasive technique reveals light-induced reversible reorganizations in the seconds-to-minutes time scale, which appear to be associated with functional changes in vivo.

Nantakomol, D, Dondorp, AM, Krudsood, S, Udomsangpetch, R, Pattanapanyasat, K, Combes, V, Grau, GE, White, NJ, Viriyavejakul, P, Day, NPJ & Chotivanich, K 2011, 'Circulating Red Cell–derived Microparticles in Human Malaria', The Journal of Infectious Diseases, vol. 203, no. 5, pp. 700-706.
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Naughton, S, Parker, D, Seemann, T, Thomas, T, Turnbull, L, Rose, B, Bye, P, Cordwell, S, Whitchurch, C & Manos, J 2011, 'Pseudomonas aeruginosa AES-1 Exhibits Increased Virulence Gene Expression during Chronic Infection of Cystic Fibrosis Lung', PLOS ONE, vol. 6, no. 9, pp. e24526-e24526.
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Pseudomonas aeruginosa, the leading cause of morbidity and mortality in people with cystic fibrosis (CF), adapts for survival in the CF lung through both mutation and gene expression changes. Frequent clonal strains such as the Australian Epidemic Strain-1 (AES-1), have increased ability to establish infection in the CF lung and to superimpose and replace infrequent clonal strains. Little is known about the factors underpinning these properties. Analysis has been hampered by lack of expression array templates containing CF-strain specific genes. We sequenced the genome of an acute infection AES-1 isolate from a CF infant (AES-1R) and constructed a non-redundant micro-array (PANarray) comprising AES-1R and seven other sequenced P. aeruginosa genomes. The unclosed AES-1R genome comprised 6.254Mbp and contained 6957 putative genes, including 338 not found in the other seven genomes. The PANarray contained 12,543 gene probe spots; comprising 12,147 P. aeruginosa gene probes, 326 quality-control probes and 70 probes for non-P. aeruginosa genes, including phage and plant genes. We grew AES-1R and its isogenic pair AES-1M, taken from the same patient 10.5 years later and not eradicated in the intervening period, in our validated artificial sputum medium (ASMDM) and used the PANarray to compare gene expression of both in duplicate. 675 genes were differentially expressed between the isogenic pairs, including upregulation of alginate, biofilm, persistence genes and virulence-related genes such as dihydroorotase, uridylate kinase and cardiolipin synthase, in AES-1M. Non-PAO1 genes upregulated in AES-1M included pathogenesis-related (PAGI-5) genes present in strains PACS2 and PA7, and numerous phage genes. Elucidation of these genes' roles could lead to targeted treatment strategies for chronically infected CF patients.

Neville, SE, Palmer, MJ & Wand, MP 2011, 'GENERALIZED EXTREME VALUE ADDITIVE MODEL ANALYSIS VIA MEAN FIELD VARIATIONAL BAYES', Australian & New Zealand Journal of Statistics, vol. 53, no. 3, pp. 305-330.
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We develop Mean Field Variational Bayes methodology for fast approximate inference in Bayesian Generalized Extreme Value additive model analysis. Such models are useful for flexibly assessing the impact of continuous predictor variables on sample extreme

Ngo, L, Ryan, LM, Mezzetti, M, Bois, FY & Smith, TJ 2011, 'Estimating metabolic rate for butadiene at steady state using a Bayesian physiologically-based pharmacokinetic model', ENVIRONMENTAL AND ECOLOGICAL STATISTICS, vol. 18, no. 1, pp. 131-146.
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In a study of 133 volunteer subjects, demographic, physiologic and pharmacokinetic data through exposure to 1,3-Butadiene (BD) were collected in order to estimate the percentage of BD concentration metabolized at steady state, and to determine whether this percentage varies across gender, racial, and age groups. During the 20 min of continuous exposure to 2 parts per million (ppm) of BD, five measurements of exhaled concentration were made on each subject. In the following 40 min washout period, another five measurements were collected. A Bayesian hierarchical compartmental physiologically-based pharmacokinetic model (PKPB) was used. Using prior information on the model parameters, Markov Chain Monte Carlo (MCMC) simulation was conducted to obtain posterior distributions. The overall estimate of the mean percent of BD metabolized at steady state was 12.7% (95% credible interval: 7.7-17.8%). There was no significant difference in gender with males having a mean of 13.5%, and females 12.3%. Among the racial groups, Hispanic (13.9%), White (13.0%), Asian (12.1%), and Black (10.9%), the significant difference came from the difference between Black and Hispanic with a 95% credible interval from -5.63 to -0.30%. Those older than 30 years had a mean of 12.2% versus 12.9% for the younger group; although this was not a statistically significant difference. Given a constant inhalation input of 2 ppm, at steady state, the overall mean exhaled concentration was estimated to be 1.75ppm (95% credible interval: 1.64-1.84). An equivalent parameter, first-order metabolic rate constant, was also estimated and found to be consistent with the percent of BD metabolized at steady state across gender, race, and age strata.

Nicorovici, N-AP, McPhedran, RC & Botten, LC 2011, 'Relative local density of states and cloaking in finite clusters of coated cylinders', WAVES IN RANDOM AND COMPLEX MEDIA, vol. 21, no. 2, pp. 248-277.
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We describe a method for accurate calculation of the Relative Local Density of States (RLDOS) as a function of frequency and position in finite sets of coated cylinders. The RLDOS is important, since it describes the interaction between sources and their

Nicotra, AB, Leigh, A, Boyce, CK, Jones, CS, Niklas, KJ, Royer, DL & Tsukaya, H 2011, 'The evolution and functional significance of leaf shape in the angiosperms', Functional Plant Biology, vol. 38, no. 7, pp. 535-535.
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Angiosperm leaves manifest a remarkable diversity of shapes that range from developmental sequences within a shoot and within crown response to microenvironment to variation among species within and between communities and among orders or families. It is generally assumed that because photosynthetic leaves are critical to plant growth and survival, variation in their shape reflects natural selection operating on function. Several non-mutually exclusive theories have been proposed to explain leaf shape diversity. These include: thermoregulation of leaves especially in arid and hot environments, hydraulic constraints, patterns of leaf expansion in deciduous species, biomechanical constraints, adaptations to avoid herbivory, adaptations to optimise light interception and even that leaf shape variation is a response to selection on flower form. However, the relative importance, or likelihood, of each of these factors is unclear. Here we review the evolutionary context of leaf shape diversification, discuss the proximal mechanisms that generate the diversity in extant systems, and consider the evidence for each the above hypotheses in the context of the functional significance of leaf shape. The synthesis of these broad ranging areas helps to identify points of conceptual convergence for ongoing discussion and integrated directions for future research.

Orwa, JO, Santori, C, Fu, KMC, Gibson, B, Simpson, D, Aharonovich, I, Stacey, A, Cimmino, A, Balog, P, Markham, M, Twitchen, D, Greentree, AD, Beausoleil, RG & Prawer, S 2011, 'Engineering of nitrogen-vacancy color centers in high purity diamond by ion implantation and annealing', JOURNAL OF APPLIED PHYSICS, vol. 109, no. 8, p. 083530.
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The negatively-charged nitrogen-vacancy (NV) center is the most studied optical center in diamond and is very important for applications in quantum information science. Many proposals for integrating NV centers in quantum and sensing applications rely on their tailored fabrication in ultra pure host material. In this study, we use ion implantation to controllably introduce nitrogen into high purity, low nitrogen chemical vapor deposition diamond samples. The properties of the resulting NV centers are studied as a function of implantation temperature, annealing temperature, and implantation fluence. We compare the implanted NV centers with native NV centers present deep in the bulk of the as-grown samples. The results for implanted NV centers are promising but indicate, at this stage, that the deep native NV centers possess overall superior optical properties. In particular, the implanted NV centers obtained after annealing at 2000 !C under a stabilizing pressure of 8 GPa showed an ensemble linewidth of 0.17 nm compared to 0.61 nm after annealing at 1000 !C. Over the same temperature range, the ensemble NV"/NV0 ratio increased by a factor of #5, although this was accompanied by an overall decrease in the NV count.

Ostrowski, M, Tetu, S, Hassan, K, Penesyan, A, Lim, K, Elbourne, L, Li, L, Varkey, D & Paulsen, I 2011, 'From omics to systems biology: Exploring the mystery box of microbial life', Microbiology Australia, vol. 32, no. 4, pp. 147-147.
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Microbial molecular biology has traditionally used very reductionist approaches; for example, find a gene of interest, clone it or knock it out and see if you can detect a phenotype. The genomics era has opened up the possibility of analysing microbes and communities at a systems level by combining high-throughput experimental data from genomic, transcriptomic, proteomic and phenomic techniques. This parallels earlier reductionist approaches by going from DNA to RNA to protein to phenotype, albeit on a global rather than individual gene scale.

Pakpour, AH, Yekaninejad, MS & Chen, H 2011, 'Mothers’ perception of obesity in schoolchildren: a survey and the impact of an educational intervention', Jornal de Pediatria, vol. 87, no. 2, pp. 169-174.
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Objectives: To investigate mothers' awareness of their children's weight problem, and to evaluate the impact of an educational intervention on improving mothers' recognition of obesity in their children. Methods: Twelve primary schools from Tehran, Iran,

Pant, R, Li, E, Choi, D-Y, Poulton, CG, Madden, SJ, Luther-Davies, B & Eggleton, BJ 2011, 'Cavity enhanced stimulated Brillouin scattering in an optical chip for multiorder Stokes generation', Optics Letters, vol. 36, no. 18, pp. 3687-3687.
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We report the first demonstration of on-chip cascaded stimulated Brillouin scattering (SBS). Cascaded SBS is characterized in a 4 cm long chalcogenide (As(2)S(3)) rib waveguide where the end facet reflections provide a monolithic Fabry-Perot (FP) resonator. The presence of the FP cavity reduces the Brillouin gain threshold, which enables observation of cascaded SBS at reduced pump powers. We observe up to three orders of Stokes waves in the backscattered signal at a coupled peak power of 1.34 W. Anti-Stokes waves due to four-wave mixing between the pump and the Stokes wave were observed in the forward spectrum.

Pant, R, Poulton, CG, Choi, D-Y, Mcfarlane, H, Hile, S, Li, E, Thevenaz, L, Luther-Davies, B, Madden, SJ & Eggleton, BJ 2011, 'On-chip stimulated Brillouin scattering', Optics Express, vol. 19, no. 9, pp. 8285-8285.
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We demonstrate on-chip stimulated Brillouin scattering (SBS) in an As2S3 chalcogenide rib waveguide. SBS was characterized in a 7cm long waveguide with a cross-section 4£gm x 850nm using the backscattered signal and pump-probe technique. The measured Brillouin shift and its full-width at half-maximum (FWHM) linewidth were ~7.7 GHz and 34 MHz, respectively. Probe vs. pump power measurements at the Brillouin shift were used to obtain the gain coefficient from an exponential fit. The Brillouin gain coefficient obtained was 0.715 x 10{9 m/W. A probe gain of 16 dB was obtained for a CW pump power of ~300 mW.

Park, J-H, Gail, MH, Weinberg, CR, Carroll, RJ, Chung, CC, Wang, Z, Chanock, SJ, Fraumeni, JF & Chatterjee, N 2011, 'Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants', Proceedings of the National Academy of Sciences, vol. 108, no. 44, pp. 18026-18031.
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Recent discoveries of hundreds of common susceptibility SNPs from genome-wide association studies provide a unique opportunity to examine population genetic models for complex traits. In this report, we investigate distributions of various population genetic parameters and their interrelationships using estimates of allele frequencies and effect-size parameters for about 400 susceptibility SNPs across a spectrum of qualitative and quantitative traits. We calibrate our analysis by statistical power for detection of SNPs to account for overrepresentation of variants with larger effect sizes in currently known SNPs that are expected due to statistical power for discovery. Across all qualitative disease traits, minor alleles conferred “risk” more often than “protection.” Across all traits, an inverse relationship existed between “regression effects” and allele frequencies. Both of these trends were remarkably strong for type I diabetes, a trait that is most likely to be influenced by selection, but were modest for other traits such as human height or late-onset diseases such as type II diabetes and cancers. Across all traits, the estimated effect-size distribution suggested the existence of increasingly large numbers of susceptibility SNPs with decreasingly small effects. For most traits, the set of SNPs with intermediate minor allele frequencies (5–20%) contained an unusually small number of susceptibility loci and explained a relatively small fraction of heritability compared with what would be expected from the distribution of SNPs in the general population. These trends could have several implications for future studies of common and uncommon variants.

Peng, D, Huete, AR, Huang, J, Wang, F & Sun, H 2011, 'Detection and estimation of mixed paddy rice cropping patterns with MODIS data', INTERNATIONAL JOURNAL OF APPLIED EARTH OBSERVATION AND GEOINFORMATION, vol. 13, no. 1, pp. 13-23.
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In this paper, we developed a more sophisticated method for detection and estimation of mixed paddy rice agriculture from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data. Previous research demonstrated that MODIS data can be used to map paddy rice fields and to distinguish rice from other crops at large, continental scales with combined Enhanced Vegetation Index (EVI) and Land Surface Water Index (LSWI) analysis during the flooding and rice transplanting stage. Our approach improves upon this methodology by incorporating mixed rice cropping patterns that include single-season rice crops, early-season rice, and late-season rice cropping systems. A variable EVI/LSWI threshold function, calibrated to more local rice management practices, was used to recognize rice fields at the flooding stage. We developed our approach with MODIS data in Hunan Province, China, an area with significant flooded paddy rice agriculture and mixed rice cropping patterns. We further mapped the aerial coverage and distribution of early, late, and single paddy rice crops for several years from 2000 to 2007 in order to quantify temporal trends in rice crop coverage, growth and management systems. Our results were validated with finer resolution (2.5 m) Satellite Pour l'Observation de la Terre 5 High Resolution Geometric (SPOT 5 HRG) data, land-use data at the scale of 1/10,000 and with county-level rice area statistical data. The results showed that all three paddy rice crop patterns could be discriminated and their spatial distribution quantified. We show the area of single crop rice to have increased annually and almost doubling in extent from 2000 to 2007, with simultaneous, but unique declines in the extent of early and late paddy rice. These results were significantly positive correlated and consistent with agricultural statistical data at the county level (P<0.01).

Perez, A, AlKhamis, M, Carlsson, U, Brito, B, Carrasco-Medanic, R, Whedbee, Z & Willeberg, P 2011, 'Global animal disease surveillance', Spatial and Spatio-temporal Epidemiology, vol. 2, no. 3, pp. 135-145.
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Development and implementation of global animal disease surveillance has been limited by the lack of information systems that enable near real-time data capturing, sharing, analysis, and related decision- and policy-making. The objective of this paper is to describe requirements for global animal disease surveillance, including design and functionality of tools and methods for visualization and analysis of animal disease data. The paper also explores the potential application of techniques for spatial and spatio-temporal analysis on global animal disease surveillance, including for example, landscape genetics, social network analysis, and Bayesian modeling. Finally, highly pathogenic avian influenza data from Denmark and Sweden are used to illustrate the potential application of a novel system (Disease BioPortal) for data sharing, visualization, and analysis for regional and global surveillance efforts. © 2011 Elsevier Ltd.

Pernice, M, Dunn, SR, Miard, T, Dufour, S, Dove, S & Hoegh-Guldberg, O 2011, 'Regulation of Apoptotic Mediators Reveals Dynamic Responses to Thermal Stress in the Reef Building Coral Acropora millepora', PLoS ONE, vol. 6, no. 1, pp. e16095-e16095.
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Petrou, K & Ralph, PJ 2011, 'Photosynthesis and net primary productivity in three Antarctic diatoms: possible significance for their distribution in the Antarctic marine ecosystem', MARINE ECOLOGY PROGRESS SERIES, vol. 437, pp. 27-40.
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Photosynthesis and net primary productivity were measured in 3 Antarctic diatoms, Fragilariopsis cylindrus, Pseudo-nitzschia subcurvata and Chaetoceros sp., exposed to rapid changes in temperature and salinity representing a range of conditions found during a seasonal cycle. Measured differences in fluorescence-derived photosynthetic activity and oxygen evolution suggested that some alternative electron cycling activity was present under high irradiances. F. cylindrus displayed the highest rates of relative electron transport and net primary productivity under all salinity and temperature combinations and showed adaptive traits towards the sea-ice-like environment. P. subcurvata displayed a preference for low saline conditions where production rates were greatest. However, there was evidence of photosynthetic sensitivity to the lowest temperatures and highest salinities, suggesting a lack of adaptation for dealing with sea-ice-like conditions. Chaetoceros sp. showed high plasticity, acclimating well to all conditions but performing best under pelagic conditions. The study shows species-specific sensitivities to environmental change, highlighting photosynthetic capacity as a potentially important mechanism in ecological niche adaptation. When these data were modelled over different seasons, integrated daily net primary production was greatest under summer pelagic conditions. The findings from this study support the general observations of light control and seasonal development of net primary productivity and species succession in the Antarctic marine ecosystem.

Petrou, K, Doblin, MA & Ralph, PJ 2011, 'Heterogeneity in the photoprotective capacity of three Antarctic diatoms during short-term changes in salinity and temperature', MARINE BIOLOGY, vol. 158, no. 5, pp. 1029-1041.
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The Antarctic marine ecosystem changes seasonally, forming a temporal continuum of specialised niche habitats including open ocean, sea ice and meltwater environments. The ability for phytoplankton to acclimate rapidly to the changed conditions of these environments depends on the speciesâ physiology and photosynthetic plasticity and may ultimately determine their long-term ecological niche adaptation. This study investigated the photophysiological plasticity and rapid acclimation response of three Antarctic diatomsâFragilariopsis cylindrus, Pseudo-nitzschia subcurvata and Chaetoceros sp.âto a selected range of temperatures and salinities representative of the sea ice, meltwater and pelagic habitats in the Antarctic. Fragilariopsis cylindrus displayed physiological traits typical of adaptation to the sea ice environment. Equally, this species showed photosynthetic plasticity, acclimating to the range of environmental conditions, explaining the prevalence of this species in all Antarctic habitats. Pseudo-nitzschia subcurvata displayed a preference for the meltwater environment, but unlike F. cylindrus, photoprotective capacity was low and regulated via changes in PSII antenna size. Chaetoceros sp. had high plasticity in non-photochemical quenching, suggesting adaptation to variable light conditions experienced in the wind-mixed pelagic environment. While only capturing short-term responses, this study highlights the diversity in photoprotective capacity that exists amongst three dominant Antarctic diatom species and provides insight into links between ecological niche adaptation and speciesâ distribution

Petrou, K, Hassler, CS, Doblin, MA, Shelly, K, Schoemann, V, van den Enden, R, Wright, S & Ralph, PJ 2011, 'Iron-limitation and high light stress on phytoplankton populations from the Australian Sub-Antarctic Zone (SAZ)', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 58, no. 21-22, pp. 2200-2211.
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The high nutrient low chlorophyll (HNLC) surface waters of the Southern Ocean are characterised by high concentrations of nitrate and phosphate, low concentrations of dissolved iron and deep vertical mixing. Future climate scenarios predict increased sur

Petrou, K, Hill, R, Doblin, MA, McMinn, A, Johnson, R, Wright, SW & Ralph, PJ 2011, 'PHOTOPROTECTION OF SEA-ICE MICROALGAL COMMUNITIES FROM THE EAST ANTARCTIC PACK ICE', JOURNAL OF PHYCOLOGY, vol. 47, no. 1, pp. 77-86.
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All photosynthetic organisms endeavor to balance energy supply with demand. For sea-ice diatoms, as with all marine photoautotrophs, light is the most important factor for determining growth and carbonfixation rates. Light varies from extremely low to often relatively high irradiances within the sea-ice environment, meaning that sea-ice algae require moderate physiological plasticity that is necessary for rapid light acclimation and photoprotection. This study investigated photoprotective mechanisms employed by bottom Antarctic sea-ice algae in response to relatively high irradiances to understand how they acclimate to the environmental conditions presented during early spring, as the light climate begins to intensify and snow and sea-ice thinning commences.

Phyu, YL, Palmer, CG, Warne, MSJ, Hose, GC, Chapman, JC & Lim, RP 2011, 'A comparison of mixture toxicity assessment: Examining the chronic toxicity of atrazine, permethrin and chlorothalonil in mixtures to Ceriodaphnia cf. dubia', CHEMOSPHERE, vol. 85, no. 10, pp. 1568-1573.
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Pesticides predominantly occur in aquatic ecosystems as mixtures of varying complexity, yet relatively few studies have examined the toxicity of pesticide mixtures. Atrazine, chlorothalonil and permethrin are widely used pesticides that have different mo

Piefer, LA, Stehm, RE, Krenek, KA, Weeks, BR, Carroll, RJ, Byrne, DH, Talcott, ST & Turner, ND 2011, 'Chlorogenic acid reduced DSS‐induced injury and NF‐κB activation in a rat colitis model', The FASEB Journal, vol. 25, no. S1.
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Pike, DA, Webb, JK & Andrews, RM 2011, 'Social and Thermal Cues Influence Nest-site Selection in a Nocturnal Gecko, Oedura lesueurii', ETHOLOGY, vol. 117, no. 9, pp. 796-801.
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In oviparous species lacking parental care, successful reproduction depends on females selecting nest sites that facilitate embryonic development. Such sites may be limited in the environment, which can lead to multiple females using the same nest site simultaneously. However, there are several alternative explanations for communal nesting, including natal homing, predator satiation, and adaptive benefits to offspring. We used laboratory experiments to evaluate three hypotheses about nest-site selection in velvet geckos (Oedura lesueurii), which often nest communally. We investigated whether the trend to nest communally is influenced by the following: (1) evidence of previous nesting (hatched eggshells); (2) body size; and/or (3) thermal regimes. When given the choice, females laid their eggs in shelters containing hatched eggshells rather than in empty shelters, and this was not influenced by body size. Females selected nest sites that were cooler than their own mean selected body temperatures, suggesting that thermal requirements of their developing embryos could outweigh their own thermoregulatory preferences. Field observations of natal homing and high predation rates on gravid females suggest that imprinting on nest sites and/or predator swamping also play roles in communal nesting. Collectively, our results suggest that female velvet geckos use multiple cues to select appropriate nest sites, and hence that multiple mechanisms result in communal nesting behavior in this species.

Pike, DA, Webb, JK & Shine, R 2011, 'Chainsawing for conservation: Ecologically informed tree removal for habitat management', Ecological Management & Restoration, vol. 12, no. 2, pp. 110-118.
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In many ecosystems, increases in vegetation density and the resulting closure of forest canopies are threatening the viability of species that depend upon open, sunlight- exposed habitats. Consequently, we need to develop management strategies that recreate open habitats while minimizing the impacts on non-target areas. Selective logging creates canopy gaps, but may result in undesirable effects in other respects. Thus, chainsaws have not been a popular tool for conservation. We conducted a landscape-scale experiment to test whether selective tree removal can restore patch-level habitat quality for Australias most endangered snake (Hoplocephalus bungaroides) and its main prey (the lizard Oedura lesueurii). We selectively removed canopy trees surrounding 25 overgrown rock outcrops and compared the resultant habitat structure and abiotic conditions to 30 overgrown, shady outcrops and 20 open, sunny outcrops. Removing vegetation decreased canopy cover by 19% in experimental plots and increased incident radiation and thermal regimes. These changes increased the availability of suitable shelter sites for our target species by 131%. At the landscape scale, our manipulations had a trivial effect on forest habitat; by increasing the area of sun-exposed outcrops, we decreased forest cover by <0.1%. Our results show that targeted canopy removal can increase the availability of sun-exposed habitat patches for endangered species in biologically meaningful ways. Thus, selective tree felling may be an effective conservation tool for open-habitat specialists threatened by vegetation overgrowth.

Pike, DA, Webb, JK & Shine, R 2011, 'Removing forest canopy cover restores a reptile assemblage', ECOLOGICAL APPLICATIONS, vol. 21, no. 1, pp. 274-280.
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Humans are rapidly altering natural systems, leading to changes in the distribution and abundance of species. However, so many changes are occurring simultaneously (e.g., climate change, habitat fragmentation) that it is difficult to determine the cause of population fluctuations from correlational studies. We used a manipulative field experiment to determine whether forest canopy cover directly influences reptile assemblages on rock outcrops in southeastern Australia. Our experimental design consisted of three types of rock outcrops: (1) shady sites in which overgrown vegetation was manually removed (n=25); (2) overgrown controls (n= 30); and (3) sun-exposed controls (n= 20). Following canopy removal, we monitored reptile responses over 30 months. Canopy removal increased reptile species richness, the proportion of shelter sites used by reptiles, and relative abundances of five species that prefer sun-exposed habitats. Our manipulation also decreased the abundances of two shade-tolerant species. Canopy cover thus directly influences this reptile assemblage, with the effects of canopy removal being dependent on each species' habitat preferences (i.e., selection or avoidance of sun-exposed habitat). Our study suggests that increases in canopy cover can cause declines of open-habitat specialists, as previously suggested by correlative studies from a wide range of taxa. Given that reptile colonization of manipulated outcrops occurred rapidly, artificially opening the canopy in ecologically informed ways could help to conserve imperiled species with patchy distributions and low vagility that are threatened by vegetation overgrowth. One such species is Australia's most endangered snake, the broadheaded snake (Hoplocephalus bungaroides

Pissuwan, D, Niidome, T & Cortie, MB 2011, 'The forthcoming applications of gold nanoparticles in drug and gene delivery systems', JOURNAL OF CONTROLLED RELEASE, vol. 149, no. 1, pp. 65-71.
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The unique optical, chemical, and biological properties of gold nanoparticles have resulted in them becoming of clinical interest in several applications including drug and gene delivery. The attractive features of gold nanoparticles include their surface plasmon resonance, the controlled manner in which they interact with thiol groups, and their non-toxic nature. These attributes can be exploited to provide an effective and selective platform to obtain a targeted intracellular release of some substance. The use of gold nanoparticles can also increase the stability of the payload. Here we review recent advances in the use of gold nanoparticles in drug and gene delivery systems. The topics of surface modification, site-specificity and drugs and gene and gene delivery are discussed.

Platen, E & Hulley, H 2011, 'A visual criterion for identifying Itô diffusions as martingales or strict local martingales', Seminar on Stochastic Analysis, Random Fields and Applications, vol. 6, pp. 147-157.

Platen, E & West, J 2011, 'Intraday Empirical Analysis of Electricity Price Behaviour', Communications on Stochastic Analysis, vol. 5, no. 4, pp. 721-744.
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This paper proposes an approach to the intraday analysis of the dynamics of electricity prices. The growth optimal portfolio (GOP) is used as a reference unit in a continuous financial electricity price model. A diversified global portfolio in the form a market capitalisation weighted index approx- imates the GOP. The GOP, measured in units of electricity, is normalised and then modelled as a time transformed square root process of dimension four. The dynamics of the resulting process is empirically verified. Intra- day spot electricity prices from the US and Australian markets are used for this analysis. The empirical findings identify a simple but realistic model for examining the volatile behaviour of electricity prices. The proposed model reflects the historical price evolution reasonably well by using only a few ro- bust and readily observable parameters. The evolution of the transformed time is modelled via a rapidly evolving market activity. A periodic, ergodic process with deterministic volatility is used to model market activity.

Ponton, F, Chapuis, M-P, Pernice, M, Sword, GA & Simpson, SJ 2011, 'Evaluation of potential reference genes for reverse transcription-qPCR studies of physiological responses in Drosophila melanogaster', Journal of Insect Physiology, vol. 57, no. 6, pp. 840-850.
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Porkovich, AJ, Arnold, MD, Kouzmina, G, Hingley, B, Dowd, A & Cortie, MB 2011, 'Calorimetric Sensor for Use in Hydrogen Peroxide Aqueous Solutions', SENSOR LETTERS, vol. 9, no. 2, pp. 695-697.
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A sensor for characterising aqueous solutions of hydrogen peroxide is described. The sensor is based on the calorimetric signal obtained when catalysing the decomposition of H(2)O(2). The system is quick and simple, and is suitable for determinations of H(2)O(2) concentration between 0% and at least 50% (w/w).

Preston, JA, Thorburn, AN, Starkey, MR, Beckett, EL, Horvat, JC, Wade, MA, O'Sullivan, BJ, Thomas, R, Beagley, KW, Gibson, PG, Foster, PS & Hansbro, PM 2011, 'Streptococcus pneumoniae infection suppresses allergic airways disease by inducing regulatory T-cells', European Respiratory Journal, vol. 37, no. 1, pp. 53-64.
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Price-Carter, M, Roy-Chowdhury, P, Pope, CE, Paine, S, De Lisle, GW, Collins, DM, Nicol, C & Carter, PE 2011, 'The evolution and distribution of phage ST160 within Salmonella enterica serotype Typhimurium', EPIDEMIOLOGY AND INFECTION, vol. 139, no. 8, pp. 1262-1271.
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Salmonellosis is an internationally important disease of mammals and birds. Unique epidemics in New Zealand in the recent past include two Salmonella serovars: Salmonella enterica subsp. enterica serovar Typhimurium definitive type (DT) 160 (S. Typhimurium DT160) and S. Brandenburg. Although not a major threat internationally, in New Zealand S. Typhimurium DT160 has been the most common serovar isolated from humans, and continues to cause significant losses in wildlife. We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost identical to phage SE1 but has two regions not found in SE1 which are identical to the P22-like phage ST64T, suggesting that ST160 evolved from SE1 via two recombination events with ST64T. All of the New Zealand isolates of DT160 were identical indicating the clonal spread of this particular Salmonella. Some overseas isolates of S. Typhimurium DT160 differed from the New Zealand strain and contained SE1 phage rather than ST160. ST160 was also identified in New Zealand isolates of S. Typhimurium DT74 and S. Typhimurium RDNC-April06 and in S. Typhimurium DT160 isolates from the USA. The emergence of S. Typhimurium DT160 as a significant pathogen in New Zealand is postulated to have occurred due to the sensitivity of the Salmonella strains to the ST160 phage when S. Typhimurium DT160 first arrived.

