Publications

Fatima-Shad, K & Bradley, K 2012, Patch ClampTechnique for Looking at Serotonin Receptors in B103 Cell Lines: A Black Box Test.

Kumar, M & Reddy, CRK 2012, Oxidative stress tolerance mechanisms in marine macroalgae (Seaweeds): Oxidative stress in seaweeds., LAP Lambert Academic Publishing.

Perry, Y, Varlow, M, Dedousis-Wallace, A, Murrihy, RC, Ellis, DM & Kidman, A 2012, Moving forward : introduction to CBT for psychosis : a reference manual for mental health professional, 1, Foundation for Life Sciences and NSW Health, Sydney.

Azizur Rahman, M, Lim, R & Hasegawa, H 2012, 'Biodegradable chelating ligands for iron and arsenic bioavailability and uptake in rice (Oryza sativa L.)' in Ng, JC, Noller, BN, Naidu, R, Bundschuh, J & Bhattacharya, P (eds), Understanding the Geological and Medical Interface of Arsenic, CRC Press, AK Leiden, The Netherlands, pp. 394-396.
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Biodegradable chelating ligands Ethylenediaminedisuccinic acid (EDDS), Hydroxyimi-nodisuccinic acid (HIDS) and Methylglycindiacetic Acid (MGDA) for iron (Fe) and arsenic (As) bioavailability and uptake were investigated using hydroponic rice (Oryza sativa L.). The growth of rice seedlings decreased significantly (P < 0.05) with increasing pH. The highest growth was observed at pH 7 which was related to Fe concentrations in roots and shoots. As and Fe uptake in rice roots was increased by significantly (P < 0.05) by EDDS and HIDS, while their translocation to shoots were not influenced by the ligands. EDDS and HIDS were more efficient in As and Fe uptake than MGDA indicating that EDDS and HIDS would be good ligands for the increase of Fe uptake and Fe phytoextraction. © 2012 Taylor & Francis Group.

Bardet, N 2012, 'Introduction' in Segal, G & Goodman, DSG (eds), Towards Recovery in Pacific Asia, EDP Sciences, London UK, pp. 3-4.
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Bhosale, SV, Wilman, BE & Langford, SJ 2012, 'Nanostructured Materials Based on Core‐Substituted Naphthalene Diimides' in Molecules at Work, Wiley, pp. 97-111.
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Bhosale, SV, Wilman, BE & Langford, SJ 2012, 'Yoctoliter‐Sized Vessels as Potential Biological Models' in Molecules at Work, Wiley, pp. 1-12.
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Bohic, S, Hare, D, Daoust, A, Cloetens, P & Barbier, EL 2012, 'Spatially resolved imaging methods to probe metals in the brain: from subcellular to organ level' in Linert, W & Kozlowski, H (eds), Metal Ions in Neurological Systems, Springer Vienna, Vienna, pp. 211-222.
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Very little is known about the subcellular distribution of metal ions in cells. Some metals such as zinc, copper, and iron are essential and play an important role in the cell metabolism. Dysfunctions in this delicate housekeeping may be at the origin of major diseases. There is also a prevalent use of metals in a wide range of diagnostic agents and drugs for the diagnosis or treatment of a variety of disorders. This is becoming more and more of a concern in the field of nanomedicine with the increasing development and use of nanoparticles, which are suspected of causing adverse effects on cells and organ tissues and particularly the brain. Various analytical methods are developing into well-suited sub-micrometer analytical tools for addressing new problems when studying the role of metals in the brain. In the present review, we describe the possibilities and some current applications offered by three major techniques that cover imaging of metals from subcellular to organ level, namely synchrotron-based X-ray microspectroscopy, laser ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS) and, less thoroughly addressed, the capabilities of magnetic resonance imaging (MRI) for in vivo imaging of metals in the brain

Booth, DJ, Figueira, WF, Jenkins, G & Lenanton, R 2012, 'Temperate Fish' in Poloczanska, ES, Hobday, AJ & Richardson, AJ (eds), A Marine Climate Change Impacts and Adaptation Report Card for Australia 2012, National Climate Change Adaptation Research Facility, Australia, pp. 307-322.
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Since the first report card, little on-the-ground research on range shifts of temperate fishes has been reported. Several reviews of range shifts of Australian coastal fishes (Booth et al 2011 and Madin et al. 2012) have highlighted approaches for collecting and applying the data. Research in Western Australia (e.g. Langlois et al 2010, Cheung et al. 2011) has shown that many species of groundfish and reef fish are distributed latitudinally based on clear water temperature gradients, suggesting that climate-change SST increases/differences will significantly affect ranges. Langlois et al. 2010 conclude that the old climatically buffered, oligotrophic seascape of southwestern Australia has provided a simple system in which the consistent influence of Temperate Fish 308 www.oceanclimatechange.org.au physiological gradients on the abundance and distribution of fish species can be observed'.

Callaghan, R, George, AM & Kerr, ID 2012, '8.8 Molecular Aspects of the Translocation Process by ABC Proteins' in Ferguson, S (ed), Comprehensive Biophysics, Elsevier, Oxford, pp. 145-173.
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Castro Aguilar, JL, Smith, G, Gentle, AR & Chen, D 2012, 'Making cool roofs compatible with low heating and cooling loads' in Mendez-Vilas, A, BrownWalker & Raton, B (eds), Fuelling the Future: Advances in Science and Technologies for Energy Generation, Transmission and St, Brown Walker Press, United States, pp. 530-534.

Cranfield, CG, Kloda, A, Nomura, T, Petrov, E, Battle, A, Constantine, M & Martinac, B 2012, 'Force from Lipids: A Multidisciplinary Approach to Study Bacterial Mechanosensitive Ion Channels' in Kamkin & Lozinsky (eds), Mechanically Gated Channels and their Regulation, Springer Netherlands, USA, pp. 1-33.
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Gale, PA & Haynes, CJE 2012, 'Anion Receptors Containing Heterocyclic Rings', Wiley.
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Abstract Heterocyclic groups can play key roles as hydrogen bond donors and charged components in a wide range of anion receptors. This chapter reviews the roles the heterocycles play in anion recognition, covering pyrrole‐based systems (both macrocyclic and acyclic, including synthetic systems and natural products such as prodigiosin), indole‐based receptors, and foldamers‐ and charged‐imidazolium‐based hosts. The chemistry of pyridine‐ and quinoline‐based receptors, including metal‐templated systems that employ transition metals to assemble simple organic components, and the role of bipyridinium in anion complexation and sensing are also reviewed. Finally, the chemistry of 1,2,3‐triazoles as components of hosts that use CH· · ·anion hydrogen bonds to complex anionic guests is examined.

Goerigk, L, Falklöf, O, Collyer, CA & Reimers, JR 2012, 'First Steps Towards Quantum Refinement of Protein X-Ray Structures' in Zeng, J, Zhang, R & Treutlein, HR (eds), Quantum Simulations of Materials and Biological Systems, Springer Netherlands, Dordrecht, pp. 87-120.
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© Springer Science+Business Media Dordrecht 2012. Using standard force-fields and empirical restraints in protein refinement has proven to be a key tool in X-ray protein structure determination. However, detailed analysis of the resulting structural models sometimes reveals chemically unreasonable features, originating in many cases from the representation of multiple configurations using some averaged structure. Quantum chemical methods and computational capabilities have now come to the point at which full quantum refinement of protein structure is feasible, but only complete (meaning real ensembles of) chemical structures may be considered. Density functional theory (DFT) is currently the most popular quantum chemical approach but a large number of approximate functionals are available and most of these do not correctly describe the biologically important London dispersion effects. For small molecules it has been shown that efficient dispersion corrections can overcome this problem, without additional computational effort. We show that this is also the case using linear-scaling dispersion-corrected DFT to refine protein X-ray structures. The study considers the effect on the R factors (i.e. the agreement between modeled and observed diffraction data) when DFT is used to optimize atomic coordinates from the traditionally refined X-ray structure of triclinic hen egg white lysozyme, resolved to 0.65… This particular system was chosen as an ensemble of 8 chemically realistic structures, which are used for the representation of observed structural variability within the crystallographic unit cell and which has been recently published [Falklöf et al. in Theor. Chem. Acc. 131:1076, 2012]. Optimizing only isolated residues within the protein for which all neighboring functional groups are fully identified, we show that in many cases dispersion-corrected DFT (and also Hartree-Fock) optimization competes with conventional refinement techniques. Significant cor...

Heather, A & McGrath, K 2012, 'Cardiovascular disease and inflammation' in Garg, ML & Wood, LG (eds), Nutrition and Physical Activity in Inflammatory Diseases, CABI, United Kingdom, pp. 243-259.

Huete, A 2012, 'Soil Properties' in Njoku Eni, G (ed), Encyclopedia of Remote Sensing, Springer, Germany, pp. 1-6.
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Soils. Soils are three-dimensional living bodies, with spatially variable biologic, physical, and chemical properties, that form the outer skin of the Earths terrestrial surface. Soil formation. Soils form slowly over time and develop distinguishing properties as a function of climate, geologic and organic parent materials, topography, time, vegetation type, and land use history. Soil profile. The vertical depth of a soil body varies from a few centimeters up to several meters and contain a series of soil horizons. The surface layers are termed the O (organic) or A (mineral) horizons, while a lower zone of clay accumulation is the B horizon, and the lowest zone that interfaces with the parent material is the C horizon.

Kordzakhia, N, Novikov, A & Tsitsiashvili, G 2012, 'On ruin probabilities in risk models with interest rate' in Mathematical and Statistical Methods for Actuarial Sciences and Finance, Springer Milan, pp. 245-253.
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Larkum, AWD 2012, 'Harvesting solar energy through natural or artificial photosynthesis: Scientific, social, political and economic implications' in Wydrzynski, TJ & Hillier, W (eds), Molecular Solar Fuels, Royal Society of Chemistry, United Kingdom, pp. 1-19.
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Natural photosynthesis is an inherently inefficient process that developed millions or even billions of years ago. Thus present systems for harvesting solar energy in the form of organic carbon are inefficient compared with solar photovoltaic cells. The highest productivities are about 1% compared with ~10% for solar cells. Somewhat higher rates can be envisaged in the future but only through the use of a high solar footprint (the area of the Earth's surface needed to sustain a certain energy output), i.e. by using extra energy, which in a long-term sustainable world can come only from solar energy. While bioenergy production from algae may be lead to even greater efficiencies in the future it seems that this will only come about by an even higher solar footprint. Additionally, while bioenergy production may seem to be favourable in terms of carbon footprint, in practice there are several unfavourable outcomes. Further, bioenergy production immediately conflicts with use of the Earth's surface for food production and/or the need to maintain biodiversity. Thus artificial photosynthesis with very much higher expected efficiencies than natural photosynthesis is a worthwhile goal, in that it could potentially compete in efficiency with energy production by photovoltaic cells.

Lobo, C & Toth, M 2012, 'Continuum modeling of electron beam induced processes' in Utke, I, Moshkalev, SA & Russell, P (eds), Nanofabrication Using Focused Ion and Electron Beams: Principles and Applications, Oxford University Press, New York, USA, pp. 286-320.
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Gas-mediated focused electron beam induced etching (FEBIE) and deposition (FEBID), collectively referred to here as FEBIED, permit nanoscale modification of surface material via chemical reactions involving electron-dissociated precursor molecules. Electrons crossing the solid-vacuum interface usually possess a wide range of energies, are capable of breaking most bonds in typical precursor adsorbates and dissociation products, and can therefore generate a wide range of mobile, chemically active species. Adsorption, desorption, diffusion, and dissociation of these species all contribute to the development of nanostructures fabricated by FEBIED processes. Furthermore, these nanostructures are often electron-sensitive, and thus their structure evolves during deposition. The wide range of processes behind FEBIED yields very complex behavior that is yet to be modeled realistically fifty years after Christy first proposed a simple analytical model of deposition induced by a broad (defocused) electron beam [1]. A complete description of FEBIED requires a realistic model of electron-gas and electron-solid interactions, the spatial and energy distributions of secondary and backscattered electrons, electron interactions with adsorbates, and the behavior of adsorbates and dissociation products at the solid-vacuum interface.

Marsh, J, Gloeckl, S, Tyndall, J & Huston, WM 2012, 'The role of HTRA as a chaperone and protease in bacterial pathogenesis' in Boulanger, A & Blanc, M (eds), Bacterial Pathogens: Virulence Mechanisms, Diagnosis and Management, Nova Science Publishers, Inc, Happauge, New York, pp. 117-164.
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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. © 2012 Nova Science Publishers, Inc.

Platen, E & Rendek, RJ 2012, 'Simulation of diversified portfolios in a continuous financial markets' in Zhang, T & Zhou, X (eds), Stochastic Analysis and Applications to Finance: Essays in Honour of Jia-an Yan, World Scientific Publishing, USA, pp. 385-410.

Platen, E & Semmler, W 2012, 'A dynamic portfolio approach to asset markets and monetary policy' in Cohen, SN, Madan, D, Siu, TK & Yang, H (eds), Advances in Statistics, Probability and Actuarial Science: Stochastic Processes, Finance and Control, World Scientific Publishing, USA, pp. 347-373.

Robbins, RL & Booth, DJ 2012, 'Seasonal Sexual and Size Segregation of White Sharks, Carcharodon carcharias, at the Neptune Islands, South Australia' in Global Perspectives on the Biology and Life History of the White Shark, CRC Press, pp. 312-325.
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The seasonal temporal sexual and size segregation of White Sharks, Carcharodon carcharias, at the Neptune Islands, South Australia, is described. Under baited conditions, using chum to attract sharks to the vessel, the sex and size of White Sharks were recorded over a 3-yr. period from April 2001 to February 2004. Sexual and size segregation was observed in this species. There was a high degree of interannual variability in the data with the number of subadult males increasing and mature males decreasing over the 3 yrs. of the study. An overall trend was observed for larger White Sharks to be recorded in the winter/spring months (June to September) and smaller sharks in other months. Sea-surface temperature appeared to be related to sexual and size segregation in this species. It was found to be negatively related to subadult and mature male numbers, whereas no significant relationships with temperature were found for females of either size grouping, although female abundance tended to cluster toward the higher temperature ranges (15.7-18.1°C). The significantly lower temperatures in 2003 may explain the absence of females in this year. It is speculated that females may favor warmer waters to promote and accelerate embryonic development of young as a result of comparatively increased internal core body temperatures.

Robinson, MW, Dalton, JP, O'Neill, SM & Donnelly, SM 2012, 'Mechanisms of Immune Modulation by Fasciola hepatica : Importance for Vaccine Development and for Novel Immunotherapeutics' in Caffrey, CR (ed), Parasitic Helminths: Targets, Screens, Drugs and Vaccines, Wiley, Germany, pp. 451-463.
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The liver fluke Fasciola hepatica can live for long periods in its definitive mammalian host. This longevity is related to the parasite's ability to modulate host immune responses to benefit its survival (i.e., suppression of Th1/Th17 responses and the promotion of strong Th2/Treg-mediated responses). Various reports indicate that this immune regulation may reduce the capacity of animals to resist other bystander infections (e.g., F. hepatica-infected mice exhibit reduced protective immune responses to the respiratory bacterium, Bordetella pertussis). Experiments in cattle infected with F. hepatica revealed reductions in interferon-γ responses to coinfections with Mycobacterium bovis. Molecules secreted by the parasite such as cathepsin L cysteine peptidases, the antioxidant peroxiredoxin, and a cathelicidin-like defense molecule play central roles in manipulating the function of host innate immune cells, and thus the development of protective adaptive immune responses. While these molecules influence innate immune cells in distinct ways, they likely function in concert to establish the potent Th2/Treg-mediated immune environment in the host. Vaccines that prevent the action of these immunomodulatory molecules may not only protect animals against liver fluke disease, but reduce their susceptibility to coincident parasitic or microbial infections. Taking a broader view, understanding how the liver fluke influences host immunity via specific cell surface receptors and intracellular signaling pathways could reveal strategies to selectively suppress certain inflammatory processes, and eventually lead to immunotherapeutic treatments for conditions such as arthritis, inflammatory bowel disease, and diabetes. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA.

Ursin, R, Langford, N & Poppe, A 2012, 'Quantum key distribution' in Advanced Optical Wireless Communication Systems, Cambridge University Press, pp. 305-327.
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© Cambridge University Press 2012. Motivation The ability to guarantee security and privacy in communication are critical factors in encouraging people to accept and trust new tools and methods for today's information-based society (e.g. in eCommerce or eHealth) and for future services (e.g. eGovernment, eVoting). Cybercrime already hinders these new possibilities by creating widespread mistrust in these new services. Another problem is that a (perhaps unpublicized) break-through in mathematics or computer science could completely compromise current state-of-the-art encryption methods overnight, even those which are the basis of all existing internet banking transactions. This is because the security of cutting-edge public-key cryptography (conventional cryptography) relies on the computational difficulty of certain mathematical tasks, meaning that conventional cryptography alone can neither provide any evidence of eavesdropping nor guarantee strong security. The trend towards faster electronics provides the ability to handle longer keys, thus providing better security, but also increases the possibility to break keys. This also has another worrying effect: even using today's most advanced available security technology to protect data during communication with best practice and without making any mistakes, the ongoing improvements in technology (which hence require longer key lengths to ensure security) mean that today's transmitted data will not be secure for more than a few years. Thus, while encrypted data might be safe today, it can still be stored by the adversary now and then broken later on once the future technology has caught up with today's encryption. Alternatively, modern quantum cryptography has created a new paradigm for cryptographic communication, which provides strong, long-term security and incontrovertible evidence of any attempted eavesdropping which is based on theoretically and experimentally proven laws of nature.

Wang, B, Ranjbartoreh, AR & Wang, G 2012, 'Controlled size and shape of graphene and its application in li-ion battery' in Ru-Shi Liu (ed), Controlled Nanofabrication: Advances and Applications, Pan Stanford Publishing, USA, pp. 623-656.
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Graphene is one-atom-thick film of carbon atoms packed in honeycomb structure with exceptional electrical, thermal, optical, and mechanical properties, which opened up new horizons for next generation nanotechnology-based devices. Two University of Manchester scientists, Andre Geim and Konstantin Novoselov, were awarded the 2010 Nobel Prize in physics 'for groundbreaking experiments regarding the two-dimensional material graphene'. This chapter reviews the brief history and development of graphene, considers its properties, characterizations and the synthesis methods, and provides a few examples for its advanced application in lithium-ion battery. © 2013 Pan Stanford Publishing Pte. Ltd. All rights reserved.

Zaslawski, C 2012, 'An Evidence-Based Review of Acupuncture as an Adjunctive Therapy in Comprehensive Cancer Care' in Soh, KS, Kang, KA & Harrison, DK (eds), The Primo Vascular System, Springer New York, United States, pp. 319-325.
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The use of acupuncture as an adjunctive therapy for cancer has been increasing over several decades. While there has only been one Cochrane review completed in this area, with another at the protocol stage, several high-quality RCTs have been published in the last decade. These studies have focused on the effect of acupuncture on managing many of the disabling symptoms associated with radiation therapy, chemotherapy or surgical intervention. These include conditions such as nausea, pain control, xerostomia and fatigue. This chapter will report on the current evidence for using acupuncture for these conditions as well as some of the problems associated with designing and implementing a rigorous acupuncture clinical trial

Zaslawski, CJ & Lee, MS 2012, 'International standardization of East Asian medicine: the quest for standardization' in Scheid, V & MacPherson, H (eds), Integrating East Asian Medicine into Contemporary Healthcare, Elsevier, London, pp. 89-104.

Abdul, JM, Colville, A, Lim, R, Vigneswaran, S & Kandasamy, J 2012, 'Use of duckweed (Lemna disperma) to assess the phytotoxicity of the products of Fenton oxidation of metsulfuron methyl', Ecotoxicology and Environmental Safety, vol. 83, pp. 89-95.
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Because of pressure on water supplies world-wide, there is increasing interest in methods of remediating contaminated ground waters. However, with some remediation processes, the breakdown products are more toxic than the original contaminant. Organic matter and salinity may also influence degradation efficiency. This study tested the efficiency of Fenton oxidation in degrading the sulfonylurea herbicide metsulfuron methyl (MeS), and tested the reaction products for phytotoxicity with the Lemna (duckweed) bioassay. The efficiency of degradation by Fentonâs reagent (Fe2þ ¼0.09 mM; H2O2¼1.76mM, 4 h) decreased with increasing initial MeS concentration, from 98% with 5 mg/L MeS, to 63% with 70 mg/L MeS. Addition of NaCl (10 mM) and organic matter (humic acid at 0.2 and 2.0 mg C/L as Total Organic Carbon) reduced the efficiency of degradation at low initial MeS concentrations (5 and 10mg/L), but had no effect at high concentrations. The residual Fentonâs reagent after Fentonâs oxidation was toxic to Lemna. After removal of residual iron and H2O2, the measured toxicity to Lemna in the treated samples could be explained by the concentrations of MeS as measured by HPLC/UV detection, so there was no evidence of additional toxicity or amelioration due to the by-products or formulation materials.

Afzal, S, Daoud, WA & Langford, SJ 2012, 'Self-cleaning cotton by porphyrin-sensitized visible-light photocatalysis', Journal of Materials Chemistry, vol. 22, no. 9, pp. 4083-4083.
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Aharonovich, I & Shenderova, O 2012, 'Brilliant explosions', NATURE MATERIALS, vol. 11, no. 12, pp. 996-996.
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Aharonovich, I, Lee, JC, Magyar, AP, Buckley, BB, Yale, CG, Awschalom, DD & Hu, EL 2012, 'Homoepitaxial Growth of Single Crystal Diamond Membranes for Quantum Information Processing', ADVANCED MATERIALS, vol. 24, no. 10, pp. OP54-OP59.
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Alahyarizadeh, G 2012, 'Performance enhancement of deep violet indium gallium nitride double quantum well lasers using delta barrier close to electron blocking layer', Journal of Nanophotonics, vol. 6, no. 1, pp. 063514-063514.
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Alahyarizadeh, G, Aghajani, H, Mahmodi, H, Rahmani, R & Hassan, Z 2012, 'Analytical and visual modeling of InGaN/GaN single quantum well laser based on rate equations', Optics & Laser Technology, vol. 44, no. 1, pp. 12-20.
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Alahyarizadeh, G, Ghazai, AJ, Rahmani, R, Mahmodi, H & Hassan, Z 2012, 'Simulation and optimization of deep violet InGaN double quantum well laser', Optics Communications, vol. 285, no. 5, pp. 746-750.
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Allen, JC, Seidel, P, Schlosser, T, Ramsay, EE, Ge, Q & Ammit, AJ 2012, 'Cyclin D1 in ASM Cells from Asthmatics Is Insensitive to Corticosteroid Inhibition', Journal of Allergy, vol. 2012, pp. 1-6.
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Hyperplasia of airway smooth muscle (ASM) is a feature of the remodelled airway in asthmatics. We examined the antiproliferative effectiveness of the corticosteroid dexamethasone on expression of the key regulator of G1 cell cycle progression—cyclin D1—in ASM cells from nonasthmatics and asthmatics stimulated with the mitogen platelet-derived growth factor BB. While cyclin D1 mRNA and protein expression were repressed in cells from nonasthmatics in contrast, cyclin D1 expression in asthmatics was resistant to inhibition by dexamethasone. This was independent of a repressive effect on glucocorticoid receptor translocation. Our results corroborate evidence demonstrating that corticosteroids inhibit mitogen-induced proliferation only in ASM cells from subjects without asthma and suggest that there are corticosteroid-insensitive proliferative pathways in asthmatics.

Allen-Hall, A & McNevin, D 2012, 'Human tissue preservation for disaster victim identification (DVI) in tropical climates', Forensic Science International: Genetics, vol. 6, no. 5, pp. 653-657.
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Allsop, DJ, Copeland, J, Norberg, MM, Fu, S, Molnar, A, Lewis, J & Budney, AJ 2012, 'Quantifying the Clinical Significance of Cannabis Withdrawal', PLOS ONE, vol. 7, no. 9, p. e44864.
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Background and Aims: Questions over the clinical significance of cannabis withdrawal have hindered its inclusion as a discrete cannabis induced psychiatric condition in the Diagnostic and Statistical Manual of Mental Disorders (DSM IV). This study aims to quantify functional impairment to normal daily activities from cannabis withdrawal, and looks at the factors predicting functional impairment. In addition the study tests the influence of functional impairment from cannabis withdrawal on cannabis use during and after an abstinence attempt. Methods and Results: A volunteer sample of 49 non-treatment seeking cannabis users who met DSM-IV criteria for dependence provided daily withdrawal-related functional impairment scores during a one-week baseline phase and two weeks of monitored abstinence from cannabis with a one month follow up. Functional impairment from withdrawal symptoms was strongly associated with symptom severity (p = 0.0001). Participants with more severe cannabis dependence before the abstinence attempt reported greater functional impairment from cannabis withdrawal (p = 0.03). Relapse to cannabis use during the abstinence period was associated with greater functional impairment from a subset of withdrawal symptoms in high dependence users. Higher levels of functional impairment during the abstinence attempt predicted higher levels of cannabis use at one month follow up (p = 0.001). Conclusions: Cannabis withdrawal is clinically significant because it is associated with functional impairment to normal daily activities, as well as relapse to cannabis use. Sample size in the relapse group was small and the use of a non-treatment seeking population requires findings to be replicated in clinical samples. Tailoring treatments to target withdrawal symptoms contributing to functional impairment during a quit attempt may improve treatment outcomes. © 2012 Allsop et al.

Alrashdan, YA, Alkhouri, H, Chen, E, Lalor, DJ, Poniris, M, Henness, S, Brightling, CE, Burgess, JK, Armour, CL, Ammit, AJ & Margaret Hughes, J 2012, 'Asthmatic airway smooth muscle CXCL10 production: mitogen-activated protein kinase JNK involvement', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 302, no. 10, pp. L1118-L1127.
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CXCL10 (IP10) is involved in mast cell migration to airway smooth muscle (ASM) bundles in asthma. We aimed to investigate the role of cytokine-induced MAPK activation in CXCL10 production by ASM cells from people with and without asthma. Confluent growth-arrested ASM cells were treated with inhibitors of the MAPKs ERK, p38, and JNK and transcription factor NF-κB, or vehicle, and stimulated with IL-1β, TNF-α, or IFN-γ, alone or combined (cytomix). CXCL10 mRNA and protein, JNK, NF-κB p65 phosphorylation, and Iκ-Bα protein degradation were assessed using real-time PCR, ELISA, and immunoblotting, respectively. Cytomix, IL-1β, and TNF-α induced CXCL10 mRNA expression more rapidly in asthmatic than nonasthmatic ASM cells. IL-1β and/or TNF-α combined with IFN-γ synergistically increased asthmatic ASM cell CXCL10 release. Inhibitor effects were similar in asthmatic and nonasthmatic cells, but cytomix-induced release was least affected, with only JNK and NF-κB inhibitors halving it. Notably, JNK phosphorylation was markedly less in asthmatic compared with nonasthmatic cells. However, in both, the JNK inhibitor SP600125 reduced JNK phosphorylation and CXCL10 mRNA levels but did not affect CXCL10 mRNA stability or Iκ-Bα degradation. Together, the JNK and NF-κB inhibitors completely inhibited their CXCL10 release. We concluded that, in asthmatic compared with nonasthmatic ASM cells, JNK activation was reduced and CXCL10 gene expression was more rapid following cytomix stimulation. However, in both, JNK activation did not regulate early events leading to NF-κB activation. Thus JNK and NF-κB provide independent therapeutic targets for limiting CXCL10 production and mast cell migration to the ASM in asthma.

Angrisano, F, Riglar, DT, Sturm, A, Volz, JC, Delves, MJ, Zuccala, ES, Turnbull, L, Dekiwadia, C, Olshina, MA, Marapana, DS, Wong, W, Mollard, V, Bradin, CH, Tonkin, CJ, Gunning, PW, Ralph, SA, Whitchurch, CB, Sinden, RE, Cowman, AF, McFadden, GI & Baum, J 2012, 'Spatial Localisation of Actin Filaments across Developmental Stages of the Malaria Parasite', PLOS ONE, vol. 7, no. 2, p. e32188.
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Actin dynamics have been implicated in a variety of developmental processes during the malaria parasite lifecycle. Parasite motility, in particular, is thought to critically depend on an actomyosin motor located in the outer pellicle of the parasite cell. Efforts to understand the diverse roles actin plays have, however, been hampered by an inability to detect microfilaments under native conditions. To visualise the spatial dynamics of actin we generated a parasite-specific actin antibody that shows preferential recognition of filamentous actin and applied this tool to different lifecycle stages (merozoites, sporozoites and ookinetes) of the human and mouse malaria parasite species Plasmodium falciparum and P. berghei along with tachyzoites from the related apicomplexan parasite Toxoplasma gondii. Actin filament distribution was found associated with three core compartments: the nuclear periphery, pellicular membranes of motile or invasive parasite forms and in a ring-like distribution at the tight junction during merozoite invasion of erythrocytes in both human and mouse malaria parasites. Localisation at the nuclear periphery is consistent with an emerging role of actin in facilitating parasite gene regulation. During invasion, we show that the actin ring at the parasite-host cell tight junction is dependent on dynamic filament turnover. Super-resolution imaging places this ring posterior to, and not concentric with, the junction marker rhoptry neck protein 4. This implies motor force relies on the engagement of dynamic microfilaments at zones of traction, though not necessarily directly through receptor-ligand interactions at sites of adhesion during invasion. Combined, these observations extend current understanding of the diverse roles actin plays in malaria parasite development and apicomplexan cell motility, in particular refining understanding on the linkage of the internal parasite gliding motor with the extra-cellular milieu. © 2012 Angrisano et al.

Angus, K, Thomas, P & Guerbois, J-P 2012, 'Synthesis and characterisation of cobaltite and ferrite spinels using thermogravimetric analysis and X-ray crystallography', Journal of Thermal Analysis and Calorimetry, vol. 108, no. 2, pp. 449-452.
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The synthesis for a series of ferrite (M IIFe 2O 4) and cobaltite (M IICo 2O 4) spinels was investigated where M II is Mg, Co, Ni, Cu or Zn. The ferrites were prepared at a calcination temperature of 800 °C; the cobaltites at 500 °C. TG-MS indicated that reduction of CoIII to CoII occurs at ca. 800 °C, hence, the lower calcination temperature. For both the ferrites and the cobaltites, the evolution of water and CO 2 during the calcination suggests the presence of both species in the precipitates. The observed mass losses indicated that the precursor basic carbonate precipitates for the cobaltite synthesis were predominantly carbonate, while the precursor basic carbonate precipitates for ferrite synthesis were predominantly hydroxide in character. XRD data showed successful synthesis of the ferrites with minimal contamination from the parent oxides, while the cobaltites were observed to be predominantly of the spinel structure. © Akadémiai Kiadó, Budapest, Hungary 2011.

Asatryan, AA, Botten, LC, Byrne, MA, Freilikher, VD, Gredeskul, SA, Shadrivov, IV, McPhedran, RC & Kivshar, YS 2012, 'Transmission and Anderson localization in dispersive metamaterials', PHYSICAL REVIEW B, vol. 85, no. 4, pp. 1-11.
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Comprehensive theoretical and numerical studies of the effects of dispersion and absorption on the Anderson localization of classical waves in weakly disordered, one-dimensional stacks composed of dispersive metamaterials and normal materials are presented. An asymptotic analysis for studying the effects of dispersion and absorption is developed. It is shown that the localization of waves in random stacks composed entirely of either metamaterial or normal dielectric layers is completely suppressed at frequencies where the magnetic permeability or the dielectric permittivity is zero. In mixed stacks of alternating layers of normal and metamaterials with disorder present in either the dielectric permittivity or the magnetic permeability, localization is substantially suppressed not only at these frequencies but in essentially wider frequency ranges. When both the permittivity and the permeability are random, the localization behavior is similar to that in monotype stacks. At the transition from a double negative metamaterial to a single negative metamaterial, the transmission length drops dramatically in a manner that might be useful in optical switching. Polarization effects are also considered and it is shown that localization is suppressed at the Brewster angle, in a manner dependent on both the polarization and the nature of the disorder. Theoretical predictions are in excellent agreement with numerical calculations. © 2012 American Physical Society.

Ayres, DL, Darling, A, Zwickl, DJ, Beerli, P, Holder, MT, Lewis, PO, Huelsenbeck, JP, Ronquist, F, Swofford, DL, Cummings, MP, Rambaut, A & Suchard, MA 2012, 'BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics', Systematic Biology, vol. 61, no. 1, pp. 170-173.
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Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. © 2011 The Author(s).

Bai, S, Chen, S, Shen, X, Zhu, G & Wang, G 2012, 'Nanocomposites of hematite (alpha-Fe2O3) nanospindles with crumpled reduced graphene oxide nanosheets as high-performance anode material for lithium-ion batteries', RSC ADVANCES, vol. 2, no. 29, pp. 10977-10984.
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Nanocomposites of Fe2O3 nanospindles with crumpled reduced graphene oxide (RGO) nanosheets were prepared using a facile solvothermal synthesis method. The RGO-Fe2O3 nanocomposite with about 24.4 wt% RGO demonstrated an excellent electrochemical performance as a promising anode material for lithium-ion batteries (LIBs), which achieved a high reversible capacity of 969 mA h g-1 after 100 cycles at a current density of 100 mA g-1 (0.1 C). Furthermore, it also exhibited a large capacity of 336 mA h g-1 after 100 cycles at the high rate of 5 C. The cycling performance and reversible capacities of the RGO-Fe 2O3 composites were much better than those of bare Fe 2O3 nanospindles and pure RGO nanosheets, as well as previously reported RGO-Fe2O3 nanocomposites. The enhanced performance towards lithium storage can be ascribed to the crumpled RGO nanosheets, which may act as efficient volume buffer and electron conductor in the composites. The strategy proposed here could be extended to produce other nanocomposites based on crumpled graphene nanosheets for various applications. © 2012 The Royal Society of Chemistry.

Baker, AC & Murray, BR 2012, 'Seasonal intrusion of litterfall from non-native pine plantations into surrounding native woodland: Implications for management of an invasive plantation species', FOREST ECOLOGY AND MANAGEMENT, vol. 277, pp. 25-37.
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Radiata pine (. Pinus radiata) is commonly grown throughout the world as a major plantation species. Non-native radiata pine plantations are often established as monocultures amongst large tracts of remnant native vegetation. While the direct impacts on native biodiversity of such vegetation replacement have been well documented, much less is known about how plant litterfall from such plantations influences ecosystem dynamics beyond the confines of the plantation limits. In this study, we assessed the inputs of plant litterfall from radiata pine plantations into surrounding native woodland vegetation over a two-year period in south-eastern Australia. We found that pine litter was a significant and even dominant component of litterfall at certain times of the year, typically autumn and winter, when quantities of pine needles falling were up to three times the fall of native leaves. Pine litter was found to be lower in quality than native litter, containing less carbon (C) and nitrogen (N) and having a higher C:N ratio than native litter. Although the comparatively larger inputs of pine litter resulted in C and N inputs that were 2-3 times those of native litter during some seasons, the influx of low-quality pine litter is likely to decompose slowly and immobilise N, thereby limiting the availability of N for plant growth in the long term. The intrusion of large quantities of pine litter into native eucalypt woodland may have a suite of further short and long term impacts on native biodiversity through a number of mechanisms including alteration of leaf-litter invertebrate communities, increased fire intensity and changes in microclimate. These impacts may be alleviated by preventing pine litter entering woodland communities through the use of modified buffer zones and by employing appropriate plantation design. We discuss the merits and shortfalls of various options available to land mangers to minimise pine-litter intrusion into adjacent native woodland...

Baldi, DL, Higginson, EE, Hocking, DM, Praszkier, J, Cavaliere, R, James, CE, Bennett-Wood, V, Azzopardi, KI, Turnbull, L, Lithgow, T, Robins-Browne, RM, Whitchurch, CB & Tauschek, M 2012, 'The Type II Secretion System and Its Ubiquitous Lipoprotein Substrate, SslE, Are Required for Biofilm Formation and Virulence of Enteropathogenic Escherichia coli', INFECTION AND IMMUNITY, vol. 80, no. 6, pp. 2042-2052.
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Enteropathogenic Escherichia coli (EPEC) is a major cause of diarrhea in infants in developing countries. We have identified a functional type II secretion system (T2SS) in EPEC that is homologous to the pathway responsible for the secretion of heat-labile enterotoxin by enterotoxigenic E. coli. The wild-type EPEC T2SS was able to secrete a heat-labile enterotoxin reporter, but an isogenic T2SS mutant could not. We showed that the major substrate of the T2SS in EPEC is SslE, an outer membrane lipoprotein (formerly known as YghJ), and that a functional T2SS is essential for biofilm formation by EPEC. T2SS and SslE mutants were arrested at the microcolony stage of biofilm formation, suggesting that the T2SS is involved in the development of mature biofilms and that SslE is a dominant effector of biofilm development. Moreover, the T2SS was required for virulence, as infection of rabbits with a rabbit-specific EPEC strain carrying a mutation in either the T2SS or SslE resulted in significantly reduced intestinal colonization and milder disease. © 2012, American Society for Microbiology.

Banik, GR, Birch, D, Stark, D & Ellis, JT 2012, 'A microscopic description and ultrastructural characterisation of Dientamoeba fragilis: An emerging cause of human enteric disease', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 42, no. 2, pp. 139-153.
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Dientamoeba fragilis is a pathogenic trichomonad found in the gastrointestinal tract of humans and is implicated as a cause of diarrhoea. Despite its discovery over a century ago, there has been no recent thorough description of this parasite by microscopy. Scanning electron microscopy, transmission electron microscopy, confocal and light microscopy were therefore used to characterise D. fragilis populations growing in xenic culture. Two different populations smooth and ruffled cells were identifiable by scanning electron microscopy. No flagella, pelta structures, undulating membrane or pseudocyst-like forms were present. The organelles in D. fragilis were analysed by transmission electron microscopy; like Trichomonas and Histomonas, D. fragilis contains hydrogenosomes that presumably represent the site of anaerobic respiration. The nuclear morphology of D. fragilis trophozoites grown in vitro and trophozoites from clinical isolates were also compared by confocal microscopy and light microscopy. The majority of cells grown in culture were mononucleate while most cells in permanent stained faecal smears were binucleate. The two nuclei of D. fragilis are morphologically indistinguishable and contain equivalent amounts of DNA as determined by DAPI staining. The approximate cell and nuclear volume of four isolates of D. fragilis were measured and shown to be comparable to other trichomonads. In addition, the discovery of a virus-like particle is reported, to our knowledge for the first time in D. fragilis. This study therefore provides extensive and novel details of the ultrastructure of a neglected protozoan parasite that is an emerging cause of human disease.

Baraket, M, Oliver, BGG, Burgess, JK, Lim, S, King, GG & Black, JL 2012, 'Is low dose inhaled corticosteroid therapy as effective for inflammation and remodeling in asthma? A randomized, parallel group study', Respiratory Research, vol. 13, no. 1, pp. 11-11.
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Background: While most of the clinical benefits of inhaled corticosteroid (ICS) therapy may occur at low doses, results of dose-ranging studies are inconsistent. Although symptom/lung function response to low and high dose ICS medication is comparable, it is uncertain whether low dose ICSs are as effective as high dose in the treatment of inflammation and remodeling.Methods: 22 mild or moderate asthmatic adult subjects (corticosteroid free for > 2 months) participated in a randomized, parallel group study to compare effects of fluticasone propionate (FP) 200 mcg/day and 1000 mcg/day. Alveolar macrophage (AM)-derived cytokines and basement membrane thickness (BMT) were measured at baseline and after 7 weeks treatment while symptoms, spirometry, exhaled nitric oxide (eNO) and airway hyperresponsiveness (AHR) to mannitol at baseline and 6 weeks.Results: FP improved spirometry, eNO, symptoms and AHR with no difference between low and high dose FP. Both high and low dose FP reduced GM-CSF, TNF-alpha and IL-1ra, with no change in BMT and with no differences between low and high dose FP.Conclusions: 200 μg/day of FP was as effective as 1000 μg/day in improving asthma control, airway inflammation, lung function and AHR in adults in the short term. Future studies should examine potential differential effects between low and high dose combination therapy (ICS/long acting beta agonist) on inflammation and airway remodeling over longer treatment periods. © 2012 Baraket et al; licensee BioMed Central Ltd.