Price-Rees, SJ, Webb, JK & Shine, R 2011, 'School for Skinks: Can Conditioned Taste Aversion Enable Bluetongue Lizards (Tiliqua scincoides) to Avoid Toxic Cane Toads (Rhinella marina) as Prey?', ETHOLOGY, vol. 117, no. 9, pp. 749-757.
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The invasion of cane toads (Rhinella marina) through Australia imperils native predators that are killed if they consume these toxic anurans. The magnitude of impact depends upon the predators' capacity for aversion learning: toad impact is lower if predators can learn not to attack toads. In laboratory trials, we assessed whether bluetongue lizards (Tiliqua scincoides) - a species under severe threat from toads - are capable of learned taste aversion and whether we can facilitate that learning by exposing lizards to toad tissue combined with a nausea-inducing chemical (lithium chloride). Captive bluetongues rapidly learned to avoid the 'unpalatable' food. Taste aversion also developed (albeit less strongly) in response to meals of minced cane toad alone. Our data suggest that taste aversion learning may help bluetongue lizards survive the onslaught of cane toads, but that many encounters will be fatal because the toxin content of toads is so high relative to lizard tolerance of those toxins. Thus, baiting with nausea-inducing (but non-lethal) toad products might provide a feasible management option to reduce the impact of cane toad invasion on these native predators.

Raetsep, M, Cai, Z-L, Reimers, JR & Freiberg, A 2011, 'Demonstration and interpretation of significant asymmetry in the low-resolution and high-resolution Q(y) fluorescence and absorption spectra of bacteriochlorophyll a', JOURNAL OF CHEMICAL PHYSICS, vol. 134, no. 2.
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Low- and high-resolution absorption and fluorescence emission Qy spectra of bacteriochlorophyll a (BChl a) were recorded, along with homogeneous band line shapes, revealing significant asymmetry between the absorption and emission profiles that are interpreted using a priori spectral calculations. The spectra were recorded in a range of organic solvents facilitating both penta- and hexa-coordination of Mg at ambient and cryogenic temperatures. Detailed vibrational structure in the ground electronic state, virtually independent of Mg coordination, was revealed at 4.5 K by a hole-burning fluorescence line-narrowing technique, complementing the high-resolution spectrum of the excited state measured previously by hole burning to provide the first complete description of the Qy absorption and fluorescence spectra of BChl a. Spectral asymmetry persists from 4.5 to 298 K. Time-dependent density-functional theory calculations of the gas-phase absorption and emission spectra obtained using the CAM-B3LYP density functional, curvilinear coordinates, and stretch-bend-torsion scaling factors fitted to data for free-base porphyrin quantitatively predict the observed frequencies of the most-significant vibrational modes as well as the observed absorption/emission asymmetry. Most other semi-empirical, density-functional, and ab initio computational methods severely overestimate the electron-vibrational coupling and its asymmetry. It is shown that the asymmetry arises primarily through Duschinsky rotation.

Raghu, AV, Unnikrishnan, K, Geetha, SP, Martin, G & Balachandran, I 2011, 'Plant regeneration and production of embelin from organogenic and embryogenic callus cultures of Embelia ribes Burm. f.-a vulnerable medicinal plant', IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT, vol. 47, no. 4, pp. 506-515.
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Randolph, S, Toth, M, Cullen, J, Chandler, C & Lobo, C 2011, 'Kinetics of gas mediated electron beam induced etching', Applied Physics Letters, vol. 99, no. 21, pp. 213103-213103.
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Electron beam induced etching (EBIE) is a high resolution, direct write, chemical dry etch process in which surface-adsorbed precursor molecules are activated by an electron beam. We show that nanoscale EBIE is rate limited through at least two mechanisms ascribed to adsorbate depletion and the transport of gaseous precursor molecules into an etch pit during etching, respectively. The latter has, to date, not been accounted for in models of EBIE and is needed to reproduce etch kinetics which govern the time-evolution of etch pits, EBIE throughput, and spatial resolution.

Raymond, J, van Oorschot, RAH, Walsh, SJ, Gunn, PR & Roux, CP 2011, 'How far have we come with trace DNA since 2004? The Australian and New Zealand experience', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 43, no. 4, pp. 231-244.
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In 2004, a survey was sent to forensic organisations in every jurisdiction in Australia and New Zealand, benchmarking practices in relation to trace DNA analysis. Concerning issues were identified such as a lack of standard training protocols, little ongoing training or proficiency testing, and poor information gathering and sharing. To assess the changes occurring in the five years since this survey, a follow-up was devised and distributed to the same organisations in early 2009. Seventy-seven surveys were received from persons active in the field of trace DNA including crime scene and laboratory personnel, and managers. The major difference noted between the two surveys was the implementation of new technologies, primarily robotic automation and subsequent changes in extraction methodology. Disappointingly, training, research and proficiency test levels were still found to be lacking, a concern given the findings of recent international forensic reviews. A major deficiency still noted from the 2004 survey was the absence of effective data management systems, indicating that the wider intelligence-led application of this evidence is not fully utilised. Reviewing the methods and processes of the dissemination of forensic data in the policing environment has the potential to broaden its application to crime prevention strategies

Reid, DD, Robbins, WD & Peddemors, VM 2011, 'Decadal trends in shark catches and effort from the New South Wales, Australia, Shark Meshing Program 1950-2010', MARINE AND FRESHWATER RESEARCH, vol. 62, no. 6, pp. 676-693.
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Reim, KF, Michelberger, P, Lee, KC, Nunn, J, Langford, NK & Walmsley, IA 2011, 'Single-Photon-Level Quantum Memory at Room Temperature', Physical Review Letters, vol. 107, no. 5.
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Reimers, GJ, Jackson, CL, Rickards, J, Chan, PY, Cohn, JS, Rye, K-A, Barter, PJ & Rodgers, KJ 2011, 'Inhibition of rupture of established atherosclerotic plaques by treatment with apolipoprotein A-I', CARDIOVASCULAR RESEARCH, vol. 91, no. 1, pp. 37-44.
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Aims Plasma concentrations of high-density lipoprotein (HDL)-cholesterol correlate inversely with the incidence of myocardial infarction in humans. We investigated the effect of treatment with human apolipoprotein A-I (apoA-I), the principal protein of HDL, on plaque disruption in an animal model. Methods and results Seventy apolipoprotein E knockout mice were induced to develop atherosclerotic lesions in the brachiocephalic artery by feeding a high-fat diet for 9 weeks. Mice then received twice-weekly treatment with human apoA-I (8 mg/kg) or vehicle, for 2 weeks. The incidence of acute plaque disruption was reduced by 65% in mice receiving apoA-I (P < 0.01). Plaques in treated mice had a more stable phenotype, with an increase in smooth muscle cell (SMC): macrophage ratio (P = 0.05), principally the consequence of an increase in the number of SMC in plaques. In the fibrous cap, there were reductions in matrix metalloproteinase-13 (-69%, P < 0.0001) and S100A4, a marker of SMC de-differentiation (-60%, P < 0.0001). These results indicate that 2 weeks of treatment with small amounts of human apoA-I produces more stable plaques in a mouse model.

Ren, D, Fu, R, Leslie, LM & Dickinson, RE 2011, 'Modeling the mudslide aftermath of the 2007 Southern California Wildfires', Natural Hazards, vol. 57, no. 2, pp. 327-343.
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Ren, D, Fu, R, Leslie, LM & Dickinson, RE 2011, 'Predicting Storm-triggered Landslides', Bulletin of the American Meteorological Society, vol. 92, no. 2, pp. 129-139.
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Ren, D, Fu, R, Leslie, LM, Chen, J, Wilson, CR & Karoly, DJ 2011, 'The Greenland Ice Sheet Response to Transient Climate Change', Journal of Climate, vol. 24, no. 13, pp. 3469-3483.
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Abstract This study applies a multiphase, multiple-rheology, scalable, and extensible geofluid model to the Greenland Ice Sheet (GrIS). The model is driven by monthly atmospheric forcing from global climate model simulations. Novel features of the model, referred to as the scalable and extensible geofluid modeling system (SEGMENT-Ice), include using the full Navier–Stokes equations to account for nonlocal dynamic balance and its influence on ice flow, and a granular sliding layer between the bottom ice layer and the lithosphere layer to provide a mechanism for possible large-scale surges in a warmer future climate (granular basal layer is for certain specific regions, though). Monthly climate of SEGMENT-Ice allows an investigation of detailed features such as seasonal melt area extent (SME) over Greenland. The model reproduced reasonably well the annual maximum SME and total ice mass lost rate when compared observations from the Special Sensing Microwave Imager (SSM/I) and Gravity Recovery and Climate Experiment (GRACE) over the past few decades. The SEGMENT-Ice simulations are driven by projections from two relatively high-resolution climate models, the NCAR Community Climate System Model, version 3 (CCSM3) and the Model for Interdisciplinary Research on Climate 3.2, high-resolution version [MIROC3.2(hires)], under a realistic twenty-first-century greenhouse gas emission scenario. They suggest that the surface flow would be enhanced over the entire GrIS owing to a reduction of ice viscosity as the temperature increases, despite the small change in the ice surface topography over the interior of Greenland. With increased surface flow speed, strain heating induces more rapid heating in the ice at levels deeper than due to diffusion alone. Basal sliding, especially for granular sediments, provides an efficient mechanism for fast-glacier acceleration and enhanced mass loss. This mechanis...

Ren, D, Fu, R, Leslie, LM, Karoly, DJ, Chen, J & Wilson, C 2011, 'A multirheology ice model: Formulation and application to the Greenland ice sheet', Journal of Geophysical Research, vol. 116, no. D5.
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Riglar, DT, Richard, D, Wilson, DW, Boyle, MJ, Dekiwadia, C, Turnbull, L, Angrisano, F, Marapana, DS, Rogers, KL, Whitchurch, CB, Beeson, JG, Cowman, AF, Ralph, SA & Baum, J 2011, 'Super-Resolution Dissection of Coordinated Events during Malaria Parasite Invasion of the Human Erythrocyte', CELL HOST & MICROBE, vol. 9, no. 1, pp. 9-20.
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Erythrocyte invasion by the merozoite is an obligatory stage in Plasmodium parasite infection and essential to malaria disease progression. Attempts to study this process have been hindered by the poor invasion synchrony of merozoites from the only in vi

Ritchie, LE, Carroll, RJ, Weeks, BR, McDonough, CM, Dykes, L, Rooney, LW & Turner, ND 2011, 'Reduction in DSS‐induced enhancement of colonic injury and NF‐κB activation in rats consuming a diet containing black sorghum bran', The FASEB Journal, vol. 25, no. S1.
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Robbins, WD, Peddemors, VM & Kennelly, SJ 2011, 'Assessment of permanent magnets and electropositive metals to reduce the line-based capture of Galapagos sharks, Carcharhinus galapagensis', FISHERIES RESEARCH, vol. 109, no. 1, pp. 100-106.
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Roberts, T, Barratt, J, Harkness, J, Ellis, J & Stark, D 2011, 'Comparison of Microscopy, Culture, and Conventional Polymerase Chain Reaction for Detection of Blastocystis sp in Clinical Stool Samples', AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, vol. 84, no. 2, pp. 308-312.
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We tested 513 stool samples from patients in Sydney, Australia for Blastocystis by using five diagnostic techniques: microscopy of a permanently stained smear using a modified iron-hematoxylin stain, two xenic culture systems (a modified Boeck and Drbohlav's medium and tryptone, yeast extract, glucose, methionine-9 medium), and two published conventional polymerase chain reaction methods specific for the small subunit ribosomal DNA. Ninety-eight (19%) samples were positive for Blastocystis in one or more of the diagnostic techniques. The PCR 2 method was the most sensitive at detecting Blastocystis with a sensitivity of 94%, and the least sensitive was microscopy of the permanent stain (48%). Subtype 3 was the most predominant subtype (present in 43% of samples assigned to this group). This study highlights the low sensitivity of microscopy when used as the sole diagnostic modality for detection of Blastocystis sp

Robinson, MW, Corvo, I, Jones, PM, George, AM, Padula, MP, To, J, Cancela, M, Rinaldi, G, Tort, JF, Roche, L & Dalton, JP 2011, 'Collagenolytic Activities of the Major Secreted Cathepsin L Peptidases Involved in the Virulence of the Helminth Pathogen, Fasciola hepatica', PLoS Neglected Tropical Diseases, vol. 5, no. 4, pp. e1012-e1012.
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Background: The temporal expression and secretion of distinct members of a family of virulence-associated cathepsin L cysteine peptidases (FhCL) correlates with the entry and migration of the helminth pathogen Fasciola hepatica in the host. Thus, infective larvae traversing the gut wall secrete cathepsin L3 (FhCL3), liver migrating juvenile parasites secrete both FhCL1 and FhCL2 while the mature bile duct parasites, which are obligate blood feeders, secrete predominantly FhCL1 but also FhCL2. Methodology/Principal Findings: Here we show that FhCL1, FhCL2 and FhCL3 exhibit differences in their kinetic parameters towards a range of peptide substrates. Uniquely, FhCL2 and FhCL3 readily cleave substrates with Pro in the P2 position and peptide substrates mimicking the repeating Gly-Pro-Xaa motifs that occur within the primary sequence of collagen. FhCL1, FhCL2 and FhCL3 hydrolysed native type I and II collagen at neutral pH but while FhCL1 cleaved only non-collagenous (NC, non-Gly-X-Y) domains FhCL2 and FhCL3 exhibited collagenase activity by cleaving at multiple sites within the alpha 1 and alpha 2 triple helix regions (Col domains). Molecular simulations created for FhCL1, FhCL2 and FhCL3 complexed to various seven-residue peptides supports the idea that Trp67 and Tyr67 in the S2 subsite of the active sites of FhCL3 and FhCL2, respectively, are critical to conferring the unique collagenase-like activity to these enzymes by accommodating either Gly or Pro residues at P2 in the substrate. The data also suggests that FhCL3 accommodates hydroxyproline (Hyp)-Gly at P3-P2 better than FhCL2 explaining the observed greater ability of FhCL3 to digest type I and II collagens compared to FhCL2 and why these enzymes cleave at different positions within the Col domains. Conclusions/Significance: These studies further our understanding of how this helminth parasite regulates peptidase expression to ensure infection, migration and establishment in host tissues.

Robinson, MW, Donnelly, S, Hutchinson, AT, To, J, Taylor, NL, Norton, RS, Perugini, MA & Dalton, JP 2011, 'A Family of Helminth Molecules that Modulate Innate Cell Responses via Molecular Mimicry of Host Antimicrobial Peptides', PLOS PATHOGENS, vol. 7, no. 5, pp. 1-15.
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Over the last decade a significant number of studies have highlighted the central role of host antimicrobial (or defence) peptides in modulating the response of innate immune cells to pathogen-associated ligands. In humans, the most widely studied antimicrobial peptide is LL-37, a 37-residue peptide containing an amphipathic helix that is released via proteolytic cleavage of the precursor protein CAP18. Owing to its ability to protect against lethal endotoxaemia and clinically-relevant bacterial infections, LL-37 and its derivatives are seen as attractive candidates for anti-sepsis therapies. We have identified a novel family of molecules secreted by parasitic helminths (helminth defence molecules; HDMs) that exhibit similar biochemical and functional characteristics to human defence peptides, particularly CAP18. The HDM secreted by Fasciola hepatica (FhHDM-1) adopts a predominantly alpha-helical structure in solution. Processing of FhHDM-1 by F. hepatica cathepsin L1 releases a 34-residue C-terminal fragment containing a conserved amphipathic helix. This is analogous to the proteolytic processing of CAP18 to release LL-37, which modulates innate cell activation by classical toll-like receptor (TLR) ligands such as lipopolysaccharide (LPS). We show that full-length recombinant FhHDM-1 and a peptide analogue of the amphipathic C-terminus bind directly to LPS in a concentration-dependent manner, reducing its interaction with both LPS-binding protein (LBP) and the surface of macrophages. Furthermore, FhHDM-1 and the amphipathic C-terminal peptide protect mice against LPS-induced inflammation by significantly reducing the release of inflammatory mediators from macrophages. We propose that HDMs, by mimicking the function of host defence peptides, represent a novel family of innate cell modulators with therapeutic potential in anti-sepsis treatments and prevention of inflammation.

Roest, R, Latella, BA, Heness, G & Ben-Nissan, B 2011, 'Adhesion of sol–gel derived hydroxyapatite nanocoatings on anodised pure titanium and titanium (Ti6Al4V) alloy substrates', Surface and Coatings Technology, vol. 205, no. 11, pp. 3520-3529.
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The mechanical properties and adhesion behaviour of sol-gel derived hydroxyapatite (HA) nanocoatings on commercially pure (cp) titanium (Ti) and Ti6Al4V alloy have been determined and related to anodising treatment. The surface roughness, wetting and coating characteristics were examined using profilometry, contact angle, scanning electron microscopy (SEM) and X-ray diffraction (XRD). Nano-indentation was used to determine the Young's modulus and hardness of the coatings, while microtensile tests were used to introduce controlled strains in the coatings through the cp Ti and TiAl6V4 alloy substrates, from which the strength, fracture toughness and adhesion behaviour could be ascertained based on multiple cracking and delamination events. The toughness of the HA coatings is found to be slightly lower to that of equivalent bulk pure HA ceramics. The substrate and the anodized layer thickness have the most influence on the interfacial adhesion of HA, with nanocoatings on Ti6Al4V exhibiting superior interfacial bonding in comparison to cp Ti.

Rosic, NN, Pernice, M, Dove, S, Dunn, S & Hoegh-Guldberg, O 2011, 'Gene expression profiles of cytosolic heat shock proteins Hsp70 and Hsp90 from symbiotic dinoflagellates in response to thermal stress: possible implications for coral bleaching', CELL STRESS & CHAPERONES, vol. 16, no. 1, pp. 69-80.
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Rosic, NN, Pernice, M, Rodriguez-Lanetty, M & Hoegh-Guldberg, O 2011, 'Validation of Housekeeping Genes for Gene Expression Studies in Symbiodinium Exposed to Thermal and Light Stress', Marine Biotechnology, vol. 13, no. 3, pp. 355-365.
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Roux, C 2011, 'Forensic science – A teenager in identity crisis?', Australian Journal of Forensic Sciences, vol. 43, no. 2-3, pp. 79-83.
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In contrast with its high pro?le in popular culture, forensic science has been increasingly challenged in recent years. As reminded by Crispino et al. in this issue, forensic scientists have variously been labelled `craftsmen, accused of carrying `a misleading title, of having `no understanding of scienti?c methodology, of issuing `clearly absurd or `preposterous conclusions of individualisation, and practising a marginal, pseudo- if not junk-science. Unsurprisingly, these views are not shared by everyone. It is also obvious that such challenges and comments have been more common in the USA, especially in the post-Daubert and post-NAS eras than in Australia and in New Zealand. However, such criticisms cannot remain unheard by those involved in forensic science. The Antipodean, and indeed worldwide, forensic science community must consider these criticisms with all the rigor and seriousness that we should expect from a con?dent, mature and distinctive scienti?c discipline. But in all truth, despite the goodwill demonstrated by its individual practitioners, is forensic science really such a discipline?

Šafránek, D, Červený, J, Klement, M, Pospíšilová, J, Brim, L, Lazár, D & Nedbal, L 2011, 'E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes', Biosystems, vol. 103, no. 2, pp. 115-124.
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Salam, S, Islam, M, Alam, M, Akram, A, Ikram, M, Mahmood, A, Khan, M & Mujahid, M 2011, 'The effect of processing conditions on the structural morphology and physical properties of ZnO and CdS thin films produced via sol–gel synthesis and chemical bath deposition techniques', Advances in Natural Sciences: Nanoscience and Nanotechnology, vol. 2, no. 4, pp. 045001-045001.
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Abstract Cadmium sulfide (CdS) and zinc oxide (ZnO) are used in thin film solar cells as buffer layer and transparent conducting oxide, respectively. The effect of annealing conditions on the morphology and physical properties of CdS and ZnO films prepared using chemical bath deposition and sol–gel synthesis techniques, respectively, was investigated. CdS films obtained from the chemical bath deposition (CBD) process were found to be polycrystalline with dense granular morphology. Electrical characterization of the films annealed at 400 °C for 10 min yielded values of 2.2×10−3 Ω cm and 8.3×1012  cm −3 for resistivity and carrier concentration, respectively. Scanning electron microscopy (SEM) and x-ray diffraction (XRD) studies of intrinsic zinc oxide (i-ZnO) films revealed flake-like morphology and transformation of the as-deposited amorphous structure into a hexagonal wurtzite crystal structure upon annealing at 500 °C for 2 h. Optical and electrical characterization results showed that such films had ∼80% transmittance and resistivity values as low as 6.4×102 Ω cm. These films are being explored for fabrication and testing of copper-indium-gallium-(di)selenide (CIGS) thin film solar cells obtained from simple, cost-effective, solution-based synthesis routes.

Samoc, M, Corkery, TC, McDonagh, AM, Cifuentes, MP & Humphrey, MG 2011, 'Organometallic Complexes for Non-linear Optics. 49.* Third-Order Non-linear Optical Spectral Dependence Studies of Arylalkynylruthenium Dendrimers', Australian Journal of Chemistry, vol. 64, no. 9, pp. 1269-1269.
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The cubic hyperpolarizabilities of 1,3,5-(trans-[RuCl(dppe)2(C≡CC6H4-4-C≡C)])3C6H3 (1), 1,3,5-(trans-[Ru(C≡CPh)(dppe)2(C≡CC6H4-4-C≡C)])3C6H3 (2), 1,3,5-(trans-[Ru(C≡CC6H4-4-NO2)(dppe)2(C≡CC6H4-4-C≡C)])3C6H3 (3), 1,3,5-{trans-[Ru(C≡C-3,5-(trans-[Ru(C≡CPh)(dppe)2(C≡CC6H4-4-C≡C)])2C6H3)(dppe)2(C≡CC6H4-4-C≡C)]}3C6H3 (4), and 1,3,5-{trans-[Ru(C≡C-3,5-(trans-[Ru(C≡CC6H4-4-NO2)(dppe)2(C≡CC6H4-4-C≡C)])2C6H3)(dppe)2(C≡CC6H4-4-C≡C)]}3C6H3 (5) have been assessed over the spectral range 520–1600 nm using the Z-scan technique and ~150 fs pulses. All complexes exhibit negative values of γreal (corresponding to self-defocusing behaviour) and significant positive values of γimag (corresponding to two-photon absorption) at short wavelengths (up to 1000 nm). The maximal values of γreal and γimag increase in magnitude on dendrimer generation increase (proceeding from 2 to 4 or 3 to 5). The open-aperture Z-scan results have been used to confirm and contrast the two-photon (2PA) and three-photon absorption (3PA) behaviour of 1–5, the data being consistent with the existence of 2PA at the short wavelength range, but with significant 3PA at longer wavelengths for 1–3 and 5, a record 3PA coefficient for an inorganic complex for 5 at 1180 nm, and appreciable 3PA at the telecommunications wavelength of 1300 nm.

Sanchez-Camara, J, Martin-Smith, K, Booth, DJ, Fritschi, J & Turon, X 2011, 'Demographics and vulnerability of a unique Australian fish, the weedy seadragon Phyllopteryx taeniolatus', MARINE ECOLOGY PROGRESS SERIES, vol. 422, pp. 253-264.
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The weedy seadragon Phyllopteryx taeniolatus is a vulnerable and endemic Australian fish and also an icon and flagship species for marine conservation. However, little is known about its population dynamics, which hinders the establishment of conservation policies. We have previously demonstrated seadragons to be highly site-attached, so we estimated population densities, growth and survival of weedy seadragons using mark-recapture techniques at 5 sites in New South Wales (NSW, 34 S) and Tasmania (TAS, 43 S), near the northern and southeastern limit of distribution for the species, over a 7 yr period. Population densities varied from ca. 10 to 70 seadragons ha.1 depending on site and year. There was a significant decline in the number of weedy seadragon sightings per unit area searched in 2 out of 3 study sites near Sydney, NSW, from 2001 to 2007. There was also a decline at one of the 2 sites surveyed in the lower Derwent Estuary, TAS, in 2009 compared to 2003 and 2004. Survival rates at NSW sites ranged from 0.62 to 0.65 yr.1 and were higher at TAS sites where they ranged from 0.71 to 0.77 yr.1. Birth occurred approximately 3 mo later and seadragons exhibited significant slower growth in TAS (maximum adult size ~ growth rate parameter, L ~ k = 31.02) compared to NSW (L ~ k = 55.15). This study is the first population assessment of seadragons over ecologically relevant spatial and temporal scales, and shows differences in the dynamics of populations at different latitudes. It also shows declines in some populations at widely separated sites. Determining whether these declines are natural interannual fluctuations or whether they are caused by environmental or habitat changes must be a priority for conservation.

Sastraruji, T, Chaiyong, S, Jatisatienr, A, Pyne, SG, Ung, AT & Lie, W 2011, 'Phytochemical Studies on Stemona aphylla: Isolation of a New Stemofoline Alkaloid and Six New Stemofurans', JOURNAL OF NATURAL PRODUCTS, vol. 74, no. 1, pp. 60-64.
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A new stemofoline alkaloid, (2'S)-hydroxy-(11S,12R)-dihydrostemofoline (3), new stemofurans M-R (8-13), and known compounds stemofoline (1), (2?S)-hydroxystemofoline (2), stemofuran E (4), stemofuran F (5), stemofuran J (6), and stilbostemin F (7) have been isolated from the root extracts of Stemona aphylla. The structures and relative configurations of these new compounds have been determined by spectroscopic data interpretation and from semisynthetic studies. These natural and semisynthetic alkaloids were tested for acetylcholinesterase inhibitory activities and were found to be 10-20 times less active than 1?,2?-didehydrostemofoline itself. Stemofurans 4, 6, 8, 11, and 13 were tested for their antibacterial and antifungal activities. Three of these showed antibacterial activities against MRSA with MIC values of 15.6 ?g/mL

Scott, NE, Parker, BL, Connolly, AM, Paulech, J, Edwards, AVG, Crossett, B, Falconer, L, Kolarich, D, Djordjevic, SP, Højrup, P, Packer, NH, Larsen, MR & Cordwell, SJ 2011, 'Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID, Higher Energy Collisional Dissociation, and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni', Molecular & Cellular Proteomics, vol. 10, no. 2, pp. S1-S18.
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Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E) XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or beta-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation ( CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism.

Seidel, P, Roth, M, Ge, Q, Merfort, I, S'ng, CT & Ammit, AJ 2011, 'I B  glutathionylation and reduced histone H3 phosphorylation inhibit eotaxin and RANTES', European Respiratory Journal, vol. 38, no. 6, pp. 1444-1452.
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Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Ricken, R, Min, Y, Sohler, W, Kivshar, YS & Pertsch, T 2011, 'Spectral pulse transformations and phase transitions in quadratic nonlinear waveguide arrays', Optics Express, vol. 19, no. 23, pp. 23188-23188.
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Seymour, LM, Falconer, L, Deutscher, AT, Minion, FC, Padula, MP, Dixon, NE, Djordjevic, SP & Walker, MJ 2011, 'Mhp107 Is a Member of the Multifunctional Adhesin Family of Mycoplasma hyopneumoniae', Journal of Biological Chemistry, vol. 286, no. 12, pp. 10097-10104.
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Mycoplasma hyopneumoniae is the causative pathogen of porcine enzootic pneumonia, an economically significant disease that disrupts the mucociliary escalator in the swine respiratory tract. Expression of Mhp107, a P97 paralog encoded by the gene mhp107, was confirmed using ESI-MS/MS. To investigate the function of Mhp107, three recombinant proteins, F1Mhp107, F2Mhp107, and F3Mhp107, spanning the N-terminal, central, and C-terminal regions of Mhp107 were constructed. Colonization of swine by M. hyopneumoniae requires adherence of the bacterium to ciliated cells of the respiratory tract. Recent studies have identified a number of M. hyopneumoniae adhesins that bind heparin, fibronectin, and plasminogen. F1Mhp107 was found to bind porcine heparin (KD ~90 nm) in a dose-dependent and saturable manner, whereas F3Mhp107 bound fibronectin (KD ~180 nm) at physiologically relevant concentrations. F1Mhp107 also bound porcine plasminogen (KD = 24 nm) in a dose-dependent and physiologically relevant manner. Microspheres coated with F3Mhp107 mediate adherence to porcine kidney epithelial-like (PK15) cells, and all three recombinant proteins (F1Mhp107-F3Mhp107) bound swine respiratory cilia. Together, these findings indicate that Mhp107 is a member of the multifunctional M. hyopneumoniae adhesin family of surface proteins and contributes to both adherence to the host and pathogenesis.