Bargain, A, Robin, M, Le Men, E, Huete, A & Barille, L 2012, 'Spectral response of the seagrass Zostera noltii with different sediment backgrounds', AQUATIC BOTANY, vol. 98, no. 1, pp. 45-56.
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The efficiency of vegetation indices (VIs) to estimate the above-ground biomass of the seagrass species Zostera noltii Hornem. from remote sensing was tested experimentally on different substrata, since terrestrial vegetation studies have shown that VIs can be adversely influenced by the spectral properties of soils and background surfaces. Leaves placed on medium sand, fine sand and autoclaved fine sand were incrementally removed, and the spectral reflectance was measured in the 400-900nm wavelength range. Several VIs were evaluated: ratios using visible and near infrared wavelengths, narrow-band indices, indices based on derivative analysis and continuum removal. Background spectral reflectance was clearly visible in the leaf reflectance spectra, showing marked brightness and spectral contrast variations for the same amount of vegetation. Paradoxically, indices used to minimize soil effects, such as the Soil-Adjusted Vegetation Index (SAVI) and the Modified second Soil-Adjusted Vegetation Index (MSAVI 2) showed a high sensitivity to background effects. Similar results were found for the widely used Normalized Difference Vegetation Index (NDVI) and for Pigment Specific Simple Ratios (PSSRs). In fact, background effects were most reduced for VIs integrating a blue band correction, namely the modified specific ratio (mSR (705)), the modified Normalized Difference (mND (705)), and two modified NDVIs proposed in this study. However, these indices showed a faster saturation for high seagrass biomass. The background effects were also substantially reduced using Modified Gaussian Model indices at 620 and 675nm. The blue band corrected VIs should now be tested for air-borne or satellite remote sensing applications, but some require sensors with a hyperspectral resolution. Nevertheless, this type of index can be applied to analyse broad band multispectral satellite images with a blue band. © 2011 Elsevier B.V.

Barraud, N, Kardak, BG, Yepuri, NR, Howlin, RP, Webb, JS, Faust, SN, Kjelleberg, S, Rice, SA & Kelso, MJ 2012, 'Cephalosporin‐3′‐diazeniumdiolates: Targeted NO‐Donor Prodrugs for Dispersing Bacterial Biofilms', Angewandte Chemie International Edition, vol. 51, no. 36, pp. 9057-9060.
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Barraud, N, Kardak, BG, Yepuri, NR, Howlin, RP, Webb, JS, Faust, SN, Kjelleberg, S, Rice, SA & Kelso, MJ 2012, 'Cephalosporin‐3′‐diazeniumdiolates: Targeted NO‐Donor Prodrugs for Dispersing Bacterial Biofilms', Angewandte Chemie, vol. 124, no. 36, pp. 9191-9194.
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Bates, GW, Davidson, JE, Forgan, RS, Gale, PA, Henderson, DK, King, MG, Light, ME, Moore, SJ, Tasker, PA & Tong, CC 2012, 'A dual host approach to NiSO₄ extraction', Supramolecular Chemistry, vol. 24, no. 2, pp. 117-126.
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Beckett, EL, Phipps, S, Starkey, MR, Horvat, JC, Beagley, KW, Foster, PS & Hansbro, PM 2012, 'TLR2, but Not TLR4, Is Required for Effective Host Defence against Chlamydia Respiratory Tract Infection in Early Life', PLoS ONE, vol. 7, no. 6, pp. e39460-e39460.
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Chlamydia pneumoniae commonly causes respiratory tract infections in children, and epidemiological investigations strongly link infection to the pathogenesis of asthma. The immune system in early life is immature and may not respond appropriately to pathogens. Toll-like receptor (TLR)2 and 4 are regarded as the primary pattern recognition receptors that sense bacteria, however their contribution to innate and adaptive immunity in early life remains poorly defined. We investigated the role of TLR2 and 4 in the induction of immune responses to Chlamydia muridarum respiratory infection, in neonatal wild-type (Wt) or TLR2-deficient (-/-), 4-/- or 2/4-/- BALB/c mice. Wt mice had moderate disease and infection. TLR2-/- mice had more severe disease and more intense and prolonged infection compared to other groups. TLR4-/- mice were asymptomatic. TLR2/4-/- mice had severe early disease and persistent infection, which resolved thereafter consistent with the absence of symptoms in TLR4-/- mice. Wt mice mounted robust innate and adaptive responses with an influx of natural killer (NK) cells, neutrophils, myeloid (mDCs) and plasmacytoid (pDCs) dendritic cells, and activated CD4+ and CD8+ T-cells into the lungs. Wt mice also had effective production of interferon (IFN)γ in the lymph nodes and lung, and proliferation of lymph node T-cells. TLR2-/- mice had more intense and persistent innate (particularly neutrophil) and adaptive cell responses and IL-17 expression in the lung, however IFNγ responses and T-cell proliferation were reduced. TLR2/4-/- mice had reduced innate and adaptive responses. Most importantly, neutrophil phagocytosis was impaired in the absence of TLR2. Thus, TLR2 expression, particularly on neutrophils, is required for effective control of Chlamydia respiratory infection in early life. Loss of control of infection leads to enhanced but ineffective TLR4-mediated inflammatory responses that prolong disease symptoms. This indicates that TLR2 agonists...

Behrendt, L, Larkum, AWD, Trampe, E, Norman, A, Sorensen, SJ & Kuhl, M 2012, 'Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella', ISME JOURNAL, vol. 6, no. 6, pp. 1222-1237.
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We assessed the microbial diversity and microenvironmental niche characteristics in the didemnid ascidian Lissoclinum patella using 16S rRNA gene sequencing, microsensor and imaging techniques. L. patella harbors three distinct microbial communities spatially separated by few millimeters of tunic tissue: (i) a biofilm on its upper surface exposed to high irradiance and O-2 levels, (ii) a cloacal cavity dominated by the prochlorophyte Prochloron spp. characterized by strong depletion of visible light and a dynamic chemical microenvironment ranging from hyperoxia in light to anoxia in darkness and (iii) a biofilm covering the underside of the animal, where light is depleted of visible wavelengths and enriched in near-infrared radiation (NIR). Variable chlorophyll fluorescence imaging demonstrated photosynthetic activity, and hyperspectral imaging revealed a diversity of photopigments in all microhabitats. Amplicon sequencing revealed the dominance of cyanobacteria in all three layers. Sequences representing the chlorophyll d containing cyanobacterium Acaryochloris marina and anoxygenic phototrophs were abundant on the underside of the ascidian in shallow waters but declined in deeper waters. This depth dependency was supported by a negative correlation between A. marina abundance and collection depth, explained by the increased attenuation of NIR as a function of water depth. The combination of microenvironmental analysis and fine-scale sampling techniques used in this investigation gives valuable first insights into the distribution, abundance and diversity of bacterial communities associated with tropical ascidians. In particular, we show that microenvironments and microbial diversity can vary significantly over scales of a few millimeters in such habitats; which is information easily lost by bulk sampling

Behrendt, L, Schrameyer, V, Qvortrup, K, Lundin, L, Sorensen, SJ, Larkum, AWD & Kuehl, M 2012, 'Biofilm Growth and Near-Infrared Radiation-Driven Photosynthesis of the Chlorophyll d-Containing Cyanobacterium Acaryochloris marina', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 78, no. 11, pp. 3896-3904.
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The cyanobacterium Acaryochloris marina is the only known phototroph harboring chlorophyll (Chl) d. It is easy to cultivate it in a planktonic growth mode, and A. marina cultures have been subject to detailed biochemical and biophysical characterization. In natural situations, A. marina is mainly found associated with surfaces, but this growth mode has not been studied yet. Here, we show that the A. marina type strain MBIC11017 inoculated into alginate beads forms dense biofilm-like cell clusters, as in natural A. marina biofilms, characterized by strong O-2 concentration gradients that change with irradiance. Biofilm growth under both visible radiation (VIS, 400 to 700 nm) and near-infrared radiation (NIR, similar to 700 to 730 nm) yielded maximal cell-specific growth rates of 0.38 per day and 0.64 per day, respectively. The population doubling times were 1.09 and 1.82 days for NIR and visible light, respectively. The photosynthesis versus irradiance curves showed saturation at a photon irradiance of E-k (saturating irradiance) >250 mu mol photons m(-2) s(-1) for blue light but no clear saturation at 365 mu mol photons m(-2) s(-1) for NIR. The maximal gross photosynthesis rates in the aggregates were similar to 1,272 mu mol O-2 mg Chl d(-1) h(-1) (NIR) and similar to 1,128 mu mol O-2 mg Chl d(-1) h(-1) (VIS). The photosynthetic efficiency (alpha) values were higher in NIR-irradiated cells [(268 +/- 0.29) x 10(-6) m(2) mg Chl d(-1) (mean +/- standard deviation)] than under blue light [(231 +/- 0.22) x 10(-6) m(2) mg Chl d(-1)]. A. marina is well adapted to a biofilm growth mode under both visible and NIR irradiance and under O-2 conditions ranging from anoxia to hyperoxia, explaining its presence in natural niches with similar environmental conditions.

Bennett, WW, Teasdale, PR, Welsh, DT, Panther, JG, Stewart, RR, Price, HL & Jolley, DF 2012, 'Inorganic arsenic and iron(II) distributions in sediment porewaters investigated by a combined DGT–colourimetric DET technique', Environmental Chemistry, vol. 9, no. 1, pp. 31-31.
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Environmental contextContamination of aquatic ecosystems with inorganic arsenic is a concern for both environmental and human health. Sediments are an important sink for dissolved arsenic, but they may also act as a source of arsenic because of human-induced changes in aquatic systems. This paper describes a new approach for investigating the status of inorganic arsenic in sediments, based on recent developments in diffusion-based sediment sampling techniques.AbstractA new approach for investigating the biogeochemistry of inorganic arsenic and iron(II) in freshwater, estuarine and marine sediments is reported. The recently developed Metsorb diffusive gradients in thin films (DGT) technique for the measurement of total inorganic arsenic and the colourimetric diffusive equilibration in thin films (DET) technique for the measurement of iron(II), were utilised in combination to determine co-located depth profiles of both solutes in sediment porewaters. DGT-measured porewater arsenic concentrations were typically less than 40 nM, whereas iron(II) concentrations reached up to 704 µM. Statistically significant (P < 0.0002) correlations between porewater arsenic and iron(II) profiles were observed (R > 0.92) in mesocosms of each sediment type. This approach to investigating arsenic and iron geochemistry in sediments allows the in-situ determination of arsenic and iron species at exactly the same location in the sediment at 3-mm resolution for arsenic and 1-mm resolution for iron(II). The technique was capable of detecting very low concentrations of arsenic, with a detection limit of 0.27 nM (0.02 µg L–1) for a 48-h deployment time. Porewater iron(II), which is often present over a wide range of concentrations, was detectable up to 2000 µM. This study shows the application of these recently developed DGT and DET techniques for the in-situ investigation of inorganic arsenic and iron biogeochemistry in sediments. This approach has the potential to...

Berger, F, Cao, XF, Chandler, V, Dennis, L, Martienssen, R, Meyers, B, Pikaard, C, Peacock, J, Richards, E, Wagner, D, Weigel, D, Colot, V, Deal, R, Dean, C, Ecker, J, Gehring, M, Gong, Z, Gregory, B, Rodrigo, G, Gutierrez-Marcos, J, Hasebe, M, Hwang, ID, Jacobsen, S, Kakutani, T, Li, J, Michaels, S, Noh, YS, Provart, N & Vaughn, M 2012, 'Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment', The Plant Cell, vol. 24, no. 6, pp. 2257-2261.
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© 2012 American Society of Plant Biologists. All rights reserved. We have entered a new era in agricultural and biomedical science made possible by remarkable advances in DNA sequencing technologies. The complete sequence of an individual’s set of chromosomes (collectively, its genome) provides a primary genetic code for what makes that individual unique, just as the contents of every personal computer reflect the unique attributes of its owner. But a second code, composed of “epigenetic” layers of information, affects the accessibility of the stored information and the execution of specific tasks. Nature’s second code is enigmatic and must be deciphered if we are to fully understand and optimize the genetic potential of crop plants. The goal of the Epigenomics of Plants International Consortium is to crack this second code, and ultimately master its control, to help catalyze a new green revolution.

Bertrand, RL, Senadheera, S, Tanoto, A, Tan, KL, Howitt, L, Chen, H, Murphy, TV, Sandow, SL, Liu, L & Bertrand, PP 2012, 'Serotonin availability in rat colon is reduced during a Western diet model of obesity', American Journal of Physiology-Gastrointestinal and Liver Physiology, vol. 303, no. 3, pp. G424-G434.
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Constipation and slowed transit are associated with diet-induced obesity, although the mechanisms by which this occurs are unclear. Enterochromaffin (EC) cells within the intestinal epithelium respond to mechanical stimulation with the release of serotonin [5-hydroxytryptamine (5-HT)], which promotes transit. Thus our aim was to characterize 5-HT availability in the rat colon of a physiologically relevant model of diet-induced obesity. EC cell numbers were determined immunohistochemically in chow-fed (CF) and Western diet-fed (WD) rats, while electrochemical methods were used to measure mechanically evoked (peak) and steady-state (SS) 5-HT levels. Fluoxetine was used to block the 5-HT reuptake transporter (SERT), and the levels of mRNA for tryptophan hydroxylase 1 and SERT were determined by quantitative PCR, and SERT protein was determined by Western blot. In WD rats, there was a significant decrease in the total number of EC cells per crypt (0.86 ± 0.06 and 0.71 ± 0.05 in CF and WD, respectively), which was supported by a reduction in the levels of 5-HT in WD rats (2.9 ± 1.0 and 10.5 ± 2.6 μM at SS and peak, respectively) compared with CF rats (7.3 ± 0.4 and 18.4 ± 3.4 μM at SS and peak, respectively). SERT-dependent uptake of 5-HT was unchanged, which was supported by a lack of change in SERT protein levels. In WD rats, there was no change in tryptophan hydroxylase 1 mRNA but an increase in SERT mRNA. In conclusion, our data show that foods typical of a WD are associated with decreased 5-HT availability in rat colon. Decreased 5-HT availability is driven primarily by a reduction in the numbers and/or 5-HT content of EC cells, which are likely to be associated with decreased intestinal motility in vivo.

Bhosale, SV, Hackbarth, S, Langford, SJ & Bhosale, SV 2012, 'Light‐Induced Electron Transfer over Distances of 5, 10, and 15 Å within Water‐Filled Yoctowells', Chemistry – An Asian Journal, vol. 7, no. 1, pp. 176-182.
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AbstractA small series of variable‐depth yoctowell cavities with ′functional′ walls on aminated silica particles and gold electrodes has been established. The dimensions of the gaps formed were 2.2 nm in diameter with varying ′functional′ depths of 5, 10, and 15 Å, depending on the length of bolaphiles applied and the position of the positive rim; these gaps were prepared through a Michael addition of the incorporated ene‐amide groups. Using this construct and electrostatic interactions between the positive rim and anionic quinones as a means of immobilization, a porphyrin–quinone dyad system has been prepared. The distance between the donor and acceptor was changed systematically in aqueous solution, whilst maintaining a similar environment in each case. Upon photoexcitation of the porphyrin, efficient electron transfer occurs between the porphyrin and quinone units in a distance‐dependent manner on the nanosecond timescale.

Biagini, F, Cretarola, A & Platen, E 2012, 'Local Risk-Minimization under the Benchmark Approach', Mathematics and Financial Economics, vol. 8, no. 2, pp. 109-134.
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We study the pricing and hedging of derivatives in incomplete financialmarkets by considering the local risk-minimization method in the context of thebenchmark approach, which will be called benchmarked local risk-minimization.We show that the proposed benchmarked local risk-minimization allows to handleunder extremely weak assumptions a much richer modeling world than theclassical methodology.

Bishop, J, Lobo, CJ, Martin, A, Ford, M, Phillips, M & Toth, M 2012, 'Role of Activated Chemisorption in Gas-Mediated Electron Beam Induced Deposition', Physical Review Letters, vol. 109, no. 14, p. 146103.
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Models of adsorbate dissociation by energetic electrons are generalized to account for activated sticking and chemisorption, and used to simulate the rate kinetics of electron beam induced chemical vapor deposition (EBID). The model predicts a novel temperature dependence caused by thermal transitions from physisorbed to chemisorbed states that govern adsorbate coverage and EBID rates at elevated temperatures. We verify these results by experiments that also show how EBID can be used to deposit high purity materials and characterize the rates and energy barriers that govern adsorption. © 2012 American Physical Society.

Bishop, J, Toth, M, Phillips, M & Lobo, C 2012, 'Effects of oxygen on electron beam induced deposition of SiO2 using physisorbed and chemisorbed tetraethoxysilane', Applied Physics Letters, vol. 101, no. 21, pp. 211605-211605.
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Electron beam induced deposition (EBID) is limited by low throughput and purity of as-grown material. Co-injection of O2 with the growth precursor is known to increase both the purity and deposition rate of materials such as SiO2 at room temperature. Here, we show that O2 inhibits rather than enhances EBID from tetraethoxysilane (TEOS) precursor at elevated temperatures. This behavior is attributed to surface site competition between chemisorbates at elevated temperature, and TEOS decomposition by atomic oxygen produced through electron dissociation of physisorbed O2 at room temperature.

Blanes, L, Coltro, WKT, Saito, RM, Van Gramberg, A, Lucio do Lago, C & Doble, P 2012, 'High‐voltage power supplies to capillary and microchip electrophoresis', ELECTROPHORESIS, vol. 33, no. 6, pp. 893-898.
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Over the past years, the development of capillary electrophoresis (CE) and microchip electrophoresis (ME) systems has grown due to instrumental simplicity and wide application. In both CE and ME, the application of a high voltage (HV) is a crucial step in the electrokinetic (EK) injection and separation processes. Particularly on ME devices, EK injection is often performed with three different modes: gated, pinched, and unpinched. In all these cases, different potential values may be applied to one or multiple channels to control the injection of small sample volumes as well as the separation process. For this reason, the construction of reliable HV power supplies (HVPS) is required. This review covers the advances of the development of commercial and laboratory‐built HVPS for CE and ME. Moreover, it intends to be a guide for new developers of electrophoresis instrumentation.

Blumenthal, A, Nagalingam, G, Huch, JH, Walker, L, Guillemin, GJ, Smythe, GA, Ehrt, S, Britton, WJ & Saunders, BM 2012, 'M. tuberculosis Induces Potent Activation of IDO-1, but This Is Not Essential for the Immunological Control of Infection', PLoS ONE, vol. 7, no. 5, pp. e37314-e37314.
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Bogema, DR, Deutscher, AT, Woolley, LK, Seymour, LM, Raymond, BBA, Tacchi, JL, Padula, MP, Dixon, NE, Minion, FC, Jenkins, C, Walker, MJ & Djordjevic, SP 2012, 'Characterization of Cleavage Events in the Multifunctional Cilium Adhesin Mhp684 (P146) Reveals a Mechanism by Which Mycoplasma hyopneumoniae Regulates Surface Topography', MBIO, vol. 3, no. 2, pp. 1-11.
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Mycoplasma hyopneumoniae causes enormous economic losses to swine production worldwide by colonizing the ciliated epithelium in the porcine respiratory tract, resulting in widespread damage to the mucociliary escalator, prolonged inflammation, reduced weight gain, and secondary infections. Protein Mhp684 (P146) comprises 1,317 amino acids, and while the N-terminal 400 residues display significant sequence identity to the archetype cilium adhesin P97, the remainder of the molecule is novel and displays unusual motifs. Proteome analysis shows that P146 preprotein is endogenously cleaved into three major fragments identified here as P50P146, P40P146, and P85P146 that reside on the cell surface. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) identified a semitryptic peptide that delineated a major cleavage site in Mhp684. Cleavage occurred at the phenylalanine residue within sequence 672ATEF↓QQ677, consistent with a cleavage motif resembling S/T-X-F↓XD/E recently identified in Mhp683 and other P97/P102 family members. Biotinylated surface proteins recovered by avidin chromatography and separated by two-dimensional gel electrophoresis (2-D GE) showed that more-extensive endoproteolytic cleavage of P146 occurs. Recombinant fragments F1P146-F3P146 that mimic P50P146, P40P146, and P85P146 were constructed and shown to bind porcine epithelial cilia and biotinylated heparin with physiologically relevant affinity. Recombinant versions of F3P146 generated from M. hyopneumoniae strain J and 232 sequences strongly bind porcine plasminogen, and the removal of their respective C-terminal lysine and arginine residues significantly reduces this interaction. These data reveal that P146 is an extensively processed, multifunctional adhesin of M. hyopneumoniae. Extensive cleavage coupled with variable cleavage efficiency provides a mechanism by which M. hyopneumoniae regulates protein topography. © 2012 Bogema et al.

Booth, D 2012, 'Science under siege-comment on Kearney article: Faith, vested interests and the scientific method: a critique of Kearney', Australian Zoologist, vol. 36, no. 2, pp. 143-144.
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Borger, P, Oliver, B, Heijink, I & Hardavella, G 2012, 'Beyond the Immune System: The Role of Resident Cells in Asthma and COPD', Journal of Allergy, vol. 2012, pp. 1-3.
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Bosman, M, Anstis, GR, Keast, VJ, Clarke, JD & Cortie, MB 2012, 'Light Splitting in Nanoporous Gold and Silver', ACS NANO, vol. 6, no. 1, pp. 319-326.
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Nanoporous gold and silver exhibit strong, omnidirectional broad-band absorption in the far-field. Even though they consist entirely of gold or silver atoms, these materials appear black and dull, in great contrast with the familiar luster of continuous

Bosse, Y 2012, 'Comments on Point:Counterpoint: Alterations in airway smooth muscle phenotype do/do not cause airway hyperresponsiveness in asthma', Journal of Applied Physiology, vol. 113, no. 5, pp. 844-846.
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Bosse, Y, Vagula, MC, Rawding, RS, Pun, M, Black, JL, Burgess, J, Oliver, B, Berger, P, Marthan, R & Adner, M 2012, 'Comments on Point:Counterpoint: Alterations in airway smooth muscle phenotype do/do not cause airway hyperresponsiveness in asthma.', J Appl Physiol (1985), vol. 113, no. 5, pp. 844-846.
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Bowen, MT, Keats, K, Kendig, MD, Cakic, V, Callaghan, PD & McGregor, IS 2012, 'Aggregation in quads but not pairs of rats exposed to cat odor or bright light', Behavioural Processes, vol. 90, no. 3, pp. 331-336.
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Boyle, J, Crilly, J, Keijzers, G, Wallis, M, Lind, J, Sparks, R & Ryan, L 2012, 'Impact of influenza across 27 public emergency departments in Australia: a 5-year descriptive study', EMERGENCY MEDICINE JOURNAL, vol. 29, no. 9, pp. 725-731.
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Objective: To describe the incidence, characteristics and outcomes of patients with influenza-like symptoms presenting to 27 public hospital emergency departments (EDs) in Queensland, Australia. Methods: A descriptive retrospective study covering 5 years (2005-9) of historical data from 27 hospital EDs was undertaken. State-wide hospital ED Information System data were analysed. Annual comparisons between influenza and non-influenza cases were made across the southern hemisphere influenza season (June-September) each year. Results: Influenza-related presentations increased significantly over the 5 years from 3.4% in 2005 to 9.4% in 2009, reflecting a 276% relative increase. Differences over time regarding characteristics of patients with influenza-like symptoms, based on the influenza season, occurred for admission rate (decreased over time from 28% in 2005 to 18% in 2009), length of stay (decreased over time from a median of 210 min in 2005 to 164 min in 2009) and access block (increased over time from 33% to 41%). Also, every year there was a significantly (p<0.001) higher percentage of access block in the influenza cohort than in the non-influenza cohort. Conclusions: Although there was a large increase over time in influenza-related ED presentations, most patients were discharged home from the ED. Special consideration of health service delivery management (eg, establishing an 'influenza clinic border protection and public rollout of vaccination, beginning with those most at risk') for this group of patients is warranted but requires evaluation. These results may inform planning for service delivery models during the influenza season.

Brading, P, Warner, ME, Davey, P, Smith, DJ, Achterberg, EP & Suggett, DJ 2012, 'Erratum: Differential effects of ocean acidification on growth and photosynthesis among phylotypes of Symbiodinium (Dinophyceae)', Limnology and Oceanography, vol. 57, no. 4, pp. 1255-1255.
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Brown, JJ & Honchar, O 2012, 'Design and Estimation of Surveys to Measure Data Quality Aspects of Administrative Data', Lithuanian Journal of Statistics, vol. 51, no. 1, pp. 5-16.
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National Statistics Institutes (NSIs) have been increasingly seeking to replace or enhance traditional survey-based data sources with administrative data sources; with the aim to improve overall quality in the absence of a definitive register of the population. The Beyond 2011 Census Programme in England and Wales is an example of looking to replace a traditional census with administrative data collected for another purpose by a different organisation, when there is no definitive register as a starting point. There are also similar projects across NSIs within the area of business surveys looking to use administrative sources to reduce cost and burden. In this paper we start with considering all aspects of a quality framework for administrative data and then focus on the elements relevant to data quality such as accuracy and coherence. We fit these concepts into the framework for total survey error highlighting the components an NSI needs to measure to produce estimates based on the administrative data. We then explore the use of both dependent and independent quality surveys to adjust the administrative data for `measurement and `coverage aspects to improve the quality of estimates produced from the administrative data.

Brown, R, Kabani, K, Favaloro, J, Yang, S, Ho, PJ, Gibson, J, Fromm, P, Suen, H, Woodland, N, Nassif, N, Hart, D & Joshua, D 2012, 'CD86(+) or HLA-G(+) can be transferred via trogocytosis from myeloma cells to T cells and are associated with poor prognosis', BLOOD, vol. 120, no. 10, pp. 2055-2063.
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The transfer of membrane proteins between cells during contact, known as trogocytosis, can create novel cells with a unique phenotype and altered function. We demonstrate that trogocytosis is more common in multiple myeloma (MM) than chronic lymphocytic leukemia and Waldenstrom macroglobulinaemia; that T cells are more probable to be recipients than B or natural killer cells; that trogocytosis occurs independently of either the T-cell receptor or HLA compatibility; and that after trogocytosis, T cells with acquired antigens can become novel regulators of T-cell proliferation. We screened 168 patients with MM and found that CD86 and human leukocyte antigen G (HLA-G) were antigens commonly acquired by T cells from malignant plasma cells. CD3 +CD86acq+ and CD3+ HLA-Gacq+ cells were more prevalent in bone marrow than peripheral blood samples. The presence of either CD86 or HLA-G on malignant plasma cells was associated with a poor prognosis. CD38++ side population cells expressed HLA-G, suggesting that these putative myeloma stem cells could generate immune tolerance. HLA-G+ T cells had a regulatory potency similar to natural Tregs, thus providing another novel mechanism for MM to avoid effective immune surveillance. © 2012 by The American Society of Hematology.

Browne, EC, Langford, SJ & Abbott, BM 2012, 'Peptide Nucleic Acid Monomers: A Convenient and Efficient Synthetic Approach to Fmoc/Boc Monomers', Australian Journal of Chemistry, vol. 65, no. 5, pp. 539-539.
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A convenient and cost-effective method for the synthesis of Fmoc/Boc-protected peptide nucleic acid monomers is described. The Fmoc/Boc strategy was developed in order to eliminate the solubility issues during peptide nucleic acid solid-phase synthesis, in particular that of the cytosine monomer, that occurred when using the commercialized Bhoc chemistry approach.

Brownless, JS, Lawrence, FJ, Mahmoodian, S, Dossou, KB, Botten, LC & de Sterke, CM 2012, 'Supermodes of hexagonal lattice waveguide arrays', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, vol. 29, no. 6, pp. 1338-1346.
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We present a semianalytical formulation for calculating the supermodes and corresponding Bloch factors of light in hexagonal lattice photonic crystal waveguide arrays. We then use this formulation to easily calculate dispersion curves and predict propagation in systems too large to calculate using standard numerical methods. © 2012 Optical Society of America.

Brymora, A, Duggin, IG, Berven, LA, van Dam, EM, Roufogalis, BD & Robinson, PJ 2012, 'Identification and Characterisation of the RalA-ERp57 Interaction: Evidence for GDI Activity of ERp57', PLOS ONE, vol. 7, no. 11, pp. 1-11.
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RalA is a membrane-associated small GTPase that regulates vesicle trafficking. Here we identify a specific interaction between RalA and ERp57, an oxidoreductase and signalling protein. ERp57 bound specifically to the GDP-bound form of RalA, but not the GTP-bound form, and inhibited the dissociation of GDP from RalA in vitro. These activities were inhibited by reducing agents, but no disulphide bonds were detected between RalA and ERp57. Mutation of all four of ERp57's active site cysteine residues blocked sensitivity to reducing agents, suggesting that redox-dependent conformational changes in ERp57 affect binding to RalA. Mutations in the switch II region of the GTPase domain of RalA specifically reduced or abolished binding to ERp57, but did not block GTP-specific binding to known RalA effectors, the exocyst and RalBP1. Oxidative treatment of A431 cells with H(2)O(2) inhibited cellular RalA activity, and the effect was exacerbated by expression of recombinant ERp57. The oxidative treatment significantly increased the amount of RalA localised to the cytosol. These findings suggest that ERp57 regulates RalA signalling by acting as a redox-sensitive guanine-nucleotide dissociation inhibitor (RalGDI).

Bucolo, C, Leggio, GM, Maltese, A, Castorina, A, D’Agata, V & Drago, F 2012, 'Dopamine-3 receptor modulates intraocular pressure: Implications for glaucoma', Biochemical Pharmacology, vol. 83, no. 5, pp. 680-686.
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Busschaert, N, Kirby, IL, Young, S, Coles, SJ, Horton, PN, Light, ME & Gale, PA 2012, 'Squaramides as Potent Transmembrane Anion Transporters', Angewandte Chemie International Edition, vol. 51, no. 18, pp. 4426-4430.
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Busschaert, N, Kirby, IL, Young, S, Coles, SJ, Horton, PN, Light, ME & Gale, PA 2012, 'Squaramides as Potent Transmembrane Anion Transporters', Angewandte Chemie, vol. 124, no. 18, pp. 4502-4506.
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Buxton, L, Takahashi, S, Hill, R & Ralph, PJ 2012, 'VARIABILITY IN THE PRIMARY SITE OF PHOTOSYNTHETIC DAMAGE IN SYMBIODINIUM SP (DINOPHYCEAE) EXPOSED TO THERMAL STRESS', JOURNAL OF PHYCOLOGY, vol. 48, no. 1, pp. 117-126.
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Exposure to elevated temperature is known to cause photosynthetic inhibition in the coral symbiont Symbiodinium sp. Through the use of the artificial electron acceptor, methyl viologen, this study identified how reduced photosynthetic capacity occurs as a result of inhibition up- and/or downstream of ferredoxin in Symbiodinium sp. in hospite and in culture. Heterogeneity between coral species and symbiont clades was identified in the thermal sensitivity of photosynthesis in the symbionts of the scleractinian corals Stylophora pistillata and Pocillopora damicornis, as well as among Symbiodinium cultures of clades A, B, and C. The in hospite symbionts of S. pistillata and the cultured clade C Symbiodinium both exhibited similar patterns in that their primary site of thermal inhibition occurred downstream of ferredoxin at 32 degrees C. In contrast, the primary site of thermal inhibition occurred upstream of ferredoxin in clades A and B at 32 degrees C, while at 34 degrees C, all samples showed combined up- and downstream inhibition. Although clade C is common to both P. damicornis and S. pistillata, the manner of thermal inhibition was not consistent when observed in hospite. Results showed that there is heterogeneity in the primal site of thermal damage in Symbiodinium among coral species and symbiont clades.

Byrnes, A, Pant, R, Li, E, Choi, D-Y, Poulton, CG, Fan, S, Madden, S, Luther-Davies, B & Eggleton, BJ 2012, 'Photonic chip based tunable and reconfigurable narrowband microwave photonic filter using stimulated Brillouin scattering', OPTICS EXPRESS, vol. 20, no. 17, pp. 18836-18845.
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We report the first demonstration of a photonic chip based dynamically reconfigurablewidely tunablenarrow pass-bandhigh Q microwave photonic filter (MPF). We exploit stimulated Brillouin scattering (SBS) in a 6.5 cm long chalcogenide (As2S3) photonic chip to demonstrate a MPF that exhibited a high quality factor of ∼520 and narrow bandwidth and was dynamically reconfigurable and widely tunable. It maintained a stable 3 dB bandwidth of 23 ± 2MHz and amplitude of 20 ± 2 dB over a large frequency tuning range of 2-12 GHz. By tailoring the pump spectrumwe reconfigured the 3 dB bandwidth of the MPF from ∼20 MHz to ∼40 MHz and tuned the shape factor from 3.5 to 2 resulting in a nearly flat-topped filter profile. This demonstration represents a significant advance in integrated microwave photonics with potential applications in on-chip microwave signal processing for RADAR and analogue communications. © 2012 Optical Society of America.

Cadillo-Quiroz, H, Didelot, X, Held, NL, Herrera, A, Darling, A, Reno, ML, Krause, DJ & Whitaker, RJ 2012, 'Patterns of Gene Flow Define Species of Thermophilic Archaea', PLoS Biology, vol. 10, no. 2, pp. e1001265-e1001265.
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Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic 'continents,' indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation. © 2012 Cadillo-Quiroz et al.

Cai, H, Li, K, Shen, M, Wen, S, Luo, Y, Peng, C, Zhang, G & Shi, X 2012, 'Facile assembly of Fe3O4@Au nanocomposite particles for dual mode magnetic resonance and computed tomography imaging applications', Journal of Materials Chemistry, vol. 22, no. 30, pp. 15110-15110.
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Cai, T, Lin, X & Carroll, RJ 2012, 'Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test', Biostatistics, vol. 13, no. 4, pp. 776-790.
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In recent years, genome-wide association studies (GWAS) and gene-expression profiling have generated a large number of valuable datasets for assessing how genetic variations are related to disease outcomes. With such datasets, it is often of interest to assess the overall effect of a set of genetic markers, assembled based on biological knowledge. Genetic marker-set analyses have been advocated as more reliable and powerful approaches compared with the traditional marginal approaches (Curtis and others, 2005. Pathways to the analysis of microarray data. TRENDS in Biotechnology 23, 429-435; Efroni and others, 2007. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS One 2, 425). Procedures for testing the overall effect of a marker-set have been actively studied in recent years. For example, score tests derived under an Empirical Bayes (EB) framework (Liu and others, 2007. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63, 1079-1088; Liu and others, 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC bioinformatics 9, 292-2; Wu and others, 2010. Powerful SNP-set analysis for case-control genome-wide association studies. American Journal of Human Genetics 86, 929) have been proposed as powerful alternatives to the standard Rao score test (Rao, 1948. Large sample tests of statistical hypotheses concerning several parameters with applications to problems of estimation. Mathematical Proceedings of the Cambridge Philosophical Society, 44, 50-57). The advantages of these EB-based tests are most apparent when the markers are correlated, due to the reduction in the degrees of freedom. In this paper, we propose an adaptive score test which up-or down-weights the contributions from each member of the marker-set based on the Z-sc...

Calander, N, Jin, D & Goldys, EM 2012, 'Taking Plasmonic Core–Shell Nanoparticles Toward Laser Threshold', The Journal of Physical Chemistry C, vol. 116, no. 13, pp. 7546-7551.
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The first experimental demonstration of lasing plasmonic nanoparticles in 2009 ignited interest in active plasmonic structures with optical gain. However, the understanding of lasing in plasmonic nanoparticles is largely incomplete, and even less is known about their characteristics as they are taken toward the lasing threshold. Here we present a computational method and predictions of the lasing wavelength and threshold gain for spherical core-shell nanostructures with a metal core and a gain medium in the shell. We demonstrate that light scattering provides a simple diagnostics method to establish how far a specific nanoparticle is from reaching the lasing threshold. We also show that these structures can enhance the electric field by a factor of over 1500 (at 99.9% of threshold gain) and beyond, taking biosensing with these “ smart dustâ€' nanoparticles into the single molecule sensitivity regime. © 2012 American Chemical Society.

Camp, E & Fraser, D 2012, 'Influence of conservation education dive briefings as a management tool on the timing and nature of recreational SCUBA diving impacts on coral reefs', Ocean & Coastal Management, vol. 61, pp. 30-37.
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Carroll, L, Hawkins, CL, Fu, S, Storkey, C, Schiesser, H & Davies, MJ 2012, 'Seleno compounds are effective catalytic scavengers of myeloperoxidase-derived oxidants', FREE RADICAL BIOLOGY AND MEDICINE, vol. 53, pp. S97-S97.
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Carroll, R, Delaigle, A & Hall, P 2012, 'Deconvolution When Classifying Noisy Data Involving Transformations', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 107, no. 499, pp. 1166-1177.
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In the present study, we consider the problem of classifying spatial data distorted by a linear transformation or convolution and contaminated by additive random noise. In this setting, we show that classifier performance can be improved if we carefully invert the data before the classifier is applied. However, the inverse transformation is not constructed so as to recover the original signal, and in fact, we show that taking the latter approach is generally inadvisable. We introduce a fully data-driven procedure based on cross-validation, and use several classifiers to illustrate numerical properties of our approach. Theoretical arguments are given in support of our claims. Our procedure is applied to data generated by light detection and ranging (Lidar) technology, where we improve on earlier approaches to classifying aerosols. This article has supplementary materials online. © 2012 American Statistical Association.

Carroll, RJ, Midthune, D, Subar, AF, Shumakovich, M, Freedman, LS, Thompson, FE & Kipnis, V 2012, 'Taking Advantage of the Strengths of 2 Different Dietary Assessment Instruments to Improve Intake Estimates for Nutritional Epidemiology', American Journal of Epidemiology, vol. 175, no. 4, pp. 340-347.
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With the advent of Internet-based 24-hour recall (24HR) instruments, it is now possible to envision their use in cohort studies investigating the relation between nutrition and disease. Understanding that all dietary assessment instruments are subject to measurement errors and correcting for them under the assumption that the 24HR is unbiased for usual intake, here the authors simultaneously address precision, power, and sample size under the following 3 conditions: 1) 1-12 24HRs; 2) a single calibrated food frequency questionnaire (FFQ); and 3) a combination of 24HR and FFQ data. Using data from the Eating at America's Table Study (1997-1998), the authors found that 4-6 administrations of the 24HR is optimal for most nutrients and food groups and that combined use of multiple 24HR and FFQ data sometimes provides data superior to use of either method alone, especially for foods that are not regularly consumed. For all food groups but the most rarely consumed, use of 2-4 recalls alone, with or without additional FFQ data, was superior to use of FFQ data alone. Thus, if self-administered automated 24HRs are to be used in cohort studies, 4-6 administrations of the 24HR should be considered along with administration of an FFQ. © 2012 The Author.

Castorina, A, Giunta, S, Scuderi, S & D’Agata, V 2012, 'Involvement of PACAP/ADNP Signaling in the Resistance to Cell Death in Malignant Peripheral Nerve Sheath Tumor (MPNST) Cells', Journal of Molecular Neuroscience, vol. 48, no. 3, pp. 674-683.
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Ceh, J, Raina, J-B, Soo, RM, van Keulen, M & Bourne, DG 2012, 'Coral-Bacterial Communities before and after a Coral Mass Spawning Event on Ningaloo Reef', PLoS ONE, vol. 7, no. 5, pp. e36920-e36920.
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Bacteria associated with three coral species, Acropora tenuis, Pocillopora damicornis and Tubastrea faulkneri, were assessed before and after coral mass spawning on Ningaloo Reef in Western Australia. Two colonies of each species were sampled before and after the mass spawning event and two additional samples were collected for P. damicornis after planulation. A variable 470 bp region of the 16 S rRNA gene was selected for pyrosequencing to provide an understanding of potential variations in coral-associated bacterial diversity and community structure. Bacterial diversity increased for all coral species after spawning as assessed by Chao1 diversity indicators. Minimal changes in community structure were observed at the class level and data at the taxonomical level of genus incorporated into a PCA analysis indicated that despite bacterial diversity increasing after spawning, coral-associated community structure did not shift greatly with samples grouped according to species. However, interesting changes could be detected from the dataset; for example, a-Proteobacteria increased in relative abundance after coral spawning and particularly the Roseobacter clade was found to be prominent in all coral species, indicating that this group may be important in coral reproduction.

Chadwick, S, Maynard, P, Kirkbride, P, Lennard, C, McDonagh, A, Spindler, X & Roux, C 2012, 'Styryl dye coated metal oxide powders for the detection of latent fingermarks on non-porous surfaces', FORENSIC SCIENCE INTERNATIONAL, vol. 219, no. 1-3, pp. 208-214.
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Conventional fingermark powders rely on contrast induced by absorption/reflection (e.g. black powder) or luminescence in the visible region (e.g. Blitz Green ®). In most cases, these powders provide sufficient contrast; however, in some circumstances surface characteristics can interfere with the visualisation of powdered fingermarks. Visualisation in the near infra-red (NIR) region, however, has been shown to eliminate interferences commonly encountered in the visible region. In this study, a mixture of rhodamine 6G and the NIR laser dye styryl 11 (STaR 11) was coated onto an aluminium oxide nanopowder and then mixed with silver magnetic powder to develop and visualise fingermarks in the NIR. When compared to Blitz Green ®, it was determined that the STaR 11 magnetic powder was better suited for marks deposited on textured surfaces and for older marks, whereas Blitz Green ® performed better on smooth glossy surfaces. The ability of the STaR 11 mixed dye formulation to be visualised in both the visible and NIR regions also provides a significant advantage over conventional luminescent fingermark powders. © 2012 Elsevier Ireland Ltd.