Shi, X, Wang, Wen, Shen, Guo, Cao & Wang 2011, 'Aminopropyltriethoxysilane-mediated surface functionalization of hydroxyapatite nanoparticles: synthesis, characterization, and in vitro toxicity assay', International Journal of Nanomedicine, vol. 6, pp. 3449-3449.
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Shill, M 2011, 'Injection Practices at Primary Healthcare Units in Bangladesh: Experience at Six Upazilla Health Complexes', Australasian Medical Journal, pp. 26-42.
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Shukla, MK, Kumar, M, Prasad, K, Reddy, CRK & Jha, B 2011, 'Partial characterization of sulfohydrolase from Gracilaria dura and evaluation of its potential application in improvement of the agar quality', Carbohydrate Polymers, vol. 85, no. 1, pp. 157-163.
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Siegle, JS, Hansbro, N, Dong, C, Angkasekwinai, P, Foster, PS & Kumar, RK 2011, 'Blocking induction of T helper type 2 responses prevents development of disease in a model of childhood asthma', Clinical and Experimental Immunology, vol. 165, no. 1, pp. 19-28.
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Summary Early-life respiratory viral infections are linked to subsequent development of allergic asthma in children. We assessed the underlying immunological mechanisms in a novel model of the induction phase of childhood asthma. BALB/c mice were infected neonatally with pneumonia virus of mice, then sensitized intranasally with ovalbumin following recovery. Animals were challenged with low levels of aerosolized ovalbumin for 4 weeks to induce changes of chronic asthma, then received a single moderate-level challenge to elicit mild acute allergic inflammation. To inhibit the initial induction of a T helper type 2 (Th2) response, we administered neutralizing antibodies against interleukin (IL)-4 or IL-25, then assessed development of airway inflammation and remodelling. Anti-IL-4 administered during chronic challenge prevented development of chronic and acute allergic inflammation, as well as goblet cell hyperplasia/metaplasia, but features of remodelling such as subepithelial fibrosis and epithelial hypertrophy were unaffected. In contrast, anti-IL-25 had limited effects on the airway inflammatory response but prevented key changes of remodelling, although it had no effect on goblet cells. Both antibodies suppressed development of a Th2 response, while anti-IL-25 also promoted a Th17 response. In further experiments, anti-IL-25 was administered in early life alone, and again had limited effects on airway inflammation, but prevented development of airway wall remodelling. We conclude that in this murine model of childhood asthma, administration of anti-IL-4 or anti-IL-25 prevents development of some key features of asthma, suggesting that suppression of development of a Th2 response during the neonatal period or later in childhood could be effective for primary prevention.

Simberloff, D, Alexander, J, Allendorf, F, Aronson, J, Antunes, PM, Bacher, S, Bardgett, R, Bertolino, S, Bishop, M, Blackburn, TM, Blakeslee, A, Blumenthal, D, Bortolus, A, Buckley, R, Buckley, Y, Byers, J, Callaway, RM, Campbell, F, Campbell, K, Campbell, M, Carlton, JT, Cassey, P, Catford, J, Celesti-Grapow, L, Chapman, J, Clark, P, Clewell, A, Clode, JC, Chang, A, Chytry, M, Clout, M, Cohen, A, Cowan, P, Cowie, RH, Crall, AW, Crooks, J, Deveney, M, Dixon, K, Dobbs, FC, Duffy, DC, Duncan, R, Ehrlich, PR, Eldredge, L, Evenhuis, N, Fausch, KD, Feldhaar, H, Firn, J, Fowler, A, Galil, B, Garcia-Berthou, E, Geller, J, Genovesi, P, Gerber, E, Gherardi, F, Gollasch, S, Gordon, D, Graham, J, Gribben, P, Griffen, B, Grosholz, ED, Hewitt, C, Hierro, JL, Hulme, P, Hutchings, P, Jarosik, V, Jeschke, JM, Johnson, C, Johnson, L, Johnston, EL, Jones, CG, Keller, R, King, CM, Knols, BGJ, Kollmann, J, Kompas, T, Kotanen, PM, Kowarik, I, Kuehn, I, Kumschick, S, Leung, B, Liebhold, A, MacIsaac, H, Mack, R, McCullough, DG, McDonald, R, Merritt, DM, Meyerson, L, Minchin, D, Mooney, HA, Morisette, JT, Moyle, P, Heinz, M-S, Murray, BR, Nehring, S, Nelson, W, Nentwig, W, Novak, SJ, Occhipinti, A, Ojaveer, H, Osborne, B, Ostfeld, RS, Parker, J, Pederson, J, Pergl, J, Phillips, ML, Pysek, P, Rejmanek, M, Ricciardi, A, Ricotta, C, Richardson, D, Rilov, G, Ritchie, E, Robertson, PA, Roman, J, Ruiz, G, Schaefer, H, Schaffelke, B, Schierenbeck, KA, Schmitz, DC, Schwindt, E, Seeb, J, Smith, LD, Smith, GF, Stohlgren, T, Strayer, DL, Strong, D, Sutherland, WJ, Therriault, T, Thuiller, W, Torchin, M, van der Putten, WH, Vila, M, Von Holle, B, Wallentinus, I, Wardle, D, Williamson, M, Wilson, J, Winter, M, Wolfe, LM, Wright, J, Wonham, M, Zabin, C & Signatories 2011, 'Non-natives: 141 scientists object', NATURE, vol. 475, no. 7354, pp. 36-36.

Singh, RP, Gupta, V, Kumari, P, Kumar, M, Reddy, CRK, Prasad, K & Jha, B 2011, 'Purification and partial characterization of an extracellular alginate lyase from Aspergillus oryzae isolated from brown seaweed', Journal of Applied Phycology, vol. 23, no. 4, pp. 755-762.
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Sinutok, S, Hill, R, Doblin, MA, Wuhrer, R & Ralph, PJ 2011, 'Warmer more acidic conditions cause decreased productivity and calcification in subtropical coral reef sediment-dwelling calcifiers', LIMNOLOGY AND OCEANOGRAPHY, vol. 56, no. 4, pp. 1200-1212.
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The effects of elevated CO(2) and temperature on photosynthesis and calcification in the calcifying algae Halimeda macroloba and Halimeda cylindracea and the symbiont-bearing benthic foraminifera Marginopora vertebralis were investigated through exposure to a combination of four temperatures (28 degrees C, 30 degrees C, 32 degrees C, and 34 degrees C) and four CO(2) levels (39, 61, 101, and 203 Pa; pH 8.1, 7.9, 7.7, and 7.4, respectively). Elevated CO(2) caused a profound decline in photosynthetic efficiency (F(V) : F(M)), calcification, and growth in all species. After five weeks at 34 degrees C under all CO(2) levels, all species died. Chlorophyll (Chl) a and b concentration in Halimeda spp. significantly decreased in 203 Pa, 32 degrees C and 34 degrees C treatments, but Chl a and Chl c(2) concentration in M. vertebralis was not affected by temperature alone, with significant declines in the 61, 101, and 203 Pa treatments at 28 degrees C. Significant decreases in F(V) : F(M) in all species were found after 5 weeks of exposure to elevated CO(2) (203 Pa in all temperature treatments) and temperature (32 degrees C and 34 degrees C in all pH treatments). The rate of oxygen production declined at 61, 101, and 203 Pa in all temperature treatments for all species. The elevated CO(2) and temperature treatments greatly reduced calcification (growth and crystal size) in M. vertebralis and, to a lesser extent, in Halimeda spp. These findings indicate that 32 degrees C and 101 Pa CO(2), are the upper limits for survival of these species on Heron Island reef, and we conclude that these species will be highly vulnerable to the predicted future climate change scenarios of elevated temperature and ocean acidification.

Smedley, EJ, Stelzer-Braid, S, Ressler, K-A, Melling, P, Bowden, S, McCaw, R, White, PA, Vickers, CR, Rawlinson, WD & Ferson, MJ 2011, 'Transmission of hepatitis C virus to recipients of parenteral vitamin therapy in a primary care facility', Journal of Clinical Virology, vol. 51, no. 2, pp. 105-109.
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Smith, CA, Zaslawski, CJ, Zheng, Z, Cobbin, D, Cochrane, S, Lenon, GB, Loyeung, B, Meier, PC, Walsh, S, Xue, CC, Zhang, AL, Zhu, X & Bensoussan, A 2011, 'Development of an Instrument to Assess the Quality of Acupuncture: Results from a Delphi Process', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 17, no. 5, pp. 441-452.
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Background: Quality acupuncture influences the outcomes of clinical research, and issues associated with effective administration of acupuncture in randomized controlled trials need to be addressed when appraising studies. Objective: The study objective was to achieve consensus on domains and items for inclusion in a rating scale to assess quality acupuncture administered in clinical research. Study design and subjects: An active group of Australian acupuncture researchers initially identified a pool of items assessing quality. The Delphi consensus process was then used to select and reduce the number of items, and an additional expert panel of 42 researchers were invited to participate. Participants initially ranked items along a five-point scale for the first Delphi round, and indicated an agree or disagree response during the second round. For an item to be retained into the second round, an item had to attain greater than 80% agreement that the item described a dimension of quality acupuncture and related study design. Results: Thirty-two (32) experts agreed to participate in the study. After two rounds of the Delphi process, consensus was reached on 14 domains and 26 items relating to quality acupuncture. Domains, items, and minimum standards related to study design; rationale of the intervention; criteria relating to needling stimulation either manual or electrostimulation; duration and frequency of treatment; and practitioner training. Conclusions: Items for inclusion in an instrument to assess quality acupuncture in clinical research were identified. Further development of the instrument including relative weighting of items and reliability testing is under way.

Smith, GB 2011, 'Commentary: Environmental nanophotonics and energy', JOURNAL OF NANOPHOTONICS, vol. 5.
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Smith, GB 2011, 'Commentary: Environmental nanophotonics and energy (vol 5, 050301, 2011)', JOURNAL OF NANOPHOTONICS, vol. 5.

Smith, KR, Suppiah, V, O'Connor, K, Berg, T, Weltman, M, Abate, M, Spengler, U, Bassendine, M, Matthews, G, Irving, WL, Powell, E, Riordan, S, Ahlenstiel, G, Stewart, GJ, Bahlo, M, George, J & Booth, DR 2011, 'Identification of improved IL28B SNPs and haplotypes for prediction of drug response in treatment of hepatitis C using massively parallel sequencing in a cross-sectional European cohort', Genome Medicine, vol. 3, no. 8, pp. 57-57.
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Solntsev, AS, Sukhorukov, AA, Neshev, DN, Iliew, R, Geiss, R, Pertsch, T & Kivshar, YS 2011, 'Cascaded third harmonic generation in lithium niobate nanowaveguides', Applied Physics Letters, vol. 98, no. 23, pp. 231110-231110.
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We predict highly efficient third harmonic generation through simultaneous phase-matching of second-harmonic generation and sum-frequency generation in lithium niobate nanowaveguides, enabled due to strong modal dispersion. We demonstrate that the waveguide size which corresponds to phase-matching is also optimal for highest mode confinement and therefore for strongly enhanced conversion efficiency.

Somaweera, R, Webb, JK & Shine, R 2011, 'Determinants of Habitat Selection by Hatchling Australian Freshwater Crocodiles', PLOS ONE, vol. 6, no. 12, p. e28533.
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Animals almost always use habitats non-randomly, but the costs and benefits of using specific habitat types remain unknown for many types of organisms. In a large lake in northwestern Australia (Lake Argyle), most hatchling (<12-month-old) freshwater crocodiles (Crocodylus johnstoni) are found in floating vegetation mats or grassy banks rather than the more widely available open banks. Mean body sizes of young crocodiles did not differ among the three habitat types. We tested four potential explanations for non-random habitat selection: proximity to nesting sites, thermal conditions, food availability, and exposure to predation. The three alternative habitat types did not differ in proximity to nesting sites, or in thermal conditions. Habitats with higher food availability harboured more hatchlings, and feeding rates (obtained by stomach-flushing of recently-captured crocodiles) were highest in such areas. Predation risk may also differ among habitats: we were twice as likely to capture a crocodile after seeing it in open-bank sites than in the other two habitat types. Thus, habitat selection of hatchling crocodiles in this system may be driven both by prey availability and by predation risk.

Somaweera, R, Webb, JK & Shine, R 2011, 'It's a dog-eat-croc world: dingo predation on the nests of freshwater crocodiles in tropical Australia', ECOLOGICAL RESEARCH, vol. 26, no. 5, pp. 957-967.
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Predation on eggs is an important source of mortality for many long-lived organisms, but causes of egg mortality from specific predators remain poorly known in most cases. Understanding the identity of predators, and the rates and determinants of their effects on a cohort of recruits, can provide a valuable background for attempts to exploit, control or conserve populations. We used remotely triggered cameras to study predation on the nests of freshwater crocodiles (Crocodylus johnstoni) inhabiting Lake Argyle, in tropical Australia. We also supplemented our work on natural crocodile nests with artificial nests. Overall, 80 of 111 natural nests were opened by predators, and predation occurred throughout the study period (7 weeks). Unlike in other parts of the species' range, most nest-robbers were dingoes (Canis lupus dingo, responsible for 98% of all predator visits in the northern sites, and 54% in the Ord River site), with minimal additional predation by reptiles and birds. Contrary to expectation, rates of nest predation were not influenced by spatial clumping of nests: the probability of predation per nest did not change with total numbers of nests laid in an area, and artificially aggregated versus dispersed nests experienced similar levels of predation. Nest vulnerability was linked to abiotic features including slope of surrounding banks, compactness of nesting substrate, and distance from the nearest forest. Abundant aquatic food resources support a large crocodile population, but a lack of suitable nest-sites forces the crocodiles to concentrate nesting in small areas readily accessible to wide-ranging nest predators. Collectively, our results suggest that distinctive attributes of the lakeside landscape alter predator guilds and fashion unique predator-prey interactions.

Somaweera, R, Webb, JK, Brown, GP & Shine, R 2011, 'Hatchling Australian freshwater crocodiles rapidly learn to avoid toxic invasive cane toads', BEHAVIOUR, vol. 148, no. 4, pp. 501-517.
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Predicting the ecological impacts of invasive species on native fauna is a formidable challenge for conservation biologists. One way to deal with that challenge is to stage encounters between the invader and native species in the laboratory, to illuminate likely outcomes of encounters in the wild. The invasion of the highly toxic cane toad Rhinella marina across tropical Australia threatens many frog-eating predators, including freshwater crocodiles (Crocodylus johnstoni). To predict the impact of cane toads on crocodiles, we need to know whether crocodiles will attack cane toads, and whether predators that survive the toads' poisons will learn to avoid toads. We quantified these traits under laboratory conditions in hatchling freshwater crocodiles from Lake Argyle in Western Australia. All toad-naive hatchling crocodiles attacked toads during their first encounter, and none showed signs of overt illness after consuming toads. However, crocodiles rapidly learnt to avoid toads as prey, and only four out of the 10 crocodiles attacked toads during subsequent encounters. Compared to control (toad-naive) conspecifics, toad-smart crocodiles inflicted fewer bites on toads, held toads in their mouths for shorter time periods, and were more likely to reject toads as prey. In the field, toads were consumed more rarely than native frogs. Our results show that hatchling freshwater crocodiles can rapidly learn to avoid cane toads as prey. Hence, even if toads cause mortality of larger crocodiles (as happens in some areas), populations may recover via hatchling recruitment.

Sommer, B, Harrison, PL, Brooks, L & Scheffers, SR 2011, 'Coral Community Decline at Bonaire, Southern Caribbean', Bulletin of Marine Science, vol. 87, no. 3, pp. 541-565.
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Song, DF, Sommerville, D, Brown, AG, Shimmon, RG, Reedy, BJ & Tahtouh, M 2011, 'Thermal development of latent fingermarks on porous surfaces-Further observations and refinements', FORENSIC SCIENCE INTERNATIONAL, vol. 204, no. 1-3, pp. 97-110.
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In a further study of the thermal development of fingermarks on paper and similar surfaces, it is demonstrated that direct contact heating of the substrate using coated or ceramic surfaces at temperatures in excess of 230 8C produces results superior to those obtained using hot air. Fingermarks can also be developed in this way on other cellulose-based substrates such as wood and cotton fabric, though ridge detail is difficult to obtain in the latter case. Fluorescence spectroscopy indicates that the phenomena observed during the thermal development of fingermarks can be reproduced simply by heating untreated white copy paper or filter paper, or these papers treated with solutions of sodium chloride or alanine. There is no evidence to suggest that the observed fluorescence of fingermarks heated on paper is due to a reaction of fingermark constituents on or with the paper. Instead, we maintain that the ridge contrast observed first as fluorescence, and later as brown charring, is simply an acceleration of the thermal degradation of the paper. Thermal degradation of cellulose, amajor constituent of paper and wood, is known to give rise to a fluorescent product if sufficient oxygen is available [15]. However, the absence of atmospheric oxygen has only a slight effect on the thermal development of fingermarks, indicating that there is sufficient oxygen already present in paper to allow the formation of the fluorescent and charred products. In a depletion study comparing thermal development of fingermarks on paper with development using ninhydrin, the thermal technique was found to be as sensitive as ninhydrin for six out of seven donors.

Sparks, R, Carter, C, Graham, P, Muscatello, D, Churches, T, Kaldor, J, Turner, R, Zheng, W & Ryan, L 2011, 'Understanding sources of variation in syndromic surveillance for early warning of natural or intentional disease outbreaks (vol 42, pg 613, 2010)', IIE TRANSACTIONS, vol. 43, no. 3, pp. 231-231.
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Speer, MS, Leslie, LM & Fierro, AO 2011, 'Australian east coast rainfall decline related to large scale climate drivers', Climate Dynamics, vol. 36, no. 7-8, pp. 1419-1429.
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Spindler, X, Hofstetter, O, McDonagh, AM, Roux, C & Lennard, C 2011, 'Enhancement of latent fingermarks on non-porous surfaces using anti-L-amino acid antibodies conjugated to gold nanoparticles', CHEMICAL COMMUNICATIONS, vol. 47, no. 19, pp. 5602-5604.
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Enantioselective anti-L-amino acid antibodies conjugated to gold nanoparticles are shown to facilitate the detection of latent fingermarks by interacting with amino acids present in friction ridge secretions. This antibody-based system is particularly effective for the enhancement of aged and dried fingermarks on non-porous surfaces, an area unexploited by current techniques.

Spindler, X, Shimmon, R, Roux, C & Lennard, C 2011, 'The effect of zinc chloride, humidity and the substrate on the reaction of 1,2-indanedione-zinc with amino acids in latent fingermark secretions', FORENSIC SCIENCE INTERNATIONAL, vol. 212, no. 1-3, pp. 150-157.
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Anecdotal evidence from forensic practitioners and studies conducted under controlled conditions have indicated that the reaction between 1,2-indanedione and the amino acids present in latent fingermark deposits is highly susceptible to ambient humidity. The addition of catalytic amounts of zinc chloride to the 1,2-indanedione working solution usually in the order of 1:25 to 1:4 molar ratio (indanedione:zinc) significantly improves the colour and luminescence of fingermarks treated under dry conditions but appears to have a negligible effect on fingermarks treated in humid environments. The results presented in this paper confirmed that zinc(II) ions added to the 1,2-indanedione working solution act as a Lewis acid catalyst, stabilising a key intermediate during a rate-limiting hydrolysis step. Furthermore, studying the reaction using a chromatography-grade cellulose substrate method previously reported confirmed that cellulose substrates play a major role in facilitating the indanedione-amino acid reaction by acting as a surface catalyst in the early stages of the reaction and by directing the formation of the desired luminescent product (Joullie´ s Pink).

Sprouster, DJ, Ruffell, S, Bradby, JE, Williams, JS, Lockrey, MN, Phillips, MR, Major, RC & Warren, OL 2011, 'Structural characterization of B-doped diamond nanoindentation tips', JOURNAL OF MATERIALS RESEARCH, vol. 26, no. 24, pp. 3051-3057.
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We report on the electrical and structural properties of boron-doped diamond tips commonly used for in-situ electromechanical testing during nanoindentation. The boron dopant environment, as evidenced by cathodoluminescence (CL) microscopy, revealed significantly different boron states within each tip. Characteristic emission bands of both electrically activated and nonelectrically activated boron centers were identified in all boron-doped tips. Surface CL mapping also revealed vastly different surface properties, confirming a high amount of nonelectrically activated boron clusters at the tip surface. Raman microspectroscopy analysis showed that structural characteristics at the atomic scale for boron-doped tips also differ significantly when compared to an undoped diamond tip. Furthermore, the active boron concentration, as inferred via the Raman analysis, varied greatly from tip-to-tip. It was found that tips (or tip areas) with low overall boron concentration have a higher number of electrically inactive boron, and thus non-Ohmic contacts were made when these tips contacted metallic substrates. Conversely, tips that have higher boron concentrations and a higher number of electrically active boron centers display Ohmic-like contacts. Our results demonstrate the necessity to understand and fully characterize the boron environments, boron concentrations, and atomic structure of the tips prior to performing in situ electromechanical experiments, particularly if quantitative electrical data are required.

Stanley, AC, de Labastida Rivera, F, Haque, A, Sheel, M, Zhou, Y, Amante, FH, Bunn, PT, Randall, LM, Pfeffer, K, Scheu, S, Hickey, MJ, Saunders, BM, Ware, C, Hill, GR, Tamada, K, Kaye, PM & Engwerda, CR 2011, 'Critical Roles for LIGHT and Its Receptors in Generating T Cell-Mediated Immunity during Leishmania donovani Infection', PLoS Pathogens, vol. 7, no. 10, pp. e1002279-e1002279.
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Stappers, BW, Hessels, JWT, Alexov, A, Anderson, K, Coenen, T, Hassall, T, Karastergiou, A, Kondratiev, VI, Kramer, M, van Leeuwen, J, Mol, JD, Noutsos, A, Romein, JW, Weltevrede, P, Fender, R, Wijers, RAMJ, Bähren, L, Bell, ME, Broderick, J, Daw, EJ, Dhillon, VS, Eislöffel, J, Falcke, H, Griessmeier, J, Law, C, Markoff, S, Miller-Jones, JCA, Scheers, B, Spreeuw, H, Swinbank, J, ter Veen, S, Wise, MW, Wucknitz, O, Zarka, P, Anderson, J, Asgekar, A, Avruch, IM, Beck, R, Bennema, P, Bentum, MJ, Best, P, Bregman, J, Brentjens, M, van de Brink, RH, Broekema, PC, Brouw, WN, Brüggen, M, de Bruyn, AG, Butcher, HR, Ciardi, B, Conway, J, Dettmar, R-J, van Duin, A, van Enst, J, Garrett, M, Gerbers, M, Grit, T, Gunst, A, van Haarlem, MP, Hamaker, JP, Heald, G, Hoeft, M, Holties, H, Horneffer, A, Koopmans, LVE, Kuper, G, Loose, M, Maat, P, McKay-Bukowski, D, McKean, JP, Miley, G, Morganti, R, Nijboer, R, Noordam, JE, Norden, M, Olofsson, H, Pandey-Pommier, M, Polatidis, A, Reich, W, Röttgering, H, Schoenmakers, A, Sluman, J, Smirnov, O, Steinmetz, M, Sterks, CGM, Tagger, M, Tang, Y, Vermeulen, R, Vermaas, N, Vogt, C, de Vos, M, Wijnholds, SJ, Yatawatta, S & Zensus, A 2011, 'Observing pulsars and fast transients with LOFAR', Astronomy & Astrophysics, vol. 530, pp. A80-A80.
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Stark, D, Al-Qassab, SE, Barratt, JLN, Stanley, K, Roberts, T, Marriott, D, Harkness, J & Ellis, JT 2011, 'Evaluation of Multiplex Tandem Real-Time PCR for Detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in Clinical Stool Samples', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 49, no. 1, pp. 257-262.
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The aim of this study was to describe the first development and evaluation of a multiplex tandem PCR (MT-PCR) assay for the detection and identification of 4 common pathogenic protozoan parasites; Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis from human clinical samples. A total of 472 faecal samples submitted to the Department of Microbiology at St. Vincent's Hospital were included in the study. The MT-PCR assay was compared to four real-time PCR assays (RT-PCR) and microscopy by a traditional modified iron haematoxylin stain. The MT-PCR detected 28 G. intestinalis, 26 D. fragilis, 11 E. histolytica, and 9 Cryptosporidium spp. isolates. Detection and identification of the faecal protozoa by MT-PCR demonstrated 100% correlation with the RT-PCR results and when compared to RT-PCR the MT-PCR exhibited 100% sensitivity and specificity, while traditional microscopy of stained fixed faecal smears exhibited sensitivities and specificities of 56% and 100% for Cryptosporidium ssp., 38% and 99% for D. fragilis, 47% and 97% for E. histolytica and 50% and 100% for G. intestinalis respectively. No cross reactivity was detected in 100 stool samples containing various other bacterial, viral and protozoan species. The MT-PCR assay was able to provide rapid, sensitive and specific simultaneous detection and identification of the four most important diarrhoea causing protozoan parasites that infect humans. This study also highlights the lack of sensitivity demonstrated by microscopy and as such molecular methods such as MT-PCR must be considered the diagnostic method of choice for enteric protozoan parasites.

Steele, VR, Bottomley, AL, Garcia-Lara, J, Kasturiarachchi, J & Foster, SJ 2011, 'Multiple essential roles for EzrA in cell division of Staphylococcus aureus', MOLECULAR MICROBIOLOGY, vol. 80, no. 2, pp. 542-555.
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In Bacillus subtilis, EzrA is involved in preventing aberrant formation of FtsZ rings and has also been implicated in the localization cycle of Pbp1. We have identified the orthologue of EzrA in Staphylococcus aureus to be essential for growth and cell division in this organism. Phenotypic analyses following titration of EzrA levels in S. aureus have shown that the protein is required for peptidoglycan synthesis as well as for assembly of the divisome at the midcell and cytokinesis. Protein interaction studies revealed that EzrA forms a complex with both the cytoplasmic components of the division machinery and those with periplasmic domains, suggesting that EzrA may be a scaffold molecule permitting the assembly of the division complex and forming an interface between the cytoplasmic cytoskeletal element FtsZ and the peptidoglycan biosynthetic apparatus active in the periplasm.

Steinberg, PD, Rice, SA, Campbell, AH, McDougald, D & Harder, T 2011, 'Interfaces Between Bacterial and Eukaryotic 'Neuroecology'', Integrative and Comparative Biology, vol. 51, no. 5, pp. 794-806.
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Steinke, M, Brading, P, Kerrison, P, Warner, ME & Suggett, DJ 2011, 'CONCENTRATIONS OF DIMETHYLSULFONIOPROPIONATE AND DIMETHYL SULFIDE ARE STRAIN-SPECIFIC IN SYMBIOTIC DINOFLAGELLATES (SYMBIODINIUM SP., DINOPHYCEAE)1', Journal of Phycology, vol. 47, no. 4, pp. 775-783.
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Dimethyl sulfide (DMS) and dimethylsulfoniopropionate (DMSP) are sulfur compounds that may function as antioxidants in algae. Symbiotic dinoflagellates of the genus Symbiodinium show strain-specific differences in their susceptibility to temperature-induced oxidative stress and have been shown to contain high concentrations of DMSP. We investigated continuous cultures of four strains from distinct phylotypes (A1, A13, A2, and B1) that can be characterized by differential thermal tolerances. We hypothesized that strains with high thermal tolerance have higher concentrations of DMSP and DMS in comparison to strains with low thermal tolerance. DMSP concentrations were strain-specific with highest concentrations occurring in A1 (225 +/- 3.5 mmol . L(-1) cell volume [CV]) and lowest in A2 (158 +/- 3.8 mmol L) 1 CV). Both strains have high thermal tolerance. Strains with low thermal tolerance (A13 and B1) showed DMSP concentrations in between these extremes (194 +/- 19.0 and 160 +/- 6.1 mmol L(-1) CV, respectively). DMS data further confirmed this general pattern with high DMS concentrations in A1 and A13 (4.1 +/- 1.22 and 2.1 +/- 0.37 mmol . L(-1) CV, respectively) and low DMS concentrations in A2 and B1 (0.3 +/- 0.06 and 0.5 +/- 0.22 mmol . L(-1) CV, respectively). Hence, the strain-specific differences in DMSP and DMS concentrations did not match the different abilities of the four phylotypes to withstand thermal stress. Future work should quantify the possible dynamics in DMSP and DMS concentrations during periods of high oxidative stress in Symbiodinium sp. and address the role of these antioxidants in zooxanthellate cnidarians.

Stohlgren, TJ, Pysek, P, Kartesz, J, Nishino, M, Pauchard, A, Winter, M, Pino, J, Richardson, DM, Wilson, JRU, Murray, BR, Phillips, ML, Ming-yang, L, Celesti-Grapow, L & Font, X 2011, 'Widespread plant species: natives versus aliens in our changing world', BIOLOGICAL INVASIONS, vol. 13, no. 9, pp. 1931-1944.
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Estimates of the level of invasion for a region are traditionally based on relative numbers of native and alien species. However, alien species differ dramatically in the size of their invasive ranges. Here we present the first study to quantify the level of invasion for several regions of the world in terms of the most widely distributed plant species (natives vs. aliens). Aliens accounted for 51.3% of the 120 most widely distributed plant species in North America, 43.3% in New South Wales (Australia), 34.2% in Chile, 29.7% in Argentina, and 22.5% in the Republic of South Africa. However, Europe had only 1% of alien species among the most widespread species of the flora. Across regions, alien species relative to native species were either as well-distributed (10 comparisons) or more widely distributed (5 comparisons). These striking patterns highlight the profound contribution that widespread invasive alien plants make to floristic dominance patterns across different regions. Many of the most widespread species are alien plants, and, in particular, Europe and Asia appear as major contributors to the homogenization of the floras in the Americas. We recommend that spatial extent of invasion should be explicitly incorporated in assessments of invasibility, globalization, and risk assessments.

Stuken, A, Orr, RJS, Kellmann, R, Murray, SA, Neilan, BA & Jakobsen, KS 2011, 'Discovery of Nuclear-Encoded Genes for the Neurotoxin Saxitoxin in Dinoflagellates', PLOS ONE, vol. 6, no. 5, pp. e20096-0.
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Saxitoxin is a potent neurotoxin that occurs in aquatic environments worldwide. Ingestion of vector species can lead to paralytic shellfish poisoning, a severe human illness that may lead to paralysis and death. In freshwaters, the toxin is produced by p

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, de Sterke, CM & McPhedran, RC 2011, 'Modal analysis of enhanced absorption in silicon nanowire arrays', OPTICS EXPRESS, vol. 19, no. 19, pp. A1067-A1081.
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Su, D, Ahn, H & Wang, G 2011, 'Ab initio calculations on Li-ion migration in Li2FeSiO4 cathode material with a P21 symmetry structure', Applied Physics Letters, vol. 99, no. 14, pp. 141909-141909.
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We have systematically investigated the diffusion mechanism of Li ions in Li2FeSiO4 and its delithiated product LiFeSiO4 based on the P21 symmetry using the first principle method. Calculations on the energy barriers for possible spatial hopping pathways predicted that the activation barriers along the [101] direction and Li ion layer in the ac plane are relatively low, which can ensure the facile lithium diffusion along those directions. The results indicate that Li2FeSiO4 with the P21 symmetry is an ionic conductor for Li ions with two-dimensional diffusion.

SUGGETT, DJ & SMITH, DJ 2011, 'Interpreting the sign of coral bleaching as friend vs. foe', Global Change Biology, vol. 17, no. 1, pp. 45-55.
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Coral bleaching is a major concern to researchers, conservationists and the general public worldwide. To date, much of the high profile attention for bleaching has coincided with major environmental impacts and for many the term coral bleaching is synonymously associated with coral mortality (so-called `lethal bleaching episodes). While this synonymous association has undoubtedly been key in raising public support, it carries unfair representation: nonlethal bleaching is, and always has been, a phenomenon that effectively occurs regularly in nature as corals acclimatize to regular periodic changes in growth environment (days, seasons etc). In addition, corals can exhibit sublethal bleaching during extreme environmental conditions whereby mortality does not occur and corals can potentially subsequently recover once ambient environmental conditions return. Perhaps not surprisingly it is the frequency and extent of these non and sublethal processes that yield key evidence as to how coral species and reef systems will likely withstand environmental and thus climatic change. Observations of non and sublethal bleaching (and subsequent recovery) are arguably not as readily reported as those of lethal bleaching since (1) the convenient tools used to quantify bleaching yield major ambiguity (and hence high potential for misidentification) as to the severity of bleaching; and (2) lethal bleaching events inevitably receive higher profile (media) attention and so are more readily reported. Under-representation of non and sublethal bleaching signs may over-classify the severity of bleaching, under-estimate the potential resilience of reefs against environmental change, and thus ultimately limit (if not depreciate) the validity and effectiveness of reef management policies and practices. While bleaching induced coral mortality must remain our key concern it must be better placed within the context of bleaching signs that do not result in a long-term loss of reefviability.

Suglia, SF, Ryan, L, Bellinger, DC, Enlow, MB & Wright, RJ 2011, 'Children's Exposure to Violence and Distress Symptoms: Influence of Caretakers' Psychological Functioning', INTERNATIONAL JOURNAL OF BEHAVIORAL MEDICINE, vol. 18, no. 1, pp. 35-43.
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Background Previous studies linking violence exposure to adverse child behavior have typically relied on parental report of child symptoms without accounting for the informant's mental well-being, despite evidence that parental mental health can influence children's mental health and the parent's report of distress symptoms. Purpose We assess the influence of maternal depression on the violence exposure and child distress association in a subset of the Maternal Infant Smoking Study of East Boston, a prospective birth cohort. Results Among the 162 children ages 7 to 11, 51% were boys and 43% self-identified as Hispanic. When using child self-report, increased violence exposure was significantly associated with a broader range of distress symptoms (numbness, arousal, intrusion, avoidance subscales) compared to parent reported findings, which were only significantly related to the intrusion and avoidance subscales. Moreover, a significant mediation effect of maternal depression on the violence and distress association was noted only when mother's report of exposure and outcome was used. Conclusion Considering both parent and child self-report of violence is necessary to obtain a complete picture of violence exposure because parents and children may be offering different, although equally valid information. The influence of maternal depressive symptoms on preadolescent's distress symptoms may be attributed to reporting bias as opposed to more direct effects; thus, the parent's psychological functioning should be taken into consideration when relying on parental report of the child's psychological functioning.

Sun, B, Chen, Z, Kim, H-S, Ahn, H & Wang, G 2011, 'MnO/C core-shell nanorods as high capacity anode materials for lithium-ion batteries', JOURNAL OF POWER SOURCES, vol. 196, no. 6, pp. 3346-3349.
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MnO/C core-shell nanorods were synthesized by an in situ reduction method using MnO2 nanowires as precursor and block copolymer F127 as carbon source. Field emission scanning electron microscopy and transmission electron microscopy analysis indicated that a thin carbon layer was coated on the surfaces of the individual MnO nanorods. The electrochemical properties were evaluated by cyclic voltammetry and galvanostatic charge-discharge techniques. The as-prepared MnO/C core-shell nanorods exhibit a higher specific capacity than MnO microparticles as anode material for lithium ion batteries.

Szewcow, R, Robertson, J & Roux, CP 2011, 'The influence of front-loading and top-loading washing machines on the persistence, redistribution and secondary transfer of textile fibres during laundering', Australian Journal of Forensic Sciences, vol. 43, no. 4, pp. 263-273.
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This study investigated the influence of several factors on the redistribution of extraneous textile fibres on garments during machine washing. Cotton T-shirts were seeded with known numbers of acrylic, wool and viscose target fibres in controlled positions and laundered in top- and front-loading machines, both individually and accompanied by undergarments. The persistence of target fibres was low (generally <10%), but never zero. Between 50% and 100% of recovered fibres were redistributed away from the primary contact area. A secondary transfer of target fibres always occurred to at least one undergarment, 90% of experiments resulting in fibres transferred to the inside surface of the undergarments. This implies that whilst valuable fibre evidence may be recovered from garments after machine washing, the location of recovered fibres should not be relied upon to corroborate alleged scenarios when it is known or suspected that the garment under investigation has been laundered.

Tahtouh, M, Kalman, JR & Reedy, BJ 2011, 'Synthesis and Characterization of Four Alkyl 2-Cyanoacrylate Monomers and Their Precursors for Use in Latent Fingerprint Detection', JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, vol. 49, no. 1, pp. 257-277.
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Four novel cyanoacrylates, 2-cyanoethyl 2-cyanoacrylate, 1-cyanoethyl 2-cyanoacrylate, trideuteromethyl 2-cyanoacrylate and pentadeuteroethyl 2-cyanoacrylate have been synthesized using a Die Is-Alder protection/deprotection route involving anthracene. The common route for the synthesis of alkyl 2-cyanoacrylates was found to be unsatisfactory for the production of small quantities of the targeted cyanoacrylates, which have potential as reagents for the mid-infrared spectral imaging of fingerprints on difficult surfaces.

Tahtouh, M, Scott, SA, Kalman, JR & Reedy, BJ 2011, 'Four novel alkyl 2-cyanoacylate monomers and their use in latent fingermark detection by mid-infrared spectral imaging', FORENSIC SCIENCE INTERNATIONAL, vol. 207, no. 1-3, pp. 223-238.
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Four novel alkyl 2-cyanoacrylate monomers (alkyl = 1-cyanoethyl, 2-cyanoethyl, trideuteromethyl and pentadeuteroethyl) have been tested for their ability to develop latent fingermarks that can then be visualized usingmid-infrared spectral (chemical) imaging. Each of the fourmonomers was chosen for its potential to produce a strong, isolated infrared spectral band in its corresponding polymer (to provide spectral contrast against most backgrounds), as well as for its potential ability to be fumed onto fingermarks in the manner of conventional ethyl 2-cyanoacrylate (superglue). With the exception of the 2-cyanoethyl 2-cyanoacrylate, which had to be fumed under reduced pressure, all of themonomers were found to be sufficiently volatile to be fumed in a conventional fuming cabinet. All four monomers polymerized selectively on fingermark ridges on a variety of non-porous and semi-porous surfaces, leading to excellent development of the fingermarks. Unfortunately, although high quality mid-infrared spectral images of the fingermarks could be formed for all of the polymers at various frequencies, the new CBBN or CD stretching vibrations did not give rise to strong enough absorption intensities for good contrast on difficult backgrounds such as polymer banknotes. However, in the 1-cyanoethyl 2- cyanoacrylate polymer, the presence of the additional nitrile group had the unintended but desirable effect of shifting the strong C55O absorption to higher frequencies, moving it away from interfering banknote absorptions. This enabled fingermark contrast to be achieved even against the intaglio printing on the banknotes.

Tan, Y, Kamal, MA, Wang, Z-Z, Xiao, W, Seale, JP & Qu, X 2011, 'Chinese herbal extracts (SK0506) as a potential candidate for the therapy of the metabolic syndrome', Clinical Science, vol. 120, no. 7, pp. 297-305.
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The metabolic syndrome has reached epidemic proportions worldwide, but currently there is a lack of effective therapies for this multifactorial endocrine disease. TCM (traditional Chinese medicine) has been utilized to treat a wide variety of diseases for centuries in the People's Republic of China, subsequently becoming a promising source for the development of new therapeutic agents. Chinese medicinal herbs Gynostemma pentaphyllum, Coptis chinensis and Salvia miltiorrhiza have been shown to have anti-atherosclerotic and antidiabetic properties. In this study, we have investigated the metabolic effects of a mixture of these three herbal extracts (SK0506) in a rodent model of the metabolic syndrome induced by an HFD (high-fat diet). SD (Sprague–Dawley) rats that were fed on an HFD for 4 weeks gained 33% more weight compared with chow-fed rats (P&lt;0.05). Four weeks treatment with SK0506 prevented weight gain with decreased visceral fat (P&lt;0.01 compared with vehicle treatment). SK0506 also significantly reduced plasma triacylglycerols (triglycerides), NEFAs (non-esterified fatty acids) and cholesterol. SK0506 exerted similar effects to RSG (rosiglitazone) on impaired glucose intolerance. SK0506 also significantly enhanced glucose uptake and glycogen synthesis in adipose tissue during hyperinsulinaemic–euglycaemic clamp. Western blotting analysis revealed that SK0506 enhanced GLUT4 (glucose transporter 4) expression in adipose tissue, and RSG markedly up-regulated GLUT4 translocation in skeletal muscle. Overall, the present study has discovered that SK0506 can reverse several components of the metabolic syndrome primarily through acting on hyperlipidaemia and visceral obesity. The results from the present study suggest that it is worthwhile to conduct a randomized clinical trial to confirm the potential that SK0506 may be a new oral agent for treating the metabolic syndrome and preventing Type 2 diabetes.

Tan, Y, Sun, L-Q, Kamal, MA, Wang, X, Seale, JP & Qu, X 2011, 'Suppression of retinol-binding protein 4 with RNA oligonucleotide prevents high-fat diet-induced metabolic syndrome and non-alcoholic fatty liver disease in mice', Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, vol. 1811, no. 12, pp. 1045-1053.
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Conflicting data have been reported regarding the role of retinol-binding protein (RBP4) in insulin resistance, obesity, type 2 diabetes and non-alcoholic fatty liver disease (NAFLD). In this study, we used pharmacological methods to investigate the role

Tang, J, Dunlop, RA, Rowe, A, Rodgers, KJ & Ramzan, I 2011, 'Kavalactones Yangonin and Methysticin Induce Apoptosis in Human Hepatocytes (HepG2) In Vitro', PHYTOTHERAPY RESEARCH, vol. 25, no. 3, pp. 417-423.
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While cases of severe kava hepatotoxicity have been reported, studies examining the toxicity of individual kavalactones are limited. The present study examined the in vitro hepatotoxicity of kavain, methysticin and yangonin on human hepatocytes (HepG2) and the possible mechanism(s) involved. Cytotoxicity was assessed using lactate dehydrogenase (LDH) and ethidium bromide (EB) assays. The mode of cell death was analysed with acridine orange/ethidium bromide dual staining with fluorescence microscopy. Glutathione oxidation was measured using the ortho-phthalaldehyde (OPT) fluorescence assay. Kavain had minimal cytotoxicity, methysticin showed moderate concentration-dependent toxicity and yangonin displayed marked toxicity with ~40% reduction in viability in the EB assay. Acridine orange/ethidium bromide staining showed the predominant mode of cell death was apoptosis rather than necrosis. No significant changes were observed in glutathione levels, excluding this as the primary mechanism of cell death in this model. Further studies may elucidate the precise apoptotic pathways responsible and whether toxic kavalactone metabolites are involved.

Teng, Y, Zhou, J, Luo, F, Lin, G & Qiu, J 2011, 'Controllable space selective precipitation of copper nanoparticles in borosilicate glasses using ultrafast laser irradiation', Journal of Non-Crystalline Solids, vol. 357, no. 11-13, pp. 2380-2383.
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Transparent glasses containing copper nanoparticles are promising materials for ultrafast all-optical switches in the THz region due to their wide range of resonant absorption frequencies, ultrafast time response, as well as large third-order nonlinear optical coefficients associated with the surface plasmon resonance (SPR) in the visible region. In this paper, three dimension controllable precipitation of copper nanoparticles inside a borosilicate glass by irradiation of femtosecond laser pulses is studied. According to the designed program, different patterns made up of copper nanoparticles can be induced inside the glass sample. Absorption spectra are used to confirm the precipitation of copper nanoparticles. The precipitated nanoparticles can be space-selectively “dissolved” by the second time femtosecond laser irradiation. The involved mechanisms are discussed.

Teng, Y, Zhou, J, Ma, Z, Smedskjaer, MM & Qiu, J 2011, 'Persistent Near Infrared Phosphorescence from Rare Earth Ions Co-doped Strontium Aluminate Phosphors', Journal of The Electrochemical Society, vol. 158, no. 2, pp. K17-K17.
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SrAl2O4SrAl2O4 phosphors co-doped with Eu2+Eu2+ , Dy3+Dy3+ , and Nd3+Nd3+ ions are synthesized through a citric acid assisted sol-gel combustion process. The crystalline phases and crystallinity of the synthesized phosphors are studied by X-ray diffraction analysis. Strong persistent phosphorescence at 882nm882nm is observed as a consequence of irradiation by ultraviolet light at 370nm370nm due to the persistent energy transfer from excited Eu2+Eu2+ ions to Nd3+Nd3+ ions. The optimum doping concentration of Nd3+Nd3+ ions is estimated to be ∼2%∼2% , when the concentration of Eu2+Eu2+ and Dy3+Dy3+ ions are 1 and 1.5%, respectively, considering the energy transfer efficiency and the near infrared phosphorescence intensity.

Thomas, GL, Hsieh, YSY, Chun, CKY, Cai, Z-L, Reimers, JR & Payne, RJ 2011, 'Peptide Ligations Accelerated by N-Terminal Aspartate and Glutamate Residues', ORGANIC LETTERS, vol. 13, no. 18, pp. 4770-4773.
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A novel application of intramolecular base catalysis confers enhanced reaction rates for aminolysis ligations between peptide thioesters and peptides bearing N-terminal aspartate or glutamate residues. The broad scope of this process and its application in the total synthesis of the diabetes drug exenatide is demonstrated.

Thomas, PS, Stuart, BH, McGowan, N, Guerbois, JP, Berkahn, M & Daniel, V 2011, 'A study of ochres from an Australian aboriginal bark painting using thermal methods', JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY, vol. 104, no. 2, pp. 507-513.
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The potential of thermogravimetric analysis (TG) as a tool for the characterisation of ochre paint used in indigenous Australian bark paintings has been investigated. TG has been combined with differential scanning calorimetry (DSC) and mass spectrometry

Thomas-Peter, N, Langford, NK, Datta, A, Zhang, L, Smith, BJ, Spring, JB, Metcalf, BJ, Coldenstrodt-Ronge, HB, Hu, M, Nunn, J & Walmsley, IA 2011, 'Integrated Photonic Sensing', New J. Phys., vol. 13, p. 055024.
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Loss is a critical roadblock to achieving photonic quantum-enhanced technologies. We explore a modular platform for implementing integrated photonics experiments and consider the effects of loss at different stages of these experiments, including state preparation, manipulation and measurement. We frame our discussion mainly in the context of quantum sensing and focus particularly on the use of loss-tolerant Holland-Burnett states for optical phase estimation. In particular, we discuss spontaneous four-wave mixing in standard birefringent fibre as a source of pure, heralded single photons and present methods of optimising such sources. We also outline a route to programmable circuits which allow the control of photonic interactions even in the presence of fabrication imperfections and describe a ratiometric characterisation method for beam splitters which allows the characterisation of complex circuits without the need for full process tomography. Finally, we present a framework for performing state tomography on heralded states using lossy measurement devices. This is motivated by a calculation of the effects of fabrication imperfections on precision measurement using Holland-Burnett states.

Thompson, PA, Bonham, P, Waite, AM, Clementson, LA, Cherukuru, N, Hassler, C & Doblin, MA 2011, 'Contrasting oceanographic conditions and phytoplankton communities on the east and west coasts of Australia', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 58, no. 5, pp. 645-663.
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The composition and dynamics of the phytoplankton communities and hydrographic factors that control them are described for eastern and western Australia with a focus on the Eastern Australian Current (EAC) and Leeuwin Current (LC) between 27.5 degrees and 34.51S latitude.

Tian, H, Li, B, Wang, H, Li, Y, Wang, J, Zhao, S, Zhu, J, Wang, Q, Liu, W, Yao, X & Tang, Y 2011, 'A nanocontainer that releases a fluorescence sensor for cadmium ions in water and its biological applications', Journal of Materials Chemistry, vol. 21, no. 28, pp. 10298-10298.
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Tohidi-Esfahani, D, Graham, LD, Hannan, GN, Simpson, AM & Hill, RJ 2011, 'An ecdysone receptor from the pentatomomorphan, Nezara viridula, shows similar affinities for moulting hormones makisterone A and 20-hydroxyecdysone', Insect Biochemistry and Molecular Biology, vol. 41, no. 2, pp. 77-89.
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It has been suggested that Pentatomomorpha utilise the C(28) ecdysteroid, makisterone A (MakA), as the major moulting hormone rather than the more common C(27) hormone, 20-hydroxyecdsyone (20E). The present study is the first to examine this postulate at

Tohidi-Esfahani, D, Lawrence, MC, Graham, LD, Hannan, GN, Simpson, AM & Hill, RJ 2011, 'Isoforms of the heteropteran Nezara viridula ecdysone receptor: protein characterisation, RH5992 insecticide binding and homology modelling', Pest Management Science, vol. 67, no. 11, pp. 1457-1467.
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Abstract: BACKGROUND: Certain bisacylhydrazine compounds such as tebufenozide (RH5992) have been shown to act as order-specific insecticides. Their compatibility with predatory Heteroptera, which are used as biological control agents, has also been demonstrated. However, the molecular mode of action of these ecdysone agonists has not been explored in a heteropteran, much less one that is a significant agricultural pest, such as Nezara viridula. RESULTS: Alternatively spliced ligand-binding regions of the N. viridula ecdysone receptor were expressed, purified and characterised by 2D gel analysis, mass spectrometry, homology modelling and competitive binding of a bisacylhydrazine insecticidal compound (RH5992) and various ecdysteroids. Ligand binding by the two splice isoforms was indistinguishable, and relative affinities were found to occur in the order muristerone A > ponasterone A > 20-hydroxyecdysone > inokosterone > RH5992 > alpha-ecdysone. CONCLUSION: The predicted difference in amino acid sequence between the ligand-binding domains of the N. viridula ecdysone receptor splice variants was verified by mass spectrometry. Both splice variant isoforms exhibit a greater affinity for the bisacylhydrazine insecticide RH5992 than do the other hemipteran ecdysone receptors characterised to date. Their affinities for a range of ecdysteroids also distinguish them from the ecdysone receptors of other Hemiptera characterised thus far. Homology models of both N. viridula receptor isoforms provide further insight into the bisacylhydrazine- and ecdysteroid-binding properties of these receptors, including their similar affinity for 20-hydroxyecdysone and the postulated pentatomomorphan moulting hormonemakisterone A.

Tolmachev, SY, Ketterer, ME, Hare, D, Doble, P & James, AC 2011, 'The US Transuranium and Uranium Registries: forty years' experience and new directions in the analysis of actinides in human tissues', Proceedings in Radiochemistry, vol. 1, no. 1, pp. 173-181.
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Abstract The US Transuranium and Uranium Registries (USTUR) studies the distribution, biokinetics and tissue dosimetry of actinide elements through radiochemical analysis of autopsy tissues voluntarily donated by occupationally exposed persons. The paper provides an overview of the analytical methods for plutonium (Pu), americium (Am) and uranium (U) isotopic determination in human tissues currently applied at USTUR. The results of inter-comparing 239+240Pu, 241Am and 234,235,238U determinations by sector field inductively coupled mass spectrometry (SF-ICP-MS), α-spectrometry (AS) and kinetic phosphorescence analysis (KPA) are discussed. SF-ICP-MS is a major advance over AS and KPA in enabling the measurement of the 240Pu/ 239Pu atom ratio, the short-lived β-emitter 241Pu, and long-lived 236U. For the first time, 241Am and 241Pu were measured in human tissues using SF-ICP-MS. The paper also presents a new avenue of USTUR research in the application of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to elemental bio-imaging (EBI) of the actinides in human tissues.

Tovey, ER, Ng, DSY, Stelzer-Braid, S, Rawlinson, WD & Oliver, BG 2011, 'Retraction notice to “Children with asthma and no URTI, more commonly have rhinovirus in their exhaled breath, than in mucous”', Journal of Allergy and Clinical Immunology, vol. 127, no. 2, pp. 551-551.
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Traut, T, Kriel, FH, Zyl, WEV & Williams, DBG 2011, 'Chlorido{N-[2-(diphenylphosphanyl)benzyl]-1-(pyridin-2-yl)methanamine-κP}gold(I)', Acta Crystallographica Section E Structure Reports Online, vol. 67, no. 11, pp. m1625-m1625.
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In the title compound, [AuCl(C 25 H 23 N 2 P)], the Au I atom is in a typical almost linear coordination environment defined by phosphane P and Cl atoms [bond angle = 175.48 (4)°]. Helical supra-molecular chains along the b axis and mediated by N - H⋯Cl hydrogen bonds feature in the crystal packing. © Traut et al. 2011.

Trian, T, Burgess, JK, Niimi, K, Moir, LM, Ge, Q, Berger, P, Liggett, SB, Black, JL & Oliver, BG 2011, 'beta(2)-Agonist Induced cAMP Is Decreased in Asthmatic Airway Smooth Muscle Due to Increased PDE4D', PLOS ONE, vol. 6, no. 5, pp. 1-7.
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Background and Objective: Asthma is associated with airway narrowing in response to bronchoconstricting stimuli and increased airway smooth muscle (ASM) mass. In addition, some studies have suggested impaired b-agonist induced ASM relaxation in asthmatics, but the mechanism is not known. Objective: To characterize the potential defect in b-agonist induced cAMP in ASM derived from asthmatic in comparison to non-asthmatic subjects and to investigate its mechanism. Methods: We examined b2-adrenergic (b2AR) receptor expression and basal b-agonist and forskolin (direct activator of adenylyl cyclase) stimulated cAMP production in asthmatic cultured ASM (n = 15) and non-asthmatic ASM (n = 22). Based on these results, PDE activity, PDE4D expression and cell proliferation were determined. Results: In the presence of IBMX, a pan PDE inhibitor, asthmatic ASM had ,50% lower cAMP production in response to isoproterenol, albuterol, formoterol, and forskolin compared to non-asthmatic ASM. However when PDE4 was specifically inhibited, cAMP production by the agonists and forskolin was normalized in asthmatic ASM. We then measured the amount and activity of PDE4, and found ,2-fold greater expression and activity in asthmatic ASM compared to non-asthmatic ASM. Furthermore, inhibition of PDE4 reduced asthmatic ASM proliferation but not that of non-asthmatic ASM. Conclusion: Decreased b-agonist induced cAMP in ASM from asthmatics results from enhanced degradation due to increased PDE4D expression. Clinical manifestations of this dysregulation would be suboptimal b-agonist-mediated bronchodilation and possibly reduced control over increasing ASM mass. These phenotypes appear to be ``hard-wired into ASM from asthmatics, as they do not require an inflammatory environment in culture to be observed.

Trivedi, N, Gupta, V, Kumar, M, Kumari, P, C.R.K.Reddy & Jha, B 2011, 'An alkali-halotolerant cellulase from Bacillus flexus isolated from green seaweed Ulva lactuca', Carbohydrate Polymers, vol. 83, no. 2, pp. 891-897.
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Abstract An extracellular alkali-halotolerant cellulase from the strain Bacillus flexus NT isolated from Ulva lactuca was purified to homogeneity with a recovery of 25.03% and purity fold of 22.31. The molecular weight of the enzyme was about 97 kDa and the Vmax and Km was 370.17 U/ml/min and 6.18 mg/ml respectively. The optimum pH and temperature for enzyme activity was 10 and 45 °C respectively. The enzymatic hydrolysis of the CMC was confirmed with GPC and GC-MS analysis. The stabilized activity of the enzyme even at high pH of 9.0–12.0 and residual activity of about 70% at salt concentration (NaCl 15%) revealed for its alkali-halotolerance nature. The metal ions Cd2+ and Li1+ were found as inducers while Cr2+, Co2+, Zn2+ and metal chelator EDTA have significantly inhibited the enzyme activity. Enzyme activity was insensitive to ethanol and isopropanol while partially inhibited by acetone, cyclohexane and benzene.

Trivedi, N, Gupta, V, Kumar, M, Kumari, P, Reddy, CRK & Jha, B 2011, 'Solvent tolerant marine bacterium Bacillus aquimaris secreting organic solvent stable alkaline cellulase', Chemosphere, vol. 83, no. 5, pp. 706-712.
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Ulstrup, KE, Kuhl, M, van Oppen, MJH, Cooper, TF & Ralph, PJ 2011, 'Variation in photosynthesis and respiration in geographically distinct populations of two reef-building coral species', AQUATIC BIOLOGY, vol. 12, no. 3, pp. 241-248.
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Studies of the regulation and importance of physiological processes such as coral photosynthesis and respiration on coral reefs require knowledge of spatio-temporal patterns of variability at different scales. Oxygen microelectrodes were used to measure photosynthesis and dark respiration of 2 corals, Pocillopora damicornis and Turbinaria reniformis, in the northern (Lizard Island) and central (Davies and Broadhurst Reefs) regions of the Great Barrier Reef (GBR) in winter and summer. Genetic characterisation of Symbiodinium revealed that P. damicornis hosted a single symbiont type (Symbiodinium C1) in both regions, whereas T. reniformis harboured 2 types, dependent on location. Colonies at Lizard Island harboured Symbiodinium D, whereas colonies at Davies Reef harboured Symbiodinium C2. Rates of gross photosynthesis were greater in the central than in the northern GBR in summer. A similar pattern was detected for dark respiration rates in T. reniformis. No seasonal change in either photosynthesis or dark respiration was evident in the northern GBR, possibly due to less annual variability in light conditions, and for T. reniformis, additionally the presence of Symbiodinium D. These results highlight that environmental conditions coupled with regional-scale distribution of Symbiodinium are likely to exert important influences on respiration and photosynthetic performance of reef-building corals.

Ung, AT, Pyne, SG, Jeoffreys, GR, Skelton, BW & White, AH 2011, 'ChemInform Abstract: Synthesis of 2-Acetyl-5-(1,2,3,4,5,6-hexahydroxyhexyl)thiazoles.', ChemInform, vol. 42, no. 29, pp. no-no.
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Ung, AT, Pyne, SG, Jeoffreys, GR, Skelton, BW & White, AH 2011, 'Synthesis of 2-acetyl-5-(1,2,3,4,5,6-hexahydroxyhexyl)thiazoles', MONATSHEFTE FUR CHEMIE, vol. 142, no. 3, pp. 297-303.
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The syntheses of two diastereoisomers of 2-acetyl-5-(1,2,3,4,5,6-hexahydroxyhexyl) thiazole are reported. The synthesis of these diastereoisomers involved the coupling of 5-metallated 2-(1,1-dimethoxyethyl)thiazole with a Weinreb amide derived from d-gluconolactone, followed by asymmetric reduction of the ketone thus prepared. The stereochemistries and structures of some key compounds were determined by single-crystal X-ray structural analysis.

van den Broek, J, Peach, M & Booth, D 2011, 'The reproductive biology of the common stingareeTrygonoptera testacea(Urolophidae) in eastern Australia', Australian Zoologist, vol. 35, no. 3, pp. 627-632.
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The common stingaree, Trygonoptera testacea, is abundant on the continental shelf of eastern Australia but little is known of its ~cology and reproduction despite it being a common component of the demersal trawl fishery. Specimens of T testacea were collected from bycatch to investigate the species' reproductive biology. Males were found to mature at a disc width of 22 cm, while females reached sexual maturity at 26 cm disc width. Of all the I testacea examined, 53% of males (n= 159) and 16% of females (n=62) were se~ually mature. Only the left uterus and ovary were found to be functional in female I testacea. One gravid female carrying two near term embryos was sampled in February 2004. Many other females daught during the same trawl were observed aborting embryos providing a tentative estimate parturitiàn period, which appears to be between the months of February and April. Although further investigation is required to determine if I testacea populations are threatened by fishing pressures, the current study has provided key demographic parameters vital for the design of a management plan for I testacea and similar populations.

van der Heyde, HC, Gramaglia, I, Combes, V, George, TC & Grau, GE 2011, 'Flow Cytometric Analysis of Microparticles', Methods in Molecular Biology, vol. 699, pp. 337-354.
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Cell-derived microparticles (MPs) are increasingly recognized as important cell-to-cell signaling mechanisms and may exhibit important functions in homeostasis but also in pathogenesis. Indeed, MPs are associated with a number of diseases inhibiting their production that protects against pathogenesis. MPs are distinct from exosomes and apoptotic bodies, often exhibiting the membrane proteins of the activated or apoptotic cell from which they are derived. Electron microscopic analyses have shown that MPs are produced by all cell types tested to date, and ELISA-based assays have established that increased numbers of MPs are produced following cell activation. These approaches do not, however, determine the exact number of MPs and distribution of functional proteins on their surface. Flow cytometry represents an obvious approach to analyze MPs, and we present here a method to assess the number and phenotype of MPs by using a conventional flow cytometer. We also present the caveats with this method and describe a new imaging flow cytometry approach that overcomes these limitations.