Chan, SW, Dunlop, RA, Rowe, A, Double, KL & Rodgers, KJ 2012, 'L-DOPA is incorporated into brain proteins of patients treated for Parkinson's disease, inducing toxicity in human neuroblastoma cells in vitro', EXPERIMENTAL NEUROLOGY, vol. 238, no. 1, pp. 29-37.
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Levodopa (l-dopa), a close structural analogue of the protein amino acid l-tyrosine, can substitute for l-tyrosine in protein synthesis and be mistakenly incorporated into newly synthesised proteins in vitro. We show that l- dopa-containing proteins are present in the brain in l-DOPA-treated Parkinson's disease patients and accumulate in specific brain regions. In vitro studies demonstrate that substitution of l-tyrosine residues in proteins with l-DOPA causes protein misfolding and promotes protein aggregation in SH-SY5Y neuroblastoma cells resulting in the appearance of autofluorescent bodies. We show that the presence of l-DOPA-containing proteins causes profound changes in mitochondria and stimulates the formation of autophagic vacuoles in cells. Unlike l-DOPA, which is toxic to cells through its ability to generate radicals, proteins containing incorporated l-DOPA are toxic to SH-SY5Y cells by a mechanism independent of oxidative stress and resistant to antioxidants. These data suggest that the accumulation of l-DOPA-containing proteins in vulnerable cells might negatively impact on cell function. © 2011 Elsevier Inc.

Che, W, Manetsch, M, Quante, T, Rahman, MM, Patel, BS, Ge, Q & Ammit, AJ 2012, 'Sphingosine 1-phosphate induces MKP-1 expression via p38 MAPK- and CREB-mediated pathways in airway smooth muscle cells', Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol. 1823, no. 10, pp. 1658-1665.
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Chen, H, Saad, S, Sandow, SL & Bertrand, PP 2012, 'Cigarette Smoking and Brain Regulation of Energy Homeostasis', Frontiers in Pharmacology, vol. 3, no. 147, pp. 1-8.
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Cigarette smoking is an addictive behavior, and is the primary cause of cardiovascular and pulmonary disease, and cancer (among other diseases). Cigarette smoke contains thousands of components that may affect caloric intake and energy expenditure, although nicotine is the major addictive substance present, and has the best described actions. Nicotine exposure from cigarette smoke can change brain feeding regulation to reduce appetite via both energy homeostatic and reward mechanisms, causing a negative energy state which is characterized by reduced energy intake and increased energy expenditure that are linked to low body weight. These findings have led to the public perception that smoking is associated with weight loss. However, its effects at reducing abdominal fat mass (a predisposing factor for glucose intolerance and insulin resistance) are marginal, and its promotion of lean body mass loss in animal studies suggests a limited potential for treatment in obesity. Smoking during pregnancy puts pressure on the mother's metabolic system and is a significant contributor to adverse pregnancy outcomes. Smoking is a predictor of future risk for respiratory dysfunction, social behavioral problems, cardiovascular disease, obesity, and type-2 diabetes. Catch-up growth is normally observed in children exposed to intrauterine smoke, which has been linked to subsequent childhood obesity. Nicotine can have a profound impact on the developing fetal brain, via its ability to rapidly and fully pass the placenta. In animal studies this has been linked with abnormal hypothalamic gene expression of appetite regulators such as downregulation of NPY and POMC in the arcuate nucleus of the hypothalamus. Maternal smoking or nicotine replacement leads to unhealthy eating habits (such as junk food addiction) and other behavioral disorders in the offspring.

Chen, H, Simar, D, Ting, JHY, Erkelens, JRS & Morris, MJ 2012, 'Leucine Improves Glucose and Lipid Status in Offspring from Obese Dams, Dependent on Diet Type, but not Caloric Intake', Journal of Neuroendocrinology, vol. 24, no. 10, pp. 1356-1364.
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Previously, we showed that offspring from obese rat dams were hyperphagic, with increased adiposity, hyperlipidaemia and glucose intolerance associated with increased orexigenic neuropeptide expression after fasting. Mammalian target of rapamycin (mTOR) can inhibit food intake through a hypothalamic action. As we previously showed that maternal obesity down‐regulated hypothalamic mTOR, in the present study, we hypothesised that dietary leucine supplementation would activate hypothalamic mTOR to reduce food intake, thus limiting metabolic disorders in offspring from obese dams, regardless of postweaning diet. Obesity was induced in Sprague–Dawley females by high‐fat diet (HFD) for 5 weeks before mating, throughout gestation and lactation. Male pups from HFD‐fed mothers were weaned onto chow or HFD; within each dietary group, half were supplied with leucine via drinking water (1.5%) versus water control for 10 weeks. Those from chow‐fed mothers were fed chow and water. Maternal obesity led to increased adiposity in chow‐fed offspring. Postweaning HFD consumption exaggerated adiposity, hyperglycaemia, hyperinsulinaemia and hyperlipidaemia. Supplementation with leucine doubled leucine intake and increased hypothalamic mTOR activation; however, appetite regulation was not affected. A reduction in blood lipid levels was observed in offspring regardless of diet, as well as improved glucose tolerance in HFD‐fed rats. In HFD‐fed rats, up‐regulated carnitine palmitoyl‐transferase‐1 and peroxisome‐proliferator‐activated receptor‐γ coactivator‐1α in muscle and glucose transporter 4 in fat suggested that leucine improved peripheral fat oxidation and glucose transport. Leucine is able to improve peripheral glucose and lipid metabolism independent of appetite and weight regulation, suggesting its potential application in the management of metabolic disorders.

Chen, PY, Byrne, MA, Asatryan, AA, Botten, LC, Dossou, KB, Tuniz, A, McPhedran, RC, de Sterke, CM, Poulton, CG & Steel, MJ 2012, 'Plane-wave scattering by a photonic crystal slab: Multipole modal formulation and accuracy', WAVES IN RANDOM AND COMPLEX MEDIA, vol. 22, no. 4, pp. 531-570.
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The optical properties of photonic crystal slabs are often simulated with general three-dimensional methods such as finite-difference time-domain. Here we develop a multipole modal method, which is specialized to exploit two symmetries of the photonic crystal slab: the slab's vertically invariant nature allows the field to be expressed in Bloch modes, while the cylindrical inclusions allow the Bloch modes themselves to be expressed in the multipole basis. We find the multipole method to be fast and efficient in finding the Bloch modes, with convergence approaching the numerical accuracy possible. By matching the Bloch modes to plane waves at the top and bottom interfaces of the photonic crystal, the field scattered by the slab is calculated. Values of transmittance and reflectance accurate to 2-3 digits are easily and quickly achieved, whereas 5-6 digits are possible with greater numbers of modes and plane waves in field expansions. Higher accuracy is limited by Gibbs-related phenomena arising from the matching at the interface of necessarily discontinuous Bloch modes to necessarily continuous plane waves. We believe this limit may be present in all modal methods that use Bloch modes to expand the field within the photonic crystal. © 2012 Taylor and Francis Group, LLC.

Chen, S, Wang, Y, Ahn, H & Wang, G 2012, 'Microwave hydrothermal synthesis of high performance tin-graphene nanocomposites for lithium ion batteries', JOURNAL OF POWER SOURCES, vol. 216, no. October 2012, pp. 22-27.
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Tin-graphene nanocomposites are prepared by a combination of microwave hydrothermal synthesis and a one-step hydrogen gas reduction. Altering the weight ratio between tin and graphene nanosheets has critical influences on their morphologies and electrochemical performances. Field emission scanning electron microscope (FESEM) and transmission electron microscope (TEM) analysis confirm the homogeneous distribution of tin nanoparticles on the surface of graphene nanosheets. When applied as an anode material in lithium ion batteries, tin-graphene nanocomposite exhibits a high lithium storage capacity of 1407 mAh g -1. The as-prepared tin-graphene nanocomposite also demonstrates an excellent high rate capacity and a stable cycle performance. The superior electrochemical performance could be attributed to the synergistic effect of the three-dimensional nanoarchitecture, in which tin nanoparticles are sandwiched between highly conductive and flexible graphene nanosheets. © 2012 Elsevier B.V.

Chen, S, Yeoh, W, Liu, Q & Wang, G 2012, 'Chemical-free synthesis of graphene-carbon nanotube hybrid materials for reversible lithium storage in lithium-ion batteries', CARBON, vol. 50, no. 12, pp. 4557-4565.
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Graphene-carbon nanotube hybrid materials were successfully prepared through the π-π interaction without using any chemical reagent. We found that the ratio between carbon nanotube and graphene had critical influences on the state in aqueous solution and morphology of hybrid materials. Field emission scanning electron microscope and transmission electron microscope analysis confirmed that graphene nanosheets wrap around individual carbon nanotubes and form a homogeneous three-dimensional hybrid nanostructure. When applied as an anode material in lithium ion batteries, graphene-carbon nanotube hybrid materials demonstrated a high reversible lithium storage capacity, a high Coulombic efficiency and an excellent cyclability. © 2012 Elsevier Ltd. All rights reserved.

Cheridito, P, Nikeghbali, A & Platen, E 2012, 'Processes of Class Sigma, Last Passage Times, and Drawdowns', SIAM JOURNAL ON FINANCIAL MATHEMATICS, vol. 3, no. 1, pp. 280-303.
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We propose a general framework for studying last passage times, suprema, and drawdowns of a large class of continuous-time stochastic processes. Our approach is based on processes of class Sigma and the more general concept of two processes, one of which moves only when the other is at the origin. After investigating certain transformations of such processes and their convergence properties, we provide three general representation results. The first allows the recovery of a process of class Sigma from its final value and the last time it visited the origin. In many situations this gives access to the distribution of the last time a stochastic process attains a certain level or is equal to its running maximum. It also leads to recently discovered formulas expressing option prices in terms of last passage times. Our second representation result is a stochastic integral representation that will allow us to price and hedge options on the running maximum of an underlying that are triggered when the underlying drops to a given level or, alternatively, when the drawdown or relative drawdown of the underlying attains a given height. The third representation gives conditional expectations of certain functionals of processes of class Sigma. It can be used to deduce the distributions of a variety of interesting random variables such as running maxima, drawdowns, and maximum drawdowns of suitably stopped processes.

Chew, K-L, Langtry, T, Zinder, Y, Yu, Q & Li, L 2012, 'Estimation of biochemical parameters from leaf photosynthesis', ANZIAM Journal, vol. 53, no. EMAC2011, pp. 218-218.
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The objective of measuring leaf photosynthesis using infrared gas analysis is to determine key indicators of plant eco-physiology, including light and CO2 compensation and saturation points, and critical thresholds of temperature. These and other biochemical parameters in photosynthesis models define specific response curves of photosynthetic rate to environmental variables, such as light intensity, temperature, and CO2. Since these parameters cannot regularly be measured in the field, modellers normally adopt laboratory values as universal ones even though the values of these parameters may vary across plant species. This study investigates the identification of parameter values from data sets obtained from field measurement

Cho, Y, Turner, ND, Davidson, LA, Chapkin, RS, Carroll, RJ & Lupton, JR 2012, 'A chemoprotective fish oil/pectin diet enhances apoptosis via Bcl-2 promoter methylation in rat azoxymethane-induced carcinomas', Experimental Biology and Medicine, vol. 237, no. 12, pp. 1387-1393.
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We have demonstrated that diets containing fish oil and pectin (FO/P) reduce colon tumor incidence relative to control (corn oil and cellulose [CO/C]) in part by inducing apoptosis of DNA-damaged colon cells. Relative to FO/P, CO/C promotes colonocyte expression of the antiapoptotic modulator, Bcl-2, and Bcl-2 promoter methylation is altered in colon cancer. To determine if FO/P, compared with CO/C, limits Bcl-2 expression by enhancing promoter methylation in colon tumors, we examined Bcl-2 promoter methylation, mRNA levels, colonocyte apoptosis and colon tumor incidence in azoxymethane (AOM)-injected rats. Rats were provided diets containing FO/P or CO/C, and were terminated 16 and 34 weeks after AOM injection. DNA isolated from paraformaldehyde-fixed colon tumors and uninvolved tissue was bisulfite modified and amplified by quantitative reverese transcriptase-polymerase chain reaction to assess DNA methylation in Bcl-2 cytosine-guanosine islands. FO/P increased Bcl-2 promoter methylation (P = 0.009) in tumor tissues and colonocyte apoptosis (P = 0.020) relative to CO/C. An inverse correlation between Bcl-2 DNA methylation and Bcl-2 mRNA levels was observed in the tumors. We conclude that dietary FO/P promotes apoptosis in part by enhancing Bcl-2 promoter methylation. These Bcl-2 promoter methylation responses, measured in vivo, contribute to our understanding of the mechanisms involved in chemoprevention of colon cancer by diets containing FO/P.

Choi, AH, Matinlinna, JP & Ben-Nissan, B 2012, 'Finite element stress analysis of Ti-6Al-4V and partially stabilized zirconia dental implant during clenching', Acta Odontologica Scandinavica, vol. 70, no. 5, pp. 353-361.
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Objective. The purpose of this paper is to compare the differences in stress between Ti-6Al-4V and PS-ZrO2 dental implant during clenching and whether these changes are clinically signi?cant to limit the use of zirconia in oral implantology. Materials and methods. The model geometry was derived from position measurements taken from 28 diamond blade cut cross-sections of an average size human adult edentulous mandible and generated using a special sequencing method. Data on anatomical, structural, functional aspects and material properties were obtained from measurements and published data. Ti- 6Al-4V and PS-ZrO2 dental implants were modelled as cylindrical structure with a diameter of 3.26 mm and length of 12.00 mm was placed in the ?rst molar region on the right hemimandible. Results. The analysis revealed an increase of 23% in the averaged tensile and compressive stress and an increase of 8% in the averaged Von Mises stress were recorded in the boneimplant interface when PS-ZrO2 dental implant was used instead of Ti-6Al-4V dental implant. The results also revealed only relatively low levels of stresses were transferred from the implant to the surrounding cortical and cancellous bone, with the majority of the stresses transferred to the cortical bone. Conclusion. Even though high magnitudes of tensile, compressive and Von Mises stresses were recorded on the Ti-6Al-4V and PS-ZrO2 dental implants and in the surrounding osseous structures, the stresses may not be clinically critical since the mechanical properties of the implant material and the cortical and cancellous bone could withstand stress magnitudes far greater than those recorded in this analysis.

Choi, T-Y, Lee, MS, Kim, T-H, Zaslawski, C & Ernst, E 2012, 'Acupuncture for the treatment of cancer pain: a systematic review of randomised clinical trials', SUPPORTIVE CARE IN CANCER, vol. 20, no. 6, pp. 1147-1158.
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Purpose: Controlling cancer-related pain is an important component in the palliative care of cancer patients. The objective of this review was to assess the effectiveness of acupuncture for treating cancer pain. Methods: Fourteen databases were searched from their inception through April 2011. Randomised clinical trials (RCTs) were included if acupuncture was used as the sole treatment or as a part of a combination therapy for cancer pain. Studies were included if they were controlled with a placebo or controlled against a drug-therapy or no-treatment group. The Cochrane criteria were used to assess the risk of bias. Results: A total of 15 RCTs met our inclusion criteria. All of the included RCTs were associated with a high risk of bias. The majority of acupuncture treatments or combination therapies with analgesics exhibited favourable effects compared with conventional treatments in individual studies. However, a meta-analysis suggested that acupuncture did not generate a better effect than drug therapy (n=886; risk ratio (RR), 1.12; 95% CI 0.98 to 1.28; P=0.09). The comparison between acupuncture plus drug therapy and drug therapy alone demonstrated a significant difference in favour of the combination therapy (n=437; RR, 1.36; 95% CI 1.13 to 1.64; P=0.003). The results of this systematic review provide no strong evidence for the effectiveness of acupuncture in the management of cancer pain. Conclusion: The total number of RCTs included in the analysis and their methodological quality were too low to draw firm conclusions. Future rigorous RCTs will be necessary to assess the clinical efficacy of acupuncture in this area. © Springer-Verlag 2012.

Chong, G, Kimyon, O, Rice, SA, Kjelleberg, S & Manefield, M 2012, 'The presence and role of bacterial quorum sensing in activated sludge', Microbial Biotechnology, vol. 5, no. 5, pp. 621-633.
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SummaryActivated sludge used for wastewater treatment globally is composed of a high‐density microbial community of great biotechnological significance. In this study the presence and purpose of quorum sensing via N‐acylated‐l‐homoserine lactones (AHLs) in activated sludge was explored. The presence of N‐heptanoyl‐l‐homoserine lactone in organic extracts of sludge was demonstrated along with activation of a LuxR‐based AHL monitor strain deployed in sludge, indicating AHL‐mediated gene expression is active in sludge flocculates but not in the bulk aqueous phase. Bacterial isolates from activated sludge were screened for AHL production and expression of phenotypes commonly but not exclusively regulated by AHL‐mediated gene transcription. N‐acylated‐l‐homoserine lactone and exoenzyme production were frequently observed among the isolates. N‐acylated‐l‐homoserine lactone addition to sludge upregulated chitinase activity and an AHL‐ and chitinase‐producing isolate closely related to Aeromonas hydrophila...

Chong, HS, Campbell, L, Padula, MP, Hill, C, Harry, E, Li, SS, Wilkins, MR, Herbert, B & Carter, D 2012, 'Time-Course Proteome Analysis Reveals the Dynamic Response of Cryptococcus gattii Cells to Fluconazole', PLoS ONE, vol. 7, no. 8, pp. e42835-e42835.
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Cryptococcus gattii is an encapsulated fungus capable of causing fatal disease in immunocompetent humans and animals. As current antifungal therapies are few and limited in efficacy, and resistance is an emerging issue, the development of new treatment strategies is urgently required. The current study undertook a time-course analysis of the proteome of C. gattii during treatment with fluconazole (FLC), which is used widely in prophylactic and maintenance therapies. The aims were to analyze the overall cellular response to FLC, and to find fungal proteins involved in this response that might be useful targets in therapies that augment the antifungal activity of FLC. During FLC treatment, an increase in stress response, ATP synthesis and mitochondrial respiratory chain proteins, and a decrease in most ribosomal proteins was observed, suggesting that ATP-dependent efflux pumps had been initiated for survival and that the maintenance of ribosome synthesis was differentially expressed. Two proteins involved in fungal specific pathways were responsive to FLC. An integrative network analysis revealed co-ordinated processes involved in drug response, and highlighted hubs in the network representing essential proteins that are required for cell viability. This work demonstrates the dynamic cellular response of a typical susceptible isolate of C. gattii to FLC, and identified a number of proteins and pathways that could be targeted to augment the activity of FLC. © 2012 Chong et al.

Chou, J, Austin, C, Doble, P, Ben-Nissan, B & Milthorpe, B 2012, 'Trace elemental imaging of coralline hydroxyapatite by laser-ablation inductively coupled plasma-mass spectroscopy', Journal of Tissue Engineering and Regenerative Medicine, vol. 8, no. 7, pp. n/a-n/a.
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Clifton, J, Etienne, M, Barnes, DKA, Barnes, RSK, Suggett, DJ & Smith, DJ 2012, 'Marine conservation policy in Seychelles: Current constraints and prospects for improvement', Marine Policy, vol. 36, no. 3, pp. 823-831.
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The marine assets of Seychelles are fundamental to the national economy through generating income derived from tourism and fisheries. Marine management institutions and policies have undergone radical changes since 2008, reflecting a number of drivers and initiatives at international and national levels. Through using the example of Curieuse Marine National Park in the inner Seychelles, we demonstrate how these are affecting marine conservation with respect to coastal development, governance of marine protected areas and livelihood security within resource-dependent communities. These issues are of significance with respect to the current and future viability of marine conservation and resource management in Seychelles. Potential mitigating strategies are suggested which could lead to more effective governance and conservation of marine protected areas in Seychelles and similar small island developing states. © 2011 Elsevier Ltd.

Clifton, LA, Johnson, CL, Solovyova, AS, Callow, P, Weiss, KL, Ridley, H, Le Brun, AP, Kinane, CJ, Webster, JRP, Holt, SA & Lakey, JH 2012, 'Low Resolution Structure and Dynamics of a Colicin-Receptor Complex Determined by Neutron Scattering', Journal of Biological Chemistry, vol. 287, no. 1, pp. 337-346.
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Collier, BA, Groce, JE, Morrison, ML, Newnam, JC, Campomizzi, AJ, Farrell, SL, Mathewson, HA, Snelgrove, RT, Carroll, RJ & Wilkins, RN 2012, 'Predicting patch occupancy in fragmented landscapes at the rangewide scale for an endangered species: an example of an American warbler', Diversity and Distributions, vol. 18, no. 2, pp. 158-167.
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AbstractAim  Our objective was to identify the distribution of the endangered golden‐cheeked warbler (Setophaga chrysoparia) in fragmented oak–juniper woodlands by applying a geoadditive semiparametric occupancy model to better assist decision‐makers in identifying suitable habitat across the species breeding range on which conservation or mitigation activities can be focused and thus prioritize management and conservation planning.Location  Texas, USA.Methods  We used repeated double‐observer detection/non‐detection surveys of randomly selected (n = 287) patches of potential habitat to evaluate warbler patch‐scale presence across the species breeding range. We used a geoadditive semiparametric occupancy model with remotely sensed habitat metrics (patch size and landscape composition) to predict patch‐scale occupancy of golden‐cheeked warblers in the fragmented oak–juniper woodlands of central Texas, USA.Results  Our spatially explicit model indicated that golden‐cheeked warbler patch occupancy declined from south to north within the breeding range concomitant with reductions in the availability of large habitat patches. We found that 59% of woodland patches, primarily in the northern and central portions of the warbler’s range, were predicted to have occupancy probabilities ≤0.10 with only 3% of patches predicted to have occupancy probabilities >0.90. Our model exhibited high prediction accuracy (area under curve = 0.91) when validated using independently collected warbler occurrence data.Main conclusions  We have identified a distinct spatial occurrence gradient for golden‐cheeked warblers as well as a relationship between two measurable landscape characteristics. Because habitat‐occ...

Combes, V, Guillemin, GJ, Chan-Ling, T, Hunt, NH & Grau, GER 2012, 'The crossroads of neuroinflammation in infectious diseases: endothelial cells and astrocytes', Trends in Parasitology, vol. 28, no. 8, pp. 311-319.
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Homeostasis implies constant operational defence mechanisms, against both external and internal threats. Infectious agents are prominent among such threats. During infection, the host elicits the release of a vast array of molecules and numerous cell-cell interactions are triggered. These pleiomorphic mediators and cellular effects are of prime importance in the defence of the host, both in the systemic circulation and at sites of tissue injury, for example, the blood-brain barrier (BBB). Here, we focus on the interactions between the endothelium, astrocytes, and the molecules they release. Our review addresses these interactions during infectious neurological diseases of various origins, especially cerebral malaria (CM). Two novel elements of the interplay between endothelium and astrocytes, microparticles and the kynurenine pathway, will also be discussed. © 2012 Elsevier Ltd.

Cortez, DP, Growns, IO, Mitrovic, SM & Lim, RP 2012, 'Effects of a gradient in river regulation on the longitudinal trends in water quality and benthic algal and macroinvertebrate assemblages in the Hunter River, Australia', MARINE AND FRESHWATER RESEARCH, vol. 63, no. 6, pp. 494-504.
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River regulation impacts lotic ecosystem processes; however, the effect of a gradient of regulation on these attributes has rarely been studied. This study examined the effects of a river regulation gradient on longitudinal trends in water quality and be

Cortie, MB, Liu, F, Arnold, MD & Niidome, Y 2012, 'Multimode Resonances in Silver Nanocuboids', LANGMUIR, vol. 28, no. 24, pp. 9103-9112.
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A rich variety of dipolar and higher order plasmon resonances have been predicted for nanoscale cubes and parallopipeds of silver, in contrast to the simple dipolar modes found on silver nanospheres or nanorods. However, in general, these multimode reson

Cotton, S, Donnelly, S, Robinson, MW, Dalton, JP & Thivierge, K 2012, 'Defense peptides secreted by helminth pathogens: antimicrobial and/or immunomodulator molecules?', FRONTIERS IN IMMUNOLOGY, vol. 3, no. AUG, pp. 1-7.
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Host defense peptides (HDPs) are an evolutionarily conserved component of the innate immune response found in all living species. They possess antimicrobial activities against a broad range of organisms including bacteria, fungi, eukaryotic parasites, and viruses. HDPs also have the ability to enhance immune responses by acting as immunomodulators. We discovered a new family of HDPs derived from pathogenic helminth (worms) that cause enormous disease in animals and humans worldwide. The discovery of these peptides was based on their similar biochemical and functional characteristics to the human defense peptide LL-37. We propose that these new peptides modulate the immune response via molecular mimicry of mammalian HDPs thus providing a mechanism behind the anti-inflammatory properties of helminth infections. © 2012 Cotton, Donnelly, Robinson, Dalton and Thivierge.

Courtenay, G, Smith, DR & Gladstone, W 2012, 'Occupational health issues in marine and freshwater research', JOURNAL OF OCCUPATIONAL MEDICINE AND TOXICOLOGY, vol. 7, no. 4, pp. 1-11.
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Marine and freshwater scientists are potentially exposed to a wide variety of occupational hazards. Depending on the focus of their research, risks may include animal attacks, physiological stresses, exposure to toxins and carcinogens, and dangerous environmental conditions. Many of these hazards have been investigated amongst the general population in their recreational use of the environment; however, very few studies have specifically related potential hazards to occupational exposure. For example, while the incidence of shark and crocodile attacks may invoke strong emotions and the occupational risk of working with these animals is certainly real, many more people are stung by jellyfish or bitten by snakes or dogs each year. Furthermore, a large proportion of SCUBA-related injuries and deaths are incurred by novice or uncertified divers, rather than professional divers using aquatic environments. Nonetheless, marine and freshwater research remains a potentially risky occupation, and the likelihood of death, injury and long-term health impacts still needs to be seriously considered.

Couttas, TA, Raftery, MJ, Padula, MP, Herbert, BR & Wilkins, MR 2012, 'Methylation of translation‐associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases', PROTEOMICS, vol. 12, no. 7, pp. 960-972.
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This study aimed to identify sites of lysine methylation in Saccharomyces cerevisiae and the associated methyltransferases. Hexapeptide ligand affinity chromatography was used to normalize the abundance levels of proteins in whole cell lysate. MS/MS, in association with antibody‐based detection, was then used to identify lysine methylated proteins and the precise sites of modification. Lysine methylation was found on the proteins elongation factor (EF) 1‐α, 2, and 3A, as well as ribosomal proteins 40S S18‐A/B, 60S L11‐A/B, L18‐A/B, and L42‐A/B. Precise sites were mapped in all cases. Single‐gene knockouts of known and putative methyltransferase(s), in association with MS/MS, showed that EF1‐α is monomet...

Cox, RP, Higginbotham, HF, Graystone, BA, Sandanayake, S, Langford, SJ & Bell, TDM 2012, 'A new fluorescent H+ sensor based on core-substituted naphthalene diimide', Chemical Physics Letters, vol. 521, pp. 59-63.
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Craddock, M & Lennox, KA 2012, 'Lie symmetry methods for multi-dimensional parabolic PDEs and diffusions', Journal of Differential Equations, vol. 252, no. 1, pp. 56-90.
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In this paper we introduce new methods based upon integrating Lie symmetries for the construction of explicit fundamental solutions of multi-dimensional second order parabolic PDEs. We present applications to the problem of finding transition probability

Croak, BM, Pike, DA, Webb, JK & Shine, R 2012, 'Habitat Selection in a Rocky Landscape: Experimentally Decoupling the Influence of Retreat Site Attributes from That of Landscape Features', PLOS ONE, vol. 7, no. 6, pp. 1-8.
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Organisms selecting retreat sites may evaluate not only the quality of the specific shelter, but also the proximity of that site to resources in the surrounding area. Distinguishing between habitat selection at these two spatial scales is complicated by co-variation among microhabitat factors (i.e., the attributes of individual retreat sites often correlate with their proximity to landscape features). Disentangling this co-variation may facilitate the restoration or conservation of threatened systems. To experimentally examine the role of landscape attributes in determining retreat-site quality for saxicolous ectotherms, we deployed 198 identical artificial rocks in open (sun-exposed) sites on sandstone outcrops in southeastern Australia, and recorded faunal usage of those retreat sites over the next 29 months. Several landscape-scale attributes were associated with occupancy of experimental rocks, but different features were important for different species. For example, endangered broad-headed snakes (Hoplocephalus bungaroides) preferred retreat sites close to cliff edges, flat rock spiders (Hemicloea major) preferred small outcrops, and velvet geckos (Oedura lesueurii) preferred rocks close to the cliff edge with higher-than-average sun exposure. Standardized retreat sites can provide robust experimental data on the effects of landscape-scale attributes on retreat site selection, revealing interspecific divergences among sympatric taxa that use similar habitats. © 2012 Croak et al.

Cui, PH, Rawling, T, Bourget, K, Kim, T, Duke, CC, Doddareddy, MR, Hibbs, DE, Zhou, F, Tattam, BN, Petrovic, N & Murray, M 2012, 'Antiproliferative and Antimigratory Actions of Synthetic Long Chain n-3 Monounsaturated Fatty Acids in Breast Cancer Cells That Overexpress Cyclooxygenase-2', Journal of Medicinal Chemistry, vol. 55, no. 16, pp. 7163-7172.
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Cyclooxygenase-2 (COX-2) is overexpressed in many human cancers and converts the n-6 polyunsaturated fatty acid (PUFA) arachidonic acid to prostaglandin E2 (PGE2), which drives tumorigenesis; in contrast, n-3 PUFA inhibit tumorigenesis. We tested the hypothesis that these antitumor actions of n-3 PUFA may involve the n-3 olefinic bond. n-3 Monounsaturated fatty acids (MUFAs) of chain length C16C22 were synthesized and evaluated in MDA-MB-468 breast cancer cells that stably overexpressed COX-2 (MDA-COX-2 cells). Longer chain (C19C22) n-3 MUFAs inhibited proliferation, activated apoptosis, decreased PGE2 formation, and decreased cell invasion; C16C18 analogues were less active. Molecular modeling showed that interactions of Arg120, Tyr355, and several hydrophobic amino acid residues in the COX-2 active site with C19C22 MUFA analogues were favored. Thus, longer-chain n-3 MUFAs may be prototypes of novel anticancer agents that decrease the formation of PGE2 in tumor cells that contain high levels of COX-2.

Curtis, EM, Leigh, A & Rayburg, S 2012, 'Relationships among leaf traits of Australian arid zone plants: alternative modes of thermal protection', Australian Journal of Botany, vol. 60, no. 6, pp. 471-471.
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Despite the importance of leaf traits that protect against critically high leaf temperatures, relationships among such traits have not been investigated. Further, while some leaf trait relationships are well documented across biomes, little is known about such associations within a biome. This study investigated relationships between nine leaf traits that protect leaves against excessively high temperatures in 95 Australian arid zone species. Seven morphological traits were measured: leaf area, length, width, thickness, leaf mass per area, water content, and an inverse measure of pendulousness. Two spectral properties were measured: reflectance of visible and near-infrared radiation. Three key findings emerged: (1) leaf pendulousness increased with leaf size and leaf mass per area, the former relationship suggesting that pendulousness affords thermal protection when leaves are large; (2) leaf mass per area increased with thickness and decreased with water content, indicating alternative means for protection through increasing thermal mass; (3) spectral reflectance increased with leaf mass per area and thickness and decreased with water content. The consistent co-variation of thermal protective traits with leaf mass per area, a trait not usually associated with thermal protection, suggests that these traits fall along the leaf economics spectrum, with leaf longevity increasing through protection not only against structural damage but also against heat stress.

Daniels, WD, Garcia, TP, Carroll, RJ, Patil, BS & Turner, ND 2012, 'Suppression of early colon cancer lesions by apigenin and naringenin is in part due to their downregulation of p21, TLR‐4, and MCT‐1 expression', The FASEB Journal, vol. 26, no. S1.
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We have shown that apigenin and naringenin (flavonoids) suppress colon carcinogenesis by inducing apoptosis and suppressing proliferation in rats. The goal of this experiment was to test the hypothesis that apigenin and naringenin affect proliferation and apoptosis by regulating expression of genes involved in microbial recognition (TLR‐2, TLR‐4), short‐chain fatty acid transport (MCT‐1), cell cycle (p21), and apoptosis (Bax, Bcl‐2, Fas). Rats received diets (0.02% naringenin, 0.1% apigenin, or control) for 10 wk and were treated with AOM at wk 3 and 4. Apigenin suppressed (p<0.05) MCT‐1 expression compared to control, with naringenin being intermediate. Apigenin and naringenin suppressed (p<0.01) p21 expression. Expression of TLR‐4, a promoter of proliferation, also was suppressed by apigenin and naringenin (p<0.04). Diet did not affect expression of Bax, Bcl‐2, Fas, or TLR‐2. Considering MCT‐1 is a butyrate transporter and butyrate induces colonocyte p21 expression, it is possible that suppression of p21 by apigenin and naringenin may be a MCT‐1 mediated effect. Reduction of MCT‐1, p21, and TLR‐4 expression by apigenin and naringenin could have contributed to apoptosis induction and suppression of proliferation. Thus, both apigenin and naringenin were able to reduce colon carcinogenesis through their influence on expression of genes involved in multiple pathways. Funding USDA 2010‐34402‐20875.

Davie, AW, Mitrovic, SM & Lim, RP 2012, 'Succession and accrual of benthic algae on cobbles of an upland river following scouring', INLAND WATERS, vol. 2, no. 2, pp. 89-100.
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Flow releases from dams can be used to scour benthic algae, simulating the effects of natural spates and maintaining benthic algae in an early successional stage for increased grazer palatability. The timing of releases needs to consider the natural periodicity of flow events and the speed of regrowth and community succession changes. We studied benthic algal regrowth and succession using manipulative field experiments during summer and winter in the upland regulated Severn River, New South Wales, Australia. Benthic algal biomass accrual as chlorophyll a and community changes were determined after artificially scoured cobbles were returned to the river. In summer, algal biomass and diversity on scoured cobbles took 2 weeks to return to levels similar to reference cobbles and 5 weeks in winter. Chlorophyll a during summer was initially 0.24 ± 0.06 mg m-2 on scoured cobbles, but by day 16 had increased to 9.74 ± 1.97 mg m-2 and was no longer significantly different from reference cobbles. In winter, chlorophyll a was initially 0.47 ± 0.13 mg m-2 on scoured cobbles, but by day 37 had increased to 44.7 ± 10.9 mg m-2 and was no longer significantly different from reference cobbles. Peak chlorophyll a accrual during summer and winter was 1.64 and 2.63 mg m-2 d-1, respectively. Early succession in both experiments was dominated by diatoms such as Cocconeis, Synedra, and Fragilaria. A proliferation of the filamentous green alga Stigeoclonium was indicative of a late succession community. The implications for flow management based on resetting of benthic algae by scouring in riffle reaches of rivers are discussed.

Davila, YC, Elle, E, Vamosi, JC, Hermanutz, L, Kerr, JT, Lortie, CJ, Westwood, AR, Woodcock, TS & Worley, AC 2012, 'Ecosystem services of pollinator diversity: a review of the relationship with pollen limitation of plant reproduction', BOTANY-BOTANIQUE, vol. 90, no. 7, pp. 535-543.
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Recent work on the ecosystem service of biodiversity suggests that higher pollinator diversity could lower pollen limitation, but these two aspects of plant-pollinator communities have only rarely been causally connected. Here we present a review of studies that produced quantitative assessments of both pollinator diversity and evenness as well as pollen limitation of focal plant species. Although pollen limitation is expected to be lower when pollinator diversity is high, our analysis suggests this relationship is weak. The relationship may be obscured when features of the plant species (e.g., average level of specialization) are confounded with features of the plant communities (e.g., habitat). We encourage researchers investigating pollen limitation to consider including measures of diversity of the floral visitors, and their effectiveness. These data would permit a more powerful test of the relationships among these variables and improve our understanding of the critical elements of stable plant-pollinator networks.

Davis, J, Short, K, Lumpkin, G, Whittle, K, Wuhrer, R & Phillips, MR 2012, 'EBSD Studies of Ion Implanted Duplex Stainless Steel', Microscopy and Microanalysis, vol. 18, no. S2, pp. 1346-1347.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Dawes, FE, Bulach, DM, Kuzevski, A, Bettelheim, KA, Venturini, C, Djordjevic, SP & Walker, MJ 2012, 'Molecular Characterization of a 21.4 Kilobase Antibiotic Resistance Plasmid from an α-Hemolytic Escherichia coli O108:H- Human Clinical Isolate', PLoS ONE, vol. 7, no. 4, pp. e34718-e34718.
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This study characterizes the 21.4 kilobase plasmid pECTm80 isolated from Escherichia coli strain 80, an α hemolytic human clinical diarrhoeal isolate (serotype O108:H-). DNA sequence analysis of pECTm80 revealed it belonged to incompatibility group X1, and contained plasmid partition and toxin-antitoxin systems, an R6K-like triple origin (ori) replication system, genes required for replication regulation, insertion sequences IS1R, ISEc37 and a truncated transposase gene (Tn3-like ΔtnpA) of the Tn3 family, and carried a class 2 integron. The class 2 integron of pECTm80 contains an intact cassette array dfrA1-sat2, encoding resistance to trimethoprim and streptothricin, and an aadA1 gene cassette truncated by the insertion of IS1R. The complex plasmid replication system includes α, β and γ origins of replication. Pairwise BLASTn comparison of pECTm80 with plasmid pE001 reveals a conserved plasmid backbone suggestive of a common ancestral lineage. Plasmid pECTm80 is of potential clinical importance, as it carries multiple genes to ensure its stable maintenance through successive bacterial cell divisions and multiple antibiotic resistance genes. © 2012 Dawes et al.

De Grazia, A, Mikhael, M, Stojanovska, N, Reedy, B, Shimmon, R & Tahtouh, M 2012, 'Diacetylene copolymers for fingermark development', FORENSIC SCIENCE INTERNATIONAL, vol. 216, no. 1-3, pp. 189-197.
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In 1979, Miller and Patel showed that a solution containing two diacetylene monomers, 2,4-hexadiyne-1,6-bis(phenylurethane) (HDDPU) and 2,4-hexadiyne-1,6-bis(p-chlorophenylurethane) (HDDCPU) could be used to develop latent fingermarks on a non-porous surface. In the current work, the same mixture (HDDPU:HDDCPU = 10:1, in acetone solution) was used to develop fingermarks on a wide variety of surfaces, both non-porous and porous, including paper. An airbrush system was optimized for the application of the reagent solution. Once the solution evaporates on a surface, the monomers co-crystallize in different ways, depending upon a number of factors, including the surface residue. Active co-crystallization leads (with heat or radiation) to the formation of purple polymer, while inactive crystallization results in a non-polymerizable white deposit. Fingermark contrast was achieved as a result of active co-crystallization (giving purple polymer) in either the ridges or the furrows, depending upon the surface and other factors. A general observation (supported by spot tests with linseed oil, salt and amino acid solutions) was that on paper, oily materials are more likely to lead to the formation of the purple polymer, while the presence of water inhibits polymerization.

De Silva, KSB, Gambhir, S, Wang, XL, Xu, X, Li, WX, Officer, DL, Wexler, D, Wallace, GG & Dou, SX 2012, 'The effect of reduced graphene oxide addition on the superconductivity of MgB2', JOURNAL OF MATERIALS CHEMISTRY, vol. 22, no. 28, pp. 13941-13946.
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Reduced graphene oxide (rGO) and highly reduced chemically converted graphene (rCCG) samples were prepared under different processing conditions and were doped into MgB 2 by a diffusion process at 800 °C for 10 hours. It was demonstrated that a small addition rCCG can significantly improve the superconducting properties of MgB 2. Doping of MgB 2 with 1 mol% of rCCG resulted in a J c of 5.45 × 10 5 A cm -2 at 20 K in self-fields, which is nearly 32% improvement over that of the undoped sample. This is a significant improvement as most carbon sources adversely affect the J c performance at the zero field. © 2012 The Royal Society of Chemistry.

De Silva, KSB, Xu, X, Wang, XL, Wexler, D, Attard, D, Xiang, F & Dou, SX 2012, 'A significant improvement in the superconducting properties of MgB2 by co-doping with graphene and nano-SiC', SCRIPTA MATERIALIA, vol. 67, no. 10, pp. 802-805.
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Dearnley, MK, Yeoman, JA, Hanssen, E, Kenny, S, Turnbull, L, Whitchurch, CB, Tilley, L & Dixon, MWA 2012, 'Origin, composition, organization and function of the inner membrane complex of Plasmodium falciparum gametocytes', JOURNAL OF CELL SCIENCE, vol. 125, no. 8, pp. 2053-2063.
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The most virulent of the human malaria parasites, Plasmodium falciparum, undergoes a remarkable morphological transformation as it prepares itself for sexual reproduction and transmission via mosquitoes. Indeed P. falciparum is named for the unique falciform or crescent shape of the mature sexual stages. Once the metamorphosis is completed, the mature gametocyte releases from sequestration sites and enters the circulation, thus making it accessible to feeding mosquitoes. Early ultrastructural studies showed that gametocyte elongation is driven by the assembly of a system of flattened cisternal membrane compartments underneath the parasite plasma membrane and a supporting network of microtubules. Here we describe the molecular composition and origin of the sub-pellicular membrane complex, and show that it is analogous to the inner membrane complex, an organelle with structural and motor functions that is well conserved across the apicomplexa. We identify novel crosslinking elements that might help stabilize the inner membrane complex during gametocyte development. We show that changes in gametocyte morphology are associated with an increase in cellular deformability and postulate that this enables the gametocytes to circulate in the bloodstream without being detected and removed by the mechanical filtering mechanisms in the spleen of the host. © 2012.

Demers, H, Poirier-Demers, N, Phillips, MR, de Jonge, N & Drouin, D 2012, 'Three-Dimensional Electron Energy Deposition Modeling of Cathodoluminescence Emission near Threading Dislocations in GaN and Electron-Beam Lithography Exposure Parameters for a PMMA Resist', MICROSCOPY AND MICROANALYSIS, vol. 18, no. 6, pp. 1220-1228.
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The Monte Carlo software CASINO has been expanded with new modules for the simulation of complex beam scanning patterns, for the simulation of cathodoluminescence (CL), and for the calculation of electron energy deposition in subregions of a three-dimensional (3D) volume. Two examples are presented of the application of these new capabilities of CASINO. First, the CL emission near threading dislocations in gallium nitride (GaN) was modeled. The CL emission simulation of threading dislocations in GaN demonstrated that a better signal-to-noise ratio was obtained with lower incident electron energy than with higher energy. Second, the capability to simulate the distribution of the deposited energy in 3D was used to determine exposure parameters for polymethylmethacrylate resist using electron-beam lithography (EBL). The energy deposition dose in the resist was compared for two different multibeam EBL schemes by changing the incident electron energy. © 2012 Microscopy Society of America.

Deplazes, E, Jayatilaka, D & Corry, B 2012, 'ExiFRET: flexible tool for understanding FRET in complex geometries', Journal of Biomedical Optics, vol. 17, no. 1, pp. 011005-011005.
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Deplazes, E, Louhivuori, M, Jayatilaka, D, Marrink, SJ & Corry, B 2012, 'Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations', PLoS Computational Biology, vol. 8, no. 9, pp. e1002683-e1002683.
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Deutscher, AT, Tacchi, JL, Minion, FC, Padula, MP, Crossett, B, Bogema, DR, Jenkins, C, Kuit, TA, Walker, MJ & Djordjevic, SP 2012, 'Mycoplasma hyopneumoniae Surface Proteins Mhp385 and Mhp384 Bind Host Cilia and Glycosaminoglycans and Are Endoproteolytically Processed by Proteases That Recognize Different Cleavage Motifs', JOURNAL OF PROTEOME RESEARCH, vol. 11, no. 3, pp. 1924-1936.
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P97 and P102 paralogues occur as endoproteolytic cleavage fragments on the surface of Mycoplasma hyopneumoniae that bind glycosaminoglycans, plasminogen, and fibronectin and perform essential roles in colonization of ciliated epithelia. We show that the P102 paralogue Mhp384 is efficiently cleaved at an S/T-X-F↓X-D/E-like site, creating P60 384 and P50 384. The P97 paralogue Mhp385 is inefficiently cleaved, with tryptic peptides from a 115 kDa protein (P115 385) and 88 kDa (P88 385) and 27 kDa (P27 385) cleavage fragments identified by LC-MS/MS. This is the first time a preprotein belonging to the P97 and P102 paralogue families has been identified by mass spectrometry. The semitryptic peptide 752IQFELEPISLNV 763 denotes the C-terminus of P88 385 and defines the novel cleavage site 761L-N-V↓A-V- S 766 in Mhp385. P115 385, P88 385, P27 385, P60 384, and P50 384 were shown to reside extracellularly, though it is unknown how the fragments remain attached to the cell surface. Heparin- and cilium-binding sites were identified within P60 384, P50 384, and P88 385. No primary function was attributed to P27 385; however, this molecule contains four tandem R1 repeats with similarity to porcine collagen type VI (α3 chain). P97 and P102 paralogue families are adhesins targeted by several proteases with different cleavage efficiencies, and this process generates combinatorial complexity on the surface of M. hyopneumoniae. © 2012 American Chemical Society.

Didelot, X, Meric, G, Falush, D & Darling, AE 2012, 'Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli', BMC GENOMICS, vol. 13, pp. 1-15.
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Background: Escherichia coli is an important species of bacteria that can live as a harmless inhabitant of the guts of many animals, as a pathogen causing life-threatening conditions or freely in the non-host environment. This diversity of lifestyles has

Ding, Y, Xie, H, Peng, T, Lu, Y, Jin, D, Teng, J, Ren, Q & Xi, P 2012, 'Laser oblique scanning optical microscopy (LOSOM) for phase relief imaging', OPTICS EXPRESS, vol. 20, no. 13, pp. 14100-14108.
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The visualization of optical phase can provide abundant information when imaging transparent specimen. We present a novel phase sensitive imaging design capable of obtaining phase contours of transparent biological cells through laser oblique scanning optical microscope (LOSOM). LOSOM is based on the introduction of a fluorescent medium behind the specimen to generate a differential phase-sensitive image, thus, the complicated phase retardation alignment procedure associated with differential interference contrast (DIC) microscopy can be eliminated. Moreover, multi-modality fluorescence and phase relief imaging can be attained in a single system with fluorescently labeled specimens. © 2012 Optical Society of America.

Donovan, C, Tan, X & Bourke, JE 2012, 'PPARγLigands Regulate Noncontractile and Contractile Functions of Airway Smooth Muscle: Implications for Asthma Therapy', PPAR Research, vol. 2012, pp. 1-13.
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In asthma, the increase in airway smooth muscle (ASM) can contribute to inflammation, airway wall remodeling and airway hyperresponsiveness (AHR). Targetting peroxisome proliferator-activated receptorγ(PPARγ), a receptor upregulated in ASM in asthmatic airways, may provide a novel approach to regulate these contributions. This review summarises experimental evidence that PPARγligands, such as rosiglitazone (RGZ) and pioglitazone (PGZ), inhibit proliferation and inflammatory cytokine production from ASMin vitro. In addition, inhaled administration of these ligands reduces inflammatory cell infiltration and airway remodelling in mouse models of allergen-induced airways disease. PPARγligands can also regulate ASM contractility, with acute treatment eliciting relaxation of mouse tracheain vitrothrough a PPARγ-independent mechanism. Chronic treatment can protect against the loss of bronchodilator sensitivity toβ2-adrenoceptor agonists and inhibit the development of AHR associated with exposure to nicotinein uteroor following allergen challenge. Of particular interest, a small clinical trial has shown that oral RGZ treatment improves lung function in smokers with asthma, a group that is generally unresponsive to conventional steroid treatment. These combined findings support further investigation of the potential for PPARγagonists to target the noncontractile and contractile functions of ASM to improve outcomes for patients with poorly controlled asthma.

Dooley, AH & Golodets, VY 2012, 'On the entropy of actions of nilpotent Lie groups and their lattice subgroups', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 32, pp. 535-573.
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Dooley, AH & Hagihara, R 2012, 'Computing the critical dimensions of Bratteli-Vershik systems with multiple edges', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 32, pp. 103-117.
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Dooley, AH & Rudolph, DJ 2012, 'Non-uniqueness in G-measures', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 32, pp. 575-586.
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Dooley, AH & Zhang, G 2012, 'Co-induction in dynamical systems', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 32, pp. 919-940.
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Dossou, KB & Botten, LC 2012, 'A combined three-dimensional finite element and scattering matrix method for the analysis of plane wave diffraction by bi-periodic, multilayered structures', JOURNAL OF COMPUTATIONAL PHYSICS, vol. 231, no. 20, pp. 6969-6989.
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A three-dimensional finite element method (FEM) for the analysis of plane wave diffraction by a bi-periodic slab is described and implemented. A scattering matrix formalism based on the FEM allows the efficient treatment of light reflection and transmission by multilayer bi-periodic structures, and the computation of Bloch modes of three-dimensional arrays. Numerical simulations, which show the accuracy and flexibility of the FEM, are presented. © 2012 Elsevier Inc.

Dossou, KB, Botten, LC, Asatryan, AA, Sturmberg, BCP, Byrne, MA, Poulton, CG, McPhedran, RC & de Sterke, CM 2012, 'Modal formulation for diffraction by absorbing photonic crystal slabs', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, vol. 29, no. 5, pp. 817-831.
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A finite element-based modal formulation of diffraction of a plane wave by an absorbing photonic crystal slab of arbitrary geometry is developed for photovoltaic applications. The semianalytic approach allows efficient and accurate calculation of the absorption of an array with a complex unit cell. This approach gives direct physical insight into the absorption mechanism in such structures, which can be used to enhance the absorption. The verification and validation of this approach is applied to a silicon nanowire array, and the efficiency and accuracy of the method is demonstrated. The method is ideally suited to studying the manner in which spectral properties (e.g., absorption) vary with the thickness of the array, and we demonstrate this with efficient calculations that can identify an optimal geometry. © 2012 Optical Society of America.

Dubern, J-F, Cigana, C, Lazenby, J, De Simone, M, Juhas, M, Schwager, S, Eberl, L, Doring, G, Williams, P, Bragonzi, A & Camara, M 2012, '86 Genome wide random screening strategy for the discovery of novel antimicrobial targets in Pseudomonas aeruginosa', Journal of Cystic Fibrosis, vol. 11, pp. S78-S78.
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Dubey, S, Croak, B, Pike, D, Webb, J & Shine, R 2012, 'Phylogeography and dispersal in the velvet gecko (Oedura lesueurii), and potential implications for conservation of an endangered snake (Hoplocephalus bungaroides)', BMC Evolutionary Biology, vol. 12, no. 1, pp. 67-67.
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Background: To conserve critically endangered predators, we also need to conserve the prey species upon which they depend. Velvet geckos (Oedura lesueurii) are a primary prey for the endangered broad-headed snake (Hoplocephalus bungaroides), which is restricted to sandstone habitats in southeastern Australia. We sequenced the ND2 gene from 179 velvet geckos, to clarify the lizards phylogeographic history and landscape genetics. We also analysed 260 records from a longterm (3-year) capture-mark-recapture program at three sites, to evaluate dispersal rates of geckos as a function of locality, sex and body size. Results: The genetic analyses revealed three ancient lineages in the north, south and centre of the species current range. Estimates of gene flow suggest low dispersal rates, constrained by the availability of contiguous rocky habitat. Mark-recapture records confirm that these lizards are highly sedentary, with most animals moving<30m from their original capture site even over multi-year periods. Conclusion: The low vagility of these lizards suggests that they will be slow to colonise vacant habitat patches; and hence, efforts to restore degraded habitats for broad-headed snakes may need to include translocation of lizards. © 2012 Dubey et al.; licensee BioMed Central Ltd.

Dunn, SR, Pernice, M, Green, K, Hoegh-Guldberg, O & Dove, SG 2012, 'Thermal Stress Promotes Host Mitochondrial Degradation in Symbiotic Cnidarians: Are the Batteries of the Reef Going to Run Out?', PLoS ONE, vol. 7, no. 7, pp. e39024-e39024.
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The symbiotic relationship between cnidarians and their dinoflagellate symbionts, Symbiodinium spp, which underpins the formation of tropical coral reefs, can be destabilized by rapid changes to environmental conditions. Although some studies have concluded that a breakdown in the symbiosis begins with increased reactive oxygen species (ROS) generation within the symbiont due to a decoupling of photosynthesis, others have reported the release of viable symbionts via a variety of host cell derived mechanisms. We explored an alternative model focused upon changes in host cnidarian mitochondrial integrity in response to thermal stress. Mitochondria are often likened to being batteries of the cell, providing energy in the form of ATP, and controlling cellular pathway activation and ROS generation. The overall morphology of host mitochondria was compared to that of associated symbionts under an experimental thermal stress using confocal and electron microscopy. The results demonstrate that hyperthermic stress induces the degradation of cnidarian host mitochondria that is independent of symbiont cellular deterioration. The potential sites of host mitochondrial disruption were also assessed by measuring changes in the expression of genes associated with electron transport and ATP synthesis using quantitative RT-PCR. The primary site of degradation appeared to be downstream of complex III of the electron transport chain with a significant reduction in host cytochrome c and ATP synthase expression. The consequences of reduced expression could limit the capacity of the host to mitigate ROS generation and maintain both organelle integrity and cellular energy supplies. The disruption of host mitochondria, cellular homeostasis, and subsequent cell death irrespective of symbiont integrity highlights the importance of the host response to thermal stress and in symbiosis dysfunction that has substantial implications for understanding how coral reefs will survive in the...

Edgar, JA, McDonagh, AM & Cortie, MB 2012, 'Formation of Gold Nanorods by a Stochastic 'Popcorn' Mechanism', ACS NANO, vol. 6, no. 2, pp. 1116-1125.
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Gold nanorods have significant technological potential and are of broad interest to the nanotechnology community. The discovery of the seeded, wet-chemical synthetic process to produce them may be regarded as a landmark in the control of metal nanoparticle shape. However, the mechanism by which the initial spherical gold seeds acquire anisotropy is a critical, yet poorly understood, factor. Here we examine the very early stages of rod growth using a combination of techniques including cryogenic transmission electron microscopy, optical spectroscopy, and computational modeling. Reconciliation of the available experimental observations can only be achieved by invoking a stochastic, 'popcorn'-like mechanism of growth, in which individual seeds lie quiescent for some time before suddenly and rapidly growing into rods. This is quite different from the steady, concurrent growth of nanorods that has been previously generally assumed. Furthermore we propose that the shape is controlled by the ratio of surface energy of rod sides to rod ends, with values of this quantity in the range of 0.3-0.8 indicated for typical growth solutions. © 2012 American Chemical Society.

El Saliby, I, Shahid, M, McDonagh, A, Shon, HK & Kim, J-H 2012, 'Photodesorption of organic matter from titanium dioxide particles in aqueous media', Journal of Industrial and Engineering Chemistry, vol. 18, no. 5, pp. 1774-1780.
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Photo-induced desorption of organic compounds from TiO2 particles in aqueous media during photocatalysis has promising applications in water treatment. Photodesorption is a relatively fast phenomenon that facilitates the regeneration of photocatalysts with low energy consumption while concentrating the waste products in an energy and water efficient process. We propose that this transport phenomenon involves a significantly reduced affinity between the photocatalyst and pollutants upon UV illumination, and leads to the rapid detachment/decomposition of adsorbed pollutants. In this study, we report the effect of experimental conditions (pH, photocatalyst loading, organic loading, UV light irradiation and flow rate) on this phenomenon in a recirculating photocatalysis continuous reactor. Initially, organic compounds were allowed to adsorb on the surface of the photocatalyst (Degussa P25) until adsorption equilibrium was achieved. The photodesorption phenomenon was observed shortly after UVlight illumination of TiO2 but before the bulk photocatalytic oxidation takes place. The pH of the solution was found to affect both the adsorption and the desorption percentages revealing the role of particle charge on this phenomenon. Additionally, a 1 g/L loading of photocatalyst showed an optimum photodesorption rate using a single strength synthetic wastewater at pH 7.

Elder, M 2012, 'A short introduction to self-similar groups', The Australian Mathematical Society. Gazette, vol. 39, pp. 125-133.

Elder, M, Elston, G & Ostheimer, G 2012, 'On groups that have normal forms computable in logspace', Journal of Algebra, vol. 381, pp. 260-281.
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We consider the class of finitely generated groups which have a normal formcomputable in logspace. We prove that the class of such groups is closed underfinite extensions, finite index subgroups, direct products, wreath products,and also certain free products, and includes the solvable Baumslag-Solitargroups, as well as non-residually finite (and hence non-linear) examples. Wedefine a group to be logspace embeddable if it embeds in a group with normalforms computable in logspace. We prove that finitely generated nilpotent groupsare logspace embeddable. It follows that all groups of polynomial growth arelogspace embeddable.

Ellis, J, Goodswen, S, Kennedy, PJ & Bush, S 2012, 'The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses', Bioinformatics and Biology Insights, vol. 6, pp. BBI.S9954-BBI.S9954.
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In this study, the BALB/c and Qs mouse responses to infection by the parasite Neospora caninum were investigated in order to identify host response mechanisms. Investigation was done using gene set (enrichment) analyses of microarray data. GSEA, MANOVA, Romer, subGSE and SAM-GS were used to study the contrasts Neospora strain type, Mouse type (BALB/c and Qs) and time post infection (6 hours post infection and 10 days post infection). The analyses show that the major signal in the core mouse response to infection is from time post infection and can be defined by gene ontology terms Protein Kinase Activity, Cell Proliferation and Transcription Initiation. Several terms linked to signaling, morphogenesis, response and fat metabolism were also identified. At 10 days post infection, genes associated with fatty acid metabolism were identified as up regulated in expression. The value of gene set (enrichment) analyses in the analysis of microarray data is discussed.

England, DG, Michelberger, PS, Champion, TFM, Reim, KF, Lee, KC, Sprague, MR, Jin, X-M, Langford, NK, Kolthammer, WS, Nunn, J & Walmsley, IA 2012, 'High-fidelity polarization storage in a gigahertz bandwidth quantum memory', Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 45, no. 12, pp. 124008-124008.
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Essilfie, A-T, Simpson, JL, Dunkley, ML, Morgan, LC, Oliver, BG, Gibson, PG, Foster, PS & Hansbro, PM 2012, 'Combined Haemophilus influenzae respiratory infection and allergic airways disease drives chronic infection and features of neutrophilic asthma', THORAX, vol. 67, no. 7, pp. 588-599.
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Background: 20-30% of patients with asthma have neutrophilic airway inflammation and reduced responsiveness to steroid therapy. They often have chronic airway bacterial colonisation and Haemophilus influenzae is one of the most commonly isolated bacteria. The relationship between chronic airway colonisation and the development of steroid-resistant neutrophilic asthma is unclear. Objectives: To investigate the relationship between H influenzae respiratory infection and neutrophilic asthma using mouse models of infection and ovalbumin (OVA)- induced allergic airways disease. Methods: BALB/c mice were intratracheally infected with H influenzae (day 10), intraperitoneally sensitised (day 0) and intranasally challenged (day 12-15) with OVA. Treatment groups were administered dexamethasone intranasally during OVA challenge. Infection, allergic airways disease, steroid sensitivity and immune responses were assessed (days 11, 16 and 21). Results: The combination of H influenzae infection and allergic airways disease resulted in chronic lung infection that was detected on days 11, 16 and 21 (21, 26 and 31 days after infection). Neutrophilic allergic airways disease and T helper 17 cell development were induced, which did not require active infection. Importantly, all features of neutrophilic allergic airways disease were steroid resistant. Toll-like receptor 4 expression and activation of phagocytes was reduced, but most significantly the influx and/or development of phagocytosing neutrophils and macrophages into the airways was inhibited. Conclusions: The combination of infection and allergic airways disease promotes bacterial persistence, leading to the development of a phenotype similar to steroid-resistant neutrophilic asthma and which may result from dysfunction in innate immune cells. This indicates that targeting bacterial infection in steroid-resistant asthma may have therapeutic benefit.

Everest-Dass, AV, Jin, D, Thaysen-Andersen, M, Nevalainen, H, Kolarich, D & Packer, NH 2012, 'Comparative structural analysis of the glycosylation of salivary and buccal cell proteins: innate protection against infection by Candida albicans', Glycobiology, vol. 22, no. 11, pp. 1465-1479.
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Mucosal epithelial surfaces, such as line the oral cavity, are common sites of microbial colonization by bacteria, yeast and fungi. The microbial interactions involve adherence between the glycans on the host cells and the carbohydrate-binding proteins of the pathogen. Saliva constantly bathes the buccal cells of the epithelial surface of the mouth and we postulate that the sugars on the salivary glycoproteins provide an innate host immune mechanism against infection by competitively inhibiting pathogen binding to the cell membranes. The structures of the N-and O-linked oligosaccharides on the glycoproteins of saliva and buccal cell membranes were analyzed using capillary carbon liquid chromatography-electrospray ionization MS/MS. The 190 glycan structures that were characterized were qualitatively similar, but differed quantitatively, between saliva and epithelial buccal cell membrane proteins. The similar relative abundance of the terminal glycan epitope structures (e.g. ABO(H) blood group, sialylation and Lewis-type antigens) on saliva and buccal cell membrane glycoproteins indicated that the terminal N-and O-linked glycan substructures in saliva could be acting as decoy-binding receptors to competitively inhibit the attachment of pathogens to the surface of the oral mucosa. A flow cytometry-based binding assay quantified the interaction between buccal cells and the commensal oral pathogen Candida albicans. Whole saliva and released glycans from salivary proteins inhibited the interaction of C. albicans with buccal epithelial cells, confirming the protective role of the glycans on salivary glycoproteins against pathogen infection. © 2012 The Author.

Exton, DA, Suggett, DJ, Steinke, M & McGenity, TJ 2012, 'Spatial and temporal variability of biogenic isoprene emissions from a temperate estuary', Global Biogeochemical Cycles, vol. 26, no. 2, pp. n/a-n/a.
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Isoprene is important for its atmospheric impacts and the ecophysiological benefits it affords to emitting organisms; however, isoprene emissions from marine systems remain vastly understudied compared to terrestrial systems. This study investigates for the first time drivers of isoprene production in a temperate estuary, and the role this production may play in enabling organisms to tolerate the inherently wide range of environmental conditions. Intertidal sediment cores as well as high and low tide water samples were collected from four sites along the Colne Estuary, UK, every six weeks over a year. Isoprene concentrations in the water were significantly higher at low than high tide, and decreased toward the mouth of the estuary; sediment production showed no spatial variability. Diel isoprene concentration increased with light availability and decreased with tidal height; nighttime production was 79% lower than daytime production. Seasonal isoprene production and water concentrations were highest for the warmest months, with production strongly correlated with light (r2 = 0.800) and temperature (r2 = 0.752). Intertidal microphytobenthic communities were found to be the primary source of isoprene, with tidal action acting as a concentrating factor for isoprene entering the water column. Using these data we estimated an annual production rate for this estuary of 681 μmol m−2 y−1. This value falls at the upper end of other marine estimates and highlights the potentially significant role of estuaries as isoprene sources. The control of estuarine isoprene production by environmental processes identified here further suggests that such emissions may be altered by future environmental change.

Eyles, M 2012, 'Many fingers in the pie', Food Australia, vol. 64, no. 1, pp. 32-33.

Fagerlind, MG, Webb, JS, Barraud, N, McDougald, D, Jansson, A, Nilsson, P, Harlén, M, Kjelleberg, S & Rice, SA 2012, 'Dynamic modelling of cell death during biofilm development', Journal of Theoretical Biology, vol. 295, pp. 23-36.
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Faille, D, El‐Assaad, F, Mitchell, AJ, Alessi, M, Chimini, G, Fusai, T, Grau, GE & Combes, V 2012, 'Endocytosis and intracellular processing of platelet microparticles by brain endothelial cells', Journal of Cellular and Molecular Medicine, vol. 16, no. 8, pp. 1731-1738.
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AbstractPlatelet‐derived microparticles (PMP) bind and modify the phenotype of many cell types including endothelial cells. Recently, we showed that PMP were internalized by human brain endothelial cells (HBEC). Here we intend to better characterize the internalization mechanisms of PMP and their intracellular fate. Confocal microscopy analysis of PKH67‐labelled PMP distribution in HBEC showed PMP in early endosome antigen 1 positive endosomes and in LysoTracker‐labelled lysosomes, confirming a role for endocytosis in PMP internalization. No fusion of calcein‐loaded PMP with HBEC membranes was observed. Quantification of PMP endocytosis using flow cytometry revealed that it was partially inhibited by trypsin digestion of PMP surface proteins and by extracellular Ca2+ chelation by EDTA, suggesting a partial role for receptor‐mediated endocytosis in PMP uptake. This endocytosis was independent of endothelial receptors such as intercellular adhesion molecule‐1 and vascular cell adhesion molecule‐1 and was not increased by tumour necrosis factor stimulation of HBEC. Platelet‐derived microparticle internalization was dramatically increased in the presence of decomplemented serum, suggesting a role for PMP opsonin‐dependent phagocytosis. Platelet‐derived microparticle uptake was greatly diminished by treatment of HBEC with cytochalasin D, an inhibitor of microfilament formation required for both phagocytosis and macropinocytosis, with methyl‐β‐cyclodextrin that depletes membrane cholesterol needed for macropinocytosis and with amiloride that inhibits the Na+/H+ exchanger involved in macropinocytosis. In conclusion, PMP are taken up by active endocytosis in HBEC, involving mechanisms consistent with both phagocytosis and macropinocytosis. These findings identify new processes by which PMP could modify endothelial cell phenotype and functions.

Faiz, A & Burgess, JK 2012, 'How Can Microarrays Unlock Asthma?', Journal of Allergy, vol. 2012, pp. 1-15.
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Asthma is a complex disease regulated by the interplay of a large number of underlying mechanisms which contribute to the overall pathology. Despite various breakthroughs identifying genes related to asthma, our understanding of the importance of the genetic background remains limited. Although current therapies for asthma are relatively effective, subpopulations of asthmatics do not respond to these regimens. By unlocking the role of these underlying mechanisms, a source of novel and more effective treatments may be identified. In the new age of high-throughput technologies, gene-expression microarrays provide a quick and effective method of identifying novel genes and pathways, which would be impossible to discover using an individual gene screening approach. In this review we follow the history of expression microarray technologies and describe their contributions to advancing our current knowledge and understanding of asthma pathology.

Falconer, RJ & Markelz, AG 2012, 'Terahertz Spectroscopic Analysis of Peptides and Proteins', Journal of Infrared, Millimeter, and Terahertz Waves, vol. 33, no. 10, pp. 973-988.
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Falklof, O, Collyer, CA & Reimers, JR 2012, 'Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations', THEORETICAL CHEMISTRY ACCOUNTS, vol. 131, no. 1.
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© Springer-Verlag 2012. The refinement of protein crystal structures currently involves the use of empirical restraints and force fields that are known to work well in many situations but nevertheless yield structural models with some features that are inconsistent with detailed chemical analysis and therefore warrant further improvement. Ab initio electronic structure computational methods have now advanced to the point at which they can deliver reliable results for macromolecules in realistic times using linear-scaling algorithms. The replacement of empirical force fields with ab initio methods in a final refinement stage could allow new structural features to be identified in complex structures, reduce errors and remove computational bias from structural models. In contrast to empirical approaches, ab initio refinements can only be performed on models that obey basic qualitative chemical rules, imposing constraints on the parameter space of existing refinements, and this in turn inhibits the inclusion of unlikely structural features. Here, we focus on methods for determining an appropriate ensemble of initial structural models for an ab initio X-ray refinement, modeling as an example the high-resolution single-crystal X-ray diffraction data reported for the structure of lysozyme (PDB entry “2VB1”). The AMBER force field is used in a Monte Carlo calculation to determine an ensemble of 8 structures that together embody all of the partial atomic occupancies noted in the original refinement, correlating these variations into a set of feasible chemical structures while simultaneously retaining consistency with the X-ray diffraction data. Subsequent analysis of these results strongly suggests that the occupancies in the empirically refined model are inconsistent with protein energetic considerations, thus depicting the 2VB1 structure as a deep-lying minimum in its optimized parameter space that actually embodies chemically unreasonable features. Indeed, de...

Fane, AG, Wang, R, Tang, CY, Nielsen, CH, Rice, S & Chong, TH 2012, 'REMOVED: Bio-Inspired Enhancement of Membrane Desalination', Procedia Engineering, vol. 44, pp. 591-593.
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Fang, J, Aharonovich, I, Leychenko, I, Ostrikov, KK, Spizzirri, PG, Rubanov, S & Prawer, S 2012, 'Plasma-Enabled Growth of Single-Crystalline SiC/AlSiC Core-Shell Nanowires on Porous Alumina Templates', CRYSTAL GROWTH & DESIGN, vol. 12, no. 6, pp. 2917-2922.
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We report the catalyst-free synthesis of the arrays of core-shell, ultrathin, size-uniform SiC/AlSiC nanowires on the top of a periodic anodic aluminum oxide template. The nanowires were grown using an environmentally friendly, silane-free process by exposing the silicon supported porous alumina template to CH 4 + H 2 plasmas. High-resolution scanning and transmission electron microscopy studies revealed that the nanowires have a single-crystalline core with a diameter of about 10 nm and a thin (1-2 nm) amorphous AlSiC shell. Because of their remarkable length, high aspect ratio, and very high surface area-to-volume ratio, these unique structures are promising for nanoelectronic and nanophotonic applications that require efficient electron emission, light scattering, etc. A mechanism for nanowire growth is proposed based upon the reduction of the alumina template to nanosized metallic aluminum droplets forming between nanopores. The subsequent incorporation of silicon and carbon atoms from the plasma leads to nucleation and growth from the top of the alumina template. © 2012 American Chemical Society.

Farrell, H, Gentien, P, Fernand, L, Lunven, M, Reguera, B, Gonzalez-Gil, S & Raine, R 2012, 'Scales characterising a high density thin layer of Dinophysis acuta Ehrenberg and its transport within a coastal jet', HARMFUL ALGAE, vol. 15, pp. 36-46.
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An investigation into the distribution of Dinophysis spp. in coastal waters off the south coast of Ireland was carried out in July 2007. Dinophysis acuta was present as a sub surface layer containing up to 55,000cellsL -1. The population had a high percentage of viable cells (mean: 89%; median: 94%; n=24) with a high specific division rate (∼0.55d -1). The layer, of approximately 5m thickness, did not coincide with the fluorescence maximum and was present as a patch of horizontal dimension less than 10km×7km. Both conventional and towed undulating CTD used in conjunction with high vertical resolution sampling methods showed the patch of Dinophysis to move with a similar speed and direction as the coastal flow, which ran parallel to the coast in the form of a coastal jet with speed of the order of 6.5-7kmday -1. The implications of the alongshore transport of populations of harmful species in coastal jets for monitoring programmes and predictive models are discussed. © 2011 Elsevier B.V.

Feito, R, Valcárcel, Y & Catalá, M 2012, 'Biomarker assessment of toxicity with miniaturised bioassays: diclofenac as a case study', Ecotoxicology, vol. 21, no. 1, pp. 289-296.
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Fletcher, SM, Stark, D, Harkness, J & Ellisa, J 2012, 'Enteric Protozoa in the Developed World: a Public Health Perspective', CLINICAL MICROBIOLOGY REVIEWS, vol. 25, no. 3, pp. 420-449.
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Several enteric protozoa cause severe morbidity and mortality in both humans and animals worldwide. In developed settings, enteric protozoa are often ignored as a cause of diarrheal illness due to better hygiene conditions, and as such, very little effort is used toward laboratory diagnosis. Although these protozoa contribute to the high burden of infectious diseases, estimates of their true prevalence are sometimes affected by the lack of sensitive diagnostic techniques to detect them in clinical and environmental specimens. Despite recent advances in the epidemiology, molecular biology, and treatment of protozoan illnesses, gaps in knowledge still exist, requiring further research. There is evidence that climate-related changes will contribute to their burden due to displacement of ecosystems and human and animal populations, increases in atmospheric temperature, flooding and other environmental conditions suitable for transmission, and the need for the reuse of alternative water sources to meet growing population needs. This review discusses the common enteric protozoa from a public health perspective, highlighting their epidemiology, modes of transmission, prevention, and control. It also discusses the potential impact of climate changes on their epidemiology and the issues surrounding waterborne transmission and suggests a multidisciplinary approach to their prevention and control.

Fogarty, S, Harris, D, Zaslawski, C, McAinch, AJ & Stojanovska, L 2012, 'Development of a Chinese Medicine Pattern Severity Index for Understanding Eating Disorders', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 18, no. 6, pp. 597-606.
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Introduction: Eating disorders commonly affect young girls and women. Four eating disorders are analyzed in this study: anorexia nervosa (AN), bulimia nervosa (BN), eating disorders not otherwise specified (EDNOS), and binge eating disorder (BED). Eating disorders are a modern concept and as such there is no critically appraised research on how Traditional Chinese Medicine (TCM) conceptualizes of or treats eating disorders. The purpose of this study is to identify and quantify the TCM patterns relevant to eating disorders based on a systematic evaluation of the results of a self-reported questionnaire. Methods: One hundred and ninety-six (196) female participants (142 with a self-reported eating disorder and 54 with no eating disorder) completed an online survey, designed to collect data on their current general health and, where relevant, their eating disorder. The Berle methodology was used to identify TCM patterns involved in eating disorders to tabulate and score the number of signs and symptoms experienced by the participants. Results: For many of the TCM patterns, statistically significant differences were found between presentation severity across the four eating disorders. Conclusions: For the first time, there is evidence-based research to classify the TCM patterns involved in AN, BN, EDNOS, and BED. Evidence is given to support the anecdotal theories of TCM patterns involved in eating disorder presentation. These results have relevance on how eating disorders are treated and viewed by TCM practitioners. © Copyright 2012, Mary Ann Liebert, Inc. 2012.

Fowler, AM & Booth, DJ 2012, 'Evidence of sustained populations of a small reef fish on artificial structures. Does depth affect production on artificial reefs?', JOURNAL OF FISH BIOLOGY, vol. 80, no. 3, pp. 613-629.
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The length frequencies and age structures of resident Pseudanthias rubrizonatus (n = 407), a small protogynous serranid, were measured at four isolated artificial structures on the continental shelf of north-western Australia between June and August 2008, to determine whether these structures supported full (complete size and age-structured) populations of this species. The artificial structures were located in depths between 82 and 135 m, and growth rates of juveniles and adults, and body condition of adults, were compared among structures to determine the effect of depth on potential production. All life-history stages, including recently settled juveniles, females and terminal males, of P. rubrizonatus were caught, ranging in standard length (L s) from 16·9 to 96·5 mm. Presumed ages estimated from whole and sectioned otoliths ranged between 22 days and 5 years, and parameter ±s.e. estimates of the von Bertalanffy growth model were L ∞ = 152 ± 34 mm, k = 0·15(±0·05) and t 0 = -1·15(±0·15). Estimated annual growth rates were similar between shallow and deep artificial structures; however, otolith lengths and recent growth of juveniles differed among individual structures, irrespective of depth. The artificial structures therefore sustained full populations of P. rubrizonatus, from recently settled juveniles through to adults; however, confirmation of the maximum age attainable for the species is required from natural populations. Depth placement of artificial reefs may not affect the production of fish species with naturally wide depth ranges. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Fowler, AM & Booth, DJ 2012, 'How well do sunken vessels approximate fish assemblages on coral reefs? Conservation implications of vessel-reef deployments', MARINE BIOLOGY, vol. 159, no. 12, pp. 2787-2796.
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The amount of artificial habitat (termed 'artificial reef', AR) in marine systems is rapidly increasing, yet the effect of most types of AR on reef communities remains unknown. We examined the role of well-established vessel-reefs in structuring coral reef fish assemblages by comparing assemblages on 7 World War II wrecks (>65 years old) to those on interspersed coral patch reefs of comparable size in a tropical lagoon. Fish abundance, species richness, diversity and feeding guild structure on wrecks were similar to natural reefs; however, species composition differed between the two reef types (R = 0.189-0.341, average dissimilarity: 67.3-68.8 %). Despite being more species-rich and diverse, fish assemblages on larger wrecks were less similar to assemblages on their adjacent natural reefs than smaller wrecks. Wrecks may also have affected fish abundance on adjacent natural reefs, with reefs adjacent to larger wrecks supporting higher abundances than reefs adjacent to smaller wrecks. Our results indicate that increases in vessel-reef habitat may not greatly affect reef fish assemblage parameters, but may affect the relative abundances of particular species. © 2012 Springer-Verlag.

Fronzi, M, Cereda, S, Tateyama, Y, De Vita, A & Traversa, E 2012, 'Ab initioinvestigation of defect formation at ZrO2-CeO2interfaces', Physical Review B, vol. 86, no. 8.
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The structural and electronic properties of low index (100) and (111) ZrO 2 -CeO 2 interfaces are analyzed on the basis of density functional theory calculations. The formation energy and relative stability of substitutional defects, oxygen vacancies, and vacancy-dopant complexes are investigated for the (100) orientation. By comparing these results with the ones obtained in bulk structures, we provide a possible explanation for the higher experimental ionic conductivity measured at the interface. © 2012 American Physical Society.

Fu, H, Jiang, X, Yang, X, Yu, A, Su, D & Wang, G 2012, 'Glycothermal synthesis of assembled vanadium oxide nanostructures for gas sensing', Journal of Nanoparticle Research, vol. 14, no. 6, pp. 1-14.
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This study demonstrates a facile but effective glycothermal method to synthesize vanadium oxide nanostructures for gas sensing detection. In this method, sodium orthovanadate was first dispersed and heated in ethylene glycol at 120-180 °C for a few hours, and then the precipitates were collected, rinsed, and sintered at high temperatures (e.g., 600°C) for V 2O 5 in air and V 2O 3 in nitrogen, respectively. The as-prepared vanadium oxide particles are nanorods (200 nm × 1 μm) and can assemble into microspheres or urchin-like structures with a diameter of ~3 μm. The experimental parameters (temperature, time, and surfactants) and the formation mechanisms were investigated by various advanced techniques, such as transmission electron microscope, scanning electron microscope, X-ray diffraction, Fourier transform infrared spectroscopy, and thermo-gravimetric analysis. Finally, the V 2O 5 nanoparticles were tested for sensing detection of gas species of acetone, isopropanol, and ammonia. The microurchin structures show higher sensing performance than the nanorods. Graphical Abstract: [Figure not available: see fulltext.] © 2012 Springer Science+Business Media B.V.

Fujimoto, R, Sasaki, T, Ishikawa, R, Osabe, K, Kawanabe, T & Dennis, ES 2012, 'Molecular Mechanisms of Epigenetic Variation in Plants', INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 13, no. 8, pp. 9900-9922.
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Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identifi

Fujimoto, R, Taylor, JM, Shirasawa, S, Peacock, WJ & Dennis, ES 2012, 'Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 109, no. 18, pp. 7109-7114.
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Arabidopsis thaliana shows hybrid vigor (heterosis) in progeny of crosses between Columbia-0 and C24 accessions. Hybrid vigor was evident as early as mature seeds and in seedlings 3 d after sowing (DAS). At 3 DAS, genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes that have greater than midparent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll, and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3-7 DAS period. At 10 DAS, only 118 genes had expression levels different from the expected midparent value in the hybrid, and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increases in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation, we found that an inhibitor of photosynthesis eliminated heterosis and that higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low-level heterosis (Landsberg erecta x Columbia-0), chloroplast-targeted genes were not up-regulated and leaf areas were only marginally increased.

Gale, PA, Hiscock, JR, Lalaoui, N, Light, ME, Wells, NJ & Wenzel, M 2012, 'Benzimidazole-based anion receptors: tautomeric switching and selectivity', Organic & Biomolecular Chemistry, vol. 10, no. 30, pp. 5909-5909.
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Gallagher, R, Shimmon, R & McDonagh, AM 2012, 'Synthesis and impurity profiling of MDMA prepared from commonly available starting materials', FORENSIC SCIENCE INTERNATIONAL, vol. 223, no. 1-3, pp. 306-313.
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This work examines the synthesis of 3,4-methylenedioxy-N-methylamphetamine (MDMA) from common starting materials that may be utilised by clandestine laboratory operators. Piperonal was prepared from two common starting materials, piperine (from pepper) and vanillin (a common flavouring). Piperine was converted to piperonal by ozonolysis and oxidative cleavage with potassium permanganate and tetrahydrofuran. Vanillin was converted to piperonal by demethylation with pyridine and aluminium chloride followed by methylenation with dichloromethane. The resulting piperonal samples were converted via a commonly encountered route to MDMA. The impurities that indicate a particular route were identified and the feasibility of each method was also assessed. © 2012 Elsevier Ireland Ltd.

Gautam, R, Kulow, M, Döpfer, D, Kaspar, C, Gonzales, T, Pertzborn, KM, Carroll, RJ, Grant, W & Ivanek, R 2012, 'The strain-specific dynamics ofEscherichia coliO157:H7 faecal shedding in cattle post inoculation', Journal of Biological Dynamics, vol. 6, no. 2, pp. 1052-1066.
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This study reports analysis of faecal shedding dynamics in cattle for three Escherichia coli O157:H7 (ECO157) strains (S1, S2 and S3) of different genotype and ecological history, using experimental inoculation data. The three strains were compared for their shedding frequency and level of ECO157 in faeces. A multistate Markov chain model was used to compare shedding patterns of S1 and S2. Strains S1 and S2 were detected seven to eight times more often and at 104 larger levels than strain S3. Strains S1 and S2 had similar frequencies and levels of shedding. However, the total time spent in the shedding state during colonization was on average four times longer for S1 (15 days) compared to S2 (4 days). These results indicate that an ECO157 strain effect on the frequency, level, pattern and the duration of faecal shedding may need to be considered in control of ECO157 in the cattle reservoir. © 2012 Copyright R. Gautam.