Van Dongen-Vogels, V, Seymour, JR, Middleton, JF, Mitchell, JG & Seuront, L 2011, 'Influence of local physical events on picophytoplankton spatial and temporal dynamics in South Australian continental shelf waters', JOURNAL OF PLANKTON RESEARCH, vol. 33, no. 12, pp. 1825-1841.
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We investigated the space-time dynamics of picophytoplankton in South Australian continental shelf waters from February 2008 to January 2009, focusing on localized physical events. We discriminated six picophytoplankton populations by flow cytometry, including Synechococcus (SYN1, SYN2), Prochlorococcus (PROC1, PROC2) and small and large picoeukaryotes (EUKS, EUKL). Local physical events observed included downwelling and dense waters outflowing from a nearby gulf in winter-early spring 2008, upwelling in summer and early spring 2008 and eddy formation in January 2009. Each population responded differently to these events, which resulted in up to four orders of magnitude changes in their abundances. Population-specific hotspots reflected a succession of distinct dominant communities associated with the strength of upwelling events, changes in fluorescence maximum depths and local downwelling and mixing processes. The unexpected high abundances and local dominance of Prochlorococcus in summer reflected the possible influence of eastward and westward current transports and the presence of a High-Light (PROC1)-and Low-Light (PROC2)-adapted ecotypes. This study highlights the role of localized physical events in the dominance of all three picophytoplankton groups that may be critical for the high productivity of the study region, and suggests the importance of hydroclimatic forcing for inter-annual changes in picophytoplankton communities.

Van Ly, D, King, NJC, Moir, LM, Burgess, JK, Black, JL & Oliver, BG 2011, 'Effects of β2 Agonists, Corticosteroids, and Novel Therapies on Rhinovirus-Induced Cytokine Release and Rhinovirus Replication in Primary Airway Fibroblasts', Journal of Allergy, vol. 2011, pp. 1-11.
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Rhinovirus-(RV-) induced asthma exacerbations account for high asthma-related health costs and morbidity in Australia. The cellular mechanism underlying this pathology is likely the result of RV-induced nuclear-factor-kappa-B-(NF-κB-) dependent inflammation. NF-κB may also be important in RV replication as inhibition of NF-κB inhibits replication of other viruses such as human immunodeficiency virus and cytomegalovirus. To establish the role of NF-κB inhibitors in RV-induced IL- 6 and IL-8 and RV replication, we used pharmacological inhibitors of NF-κB, and steroids and/or β2 agonists were used for comparison. Primary human lung fibroblasts were infected with RV-16 in the presence of NF-κB inhibitors: BAY-117085 and dimethyl fumarate; β2 agonist: salmeterol; and/or corticosteroids: dexamethasone; fluticasone. RV-induced IL-6 and IL-8 and RV replication were assessed using ELISAs and virus titration assays. RV replicated and increased IL-6 and IL-8 release. Salmeterol increased, while dexamethasone and fluticasone decreased RV-induced IL-6 and IL-8 (P<0.05). The NF-κB inhibitor BAY-117085 inhibited only RV-induced IL-6 (P<0.05) and dimethyl fumarate did not alter RV-induced IL-6 and IL-8. Dimethylfumarate increased RV replication whilst other drugs did not alter RV replication. These data suggest that inhibition of NF-κB alone is unlikely to be an effective treatment compared to current asthma therapeutics.

Velikova, V, Varkonyi, Z, Szabo, M, Maslenkova, L, Nogues, I, Kovacs, L, Peeva, V, Busheva, M, Garab, G, Sharkey, TD & Loreto, F 2011, 'Increased Thermostability of Thylakoid Membranes in Isoprene-Emitting Leaves Probed with Three Biophysical Techniques', PLANT PHYSIOLOGY, vol. 157, no. 2, pp. 905-916.
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Three biophysical approaches were used to get insight into increased thermostability of thylakoid membranes in isoprene- emittingplants.Arabidopsis (Arabidopsis thaliana) plants genetically modified to make isoprene and Platanus orientalis leaves, in which isoprene emission was chemically inhibited, were used. First, in the circular dichroism spectrum the transition temperature of the main band at 694 nm was higher in the presence of isoprene, indicating that the heat stability of chiral macrodomains of chloroplast membranes, and specifically the stability of ordered arrays of light-harvesting complex IIphotosystem II in the stacked region of the thylakoid grana, was improved in the presence of isoprene. Second, the decay of electrochromic absorbance changes resulting from the electric field component of the proton motive force (DA515) was evaluated following single-turnover saturating flashes. The decay of DA515 was faster in the absence of isoprene when leaves of Arabidopsis and Platanus were exposed to high temperature, indicating that isoprene protects the thylakoid membranes against leakiness at elevated temperature. Finally, thermoluminescence measurements revealed that S2QB 2 charge recombination was shifted to higher temperature in Arabidopsis and Platanus plants in the presence of isoprene, indicating higher activation energy for S2QB 2 redox pair, which enables isoprene-emitting plants to perform efficient primary photochemistry of photosystem II even at higher temperatures. The data provide biophysical evidence that isoprene improves the integrity and functionality of the thylakoid membranes at high temperature. These results contribute to our understanding of isoprene mechanism of action in plant protection against environmental stresses.

Venables, SJ, McNevin, D, Daniel, R, Sarre, SD, van Oorschot, RAH & Walsh, SJ 2011, 'An in-depth population genetic analysis of forensic short tandem repeat loci in Indonesia', Forensic Science International: Genetics Supplement Series, vol. 3, no. 1, pp. e157-e158.
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Allele frequency data and knowledge of the population genetic features of relevant populations are required to substantiate the strength of forensic DNA evidence. It is conceivable that population substructure exists within Indonesia given that it is an archipelago with over 17,000 islands and encompasses numerous distinct ethnic and linguistic groups. However, the population genetic features of forensic short tandem repeat (STR) loci in Indonesia have not been examined thoroughly. Samples from 1500 unrelated Indonesian individuals representing 31 geographic sub-populations were analysed using the AmpFℓSTR Identifiler kit (Applied Biosystems). Departures from Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE) were assessed using exact tests and results suggest that a number of the sub-populations, as well as the combined data set (N=1286), display significant departures from equilibrium. Ultimately, data from these STRs and other markers on this sample set will assist in forming genetically appropriate sub-population groupings for the purpose of constructing defensible forensic STR databases. © 2011 Elsevier Ireland Ltd. ® ®

Wagner, MR, Callsen, G, Reparaz, JS, Schulze, J-H, Kirste, R, Cobet, M, Ostapenko, IA, Rodt, S, Nenstiel, C, Kaiser, M, Hoffmann, A, Rodina, AV, Phillips, MR, Lautenschlaeger, S, Eisermann, S & Meyer, BK 2011, 'Bound excitons in ZnO: Structural defect complexes versus shallow impurity centers', PHYSICAL REVIEW B, vol. 84, no. 3.
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ZnO single crystals, epilayers, and nanostructures often exhibit a variety of narrow emission lines in the spectral range between 3.33 and 3.35 eV which are commonly attributed to deeply bound excitons (Y lines). In this work, we present a comprehensive study of the properties of the deeply bound excitons with particular focus on the Y(0) transition at 3.333 eV. The electronic and optical properties of these centers are compared to those of the shallow impurity related exciton binding centers (I lines). In contrast to the shallow donors in ZnO, the deeply bound exciton complexes exhibit a large discrepancy between the thermal activation energy and localization energy of the excitons and cannot be described by an effective mass approach. The different properties between the shallow and deeply bound excitons are also reflected by an exceptionally small coupling of the deep centers to the lattice phonons and a small splitting between their two electron satellite transitions. Based on a multitude of different experimental results including magnetophotoluminescence, magnetoabsorption, excitation spectroscopy (PLE), time resolved photoluminescence (TRPL), and uniaxial pressure measurements, a qualitative defect model is developed which explains all Y lines as radiative recombinations of excitons bound to extended structural defect complexes. These defect complexes introduce additional donor states in ZnO. Furthermore, the spatially localized character of the defect centers is visualized in contrast to the homogeneous distribution of shallow impurity centers by monochromatic cathodoluminescence imaging. A possible relation between the defect bound excitons and the green luminescence band in ZnO is discussed. The optical properties of the defect transitions are compared to similar luminescence lines related to defect and dislocation bound excitons in other II-VI and III-V semiconductors.

Walford, S-A, Wu, Y, Llewellyn, DJ & Dennis, ES 2011, 'GhMYB25-like: a key factor in early cotton fibre development', PLANT JOURNAL, vol. 65, no. 5, pp. 785-797.
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MYB transcription factors have been implicated in regulation of the development of ovule epidermal cells into the elongated seed fibres of cotton. An R2R3 MYB, GhMYB25-like, identified from its reduced expression in a fibreless mutant of cotton (Xu142 fl), is here shown to play a key role in the very early stages of fibre cell differentiation. A GhMYB25-like promoterGUS construct was expressed predominantly in the epidermal layers of cotton ovules before anthesis ()3 days post-anthesis, dpa), increasing in expression in 0-dpa ovules, primarily in those epidermal cells expanding into fibres, and then in elongating fibres at +3 dpa, declining thereafter. This was consistent with GhMYB25-like transcript abundance during fibre development. RNA interference suppression of GhMYB25-like resulted in cotton plants with fibreless seeds, but normal trichomes elsewhere, phenocopying the Xu142 fl mutant. Like Xu142 fl these plants had reduced expression of the fibreexpressed MYBs, GhMYB25 and GhMYB109, indicating that GhMYB25-like is upstream from those MYBs. This hierarchy was supported by the absence of any change in transcript level of GhMYB25-like in GhMYB25- and GhMYB109-silenced transgenic lines. Transgenic cotton with an additional copy of the native gene had elevated expression of GhMYB25-like in ovules, but no obvious increase in fibre initials, suggesting that there may be other factors that interact with GhMYB25-like to differentiate epidermal cells into fibre cells.

Wallach, M & Nowak, BF 2011, 'Understanding amoebic gill disease.', CABI Reviews, vol. 2011, no. 058, pp. 1-6.
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Abstract Amoebic gill disease (AGD) is a severely debilitating disease, which mainly affects the salmonid industry. It causes high production losses worldwide, including Tasmania, where it is the main health problem in farmed Atlantic salmon. Without the use of control procedures such as fresh water bathing and/or by maintaining fish population densities at a level commensurate with proper hygiene, this disease can often lead to the death of over 50% of infected salmon. AGD is caused by the parasitic amoeba, Neoparamoeba perurans , which binds to and inhabits the gill epithelium of growing fish. Pathology is associated with severe epithelial hyperplasia, fusion of gill lamellae, lowering of oxygen tension and pH of the blood and eventual death of the fish. In order to understand this disease process, research has been carried out, to study the immune response of fish to primary and secondary infections, the genetic basis of resistance to infection as well as how the parasite binds to the host gill tissue and induces a severe host response. Results have shown that N. perurans contains within its surface glycocalyx, high-molecular-weight mucin-like glycoproteins. These surface mucins are immunodominant, according to studies showing that they are the major antigens recognized by antibody in serum from fish exposed to the parasite, as well as when immunized with either whole parasites or subcellular fractions. Thus far, attempts to vaccinate salmon using the purified, high-molecular-weight surface antigen (HMWA) have failed to induce significant protective immunity. However, these studies have greatly aided our understanding of the molecular basis of the amoeba binding and infection process.

Wallach, MG, Webby, RJ, Islam, F, Walkden-Brown, S, Emmoth, E, Feinstein, R & Gronvik, K-O 2011, 'Cross-Protection of Chicken Immunoglobulin Y Antibodies against H5N1 and H1N1 Viruses Passively Administered in Mice', Clinical and Vaccine Immunology, vol. 18, no. 7, pp. 1083-1090.
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ABSTRACTInfluenza viruses remain a major threat to global health due to their ability to undergo change through antigenic drift and antigenic shift. We postulated that avian IgY antibodies represent a low-cost, effective, and well-tolerated approach that can easily be scaled up to produce enormous quantities of protective antibodies. These IgY antibodies can be administered passively in humans (orally and intranasally) and can be used quickly and safely to help in the fight against an influenza pandemic. In this study, we raised IgY antibodies against H1N1, H3N2, and H5N1 influenza viruses. We demonstrated that, using whole inactivated viruses alone and in combination to immunize hens, we were able to induce a high level of anti-influenza virus IgY in the sera and eggs, which lasted for at least 2 months after two immunizations. Furthermore, we found that by use ofin vitroassays to test for the ability of IgY to inhibit hemagglutination (HI test) and virus infectivity (serum neutralization test), IgYs inhibited the homologous as well as in some cases heterologous clades and strains of viruses. Using anin vivomouse model system, we found that, when administered intranasally 1 h prior to infection, IgY to H5N1 protected 100% of the mice against lethal challenge with H5N1. Of particular interest was the finding that IgY to H5N1 cross-protected against A/Puerto Rico/8/34 (H1N1) bothin vitroandin vivo. Based on our results, we conclude that anti-influenza virus IgY can be used to help prevent influenza virus infection.

Wallman, J, Roux, C & Lennard, C 2011, 'Supplement', Forensic Science, Medicine, and Pathology, vol. 7, no. 1, pp. 75-138.
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Wand, MP & Ormerod, JT 2011, 'Penalized wavelets: Embedding wavelets into semiparametric regression', Electronic Journal of Statistics, vol. 5, no. none, pp. 1654-1717.
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We introduce the concept of penalized wavelets to facilitate seamless embedding of wavelets into semiparametric regression models. In particular, we show that penalized wavelets are analogous to penalized splines; the latter being the established approach to function estimation in semiparametric regression. They differ only in the type of penalization that is appropriate. This fact is not borne out by the existing wavelet literature, where the regression modelling and fitting issues are overshadowed by computational issues such as efficiency gains afforded by the Discrete Wavelet Transform and partially obscured by a tendency to work in the wavelet coefficient space. With penalized wavelet structure in place, we then show that fitting and inference can be achieved via the same general approaches used for penalized splines: penalized least squares, maximum likelihood and best prediction within a frequentist mixed model framework, and Markov chain Monte Carlo and mean field variational Bayes within a Bayesian framework. Penalized wavelets are also shown have a close relationship with wide data (p»n) regression and benefit from ongoing research on that topic

Wand, MP, Ormerod, JT, Padoan, SA & Frühwirth, R 2011, 'Mean Field Variational Bayes for Elaborate Distributions', Bayesian Analysis, vol. 6, no. 4, pp. 847-900.
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We develop strategies for mean eld variational Bayes approximate inference for Bayesian hierarchical models containing elaborate distributions. We loosely dene elaborate distributions to be those having more complicated forms compared with common distributions such as those in the Normal and Gamma families. Examples are Asymmetric Laplace, Skew Normal and Generalized Ex- treme Value distributions. Such models suer from the diculty that the param- eter updates do not admit closed form solutions. We circumvent this problem through a combination of (a) specially tailored auxiliary variables, (b) univariate quadrature schemes and (c) nite mixture approximations of troublesome den- sity functions. An accuracy assessment is conducted and the new methodology is illustrated in an application

Wang, G, Liu, H, Liu, J, Qiao, S, Lu, GM, Munroe, P & Ahn, H 2011, 'ChemInform Abstract: Mesoporous LiFePO4/C Nanocomposite Cathode Materials for High Power Lithium Ion Batteries with Superior Performance.', ChemInform, vol. 42, no. 6, pp. no-no.
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Wang, JJJ, Chan, JSK & Choy, STB 2011, 'Stochastic volatility models with leverage and heavy-tailed distributions: A Bayesian approach using scale mixtures', Computational Statistics & Data Analysis, vol. 55, no. 1, pp. 852-862.
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Wang, L, Liu, X, Liang, H & Carroll, RJ 2011, 'Estimation and variable selection for generalized additive partial linear models', Annals of Statistics, vol. 39, no. 4, pp. 1827-1851.
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We study generalized additive partial linear models, proposing the use of polynomial spline smoothing for estimation of nonparametric functions, and deriving quasi-likelihood based estimators for the linear parameters. We establish asymptotic normality for the estimators of the parametric components. The procedure avoids solving large systems of equations as in kernel-based procedures and thus results in gains in computational simplicity. We further develop a class of variable selection procedures for the linear parameters by employing a nonconcave penalized quasi-likelihood, which is shown to have an asymptotic oracle property. Monte Carlo simulations and an empirical example are presented for illustration.

Wang, SSJ & Wand, MP 2011, 'Using Infer.NET for Statistical Analyses', The American Statistician, vol. 65, no. 2, pp. 115-126.
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We demonstrate and critique the new Bayesian inference package Infer.NET in terms of its capacity for statistical analyses. Infer.NET differs from the well-known BUGS Bayesian inference packages in that its main engine is the variational Bayes family of deterministic approximation algorithms rather than Markov chain Monte Carlo. The underlying rationale is that such deterministic algorithms can handle bigger problems due to their increased speed, despite some loss of accuracy. We find that Infer.NET is a well-designed computational framework and offers significant speed advantages over BUGS. Nevertheless, the current release is limited in terms of the breadth of models it can handle, and its inference is sometimes inaccurate. Supplemental materials accompany the online version of this article.

Wang, W, Hansbro, PM, Foster, PS & Yang, M 2011, 'An Alternate STAT6-Independent Pathway Promotes Eosinophil Influx into Blood during Allergic Airway Inflammation', PLoS ONE, vol. 6, no. 3, pp. e17766-e17766.
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Wang, Y, Chi, Q, Hush, NS, Reimers, JR, Zhang, J & Ulstrup, J 2011, 'Gold Mining by Alkanethiol Radicals: Vacancies and Pits in the Self-Assembled Monolayers of 1-Propanethiol and 1-Butanethiol on Au(111)', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 115, no. 21, pp. 10630-10639.
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Wang, Y, Chi, Q, Zhang, J, Hush, NS, Reimers, JR & Ulstrup, J 2011, 'Chain-Branching Control of the Atomic Structure of Alkanethiol-Based Gold-Sulfur Interfaces', JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 133, no. 38, pp. 14856-14859.
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Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): direct binding to the Au (111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the a carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.

Wang, Y, Luo, X-P, Lim, CED, Wong, WSF & Zhong, G 2011, 'Regulatory Effect of Peptidoglycan on the Expression of Toll-Like Receptor 2 mRNA and Proteins in Trophoblast Cell Line TEV-1 Cells', ISRN Obstetrics and Gynecology, vol. 2011, pp. 1-5.
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Objective. To investigate the regulatory effect of peptidoglycan on the expression of human Toll-like receptors 2 (TLR2) mRNA and proteins in the human extravillous trophoblast cell line (TEV-1). Methods. TEV-1 cells were incubated with different doses of peptidoglycan. The expression of TLR2 mRNA and protein was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) and immunocytochemistry SP staining. Results. TLR2 was expressed in TEV-1 cells and localized to both the cytoplasm and plasma membrane. Compared with the untreated control, TEV-1 cells incubated with 30 g/ml peptidoglycan significantly upregulated the expression of TLR2 mRNA and protein after 12 hours of treatment (). However, the expression of TLR2 mRNA and protein was decreased but had no significant difference compared with the control () after 24 hours of treatment. On the other hand, 10 g/ml peptidoglycan did not seem to have regulatory effect on mRNA and protein expression of TLR2 (). Conclusion. Peptidoglycan has a role in regulating the expression of TLR2 mRNA and protein in TEV-1 cells. It suggests that the trophoblast cells may play important role in the immune response at the fetal-maternal interface and affect the result of pregnancy by expressing TLR2.

Wang, Y, Sun, B, Park, J, Kim, W-S, Kim, H-S & Wang, G 2011, 'Morphology control and electrochemical properties of nanosize LiFePO4 cathode material synthesized by co-precipitation combined with in situ polymerization', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 509, no. 3, pp. 1040-1044.
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Nanosize carbon coated LiFePO4 cathode material was synthesized by in situ polymerization. The as-prepared LiFePO4 cathode material was systematically characterized by X-ray diffraction, thermogravimetric-differential scanning calorimetry, X-ray photo-electron spectroscopy, field-emission scanning electron microscopy, and transmission electron microscopy techniques. Field-emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) images revealed that the morphology of the LiFePO4 consists of primary particles (40-50 nm) and agglomerated secondary particles (100-110 nm). Each particle is evenly coated with an amorphous carbon layer, which has a thickness around 3-5 nm. The electrochemical properties were examined by cyclic voltammetry and charge-discharge testing. The as-prepared LiFePO4 can deliver an initial discharge capacity of 145 mAh/g, 150 mAh/g, and 134 mAh/g at 0.2 C, 1 C, and 2 C rates, respectively, and exhibits excellent cycling stability. At a higher C-rate (5 C) a slight capacity loss could be found. However after being charge-discharge at lower C-rates, LiFePO4 can be regenerated and deliver the discharge capacity of 145 mAh/g at 0.2 C. (C) 2010 Elsevier B.V. All rights reserved.

Wassmer, SC, Combes, V & Grau, GER 2011, 'Platelets and microparticles in cerebral malaria: the unusual suspects', Drug Discovery Today: Disease Mechanisms, vol. 8, no. 1-2, pp. e15-e23.
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Platelets and microparticles might have a crucial role in the pathogenesis of cerebral malaria by assisting in the binding of infected erythrocytes to the cerebral vasculature and mediating numerous inflammatory and immune processes. The present review compiles a selection of the recent findings on their interactions with microvascular endothelium, infected erythrocytes and immune cells that may influence the development of cerebral malaria. Crown Copyright © 2011 Published by Elsevier Ltd. All rights reserved.

Watkins, H, Joss, DT, Grahn, T, Page, RD, Carroll, RJ, Dewald, A, Greenlees, PT, Hackstein, M, Herzberg, R-D, Jakobsson, U, Jones, PM, Julin, R, Juutinen, S, Ketelhut, S, Kröll, 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 2011, 'Lifetime measurements probing triple shape coexistence in175Au', Physical Review C, vol. 84, no. 5.
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Waugh, CA, Huston, WM, Noad, MJ & Bengtson Nash, S 2011, 'Cytochrome P450 isozyme protein verified in the skin of southern hemisphere humpback whales (Megaptera novaeangliae): Implications for biochemical biomarker assessment', Marine Pollution Bulletin, vol. 62, no. 4, pp. 758-761.
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Weatherby, K, Murray, S, Carter, D & Slapeta, J 2011, 'Surface and Flagella Morphology of the Motile Form of Chromera velia Revealed by Field-Emission Scanning Electron Microscopy', PROTIST, vol. 162, no. 1, pp. 142-153.
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Chromera velia (Chromerida; Alveolata) is an autotrophic protist isolated from stony corals. Ch. velia possesses a chloroplast thought to be most closely related to the apicoplasts of non-photosynthetic apicomplexa. Phylogenetic analyses place Ch. velia as a close relative of parasitic apicomplexa and predatory colpodellids. We have used field-emission scanning electron microscopy of cells sputter-coated with gold or chromium and non-coated cells to characterise the surface ultrastructure of the motile form of Ch. velia. In overall morphology the biflagellated Ch. velia cells resemble the colpodellid Colpodella edax, but with some notable differences. The ventral side of the flagellated Ch. velia cell has two grooves extending from the anterior flagella insertion point with a ridge rising towards the anterior apex of the cell. The anterior flagellum is shorter than the posterior flagellum and possesses a distinct, small curved appendage. The insertion point of the anterior flagellum is partly enclosed by a flap extending from the cell. The posterior flagellum is approximately four times the length of the cell and possesses mastigonemes. The combination of coating techniques proved superior to the commonly used gold coating to determine fine surface ultrastructure. This new ultrastructural information for Ch. velia allowed us to emend its diagnosis.

Webb, JK, Pearson, D & Shine, R 2011, 'A small dasyurid predator (Sminthopsis virginiae) rapidly learns to avoid a toxic invader', WILDLIFE RESEARCH, vol. 38, no. 8, pp. 726-731.
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Context. Invasive species are a leading cause of extinctions, yet predicting their ecological impacts poses a formidable challenge for conservation biologists. When native predators are naive to invaders, they may lack appropriate behaviours to deal with

Wei, J, Carroll, RJ & Maity, A 2011, 'Testing for constant nonparametric effects in general semiparametric regression models with interactions', Statistics & Probability Letters, vol. 81, no. 7, pp. 717-723.
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Wei, J, Yee, C, Ramanathan, P, Bendall, LJ & Williamson, P 2011, 'Variation in immunophenotype of lactating mice', Journal of Reproductive Immunology, vol. 89, no. 2, pp. 178-184.
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Weir, MP, Heriot, SY, Martin, SJ, Parnell, AJ, Holt, SA, Webster, JRP & Jones, RAL 2011, 'Voltage-Induced Swelling and Deswelling of Weak Polybase Brushes', Langmuir, vol. 27, no. 17, pp. 11000-11007.
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Wenzel, M, Light, ME, Davis, AP & Gale, PA 2011, 'Thiourea isosteres as anion receptors and transmembrane transporters', Chemical Communications, vol. 47, no. 27, pp. 7641-7641.
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Weyermann, C, Roux, C & Champod, C 2011, 'Initial Results on the Composition of Fingerprints and its Evolution as a Functionof Time by GC/MS Analysis', JOURNAL OF FORENSIC SCIENCES, vol. 56, no. 1, pp. 102-108.
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Determining the time since deposition of fingermarks may prove necessary to assess their relevance to criminal investigations. The crucial factor is the initial composition of fingermarks, because it represents the starting point of any aging model. This study mainly aimed to characterize the initial composition of fingerprints, which show a high variability between donors (inter-variability), but also to investigate the variations among fingerprints from the same donor (intra-variability). Solutions to reduce this initial variability using squalene and cholesterol as target compounds are proposed and should be further investigated. The influence of substrates was also evaluated, and the initial composition was observed to be larger on porous surface than nonporous surfaces. Preliminary aging of fingerprints over 30 days was finally studied on a porous and a nonporous substrate to evaluate the potential for dating of fingermarks. Squalene was observed to decrease in a faster rate on a nonporous substrate.

Whiting, R, Shen, Q, Hung, WT, Cordato, D & Chan, DKY 2011, 'Predictors for 5-year survival in a prospective cohort of elderly stroke patients', ACTA NEUROLOGICA SCANDINAVICA, vol. 124, no. 5, pp. 309-316.
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Objectives - To examine predictors for 5-year survival in elderly stroke patients. Materials and Methods - Prospective cohort study of 186 consecutive acute stroke patients aged >= 65 years admitted to Bankstown-Lidcombe Hospital, Australia 03/2002 to 03

Wilksch, JJ, Yang, J, Clements, A, Gabbe, JL, Short, KR, Cao, H, Cavaliere, R, James, CE, Whitchurch, CB, Schembri, MA, Chuah, MLC, Liang, Z-X, Wijburg, OL, Jenney, AW, Lithgow, T & Strugnell, RA 2011, 'MrkH, a Novel c-di-GMP-Dependent Transcriptional Activator, Controls Klebsiella pneumoniae Biofilm Formation by Regulating Type 3 Fimbriae Expression', PLOS PATHOGENS, vol. 7, no. 8.
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Williams, DBG & Mbatha, GB 2011, 'The synthesis and characterisation of carbohydrate-functionalised porphyrazines', Dyes and Pigments, vol. 88, no. 1, pp. 65-74.
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A synthetic pathway to the incorporation of mono- and disaccharide carbohydrate moieties into porphyrazine systems was demonstrated. A range of selectively protected monosaccharide precursors was coupled to a small variety of phthalonitriles; the intermediates were co-macrocyclised to form hybrid porphyrazines in Linstead macrocyclisation reactions. Demetallisation of Mg-porphyrazine products was readily effected to afford the free-base pigments, which were subsequently converted into their zinc or nickel complexes. Some porphyrazines were deprotected of their isopropylidene groups (on the carbohydrate moieties) under acidic conditions to reveal polar OH groups. The extraction coefficients of the porphyrazines between 2-octanol and phosphate buffered saline solution were measured. Comparison of the partition coefficients of the carbohydrate-substituted porphyrazines and their deprotected counterparts revealed that structural alteration offers a way to significantly increase the hydrophilicity of substituted porphyrazines. © 2010 Elsevier Ltd. All rights reserved.

Williams, DBG, George, MJ, Meyer, R & Marjanovic, L 2011, 'Bubbles in Solvent Microextraction: The Influence of Intentionally Introduced Bubbles on Extraction Efficiency', Analytical Chemistry, vol. 83, no. 17, pp. 6713-6716.
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Williams, DBG, Kotze, PDR, Ferreira, AC & Holzapfel, CW 2011, 'Phosphine-Borane Complexes: in situ Deprotection and Application as Ligands in the Rh- or Pd-Catalysed Hydroformylation Reaction', Journal of the Iranian Chemical Society, vol. 8, no. 1, pp. 240-246.
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Triarylphosphine-borane complexes are directly useful in the Rh-catalysed hydroformylation reaction of 1-octene (or Pdcatalysed hydroformylation of 1-pentene). Mild reaction conditions provide similar yields and selectivities of the anticipated aldehyde products to reactions making use of the corresponding free phosphines as ligands. The mono- or bidentate P-B adducts undergo in situ CO-mediated deprotection the produce the free phosphine ligands. The results demonstrate that phosphine-borane complexes may be directly applied to carbonylation reactions without a prior deprotection step, with little to no change in the reaction outcome.