Ge, Q, Moir, LM, Trian, T, Niimi, K, Poniris, M, Shepherd, PR, Black, JL, Oliver, BG & Burgess, JK 2012, 'The phosphoinositide 3 '-kinase p110 delta modulates contractile protein production and IL-6 release in human airway smooth muscle', JOURNAL OF CELLULAR PHYSIOLOGY, vol. 227, no. 8, pp. 3044-3052.
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Transforming growth factor (TGF) ß1 increases pro-inflammatory cytokines and contractile protein expression by human airway smooth muscle (ASM) cells, which could augment airway inflammation and hyperresponsiveness. Phosphoinositide 3' kinase (PI3K) is one of the signaling pathways implicated in TGFß1 stimulation, and may be altered in asthmatic airways. This study compared the expression of PI3K isoforms by ASM cells from donors with asthma (A), chronic obstructive pulmonary disease (COPD), or neither disease (NA), and investigated the role of PI3K isoforms in the production of TGFß1 induced pro-inflammatory cytokine and contractile proteins in ASM cells. A cells expressed higher basal levels of p110d mRNA compared to NA and COPD cells; however COPD cells produced more p110d protein. TGFß1 increased 110d mRNA expression to the same extent in the three groups. Neither the p110d inhibitor IC87114 (1, 10, 30?µM), the p110ß inhibitor TGX221 (0.1, 1, 10?µM) nor the PI3K pan inhibitor LY294002 (3, 10?µM) had any effect on basal IL-6, calponin or smooth muscle a-actin (a-SMA) expression. However, TGFß1 increased calponin and a-SMA expression was inhibited by IC87114 and LY294002 in all three groups. IC87114, TGX221, and LY294002 reduced TGFß1 induced IL-6 release in a dose related manner in all groups of ASM cells. PI3K p110d is important for TGFß1 induced production of the contractile proteins calponin and a-SMA and the proinflammatory cytokine IL-6 in ASM cells, and may therefore be relevant as a potential therapeutic target to treat both inflammation and airway remodeling.

George, AM & Jones, PM 2012, 'Perspectives on the structure–function of ABC transporters: The Switch and Constant Contact Models', Progress in Biophysics and Molecular Biology, vol. 109, no. 3, pp. 95-107.
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ABC transporters constitute one of the largest protein families across the kingdoms of archaea, eubacteria and eukarya. They couple ATP hydrolysis to vectorial translocation of diverse substrates across membranes. The ABC transporter architecture comprises two transmembrane domains and two cytosolic ATP-binding cassettes. During 2002-2012, nine prokaryotic ABC transporter structures and two eukaryotic structures have been solved to medium resolution. Despite a wealth of biochemical, biophysical, and structural data, fundamental questions remain regarding the coupling of ATP hydrolysis to unidirectional substrate translocation, and the mechanistic suite of steps involved. The mechanics of the ATP cassette dimer is defined most popularly by the 'Switch Model', which proposes that hydrolysis in each protomer is sequential, and that as the sites are freed of nucleotide, the protomers lose contact across a large solvent-filled gap of 20-30 angstrom: as captured in several X-ray solved structures. Our 'Constant Contact' model for the operational mechanics of ATP binding and hydrolysis in the ATP-binding cassettes is derived from the 'alternating sites' model, proposed in 1995, and which requires an intrinsic asymmetry in the ATP sites, but does not require the partner protomers to lose contact. Thus one of the most debated issues regarding the function of ABC transporters is whether the cooperative mechanics of ATP hydrolysis requires the ATP cassettes to separate or remain in constant contact and this dilemma is discussed at length in this review.

Gerace, D, Ren, B, Hawthorne, WJ, Byrne, MR, Phillips, P, OʼBrien, BA, Nassif, N, Alexander, IE & Simpson, AM 2012, 'Pancreatic Transdifferentiation in Porcine Liver Following Lentiviral Delivery of Human Furin-Cleavable Insulin', Transplantation Journal, vol. 94, no. 10S, pp. 172-172.
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Ghassabian, S, Rawling, T, Zhou, F, Doddareddy, MR, Tattam, BN, Hibbs, DE, Edwards, RJ, Cui, PH & Murray, M 2012, 'Role of human CYP3A4 in the biotransformation of sorafenib to its major oxidized metabolites', Biochemical Pharmacology, vol. 84, no. 2, pp. 215-223.
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The tyrosine kinase inhibitor drug sorafenib is used in the treatment of liver and renal cancers but adverse effects may necessitate dose interruption and under-dosage may lead to therapeutic failure. Sorafenib also undergoes cytochrome P450 (CYP)-dependent biotransformation to the N-oxide and other metabolites. However, although CYPs are major determinants of efficacy and toxicity the roles of these enzymes in the formation of multiple sorafenib metabolites are unclear. In the present study CYP-mediated pathways of sorafenib oxidation in human liver were evaluated. cDNA-expressed CYP3A4 was the major catalyst in the formation of the principal N-oxide and N-hydroxymethyl metabolites of sorafenib, as well as the minor N-desmethyl metabolite. In contrast, CYP3A5 exhibited only ~5% of the activity of CYP3A4 and eleven other CYPs and three flavin-containing monooxygenases were inactive. In human hepatic microsomes metabolite formation was correlated with CYP3A4-mediated midazolam 1'-hydroxylation, but not with other CYP-specific substrate oxidations. In accord with these findings the CYP3A4 inhibitor ketoconazole selectively inhibited microsomal sorafenib oxidation pathways. From computational modeling studies atoms in the structure of sorafenib that undergo biotransformation were within ~5.4 Å of the CYP3A4 heme. Important hydrogen bonding interactions between sorafenib and amino acids Ser-119 and Glu-374 in the active center of CYP3A4 were identified. These findings indicate that sorafenib is oxidized selectively by human CYP3A4. This information could be adapted in individualized approaches to optimize sorafenib safety and efficacy in cancer patients.

Gilbert, JA, Hill, R, Doblin, MA & Ralph, PJ 2012, 'Microbial consortia increase thermal tolerance of corals', MARINE BIOLOGY, vol. 159, no. 8, pp. 1763-1771.
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This study examined the response of a coral holobiont to thermal stress when the bacterial community was treated with antibiotics. Colonies of Pocillopora damicornis were exposed to broad and narrow-spectrum antibiotics targeting coral-associated α and γ-Proteobacteria. Corals were gradually heated from the control temperature of 26 to 31 °C, and measurements were made of host, zooxanthellar and microbial condition. Antibiotics artificially reduced the abundance and activity of bacteria, but had minimal effect on zooxanthellae photosynthetic efficiency or host tissue protein content. Heated corals without antibiotics showed significant declines in F V/F M, typical of thermal stress. However, heated corals treated with antibiotics showed severe tissue loss in addition to a decline in F V/F M. This study demonstrated that a disruption to the microbial consortium diminished the resilience of the holobiont. Corals exposed to antibiotics under control temperature did not bleach, suggesting that temperature may be an important factor influencing the activity, diversity and ecological function of the holobiont bacterial community. © 2012 Springer-Verlag.

Giunta, S, Castorina, A, Bucolo, C, Magro, G, Drago, F & D’Agata, V 2012, 'Early changes in pituitary adenylate cyclase-activating peptide, vasoactive intestinal peptide and related receptors expression in retina of streptozotocin-induced diabetic rats', Peptides, vol. 37, no. 1, pp. 32-39.
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Giunta, S, Castorina, A, Scuderi, S, Patti, C & D’Agata, V 2012, 'Epidermal growth factor receptor (EGFR) and neuregulin (Neu) activation in human airway epithelial cells exposed to nickel acetate', Toxicology in Vitro, vol. 26, no. 2, pp. 280-287.
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Gladstone, W, Lindfield, S, Coleman, M & Kelaher, B 2012, 'Optimisation of baited remote underwater video sampling designs for estuarine fish assemblages', JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY, vol. 429, pp. 28-35.
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Baited remote underwater video stations (BRUVS) are used for monitoring fish assemblages and assessing management effectiveness in reef environments but are infrequently used in estuaries. A review of the BRUVS literature found that most adopted sampling designs from other studies were rarely designed from pilot studies. This potentially compromises their value for monitoring natural and anthropogenic variation. The aims of this study were: (i) to assess the suitability of BRUVS for sampling fishes in estuarine habitats (seagrass beds and unvegetated sediments) and (ii) to develop an optimal and cost effective sampling methodology for each habitat. Fishes in both habitats were sampled independently using BRUVS with soak times of 30, 60, 90. min (n=4). Thirty five species of fishes were recorded including 18 species of economic importance. Mean number of species, mean total Max N and mean Max N of species did not differ among soak times. Precision was generally greater in seagrass and in both habitats it improved with increasing soak time. Bootstrapping revealed that greater improvements in precision occurred from increasing soak time rather than increasing replication. A sampling design with n=5 replicates of 90. min soak time was optimal for most variables. This sampling effort is greater than many current applications of BRUVS. The results highlight the importance of pilot studies to optimise sampling methods and develop cost effective and statistically-robust monitoring programs. © 2012 Elsevier B.V.

Glanville, EJ, Murray, SA & Seebacher, F 2012, 'Thermal adaptation in endotherms: climate and phylogeny interact to determine population-level responses in a wild rat', FUNCTIONAL ECOLOGY, vol. 26, no. 2, pp. 390-398.
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1. The ecology of endotherms is driven by their great energetic need for thermoregulation, which renders mammals and birds particularly vulnerable to environmental temperature and resource fluctuations. Important outstanding questions are whether populations are specialized to their particular climate, and to what extent gene x environment interactions determine thermal responses. 2. Here, we show that phylogenetic relatedness and climate interact to determine metabolic capacities, body temperature and morphology in a wild rat ( Rattus fuscipes). 3. Mitochondrial metabolic capacities are greater in warm climate populations, indicating that these responses are not the result of cold adaptation. However, glycolytic capacities, fur thickness and capacity for nonshivering thermogenesis are greater in cool climate populations. In populations from cooler climates, body temperatures are lower, but more variable. Together, these changes lead to substantial energy savings in cool climate populations, although all traits are constrained by phylogenetic relatedness. 4. We demonstrate for the first time that gene u environment interactions determine thermal responses in wild mammal populations, and we suggest that physiological variability among populations may render the species more resilient to climate change because it increases wholespecies performance breadth. Climate envelope modelling is therefore insufficient to predict the future impact of climate change.

Gloeckl, S, Tyndall, JDA, Stansfield, SH, Timms, P & Huston, WM 2012, 'The Active Site Residue V266 of Chlamydial HtrA Is Critical for Substrate Binding during both in vitro and in vivo Conditions', Microbial Physiology, vol. 22, no. 1, pp. 10-16.
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HtrA is a complex, multimeric chaperone and serine protease important for the virulence and survival of many bacteria. <i>Chlamydia trachomatis </i>is an obligate, intracellular bacterial pathogen that is responsible for severe disease pathology. <i>C. trachomatis </i>HtrA (CtHtrA) has been shown to be highly expressed in laboratory models of disease. In this study, molecular modelling of CtHtrA protein active site structure identified putative S1–S3 subsite residues I242, I265, and V266. These residues were altered by site-directed mutagenesis, and these changes were shown to considerably reduce protease activity on known substrates and resulted in a narrower and distinct range of substrates compared to wild type. Bacterial two-hybrid analysis revealed that CtHtrA is able to interact in vivo with a broad range of protein sequences with high affinity. Notably, however, the interaction was significantly altered in 35 out of 69 clones when residue V266 was mutated, indicating that this residue has an important function during substrate binding.

Godecke, E, Hird, K, Lalor, EE, Rai, T & Phillips, MR 2012, 'Very early poststroke aphasia therapy: a pilot randomized controlled efficacy trial', INTERNATIONAL JOURNAL OF STROKE, vol. 7, no. 8, pp. 635-644.
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Background and purpose Early stroke rehabilitation has shown benefits over spontaneous recovery. Insufficient evidence exists to determine the benefits of early aphasia intervention. We hypothesized that daily aphasia therapy would show better communication outcomes than usual care (UC) in early poststroke recovery. Method This prospective, randomized, single-blinded, controlled trial was conducted in three acute-care hospitals in Perth, Australia, each with over 200 stroke admissions annually. Patients with acute stroke causing moderate to severe aphasia were recruited at a median of three-days (range: 0-10 days) to receive daily aphasia therapy or usual care therapy. Individually tailored, impairment-based intervention was provided for the acute hospital stay or intervention phase (median: 19 days; range: 5-76). Primary outcome measures were the aphasia quotient and functional communication profile at acute hospital discharge or four-weeks poststroke, whichever came first. A random-number generator and sealed envelopes were used to randomize participants. Assessments were completed by a blinded assessor. Results Fifty-nine participants were recruited, with six withdrawals (10%) and seven deaths (12%) at six-months. Ninety percent had ischemic strokes, with 56·5% experiencing a total anterior circulation stroke. The group mean (±SD) age was 69·1 (±13·9) years. Six participants (18·75%) in the daily aphasia therapy group did not complete the minimum (150min) therapy required for this study. The daily aphasia therapy intervention phase mean therapy session time was 45min (range: 30-80) and the total mean amount of therapy for the daily aphasia therapy participants was 331min (range: 30-1415). Four (15%) participants in the usual care group received therapy. The collective total therapy provided to these participants was 295min over seven sessions. Usual care participants received an average of 10·5min of therapy per week during the intervention phase. At...

Gong, J, Jaiswal, R, Mathys, J-M, Combes, V, Grau, GER & Bebawy, M 2012, 'Microparticles and their emerging role in cancer multidrug resistance', CANCER TREATMENT REVIEWS, vol. 38, no. 3, pp. 226-234.
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Drug resistance is a major obstacle to the successful treatment of cancer as tumor cells either fail to reduce in size following chemotherapy or the cancer recurs after an initial response. The phenomenon of multidrug resistance (MDR) is particularly problematic as it involves the simultaneous resistance to numerous chemotherapeutics of different classes. MDR is predominantly attributed to the overexpression of efflux transporters such as P-glycoprotein (P-gp) and the Multidrug Resistance-Associated Protein 1 (MRP1). P-gp and MRP1 are members of the ATP Binding Cassette (ABC) superfamily of transporters and are capable of effluxing many chemotherapeutics out of cancer cells, allowing them to survive the toxic insult.Numerous strategies have been developed over the years to circumvent MDR. Of these, the discovery and implementation of P-gp and MRP1 inhibitors have been most extensively studied. However, these inhibitors have not been able to be used clinically. While research continues in this area, it must also be acknowledged that other avenues must be explored.Recently, the novel 'non-genetic' acquisition of P-gp-mediated MDR by microparticles (MPs) has been reported. MPs are vesicles 0.1-1. μm in diameter that are released via plasma membrane blebbing. They are important mediators of inflammation, coagulation and vascular homeostasis. In addition to surface P-gp protein, MPs also carry various nucleic acid species as cargo. This 'non-genetic' intercellular transfer provides an alternative pathway for the cellular acquisition and dissemination of traits and implicates MPs as important mediators in the spread of MDR and provides a novel pathway for the circumvention of MDR. © 2011 Elsevier Ltd.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2012, 'Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques', PLOS ONE, vol. 7, no. 11.
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Gräfe, M, Solntsev, AS, Keil, R, Sukhorukov, AA, Heinrich, M, Tünnermann, A, Nolte, S, Szameit, A & Kivshar, YS 2012, 'Biphoton generation in quadratic waveguide arrays: A classical optical simulation', Scientific Reports, vol. 2, no. 1.
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Greaves, IK, Groszmann, M, Dennis, ES & Peacock, WJ 2012, 'Trans-chromosomal methylation', EPIGENETICS, vol. 7, no. 8, pp. 800-805.
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The epigenome plays a vital role in helping to maintain and regulate cell functions in all organisms. Alleles with differing epigenetic marks in the same nucleus do not function in isolation but can interact in trans to modify the epigenetic state of one or both alleles. This is particularly evident when two divergent epigenomes come together in a hybrid resulting in thousands of alterations to the methylome. These changes mainly involve the methylation patterns at one allele being changed to resemble the methylation patterns of the other allele, in processes we have termed trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). These processes are primarily modulated by siRNAs and the RNA directed DNA methylation pathway. Drawing from other examples of trans-allelic interactions, we describe the process of TCM and TCdM and the effect such changes can have on genome activity. Trans-allelic epigenetic interactions may be a common occurrence in many biological systems.

Greaves, IK, Groszmann, M, Ying, H, Taylor, JM, Peacock, WJ & Dennis, ES 2012, 'Trans Chromosomal Methylation in Arabidopsis hybrids', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 109, no. 9, pp. 3570-3575.
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The heterotic hybrid offspring of Arabidopsis accessions C24 and Landsberg erecta have altered methylomes. Changes occur most frequently at loci where parental methylation levels are different. There are context-specific biases in the nonadditive methylation patterns with mCG generally increased and mCHH decreased relative to the parents. These changes are a result of two main mechanisms, Trans Chromosomal Methylation and Trans Chromosomal deMethylation, where the methylation level of one parental allele alters to resemble that of the other parent. Regions of altered methylation are enriched around genic regions and are often correlated with changes in siRNA levels. We identified examples of genes with altered expression likely to be due to methylation changes and suggest that in crosses between the C24 and Ler accessions, epigenetic controls can be important in the generation of altered transcription levels that may contribute to the increased biomass of the hybrids.

Gredeskul, SA, Kivshar, YS, Asatryan, AA, Bliokh, KY, Bliokh, YP, Freilikher, VD & Shadrivov, IV 2012, 'Anderson localization in metamaterials and other complex media (Review Article)', LOW TEMPERATURE PHYSICS, vol. 38, no. 7, pp. 570-602.
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We review some recent (mostly ours) results on the Anderson localization of light and electron waves in complex disordered systems, including: (i) left-handed metamaterials, (ii) magnetoactive optical structures, (iii) graphene superlattices, and (iv) nonlinear dielectric media. First, we demonstrate that left-handed metamaterials can significantly suppress localization of light and lead to an anomalously enhanced transmission. This suppression is essential at the long-wavelength limit in the case of normal incidence, at specific angles of oblique incidence (Brewster anomaly), and in the vicinity of the zero-ε or zero-μ frequencies for dispersive metamaterials. Remarkably, in disordered samples comprised of alternating normal and left-handed metamaterials, the reciprocal Lyapunov exponent and reciprocal transmittance increment can differ from each other. Second, we study magnetoactive multilayered structures, which exhibit nonreciprocal localization of light depending on the direction of propagation and on the polarization. At resonant frequencies or realizations, such nonreciprocity results in effectively unidirectional transport of light. Third, we discuss the analogy between the wave propagation through multilayered samples with metamaterials and the charge transport in graphene, which enables a simple physical explanation of unusual conductive properties of disordered graphene superlatices. We predict disorder-induced resonances of the transmission coefficient at oblique incidence of the Dirac quasiparticles. Finally, we demonstrate that an interplay of nonlinearity and disorder in dielectric media can lead to bistability of individual localized states excited inside the medium at resonant frequencies. This results in nonreciprocity of the wave transmission and unidirectional transport of light. © S.A. Gredeskul, Y.S. Kivshar, A.A. Asatryan, K.Y. Bliokh, Y.P. Bliokh, V.D. Freilikher, and I.V. Shadrivov, 2012.

Green, BC, Suggett, DJ, Hills, A & Steinke, M 2012, 'Optimisation of a fast DMS sensor (FDS) for real time quantification of dimethyl sulfide production by algae', Biogeochemistry, vol. 110, no. 1-3, pp. 163-172.
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Production of dimethyl sulfide (DMS) from marine samples is often quantified using gas chromatography techniques. Typically, these are labour intensive and have a slow sample turnover rate. Here we demonstrate the use of a portable fast DMS sensor (FDS) that utilises the chemiluminescent reaction of DMS and ozone to measure DMS production in aqueous samples, with a maximum frequency of 10 Hz. We have developed a protocol for quantifying DMS production that removes potential signal interference from other biogenic trace gases such as isoprene (2-methyl-1,3-butadiene) and hydrogen sulfide. The detection limit was 0. 89 pM (0. 02 ppbv) when using a DMS standard gas mixture. The lowest DMS production rates quantified with the FDS and verified using conventional gas chromatography with flame photometric detection (GC-FPD) were around 0. 01 nmol min -1. There was a strong correlation in DMS production when comparing the FDS and GC-FPD techniques with a range of marine samples (e. g., r 2 = 0. 94 for Emiliania huxleyi). However, the combined dataset showed the FDS measured 22% higher DMS production than the GC-FPD, with the differences in rates likely due to interfering gases, for example hydrogen sulfide and isoprene. This possible overestimation of DMS production is smaller than the two-fold difference in DMS production between day and night samples from a culture of E. huxleyi. The response time of the instrument to changes in DMS production is method dependent (e. g., geometry of incubation vessel, bubble size) and was approximately 4 min under our conditions when using a culture of E. huxleyi (800 ml) with aeration at 100 ml min -1. We suggest the FDS can reduce sample handling, is suitable for short- and long-term measurements of DMS production in algal cultures, and will widen the range of DMS research in marine environments. © 2011 Springer Science+Business Media B.V.

Green, DW, Li, G, Milthorpe, B & Ben-Nissan, B 2012, 'Adult stem cell coatings for regenerative medicine', Materials Today, vol. 15, no. 1-2, pp. 60-66.
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Stem cells can become potent tools for the treatment of degenerative disorders such as heart failure, eye disease and osteoarthritis. Housing stem cells inside a hydrogel coating, directly deposited around them individually and in groups, may be an important solution to the problem of increasing stem cell viability and protection in cultivation. Such coatings can target regulatory proteins and genes for maintenance, differentiation and development into tissues. Already polymer coatings are being applied directly to protect insulin producing pancreatic islet cells in the hope of treating type I diabetes. Here, we review current emerging developments in adult mesenchymal stem cell nanocoating and microcoating techniques and assess their unique practical engineering, biological and potential clinical advantages.

Green, LC, Kalitsis, P, Chang, TM, Cipetic, M, Kim, JH, Marshall, O, Turnbull, L, Whitchurch, CB, Vagnarelli, P, Samejima, K, Earnshaw, WC, Choo, KHA & Hudson, DF 2012, 'Contrasting roles of condensin I and condensin II in mitotic chromosome formation', JOURNAL OF CELL SCIENCE, vol. 125, no. 6, pp. 1591-1604.
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In vertebrates, two condensin complexes exist, condensin I and condensin II, which have differing but unresolved roles in organizing mitotic chromosomes. To dissect accurately the role of each complex in mitosis, we have made and studied the first vertebrate conditional knockouts of the genes encoding condensin I subunit CAP-H and condensin II subunit CAP-D3 in chicken DT40 cells. Live-cell imaging reveals highly distinct segregation defects. CAP-D3 (condensin II) knockout results in masses of chromatincontaining anaphase bridges. CAP-H (condensin I)-knockout anaphases have a more subtle defect, with chromatids showing fine chromatin fibres that are associated with failure of cytokinesis and cell death. Super-resolution microscopy reveals that condensin-Idepleted mitotic chromosomes are wider and shorter, with a diffuse chromosome scaffold, whereas condensin-II-depleted chromosomes retain a more defined scaffold, with chromosomes more stretched and seemingly lacking in axial rigidity. We conclude that condensin II is required primarily to provide rigidity by establishing an initial chromosome axis around which condensin I can arrange loops of chromatin. © 2012.

Gribben, L, Baxter, RC & Marsh, DJ 2012, 'Insulin-like growth factor binding protein-3 inhibits migration of endometrial cancer cells', Cancer Letters, vol. 317, no. 1, pp. 41-48.
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Gristwood, T, Duggin, IG, Wagner, M, Albers, SV & Bell, SD 2012, 'The sub-cellular localization of Sulfolobus DNA replication', NUCLEIC ACIDS RESEARCH, vol. 40, no. 12, pp. 5487-5496.
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Analyses of the DNA replication-associated proteins of hyperthermophilic archaea have yielded considerable insight into the structure and biochemical function of these evolutionarily conserved factors. However, little is known about the regulation and progression of DNA replication in the context of archaeal cells. In the current work, we describe the generation of strains of Sulfolobus solfataricus and Sulfolobus acidocaldarius that allow the incorporation of nucleoside analogues during DNA replication. We employ this technology, in conjunction with immunolocalization analyses of replisomes, to investigate the sub-cellular localization of nascent DNA and replisomes. Our data reveal a peripheral localization of replisomes in the cell. Furthermore, while the two replication forks emerging from any one of the three replication origins in the Sulfolobus chromosome remain in close proximity, the three origin loci are separated. © The Author(s) 2012. Published by Oxford University Press.

Gupta, P, Gupta, A, Agarwal, K, Tomar, P & Satija, S 2012, 'Antioxidant and cytotoxic potential of a new thienyl derivative fromTagetes erectaroots', Pharmaceutical Biology, vol. 50, no. 8, pp. 1013-1018.
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Gupta, V, Bijo, AJ, Kumar, M, Reddy, CRK & Jha, B 2012, 'Detection of Epigenetic Variations in the Protoplast-Derived Germlings of Ulva reticulata Using Methylation Sensitive Amplification Polymorphism (MSAP)', Marine Biotechnology, vol. 14, no. 6, pp. 692-700.
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Regeneration of protoplasts into de novo plants was reported for a large number of seaweed species. The regeneration of protoplasts into different morphotypes as a result of epigenetic variations was discussed for the first time in this study. The loci assessed for methylation modifications in normal filamentous thalli showed a frequency of 32. 43% as unmethylated DNA, 24. 32% as a hemimethylated, and 20. 27% as a methylation of internal cytosine at both the strands. The corresponding methylation values for disk-type thalli were 27. 02%, 32. 43%, and 14. 86%, respectively. The hypermethylation condition was apparent in the disk-type thalli with methylation ratio of 72. 97% compared to that of normal filamentous thalli with 67. 56%. The frequency of methylation polymorphic sites among the two morphotypes was 53%. The present study reveals the distinct expression of cytosine methylation and is thus correlated to differential morphogenesis of plants regenerated from cultured cells. The number of protoplasts regenerating into filamentous thalli declined with increasing temperature from 15°C, 20°C, 25°C, and 30°C. The disk-type variant had higher thermal stability at 30°C over normal filamentous thalli. Further, this variant could maintain itself for more than a year in the laboratory indicating its suitability for in vitro germplasm maintenance and propagation. © 2012 The Author(s).

Gutman, N, de Sterke, CM, Sukhorukov, AA & Botten, LC 2012, 'Slow and frozen light in optical waveguides with multiple gratings: Degenerate band edges and stationary inflection points', PHYSICAL REVIEW A, vol. 85, no. 3, pp. 1-11.
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We show that a waveguide with multiple gratings can have a modal dispersion relation which supports frozen light. This means that light can be coupled efficiently to low group velocity modes of an optical waveguide or can even have finite coupling to zero group velocity modes. These effects are associated with stationary points in the dispersion of the form ω-ω o ⊃(k⊃-k o⊃)m, for integer order m>1, around a center frequency ω o and wave number k o. Stationary points of any order can be created, not only regular band edges (m=2), but also degenerate band edges (m>2 and even) and stationary inflection points (m odd). Using the perturbation theory of matrices in Jordan normal form, the modes and their properties are calculated analytically. Efficient coupling is shown to stem from evanescent modes which must accompany the presence of high-order stationary points with m>2. © 2012 American Physical Society.

Hahn, MA, Dickson, K-A, Jackson, S, Clarkson, A, Gill, AJ & Marsh, DJ 2012, 'The tumor suppressor CDC73 interacts with the ring finger proteins RNF20 and RNF40 and is required for the maintenance of histone 2B monoubiquitination', Human Molecular Genetics, vol. 21, no. 3, pp. 559-568.
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Hall, P, Pham, T, Wand, MP & Wang, SSJ 2012, 'Asymptotic normality and valid inference for Gaussian variational approximation', Annals of Statistics, vol. 39, no. 5, pp. 2502-2532.
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We derive the precise asymptotic distributional behavior of Gaussianvariational approximate estimators of the parameters in a single-predictorPoisson mixed model. These results are the deepest yet obtained concerning thestatistical properties of a variational approximation method. Moreover, theygive rise to asymptotically valid statistical inference. A simulation studydemonstrates that Gaussian variational approximate confidence intervals possessgood to excellent coverage properties, and have a similar precision to theirexact likelihood counterparts.

Hallegraeff, GM, Blackburn, SI, Doblin, MA & Bolch, CJS 2012, 'Global toxicology, ecophysiology and population relationships of the chainforming PST dinoflagellate Gymnodinium catenatum', HARMFUL ALGAE, vol. 14, pp. 130-143.
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Increasing scientific awareness since the 1980s of the chain-forming dinoflagellate Gymnodinium catenatum has led to this species being reported with increased frequency in a globally increasing number of countries (23 at present). G. catenatum exhibits little molecular genetic variation in rDNA over its global range, in contrast to RAPD fingerprinting which points to high genetic variation within regional populations even between estuaries 50. km apart. All Australian and New Zealand strains possess a thymine nucleotide (T-gene) near the start of the 5.8S rRNA whereas all other global populations examined to date possess cytosine-nucleotide (C-gene), except for southern Japan which harbours both C-gene and T-gene strains. Together with cyst and plankton evidence this strongly suggests that both Australian and New Zealand populations have derived from southern Japan. Global dinoflagellate populations and cultures exhibit an extraordinary variation in PST profiles (STX and 21 analogues), but consistent regional patterns are evident with regard to the production of C1,2; C3,4; B1,2; and neoSTX analogues. PST profiles of cyst-derived cultures are deemed unrepresentative. Distinct ecophysiological differences exist between tropical (21-32°C) and warm-temperate ecotypes (12-18°C), but these appear unrelated to ITS genotypes and PST toxin phenotypes. On current evidence, cyst germination appears to play a minimal role in the bloom dynamics of this species, while seasonal and inter-annual bloom variations result from the physical constraints (temperature and light) on the growth of the dinoflagellates in the water column. G. catenatum exhibits a capacity to utilize many forms of nitrogen. Its chain formation and strong motility allow it to undergo retrieval migrations to exploit light and nutrient resource gradients in both stratified and mixed environments. Subtle strain-level variations in micronutrient (Se, humics) requirements and interaction with associat...

Hamidian, M, Nigro, SJ & Hall, RM 2012, 'Variants of the gentamicin and tobramycin resistance plasmid pRAY are widely distributed in Acinetobacter', Journal of Antimicrobial Chemotherapy, vol. 67, no. 12, pp. 2833-2836.
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Hansbro, PM & Jarnicki, AG 2012, 'Macrolides for macrophages in chronic obstructive pulmonary disease', Respirology, vol. 17, no. 5, pp. 739-740.
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Hansbro, PM, Starkey, MR, Kim, RY, Stevens, RL, Foster, PS & Horvat, JC 2012, 'Programming of the lung by early-life infection', Journal of Developmental Origins of Health and Disease, vol. 3, no. 03, pp. 153-158.
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Harasti, D, Martin‐Smith, K & Gladstone, W 2012, 'Population dynamics and life history of a geographically restricted seahorse, Hippocampus whitei', Journal of Fish Biology, vol. 81, no. 4, pp. 1297-1314.
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The aim of this study was to collect data on population dynamics and life history for White's seahorse Hippocampus whitei, a geographically restricted species that is listed as data deficient under the IUCN Red List. Data from H. whitei populations were collected from two regions, Port Stephens (north) and Sydney Harbour (south) in New South Wales, Australia, covering most of the known range of H. whitei, from 2005 to 2010. Over 1000 individuals were tagged using fluorescent elastomer and on subsequent recaptures were re‐measured for growth data that were used in a forced Gulland–Holt plot to develop growth parameters for use in a specialized von Bertalanffy growth‐function model. Growth parameters for Port Stephens were: females L∞ = 149·2 mm and K = 2·034 per year and males L∞ = 147·9 mm and K = 2·520 per year compared with estimates from Sydney Harbour: females L∞ = 139·8 mm and K = 1·285 per year and males L∞ = 141·6 mm and K = 1·223 per year. Whilst there was no significant difference in growth between sexes for each region, H. whitei in Port Stephens grew significantly quicker and larger and matured and reproduced at a younger age than those from Sydney Harbour. The life span of H. whitei is at least 5 years in the wild with six individuals recorded reaching this age. Data collected on breeding pairs found that H. whitei displays life‐long monogamy with three pairs observed remaining pair bonded over three consecutive breeding years. Baseline population densities were derived for two Po...

Hare, D, Austin, C & Doble, P 2012, 'Quantification strategies for elemental imaging of biological samples using laser ablation-inductively coupled plasma-mass spectrometry', ANALYST, vol. 137, no. 7, pp. 1527-1537.
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This review provides analysts with critical insights of current approaches for quantification by laser ablation-inductively coupled plasma-mass spectrometry in the field of elemental imaging. This encompasses both calibration strategies that have been used with success in imaging biological samples, as well as those with potential to improve analytical accuracy and precision if applied to imaging. Methods reviewed include the use of CRMs, laboratory prepared matrix matched standards, internal standardisation, online standard addition and a variety of novel approaches that makes elemental imaging accessible to a wider base of analysts. The importance of quantification and factors affecting its use in imaging will also be considered.

Hare, DJ, Gerlach, M & Riederer, P 2012, 'Considerations for measuring iron in post-mortem tissue of Parkinson's disease patients', JOURNAL OF NEURAL TRANSMISSION, vol. 119, no. 12, pp. 1515-1521.
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Redox-active iron is considered to be an important factor in the pathology and progression of several neurodegenerative disorders, including Parkinsons disease. The various roles of iron in normal physiology and its prevalence in the wider environment present numerous challenges to both accurate measurement and interpretation of brain iron levels. This review will discuss considerations for the analysis of iron in post-mortem samples, including how contamination, sample preparation and methods of analysis may influence results. In addition, several important factors influencing interpretation of iron levels will be considered.

Hare, DJ, Lee, JK, Beavis, AD, van Gramberg, A, George, J, Adlard, PA, Finkelstein, DI & Doble, PA 2012, 'Three-Dimensional Atlas of Iron, Copper, and Zinc in the Mouse Cerebrum and Brainstem', ANALYTICAL CHEMISTRY, vol. 84, no. 9, pp. 3990-3997.
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Atlases depicting molecular and functional features of the brain are becoming an integral part of modern neuroscience. In this study we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS) to quantitatively measure iron (Fe), copper (Cu), and zinc (Zn) levels in a serially sectioned C57BL/6 mouse brain (cerebrum and brainstem). Forty-six sections were analyzed in a single experiment of approximately 158 h in duration. We constructed a 46-plate reference atlas by aligning quantified images of metal distribution with corresponding coronal sections from the Allen Mouse Brain Reference Atlas. The 46 plates were also used to construct three-dimensional models of Fe, Cu, and Zn distribution. This atlas represents the first reconstruction of quantitative trace metal distribution through the brain by LA-ICPMS and will facilitate the study of trace metals in the brain and help to elucidate their role in neurobiology.

Haynes, CJE, Moore, SJ, Hiscock, JR, Marques, I, Costa, PJ, Félix, V & Gale, PA 2012, 'Tunable transmembrane chloride transport by bis-indolylureas', Chemical Science, vol. 3, no. 5, pp. 1436-1436.
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Hemming, MN, Walford, SA, Fieg, S, Dennis, ES & Trevaskis, B 2012, 'Identification of High-Temperature-Responsive Genes in Cereals', PLANT PHYSIOLOGY, vol. 158, no. 3, pp. 1439-1450.
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High temperature influences plant development and can reduce crop yields. We examined how ambient temperature influences reproductive development in the temperate cereals wheat (Triticum aestivum) and barley (Hordeum vulgare). High temperature resulted in rapid progression through reproductive development in long days, but inhibited early stages of reproductive development in short days. Activation of the long-day flowering response pathway through day-lengthinsensitive alleles of the PHOTOPERIOD1 gene, which result in high FLOWERING LOCUS T-like1 transcript levels, did not allow rapid early reproductive development at high temperature in short days. Furthermore, high temperature did not increase transcript levels of FLOWERING LOCUS T-like genes. These data suggest that genes or pathways other than the longday response pathway mediate developmental responses to high temperature in cereals. Transcriptome analyses suggested a possible role for vernalization-responsive genes in the developmental response to high temperature. The MADS-box floral repressor HvODDSOC2 is expressed at elevated levels at high temperature in short days, and might contribute to the inhibition of early reproductive development under these conditions. FLOWERING PROMOTING FACTOR1-like, RNase-S-like genes, and VER2-like genes were also identified as candidates for high-temperature-responsive developmental regulators. Overall, these data suggest that rising temperatures might elicit different developmental responses in cereal crops at different latitudes or times of year, due to the interaction between temperature and day length. Additionally, we suggest that different developmental regulators might mediate the response to high temperature in cereals compared to Arabidopsis (Arabidopsis thaliana).

Hemtasin, C, Ung, AT, Kanokmedhakul, S, Kanokmedhakul, K, Bishop, R, Satraruji, T & Bishop, D 2012, 'ChemInform Abstract: Synthesis of Alkaloid‐Like Compounds via the Bridging Ritter Reaction.', ChemInform, vol. 43, no. 40, pp. no-no.
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Abstract10 Alkaloid‐like compounds are prepared using alcohol (I) as starting product.

Hemtasin, C, Ung, AT, Kanokmedhakul, S, Kanokmedhakul, K, Bishop, R, Satraruji, T & Bishop, D 2012, 'Synthesis of alkaloid-like compounds via the bridging Ritter reaction', MONATSHEFTE FUR CHEMIE, vol. 143, no. 6, pp. 955-963.
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Alkaloid-like compounds containing a benzo[c]azepine core structure were successfully prepared in three steps from H-dibenzo[a,d]cyclohepten-5-ol via the bridging Ritter reaction. Biological studies of these compounds revealed that some of them are AChE inhibitors and antimalarial agents.

Henningham, A, Chiarot, E, Gillen, CM, Cole, JN, Rohde, M, Fulde, M, Ramachandran, V, Cork, AJ, Hartas, J, Magor, G, Djordjevic, SP, Cordwell, SJ, Kobe, B, Sriprakash, KS, Nizet, V, Chhatwal, GS, Margarit, IYR, Batzloff, MR & Walker, MJ 2012, 'Conserved anchorless surface proteins as group A streptococcal vaccine candidates', Journal of Molecular Medicine, vol. 90, no. 10, pp. 1197-1207.
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Streptococcus pyogenes (group A Streptococcus (GAS)) causes similar to 700 million human infections each year, resulting in over 500,000 deaths. The development of a commercial GAS vaccine is hampered by the occurrence of many unique GAS serotypes, antigenic variation within the same serotype, differences in serotype geographical distribution, and the production of antibodies cross-reactive with human tissue that may lead to autoimmune disease. Several independent studies have documented a number of GAS cell wall-associated or secreted metabolic enzymes that contain neither N-terminal leader sequences nor C-terminal cell wall anchors. Here, we applied a proteomic analysis of serotype M1T1 GAS cell wall extracts for the purpose of vaccine development. This approach catalogued several anchorless proteins and identified two protective vaccine candidates, arginine deiminase and trigger factor. These surface-exposed enzymes are expressed across multiple GAS serotypes exhibiting >= 99% amino acid sequence identity. Vaccine safety concerns are alleviated by the observation that these vaccine candidates lack human homologs, while sera from human populations suffering repeated GAS infections and high levels of autoimmune complications do not recognize these enzymes. Our study demonstrates anchorless cell surface antigens as promising vaccine candidates for the prevention of GAS disease

Hill, R, Larkum, AWD, Prasil, O, Kramer, DM, Szabo, M, Kumar, V & Ralph, PJ 2012, 'Light-induced dissociation of antenna complexes in the symbionts of scleractinian corals correlates with sensitivity to coral bleaching', CORAL REEFS, vol. 31, no. 4, pp. 963-975.
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Elevated temperatures in combination with moderate to high irradiance are known to cause bleaching events in scleractinian corals, characterised by damage to photosystem II (PSII). Photoprotective mechanisms of the symbiont can reduce the excitation pressure impinging upon PSII. In the bleaching sensitive species, Acropora millepora and Pocillopora damicornis, high light alone induced photoprotection through the xanthophyll cycle, increased content of the antioxidant carotenoid, β-carotene, as well as the dissociation of the light-harvesting chlorophyll complexes. The evidence is compatible with either the membrane-bound chlorophyll a-chlorophyll c2-peridinin-protein (acpPC) complex or the peripheral peridinin-chlorophyll-protein complex, or both, disconnecting from PSII under high light. The acpPC complex potentially showed a state transition response with redistribution towards photosystem I to reduce PSII over-excitation. This apparent acpPC dissociation/reassociation was promoted by the addition of the xanthophyll cycle inhibitor, dithiothreitol, under high irradiance. Exposure to thermal stress as well as high light promoted xanthophyll de-epoxidation and increased β-carotene content, although it did not influence light-harvesting chlorophyll complex (LHC) dissociation, indicating light, rather than temperature, controls LHC dissociation. Photoinhibition was avoided in the bleaching tolerant species, Pavona decussata, suggesting xanthophyll cycling along with LHC dissociation may have been sufficient to prevent photodamage to PSII. Symbionts of P. decussata also displayed the greatest detachment of antenna complexes, while the more thermally sensitive species, Pocillopora damicornis and A. millepora, showed less LHC dissociation, suggesting antenna movement influences bleaching susceptibility. © 2012 Springer-Verlag.

Ho, KKK, Cole, N, Chen, R, Willcox, MDP, Rice, SA & Kumar, N 2012, 'Immobilization of Antibacterial Dihydropyrrol-2-ones on Functional Polymer Supports To Prevent Bacterial Infections In Vivo', Antimicrobial Agents and Chemotherapy, vol. 56, no. 2, pp. 1138-1141.
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ABSTRACT Antibiotic-resistant Staphylococcus aureus is of great concern, as it causes a wide range of life-threatening infections. The current study demonstrates that dihydropyrrolone (DHP)-coated polyacrylamide substrates are effective in reducing the number of culturable clinical isolates of S. aureus in vitro in a dose-dependent manner and are able to reduce the pathogenic potential of staphylococcal infection in a subcutaneous infection model. Covalently bound DHPs therefore show great potential for use as an antimicrobial strategy in device-related applications.