Williams, DBG, Shaw, ML & Hughes, T 2011, 'Recyclable Pd(OAc)₂/Ligand/Al(OTf)₃ Catalyst for the Homogeneous Methoxycarbonylation and Hydrocarboxylation Reactions of Phenylacetylene', Organometallics, vol. 30, no. 18, pp. 4968-4973.
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Williams, SJ, Sornaraj, P, deCourcy-Ireland, E, Menz, RI, Kobe, B, Ellis, JG, Dodds, PN & Anderson, PA 2011, 'An Autoactive Mutant of the M Flax Rust Resistance Protein Has a Preference for Binding ATP, Whereas Wild-Type M Protein Binds ADP', Molecular Plant-Microbe Interactions®, vol. 24, no. 8, pp. 897-906.
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Resistance (R) proteins are key regulators of the plant innate immune system and are capable of pathogen detection and activation of the hypersensitive cell death immune response. To understand the molecular mechanism of R protein activation, we undertook a phenotypic and biochemical study of the flax nucleotide binding (NB)-ARC leucine-rich repeat protein, M. Using Agrobacterium-mediated transient expression in flax cotyledons, site-directed mutations of key residues within the P-loop, kinase 2, and MHD motifs within the NB-ARC domain of M were shown to affect R protein function. When purified using a yeast expression system and assayed for ATP and ADP, these mutated proteins exhibited marked differences in the quantity and identity of the bound nucleotide. ADP was bound to recombinant wild-type M protein, while the nonfunctional P-loop mutant did not have any nucleotides bound. In contrast, ATP was bound to an autoactive M protein mutated in the highly conserved MHD motif. These data provide direct evidence supporting a model of R protein function in which the “off” R protein binds ADP and activation of R protein defense signaling involves the exchange of ADP for ATP.

Wohlthat, S, Solomon, GC, Hush, NS & Reimers, JR 2011, 'Interference-induced electron- and hole-conduction asymmetry', THEORETICAL CHEMISTRY ACCOUNTS, vol. 130, no. 4-6, pp. 815-828.
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Principles established by Shephard and Paddon-Row for optimizing and controlling intramolecular electron transport through the modulation of interfering pathways are employed to design new molecules for steady-state conduction experiments aimed at manifesting electron-hole conduction asymmetry in a unique way. First, a review of the basic principles is presented through application to a pertinent model system in which a molecule containing donor and acceptor terminal linking groups with an internal multiple-pathway bridge is used to span two metal electrodes. Different interference patterns are produced depending on whether the through-molecule coupling pathways are symmetric or antisymmetric with respect to a topological bisecting plane, giving rise to asymmetric electron and hole conductances at the tight-binding (Huckel) level; this process is also described from a complementary molecular-orbital viewpoint. Subsequently, a new molecular system based on organic polyradicals is designed to allow such asymmetry to be realized in single-molecule conduction experiments. These polyradicals are analyzed using analogous simple models, density-functional theory (DFT) calculations of steady-state transmission, and intermediate neglect of differential overlap (INDO) calculations of intramolecular connectivity, verifying that polyradicals at low temperatures should show experimentally measureable electron-hole conduction asymmetry. A key feature of this system is that the polyradicals form a narrow partially occupied band of orbitals that lie within and well separated from the HOMO and LUMO orbitals of the surrounding molecular scaffold, allowing for holes and electrons to be transported through the same molecular band.

Wong, KKY, Bull, RA, Rockman, S, Scott, G, Stelzer-Braid, S & Rawlinson, W 2011, 'Correlation of polymerase replication fidelity with genetic evolution of influenza A/Fujian/411/02(H3N2) viruses', Journal of Medical Virology, vol. 83, no. 3, pp. 510-516.
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Wong, KKY, Bull, RA, Stelzer-Braid, S, Fennell, M & Rawlinson, W 2011, 'Effect of reassortment on the nucleotide and amino acid changes of human A/H3N2 RNP subunits during 1998–2009', Journal of Clinical Virology, vol. 51, no. 4, pp. 270-275.
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Wong, WSF, Lee, TCE & Lim, CED 2011, 'A retrospective study of laparoscopic-assisted vaginal hysterectomy (LAVH) in virgins and nulliparae', European Journal of Obstetrics & Gynecology and Reproductive Biology, vol. 157, no. 2, pp. 217-221.
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Wong, WSF, Lim, CED & Luo, X 2011, 'Inguinal Endometriosis: An Uncommon Differential Diagnosis as an Inguinal Tumour', ISRN Obstetrics and Gynecology, vol. 2011, pp. 1-4.
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Inguinal endometriosis can present as a rare tumor when it occurs outside the abdomen and pelvis. We present a patient with a painful tumor in the right inguinal region, where its diagnosis was made before the operation. This enabled a conservative excisional surgery to be performed. The literature is reviewed and the diagnosis as well as management are discussed.

Wuhrer, R, Moran, K, Dredge, P & Phillips, M 2011, 'Use of X-Ray Mapping to Investigate Art Works Before their Restoration', Microscopy and Microanalysis, vol. 17, no. S2, pp. 1790-1791.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Wynne, O, Horvat, JC, Kim, RY, Ong, L, Smith, R, Hansbro, PM, Clifton, VL & Hodgson, DM 2011, '131. Sex differences in the effect of neonatal infection and adult re-infection on hippocampal corticosterone receptors and stress response outcomes', Brain, Behavior, and Immunity, vol. 25, pp. S216-S217.
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Wynne, O, Horvat, JC, Kim, RY, Ong, LK, Smith, R, Hansbro, PM, Clifton, VL & Hodgson, DM 2011, 'Neonatal respiratory infection and adult re-infection: Effect on glucocorticoid and mineralocorticoid receptors in the hippocampus in BALB/c mice', Brain, Behavior, and Immunity, vol. 25, no. 6, pp. 1214-1222.
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Wynne, O, Horvat, JC, Osei-Kumah, A, Smith, R, Hansbro, PM, Clifton, VL & Hodgson, DM 2011, 'Early life infection alters adult BALB/c hippocampal gene expression in a sex specific manner', Stress, vol. 14, no. 3, pp. 247-261.
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XiaoHua, Y, JingFeng, H, YaoPing, W, JianWen, W, Pei, W, XiaoMing, W & Huete, AR 2011, 'Estimating biophysical parameters of rice with remote sensing data using support vector machines', SCIENCE CHINA-LIFE SCIENCES, vol. 54, no. 3, pp. 272-281.
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Hyperspectral reflectance (350â2500 nm) measurements were made over two experimental rice fields containing two cultivars treated with three levels of nitrogen application. Four different transformations of the reflectance data were analyzed for their capability to predict rice biophysical parameters, comprising leaf area index (LAI; m2 green leaf area mâ2 soil) and green leaf chlorophyll density (GLCD; mg chlorophyll mâ2 soil), using stepwise multiple regression (SMR) models and support vector machines (SVMs). Four transformations of the rice canopy data were made, comprising reflectances (R), first-order derivative reflectances (D1), second-order derivative reflectances (D2), and logarithm transformation of reflectances (LOG). The polynomial kernel (POLY) of the SVM using R was the best model to predict rice LAI, with a root mean square error (RMSE) of 1.0496 LAI units. The analysis of variance kernel of SVM using LOG was the best model to predict rice GLCD, with an RMSE of 523.0741 mg mâ2. The SVM approach was not only superior to SMR models for predicting the rice biophysical parameters, but also provided a useful exploratory and predictive tool for analyzing different transformations of reflectance data.

Xu, B, Tan, D, Guan, M, Teng, Y, Zhou, J, Qiu, J & Hong, Z 2011, 'Broadband Near-Infrared Luminescence from γ-ray Irradiated Bismuth-Doped Y4GeO8 Crystals', Journal of The Electrochemical Society, vol. 158, no. 9, pp. G203-G203.
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Broadband near-infrared emission centered at 1155 nm with full width at half maximum over 300 nm has been observed in c-ray irradiated bismuth-doped Y4GeO8 crystals. The luminescence was bleached completely after thermal treatment at 350C for 2 h. Absorption spectra, electron spin resonance spectra, Raman spectra, excitation and emission spectra indicate that valence state change of bismuth was induced by c-ray irradiation, and 3 P1 ! 3 P0 transition of Biþ ions is responsible for the near-infrared emission. The effect of Bi concentration on the luminescence properties of c-ray irradiated samples was also discussed.

Xu, B, Zhou, S, Guan, M, Tan, D, Teng, Y, Zhou, J, Ma, Z, Hong, Z & Qiu, J 2011, 'Unusual luminescence quenching and reviving behavior of Bi-doped germanate glasses', Optics Express, vol. 19, no. 23, pp. 23436-23436.
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Here for the first time, we report an unusual annealing temperature dependent near-infrared (NIR) luminescence quenching and reviving behavior in Bi-doped MgO-Al2O3-GeO2 glasses. Systematic characterizations of the samples by using differential thermal analysis (DTA), photoluminescence and absorption spectra, X-ray diffraction (XRD) and transmission electron microscopy (TEM) indicate that this phenomenon is associated with the reversible reaction of Bi+ and Bi0 initiated by the change of local glass structure. Excitingly, wavelength tunable luminescence is also observed and it can be ascribed to selective excitation of active Bi+ center in different sites. These results not only open a new way for controlling luminescence properties of main group elements in glass but also provide great value for improving practical active-fiber drawing process.

Xu, J, Sun, Z, Jia, L, Li, B, Zhao, L, Liu, X, Ma, Y, Tian, H, Wang, Q, Liu, W & Tang, Y 2011, 'Visible light sensitized attapulgite-based lanthanide composites: microstructure, photophysical behaviour and biological application', Dalton Transactions, vol. 40, no. 48, pp. 12909-12909.
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Xun, X, Mallick, B, Carroll, RJ & Kuchment, P 2011, 'A Bayesian Approach to Detection of Small Low Emission Sources', Inverse Problems 27 (2011), 115009 (11pp), vol. 27, no. 11.
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The article addresses the problem of detecting presence and location of a small low emission source inside of an object, when the background noise dominates. This problem arises, for instance, in some homeland security applications. The goal is to reach the signal-to-noise ratio (SNR) levels on the order of $10^{-3}$. A Bayesian approach to this problem is implemented in 2D. The method allows inference not only about the existence of the source, but also about its location. We derive Bayes factors for model selection and estimation of location based on Markov Chain Monte Carlo (MCMC) simulation. A simulation study shows that with sufficiently high total emission level, our method can effectively locate the source.

Yao, Y, Hou, S, Li, C, Chen, H & Liao, Y 2011, 'Directed Evolution of Neutral Endoglucanase Gene by Error-prone PCR', Chinese Journal of Agricultural Biotechnology, vol. 19, no. 6, pp. 1136-1143.
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Low enzymatic activity and high cost are the two main problems that limit the industrial applications of cellulose. In order to enhance the enzymatic activity of neutral endoglucanase activity, error-prone PCR was conducted to engineer the Bacillus subtilis C-36 endoglucanase gene. Two optimum mutants, b-15 and b-28 were obtained, with an endoglucanase activity 2.1 folds and 3.6 folds increased, respectively. The sequence of b-15 endoglucanase gene showed six nucleotide substitutions leading to four mutated amino acids; and b-28 endoglucanase gene showed one nucleotide substitution leading to one mutated amino acid. According to the 3D structure of endoglucanase mimicked by SWISS-MODEL, the four mutated amino acids of b-15 were either located at the corner between the fourth and fifth α-helix in the catalytic domain or at the fifth β-fold or the corner between the ninth and tenth β-fold in the carbohydrate-binding domain. And the mutation of b-28 was located at the fourth β-fold in the carbohydrate-binding domain. Following the orthogonal experiment, the mutant b-15 and b-28 could reach to an endoglucanase activity of 4.542 U/mL and 5.136 U/mL through fermentation, respectively, both of which were much higher than the wild-type control. These results have provided a base for further research of endoglucanase.

Ye, S, Jiang, N, Zhou, J, Wang, D & Qiu, J 2011, 'Optical Property and Energy Transfer in the ZnO-LiYbO₂Hybrid Phosphors under the Indirect Near-UV Excitation', Journal of The Electrochemical Society, vol. 159, no. 1, pp. H11-H15.
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The ZnO-LiYbO 2 hybrid phosphors with various Yb 2O 3 and Li 2CO 3 starting concentrations were prepared by using the solid-state reaction method in a weak reducing atmosphere. Under the excitation of ZnO absorption with near-UV photons, the intense near infrared emission originated from Yb 3+: 2+F 5/2 → 2F 7/2 transition can be observed due to the efficient energy transfer from ZnO to Yb 3+ ions. This efficient energy transfer is benefit from the introduction of Yb 3+ ions into ZnO lattice at the interfacial diffusion layers between ZnO and LiYbO 2 crystals. The luminescence decay of Yb 3+ were recorded under the excitation of ZnO intrinsic absorption at 350 nm and excitonic absorption at 395 nm, in which the rise component can be clearly observed and the simulated rise lifetime that describing the population speed are 0.006 and 0.035 ms, respectively. The obvious different population speed of Yb 3+: 2F 5/2 excited level indicates two energy transfer mechanisms from ZnO to Yb 3+: the cooperative energy transfer process under the excitation of intrinsic absorption and the phonon-assistant energy transfer process under the excitation of excitonic absorption, respectively

Yeoman, JA, Hanssen, E, Maier, AG, Klonis, N, Maco, B, Baum, J, Turnbull, L, Whitchurch, CB, Dixon, MWA & Tilley, L 2011, 'Tracking Glideosome-Associated Protein 50 Reveals the Development and Organization of the Inner Membrane Complex of Plasmodium falciparum', EUKARYOTIC CELL, vol. 10, no. 4, pp. 556-564.
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The most deadly of the human malaria parasites, Plasmodium falciparum, has different stages specialized for invasion of hepatocytes, erythrocytes, and the mosquito gut wall. In each case, host cell invasion is powered by an actin-myosin motor complex tha

Yung, PY, Burke, C, Lewis, M, Kjelleberg, S & Thomas, T 2011, 'Novel Antibacterial Proteins from the Microbial Communities Associated with the Sponge Cymbastela concentrica and the Green Alga Ulva australis', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 77, no. 4, pp. 1512-1515.
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The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaprot

Zeppel, MJB, Lewis, JD, Medlyn, B, Barton, CVM, Duursma, RA, Eamus, D, Adams, MA, Phillips, N, Ellsworth, DS, Forster, MA & Tissue, DT 2011, 'Interactive effects of elevated CO2 and drought on nocturnal water fluxes in Eucalyptus saligna', TREE PHYSIOLOGY, vol. 31, no. 9, pp. 932-944.
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Nocturnal water flux has been observed in trees under a variety of environmental conditions and can be a significant contributor to diel canopy water flux. Elevated atmospheric CO 2 (elevated [CO 2]) can have an important effect on day-time plant water fluxes, but it is not known whether it also affects nocturnal water fluxes. We examined the effects of elevated [CO 2] on nocturnal water flux of field-grown Eucalyptus saligna trees using sap flux through the tree stem expressed on a sapwood area (J s) and leaf area (E t) basis. After 19 months growth under well-watered conditions, drought was imposed by withholding water for 5 months in the summer, ending with a rain event that restored soil moisture. Reductions in J s and E t were observed during the severe drought period in the dry treatment under elevated [CO 2], but not during moderate- and post-drought periods. Elevated [CO 2] affected night-time sap flux density which included the stem recharge period, called 'total night flux' (19:00 to 05:00, J s,r), but not during the post-recharge period, which primarily consisted of canopy transpiration (23:00 to 05:00, J s,c). Elevated [CO 2] wet (EW) trees exhibited higher J s,r than ambient [CO 2] wet trees (AW) indicating greater water flux in elevated [CO 2] under well-watered conditions. However, under drought conditions, elevated [CO 2] dry (ED) trees exhibited significantly lower J s,r than ambient [CO 2] dry trees (AD), indicating less water flux during stem recharge under elevated [CO 2]. J s,c did not differ between ambient and elevated [CO 2]. Vapour pressure deficit (D) was clearly the major influence on night-time sap flux. D was positively correlated with J s,r and had its greatest impact on J s,r at high D in ambient [CO 2]. Our results suggest that elevated [CO 2] may reduce night-time water flux in E. saligna when soil water content is low and D is high. While elevated [CO 2] affected J s,r, it did not affect day-time water flux in wet soil, suggestin...

Zhang, S, Carroll, RJ, Midthune, D, Guenther, PM, Krebs-Smith, SM, Kipnis, V, Dodd, KW, Buckman, DW, Tooze, JA & Freedman, L 2011, 'A new multivariate measurement error model with zero-inflated dietary data, and its application to dietary assessment', Annals of Applied Statistics, vol. 5, no. 2B, pp. 1456-1487.
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In the United States the preferred method of obtaining dietary intake data is the 24-hour dietary recall, yet the measure of most interest is usual or long-term average daily intake, which is impossible to measure. Thus, usual dietary intake is assessed with considerable measurement error. Also, diet represents numerous foods, nutrients and other components, each of which have distinctive attributes. Sometimes, it is useful to examine intake of these components separately, but increasingly nutritionists are interested in exploring them collectively to capture overall dietary patterns. Consumption of these components varies widely: some are consumed daily by almost everyone on every day, while others are episodically consumed so that 24-hour recall data are zero-inflated. In addition, they are often correlated with each other. Finally, it is often preferable to analyze the amount of a dietary component relative to the amount of energy (calories) in a diet because dietary recommendations often vary with energy level. The quest to understand overall dietary patterns of usual intake has to this point reached a standstill. There are no statistical methods or models available to model such complex multivariate data with its measurement error and zero inflation. This paper proposes the first such model, and it proposes the first workable solution to fit such a model. After describing the model, we use survey-weighted MCMC computations to fit the model, with uncertainty estimation coming from balanced repeated replication.

Zhang, S, Krebs-Smith, SM, Midthune, D, Perez, A, Buckman, DW, Kipnis, V, Freedman, LS, Dodd, KW & Carroll, RJ 2011, 'Fitting a Bivariate Measurement Error Model for Episodically Consumed Dietary Components', The International Journal of Biostatistics, vol. 7, no. 1, pp. 1-32.
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Zhou, J, Teng, Y, Lin, G & Qiu, J 2011, 'Ultraviolet to near-infrared spectral modification in Ce3+ and Yb3+ codoped phosphate glasses', Journal of Non-Crystalline Solids, vol. 357, no. 11-13, pp. 2336-2339.
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The ultraviolet to near-infrared spectral modification in Ce3+ and Yb3+ codoped phosphate glasses was realized through the energy transfer from Ce3+ to Yb3+. The absorption spectra, fluorescence excitation and emission spectra, luminescence decay curves, and time-resolved emission spectra were measured and analyzed. The energy transfer efficiency and concentration quenching efficiency were calculated based on the decay curves of Ce3+ 340 nm emission and Yb3+ 976 nm emission. The calculated and experimental NIR emission intensities on the Yb3+ concentrations were compared and discussed.

Zhou, J, Teng, Y, Liu, X, Ma, Z & Qiu, J 2011, 'Broadband spectral conversion of visible light to near-infrared emission via energy transfer from Ce³⁺ to Nd³⁺/Yb³⁺ in YAG', Journal of Materials Research, vol. 26, no. 5, pp. 689-692.
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Abstract

Zou, JP, Le Rendu, P, Musa, I, Yang, SH, Dan, Y, Ton-That, C & Nguyen, TP 2011, 'Investigation of the optical properties of polyfluorene/ZnO nanocomposites', THIN SOLID FILMS, vol. 519, no. 12, pp. 3997-4003.
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Polyfluorene (PF) and its derivatives are very promising candidates for organic light emitting diodes (OLEDs) in lighting applications because of their high photoluminescence and electroluminescence efficiencies. Recent investigations of potential materials for OLEDs have shown that introducing n-type inorganic nanoparticles into conjugated polymers is efficient to produce stable and high performance devices. In this study, composite thin films made by incorporation of zinc oxide (ZnO) nanoparticles into a PF derivative have been prepared and their optical properties have been investigated. The prepared thin films were stored in different media (in air, in vacuum, in the dark or exposed to light) in order to study environmental influences on the material stability. Analysis of spectral data obtained from infrared (IR), Raman, UV-vis, and photoluminescence (PL) measurements shows a large enhancement in luminescence for polymer nanocomposites while using high nanoparticle concentrations (within a limit of 10% ZnO). Time-resolved PL performed on those nanocomposite films corroborated the above result: it indicated that the light-emission enhancement can be explained by efficient energy transfer from nanoparticles to the polymer chains and increase of the chain separation distance. In addition, the nanocomposites were found to be more stable than pristine polymer films whatever the storage conditions were used. It was confirmed by IR analysis that incorporation of nanoparticles into polymers prohibited the formation of fluorenonyl groups in PF chains, which was identified as the main cause of the degradation of the polymer under photo-oxidation.

Aharonovich, I, Castelletto, S & Prawer, S 1970, 'Novel Single Photon Emitters Based on Color Centers in Diamond', PHYSICS OF SEMICONDUCTORS: 30TH INTERNATIONAL CONFERENCE ON THE PHYSICS OF SEMICONDUCTORS, International Conference on the Physics of Semiconductors (ICPS), pp. 997-998.
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Single photon emitters are core components of quantum technologies. In this work new family of emitters based on chromium impurities in diamond is presented. The emitters can be fabricated by ion implantation of chromium into bulk diamond or incorporated during the growth of diamond nanocrystals. The remarkable photo-physical properties of these emitters include room temperature operation, narrow photoluminescence (PL) in the near infra red and ultra bright, fully polarized photon emission with count rate of 3.2×10 6 counts/s. These photo physical properties make the Cr centers ideal for quantum information processing, metrology, and cellular bio markers applications. © 2011 American Institute of Physics.

Asatryan, AA, Botten, LC, Byrne, MA, Freilikher, VD, Gredeskul, SA, Shadrivov, IV, McPhedran, RC & Kivshar, YA 1970, 'Dispersion effects on the Anderson localization in disordered one dimensional metamaterial stacks', Optics InfoBase Conference Papers, pp. 175-176.
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We have carried out a comprehensive study of dispersion and absorption effects on Anderson localization in one-dimensional metamaterial stacks and have shown that the field is delocalized in μ or ε-near-zero media at normal incidence.© 2011 AOS.

Asatryan, AA, Botten, LC, Byrne, MA, Freilikher, VD, Gredeskul, SA, Shadrivov, IV, McPhedran, RC & Kivshar, YA 1970, 'Dispersion effects on the Anderson localization in disordered one dimensional metamaterial stacks', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 175-176.
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We have carried out a comprehensive study of dispersion and absorption effects on Anderson localization in one-dimensional metamaterial stacks and have shown that the field is delocalized in μ or ε-near-zero media at normal incidence. © 2011 IEEE.

Asatryan, AA, Botten, LC, Byrne, MA, Freilikher, VD, Gredeskul, SA, Shadrivov, IV, McPhedran, RC, Kivshar, YA & IEEE 1970, 'Anderson delocalization in one dimensional mu or epsilon-near-zero metamaterial stacks and other dispersion effects on localization', 2011 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Lasers and Electro-Optics.
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We have carried out a comprehensive study of dispersion and absorption effects on Anderson localization in one-dimensional metamaterial stacks and have shown that the field is delocalized in μ or ε-near-zero media at normal incidence. © 2011 OSA.

Attie, O, Darling, AE & Yancopoulos, S 1970, 'The rise and fall of breakpoint reuse depending on genome resolution', BMC BIOINFORMATICS, 9th Annual Conference on Research in Computational Molecular Biology (RECOMB)/Satellite Workshop on Comparative Genomics, Biomed Central Ltd, Galway, Ireland, pp. 1-15.
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Background: During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ('synteny blocks') across species. Some years ago, a controversy erupted in genome rearrangement studies over whether rearrang

Baldeaux, J, Chan, LL & Platen, E 1970, 'Quasi-Monte Carlo methods for derivatives on realised variance of an index under the benchmark approach', ANZIAM Journal, Computational Techniques and Applications Conference, Australian Mathematical Publishing Association, Inc., Sydney, Australia, pp. 727-727.
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We apply quasi-Monte Carlo methods to the pricing of derivatives on realised variance of an index under the benchmark approach. The resulting integration problem is shown to depend on the joint density of the realised variance of the index and the terminal value of the index. Employing a transformation mapping for this joint density to the unit square reduces the diffculty of the resulting integration problem. The quasi-Monte Carlo methods compare favourably to Monte Carlo methods when applied to the given problem. © Austral. Mathematical Soc. 2011.

Brownless, JS, Lawrence, FJ, Mahmoodian, S, Dossou, KB, Botten, LC & de Sterke, CM 1970, 'Diffraction engineering with braided modes in photonic crystal waveguide arrays', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 15-17.
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We consider discrete diffraction in coupled photonic crystal waveguides in a hexagonal lattice. We show that in these structures the (discrete) diffraction coefficient depends strongly on frequency and can even change sign. This behavior does not occur in photonic crystal waveguides in square lattices. This behavior is interesting in its own right and has intriguing consequences for the propagation of discrete spatial solitons. © 2011 IEEE.

Bryant, CE, Brown, RD, Yang, S, Suen, H, Aklilu, E, Favaloro, J, Hart, DNJ, Fromm, P, Woodland, N, Nassif, N, Iland, H, Gibson, J, Ho, PJ & Joshua, DE 1970, 'Ten Year Survivors of Multiple Myeloma Demonstrate a Differential Expression of Immunological Biomarkers Including a High Incidence of Cytotoxic T-Cell Clones Which Have Not Acquired Myeloma-Associated Anergy', BLOOD, 53rd Annual Meeting and Exposition of the American Society of Hematology (ASH)., The American Society of Hematology, San Diego, California, pp. 1678-1678.

Burgess, JK, Faiz, A, Oliver, BG & Black, JL 1970, 'Gender Effects On Gene Expression In Airway Smooth Muscle Cells In Asthma', B71. CRAZY MUSCLES: AIRWAY AND LYMPHATIC SMOOTH MUSCLE AND LYMPHANGIOLEIOMYOMATOSIS (LAM), American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Burgess, JK, Grafton, K, Tjin, G, Middelburg, J, van Egmond, P, Black, JL & Oliver, BG 1970, 'The Role Of Cathepsin D In The Regulation Of Tumstatin Levels In Asthmatic Airways', C97. AIRWAY GOVERNANCE: THE AXIS OF AIRWAY MYOCYTES, MYOFIBROBLASTS AND EXTRACELLULAR MATRIX IN ASTHMATIC AND COPD REMODELING, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Chen, PY, McPhedran, RC, Asatryan, AA, Botten, LC, Poulton, CG, Steel, MJ & de Sterke, CM 1970, 'Fast simulation of slab photonic crystal structures using modal methods', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 71-72.
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A faster method of simulating 2D slabs, both metallic and dielectric, with cylindrical inclusions is proposed. The method is applicable to photonic crystal defect-row waveguides and extraordinary transmssion through metallic films, capable of producing both in-plane dispersion relations and transmission spectra. © 2011 IEEE.

Cook, A, Rayburg, S, Capon, S & Leigh, A 1970, 'Variation in seedling emergence and mortality amongst key habitat types in a semi-arid floodplain-wetland complex', 34th IAHR Congress 2011 - Balance and Uncertainty: Water in a Changing World, Incorporating the 33rd Hydrology and Water Resources Symposium and the 10th Conference on Hydraulics in Water Engineering, Congress of IAHR, the International Association of Hydro-Environment Engineering and Research, IAHR, Brisbane, pp. 3044-3051.
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The presence of water in semi-arid environments is both spatially and temporally unpredictable and variable, creating a harsh and patchy environment. When present, water stimulates the germination and growth of plants but can also result in plant (or seedling) mortality. This study investigates how seedling emergence and mortality differ between various key habitats in a semi-arid floodplain wetland complex that are characterised by contrasting wetting regimes. Sediment samples were collected from five habitats (red soils, box-hollows, riparian areas, floodplains and lakes) and used in a germination experiment. Over a 12 week period, each habitat (except lakes) showed a peak in seedling emergence in the second week after initial experimental wetting, with box-hollows showing the largest emergence response in all weeks and riparian areas showing the lowest mortality (as a percent of emerged plants). Meanwhile the lowest overall emergence occurred in lakes and the highest mortality was found in red soils. Each habitat displayed a unique emergence and mortality response over the 12 weeks of the experiment suggesting that habitat has a strong influence on seedling emergence and survivability.

Dare, J, Wilkinson, C & Rai, T 1970, 'THE FORGOTTEN AUSTRALIANS: AN INVESTIGATION OF ALCOHOL USE AMONGST SENIOR CITIZENS', DRUG AND ALCOHOL REVIEW, Australasian Professional Society on Alcohol and other Drugs (APSAD) Conference, Hobart, Tasmania, pp. 22-22.

Deng, W, Jin, D, Drozdowicz-Tomsia, K, Yuan, J, Wu, J & Goldys, EM 1970, 'Plasmonic Ag/SiO 2 composite nanoparticles doped with europium chelate and their metal enhanced fluorescence', SPIE Proceedings, SPIE BiOS, SPIE, USA.
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We report silver nanostructure-enhanced fluorescence of a europium (Eu) chelate, BHHCT-Eu-DPBT, which was covalently bound in Ag/SiO 2 nanocomposites. This design enhances the europium signal intensity by more than one order of magnitude, and accelerates the decay time from 0.3 ms down to 60 microseconds, at low excitation conditions. These nanocomposites were bright enough to be observed in time-gated fluorescence microscopy under 365 nm LED excitation. The increased brightness and reduced lifetime of such fluorescent core-shell nanocomposites will enhance their applicability for ultrasensitive bioassays and bioimaging, especially with time-gating. © 2011 SPIE.