Hoeksema, BW, Matthews, JL & Yeemin, T 2012, 'The 2010 coral bleaching event and its impact on the mushroom coral fauna of Koh Tao, western Gulf of Thailand', Phuket Marine Biological Center Research Bulletin, vol. 71, pp. 71-81.
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During two surveys of the mushroom coral fauna of Koh Tao, a total of 20 species was recorded. The first survey (June 2010) was during a coral bleaching event caused by elevated seawater temperatures. Bleaching in mushroom corals appeared to be depth-dependent at the deepest sites with less bleaching occurring below 20 m depth. Some fungiid species, like Ctenactis echinata, appeared to be less susceptible to bleaching than others. This species was affected very little and was represented by regularly coloured individuals among many bleached specimens of other mushroom coral species. Few corals of Fungia fungites showed bleaching on the shallow reef flats but many were bleached on the slopes. During the second survey (February 2011), Koh Tao's mushroom coral fauna appeared to have recovered and no trace of thermal bleaching was visible anymore.

Hoppenrath, M, Murray, S, Sparmann, SF & Leander, BS 2012, 'MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV (DINOPHYCEAE), A NEW GENUS OF MARINE SAND-DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM', JOURNAL OF PHYCOLOGY, vol. 48, no. 5, pp. 1143-1152.
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The classical athecate dinoflagellate genera (Amphidinium, Gymnodinium, Gyrodinium) have long been recognized to be polyphyletic. Amphidinium sensu lato is the most diverse of all marine benthic dinoflagellate genera; however, following the redefinition

Horsington, J, Turnbull, L, Whitchurch, CB & Newsome, TP 2012, 'Sub-viral imaging of vaccinia virus using super-resolution microscopy', JOURNAL OF VIROLOGICAL METHODS, vol. 186, no. 1-2, pp. 132-136.
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The study of host-pathogen interactions over past decades has benefited from advances in microscopy and fluorescent imaging techniques. A particularly powerful model in this field is vaccinia virus (VACV), which due to its amenability to genetic manipulation has been a productive model in advancing the understanding of the transport of subcellular cargoes. Conventional light microscopy imposes an upper limit of resolution of ∼250. nm, hence knowledge of events occurring at the sub-viral resolution is based predominantly on studies utilising electron microscopy. The development of super-resolution light microscopy presents the opportunity to bridge the gap between these two technologies. This report describes the analysis of VACV replication using fluorescent recombinant viruses, achieving sub-viral resolution with three-dimensional structured illumination microscopy. This is the first report of successfully resolving poxvirus particle morphologies at the scale of single virus particles using light microscopy. © 2012 Elsevier B.V.

Horton, RC, Kelly, TL, Lenehan, CE, Lennard, C, Lewis, SW, Lim, KF, Roux, C & Southam, DC 2012, 'Assessing Students’ Attitudes Toward Forensic Science: Collecting an Expert Consensus', Forensic Science Policy & Management: An International Journal, vol. 3, no. 4, pp. 180-188.
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HSU, AC, SEE, HV, HANSBRO, PM & WARK, PAB 2012, 'Innate immunity to influenza in chronic airways diseases', Respirology, vol. 17, no. 8, pp. 1166-1175.
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ABSTRACTInfluenza presents a unique human infectious disease that has a substantial impact on the public health, in general, and especially for those with chronic airways diseases. People with asthma and chronic obstructive pulmonary disease (COPD) are particularly vulnerable to influenza infection and experience more severe symptoms with the worsening of their pre‐existing conditions. Recent advances in reverse genetics and innate immunity has revealed several influenza virulence factors and host factors involved in influenza pathogenesis and the immune responses to infection. Early innate immunity plays a critical role of limiting viral infection and spread; however, the underlying mechanisms that lead to enhanced susceptibility to influenza infection and severe symptoms in those with asthma and COPD to infection remain un‐investigated. This review will explore the importance of early innate antiviral responses to influenza infection and how these responses are altered by influenza virus and in those with chronic airways diseases.

Hsu, AC-Y, Parsons, K, Barr, I, Lowther, S, Middleton, D, Hansbro, PM & Wark, PAB 2012, 'Critical Role of Constitutive Type I Interferon Response in Bronchial Epithelial Cell to Influenza Infection', PLoS ONE, vol. 7, no. 3, pp. e32947-e32947.
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Innate antiviral responses in bronchial epithelial cells (BECs) provide the first line of defense against respiratory viral infection and the effectiveness of this response is critically dependent on the type I interferons (IFNs). However the importance of the antiviral responses in BECs during influenza infection is not well understood. We profiled the innate immune response to infection with H3N2 and H5N1 virus using Calu-3 cells and primary BECs to model proximal airway cells. The susceptibility of BECs to influenza infection was not solely dependent on the sialic acid-bearing glycoprotein, and antiviral responses that occurred after viral endocytosis was more important in limiting viral replication. The early antiviral response and apoptosis correlated with the ability to limit viral replication. Both viruses reduced RIG-I associated antiviral responses and subsequent induction of IFN-β. However it was found that there was constitutive release of IFN-β by BECs and this was critical in inducing late antiviral signaling via type I IFN receptors, and was crucial in limiting viral infection. This study characterizes anti-influenza virus responses in airway epithelial cells and shows that constitutive IFN-β release plays a more important role in initiating protective late IFN-stimulated responses during human influenza infection in bronchial epithelial cells. © 2012 Hsu et al.

Huang, S-W, Cirmi, G, Moses, J, Hong, K-H, Bhardwaj, S, Birge, JR, Chen, L-J, Kabakova, IV, Li, E, Eggleton, BJ, Cerullo, G & Kärtner, FX 2012, 'Optical waveform synthesizer and its application to high-harmonic generation', Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 45, no. 7, pp. 074009-074009.
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Huete, AR 2012, 'Vegetation Indices, Remote Sensing and Forest Monitoring', Geography Compass, vol. 6, no. 9, pp. 513-532.
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AbstractWith increasing threats and pressure exerted on Earth’s forest resources, there are greater demands for more quantitative, timely, and accurate information on their state, functioning, and sustainability. Satellite remote sensing offers an effective way of measuring and monitoring vast forest areas in a consistent and robust manner. This complements ground forest surveys and overcomes the spatial limitations of in situ sampling of forest biophysical properties. Among the various remote sensing tools used in characterizing forests, spectral vegetation indices (VIs) are widely adopted for monitoring forest states and canopy processes. In this article I provide a brief overview on VI applications and advances made in the assessment and monitoring of forest biophysical states, functioning, phenology, and disturbance. I also address current and future challenges, demands, and limitations of VIs for long term forest monitoring and applications in climate science, hydrology, and biogeochemistry.

Hulley, H & Platen, E 2012, 'Hedging for the long run', Mathematics and Financial Economics, vol. 6, no. 2, pp. 105-124.
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In the years following the publication of Black and Scholes (J Political Econ, 81(3), 637-654, 1973), numerous alternative models have been proposed for pricing and hedging equity derivatives. Prominent examples include stochastic volatility models, jump-diffusion models, and models based on Lévy processes. These all have their own shortcomings, and evidence suggests that none is up to the task of satisfactorily pricing and hedging extremely long-dated claims. Since they all fall within the ambit of risk-neutral valuation, it is natural to speculate that the deficiencies of these models are (at least in part) attributable to the constraints imposed by the risk-neutral approach itself. To investigate this idea, we present a simple two-parameter model for a diversified equity accumulation index. Although our model does not admit an equivalent risk-neutral probability measure, it nevertheless fulfils a minimal no-arbitrage condition for an economically viable financial market. Furthermore, we demonstrate that contingent claims can be priced and hedged, without the need for an equivalent change of probability measure. Convenient formulae for the prices and hedge ratios of a number of standard European claims are derived, and a series of hedge experiments for extremely long-dated claims on the S&P 500 total return index are conducted. Our model serves also as a convenient medium for illustrating and clarifying several points on asset price bubbles and the economics of arbitrage.

Humphreys, W, Tetu, S, Elbourne, L, Gillings, M, Seymour, J, Mitchell, J & Paulsen, I 2012, 'Geochemical and microbial diversity of bundera sinkhole, an anchialine system in the eastern Indian ocean', Natura Croatica, vol. 21, no. SUPPL.1, pp. 59-63.
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The anchialine system at Bundera sinkhole, Australia, exhibits pronounced hydrogeochemical structure through depth that is reflected in the composition and distribution of the fauna. It is a strongly structured microbial ecosystem the components of which also change with depth and which is dominated by sulfur bacteria and chemolithotrophic microbial classes.

Hung, T-F, Wang, B, Tsai, C-W, Tu, M-H, Wang, G-X, Liu, R-S, Tsai, DP, Lo, M-Y, Shy, D-S & Xing, X-K 2012, 'Sulfonation of graphene nanosheet-supported platinum via a simple thermal-treatment toward its oxygen reduction activity in acid medium', International Journal of Hydrogen Energy, vol. 37, no. 19, pp. 14205-14210.
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The sulfonated graphene nanosheet-supported platinum (s-Pt/GNS) catalyst synthesized via a simple thermal-treatment in the presence of concentrated sulfuric acid was reported in this study. Influence of sulfonation on its structural, surface, morphological and catalytic characteristics of as-prepared s-Pt/GNS was explored using X-ray diffractometer, Raman spectrometry, zeta potential analyzer, scanning and transmission electron microscopes, and cyclic voltammetry. For the oxygen reduction reaction, the current density generated from the s-Pt/GNS at 0.6 V was approximately 32.5 A g-1 Pt, which was about 193% higher than that of original Pt/GNS. © 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Huston, WM, Harvie, M, Mittal, A, Timms, P & Beagley, KW 2012, 'Vaccination to protect against infection of the female reproductive tract', Expert Review of Clinical Immunology, vol. 8, no. 1, pp. 81-94.
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Infection of the female genital tract can result in serious morbidities and mortalities from reproductive disability, pelvic inflammatory disease and cancer, to impacts on the fetus, such as infant blindness. While therapeutic agents are available, frequent testing and treatment is required to prevent the occurrence of the severe disease sequelae. Hence, sexually transmitted infections remain a major public health burden with ongoing social and economic barriers to prevention and treatment. Unfortunately, while there are two success stories in the development of vaccines to protect against HPV infection of the female reproductive tract, many serious infectious agents impacting on the female reproductive tract still have no vaccines available. Vaccination to prevent infection of the female reproductive tract is an inherently difficult target, with many impacting factors, such as appropriate vaccination strategies/mechanisms to induce a suitable protective response locally in the genital tract, variation in the local immune responses due to the hormonal cycle, selection of vaccine antigen(s) that confers effective protection against multiple variants of a single pathogen (e.g., the different serovars of Chlamydia trachomatis) and timing of the vaccine administration prior to infection exposure. Despite these difficulties, there are numerous ongoing efforts to develop effective vaccines against these infectious agents and it is likely that this important human health field will see further major developments in the next 5 years.

Hutchinson, AT, Jones, DR & Raison, RL 2012, 'The ability to interact with cell membranes suggests possible biological roles for free light chain', Immunology Letters, vol. 142, no. 1-2, pp. 75-77.
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During antibody synthesis, immunoglobulin light chains are produced in excess of heavy chains and, as a consequence, can be secreted by plasma cells as free light chains (FLC). Thus, FLC were considered to be a by-product of immunoglobulin synthesis, lac

Huynh, TT, McDougald, D, Klebensberger, J, Al Qarni, B, Barraud, N, Rice, SA, Kjelleberg, S & Schleheck, D 2012, 'Glucose Starvation-Induced Dispersal of Pseudomonas aeruginosa Biofilms Is cAMP and Energy Dependent', PLoS ONE, vol. 7, no. 8, pp. e42874-e42874.
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Carbon starvation has been shown to induce a massive dispersal event in biofilms of the opportunistic pathogen Pseudomonas aeruginosa; however, the molecular pathways controlling this dispersal response remain unknown. We quantified changes in the proteome of P. aeruginosa PAO1 biofilm and planktonic cells during glucose starvation by differential peptide-fingerprint mass-spectrometry (iTRAQ). In addition, we monitored dispersal photometrically, as a decrease in turbidity/opacity of biofilms pre-grown and starved in continuous flow-cells, in order to evaluate treatments (e.g. inhibitors CCCP, arsenate, chloramphenicol, L-serine hydroxamate) and key mutants altered in biofilm development and dispersal (e.g. nirS, vfr, bdlA, rpoS, lasRrhlR, Pf4-bacteriophage and cyaA). In wild-type biofilms, dispersal started within five minutes of glucose starvation, was maximal after 2 h, and up to 60% of the original biomass had dispersed after 24 h of starvation. The changes in protein synthesis were generally not more than two fold and indicated that more than 100 proteins belonging to various classes, including carbon and energy metabolism, stress adaptation, and motility, were differentially expressed. For the different treatments, only the proton-ionophore CCCP or arsenate, an inhibitor of ATP synthesis, prevented dispersal of the biofilms. For the different mutants tested, only cyaA, the synthase of the intracellular second messenger cAMP, failed to disperse; complementation of the cyaA mutation restored the wild-type phenotype. Hence, the pathway for carbon starvation-induced biofilm dispersal in P. aeruginosa PAO1 involves ATP production via direct ATP synthesis and proton-motive force dependent step(s) and is mediated through cAMP, which is likely to control the activity of proteins involved in remodeling biofilm cells in preparation for planktonic survival. © 2012 Huynh et al.

Ichimaru, Y, Krimmer, DI, Burgess, JK, Black, JL & Oliver, BGG 2012, 'TGF-β enhances deposition of perlecan from COPD airway smooth muscle', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 302, no. 3, pp. L325-L333.
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Chronic obstructive pulmonary disease (COPD) and asthma are characterized by irreversible remodeling of the airway walls, including thickening of the airway smooth muscle layer. Perlecan is a large, multidomain, proteoglycan that is expressed in the lungs, and in other organ systems, and has been described to have a role in cell adhesion, angiogenesis, and proliferation. This study aimed to investigate functional properties of the different perlecan domains in relation to airway smooth muscle cells (ASMC). Primary human ASMC obtained from donors with asthma ( n = 13), COPD ( n = 12), or other lung disease ( n = 20) were stimulated in vitro with 1 ng/ml transforming growth factor-β1 (TGF-β1) before perlecan deposition and cytokine release were analyzed. In some experiments, inhibitors of signaling molecules were added. Perlecan domains I–V were seeded on tissue culture plates at 10 μg/ml with 1 μg/ml collagen I as a control. ASM was incubated on top of the peptides before being analyzed for attachment, proliferation, and wound healing. TGF-β1 upregulated deposition of perlecan by ASMC from COPD subjects only. TGF-β1 upregulated release of IL-6 into the supernatant of ASMC from all subjects. Inhibitors of SMAD and JNK signaling molecules decreased TGF-β1-induced perlecan deposition by COPD ASMC. Attachment of COPD ASMC was upregulated by collagen I and perlecan domains IV and V, while perlecan domain II upregulated attachment only of asthmatic ASMC. Seeding on perlecan domains did not increase proliferation of any ASMC type. TGF-β1-induced perlecan deposition may enhance attachment of migrating ASMC in vivo and thus may be a mechanism for ASMC layer hypertrophy in COPD.

Idrees, S & Ashfaq, UA 2012, 'A brief review on dengue molecular virology, diagnosis, treatment and prevalence in Pakistan', Genetic Vaccines and Therapy, vol. 10, no. 1.
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Idrees, S, Nadeem, S, Ehsan, B & Rajoka, MI 2012, 'GasCan: A novel database for gastric cancer genes and primers', International Journal Bioautomation, vol. 16, no. 2, pp. 129-134.
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GasCan is a specialized and unique database of gastric cancer protein encoding genes expressed in human and mouse. The features that make GasCan unique are the availability of gene information, availability of primers for each gene, and built in programmed sequence analysis facility that analyze gene sequences in database itself. Furthermore, DNA sequence analysis tool is provided that can be access freely. GasCan will expand in future to other species, genes and cover more useful information of other species. Flexible database design, expandability and easy access of information to all of the users are the main features of the database.

Idrees, S, Nadeem, S, Kanwal, S, Ehsan, B, Yousaf, A, Nadeem, S & Rajoka, MI 2012, 'In silico sequence analysis, homology modeling and function annotation of Ocimum basilicum hypothetical protein G1CT28_OCIBA', International Journal Bioautomation, vol. 16, no. 2, pp. 111-118.
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Ocimum basilicum is commonly known as sweet basil and belongs to the Lamiaceae Family. Ocimum basilicum has great therapeutic benefits and can be used for lowering blood pressure, as an antispasmodic as well as cleansing the blood. In the present study, subcellular localization prediction suggested that it is a cytoplasmic protein. We predicted the 3D structure of protein using homology modeling as 3D structure prediction approach. 3D structure of the protein was determined using Protein Structure Prediction Server (PS)2 selecting MODELLER as 3D structure prediction method. Quality analysis of the model indicated that it is a reliable model. Furthermore, it was discovered that Ocimum basilicum hypothetical protein G1CT28_OCIBA is involved in two biological processes, oxidation reduction and metabolic process and the biochemical function of the protein is acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, catalytic activity and oxidoreductase.

Ignatieva, K & Platen, E 2012, 'Estimating the diffusion coefficient function for a diversified world stock index', COMPUTATIONAL STATISTICS & DATA ANALYSIS, vol. 56, no. 6, pp. 1333-1349.
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This paper deals with the estimation of continuous-time diffusion processes which model the dynamics of a well diversified world stock index (WSI). We use the nonparametric kernel-based estimation to empirically identify a square root type diffusion coefficient function in the dynamics of the discounted WSI. A square root process turns out to be an excellent building block for a parsimonious model for the WSI. Its dynamics allow capturing various empirical stylized facts and long term properties of the index, as well as, the explicit computation of various financial quantities

Ivanov, IE, Boyd, CD, Newell, PD, Schwartz, ME, Turnbull, L, Johnson, MS, Whitchurch, CB, O'Toole, GA & Camesano, TA 2012, 'Atomic force and super-resolution microscopy support a role for LapA as a cell-surface biofilm adhesin of Pseudomonas fluorescens', RESEARCH IN MICROBIOLOGY, vol. 163, no. 9-10, pp. 685-691.
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Pseudomonas fluorescence Pf0-1 requires the large repeat protein LapA for stable surface attachment. This study presents direct evidence that LapA is a cell-surface-localized adhesin. Atomic force microscopy (AFM) revealed a significant 2-fold reduction in adhesion force for mutants lacking the LapA protein on the cell surface compared to the wild-type strain. Deletion of lapG, a gene encoding a periplasmic cysteine protease that functions to release LapA from the cell surface, resulted in a 2-fold increase in the force of adhesion. Three-dimensional structured illumination microscopy (3D-SIM) revealed the presence of the LapA protein on the cell surface, consistent with its role as an adhesin. The protein is only visualized in the cytoplasm for a mutant of the ABC transporter responsible for translocating LapA to the cell surface. Together, these data highlight the power of combining the use of AFM and 3D-SIM with genetic studies to demonstrate that LapA, a member of a large group of RTX-like repeat proteins, is a cell-surface adhesin. © 2012 Institut Pasteur.

Jaiswal, R, Gong, J, Sambasivam, S, Combes, V, Mathys, J-M, Davey, R, Grau, GER & Bebawy, M 2012, 'Microparticle-associated nucleic acids mediate trait dominance in cancer', FASEB JOURNAL, vol. 26, no. 1, pp. 420-429.
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Drug resistance is a major cause of cancer treatment failure, with multidrug resistance (MDR) being the most serious, whereby cancer cells display cross-resistance to structurally and functionally unrelated drugs. MDR is caused by overexpression of the efflux transporters P-glycoprotein (P-gp) and multidrug resistance-associated protein 1 (MRP1). These transporters act to maintain sublethal intracellular drug concentrations within the cancer cell, making the population treatment unresponsive. Recently, we discovered a novel nongenetic basis to MDR whereby microparticles (MPs) transfer P-gp intercellularly from MDR donor cells to drug-sensitive recipient cells. MPs isolated from MDR leukemia and breast cancer cells were cocultured with their drug-sensitive counterparts. P-gp transfer was assessed by direct immunolabeling, and acquired transcripts and regulatory microRNAs by quantitative real-time PCR. We show that MDR MPs incorporate nucleic acids; MPs change recipient cells'transcriptional environment to reflect donor MDR phenotype, and distinct pathways exist among cancers of different origin that may be dependent on donor cells'ABCB1 overexpression. We demonstrate that this pathway exists for both hematological and nonhematological malignancies. By conferring MDR and 'retemplating'the transcriptional landscape of recipient cells, MPs provide a novel pathway, having implications in the dissemination and acquisition of deleterious traits in clinical oncology. © FASEB.

Jeffries, TC, Seymour, JR, Newton, K, Smith, RJ, Seuront, L & Mitchell, JG 2012, 'Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient', BIOGEOSCIENCES, vol. 9, no. 2, pp. 815-825.
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Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes-organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem. © 2012 Author(s).

Jia, H, Schmid, B, Liu, S, Jaggi, M, Monbaron, P, Bhosale, SV, Rivadehi, S, Langford, SJ, Sanguinet, L, Levillain, E, El‐Khouly, ME, Morita, Y, Fukuzumi, S & Decurtins, S 2012, 'Tetrathiafulvalene‐Fused Porphyrins via Quinoxaline Linkers: Symmetric and Asymmetric Donor–Acceptor Systems', ChemPhysChem, vol. 13, no. 14, pp. 3370-3382.
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AbstractA tetrathiafulvalene (TTF) donor is annulated to porphyrins (P) via quinoxaline linkers to form novel symmetric P–TTF–P triads 1 a–c and asymmetric P–TTF dyads 2 a,b in good yields. These planar and extended π‐conjugated molecules absorb light over a wide region of the UV/Vis spectrum as a result of additional charge‐transfer excitations within the donor–acceptor assemblies. Quantum‐chemical calculations elucidate the nature of the electronically excited states. The compounds are electrochemically amphoteric and primarily exhibit low oxidation potentials. Cyclic voltammetric and spectroelectrochemical studies allow differentiation between the TTF and porphyrin sites with respect to the multiple redox processes occurring within these molecular assemblies. Transient absorption measurements give insight into the excited‐state events and deliver corresponding kinetic data. Femtosecond transient absorption spectra in benzonitrile may suggest the occurrence of fast charge separation from TTF to porphyrin in dyads 2 a,b but not in triads 1 a–c. Clear evidence for a photoinduced and relatively long lived charge‐separated state (385 ps lifetime) is obtained for a supramolecular coordination compound built from the ZnP–TTF dyad and a pyridine‐functionalized C60 acceptor unit. This specific excited state results in a (ZnP–TTF)⋅+⋅⋅⋅(C60py)⋅− state. The binding constant of ZnII⋅⋅⋅py is evaluated by constructing a Benesi–Hildebrand plot based on fluorescence data. This plot yields a binding constant K of 7.20×104 M−1

Jimenez, IM, Larkum, AWD, Ralph, PJ & Kuehl, M 2012, 'Thermal effects of tissue optics in symbiont-bearing reef-building corals', LIMNOLOGY AND OCEANOGRAPHY, vol. 57, no. 6, pp. 1816-1825.
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Reflectance spectroscopy and microscale temperature measurements were used to investigate links between optical and thermal properties of corals. Coral tissue heating showed a species-specific linear correlation to the absorptance of incident irradiance. Heat budgets estimated from absorptance and thermal boundary layer measurements indicated differences in the relative contribution of convection and conduction to heat loss in Porites lobata and Stylophora pistillata, and a higher heat conduction into the skeleton of the thin-tissued branching S. pistillata as compared to the massive thick-tissued P. lobata. Decreasing absorptance associated with bleaching resulted in decreased surface warming of coral tissue. Action spectra of coral tissue heating showed elevated efficiency of heating at wavelengths corresponding to absorption maxima of major zooxanthellae photopigments. Generally, energy-rich radiation (, 500 nm) showed the highest heating efficiency. Speciesspecific relationships between coral tissue heating and absorptance can be strongly affected by differences in the thermal properties of the skeleton and/or tissue arrangement within the skeletal matrix, indicating a yet unresolved potential for coral shape, size, and tissue thickness to affect heat dissipation and especially the conduction of heat into the coral skeleton.

Jimenez, IM, Larkum, AWD, Ralph, PJ & Kuhl, M 2012, 'In situ thermal dynamics of shallow water corals is affected by tidal patterns and irradiance', MARINE BIOLOGY, vol. 159, no. 8, pp. 1773-1782.
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We studied the diel variation of in situ coral temperature, irradiance and photosynthetic performance of hemispherical colonies of Porites lobata and branching colonies of Porites cylindrica during different bulk water temperature and tidal scenarios on the shallow reef flat of Heron Island, Great Barrier Reef, Australia. Our study presents in situ evidence that coral tissue surface temperatures can exceed that of the surrounding water under environmental conditions typically occurring during low tide in shallow reef or lagoon environments. Such heating may be a regular occurrence on shallow reef flats, triggered by the combined effects of high irradiance and low water flow characteristic of low Spring tides. At these times, solar heating of corals coincides with times of maximum water temperature and high irradiance, where the slow flow and consequent thick boundary layers impede heat exchange between corals and the surrounding water. Despite similar light-absorbing properties, the heating effect was more pronounced for the hemispherical P. lobata than for the branching P. cylindrica. This is consistent with previous laboratory experiments showing the evidence of interspecific variation in coral thermal environment and may result from morphologically influenced variation in convective heat transfer and/or thermal properties of the skeleton. Maximum coral surface warming did not coincide with maximum irradiance, but with maximum water temperature, well into the low-tide period with extremely low water flow in the partially drained reef flat, just prior to flushing by the rising tide. The timing of low tide thus influences the thermal exposure and photophysiological performance of corals, and the timing of tidally driven coral surface warming could potentially have different physiological impacts in the morning or in the afternoon.

Johnson, A, Archer, M, Leigh-Shaw, L, Pais, M, O’Donnell, C & Wallman, J 2012, 'Examination of forensic entomology evidence using computed tomography scanning: case studies and refinement of techniques for estimating maggot mass volumes in bodies', International Journal of Legal Medicine, vol. 126, no. 5, pp. 693-702.
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Johnson, AP, Wallman, JF & Archer, MS 2012, 'Experimental and Casework Validation of Ambient Temperature Corrections in Forensic Entomology*^,†', Journal of Forensic Sciences, vol. 57, no. 1, pp. 215-221.
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Abstract:  This paper expands on Archer (J Forensic Sci 49, 2004, 553), examining additional factors affecting ambient temperature correction of weather station data in forensic entomology. Sixteen hypothetical body discovery sites (BDSs) in Victoria and New South Wales (Australia), both in autumn and in summer, were compared to test whether the accuracy of correlation was affected by (i) length of correlation period; (ii) distance between BDS and weather station; and (iii) periodicity of ambient temperature measurements. The accuracy of correlations in data sets from real Victorian and NSW forensic entomology cases was also examined. Correlations increased weather data accuracy in all experiments, but significant differences in accuracy were found only between periodicity treatments. We found that a >5°C difference between average values of body in situ and correlation period weather station data was predictive of correlations that decreased the accuracy of ambient temperatures estimated using correlation. Practitioners should inspect their weather data sets for such differences.

Johnson, FA, Chandra, H, Brown, JJ & PADMADAS, SS 2012, 'Small Area Estimation for Policy Development: A Case Study of Child Undernutrition in Ghana', Journal of the Indian Society of Agricultural Statistics, vol. 66, no. 1, pp. 171-186.
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The demand for Small (local-level) Area Statistics has increased tremendously, particularly in countries where a decentralised approach to governance and service provision has been adopted. Most of these countries lack local-level statistics to aid policy decisions and planning. Sample surveys such as the Demographic and Health Survey provide a wide range of invaluable data at the national and regional level but cannot be used directly to produce reliable district-level estimates due to small smaple sizes. The paper illustrates the application of Small Area Estimation (SAE) techniques to derive model-based district-level estimates of child undernutrition in Ghana linking data from the 2003 Ghana Demographic and Health Survey (GDHS) and the 2000 Ghana Population and Housing Census (GPHC). The diagnostics measures show that the model-based estimates are robust when compared to the direct surevey estimates. The model-based estimates reveal considerable heterogeneity in the prevalence of undernutrition, with children living in the Northern part of the country being most disadvantaged. The estimates clearly highlight the districts where targeted child health interventions need to be strengthened. In countries where small area statistics are non-existent, SAE techniques could be crucila for designing effective policies and strengthening local-level governance.

Jokic, T, Borisov, SM, Saf, R, Nielsen, DA, Kuehl, M & Klimant, I 2012, 'Highly Photostable Near-Infrared Fluorescent pH Indicators and Sensors Based on BF2-Chelated Tetraarylazadipyrromethene Dyes', ANALYTICAL CHEMISTRY, vol. 84, no. 15, pp. 6723-6730.
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In this study, a series of new BF2-chelated tetraarylazadipyrromethane dyes are synthesized and are shown to be suitable for the preparation of on/off photoinduced electron transfer modulated fluorescent sensors. The new indicators are noncovalently entrapped in polyurethane hydrogel D4 and feature absorption maxima in the range 660â 710 nm and fluorescence emission maxima at 680â740 nm. Indicators have high molar absorption coefficients of â¼80 000 Mâ1 cmâ1, good quantum yields (up to 20%), excellent photostability and low cross-sensitivity to the ionic strength. pKa values of indicators are determined from absorbance and fluorescence measurements and range from 7 to 11, depending on the substitution pattern of electron-donating and -withdrawing functionalities. Therefore, the new indicators are suitable for exploitation and adaptation in a diverse range of analytical applications. Apparent pKa values in sensor films derived from fluorescence data show 0.5â1 pH units lower values in comparison with those derived from the absorption data due to FoÌrster resonance energy transfer from protonated to deprotonated form. A dual-lifetime referenced sensor is prepared, and application for monitoring of pH in corals is demonstrated.

Jones, PM & George, AM 2012, 'Role of the D-Loops in Allosteric Control of ATP Hydrolysis in an ABC Transporter', The Journal of Physical Chemistry A, vol. 116, no. 11, pp. 3004-3013.
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ABC transporters couple ATP hydrolysis to movement of substrates across cell membranes. They comprise two transmembrane domains and two cytosolic nucleotide-binding domains forming two active sites that hydrolyze ATP cooperatively. The mechanism of ATP hydrolysis is controversial and the structural dynamic basis of its allosteric control unknown. Here we report molecular dynamics simulations of the ATP/apo and ATP/ADP states of the bacterial ABC exporter Sav1866, in which the cytoplasmic region of the protein was simulated in explicit water for 150 ns. In the simulation of the ATP/apo state, we observed, for the first time, conformers of the active site with the canonical geometry for an in-line nucleophilic attack on the ATP gamma-phosphate. The conserved glutamate immediately downstream of the Walker B motif is the catalytic base, forming a dyad with the H-loop histidine, whereas the Q-loop glutamine has an organizing role. Each D-loop provides a coordinating residue of the attacking water, and comparison with the simulation of the ATP/ADP state suggests that via their flexibility, the D-loops modulate formation of the hydrolysis-competent state. A global switch involving a coupling helix delineates the signal transmission route by which allosteric control of ATP hydrolysis in ABC transporters is mediated.

Kabakova, IV, Yu, Z, Halliwell, D, Fonjallaz, P-Y, Tarasenko, O, de Sterke, CM & Margulis, W 2012, 'Switching and dynamic wavelength conversion in a fiber grating cavity', Journal of the Optical Society of America B, vol. 29, no. 1, pp. 155-155.
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Kabakova, IV, Zou, L, Brawley, GA, Florea, C, Aggarwal, ID, Sanghera, JS, Mägi, EC, Li, E & Eggleton, BJ 2012, 'Dynamics of photoinduced refractive index changes in As₂S₃fibers', Applied Optics, vol. 51, no. 30, pp. 7333-7333.
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Kajer, T, Hawkins, CL, Fu, S, Graham, GG & Davies, MJ 2012, 'Myeloperoxidase is inhibited by commonly used phenolic compounds', FREE RADICAL BIOLOGY AND MEDICINE, vol. 53, pp. S89-S90.
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Kan, CWS, Hahn, MA, Gard, GB, Maidens, J, Huh, JY, Marsh, DJ & Howell, VM 2012, 'Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer', BMC Cancer, vol. 12, no. 1.
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Abstract Background There is a critical need for improved diagnostic markers for high grade serous epithelial ovarian cancer (SEOC). MicroRNAs are stable in the circulation and may have utility as biomarkers of malignancy. We investigated whether levels of serum microRNA could discriminate women with high-grade SEOC from age matched healthy volunteers. Methods To identify microRNA of interest, microRNA expression profiling was performed on 4 SEOC cell lines and normal human ovarian surface epithelial cells. Total RNA was extracted from 500 μL aliquots of serum collected from patients with SEOC (n = 28) and age-matched healthy donors (n = 28). Serum microRNA levels were assessed by quantitative RT-PCR following preamplification. Results microRNA (miR)-182, miR-200a, miR-200b and miR-200c were highly overexpressed in the SEOC cell lines relative to normal human ovarian surface epithelial cells and were assessed in RNA extracted from serum as candidate biomarkers. miR-103, miR-92a and miR -638 had relatively invariant expression across all ovarian cell lines, and with small-nucleolar C/D box 48 (RNU48) were assessed in RNA extracted from serum as candidate endogenous normalizers. No correlation between serum levels and age were observed (age range 30-79 years) for any of these microRNA or RNU48. Individually, miR-200a, miR-200b and miR-200c normalized to serum volume and miR-103 were significantly higher in serum of the SEOC cohort (P < 0.05; 0.05; 0.0005 respectively) and in combination, miR-200b + miR-200c normalized to serum volume and miR-103 was the best...

Kardaras, C & Platen, E 2012, 'ON THE DYBVIG-INGERSOLL-ROSS THEOREM', MATHEMATICAL FINANCE, vol. 22, no. 4, pp. 729-740.
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The Dybvig-Ingersoll-Ross (DIR) theorem states that, in arbitrage-free term structure models, long-term yields and forward rates can never fall. We present a refined version of the DIR theorem, where we identify the reciprocal of the maturity date as the maximal order that long-term rates at earlier dates can dominate long-term rates at later dates. The viability assumption imposed on the market model is weaker than those appearing previously in the literature.

Kardaras, C, Obloj, J & Platen, E 2012, 'The numeraire property and long-term growth optimality for drawdown-constrained investments', Mathematical Finance, vol. 27, no. 1, pp. 68-95.
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We consider the portfolio choice problem for a long-run investor in a generalcontinuous semimartingale model. We suggest to use path-wise growth optimalityas the decision criterion and encode preferences through restrictions on theclass of admissible wealth processes. Specifically, the investor is onlyinterested in strategies which satisfy a given linear drawdown constraint. Thepaper introduces the numeraire property through the notion of expected relativereturn and shows that drawdown-constrained strategies with the numeraireproperty exist and are unique, but may depend on the financial planninghorizon. However, when sampled at the times of its maximum and asymptoticallyas the time-horizon becomes distant, the drawdown-constrained numeraireportfolio is given explicitly through a model-independent transformation of theunconstrained numeraire portfolio. Further, it is established that theasymptotically growth-optimal strategy is obtained as limit of numerairestrategies on finite horizons.

Kavazos, CRJ & Wallman, JF 2012, 'Community composition of carrion-breeding blowflies (Diptera: Calliphoridae) along an urban gradient in south-eastern Australia', Landscape and Urban Planning, vol. 106, no. 2, pp. 183-190.
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Kawanabe, T, Fujimoto, R, Sasaki, T, Taylor, JM & Dennis, ES 2012, 'A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis', GENE, vol. 506, no. 2, pp. 301-309.
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Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.

Keely, S, Talley, NJ & Hansbro, PM 2012, 'Pulmonary-intestinal cross-talk in mucosal inflammatory disease', Mucosal Immunology, vol. 5, no. 1, pp. 7-18.
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Chronic obstructive pulmonary disease (COPD) and inflammatory bowel diseases (IBDs) are chronic inflammatory diseases of mucosal tissues that affect the respiratory and gastrointestinal tracts, respectively. They share many similarities in epidemiological and clinical characteristics, as well as in inflammatory pathologies. Importantly, both conditions are accompanied by systemic comorbidities that are largely overlooked in both basic and clinical research. Therefore, consideration of these complications may maximize the efficacy of prevention and treatment approaches. Here, we examine both the intestinal involvement in COPD and the pulmonary manifestations of IBD. We also review the evidence for inflammatory organ cross-talk that may drive these associations, and discuss the current frontiers of research into these issues.

Kim, I, Nam, T-H, Kim, K-W, Ahn, J-H, Park, D-S, Ahn, C, Chun, BS, Wang, G & Ahn, H-J 2012, 'LiNi0.4Co0.3Mn0.3O2 thin film electrode by aerosol deposition', Nanoscale Research Letters, vol. 7, no. 1, pp. 1-15.
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Abstract LiNi0.4Co0.3Mn0.3O2 thin film electrodes are fabricated from LiNi0.4Co0.3Mn0.3O2 raw powder at room temperature without pretreatments using aerosol deposition that is much faster and easier than conventional methods such as vaporization, pulsed laser deposition, and sputtering. The LiNi0.4Co0.3Mn0.3O2 thin film is composed of fine grains maintaining the crystal structure of the LiNi0.4Co0.3Mn0.3O2 raw powder. In the cyclic voltammogram, the LiNi0.4Co0.3Mn0.3O2 thin film electrode shows a 3.9-V anodic peak and a 3.6-V cathodic peak. The initial discharge capacity is 44.6 μAh/cm2, and reversible behavior is observed in charge-discharge profiles. Based on the results, the aerosol deposition method is believed to be a potential candidate for the fabrication of thin film electrodes.

King, JS, Brown, GK, Jenkins, DJ, Ellis, JT, Fleming, PJS, Windsor, PA & Slapeta, J 2012, 'Oocysts and high seroprevalence of Neospora caninum in dogs living in remote Aboriginal communities and wild dogs in Australia', VETERINARY PARASITOLOGY, vol. 187, no. 1-2, pp. 85-92.
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Canines are definitive hosts of Neospora caninum (Apicomplexa). For horizontal transmission from canines to occur, viable oocysts of N. caninum must occur in the environment of susceptible intermediate hosts. Canids in Australia include wild dogs and Aboriginal community dogs. Wild dogs are those dogs that are not dependent on humans for survival and consist of the dingo, feral domestic dog and their hybrid genotypes. Aboriginal community dogs are dependent on humans, domesticated and owned by a family, but are free-roaming and have free access throughout the community. In this study the extent of N. caninum infection was determined in a total of 374 dogs (75 wild dogs and 299 Aboriginal community dogs) using a combination of microscopic, molecular and serological techniques. Oocysts of N. caninum were observed in the faeces of two juvenile Aboriginal community dogs (2/132; 1.5%). To estimate N. caninum prevalence, a new optimised cut-off of 18.5% inhibition for a commercial competitive ELISA was calculated using a two-graph receiver-operating characteristic (TG-ROC) analysis and IFAT as the gold standard resulting in equal sensitivity and specificity of 67.8%. Of the 263 dog sera tested the true prevalence of N. caninum antibodies was 27.0% (95% confidence limit: 10.3-44.1%). The association between the competitive ELISA results in dogs less than 12 month old and older dogs was significant (P=0.042). To our knowledge this is the first large scale parasitological survey of the Aboriginal community dogs and wild dogs from Australia. The high prevalence of N. canilium infection in Aboriginal community dogs illustrates that horizontal transmission of N. caninum is occurring in Australia. These results demonstrated that N. caninum in dogs is widespread, including the semi-arid to arid regions of north-western New South Wales and the Northern Territory. The populations of free-ranging dogs are likely to be important contributors to the sylvatic life cycle of N. caninu...

Kipnis, V, Midthune, D, Freedman, LS & Carroll, RJ 2012, 'Regression calibration with more surrogates than mismeasured variables', Statistics in Medicine, vol. 31, no. 23, pp. 2713-2732.
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In a recent paper (Weller EA, Milton DK, Eisen EA, Spiegelman D. Regression calibration for logistic regression with multiple surrogates for one exposure. Journal of Statistical Planning and Inference 2007; 137: 449‐461), the authors discussed fitting logistic regression models when a scalar main explanatory variable is measured with error by several surrogates, that is, a situation with more surrogates than variables measured with error. They compared two methods of adjusting for measurement error using a regression calibration approximate model as if it were exact. One is the standard regression calibration approach consisting of substituting an estimated conditional expectation of the true covariate given observed data in the logistic regression. The other is a novel two‐stage approach when the logistic regression is fitted to multiple surrogates, and then a linear combination of estimated slopes is formed as the estimate of interest. Applying estimated asymptotic variances for both methods in a single data set with some sensitivity analysis, the authors asserted superiority of their two‐stage approach. We investigate this claim in some detail. A troubling aspect of the proposed two‐stage method is that, unlike standard regression calibration and a natural form of maximum likelihood, the resulting estimates are not invariant to reparameterization of nuisance parameters in the model. We show, however, that, under the regression calibration approximation, the two‐stage method is asymptotically equivalent to a maximum likelihood formulation, and is therefore in theory superior to standard regression calibration. However, our extensive finite‐sample simulations in the practically important parameter space where the regression calibration model provides a good approximation failed to uncover such superiority of the two‐stage method. We also discuss extensions to different data structures. Copyright © 2012 John Wiley &...