Dooley, AH 1970, 'Intertwining operators, the Cayley transform, and the contraction of K to NM', NEW DEVELOPMENTS IN LIE THEORY AND ITS APPLICATIONS, 7th Workshop in Lie Theory and Its Applications, AMER MATHEMATICAL SOC, Cordoba, Argentina, pp. 101-108.

Dossou, KB & Botten, LC 1970, 'Computation of scattering matrices using a three dimensional finite element method', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 18-19.
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We have developed a three-dimensional vectorial finite element method (FEM) program which offers the flexibility to model 3D diffraction gratings with arbitrary geometry. The FEM satisfies the energy conservation relation and allows us to analyze periodic structures such as photonic crystals and metamaterials. © 2011 IEEE.

Dossou, KB, Botten, LC, Asatryan, AA, Sturmberg, BCP, Byrne, MA, Poulton, CG, McPhedran, RC, de Sterke, CM & IEEE 1970, 'Modal Formulation for Scattering on the Absorbing Silicon Nanowire Arrays for Photovoltaic Applications', 2011 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Lasers and Electro-Optics (CLEO), IEEE, Baltimore, MD.

Dossou, KB, Botten, LC, Asatryan, AA, Sturmberg, BPC, Byrne, MA, Poulton, CG, McPhedran, RC & de Sterke, CM 1970, 'Novel modeling techniques for photonic devices', 2011 Numerical Simulation of Optoelectronic Devices, 2011 11th International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD), IEEE, Rome, Italy, pp. 107-108.
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The combination of purely numerical methods, such as the finite element method, with an analytical treatment can lead to a powerful semi-analytical technique. We present such a technique, which combines the finite element method with a modal approach, with a focus on the modeling three-dimensional photonic structures. © 2011 IEEE.

Fiser, J, Zitek, P & Cerveny, J 1970, 'Relay Feedback Oscillator Design for Modeling Circadian Rhythms in Cyanobacteria', Volume 2: Biomedical and Biotechnology Engineering; Nanoengineering for Medicine and Biology, ASME 2011 International Mechanical Engineering Congress and Exposition, ASMEDC, Denver, CO, pp. 549-+.
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The paper introduces a relay feedback oscillator for modeling circadian rhythms in cyanobacteria. The relay feedback oscillator is equipped with low pass filter F(jω), hysteresis-type relay and negative feedback. This negative feedback represents an autoregulatory mechanism of the circadian clock and the notion of this autoregulatory mechanism is based on the well-known Goodwin biochemical oscillator [1]. The relay is responsible for the mediation of both the activation and degradation of oscillator state variables (protein concentrations) and in this way the pacemaker is constituted. Later on, low pass filter poles are identified for the purpose of modeling auto-oscillations with the free running period of 24h and the method of the pole identification consists in an ultimate frequency test providing stability margin of a single-loop composed of the filter and the relay in the feedback. Next, a relay output / input ratio of amplitudes and hysteresis are found out by the graphical test of the single-loop on the stability margin which is carried out in Bode graph. Finally, the output correspondence of relay feedback oscillator model with Miyoshi oscillator [2] is provided because the Miyoshi oscillator is well recognized among biochemical oscillators for species of cyanobacteria.

Forbes, SL, Wilson, M & Stuart, BH 1970, 'Examination of adipocere formation in Lake Ontario, Canada', Forensic Science, Medicine and Pathology, Humana Press, Sydney, pp. 75-138.

Foster, P, Li, J, Wang, W, Baines, K, Bowden, N, Hansbro, P, Gibson, P, Kumar, R & Yang, M 1970, 'IL-27 underpins steroid resistant airway hyperresponsiveness via MyD88 dependent pathways', ALLERGY, 30th Congress of the European-Academy-of-Allergy-and-Clinical-Immunology (EAACI), WILEY-BLACKWELL, Istanbul, TURKEY, pp. 442-443.

Foster, PS, Tay, HL, Kaiko, GE, Plank, MW, Mattes, J & Hansbro, PM 1970, 'MiRNA And Its Roles In Regulating Bacterial Infection In Lungs', A13. MI-RNA AND EPIGENETIC REGULATION OF LUNG DISORDERS, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Fronzi, M, De Vita, A, Tateyama, Y & Traversa, E 1970, 'ZrO₂-CeO₂ Interface Properties: A First-Principle Investigation', ECS Transactions, ECS Transactions (ECST), The Electrochemical Society, pp. 1203-1210.
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In the present work we present a Density Functional Theory approach to investigate the structural and electronic properties of the low index ZrO2-CeO2 interface. Optimizations of the crystal geometry for the separate ZrO2 and CeO2 bulks as well as the interfaces are carried out and the structural morphology is analyzed. The energy formation of the oxygen vacancies are analyzed at different values of the lattice parameter, in order to verify its dependency on the strain. This eventually allow us to identify the vacancy concentration difference between bulks and interfaces. Activation energy of the oxygen migration are also calculated in the optimized bulk as well as under strain condition as at the interfaces level, to identify eventual preferential migration channel. The effect of the doping on the lattice geometry is analyzed for the low index interfaces in order to verify its influence on the morphologic disorder and consequently on vacancy concentration.

Fukumoto, T, Thomas, P, Stuart, BH, Adam, G, Simon, P, Shimmon, R & Guerbois, JL 1970, 'Kinetic and mechanistic analysis of the polymerisation of dimethylol urea', Proceedings of the 3rd Joint Czech-Hungarian-Polish-Slovak Thermoanalytical Conference, Slovak Chemical Society, Stara Lesna, pp. 1-5.

Ge, Q, Burgess, JK, Moir, LM, Trian, T, Niimi, K, Shepherd, PR, Black, JL & Oliver, BG 1970, 'Inhibition Of Phosphoinositide 3?-Kinase P110? Decreases TGFBeta1 Induced IL-6 And Calponin Expression In Human Airway Smooth Muscle Cells', C97. AIRWAY GOVERNANCE: THE AXIS OF AIRWAY MYOCYTES, MYOFIBROBLASTS AND EXTRACELLULAR MATRIX IN ASTHMATIC AND COPD REMODELING, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Gentle, AR & Smith, G 1970, 'Performance comparisons of sky window spectral selective and high emittance radiant cooling systems under varying atmospheric conditions', Solar 2010 : Proceedings of the 48th AuSES Annual Conference, Conference of the Australian Solar Energy Society (AuSES), Australian Solar Energy Society, Canberra, Australia, pp. 1-8.
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The need for alternative low energy methods for cooling buildings is being realised. This work investigates radiative cooling as a viable option. The use of a novel convection suppressant cover material allows a durable system capable of sub-ambient temperatures. The system's performance using a high emittance radiative surface is evaluated under various atmospheric conditions.

Gerace, D, Ren, B, Byrne, MR, O'Brien, BA & Swan, A 1970, 'Pancreatic Transdifferentiation in the Livers of Non-Obese Diabetic (NOD) Mice Following Lentiviral Delivery of Furin-Cleavable Insulin', RNSH/UTS/USYD/KIMR Annual Scientific Meeting, Kolling Institute of Medical Research.

Gibson, BC, Castelletto, S, Karle, TJ, Tomljenovic-Hanic, S, Aharonovich, I, Johnson, BC, Orwa, J, Henderson, MR, Ebendorff-Heidepriem, H, Kuan, K, Afshar, SV, Monro, TM, Greentree, AD & Prawer, S 1970, 'Towards Hybrid Diamond Optical Devices', 2011 13TH INTERNATIONAL CONFERENCE ON TRANSPARENT OPTICAL NETWORKS (ICTON), 2010 12th International Conference on Transparent Optical Networks, IEEE, Munich, Germany.
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Diamond is a unique material, with a host of attributes that seem to favour is as a platform for solid-state optical approaches to quantum information processing. Amongst the many outstanding properties of diamond, the most important for these applications are that it posses the largest transparency window in the visible regime, has the highest thermal conductivity, and most importantly, hosts a large number of high dipole moment colour centres. In this paper we give an overview of the fabrication and characterisation of diamond-based optical devices at the University of Melbourne. © 2010 IEEE.

Gibson, BC, Henderson, MR, Ebendorff-Heidepriem, H, Kuan, K, Afshar V., S, Orwa, JO, Aharonovich, I, Tomljenovic-Hanic, S, Prawer, S, Monro, TM & Greentree, AD 1970, 'Single Photon Emission from Nanodiamond in Tellurite Glass', Proceedings of the International Quantum Electronics Conference and Conference on Lasers and Electro-Optics Pacific Rim 2011, International Quantum Electronics Conference, OSA.
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Gibson, BC, Henderson, MR, Ebendorff-Heidepriem, H, Kuan, K, Afshar, VS, Orwa, JO, Aharonovich, I, Tomljenovic-Hanic, S, Prawer, S, Monro, TM & Greentree, AD 1970, 'Single photon emission from nanodiamond in tellurite glass', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 721-722.
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We demonstrate single photon emission from nanodiamond containing isolated single nitrogen-vacancy quantum emitters, embedded within tellurite glass optical fibres. This hybrid diamond-glass material presents a platform for next generation quantum photonics applications. © 2011 IEEE.

Goldys, EM, Deng, W, Calander, NP, Drozdowicz-Tomsia, K & Jin, D 1970, 'Nanoscale plasmonic resonators with high Purcell factor: spontaneous and stimulated emission', SPIE Proceedings, SPIE BiOS, SPIE, USA.
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Plasmonic nanoparticles with silver cores and silica shells containing Eu fluorophores near the surface have been produced by wet chemistry method and their spontaneous emission properties characterized. Fluorescence amplification and decreased lifetime is interpreted within the Purcell framework which highlights the role of surface plasmon polariton modes of the nanoparticle. These behave as energy-storing resonators, with values of the Q factor between 50 and 170 at the fluorophore wavelength of 615 nm, and very small mode volumes, in the order of 10 4 nm 3 , producing high Purcell factors of over 4000. Comparison of experiment with theoretical calculations by using the Mie theory shows that the values of cavity Q factors are moderated by the nonradiative rate of fluorophore molecules close to metal. The criteria for laser action in such composite nanoparticles are also presented, including lasing frequencies and threshold gain. © 2011 SPIE.

Gothe, J, Leung, T, Lim, RP, Phyu, YL, Plant, R & Walker, JR 1970, 'Advocating for Biodiversity in the Hawkesbury Nepean River: critical research practices of visual communication design', Geography on the Edge, Institute of Australian Geographers, University of Wollongong, pp. 1-47.

Gu, H & Evans, I 1970, 'Study on Improving Solution Regularity for Crew Pairing Problems', 2011 IFORS Conference on World OR : Global Economy and Sustainable Environment, Melbourne, Australia.
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When producing optimised crew pairings to cover airline schedules, many airlines consider that regular pairings are easier to implement and manage, and are to be preferred if there is limited cost impact. In this paper we propose a column generation based solution approach to consider regularity, which is regarded as the repeatability of pairings in the planning horizon, as well as cost. The contributions of our method include the use of a fully dated model, an improved k-shortest path pricing algorithm and comprehensive computational results for a schedule from a large Asian airline.

Gutman, N, Botten, LC & de Sterke, CM 1970, 'Increased Optical Intensity near High Order Degenerate Photonic Band Edges for Nonlinear Applications', CLEO:2011 - Laser Applications to Photonic Applications, CLEO: Applications and Technology, OSA, Baltimore, MD.
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Gutman, N, Dupree, H, Botten, LC, Sukhorukov, AA & de Sterke, CM 1970, 'Stationary inflection points in optical waveguides: Accessible frozen light', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 60-62.
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Stationary Inflection Points (SIPs) around a frequency ω 0 are of the form ω - ω 0 ∝ k m for any positive odd integer. We show theoretically that SIPs of order m can be created in optical waveguides such as optical fiber gratings or periodic nanobeam waveguides by coupling between m modes. Remarkably, we find that at the SIP frequency significant incident energy can be coupled into the waveguide even though the group velocity of the associated mode is zero. Here we demonstrate this frozen light for cubic (k 3) and quintic (k 5) SIPs and relate it to the existence of evanescent modes at the interface and demonstrate it. © 2011 IEEE.

Hansbro, PM, Horvat, JC, Essilfie, A-T, Kim, RY, Simpson, JL, Dunkley, ML, Beagley, KW, Gibson, P & Foster, PS 1970, 'Infection-Induced Neutrophilic Allergic Airways Disease Is Resistant To Steroid Treatment', C34. NEUTROPHILS, MAST CELLS, BASOPHILS AND EOSINOPHILS IN LUNG DISEASE, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Holt, SA, Clifton, LA, Johnson, C & Lakey, JH 1970, 'Toxin Insertion Into Lipid Monolayers at the Air/Water Interface is Promoted by the Cognate Receptor Protein', BIOPHYSICAL JOURNAL, 55th Annual Meeting of the Biophysical-Society, CELL PRESS, Baltimore, MD, pp. 512-512.

Huete, A, Eamus, D, Ma, X, Restrepo-Coupe, N, Boulain, N & Hutley, L 1970, 'MONITORING PHENOLOGICAL VARIABILITY ACROSS A TROPICAL SAVANNA ARIDITY GRADIENT WITH REMOTE SENSING ACROSS SEASONAL TO ANNUALAND EXTREME EVENTS', ISPRS BHOPAL 2011 WORKSHOP EARTH OBSERVATION FOR TERRESTRIAL ECOSYSTEM, ISPRS Bhopal Workshop on Earth Observation for Terrestrial Ecosystem, COPERNICUS GESELLSCHAFT MBH, Bhopal, INDIA, pp. 19-19.

Hulley, H & Platen, E 1970, 'A Visual Criterion for Identifying Ito Diffusions as Martingales or Strict Local Martingales', SSRN Electronic Journal, Seminar on Stochastic Processes, Random Fields and Applications, Elsevier BV, Ascona, Switzerland, pp. 147-157.
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It is often important, in applications of stochastic calculus to financial modelling, to know whether a given local martingale is a martingale or a strict local martingale. We address this problem in the context of a time-homogenous diffusion process with a finite lower boundary, presented as the solution of a driftless stochastic differential equation. Our main theorem demonstrates that the question of whether or not this process is a martingale may be decided simply by examining the slope of a certain increasing function. Further results establish the connection between our theorem and other results in the literature, while a number of examples are provided to illustrate the use of our criterion.

Jackson, E, Righi, L, McGowan, E & Sapino, A 1970, 'Sphingosine Kinase 1 Correlates With a Neuroendocrine Phenotype in Breast Cancer in Vivo and in Vitro', EUROPEAN JOURNAL OF CANCER, European Multidisciplinary Cancer Congress on Integrating Basic and Translational Science, Surgery, Radiotherapy, Medical oncology, Advocacy and Care, ELSEVIER SCI LTD, Stockholm, SWEDEN, pp. S125-S125.
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Jiang, Z, Huete, A, Wang, Y & Lyapustin, A 1970, 'Evaluation of MODIS VI products using the AERONET-based surface reflectance validation network dataset', 34th International Symposium on Remote Sensing of Environment - The GEOSS Era: Towards Operational Environmental Monitoring.
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MODIS vegetation index (VI) products (MOD13) are widely used in many science applications that aim to monitor and characterize spatial and temporal vegetation dynamics from space. The quality and reliability of the MODIS VI products are vital to these studies, and thus there is a need to assess their quality. In this study, the AERONET-based Surface Reflectance Validation Network (ASRVN) dataset is used to evaluate the quality of the MODIS 1 km, 16-day composite NDVI and EVI products. Our results show a positive bias of red reflectances, which is responsible for bias in the MODIS NDVI and two-band EVI (EVI2). The negative bias of the MODIS blue reflectance nullifies this effect on the standard EVI, resulting in insignificant bias in EVI. EVI and NDVI temporal profiles match ASRVN VI profiles even during higher aerosol optical thickness (AOT) periods, indicating that the VI products are not significantly affected by aerosols.

Jin, D, Lu, Y, Zhao, J, Deng, W, Lu, J & Piper, JA 1970, 'Advances in lanthanide bioprobes and high-throughput background-free biophotonics sensing', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, Sydney, NSW, Australia, pp. 80-82.
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We report time-domain techniques of biophotonics sensing. Our bioprobes have been engineered to emit tunable luminescence across multiple sharp spectra and microsecond-long lifetimes. This offers high-throughput opportunities for cellular-level disease diagnosis at low cost. © 2011 IEEE.

Kabakova, IV, Grobnic, D, Mihailov, SJ, Mägi, EC, de Sterke, CM & Eggleton, BJ 1970, '18-fold power reduction using bragg grating-based switch in highly-nonlinear bismuth-oxide fiber', Optics InfoBase Conference Papers, Conference on Lasers and Electro-Optics (CLEO), IEEE, Baltimore, MD.
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We experimentally demonstrate a Bragg grating-based all-optical switch in a highly nonlinear Bi2O3 fiber. We achieve 18-fold power reduction for a 6.5 dB switching ratio compared with previous demonstrations in silica fibers. © OSA/ CLEO 2011.

Kabakova, IV, Grobnic, D, Mihailov, SJ, Mägi, EC, De Sterke, CM & Eggleton, BJ 1970, '18-Fold power reduction using Bragg grating-based switch in highly-nonlinear bismuth-oxide fiber', 2011 Conference on Lasers and Electro-Optics: Laser Science to Photonic Applications, CLEO 2011.
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We experimentally demonstrate a Bragg grating-based all-optical switch in a highly nonlinear Bi2O3 fiber. We achieve 18-fold power reduction for a 6.5 dB switching ratio compared with previous demonstrations in silica fibers. © 2011 OSA.

Kabakova, IV, Halliwell, D, Martijn de Sterke, C, Yu, Z, Margulis, W, Fonjallaz, PY & Tarasenko, O 1970, 'Observation of frequency shift in a dynamically tuned fiber grating cavity by a beating technique', Optics InfoBase Conference Papers.
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Dynamic frequency changes of light trapped in a fiber grating-based cavity, which is detuned by RF pulses, are detected by a simple, elegant, high-resolution method in which the trapped light beats with the incoming light. © 2011 Optical Society of America.

Kajer, T, Hawkins, CL, Fu, S, Pattison, DI, Graham, GG & Davies, MJ 1970, 'Myeloperoxidase-Derived Oxidant Production and Biological Damage are Inhibited by Acetaminophen (Paracetamol) at Pharmacologically-Relevant Levels', FREE RADICAL BIOLOGY AND MEDICINE, 18th Annual Meeting of the Society-for-Free-Radical-Biology-and-Medicine (SFRBM), ELSEVIER SCIENCE INC, Atlanta, GA, pp. S89-S89.
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Kan, DJ, Botten, LC, Poulton, CG, Asatryan, AA & Dossou, KB 1970, 'Semi-analytical formulations for the surface modes of photonic woodpiles', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, Sydney, NSW, Australia, pp. 2130-2132.
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We describe semi-analytical methods for modeling the optical surface modes of finite and semi-infinite photonic woodpiles, and find that the behavior of the surface modes depends greatly on the whether the number of layers is even or odd. We also demonstrate analytically that coupling between the top and bottom surfaces can occur even when the top layer is orthogonal to the bottom layer. The coupling strength exhibits a strong dependence on the direction of propagation; for certain directions, decoupling occurs even when the number of layers is small. The dispersion curves of two different coupled modes can anticross or be interwoven. We also describe the conditions under which coupled surface modes will exist when two woodpiles are used to create a Fabry-Pérot cavity. © 2011 IEEE.

Krimmer, DI, Burgess, JK, Black, JL & Oliver, BG 1970, 'Cigarette Smoke Extract Induced Production Of Extracellular Matrix Proteins Is Attenuated By Simvastatin', D39. NOVEL THERAPEUTICS IN PULMONARY FIBROSIS, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Krimmer, DI, Burgess, JK, Black, JL & Oliver, BG 1970, 'Exposure To Biomass Smoke Extract Enhances Fibronectin Release From Human Lung Fibroblasts', B106. BIOMASS AND OTHER INDOOR AIR POLLUTANTS, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Krimmer, DI, Ichimaru, Y, Burgess, JK, Black, JL & Oliver, BG 1970, 'Attachment Of Airway Smooth Muscle Cells Is Enhanced By Perlecan Domains II, IV, And V', C18. NOVEL MECHANISMS DRIVING AIRWAY REMODELING IN ASTHMA, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Lapine, M, Shadrivov, IV, Powell, DA & Kivshar, YS 1970, 'Magnetoelastic metamaterials', 2011 Conference on Lasers and Electro-Optics Europe and 12th European Quantum Electronics Conference (CLEO EUROPE/EQEC), 12th European Quantum Electronics Conference CLEO EUROPE/EQEC, IEEE, Munich, Germany.
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We propose and demonstrate experimentally a novel type of nonlinearity in metamaterials, which is induced by mechanical deformation of the structure. The nonlinearity arises from the introduction of an extra degree of freedom in the metamaterial, which allows for elastic displacement of the strongly interacting structural elements (see Fig. 1a). This type of nonlinearity relies on the counterplay between the electromagnetic attraction and the elastic repulsion, and the induced deformation alters the electromagnetic response of the entire structure, leading to the novel nonlinear response of the metamaterial. © 2011 IEEE.

Lin, BM, Hwang, FJ & Kononov, A 1970, 'Resource-constrained scheduling with two parallel dedicated machines subject to fixed processing sequences', The 24th Conference of the European Chapter on Combinatorial Optimization (ECCO 2011), ECCO, Amsterdam.

Lu, Y, Piper, JA, Huo, Y & Jin, D 1970, 'Cytometric investigation of rare-events featuring time-gated detection and high-speed stage scanning', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 2011-2013.
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We report a time-gated luminescence cytometric strategy to detect rare-event waterborne pathogens. The prototype system is capable of analyzing a 15mm 15mm slide containing as rare as 13 europium-labeled Giardia cysts within 5 minutes. © 2011 IEEE.

Luvall, JC, Sprigg, W, Levetin, E, Huete, A, Nickovic, S, Pejanovic, G, Van de Water, P, Myers, O, Budge, A, Crimmins, T, Krapfl, H & Zelicoff, A 1970, 'Use of MODIS Satellite Images and an Atmospheric Dust Transport Model To Evaluate Juniperus Spp. Pollen Phenology and Dispersal to Support Public Health Alerts', JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, American-Academy-of-Allergy-Asthma-and-Immunology Annual Meeting, MOSBY-ELSEVIER, San Francisco, CA, pp. AB19-AB19.
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Manetsch, M, Seidel, P, Che, W, Ge, Q, Sukkar, M & Ammit, AJ 1970, 'Effect Of H202 On The Synergistic Upregulation Of TnfAlpha-Induced Cytokines By TLR2 Ligand Engagement', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

McKemmish, LK, Kedziora, DJ, White, GR, Hushc, NS & Reimers, JR 1970, 'Molecular Design Principles for Linearly Scalable, Frequency-Based, Universal Quantum Computers', Proceedings of the International Quantum Electronics Conference and Conference on Lasers and Electro-Optics Pacific Rim 2011, International Quantum Electronics Conference, OSA, pp. 734-736.
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Minimizing of the number of strong couplings between qubits is shown to facilitate frequencybased universal quantum computers with two-qubit-gate construction difficulty that scales linearly with increasing register size, matching that known already for one-qubit gates. © 2011 AOS.

Mercer, AE, Richman, MB & Leslie, LM 1970, 'Identification of severe weather outbreaks using kernel principal component analysis', Procedia Computer Science, Complex Adaptive Systems, Elsevier BV, Chicago, Illinois, U.S.A, pp. 231-236.
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A new adaptive approach to severe weather outbreak compositing and discrimination is described for datasets of known non-tornadic and tornado outbreaks. Kernel principal component analysis (KPCA) is used to reduce the dimensionality of the dataset and provide input for cluster analysis (CA) of the outbreaks to discern meteorological characteristics unique to each outbreak type. Results are compared to traditional principal component analysis (PCA). The KPCA methodology and CA assigned outbreaks to different composite (maps that have a close correspondence) sets than did PCA and CA. The clusters associated with each method were used as training for a support vector machine classification scheme. An independent subset of the outbreak dataset was retained for cross-validation classification of outbreak type. Significant differences in the two composite methods are observed, and a support vector machine classification scheme demonstrates compelling effectiveness in distinguishing outbreak types based on the resulting composites. © 2011 Published by Elsevier Ltd.

Molnar, A, Fu, S, Doble, PA & Lewis, JH 1970, 'A sensitive method to detect and quantify delta-9 tetrahydrocannabinol in oral fluid by liquid chromatography - tandem mass spectrometry', TIAFT Bulletin, Annual Meeting of the International-Association-of-Forensic-Toxicologists (TIAFT), GI Printing & Graphics, Bonn, Germany, pp. 45-47.
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Delta9 -tetrahydrocannabinol (THC) is the major psychoactive constituent of cannabis. It causes a decrease in motor function and concentration making it hazardous for an individual to drive whilst under the inftuence of this drug. Roadside testing procedures for cannabis are therefore necessary since it is the most widely used illicit drug in Australia and around the world and is commonly implicated in drug-driving offences.

Murray, SA, Wiese, M, Stuken, A, Kellmann, R, Brett, S, Hallegraef, GM & Neilan, BA 1970, 'Quantitative assessment of coastal harmful algal blooms based on the saxitoxin biosynthesis gene, sxtA', Gordon Conference on Phycotoxins and Mycotoxins, Boston, United States.

Naumann, U, Wand, MP & George, L 1970, 'AUTOMATION IN HIGH-CONTENT FLOW CYTOMETRY SCREENING', CYTOMETRY PART B-CLINICAL CYTOMETRY, 26th Annual Meeting of the International-Clinical-Cytometry-Society, WILEY-BLACKWELL, Portland, OR, pp. 391-391.

Nevillea, SE & Wand, MP 1970, 'Generalised extreme value geoadditive model analysis via variational Bayes', Procedia Environmental Sciences, International Conference on Spatial Statistics - Mapping Global Change, Elsevier BV, Enschede, pp. 8-13.
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We devise a variationalBayes algorithm for fast approximate inference in Bayesian GeneralizedExtremeValue additive modelanalysis. Such models are useful for flexibly assessing the impact of continuous predictor variables on sample extremes. The new methodology allows large Bayesian models to be fitted and assessed without the significant computing costs of Monte Carlo methods

Ng, HY, Oliver, BG, Burgess, JK, Krymskaya, VP, Black, JL & Moir, LM 1970, 'Inhibition Of Matrix Metalloproteinase-2 (MMP-2) Decreases Migration Of TSC2-Null Mouse Embryonic Fibroblasts – Relevance To Pulmonary Lymphangioleiomyomatosis (LAM)', B71. CRAZY MUSCLES: AIRWAY AND LYMPHATIC SMOOTH MUSCLE AND LYMPHANGIOLEIOMYOMATOSIS (LAM), American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Niimi, K, Oliver, BG, Thomas, T, Moir, LM, Ge, Q, Burgess, JK & Black, JL 1970, 'Expression Of Phosphodiesterase 4D In Asthmatic And Non Asthmatic Airway Smooth Muscle Cells And Its Regulation By Formoterol', A30. NOVEL MECHANISMS OF AIRWAY SMOOTH MUSCLE CONTRACTION AND RELAXATION: ARE THESE THERAPEUTICALLY TARGETABLE?, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Oliver, BG, Tang, FS, Van Ly, D, Burgess, JK, Black, JL & Baines, KJ 1970, 'Imiquimod, Poly I:C And Rhinovirus Induce Interleukin (IL)-6 And IL-8 Release From Polymorphonuclear Cells And Peripheral Blood Mononuclear Cells: Effect Of Dexamethasone', D102. PATHOGENS IN AIRWAY DISEASE, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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O'Reilly, M, Hansbro, P, Horvatt, J, Sozo, F & Harding, R 1970, 'Inhalation of Hyperoxic Gas in the Neonatal Period Has Long-Term Effects on the Pulmonary Airways', JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE, CAMBRIDGE UNIV PRESS, pp. S70-S70.

Pant, R, Poulton, C, MacFarlane, H, Thevenaz, L, Choi, DY, Steve, J, Madden, SJ, Luther-Davies, B & Eggleton, BJ 1970, 'On-chip stimulated brillouin scattering', Optics InfoBase Conference Papers.
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We report the first demonstration of on-chip stimulated Brillouin scattering (SBS). The measured Brillouin shift and line width are ~7.7 GHz and 6 MHz in a 7 cm long chalcogenide waveguide. © 2010 Optical Society of America.

Phillips, M, Manning, TJ, Nenstiel, C, Lockrey, MN, Ton-That, C & Hoffmann, AV 1970, 'High Temperature In-Situ Cathodoluminescence Studies of the Thermal Stability of Hydrogen in p-type Magnesium Doped Gallium Nitride', Microscopy and Microanalysis, Vol 17, Supplement 2, High Temperature In-Situ Cathodoluminescence Studies of the Thermal Stability of Hydrogen in p-type, Nashville, pp. 1-2.

Plant, R, Walker, JR, Rayburg, SC, Gothe, J, Leung, TM, Phyu, YL & Lim, RP 1970, 'The 'Social Life of Pesticides': How organised irresponsibility in the Greater Sydney Basin threatens the biodiversity of the Hawkesbury-Nepean River', Institute of Australian Geographers (IAG) Conference Wollongong 2011, Wollongong, NSW.

Platen, E 1970, 'A benchmark approach to quantitative finance', Seminar Presentation, Humboldt University, Berlin, Germany.

Platen, E 1970, 'A dynamic portfolio approach to monetary policy', Southern Africa Mathematical Sciences Association (SAMSA) 2011 Conference, Livingston, Zambia.

Platen, E 1970, 'On targeted pensions', Quantitative Methods in Finance 2011 Conference, Sydney Australia.