Kofoed, MVW, Nielsen, DÅ, Revsbech, NP & Schramm, A 2012, 'Fluorescence in situ hybridization (FISH) detection of nitrite reductase transcripts (nirS mRNA) in Pseudomonas stutzeri biofilms relative to a microscale oxygen gradient', Systematic and Applied Microbiology, vol. 35, no. 8, pp. 513-517.
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Microsensor measurements of oxygen were combined with mRNA-targeted ?uorescence in situ hybridization (FISH) to relate the expression of nitrite reductase (nirS) to oxygen concentrations in arti?- cial bio?lms of the denitri?er Pseudomonas stutzeri. A distinct zone of nirS transcript-containing cells was detected at the oxicanoxic transition zone, below an oxygen threshold concentration of 0.72.5 M, depending on incubation conditions. Although not a routine technique yet, the possibility of coupling microsensor and mRNA-targeted FISH analyses described here opens for studies addressing microenvironment, identity, and actual activity of microbes in strati?ed environments at single cell resolution

Koh, B, Freeman, L & Zaslawski, C 2012, 'Alternative medicine and doping in sports.', Australas Med J, vol. 5, no. 1, pp. 18-25.
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Athletes are high achievers who may seek creative or unconventional methods to improve performance. The literature indicates that athletes are among the heaviest users of complementary and alternative medicine (CAM) and thus may pioneer population trends in CAM use. Unlike non-athletes, athletes may use CAM not just for prevention, treatment or rehabilitation from illness or injuries, but also for performance enhancement. Assuming that athletes' creative use of anything unconventional is aimed at 'legally' improving performance, CAM may be used because it is perceived as more 'natural' and erroneously assumed as not potentially doping. This failure to recognise CAMs as pharmacological agents puts athletes at risk of inadvertent doping.The general position of the World Anti-Doping Authority (WADA) is one of strict liability, an application of the legal proposition that ignorance is no excuse and the ultimate responsibility is on the athlete to ensure at all times whatever is swallowed, injected or applied to the athlete is both safe and legal for use. This means that a violation occurs whether or not the athlete intentionally or unintentionally, knowingly or unknowingly, used a prohibited substance/method or was negligent or otherwise at fault. Athletes are therefore expected to understand not only what is prohibited, but also what might potentially cause an inadvertent doping violation. Yet, as will be discussed, athlete knowledge on doping is deficient and WADA itself sometimes changes its position on prohibited methods or substances. The situation is further confounded by the conflicting stance of anti-doping experts in the media. These highly publicised disagreements may further portray inconsistencies in anti-doping guidelines and suggest to athletes that what is considered doping is dependent on the dominant political zeitgeist. Taken together, athletes may believe that unless a specific and explicit ruling is made, guidelines are open to interpret...

KOH, KS, MATZ, C, TAN, CH, LE, HL, RICE, SA, MARSHALL, DJ, STEINBERG, PD & KJELLEBERG, S 2012, 'Minimal increase in genetic diversity enhances predation resistance', Molecular Ecology, vol. 21, no. 7, pp. 1741-1753.
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AbstractThe importance of species diversity to emergent, ecological properties of communities is increasingly appreciated, but the importance of within‐species genetic diversity for analogous emergent properties of populations is only just becoming apparent. Here, the properties and effects of genetic variation on predation resistance in populations were assessed and the molecular mechanism underlying these emergent effects was investigated. Using biofilms of the ubiquitous bacterium Serratia marcescens, we tested the importance of genetic diversity in defending biofilms against protozoan grazing, a main source of mortality for bacteria in all natural ecosystems. S. marcescens biofilms established from wild‐type cells produce heritable, stable variants, which when experimentally combined, persist as a diverse assemblage and are significantly more resistant to grazing than either wild type or variant biofilms grown in monoculture. This diversity effect is biofilm‐specific, a result of either facilitation or resource partitioning among variants, with equivalent experiments using planktonic cultures and grazers resulting in dominance by a single resistant strain. The variants studied are all the result of single nucleotide polymorphisms in one regulatory gene suggesting that the benefits of genetic diversity in clonal biofilms can occur through remarkably minimal genetic change. The findings presented here provide a new insight on the integration of genetics and population ecology, in which diversity arising through minimal changes in genotype can have major ecological implications for natural populations.

Konarzewski, TK, Murray, BR & Godfree, RC 2012, 'Rapid Development of Adaptive, Climate-Driven Clinal Variation in Seed Mass in the Invasive Annual Forb Echium plantagineum L.', PLOS ONE, vol. 7, no. 12.
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We examined adaptive clinal variation in seed mass among populations of an invasive annual species, Echium plantagineum, in response to climatic selection. We collected seeds from 34 field populations from a 1,000 km long temperature and rainfall gradient across the species' introduced range in south-eastern Australia. Seeds were germinated, grown to reproductive age under common glasshouse conditions, and progeny seeds were harvested and weighed. Analyses showed that seed mass was significantly related to climatic factors, with populations sourced from hotter, more arid sites producing heavier seeds than populations from cooler and wetter sites. Seed mass was not related to edaphic factors. We also found that seed mass was significantly related to both longitude and latitude with each degree of longitude west and latitude north increasing seed mass by around 2.5% and 4% on average. There was little evidence that within-population or between-population variation in seed mass varied in a systematic manner across the study region. Our findings provide compelling evidence for development of a strong cline in seed mass across the geographic range of a widespread and highly successful invasive annual forb. Since large seed mass is known to provide reproductive assurance for plants in arid environments, our results support the hypothesis that the fitness and range potential of invasive species can increase as a result of genetic divergence of populations along broad climatic gradients. In E. plantagineum population-level differentiation has occurred in 150 years or less, indicating that the adaptation process can be rapid. © 2012 Konarzewski et al.

Kovacs, EK, Crowther, MS, Webb, JK & Dickman, CR 2012, 'Population and behavioural responses of native prey to alien predation', OECOLOGIA, vol. 168, no. 4, pp. 947-957.
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The introduction of invasive alien predators often has catastrophic effects on populations of naïve native prey, but in situations where prey survive the initial impact a predator may act as a strong selective agent for prey that can discriminate and avoid it. Using two common species of Australian small mammals that have persisted in the presence of an alien predator, the European red fox Vulpes vulpes, for over a century, we hypothesised that populations of both would perform better where the activity of the predator was low than where it was high and that prey individuals would avoid signs of the predator's presence. We found no difference in prey abundance in sites with high and low fox activity, but survival of one species-the bush rat Rattus fuscipes-was almost twofold higher where fox activity was low. Juvenile, but not adult rats, avoided fox odour on traps, as did individuals of the second prey species, the brown antechinus, Antechinus stuartii. Both species also showed reduced activity at foraging trays bearing fox odour in giving-up density (GUD) experiments, although GUDs and avoidance of fox odour declined over time. Young rats avoided fox odour more strongly where fox activity was high than where it was low, but neither adult R. fuscipes nor A. stuartii responded differently to different levels of fox activity. Conservation managers often attempt to eliminate alien predators or to protect predator-naïve prey in protected reserves. Our results suggest that, if predator pressure can be reduced, otherwise susceptible prey may survive the initial impact of an alien predator, and experience selection to discriminate cues to its presence and avoid it over the longer term. Although predator reduction is often feasible, identifying the level of reduction that will conserve prey and allow selection for avoidance remains an important challenge. © 2011 Springer-Verlag.

Krimmer, DI, Burgess, JK, Wooi, TK, Black, JL & Oliver, BGG 2012, 'Matrix Proteins from Smoke-Exposed Fibroblasts Are Pro-proliferative', American Journal of Respiratory Cell and Molecular Biology, vol. 46, no. 1, pp. 34-39.
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Airway remodeling decreases lung function in chronic obstructive pulmonary disease (COPD). Extracellular matrix (ECM) deposition is increased in remodeled airways and drives cellular processes of proliferation, migration, and inflammation. We investigated the role of cigarette smoke in altering the ECM deposited from human lung fibroblasts. Lung fibroblasts isolated from patients with COPD or other lung disease were exposed to cigarette smoke extract (CSE) and 5 ng/ml transforming growth factor-β1 for 72 hours; in some experiments, inhibitors of signaling molecules were added. Deposition of perlecan, fibronectin, and elastin were measured by ELISA, as was release of IL-8 and IL-13. Unstimulated fibroblast cells were reseeded onto deposited matrix and assessed for proliferation and cytokine release. CSE (5%) increased deposition of fibronectin and perlecan from only COPD fibroblasts. Fibronectin and perlecan deposition was attenuated by addition of the NF-κB inhibitor, BMS-345541, and the signal transduction and activator of transcription-1/3 inhibitor, pyridone 6, respectively. CSE (5%) increased IL-8 release from COPD fibroblasts more than non-COPD fibroblasts. This increase was attenuated by BMS-345541. Matrix deposited after 5%CSE stimulation increased proliferation of fibroblasts, but did not alter cytokine release. ECM produced from COPD fibroblasts after CSE exposure has proproliferative effects. Thus, the ECM in patients with COPD may create an environment that promotes airway remodeling.

Krull, CR, Ranjard, L, Landers, TJ, Ismar, SMH, Matthews, JL & Hauber, ME 2012, 'Analyses of sex and individual differences in vocalizations of Australasian gannets using a dynamic time warping algorithm', The Journal of the Acoustical Society of America, vol. 132, no. 2, pp. 1189-1198.
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The study of the evolution of sexual differences in behavioral and morphological displays requires analyses of the extent of sexual dimorphism across various sensory modalities. In the seabird family Sulidae, boobies show dramatic sexual dimorphism in their vocalizations, and gannet calls have also been suggested to be dimorphic to human observers. This study aimed to evaluate the presence of sexually dimorphic calls in the Australasian gannet (Morus serrator) through the first comprehensive description of its vocalizations recorded at two localities; Cape Kidnappers, where individuals were banded and sexed from DNA samples, and at the Muriwai gannetry, both on the North Island of New Zealand. Calls were first inspected using basic bioacoustic features to establish a library of call element types for general reference. Extensive multivariate tests, based on a dynamic time warping algorithm, subsequently revealed that no sexual differences could be detected in Australasian gannet calls. The analyses, however, indicated extensive and consistent vocal variation between individuals, particularly so in female gannets, which may serve to signal individual identity to conspecifics. This study generates predictions to identify whether differences in Australasian gannet vocalizations play perceptual and functional roles in the breeding and social biology of this long-lived biparental seabird species.

Kuehl, M, Behrendt, L, Trampe, E, Qvortrup, K, Schreiber, U, Borisov, SM, Klimant, I & Larkum, AWD 2012, 'Microenvironmental ecology of the chlorophyll b-containing symbiotic cyanobacterium Prochloron in the didernnid ascidian Lissoclinum patella', FRONTIERS IN MICROBIOLOGY, vol. 3, pp. 1-18.
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The discovery of the cyanobacterium Prochloron was the first finding of a bacterial oxyphototroph with chlorophyll (Chl) b, in addition to Chl a. It was first described as Prochloron didemni but a number of clades have since been described. Prochloron is a conspicuously large (7â25mm) unicellular cyanobacterium living in a symbiotic relationship, primarily with (sub-) tropical didemnid ascidians; it has resisted numerous cultivation attempts and appears truly obligatory symbiotic. Recently, a Prochloron draft genome was published, revealing no lack of metabolic genes that could explain the apparent inability to reproduce and sustain photosynthesis in a free-living stage. Possibly, the unsuccessful cultivation is partly due to a lack of knowledge about the microenvironmental conditions and ecophysiology of Prochloron in its natural habitat.We used microsensors, variable chlorophyll fluorescence imaging and imaging of O2 and pH to obtain a detailed insight to the microenvironmental ecology and photobiology of Prochloron in hospite in the didemnid ascidian Lissoclinum patella. The microenvironment within ascidians is characterized by steep gradients of light and chemical parameters that change rapidly with varying irradiances. The interior zone of the ascidians harboring Prochloron thus became anoxic and acidic within a few minutes of darkness, while the same zone exhibited O2 super-saturation and strongly alkaline pH after a few minutes of illumination. Photosynthesis showed lack of photoinhibition even at high irradiances equivalent to full sunlight, and photosynthesis recovered rapidly after periods of anoxia.We discuss these new insights on the ecological niche of Prochloron and possible interactions with its host and other microbes in light of its recently published genome and a recent study of the overall microbial diversity and metagenome of L. patella.

Kumar, M, Bijo, AJ, Baghel, RS, Reddy, CRK & Jha, B 2012, 'Selenium and spermine alleviate cadmium induced toxicity in the red seaweed Gracilaria dura by regulating antioxidants and DNA methylation', Plant Physiology and Biochemistry, vol. 51, pp. 129-138.
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The protective role of exogenously supplied selenium (Se) and polyamines (PAs) such as putrescine (Put) and spermine (Spm) in detoxifying the cadmium (Cd) induced toxicity was studied in the marine red alga Gracilaria dura in laboratory conditions. The Cd exposure (0.4 mM) impede the growth of alga while triggering the reactive oxygen species (ROS viz. O 2•- and H 2O 2) generation, inhibition of antioxidant system, and enhancing the lipoxygenase (LOX) activity, malondialdehyde (MDA) level and demethylation of DNA. Additions of Se (50 μM) and/or Spm (1 mM) to the culture medium in contrast to Put, efficiently ameliorated the Cd toxicity by decreasing the accumulation of ROS and MDA contents, while restoring or enhancing the level of enzymatic and nonenzymatic antioxidants and their redox ratio, phycobiliproteins and phytochelatins, over the controls. The isoforms of antioxidant enzymes namely superoxide dismutase (Mn-SOD, ∼ 150 kDa; Fe-SOD ∼120 kDa), glutathione peroxidase (GSH-Px, ∼120 and 140 kDa), glutathione reductase (GR, ∼110 kDa) regulated differentially to Se and/or Spm supplementation. Furthermore, it has also resulted in enhanced levels of endogenous PAs (specially free and bound insoluble Put and Spm) and n-6 PUFAs (C20-3, n-6 and C20-4, n-6). This is for the first time wherein Se and Spm were found to regulate the stabilization of DNA methylation by reducing the events of cytosine demethylation in a mechanism to alleviate the Cd stress in marine alga. The present findings reveal that both Se and Spm play a crucial role in controlling the Cd induced oxidative stress in G. dura. © 2011 Elsevier Masson SAS.

Labbate, M, Boucher, Y, Luu, I, Chowdhury, PR & Stokes, HW 2012, 'Integron associated mobile genes', Mobile Genetic Elements, vol. 2, no. 1, pp. 13-18.
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Lateral gene transfer (LGT) impacts on the evolution of prokaryotes in both the short and long-term. The short-term impacts of mobilized genes are a concern to humans since LGT explains the global rise of multi drug resistant pathogens seen in the past 70 years. However, LGT has been a feature of prokaryotes from the earliest days of their existence and the concept of a bifurcating tree of life is not entirely applicable to prokaryotes since most genes in extant prokaryotic genomes have probably been acquired from other lineages. Successful transfer and maintenance of a gene in a new host is understandable if it acts independently of cell networks and confers an advantage. Antibiotic resistance provides an example of this whereby a gene can be advantageous in virtually any cell across broad species backgrounds. In a longer evolutionary context however laterally transferred genes can be assimilated into even essential cell networks. How this happens is not well understood and we discuss recent work that identifies a mobile gene, unique to a cell lineage, which is detrimental to the cell when lost. We also present some additional data and believe our emerging model will be helpful in understanding how mobile genes integrate into cell networks.

Lam, CFD, Leung, KS, Heng, PA, Lim, CED & Wong, FWS 2012, 'Chinese Acupuncture Expert System (CAES)—A Useful Tool to Practice and Learn Medical Acupuncture', Journal of Medical Systems, vol. 36, no. 3, pp. 1883-1890.
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This paper describes the development of a Chinese Acupuncture Expert System (CAES) that will assist the learning and practice of medical acupuncture. This was the development of a Chinese Acupuncture Expert System which incorporated eight functional modules. These modules were 1) Add Patient Record subsystem; 2) Diagnosis subsystem ; 3) Acupuncture Prescription subsystem ; 4) Needle Insertion Position Animation subsystem ; 5) Acupuncture Points Usage Statistic subsystem ; 6) History Query subsystem; 7) Acupuncture Points Query subsystem and 8) Diagnosis Remarks and Diagnosis Record Save subsystem. Two databases were built-Patient Record database and Diagnosis (Acupuncture) Knowledge database. All the Traditional Chinese Medicine (TCM) knowledge and acupuncture treatment prescriptions were extracted from officially used TCM textbooks and received guidiance and expert advice from two acupuncturists working in this project. A Chinese Acupuncture Expert System (CAES) was built, which after the input from users of any Chinese disease symptoms and signs, it can provide a list of related TCM syndrome diagnoses based on the patients' disease symptoms and signs, and at the same time it can offer advice of the appropriate Chinese acupuncture treatment to the users. CAES also provided text descriptions and acupuncture animations showing the acupoint locations and the direction and depth of the needle insertion technique. Therefore users can easily learn acupuncture and practice it. This new acupuncture expert system will hopefully provide an easy way for users to learn and practice Chinese Acupuncture and establish its usefulness after it was fully evaluated. © Springer Science+Business Media, LLC 2011.

Langford, SJ, Latter, MJ, Wilman, BE & Bhosale, SV 2012, 'Biologically Derived Supramolecular Materials'.
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Abstract Inspired by nature and its ability to form well‐defined architectures on the nanoscale, this chapter investigates not only examples of hybrid nanostructured materials that utilize the building blocks of nature, such as DNA, biopolymers, and bilayers, but also of biomimicry.

Lapine, M, Jelinek, L & Marqués, R 2012, 'Surface mesoscopic effects in finite metamaterials', Optics Express, vol. 20, no. 16, pp. 18297-18297.
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While the effective medium treatment of unbounded metamaterials appears to be well established and firmly proven, related phenomena in finite structures have not received sufficient attention. We report on mesoscopic effects associated with the boundaries of finite discrete metamaterial samples, which can invalidate an effective medium description. We show how to avoid such effects by proper choice of boundary configuration. As all metamaterial implementations are naturally finite, we are confident that our findings are crucial for future metamaterial research. © 2012 Optical Society of America.

Lapine, M, Shadrivov, I & Kivshar, Y 2012, 'Wide-band negative permeability of nonlinear metamaterials', Scientific Reports, vol. 2, no. 1.
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We propose a novel way to achieve an exceptionally wide frequency range where metamaterial possesses negative effective permeability. This can be achieved by employing a nonlinear response of metamaterials. We demonstrate that, with an appropriate design, a frequency band exceeding 100% is available for a range of signal amplitudes. Our proposal provides a significant improvement over the linear approach, opening a road towards broadband negative refraction and its applications.

Lapine, M, Shadrivov, IV, Powell, DA & Kivshar, YS 2012, 'Magnetoelastic metamaterials', Nature Materials, vol. 11, no. 1, pp. 30-33.
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The study of advanced artificial electromagnetic materials, known as metamaterials, provides a link from material science to theoretical and applied electrodynamics, as well as to electrical engineering. Being initially intended mainly to achieve negative refraction, the concept of metamaterials quickly covered a much broader range of applications, from microwaves to optics and even acoustics. In particular, nonlinear metamaterials established a new research direction giving rise to fruitful ideas for tunable and active artificial materials. Here we introduce the concept of magnetoelastic metamaterials, where a new type of nonlinear response emerges from mutual interaction. This is achieved by providing a mechanical degree of freedom so that the electromagnetic interaction in the metamaterial lattice is coupled to elastic interaction. This enables the electromagnetically induced forces to change the metamaterial structure, dynamically tuning its effective properties. This concept leads to a new generation of metamaterials, and can be compared to such fundamental concepts of modern physics as optomechanics of photonic structures or magnetoelasticity in magnetic materials.

Larkum, AWD, Chen, M, Li, Y, Schliep, M, Trampe, E, West, J, Salih, A & Kuhl, M 2012, 'A Novel Epiphytic Chlorophyll d-containing Cyanobacterium Isolated from a Mangrove-associated Red Alga', JOURNAL OF PHYCOLOGY, vol. 48, no. 6, pp. 1320-1327.
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A new habitat and a new chlorophyll (Chl) d-containing cyanobacterium belonging to the genus Acaryochloris are reported in this study. Hyperspectral microscopy showed the presence of Chl d-containing microorganisms in epiphytic biofilms on a red alga (Gelidium caulacantheum) colonizing the pneumato-phores of a temperate mangrove (Avicennia marina). The presence of Chl d was further proven by high performance liquid chromatography (HPLC)-based pigment analysis and by confocal imaging of cultured cells. Enrichment of mangrove biofilm samples under near-infrared radiation (NIR) yielded the new Acaryochloris sp. MPGRS1, which was closely related in terms of 16S rRNA gene sequence to an isolate from the hypertrophic Salton Sea, USA. The new isolate used Chl d as its major photopigment; Chl d and Chl a contents were ~98% and 1%-2% of total cellular chlorophyll, respectively. These findings expand the variety of ecological niches known to harbor Chl d-containing cyanobacteria and support our working hypothesis that such oxyphototrophs may be ubiquitous in habitats depleted of visible light, but with sufficient NIR exposure. © 2012 Phycological Society of America.

Larkum, AWD, Ross, IL, Kruse, O & Hankamer, B 2012, 'Selection, breeding and engineering of microalgae for bioenergy and biofuel production', Trends in Biotechnology, vol. 30, no. 4, pp. 198-205.
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Microalgal production technologies are seen as increasingly attractive for bioenergy production to improve fuel security and reduce CO2 emissions. Photosynthetically derived fuels are a renewable, potentially carbon-neutral and scalable alternative reserve. Microalgae have particular promise because they can be produced on non-arable land and utilize saline and wastewater streams. Furthermore, emerging microalgal technologies can be used to produce a range of products such as biofuels, protein-rich animal feeds, chemical feedstocks (e.g. bio-plastic precursors) and higher-value products. This review focuses on the selection, breeding and engineering of microalgae for improved biomass and biofuel conversion efficiencies.

Lategan, MJ, Torpy, FR, Newby, S, Stephenson, S & Hose, GC 2012, 'Fungal Diversity of Shallow Aquifers in Southeastern Australia', GEOMICROBIOLOGY JOURNAL, vol. 29, no. 4, pp. 352-361.
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The diversity of groundwater mycobiota remains relatively unknown and unchartered. As a first description of the fungal diversity in Australian aquifers we explored the distribution, abundance and diversity of fungal assemblages in samples from an alluvial (Bylong) and two sandy (Tomago; Botany Sands) unconfined aquifers in coastal catchments of NSW, Australia. A total of 89 strains were isolated with 54 Eumycotan taxa identified. The Botany Sands aquifer, with a history of industrial chlorinated hydrocarbon contamination along a hydraulic gradient, yielded the highest richness with 23 identifiable taxa, followed by Tomago with 17 and Bylong with 14. Despite differences in geology and land use, the aquifers shared similarities in their fungal assemblages with Penicillium, Rhodotorula, Paecilomyces and Cladosporium spp. common to all sites. Fungal assemblages were notably similar between the Bylong and Tomago samples and differed from the Botany samples in composition and heterogeneity. Taxa appeared to cluster into two main groups according to their association with environmental conditions; with the taxa common to the Botany aquifer correlating strongly with higher dissolved oxygen concentrations. The diversity and spatial heterogeneity of groundwater mycobiota appeared to be influenced by both anthropogenic contaminants and associated environmental variables. Based on the criteria of ubiquity, abundance and potential sensitivity to contamination, Penicillium and Rhodotorula spp. might be fitting taxa for monitoring groundwater quality. © 2012 Copyright Taylor & Francis Group, LLC.

Lavery, TJ, Roudnew, B, Seymour, J, Mitchell, JG & Jeffries, T 2012, 'High Nutrient Transport and Cycling Potential Revealed in the Microbial Metagenome of Australian Sea Lion (Neophoca cinerea) Faeces', PLoS ONE, vol. 7, no. 5, pp. e36478-e36478.
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Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production. © 2012 Lavery et al.

Lawrence, FJ, Botten, LC, Dossou, KB, McPhedran, RC & de Sterke, CM 2012, 'A flexible Bloch mode method for computing complex band structures and impedances of two-dimensional photonic crystals', JOURNAL OF APPLIED PHYSICS, vol. 111, no. 1, pp. 1-8.
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We present a flexible method that can calculate Bloch modes, complex band structures, and impedances of two-dimensional photonic crystals from scattering data produced by widely available numerical tools. The method generalizes previous work which relied on specialized multipole and finite element method (FEM) techniques underpinning transfer matrix methods. We describe the numerical technique for mode extraction, and apply it to calculate a complex band structure and to design two photonic crystal antireflection coatings. We do this for frequencies at which other methods fail, but which nevertheless are of significant practical interest. © 2012 American Institute of Physics.

Lay, WCL, Zhang, Q, Zhang, J, McDougald, D, Tang, C, Wang, R, Liu, Y & Fane, AG 2012, 'Effect of Pharmaceuticals on the Performance of a Novel Osmotic Membrane Bioreactor (OMBR)', Separation Science and Technology, vol. 47, no. 4, pp. 543-554.
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Lear, J, Hare, D, Adlard, P, Finkelstein, D & Doble, P 2012, 'Improving acquisition times of elemental bio-imaging for quadrupole-based LA-ICP-MS', JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY, vol. 27, no. 1, pp. 159-164.
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Elemental bio-imaging experiments by quadrupole-based LA-ICP-MS normally employ scan speeds where the distance traversed in one second is equal to or less than the diameter of the laser beam. Consequently, data for a higher-resolution (pixel size = 15 µm2) image of a 5 mm2 tissue section can take upwards of 30 h to acquire. Appropriate laser scan speeds may be calculated by consideration of the relationship between laser scan speed, laser spot diameter and the total scan cycle of the quadrupole mass analyser. This paper presents a simple method to calculate the laser scan speeds capable of reducing the acquisition time by up to a factor of 5 whilst maintaining dimensional integrity of the image.

Lear, J, Hare, DJ, Fryer, F, Adlard, PA, Finkelstein, DI & Doble, PA 2012, 'High-Resolution Elemental Bioimaging of Ca, Mn, Fe, Co, Cu, and Zn Employing LA-ICP-MS and Hydrogen Reaction Gas', ANALYTICAL CHEMISTRY, vol. 84, no. 15, pp. 6707-6714.
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Imaging of trace metal distribution in tissue sections by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is typically performed using spatial resolutions of 30 µm2 and above. Higher resolution imaging is desirable for many biological applications in order to approach the dimensions of a single cell. The limiting factor for increasing resolution is sensitivity, where signal-to-noise ratios are poor due to inherent background spectral interferences and reduced sample volume with decreasing laser beam diameter. Several prominent spectral interferences are present for a number of biologically relevant isotopes, including the 40Ar16O+ spectral interference on 56Fe+. We examined if H2 as a reaction gas could improve the analytical performance of imaging experiments for a range of masses with spectral interferences. At low (<1 mL min1) H2 flow rates, greater spectral interference due to H+ adducts was observed for 55Mn, 57Fe, and 59Co. At higher flow rates of up to 3 mL H2 per minute, the spectral interferences were reduced leading to improvement in limits of analysis for masses with O- and N-based polyatomic interferences. Enhanced sensitivity with the reaction cell allowed construction of high resolution (6 µm2) imaging of 56Fe in the mouse brain that approached the dimensions of single cells.

Lee, JC, Aharonovich, I, Magyar, AP, Rol, F & Hu, EL 2012, 'Coupling of silicon-vacancy centers to a single crystal diamond cavity', OPTICS EXPRESS, vol. 20, no. 8, pp. 8891-8897.
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Optical coupling of an ensemble of silicon-vacancy (SiV) centers to single-crystal diamond microdisk cavities is demonstrated. The cavities are fabricated from a single-crystal diamond membrane generated by ion implantation and electrochemical liftoff fo

Lee, KC, Sussman, BJ, Sprague, MR, Michelberger, P, Reim, KF, Nunn, J, Langford, NK, Bustard, PJ, Jaksch, D & Walmsley, IA 2012, 'Macroscopic non-classical states and terahertz quantum processing in room-temperature diamond', Nature Photonics, vol. 6, no. 1, pp. 41-44.
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Lee, S-H, Larsen, AG, Ohkubo, K, Cai, Z-L, Reimers, JR, Fukuzumi, S & Crossley, MJ 2012, 'Long-lived long-distance photochemically induced spin-polarized charge separation in beta,beta '-pyrrolic fused ferrocene-porphyrin-fullerene systems', CHEMICAL SCIENCE, vol. 3, no. 1, pp. 257-269.
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The exceptionally long lived charge separation previously observed in a β,β′-pyrrolic-fused ferrocene-porphyrin-fullerene triad (lifetime 630 μs) and related porphyrin-fullerene dyad (lifetime 260 μs) is attributed to the production of triplet charge-separated states. Such molecular excited-state spin polarization maintained over distances of up to 23 Å is unprecedented and offers many technological applications. Electronic absorption and emission spectra, femtosecond and nanosecond time-resolved transient absorption spectra, and cyclic voltammograms of two triads and four dyads are measured and analyzed to yield rate constants, donor-acceptor couplings, free-energy changes, and reorganization energies for charge-separation and charge-recombination processes. Production of long-lived intramolecular triplet states is confirmed by electron-paramagnetic resonance spectra at 77-223 K, as is retention of spin polarization in π-conjugated ferrocenium ions. The observed rate constants were either first predicted (singlet manifold) or later confirmed (triplet manifold) by a priori semiclassical kinetics calculations for all conceivable photochemical processes, parameterized using density-functional theory and complete-active-space self-consistent-field calculations. Identified are both a ps-timescale process attributed to singlet recombination and a μs-timescale process attributed to triplet recombination. © 2012 The Royal Society of Chemistry.

Leigh, A, Sevanto, S, Ball, MC, Close, JD, Ellsworth, DS, Knight, CA, Nicotra, AB & Vogel, S 2012, 'Do thick leaves avoid thermal damage in critically low wind speeds?', New Phytologist, vol. 194, no. 2, pp. 477-487.
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• Transient lulls in air movement are rarely measured, but can cause leaf temperature to rise rapidly to critical levels. The high heat capacity of thick leaves can damp this rapid change in temperature. However, little is known about the extent to which increased leaf thickness can reduce thermal damage, or how thick leaves would need to be to have biological significance. We evaluated quantitatively the contribution of small increases in leaf thickness to the reduction in thermal damage during critically low wind speeds under desert conditions. • We employed a numerical model to investigate the effect of thickness relative to transpiration, absorptance and leaf size on damage avoidance. We used measured traits and thermotolerance thresholds of real leaves to calculate the leaf temperature response to naturally occurring variable low wind speed. • Our results demonstrated that an increase in thickness of only fractions of a millimetre can prevent excursions to damaging high temperatures. This damping effect of increased thickness was greatest when other means of reducing leaf temperature (transpiration, reflectance or reduced size) were lacking. • For perennial desert flora, we propose that increased leaf thickness is important in decreasing the incidence of extreme heat stress and, in some species, in enhancing long-term survival. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

LI, J, YANG, Z, YANG, Z, YAN, D, WU, H, LIAO, J, QIU, J, SONG, Z, YANG, Y & ZHOU, D 2012, 'Upconversion luminescence and color tunable properties in Yb-Tb codoped Ca0.15Zr0.85O1.85 inverse opal', Journal of Rare Earths, vol. 30, no. 12, pp. 1191-1194.
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Li, K, Wang, B, Su, D, Park, J, Ahn, H & Wang, G 2012, 'Enhance electrochemical performance of lithium sulfur battery through a solution-based processing technique', Journal of Power Sources, vol. 202, pp. 389-393.
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Sulfur/carbon nanocomposites have been successfully prepared by a solution-based processing technique using dimethyl sulfoxide as the solvent. The as-prepared nanocomposites were characterized by X-ray diffraction and field emission scanning electron microscopy. The electrochemical performance of sulfur/carbon nanocomposites were tested by cyclic voltammetry and galvanostatic charge/discharge cycling. When applied as the cathode material in lithium sulfur batteries, the as-prepared sulfur/carbon nanocomposites exhibited a high reversible capacity of 1220 mAh g -1 in the first cycle and maintained a satisfactory cyclability. This drastic improvement of specific capacity and cycling performance could be attributed to the reduced particle size of sulfur and the homogeneous distribution of sulfur nanoparticles on a carbon matrix, resulting from this novel solution-based processing technique. © 2011 Elsevier B.V. All rights reserved.

Li, L, Wang, Y-P, Yu, Q, Pak, B, Eamus, D, Yan, J, van Gorsel, E & Baker, IT 2012, 'Improving the responses of the Australian community land surface model (CABLE) to seasonal drought', JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, vol. 117, no. 4, p. G04002.
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Correct representations of root functioning, such as root water uptake and hydraulic redistribution, are critically important for modeling the responses of vegetation to droughts and seasonal changes in soil moisture content. However, these processes are poorly represented in global land surface models. In this study, we incorporated two root functions: a root water uptake function which assumes root water uptake efficiency varies with rooting depth, and a hydraulic redistribution function into a global land surface model, CABLE. The water uptake function developed by Lai and Katul (2000) was also compared with the default one (see Wang et al., 2010) that assumes that efficiency of water uptake per unit root length is constant. Using eddy flux measurements of CO 2 and water vapor fluxes at three sites experiencing different patterns of seasonal changes in soil water content, we showed that the two root functions significantly improved the agreement between the simulated fluxes of net ecosystem exchange and latent heat flux and soil moisture dynamics with those observed during the dry season while having little impact on the model simulation during the wet seasons at all three sites. Sensitivity analysis showed that varying several model parameters influencing soil water dynamics in CABLE did not significantly affect the model's performance. We conclude that these root functions represent a valuable improvement for land surface modeling and should be implemented into CABLE and other land surface models for studying carbon and water dynamics where rainfall varies seasonally or interannually. © 2012. American Geophysical Union. All Rights Reserved.

Li, X, McGrath, KC, Nammi, S, Heather, AK & Roufogalis, BD 2012, 'Attenuation of Liver Pro‐Inflammatory Responses by Zingiber officinale via Inhibition of NF‐kappa B Activation in High‐Fat Diet‐Fed Rats', Basic & Clinical Pharmacology & Toxicology, vol. 110, no. 3, pp. 238-244.
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Abstract:  The aim of this study was to investigate whether treatment with a ginger (Zingiber officinale) extract of high‐fat diet (HFD)‐fed rats suppresses Nuclear factor‐kappa B (NF‐κB)‐driven hepatic inflammation and to subsequently explore the molecular mechanisms in vitro. Adult male Sprague‐Dawley rats were treated with an ethanolic extract of Zingiber officinale (400 mg/kg) along with a HFD for 6 weeks. Hepatic cytokine mRNA levels, cytokine protein levels and NF‐κB activation were measured by real‐time PCR, Western blot and an NF‐κB nuclear translocation assay, respectively. In vitro, cell culture studies were carried out in human hepatocyte (HuH‐7) cells by treatment with Zingiber officinale (100 μg/mL) for 24 hr prior to interleukin‐1β (IL‐1β, 8 ng/mL)‐induced inflammation. We showed that Zingiber officinale treatment decreased cytokine gene TNFα and IL‐6 expression in HFD‐fed rats, which was associated with suppression of NF‐κB activation. In vitro, Zingiber officinale treatment decreased NF‐κB‐target inflammatory gene expression of IL‐6, IL‐8 and serum amyloid A1 (SAA1), while it suppressed NF‐κB activity, IκBα degradation and IκB kinase (IKK) activity. In conclusion, Zingiber officinale suppressed markers of hepatic inflammation in HFD‐fed rats, as demonstrated by decreased hepatic cytokine gene expression and decreased NF‐κB activation. The study demonstrates that the anti‐inflammatory effect of Zingiber officinale occurs at least in part through the NF‐κB signalling pathway.

Liao, Y, Zeng, M, Wu, Z-F, Chen, H, Wang, H-N, Wu, Q, Shan, Z & Han, X-Y 2012, 'Improving Phytase Enzyme Activity in a Recombinant phyA Mutant Phytase from Aspergillus niger N25 by Error-Prone PCR', Applied Biochemistry and Biotechnology, vol. 166, no. 3, pp. 549-562.
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Lim, CED & Cheng, NCL 2012, 'Connective tissue reflex massage to improve peripheral circulation in type 2 diabetes mellitus', Focus on Alternative and Complementary Therapies, vol. 17, no. 1, pp. 69-70.
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Castro‐Sanchez AM, Moreno‐Lorenzo C, Mataran‐Penarrocha GA, Feriche‐Fernandez‐Castanys B, Granados‐Gamez G, Quesada‐Rubio JM.Connective tissue reflex massage for type 2 diabetic patients with peripheral arterial disease: randomized controlled trial.Evid Based Complement Altern Med 2011; Article ID 804321. doi:10.1093/ecam/nep171.

Lim, CED & Cheng, NCL 2012, 'Massage therapy to improve sleep quality post coronary artery bypass graft surgery', Focus on Alternative and Complementary Therapies, vol. 17, no. 1, pp. 67-68.
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Nerbass FB, Feltrim MIZ, de Souza SA, Ykeda DS, Lorenzi‐Filho G.Effects of massage therapy on sleep quality after coronary artery bypass graft surgery.Clinics 2010; 65: 1105–10.

Lim, CED, Wong, WSF & Cheng, NCL 2012, 'Xiao Shan Zhu Lin Si's secret gynaecological Chinese medicinal formulae - grappling with an ancient disease in modern times', Journal of the Australian Traditional-Medicine Society, vol. 18, no. 1, pp. 27-29.

Liu, H, Du, X, Xing, X, Wang, G & Qiao, SZ 2012, 'Highly ordered mesoporous Cr2O3 materials with enhanced performance for gas sensors and lithium ion batteries', CHEMICAL COMMUNICATIONS, vol. 48, no. 6, pp. 865-867.
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Highly ordered mesoporous Cr 2O 3 materials with high specific surface area and narrow pore size distribution were successfully prepared by a vacuum assisted impregnation method. Both 2-dimensional hexagonal and 3-dimensional cubic Cr 2O 3 mesoporous replicas from SBA-15 and KIT-6 templates exhibit enhanced performance for gas sensors and lithium ion batteries, compared to the bulk Cr 2O 3 counterpart.

Liu, H, Su, D, Wang, G & Qiao, SZ 2012, 'An ordered mesoporous WS2 anode material with superior electrochemical performance for lithium ion batteries', JOURNAL OF MATERIALS CHEMISTRY, vol. 22, no. 34, pp. 17437-17440.
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Ordered mesoporous tungsten sulfide (WS 2) with high surface area and narrow pore size distribution was synthesized by a vacuum assisted impregnation route. The as-prepared mesoporous WS 2 exhibited a high lithium storage capacity of 805 mA h g -1 at a current of 0.1 A g -1 and an excellent high rate capability. © 2012 The Royal Society of Chemistry.

Liu, H, Su, D, Zhou, R, Sun, B, Wang, G & Qiao, SZ 2012, 'Highly Ordered Mesoporous MoS2 with Expanded Spacing of the (002) Crystal Plane for Ultrafast Lithium Ion Storage', ADVANCED ENERGY MATERIALS, vol. 2, no. 8, pp. 970-975.
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Highly ordered mesoporous MoS 2 with a high surface area and narrow pore-size distribution is synthesized by a vacuum assisted impregnation route. The mesoporous MoS 2 demonstrates an expanded d 002 spacing of 0.66 nm. The mesoporous MoS 2 electrode achieves an excellent high rate capacity of 608 mAh g -1 at the discharge current of 10 A g -1 (-15C), which places MoS 2 as a viable next generation high power source for electric vehicles. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Liu, Y, Biarnés Costa, M & Gerhardinger, C 2012, 'IL-1β Is Upregulated in the Diabetic Retina and Retinal Vessels: Cell-Specific Effect of High Glucose and IL-1β Autostimulation', PLoS ONE, vol. 7, no. 5, pp. e36949-e36949.
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Many molecular and cellular abnormalities detected in the diabetic retina support a role for IL-1β-driven neuroinflammation in the pathogenesis of diabetic retinopathy. IL-1β is well known for its role in the induction and, through autostimulation, amplification of neuroinflammation. Upregulation of IL-1β has been consistently detected in the diabetic retina; however, the mechanisms and cellular source of IL-1β overexpression are poorly understood. The aim of this study was to investigate the effect of high glucose and IL-1β itself on IL-1β expression in microglial, macroglial (astrocytes and Müller cells) and retinal vascular endothelial cells; and to study the effect of diabetes on the expression of IL-1β in isolated retinal vessels and on the temporal pattern of IL-1β upregulation and glial reactivity in the retina of streptozotocin-diabetic rats. IL-1β was quantified by RealTime RT-PCR and ELISA, glial fibrillar acidic protein, α2-macroglobulin, and ceruloplasmin by immunoblotting. We found that high glucose induced a 3-fold increase of IL-1β expression in retinal endothelial cells but not in macroglia and microglia. IL-1β induced its own synthesis in endothelial and macroglial cells but not in microglia. In retinal endothelial cells, the high glucose-induced IL-1β overexpression was prevented by calphostin C, a protein kinase C inhibitor. The retinal vessels of diabetic rats showed increased IL-1β expression as compared to non-diabetic rats. Retinal expression of IL-1β increased early after the induction of diabetes, continued to increase with progression of the disease, and was temporally associated with upregulation of markers of glial activation. These findings point to hyperglycemia as the trigger and to the endothelium as the origin of the initial retinal upregulation of IL-1β in diabetes; and to IL-1β itself, via autostimulation in endothelial and macroglial cells, as the mechanism of sustained IL-1β overexpression. Interrupting the vicious circle trig...