Ponce, G, Moran, S, Huete, A, Bresloff, C, Huxman, T, Bosch, D, Bradford, J, Buda, A, Gunter, S, McNab, H, McClaran, M, Peters, D, Sadler, J, Seyfried, M, Starks, P, Sutherland Montoya, D & Heartsill, T 1970, 'Convergence of dynamic vegetation net productivity responses to precipitation variability from 10 years of MODIS EVI', 34th International Symposium on Remote Sensing of Environment - The GEOSS Era: Towards Operational Environmental Monitoring, International Symposium on Remote Sensing of Environment (ISRSE), Sydney Convention and Exhibition Centre, Australia.
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According to Global Climate Models (GCMs) the occurrence of extreme events of precipitation will be more frequent in the future. Therefore, important challenges arise regarding climate variability, which are mainly related to the understanding of ecosystem responses to changes in precipitation patterns. Previous studies have found that Above-ground Net Primary Productivity (ANPP) was positively related to increases in annual precipitation and this relation may converge across biomes during dry years. One challenge in studying this ecosystem response at the continental scale is the lack of ANPP field measurements over extended areas. In this study, the MODIS EVI was utilized as a surrogate for ANPP and combined with precipitation datasets from twelve different experimental sites across the United States over a 10-year period. Results from this analysis confirmed that integrated-EVI for different biomes converged toward common precipitation use efficiency during water-limited periods and may be a viable surrogate for ANPP measurements for further ecological research.

Poulton, CG, Rahmani, A & Steel, MJ 1970, 'Radiation dynamics in a magneto-dielectric metamaterial cylinder', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, Sydney, NSW, Australia, pp. 1830-1831.
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We study the radiation dynamics of an electric line current source in a homogeneous, magneto-dielectric cylinder. We find that radiation by the source is most enhanced by maximizing the magnetic response of the cylinder. © 2011 IEEE.

Rahmani, A, Poulton, CG, Steel, MJ, Chaumet, PC & Bryant, GW 1970, 'Purcell effect in a magnetic cavity', CLEO:2011 - Laser Applications to Photonic Applications, CLEO: Applications and Technology, OSA, Baltimore, MD.
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Reim, KF, Michelberger, P, Lee, KC, Nunn, J, Langford, NK & Walmsley, IA 1970, 'Single-photon-level memory at room temperature', Optics InfoBase Conference Papers.
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We present an efficient broadband optical single-photon-level room-temperature memory, capable of operating with a low unconditional noise floor in the quantum regime, with memory efficiencies exceeding 30% and storage times of up to 4 μs. © 2011 Optical Society of America.

Scott Brownless, J, Mahmoodian, S, Lawrence, FJ, Dossou, KB, Botten, LC & Martijn De Sterke, C 1970, 'Guiding mechanisms and dispersion engineering in photonic crystal waveguides', Optics InfoBase Conference Papers, pp. 12-14.
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We examine the guiding mechanism of photonic crystal (PC) waveguide modes through the properties of their evanescent fields in the photonic crystal cladding, allowing an unambiguous definition of gap-guided and index-guided modes. We show that the ability to tailor the dispersion of PC waveguide modes depends on the properties of these fields. Our analysis suggests that the photonic crystal's lattice type can be used to maximize the region of the Brillouin zone where PC waveguide modes can be dispersion engineered. © 2011 AOS.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Eilenberger, F, Minardi, S, Ricken, R, Min, Y, Sohler, W, Kivshar, YS & Pertsch, T 1970, 'Nonlinear evolution of laser pulses in lithium niobate waveguide arrays', Optics InfoBase Conference Papers.
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We study experimentally and numerically the spatiotemporal evolution of short pulses in quadratic nonlinear waveguide arrays with coupled second-harmonic modes, revealing complex spectral transformations involving generation of new frequency components at the Brillouin zone edge. © 2011 Optical Society of America.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Eilenberger, F, Minardi, S, Ricken, R, Min, Y, Sohler, W, Kivshar, YS & Pertsch, T 1970, 'Nonlinear evolution of laser pulses in lithium niobate waveguide arrays', Nonlinear Optics, Nonlinear Optics: Materials, Fundamentals and Applications, OSA.
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We study experimentally and numerically the spatiotemporal evolution of short pulses in quadratic nonlinear waveguide arrays with coupled second-harmonic modes, revealing complex spectral transformations involving generation of new frequency components at the Brillouin zone edge. © 2011 Optical Society of America.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Kivshar, YS & Pertsch, T 1970, 'Nonlinear pulse transformation and phase transitions in LiNbO<inf>3</inf> waveguide arrays', 2011 Conference on Lasers and Electro-Optics Europe and 12th European Quantum Electronics Conference (CLEO EUROPE/EQEC), 12th European Quantum Electronics Conference CLEO EUROPE/EQEC, IEEE.
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Lithium niobate waveguide arrays (WGAs) [1] offer rich possibilities for all-optical shaping, switching, and routing of short optical pulses. In such systems, light from the fundamental wave (FW) is coupled by the 2 nonlinearity to the second harmonic (SH) giving rise to a strong cascaded quadratic nonlinearity. Recently a new type of phase transition in the nonlinear localised states was identified due to the competition between self-focusing and SH waveguide coupling, where the SH phase profile abruptly switches from in-phase to staggered structure as the input power is increased [2]. However, the temporal extent of the short laser pulses used in realistic experiments leads to a complex pulse reshaping in the course of propagation. Never studied experimentally before, such temporal dynamics is important for utilising the phase transition phenomenon for applications in optical switching. In this work, we study the spatio-temporal dynamics of pulses in lithium niobate WGAs and describe numerically and characterize experimentally the complex spatio-temporal nonlinear pulse transformations associated with the phase transition. © 2011 IEEE.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Kivshar, YS & Pertsch, T 1970, 'Nonlinear pulse transformation and phase transitions in LiNbO3 waveguide arrays', Optics InfoBase Conference Papers.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Ricken, R, Min, Y, Sohler, W, Kivshar, YS & Pertsch, T 1970, 'Spatio-temporal dynamics of laser pulses in lithium niobate waveguide arrays', Optics InfoBase Conference Papers, pp. 584-586.
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We study experimentally and numerically the spatiotemporal evolution of short pulses in quadratic nonlinear waveguide arrays with coupled second-harmonic modes, revealing complex spectral transformations involving generation of new frequency components at the Brillouin zone edge. © 2011 AOS.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Ricken, R, Min, Y, Sohler, W, Kivshar, YS & Pertsch, T 1970, 'Spatio-temporal dynamics of laser pulses in lithium niobate waveguide arrays', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 584-586.
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We study experimentally and numerically the spatiotemporal evolution of short pulses in quadratic nonlinear waveguide arrays with coupled second-harmonic modes, revealing complex spectral transformations involving generation of new frequency components at the Brillouin zone edge. © 2011 IEEE.

Setzpfandt, F, Sukhorukov, AA, Neshev, DN, Schiek, R, Solntsev, AS, Ricken, R, Min, Y, Sohler, W, Kivshar, YS & Pertsch, T 1970, 'Spatio-temporal dynamics of laser pulses in lithium niobate waveguide arrays', Proceedings of the International Quantum Electronics Conference and Conference on Lasers and Electro-Optics Pacific Rim 2011, International Quantum Electronics Conference, OSA.
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Smith, G, Gentle, AR & Edmonds, I 1970, 'Urban growth, albedo and global warming', Solar 2010 : Proceedings of the 48th AuSES Annual Conference, Conference of the Australian Solar Energy Society (AuSES), Australian Solar Energy Society, Canberra, pp. 1-8.
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Traditional town and city growth adds to the 'urban heat island' (UHI) problem, which raises cooling demand, degrades the microclimate and adds directly to global warming. Low solar albedos and local energy use both contribute to the UHI but it is not widely appreciated that the former can have by far the dominant impact. These relative impacts, locally and globally, are quantized per square kilometre of typical Australian urban area for shifts in solar albedo and for the extra coal power demanded. This analysis shows that as a matter of urgency urban planning rules and building codes need to change. The energy savings and global cooling associated with improved rules and codes provide a higher environmental return on investment than most renewables and other energy efficiency measures.

Smith, GB 1970, 'Green Nanotechnology', NANOSTRUCTURED THIN FILMS IV, Nanostructured Thin Films IV, The International Society for Optics and Photonics, San Diego, California, USA, pp. 1-14.
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Nanotechnology, in particular nanophotonics, is proving essential to achieving green outcomes of sustainability and renewable energy at the scales needed. Coatings, composites and polymeric structures used in windows, roof and wall coatings, energy storage, insulation and other components in energy efficient buildings will increasingly involve nanostructure, as will solar cells. Nanostructures have the potential to revolutionize thermoelectric power and may one day provide efficient refrigerant free cooling. Nanomaterials enable optimization of optical, opto-electrical and thermal responses to this urgent task. Optical harmonization of material responses to environmental energy flows involves (i) large changes in spectral response over limited wavelength bands (ii) tailoring to environmental dynamics. The latter includes engineering angle of incidence dependencies and switchable (or chromogenic) responses. Nanomaterials can be made at sufficient scale and low enough cost to be both economic and to have a high impact on a short time scale. Issues to be addressed include human safety and property changes induced during manufacture, handling and outdoor use. Unexpected bonuses have arisen in this work, for example the savings and environmental benefits of cool roofs extend beyond the more obvious benefit of reduced heat flows from the roof into the building.

Solntsev, AS, Neshev, DN & Schiek, R 1970, 'Time-resolved ultrafast all-optical switching in directional couplers with second-order nonlinearity', 2011 Conference on Lasers and Electro-Optics Europe and 12th European Quantum Electronics Conference (CLEO EUROPE/EQEC), 12th European Quantum Electronics Conference CLEO EUROPE/EQEC, IEEE.
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Nonlinear directional couplers (NLDC) allow for ultrafast all-optical switching. To date, various types of NLDCs have been studied, predominantly based on the Kerr [1] or cascaded quadratic nonlinearity [2] in second-harmonic generation (SHG). In the later case the switching can occur at lower powers because of a propagating-wave resonance effect. While a number of experiments to characterise the pulse propagation in Kerr-type couplers exist, till now the temporal behavior of short pulses in the NLDC with quadratic nonlinearity has never been studied experimentally. Several important questions such as the reason for incomplete switching and possible pulse compression factors remain unanswered. In this work we experimentally measure the pulse reshaping in a NLDC with second-order nonlinearity and show that pulse compression, break-up and back-switching play an important role in the switching process. © 2011 IEEE.

Solntsev, AS, Sukhorukov, AA & Kivshar, YS 1970, 'Modulated nanowire couplers for ultrashort pulses', 2011 Conference on Lasers and Electro-Optics Europe and 12th European Quantum Electronics Conference (CLEO EUROPE/EQEC), 12th European Quantum Electronics Conference CLEO EUROPE/EQEC, IEEE.
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High-index-contrast nanowires offer unique advantages for manipulation of optical pulses in compact photonic circuits, providing high field confinement and enabling precise dispersion engineering [1]. Furthermore, arrays of coupled nanowire waveguides [2-4] open possibilities for efficient spatio-temporal shaping and switching of optical pulses. In order to harness these opportunities, it is essential to develop approaches to simultaneously control temporal and spatial dispersion, as these characteristics can be strongly connected in nanophotonic structures. In this work, we suggest that spatio-temporal dispersion can be tailored by introducing periodic waveguide bending, and demonstrate through numerical simulations the application of this concept to suppress pulse break-up. © 2011 IEEE.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Combined photon pair generation and quantum walks in quadratic nonlinear waveguide arrays', Optics InfoBase Conference Papers.
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We study photon pair generation through spontaneous parametric down conversion ac- companied by quantum walks in arrays of quadratic nonlinear waveguides and investigate various ways to control output photon correlations. © 2011 OSA.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Combined Photon Pair Generation and Quantum Walks in Quadratic Nonlinear Waveguide Arrays', Frontiers in Optics 2011/Laser Science XXVII, Frontiers in Optics, OSA.
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We study photon pair generation through spontaneous parametric down conversion ac- companied by quantum walks in arrays of quadratic nonlinear waveguides and investigate various ways to control output photon correlations. © 2011 OSA.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon Pair Generation and Quantum Walks in Arrays of Quadratic Nonlinear Waveguides', Nonlinear Optics, Nonlinear Optics: Materials, Fundamentals and Applications, OSA.
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We study photon pair generation through spontaneous parametric down con- version accompanied by quantum walks in arrays of quadratic nonlinear waveguides and investigate various ways to control output photon correlations. © 2011 Optical Society of America.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon pair generation and quantum walks in arrays of quadratic nonlinear waveguides', Optics InfoBase Conference Papers.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon pair generation and quantum walks in arrays of quadratic nonlinear waveguides', Optics InfoBase Conference Papers.
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We study photon pair generation through spontaneous parametric down con- version accompanied by quantum walks in arrays of quadratic nonlinear waveguides and investigate various ways to control output photon correlations. © 2011 Optical Society of America.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon pair generation and quantum walks in arrays of quadratic nonlinear waveguides', 2011 Conference on Lasers and Electro-Optics Europe and 12th European Quantum Electronics Conference (CLEO EUROPE/EQEC), 12th European Quantum Electronics Conference CLEO EUROPE/EQEC, IEEE.
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Arrays of coupled optical waveguides provide a flexible platform for manipulation of optical beams and pulses [1]. Recently, the propagation of non-classical light in waveguide arrays has shown a surging attention. It was shown that quantum walks of correlated photon pairs realized through propagation in waveguide arrays can lead to nontrivial quantum correlations at the array output [2, 3]. However, all currently used schemes for quantum walks utilise correlated photon pairs generated externally to the array. Here, we propose and demonstrate numerically a novel scheme enabling simultaneous generation of correlated photon pair through spontaneous parametric downconversion (SPDC) and quantum walks inside a single photonic element - an array of quadratic nonlinear waveguides. This scheme avoids entirely the need for complex interfaces between the different photonic elements [3] and enables novel ways for control of the quantum correlations. © 2011 IEEE.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon pair generation and quantum walks in quadratic nonlinear waveguide arrays', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, pp. 962-964.
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We study photon pair generation through spontaneous parametric down conversion accompanied by quantum walks in arrays of quadratic nonlinear waveguides and investigate various ways to control output photon correlations. © 2011 IEEE.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon Pair Generation and Quantum Walks in Quadratic Nonlinear Waveguide Arrays', Proceedings of the International Quantum Electronics Conference and Conference on Lasers and Electro-Optics Pacific Rim 2011, International Quantum Electronics Conference, OSA.
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Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, de Sterke, CM, McPhedran, RC & IEEE 1970, 'Simulations of Silicon Nanowire Arrays for Photovoltaics-More Absorption with Less Silicon', 2011 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Lasers and Electro-Optics (CLEO), IEEE, Baltimore, MD.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, Martijn de Sterke, C & McPhedran, RC 1970, 'Absorption of silicon nanowire arrays on silicon and silica substrates', Optics InfoBase Conference Papers.
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Nanowire arrays are promising structures for 3rd generation photovoltaics, due to their absorption enhancement over thin films and reduction in material usage. Having previously studied the absorption mechanism of silicon nanowire arrays suspended in air, we now extend the analysis to arrays on substrates. We find that the absorption mechanism continues to be dominated by one (or more) well coupled, well concentrated, resonant modes. Whilst the substrates reduce the strength of the resonances, they can simultaneously increase short wavelength absorption. The ultimate efficiency of the arrays remains significantly greater than that of silicon thin films and with a silicon substrate exceeds that of arrays suspended in air. © 2011 OSA.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, Martijn de Sterke, C & McPhedran, RC 1970, 'Analysis of enhanced absorption in dense silicon nanowire arrays', Optics InfoBase Conference Papers, pp. 1136-1138.
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We analyze the absorption of solar radiation by dense silicon nanowire arrays, which are being considered for use in solar cells. Though it is known that these structures absorb sunlight much more efficiently than bulk silicon, the mechanism is complicated and not understood. Using a novel, semi-analytic model, we show that the enhanced absorption can be attributed to a few modes of the array, which couple well to incident light, overlap well with the silicon, and exhibit strong Fabry-Pérot resonances. For some frequencies the absorption is further enhanced by slow light effects. © 2011 AOS.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, Martijn De Sterke, C & McPhedran, RC 1970, 'Angular dependence of absorption in silicon nanowire arrays', Optics InfoBase Conference Papers.
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We use a novel modal simulation method to study the optical absorption properties of silicon nanowire arrays, which are being considered for 3rd generation photovoltaics. We have previously found the strong absorption to be derived from a small number of resonant modes and we now study the absorption as a function of angle of incidence. We find that the same few modes dominate the absorption mechanism and that the absorption remains high up to 35° off-normal irradiation. © 2011 OSA.

Suggett, DJ 1970, 'PHYSIOLOGICAL SIGNATURES OF MICROALGAL PHOTO-ACCLIMATION AND -ADAPTATION TO ENVIRONMENTAL CHANGE', EUROPEAN JOURNAL OF PHYCOLOGY, TAYLOR & FRANCIS LTD, pp. 34-35.

Suggett, DJ, Lawrenz, E, Silsbe, G, Capuzzo, E, Ylostalo, P, Forster, RM, Simis, S, Prasil, O & Kromkamp, JC 1970, 'TOWARDS PREDICTING THE MINIMUM QUANTUM REQUIREMENT FOR CARBON FIXATION IN EUROPEAN SEAS', EUROPEAN JOURNAL OF PHYCOLOGY, TAYLOR & FRANCIS LTD, pp. 54-54.

Tan, X, Alrashdan, Y, Alkhouri, H, Yaputra, V, Armour, CL, Oliver, BG & Hughes, JM 1970, 'Th1-Cytokine Induced STAT1 And JNK Phosphorylation Is Altered In Airway Smooth Muscle Cells From People With Asthma', B69. NOVEL INSIGHTS INTO AIRWAY INFLAMMATION AND REMODELING IN ASTHMA AND COPD, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Tekwe, CD, Dabney, AR & Carroll, RJ 1970, 'Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data', 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), IEEE, San Antonio, USA, pp. 97-100.
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Protein abundance in quantitative proteomics is often based on observed spectral features derived from LCMS experiments. Peak intensities are largely non-Normal in distribution. Furthermore, LC-MS data frequently have large proportions of missing peak intensities due to censoring mechanisms on low-abundance spectral features. Recognizing that the observed peak intensities detected with the LC-MS method are all positive, skewed and often left-censored, we propose using survival methodology to carry out differential expression analysis of proteins. Various standard statistical techniques including non-parametric tests such as the Kolmogorov-Smirnov and Wilcoxon-Mann-Whitney rank sum tests, and the parametric survival model, accelerated failure time model with the Weibull distribution were used to detect any differentially expressed proteins. The statistical operating characteristics of each method are explored using both real and simulated data set. ©2011 IEEE.

Thomas, T, Moir, LM, Burgess, JK, Liggett, SB, Ge, Q, Black, JL & Oliver, BG 1970, 'Beta2-Agonist Induced Camp Is Decreased In Asthmatic Airway Smooth Muscle Due To Increased PDE4D', A65. MECHANISMS OF AIRWAY RESPONSE TO INJURY (RESPIRATORY VIRUSES, CIGARETTE SMOKE, AND ASTHMA), American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Tilley, L, McMillan, P, Dixon, M, Hanssen, E, Yeoman, J, Whitchurch, C & Klonis, N 1970, 'Super-resolution optical imaging of malaria parasites', Optics InfoBase Conference Papers, pp. 368-369.
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3-D structured illumination microscopy (SIM), a super-resolution optical microscopy technique that allows an 8-fold increase in volume resolution, is providing new views of the cellular substructure of the malaria parasite, Plasmodium falciparum. © 2011 AOS.

Tomljenovic-Hanic, S, Aharonovich, I, Castelleto, S, Fairchild, BA, Ganesan, K, Gibson, BC, Greentree, AD, Orwa, J, Rubanov, S, Simpson, DA, Stacey, A, Prawer, S & IEEE 1970, 'Towards All-Diamond Optical Devices', 2010 12TH INTERNATIONAL CONFERENCE ON TRANSPARENT OPTICAL NETWORKS (ICTON), International Conference on Transparent Optical Networks, IEEE, Stockholm, Sweden.
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Diamond is emerging as an optical supermaterial, due to its wide transparency bandwidth, excellent thermooptic properties and most notably its stable , large dipole moment, room temperature, single photon emitting colour centres. In this paper we present recent progress in the characterization of non radiative and radiative decay in single impurities and the fabrication of hybrid diamond-tellurite optical structures First, we present direct imaging of the emission pattern of individual ion implanted chromium-based single photon emitters in diamond and measure their quantum efficiency. By comparing the decay rates from the single chromium emitters at different depths in the diamond crystal, we measured an average quantum efficiency of 28%. Second, a hybrid approach involving a soft glass tellurite host material has been introduced, allowing nitrogen-vacancy (NV-) diamond emitters to be built into an optical fibre. The potential of integrating Cr-related centres in hybrid optical structures is also discussed. © 2011 IEEE.

Van Ly, D, Burgess, JK, Black, JL & Oliver, BG 1970, 'The Role Of Eicosanoids In The Deposition Of The Extracellular Matrix From Airway Cells', A69. LIPID-MEDIATED SIGNALING, American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado, American Thoracic Society.
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Walmsley, IA, Nunn, J, Langford, N, Reim, K, Michelberger, P & Champion, T 1970, 'Photonic quantum memories', Optics InfoBase Conference Papers.
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We survey the state of the art in photonic quantum memories, describing different approaches to the storage and manipulation of quantum light beams and pulses, and expected applications.

Wen, S-H, Zheng, F-Y & Shi, X-Y 1970, 'Improved Biocompatibility of Polyethyleneimine Modified with Acetamide, Hydroxyl, Carboxyl Groups and PEG Chains', 2011 INTERNATIONAL FORUM ON BIOMEDICAL TEXTILE MATERIALS, PROCEEDINGS, International Forum on Biomedical Textile Materials, DONGHUA UNIV PRESS, Donghua Univ, Shanghai, PEOPLES R CHINA, pp. 189-193.

Yang, L, Thomas, P & Stuart, BH 1970, 'DSC characterisation of thermally treated low density polyethylenes in a forensic context', Proceedings of the 3rd Joint Czech-Hungarian-Polish-Slovak Thermoanalytical Conference, Slovak Chemical Society, Stara Lesna, pp. 1-5.

Zhao, J, Piper, JA, Dawes, JM, Jin, D & Goldys, EM 1970, 'Mechanisms of size-dependent lifetime quenching in luminescent upconverting colloidal NaYF<inf>4</inf>:Yb, Er nanocrystals', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, Sydney, NSW, Australia, pp. 384-386.
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Upconversion decay rates in colloidal NaYF 4 :Yb, Er nanocrystals for biolabelling depend on nanoparticle size. Lifetime dependence on various quenching mechanisims is explained using rate equations to describe the evolution of upconverting green and red luminescence. © 2011 IEEE.

Zheng, C, Schwartz, S, Chapkin, R, Carroll, R & Ivanov, I 1970, 'Feature selection for high-dimensional integrated data', Proceedings of the 12th SIAM International Conference on Data Mining, SDM 2012, 2012 SIAM International Conference on Data Mining, SIAM, Anaheim, USA, pp. 1141-1150.
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Motivated by the problem of identifying correlations between genes or features of two related biological systems, we propose a model of \emph{feature selection} in which only a subset of the predictors $X_t$ are dependent on the multidimensional variate $Y$, and the remainder of the predictors constitute a 'noise set' $X_u$ independent of $Y$. Using Monte Carlo simulations, we investigated the relative performance of two methods: thresholding and singular-value decomposition, in combination with stochastic optimization to determine 'empirical bounds' on the small-sample accuracy of an asymptotic approximation. We demonstrate utility of the thresholding and SVD feature selection methods to with respect to a recent infant intestinal gene expression and metagenomics dataset.

Zinder, Y, Nicorovici, NA & Langtry, T 1970, 'Mathematica based platform for self-paced learning', International Conference on Technology in Mathematics Teaching (ICTMT10), International Conference on Technology in Mathematics Teaching, University of Portsmouth, Portsmouth, United Kingdom, pp. 203-208.
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One of the major challenges in teaching applied mathematics is the large amount of calculation involved in many practical mathematical methods. On one hand, mastering these methods requires students to gain experience in performing all steps of a calculation. This experience is crucial for gaining an understanding of the methods, their capabilities and limitations, and cannot be replaced by black box type commercial software which simply displays the results of calculations and gives no insight into the nature of the operations performed. On the other hand, the calculations involved in many modern mathematical methods are tedious and time consuming with fatal results caused by even minor computational mistakes. The advent of computer algebra systems such as Mathematica opened new horizons in teaching mathematics. The ability to perform symbolic calculations in combination with powerful graphics and programming capabilities makes it possible to develop software that provides students with the opportunity for step by step exploration of mathematical procedures. We present the results of an ongoing research project aimed at the development of a Mathematica based platform which allows academics to develop software for self-paced learning.

Petrou, K, Jimenez Denness, IM, Chartrand, KM, Ralph, PJ & Rasheed, A DEEDI Publication 2011, Seagrass Health Study - Phase II August Update, pp. 1-54, Cairns.

Smith, P, Cleary, A, Jones, M, Johnston, S, Bremner, P, Brown, JJ & Wiggins, R Home Office 2011, A feasibility study for a survey of migrants, pp. 1-46, United Kingdom.
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Overview. The Analysis, Reserach and knowledge management Directorate (ARK) in the UK Border Agency commissioned Ipsos MORI and the Institute of Education to undertake a feasibility study for a large-scale face-to-face survey of migrants in the UK. The purpose of the feasibility study was to inform the design of a survey of migrants, looking at how to design and interview statistically robust sample and the appropriate questions to adopt such a survey. The feasibility study involved: 1. workshops with the UK Border Agency and other stakeholders to identify survey requirements; 2. the development of a definition of 'migrant' for use in the survey 3. the development of a sample design; 4. testing fieldwork recruitment and data collection methods to be used; and 5. the development of a questionnaire, including cognitive testing in several languages This report focuses on the sampling and field methods aspects of the feasibility study. A separate technical report provides details on other issues, including question development. To inform the development of the survey methodology and the survey questionnaire discussion groups and depth interviews were undertaken with representatives of economic migrant communities and individuals working with refugees and asylum seekers in England and Scotland. Key issues surrounding survey objectives, terminology, and field methods were identified. A useable survey population definition was developed after stakeholder consultaion such that, for the purpose of this study: 'A migrant is defined as someone who arrived in the UK in 1990 or later, who was a non-UK national on entry, whose usual place of residence prior to entry was not in the UK, and who has lived in the country for at least three months (one month if an asylum seeker or refugee).' It was concluded that different types of migrants will require different sampling and screening methods. Asylum sekers could be sampled directly from administrative records but other migra...

Torpy, FR Horticulture Australia 2011, Indoor Plant Technology for Health and Environmental Sustainability, pp. 1-50, Sydney.
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Final research project report

Brennan, SB, Cozzi, PJC, McGowan, EM, Tran, NT & Martiniello-Wilks, RMW 2011, 'The expression and role of microRNAs found in prostate cancer exosomes'.

Du, K & Platen, E 2011, 'Three-Benchmarked Risk Minimization for Jump Diffusion Markets'.
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The paper discusses the problem of hedging not perfectly replicable contingent claims by using a benchmark, the numerraire portfolio, as reference unit. The proposed concept of benchmarked risk minimization generalizes classical risk minimization, pioneered by Follmer, Sondermann and Schweizer. The latter relies on a quadratic criterion, requesting the square integrability of contingent claims and the existence of an equivalent risk neutral probability measure. The proposed concept of benchmarked risk minimization avoids these restrictive assumptions. It employs the real world probability measure as pricing measure and identifies the minimal possible price for the hedgable part of a contingent claim. Furthermore, the resulting benchmarked profit and loss is only driven by nontraded uncertainty and forms a martingale that starts at zero. Benchmarked profit and losses, when pooled and sufficiently independent, become in total negligible. This property is highly desirable from a risk management point of view. It is making a symptotically benchmarked risk minimization the least expensive method for pricing and hedging for an increasing number of not fully replicable benchmarked contingent claims.

Hulley, H & Platen, E 2011, 'A Visual Criterion for Identifying Ito Diffusions as Martingales or Strict Local Martingales', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 263 Abstract: It is often important, in applications of stochastic calculus to financial modelling, to know whether a given local martingale is a martingale or a strict local martingale. We address this problem in the context of a time-homogenous diffusion process with a finite lower boundary, presented as the solution of a driftless stochastic differential equation. Our main theorem demonstrates that the question of whether or not this process is a martingale may be decided simply by examining the slope of a certain increasing function. Further results establish the connection between our theorem and other results in the literature, while a number of examples are provided to illustrate the use of our criterion.

Platen, E & Du, K 2011, 'Benchmarked Risk Minimization for Jump Diffusion Markets'.

Platen, E & Tappe, S 2011, 'Affine Realizations for Levy Driven Interest Rate Models with Real-World Forward Rate Dynamics'.
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We investigate the existence of affine realizations for interest rate term structure models driven by Levy processes. Using as numeraire the growth optimal portfolio, we model the interest rate term structure under the real-world probability measure, and hence, we do not need the existence of an equivalent risk-neutral probability measure. Furthermore, we include finite dimensional external factors, thus admitting a stochastic volatility structure.

Reimers, JR 2011, 'Computational Methods for Large Systems', Wiley.
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While its results normally complement the information obtained by chemical experiments, computer computations can in some cases predict unobserved chemical phenomena Electronic-Structure Computational Methods for Large Systems gives readers a simple description of modern electronic-structure techniques. It shows what techniques are pertinent for particular problems in biotechnology and nanotechnology and provides a balanced treatment of topics that teach strengths and weaknesses, appropriate and inappropriate methods. It's a book that will enhance the your calculating confidence and improve your ability to predict new effects and solve new problems. © 2011 John Wiley & Sons, Inc.