Liu, Y, Ding, Y, Alonas, E, Zhao, W, Santangelo, PJ, Jin, D, Piper, JA, Teng, J, Ren, Q & Xi, P 2012, 'Achieving λ/10 Resolution CW STED Nanoscopy with a Ti:Sapphire Oscillator', PLoS ONE, vol. 7, no. 6, pp. e40003-e40003.
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In this report, a Ti:Sapphire oscillator was utilized to realize synchronization-free stimulated emission depletion (STED) microscopy. With pump power of 4.6 W and sample irradiance of 310 mW, we achieved super-resolution as high as 71 nm. With synchronization-free STED, we imaged 200 nm nanospheres as well as all three cytoskeletal elements (microtubules, intermediate filaments, and actin filaments), clearly demonstrating the resolving power of synchronization-free STED over conventional diffraction limited imaging. It also allowed us to discover that, Dylight 650, exhibits improved performance over ATTO647N, a fluorophore frequently used in STED. Furthermore, we applied synchronization-free STED to image fluorescently-labeled intracellular viral RNA granules, which otherwise cannot be differentiated by confocal microscopy. Thanks to the widely available Ti:Sapphire oscillators in multiphoton imaging system, this work suggests easier access to setup super-resolution microscope via the synchronization-free STED. © 2012 Liu et al.

Liu, Y, Qiu, X-S & Wang, E-H 2012, 'Sporadic Hemangioblastoma of the Kidney: a rare renal tumor', Diagnostic Pathology, vol. 7, no. 1.
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Abstract Abstract Hemangioblastoma is a benign and morphologically distinctive tumor that can occur sporadically or in association with von Hippel-Lindau disease in approximately 25% of the cases, and which involves the central nervous system in the majority of the cases. Rare occurrences of hemangioblastoma in peripheral nerves and extraneural tissues have been reported. This report describes one case of sporadic renal hemangioblastoma happened in a 16-year-old Chinese female patient, presenting with hematuria, and low back pain. Histologically, the tumors were circumscribed, and composed of sheets of large polygonal cells traversed by arborizing thin-walled blood vessels. The diagnosis of hemangioblastoma was confirmed by negative immunostaining for cytokeratin, and positive staining for α-inhibin, S100 and neuron-specific enolase (NSE). This benign neoplasm which can be mistaken for various malignancies such as renal cell carcinoma, epithelioid hemangiopericytoma and epithelioid angiomyolipoma, deserves wider recognition for its occurrence as a primary renal tumor. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5445834246942699

Lloyd, HB, Murray, BR & Gribben, PE 2012, 'Trait and abundance patterns in two marine molluscs: the influence of abiotic conditions operating across multiple spatial scales', MARINE ECOLOGY PROGRESS SERIES, vol. 463, pp. 205-214.
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Theoretical mechanisms describing species abundance distributions should also underpin geographic variation in life-history traits. However, recent studies suggest that abundance and trait patterns may not co-vary and may respond differently to abiotic conditions acting at different spatial scales. We examined patterns in abundance and body size of 2 estuarine molluscs, the arkshell Anadara trapezia and the mudsnail Batillaria australis, across their wide distributions in eastern Australia. We related abundance and body size patterns to abiotic variables including water temperature, pH, salinity, sediment redox and dissolved oxygen content at multiple spatial scales. Two hypotheses were tested: (1) geographic patterns in abundance and body size do not co-vary, and (2) patterns in abundance are more strongly influenced by abiotic conditions occurring at a large spatial scale (e.g. across latitudinal gradients) whereas body size is more strongly influenced by variation in abiotic conditions occurring at smaller scales. The influence of spatial scale and associated abiotic variables on abundance and body size distributions was determined using multiple linear regression, ANOVA and variance component analyses. Geographic variation in abundance and body size were independent of each other in both species. Abiotic variation across latitudinal gradients was the strongest predictor of abundance, but factors that varied substantially at local scales (e.g. dissolved oxygen and sediment redox) were the strongest predictors of body size. Our data indicate that geographic patterns in body size and abundance can be disconnected from each other, most likely due to differential responses to abiotic variation acting at different spatial scales. © Inter-Research 2012 · www.int-res.com.

Lobo, CJ, Martin, A, Phillips, MR & Toth, M 2012, 'Electron beam induced chemical dry etching and imaging in gaseous NH3 environments', NANOTECHNOLOGY, vol. 23, no. 37, pp. 375302-375302.
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We report the use of ammonia (NH 3) vapor as a new precursor for nanoscale electron beam induced etching (EBIE) of carbon, and an efficient imaging medium for environmental scanning electron microscopy (ESEM). Etching is demonstrated using amorphous carbonaceous nanowires grown by electron beam induced deposition (EBID). It is ascribed to carbon volatilization by hydrogen radicals generated by electron dissociation of NH 3 adsorbates. The volatilization process is also effective at preventing the buildup of residual hydrocarbon impurities that often compromise EBIE, EBID and electron imaging. We also show that ammonia is a more efficient electron imaging medium than H 2O, which up to now has been the most commonly used ESEM imaging gas. © 2012 IOP Publishing Ltd.

Loo, C-Y, Young, PM, Lee, W-H, Cavaliere, R, Whitchurch, CB & Rohanizadeh, R 2012, 'Superhydrophobic, nanotextured polyvinyl chloride films for delaying Pseudomonas aeruginosa attachment to intubation tubes and medical plastics', ACTA BIOMATERIALIA, vol. 8, no. 5, pp. 1881-1890.
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Bacterial attachment onto the surface of polymers in medical devices such as polyvinyl chloride (PVC) is influenced by the physicochemical properties of the polymer, including its surface hydrophobicity and roughness. In this study, to prevent biofilm fo

Lord, MS, Jung, M, Teoh, WY, Gunawan, C, Vassie, JA, Amal, R & Whitelock, JM 2012, 'Cellular uptake and reactive oxygen species modulation of cerium oxide nanoparticles in human monocyte cell line U937', Biomaterials, vol. 33, no. 31, pp. 7915-7924.
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Cerium oxide nanoparticles (nanoceria) are promising materials for intracellular oxygen free radical scavenging providing a potential therapy for reactive oxygen species (ROS)-mediated inflammatory processes. In this study rhombohedral-shaped nanoceria were synthesized by flame spray pyrolysis with tuneable particle diameters between 3 and 94 nm by changing the liquid precursor flow rate. Monocytes and macrophages are major players in inflammatory processes as their production of ROS species has important downstream effects on cell signalling. Therefore, this study examined the ability of the nanoceria to be internalised by the human monocytic cell line, U937, and scavenge intracellular ROS. U937 cells activated in the presence of phorbol 12-myristate 13-acetate (PMA) were found to be more responsive to the nanoceria than U937 cells, which may not be surprising given the role of monocyte/macrophages in phagocytosing foreign material. The smaller particles were found to contain more crystal lattice defects with which to scavenge ROS, however a greater proportion of both the U937 and activated U937 cell populations responded to the larger particles. Hence all nanoceria particle sizes examined in this study were equally effective in scavenging intracellular ROS. © 2012 .

Lu, J, Martin, J, Lu, Y, Zhao, J, Yuan, J, Ostrowski, M, Paulsen, I, Piper, JA & Jin, D 2012, 'Resolving Low-Expression Cell Surface Antigens by Time-Gated Orthogonal Scanning Automated Microscopy', Analytical Chemistry, vol. 84, no. 22, pp. 9674-9678.
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We report a highly sensitive method for rapid identification and quantification of rare-event cells carrying low-abundance surface biomarkers. The method applies lanthanide bioprobes and time-gated detection to effectively eliminate both nontarget organisms and background noise and utilizes the europium containing nanoparticles to further amplify the signal strength by a factor of ∼20. Of interest is that these nanoparticles did not correspondingly enhance the intensity of nonspecific binding. Thus, the dramatically improved signal-to-background ratio enables the low-expression surface antigens on single cells to be quantified. Furthermore, we applied an orthogonal scanning automated microscopy (OSAM) technique to rapidly process a large population of target-only cells on microscopy slides, leading to quantitative statistical data with high certainty. Thus, the techniques together resolved nearly all false-negative events from the interfering crowd including many false-positive events. © 2012 American Chemical Society.

Lu, Y, Xi, P, Piper, JA, Huo, Y & Jin, D 2012, 'Time-Gated Orthogonal Scanning Automated Microscopy (OSAM) for High-speed Cell Detection and Analysis', Scientific Reports, vol. 2, no. 1.
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We report a new development of orthogonal scanning automated microscopy (OSAM) incorporating time-gated detection to locate rare-event organisms regardless of autofluorescent background. The necessity of using long-lifetime (hundreds of microseconds) luminescent biolabels for time-gated detection implies long integration (dwell) time, resulting in slow scan speed. However, here we achieve high scan speed using a new 2-step orthogonal scanning strategy to realise on-the-fly time-gated detection and precise location of 1-μm lanthanide-doped microspheres with signal-to-background ratio of 8.9. This enables analysis of a 15...mm × 15...mm slide area in only 3.3 minutes. We demonstrate that detection of only a few hundred photoelectrons within 100 μs is sufficient to distinguish a target event in a prototype system using ultraviolet LED excitation. Cytometric analysis of lanthanide labelled Giardia cysts achieved a signal-to-background ratio of two orders of magnitude. Results suggest that time-gated OSAM represents a new opportunity for high-throughput background-free biosensing applications.

Lucey, T, Wuhrer, R, Moran, K, Reid, M, Huggett, P & Cortie, M 2012, 'Interfacial reactions in white iron/steel composites', JOURNAL OF MATERIALS PROCESSING TECHNOLOGY, vol. 212, no. 11, pp. 2349-2357.
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The interfacial phenomena occurring when a white iron of low melting point is cast onto a steel substrate are considered. Such layered composites offer the prospect of combining the toughness of steel and the wear-resistance of a white cast iron into a s

Lund, ME, O‘Brien, BA, Hutchinson, AT, Robinson, MW, Simpson, A, Dalton, JP & Donnelly, S 2012, 'Secreted Molecules from the Helminth Parasite Fasciola Hepatica Prevent Pro-Inflammatory Immune Responses to Prevent Autoimmune Diabetes', Transplantation Journal, vol. 94, no. 10S, pp. 232-232.
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Lund, ME, OʼBrien, BA, Hutchinson, AT, Robinson, MW, Simpson, A, Dalton, JP & Donnelly, S 2012, 'Secreted Molecules from the Helminth Parasite Fasciola Hepatica Prevent Pro-Inflammatory Immune Responses to Prevent Autoimmune Diabetes', Transplantation Journal, vol. 94, no. 10S, pp. 1131-1131.
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Luo, X, Hong, X-S, Xiong, X-D, Zeng, L-Q & Lim, CED 2012, 'A Single Nucleotide Polymorphism in EXO1 Gene Is Associated With Cervical Cancer Susceptibility in Chinese Patients', International Journal of Gynecological Cancer, vol. 22, no. 2, pp. 220-225.
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Objective: The aim of this study was to investigate the association of Exonuclease1 (EXO1) genetic polymorphism and the development of cervical carcinoma. Methods: This study was conducted with 126 patients diagnosed with cervical cancer and 278 people with no cancer history. The polymerase chain reaction-based restriction fragment length polymorphism was used to evaluate the K589E and C908G gene polymorphisms. Unconditional logistic regression analysis was used to estimate the association between the genotypes and the risk for cervical cancer. Results: This is the first study on the role of EXO1 K589E (rs1047840) and EXO1 C908G (rs10802996) polymorphisms in cervical cancer in a Chinese population. Our results indicated that the EXO1 K589G polymorphism were significantly associated with the risk for cervical cancer. Compared with the G allele EXO1 K589E, the A allele increased the risk for cervical cancer (adjusted odds ratio, 1.67; 95% confidence interval, 1.13-2.45). By contrast, we have not found a significant association between the EXO1 C908G polymorphism and cervical cancer risk (P = 0.791). Conclusion: These findings indicate that the SNPs of EXO1 K589E may contribute to cervical cancer carcinogenesis in Chinese populations. A larger population study will need to be carried out to further validate the potential association of EXO1 genetic polymorphism and cervical carcinoma. Copyright © 2012 by IGCS and ESGO.

Luong, S, Shimmon, R, Hook, J & Fu, S 2012, '2-Nitro-6-monoacetylmorphine: potential marker for monitoring the presence of 6-monoacetylmorphine in urine adulterated with potassium nitrite', ANALYTICAL AND BIOANALYTICAL CHEMISTRY, vol. 403, no. 7, pp. 2057-2063.
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6-Monoacetylmorphine (6-MAM), being a unique metabolite of heroin, is routinely tested in urine samples to monitor heroin use. However, detection of 6-MAM-related opiates such as morphine is known to be affected by in vitro urine adulteration using oxidi

Luts, J, Broderick, T & Wand, MP 2012, 'Real-time semiparametric regression', Journal of Computational and Graphical Statistics, vol. 23, no. 3, pp. 589-615.
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We develop algorithms for performing semiparametric regression analysis inreal time, with data processed as it is collected and made immediatelyavailable via modern telecommunications technologies. Our definition ofsemiparametric regression is quite broad and includes, as special cases,generalized linear mixed models, generalized additive models, geostatisticalmodels, wavelet nonparametric regression models and their various combinations.Fast updating of regression fits is achieved by couching semiparametricregression into a Bayesian hierarchical model or, equivalently, graphical modelframework and employing online mean field variational ideas. An internet siteattached to this article, realtime-semiparametric-regression.net, illustratesthe methodology for continually arriving stock market, real estate and airlinedata. Flexible real-time analyses, based on increasingly ubiquitous streamingdata sources stand to benefit.

Lynch, EA, Langille, MGI, Darling, A, Wilbanks, EG, Haltiner, C, Shao, KSY, Starr, MO, Teiling, C, Harkins, TT, Edwards, RA, Eisen, JA & Facciotti, MT 2012, 'Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux', PLoS ONE, vol. 7, no. 7, pp. e41389-e41389.
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We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model grou

Ma, R, Shimmon, R, McDonagh, A, Maynard, P, Lennard, C & Roux, C 2012, 'Fingermark detection on non-porous and semi-porous surfaces using YVO4:Er,Yb luminescent upconverting particles', FORENSIC SCIENCE INTERNATIONAL, vol. 217, no. 1-3, pp. E23-E26.
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This article describes the use of an anti-Stokes luminescent material (upconverter), yttrium vanadate doped with ytterbium and erbium (YVO 4:Er,Yb), for the development of latent fingermarks on a range of non-porous surfaces. Anti-Stokes luminescent materials emit light at shorter wavelengths than the excitation wavelength. This property is unusual in both natural and artificial materials commonly found as exhibits in forensic science casework. As a result, fingermark detection techniques based on anti-Stokes luminescence are potentially extremely sensitive and selective.Latent fingermarks on non-luminescent and inherently luminescent substrates, including Australian polymer banknotes (a well-known 'difficult' surface), were developed with YVO 4:Er,Yb by dry powder and wet powder techniques. The effectiveness of YVO 4:Er,Yb for fingermark detection was compared with that of cyanoacrylate fuming and of sodium yttrium tetrafluoride doped with ytterbium and erbium (NaYF 4:Er,Yb). The results illustrate some benefit of luminescent up-converting phosphors over traditional luminescence techniques for the detection of latent fingermarks. © 2011 Elsevier Ireland Ltd.

Ma, S, Yang, L & Carroll, RJ 2012, 'A simultaneous confidence band for sparse longitudinal regression', Statistica Sinica, vol. 22, no. 1, pp. 95-122.
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Functional data analysis has received considerable recent attention and a number of successful applications have been reported. In this paper, asymptotically simultaneous confidence bands are obtained for the mean function of the functional regression model, using piecewise constant spline estimation. Simulation experiments corroborate the asymptotic theory. The confidence band procedure is illustrated by analyzing CD4 cell counts of HIV infected patients.

Ma, Z, Ji, H, Tan, D, Dong, G, Teng, Y, Zhou, J & Qiu, J 2012, 'Porous YAG:Nd³⁺ Fibers with Excitation and Emission in the Human “NIR Optical Window” as Luminescent Drug Carriers', Chemistry – A European Journal, vol. 18, no. 9, pp. 2609-2616.
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AbstractThe design and preparation of luminescent drug carriers has been a prosperous area of research for many years. However, the excitation and/or emission wavelength of such luminescent drug carriers haven′t been optimized in the so‐called human “near infrared (NIR) optical window”, thus restricting their practical applications. Herein, we report the synthesis of electrospun porous YAG:Nd3+ (neodymium‐doped yttrium aluminum garnet) fibers with both excitation and emission in the “NIR optical window” as luminescent drug carriers. The YAG:Nd3+ porous fibers were characterized by SEM, TEM, XRD, scanning transmission electron microscopy–energy‐dispersive X‐ray spectroscopy (STEM‐EDX), and photoluminescence (PL). Ibuprofen (IBU) was used as a model drug to evaluate the drug‐loading capacities and release profiles of the samples. BMSCs (bone mesenchymal stem cells) were used as model human cells to investigate cytotoxicity. Our results indicated that the YAG:Nd3+ fibers possessed a fine, irregularly porous fibrous morphology with an average diameter of 378 nm. The florescence of the sample (1064 nm) could be excited over a wide wavelength range in the NIR region. During the release process of IBU in simulated body fluid (SBF), along with the dissolving of the drug, the solvent entered into the pores, and the emission intensity of the YAG:Nd3+ fibers at 1064 nm decreased gradually, owing to a quenching effect of the hydroxy groups, thus provided an approach to track and monitor drug release. In addition, cytotoxicity investigations revealed that these YAG:Nd3+ fibers were biocompatible with human cells. Consequently, the porous YAG:Nd3+ fibers are a promising material for applications as advanced drug carriers.

Macreadie, PI, Allen, K, Kelaher, BP, Ralph, PJ & Skilbeck, CG 2012, 'Paleoreconstruction of estuarine sediments reveal human-induced weakening of coastal carbon sinks', GLOBAL CHANGE BIOLOGY, vol. 18, no. 3, pp. 891-901.
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Human activities in coastal areas frequently cause loss of benthic macrophytes (e.g. seagrasses) and concomitant increases in microalgal production through eutrophication. Whether such changes translate into shifts in the composition of sediment detritus is largely unknown, yet such changes could impact the role these ecosystems play in sequestrating CO2. We reconstructed the sedimentary records of cores taken from two sites within Botany Bay, Sydney the site of European settlement of Australia to look for human-induced changes in dominant sources of detritus in this estuary. Cores covered a period from the present day back to the middle Holocene (6000years) according to 210Pb profiles and radiocarbon (14C) dating. Depositional histories at both sites could not be characterized by a linear sedimentation rate; sedimentation rates in the last 3050years were considerably higher than during the rest of the Holocene. C:N ratios declined and began to exhibit a microalgal source signature from around the time of European settlement, which could be explained by increased nutrient flows into the Bay caused by anthropogenic activity. Analysis of stable isotopic ratios of 12C/13C showed that the relative contribution of seagrass and C3 terrestrial plants (mangroves, saltmarsh) to detritus declined around the time of rapid industrial expansion (1950s), coinciding with an increase in the contribution of microalgal sources. We conclude that the relative contribution of microalgae to detritus has increased within Botany Bay, and that this shift is the sign of increased industrialization and concomitant eutrophication.

Macreadie, PI, Fowler, AM & Booth, DJ 2012, 'Rigs-to-reefs policy: can science trump public sentiment?', FRONTIERS IN ECOLOGY AND THE ENVIRONMENT, vol. 10, no. 4, pp. 179-180.
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Mahmoodian, S, Sipe, JE, Poulton, CG, Dossou, KB, Botten, LC, McPhedran, RC & de Sterke, CM 2012, 'Double-heterostructure cavities: From theory to design', PHYSICAL REVIEW A, vol. 86, no. 4.
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We derive a frequency-domain-based approach for radiation from double-heterostructure cavity (DHC) modes. We use this to compute the quality factors and radiation patterns of DHC modes. The semianalytic nature of our method enables us to provide a general relationship between the radiation pattern of the cavity and its geometry. We use this to provide general designs for ultrahigh-quality-factor DHCs with radiation patterns that are engineered to emit vertically. © 2012 American Physical Society.

Mahmoodian, S, Sipe, JE, Poulton, CG, Dossou, KB, Botten, LC, McPhedran, RC & de Sterke, CM 2012, 'First-principles method for high-Q photonic crystal cavity mode calculations', OPTICS EXPRESS, vol. 20, no. 20, pp. 22763-22769.
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We present a first-principles method to compute radiation properties of ultra-high quality factor photonic crystal cavities. Our Frequency-domain Approach for Radiation (FAR) can compute the far-field radiation pattern and quality factor of cavity modes ̃ 100 times more rapidly than conventional finite-difference time domain calculations. We explain how the radiation pattern depends on the perturbation used to create the cavity and on the Bloch modes of the photonic crystal. © 2012 Optical Society of America.

Manetsch, M, Che, W, Seidel, P, Chen, Y & Ammit, AJ 2012, 'MKP-1: A negative feedback effector that represses MAPK-mediated pro-inflammatory signaling pathways and cytokine secretion in human airway smooth muscle cells', Cellular Signalling, vol. 24, no. 4, pp. 907-913.
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Manetsch, M, Ramsay, EE, King, EM, Seidel, P, Che, W, Ge, Q, Hibbs, DE, Newton, R & Ammit, AJ 2012, 'Corticosteroids and β₂‐agonists upregulate mitogen‐activated protein kinase phosphatase 1: in vitro mechanisms', British Journal of Pharmacology, vol. 166, no. 7, pp. 2049-2059.
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BACKGROUND AND PURPOSEAirway remodelling is a consequence of long‐term inflammation and MAPKs are key signalling molecules that drive pro‐inflammatory pathways. The endogenous MAPK deactivator – MAPK phosphatase 1 (MKP‐1) – is a critical negative regulator of the myriad pro‐inflammatory pathways activated by MAPKs in the airway.EXPERIMENTAL APPROACHHerein we investigated the molecular mechanisms responsible for the upregulation of MKP‐1 in airway smooth muscle (ASM) by the corticosteroid dexamethasone and the β2‐agonist formoterol, added alone and in combination.KEY RESULTSMKP‐1 is a corticosteroid‐inducible gene whose expression is enhanced by long‐acting β2‐agonists in an additive manner. Formoterol induced MKP‐1 expression via the β2‐adrenoceptor and we provide the first direct evidence (utilizing overexpression of PKIα, a highly selective PKA inhibitor) to show that PKA mediates β2‐agonist‐induced MKP‐1 upregulation. Dexamethasone activated MKP‐1 transcription in ASM cells via a cis‐acting corticosteroid‐responsive region located between −1380 and −1266 bp of the MKP‐1 promoter. While the 3′‐untranslated region of MKP‐1 contains adenylate + uridylate elements responsible for regulation at the post‐transcriptional level, actinomycin D chase experiments revealed that there was no increase in MKP‐1 mRNA stability in the presence of dexamethasone, formoterol, alone or in combination. Rather, there was an additive effect of the asthma therapeutics on MKP‐1 transcription.CONCLUSIONS AND IMPLICATIONSTaken together, these studies allow us a greater understanding of the molecular basis of MKP‐1 regulation by corticosteroi...

Manetsch, M, Seidel, P, Heintz, U, Che, W, Hughes, JM, Ge, Q, Sukkar, MB & Ammit, AJ 2012, 'TLR2 ligand engagement upregulates airway smooth muscle TNFα-induced cytokine production', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 302, no. 9, pp. L838-L845.
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Airway inflammation and respiratory infections are important factors contributing to disease exacerbation in chronic airway diseases such as asthma and chronic obstructive pulmonary disease. Airway smooth muscle (ASM) cells express Toll-like receptors (TLRs) and may be involved in the amplification of airway inflammatory responses during infectious exacerbations. We determined whether infectious stimuli (mimicked using Pam3CSK4, a synthetic bacterial lipopeptide that binds to TLR2/TLR1) further enhance ASM cell inflammatory responses to TNFα in vitro and the signaling pathways involved. Human ASM cells were pretreated for 1 h with Pam3CSK4 (1 μg/ml) in the absence or presence of TNFα (10 ng/ml), and IL-6 and IL-8 release was measured after 24 h. As expected, stimulation with Pam3CSK4 or TNFα alone induced significant IL-6 and IL-8 release. Furthermore, Pam3CSK4 significantly increased TNFα-induced IL-6 and IL-8 mRNA expression and protein release and neutrophil chemotactic activity. The potentiating effect of Pam3CSK4 on TNFα-induced inflammatory responses was not due to enhanced TLR2 expression nor did it involve augmentation of NF-κB or MAPK signaling pathways. Rather, Pam3CSK4 induced cAMP response element (CRE) binding protein phosphorylation and induced CRE-mediated transcriptional regulation, suggesting that Pam3CSK4 and TNFα are acting in concert to enhance ASM cytokine secretion via parallel transcriptional pathways. Our findings suggest that ASM cells may be involved in the amplification of airway inflammatory responses during infectious exacerbations in chronic airway disease.

Manos-Turvey, A, Cergol, KM, Salam, NK, Bulloch, EMM, Chi, G, Pang, A, Britton, WJ, West, NP, Baker, EN, Lott, JS & Payne, RJ 2012, 'Synthesis and evaluation of M. tuberculosis salicylate synthase (MbtI) inhibitors designed to probe plasticity in the active site', Organic & Biomolecular Chemistry, vol. 10, no. 46, pp. 9223-9223.
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Mansell, PJ, Suggett, DJ & Smith, DJ 2012, 'Management of marine resources; combining industry and research', Journal of the Marine Biological Association of the United Kingdom, vol. 92, no. 4, pp. 643-646.
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Martinac, B & Cranfield, CG 2012, 'Shining a light on the structural dynamics of ion channels using Förster resonance energy transfer (FRET).', IPSI BgD Transactions on Advanced Research, vol. 8, pp. 19-24.

Martinez, E, Marquez, C, Ingold, A, Merlino, J, Djordjevic, SP, Stokes, HW & Chowdhury, PR 2012, 'Diverse Mobilized Class 1 Integrons Are Common in the Chromosomes of Pathogenic Pseudomonas aeruginosa Clinical Isolates', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 56, no. 4, pp. 2169-2172.
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Eleven clinical class 1 integron-containing Pseudomonas aeruginosa isolates from Australia and Uruguay were investigated for the genomic locations of these elements. Several novel class 1 integrons/transposons were found in at least four distinct locations in the chromosome, including genomic islands. These elements seem to be undergoing successful dispersal by lateral gene transfer since integrons were identified across several lineages and more than one clonal line.

Massonnet, G, Buzzini, P, Monard, F, Jochem, G, Fido, L, Bell, S, Stauber, M, Coyle, T, Roux, C, Hemmings, J, Leijenhorst, H, Van Zanten, Z, Wiggins, K, Smith, C, Chabli, S, Sauneuf, T, Rosengarten, A, Meile, C, Ketterer, S & Blumer, A 2012, 'Raman spectroscopy and microspectrophotometry of reactive dyes on cotton fibres: Analysis and detection limits', FORENSIC SCIENCE INTERNATIONAL, vol. 222, no. 1-3, pp. 200-207.
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A collaborative study on Raman spectroscopy and microspectrophotometry (MSP) was carried out by members of the ENFSI (European Network of Forensic Science Institutes) European Fibres Group (EFG) on different dyed cotton fabrics. The detection limits of the two methods were tested on two cotton sets with a dye concentration ranging from 0.5 to 0.005% (w/w). This survey shows that it is possible to detect the presence of dye in fibres with concentrations below that detectable by the traditional methods of light microscopy and microspectrophotometry (MSP). The MSP detection limit for the dyes used in this study was found to be a concentration of 0.5% (w/w). At this concentration, the fibres appear colourless with light microscopy. Raman spectroscopy clearly shows a higher potential to detect concentrations of dyes as low as 0.05% for the yellow dye RY145 and 0.005% for the blue dye RB221. This detection limit was found to depend both on the chemical composition of the dye itself and on the analytical conditions, particularly the laser wavelength. Furthermore, analysis of binary mixtures of dyes showed that while the minor dye was detected at 1.5% (w/w) (30% of the total dye concentration) using microspectrophotometry, it was detected at a level as low as 0.05% (w/w) (10% of the total dye concentration) using Raman spectroscopy.

McCauley, J 2012, 'Hendrickson Reagent (Triphenylphosphonium Anhydride Trifluoromethane Sulfonate)', Synlett, vol. 23, no. 20, pp. 2999-3000.
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McDougald, D, Rice, SA, Barraud, N, Steinberg, PD & Kjelleberg, S 2012, 'Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal', Nature Reviews Microbiology, vol. 10, no. 1, pp. 39-50.
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In most environments, bacteria reside primarily in biofilms, which are social consortia of cells that are embedded in an extracellular matrix and undergo developmental programmes resulting in a predictable biofilm 'life cycle'. Recent research on many different bacterial species has now shown that the final stage in this life cycle includes the production and release of differentiated dispersal cells. The formation of these cells and their eventual dispersal is initiated through diverse and remarkably sophisticated mechanisms, suggesting that there are strong evolutionary pressures for dispersal from an otherwise largely sessile biofilm. The evolutionary aspect of biofilm dispersal is now being explored through the integration of molecular microbiology with eukaryotic ecological and evolutionary theory, which provides a broad conceptual framework for the diversity of specific mechanisms underlying biofilm dispersal. Here, we review recent progress in this emerging field and suggest that the merging of detailed molecular mechanisms with ecological theory will significantly advance our understanding of biofilm biology and ecology. © 2011 Macmillan Publishers Limited. All rights reserved.

McGowan, EM, Tran, N, Alling, N, Yagoub, D, Sedger, LM & Martiniello-Wilks, R 2012, 'p14ARF Post-Transcriptional Regulation of Nuclear Cyclin D1 in MCF-7 Breast Cancer Cells: Discrimination between a Good and Bad Prognosis?', PLOS ONE, vol. 7, no. 7, pp. 1-16.
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As part of a cell's inherent protection against carcinogenesis, p14ARF is upregulated in response to hyperproliferative signalling to induce cell cycle arrest. This property makes p14ARF a leading candidate for cancer therapy. This study explores the consequences of reactivating p14ARF in breast cancer and the potential of targeting p14ARF in breast cancer treatment. Our results show that activation of the p14ARF-p53-p21-Rb pathway in the estrogen sensitive MCF-7 breast cancer cells induces many hallmarks of senescence including a large flat cell morphology, multinucleation, senescence-associated-β-gal staining, and rapid G1 and G2/M phase cell cycle arrest. P14ARF also induces the expression of the proto-oncogene cyclin D1, which is most often associated with a transition from G1-S phase and is highly expressed in breast cancers with poor clinical prognosis. In this study, siRNA knockdown of cyclin D1, p21 and p53 show p21 plays a pivotal role in the maintenance of high cyclin D1 expression, cell cycle and growth arrest post-p14ARF induction. High p53 and p14ARF expression and low p21/cyclin D1 did not cause cell-cycle arrest. Knockdown of cyclin D1 stops proliferation but does not reverse senescence-associated cell growth. Furthermore, cyclin D1 accumulation in the nucleus post-p14ARF activation correlated with a rapid loss of nucleolar Ki-67 protein and inhibition of DNA synthesis. Latent effects of the p14ARF-induced cellular processes resulting from high nuclear cyclin D1 accumulation included a redistribution of Ki-67 into the nucleoli, aberrant nuclear growth (multinucleation), and cell proliferation. Lastly, downregulation of cyclin D1 through inhibition of ER abrogated latent recurrence. The mediation of these latent effects by continuous expression of p14ARF further suggests a novel mechanism whereby dysregulation of cyclin D1 could have a double-edged effect. Our results suggest that p14ARF induced-senescence is related to late-onset breast c...

McGrath, KC, Li, XH, Gaus, K, Williams, P, Celermajer, DS, Handelsman, DJ & Heather, AK 2012, 'Androgens rapidly activate nuclear factor-kappa B via intracellular Ca2+ signalling in human vascular endothelial cells', Journal of Steroids & Hormonal Science, vol. S2, pp. 1-6.
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There exists a striking gender difference in the incidence of atherosclerosis. Androgen exposure may predispose men to earlier onset atherosclerosis. We previously demonstrated that the potent androgen, dihydrotestosterone, enhanced the binding of monocytes to endothelial cells, via androgen receptor/nuclear factor kappa B-dependent expression of the cell adhesion molecules, vascular cell adhesion molecule-1 and intercellular cell adhesion molecule-1. We now show that testosterone and dihydrotestosterone can also induce a novel, non-genomic pathway that leads to the rapid activation of nuclear factor-kappa B via intracellular Ca2+ signalling, initiated at the plasma membrane. Human umbilical vein endothelial cells exposed to 6-60 nM testosterone or dihydrotestosterone showed a rapid increase in intracellular calcium levels. The testosterone or dihydrotestosterone effect on increased intracellular calcium could not be abrogated by pre-incubation with androgen receptor antagonist, hydroxyflutamide, or by U73122, an inhibitor of intracellular calcium release from endoplasmic reticulum stores.

McGrath, KCY & Heather, AK 2012, 'Endoplasmic Reticulum Stress in Inflammatory Disease', Endocrinology, vol. 153, no. 7, pp. 2949-2952.
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In this issue of Endocrinology, Miani and colleagues (1) provide evidence that increased circulating levels of free fatty acids (FFA) associated with obesity induce a mild endoplasmic reticulum (ER) stress in pancreatic ß-cells that predisposes them to an augmented inflammatory response when exposed to cytokines such as IL-1ß or TNF-a. They found that rat insulinoma cells (INS-1E), or primary rat ß-cells, when exposed to the ER stressor sarcoplasmic/endoplasmic reticulum Ca2+-ATPase (SERCA) blocker (cyctopiazonic acid) or free fatty acids (FFA), followed by exposure to low-dose IL-1ß or TNF-a, had enhanced expression of the inflammatory markers CCL2, CXCL1, iNOS, and Fas. Interrogation of the molecular pathway showed augmented nuclear factor-?B (NF-?B) activation, after degradation of forkhead box O1 (FoxO1) protein. Using small interfering RNA that targeted specific ER stress pathways, the investigators demonstrated involvement of the inositol-requiring enzyme 1 (IRE1)/X-box binding protein-1s (XBP1s) pathway. The importance of these findings is that obesity-associated FFA may easily induce mild ß-cell ER stress that, in turn, triggers a heightened inflammatory response that could drive apoptosis. ß-cell apoptosis is the primary pathogenic mechanism that underlies type 1 diabetes, an area of growing concern because the worldwide incidence of type 1 diabetes is increasing at a rapid rate.

McKemmish, LK, Kedziora, DJ, White, GR, Hush, NS & Reimers, JR 2012, 'Frequency-based Quantum Computers from a Chemist's Perspective', AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 65, no. 5, pp. 512-519.
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Quantum computer elements are often designed and tested using molecular or nanoscopic components that form registers of qubits in which memory is stored and information processed. Often such registers are probed and manipulated using frequency-based techniques such as nuclear-magnetic resonance spectroscopy. A major challenge is to design molecules to act as these registers. We provide a basis for rational molecular design through consideration of the generic spectroscopic properties required for quantum computing, bypassing the need for intricate knowledge of the way these molecules are used spectroscopically. Designs in which two-qubit gate times scale similarly to those for one-qubit gates are presented. The specified spectroscopic requirements are largely independent of the type of spectroscopy used (e.g. magnetic resonance or vibrational) and are often independent of technical details of the application (e.g. broadband or high-resolution spectroscopy). This should allow the design of much larger quantum registers than have currently been demonstrated. © 2012 CSIRO.

McMinn, A, Ashworth, C, Bhagooli, R, Martin, A, Salleh, S, Ralph, P & Ryan, K 2012, 'Antarctic coastal microalgal primary production and photosynthesis', MARINE BIOLOGY, vol. 159, no. 12, pp. 2827-2837.
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Primary production in coastal Antarctica is primarily contributed from three sources: sea ice algae, phytoplankton, and microphytobenthos. Compared to other eastern Antarctic sites, the sea ice microalgal biomass at Casey Station, in spring 2005 was rela

McPhedran, RC, Botten, LC, Williamson, DJ & Nicorovici, N-AP 2012, 'The Riemann hypothesis and the zero distribution of angular lattice sums', Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 468, no. 2137, pp. 303-304.
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MeikleJohn, KA, Dowton, M & Wallman, JF 2012, 'Notes on the Distribution of 31 Species of Sarcophagidae (Diptera) in Australia, Including new Records in Australia for Eight Species', Transactions of the Royal Society of South Australia, vol. 136, no. 1, pp. 56-64.
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Meiklejohn, KA, Wallman, JF, Cameron, SL & Dowton, M 2012, 'Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera)', Invertebrate Systematics, vol. 26, no. 6, pp. 515-515.
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Carrion-breeding Sarcophagidae (Diptera) can be used to estimate the post-mortem interval in forensic cases. Difficulties with accurate morphological identifications at any life stage and a lack of documented thermobiological profiles have limited their current usefulness. The molecular-based approach of DNA barcoding, which utilises a 648-bp fragment of the mitochondrial cytochrome oxidase subunitI gene, was evaluated in a pilot study for discrimination between 16 Australian sarcophagids. The current study comprehensively evaluated barcoding for a larger taxon set of 588 Australian sarcophagids. In total, 39 of the 84 known Australian species were represented by 580 specimens, which includes 92% of potentially forensically important species. A further eight specimens could not be identified, but were included nonetheless as six unidentifiable taxa. A neighbour-joining tree was generated and nucleotide sequence divergences were calculated. All species except Sarcophaga (Fergusonimyia) bancroftorum, known for high morphological variability, were resolved as monophyletic (99.2% of cases), with bootstrap support of 100. Excluding S. bancroftorum, the mean intraspecific and interspecific variation ranged from 1.12% and 2.81–11.23%, respectively, allowing for species discrimination. DNA barcoding was therefore validated as a suitable method for molecular identification of Australian Sarcophagidae, which will aid in the implementation of this fauna in forensic entomology.

Melzer, M, Lin, G, Makarov, D & Schmidt, OG 2012, 'Stretchable Spin Valves on Elastomer Membranes by Predetermined Periodic Fracture and Random Wrinkling', Advanced Materials, vol. 24, no. 48, pp. 6468-6472.
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The first highly stretchable and sensitive spin valve sensor on elastomeric membranes are demonstrated. The sensor elements exhibit stable GMR behavior up to tensile strains of 29% in in situ stretching experiments and show no fatigue over 500 loading cycles. This remarkable stretchability is achieved by a predetermined periodic fracture mechanism that creates a meander-like pattern upon stretching. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mercer, AE, Shafer, CM, Doswell, CA, Leslie, LM & Richman, MB 2012, 'Synoptic Composites of Tornadic and Nontornadic Outbreaks', Monthly Weather Review, vol. 140, no. 8, pp. 2590-2608.
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Abstract Tornadic and nontornadic outbreaks occur within the United States and elsewhere around the world each year with devastating effect. However, few studies have considered the physical differences between these two outbreak types. To address this issue, synoptic-scale pattern composites of tornadic and nontornadic outbreaks are formulated over North America using a rotated principal component analysis (RPCA). A cluster analysis of the RPC loadings group similar outbreak events, and the resulting map types represent an idealized composite of the constituent cases in each cluster. These composites are used to initialize a Weather Research and Forecasting Model (WRF) simulation of each hypothetical composite outbreak type in an effort to determine the WRF’s capability to distinguish the outbreak type each composite represents. Synoptic-scale pattern analyses of the composites reveal strikingly different characteristics within each outbreak type, particularly in the wind fields. The tornado outbreak composites reveal a strong low- and midlevel cyclone over the eastern Rockies, which is likely responsible for the observed surface low pressure system in the plains. Composite soundings from the hypothetical outbreak centroids reveal significantly greater bulk shear and storm-relative environmental helicity values in the tornado outbreak environment, whereas instability fields are similar between the two outbreak types. The WRF simulations of the map types confirm results observed in the composite soundings.

Mertens-Walker, I, Baxter, RC & Marsh, DJ 2012, 'Gonadotropin signalling in epithelial ovarian cancer', Cancer Letters, vol. 324, no. 2, pp. 152-159.
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Midthune, DN, Carroll, RJ, Subar, AF, Freedman, LS, Thompson, FE & Kipnis, V 2012, 'Combining self‐report dietary assessment instruments to reduce the effects of measurement error', The FASEB Journal, vol. 26, no. S1.
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With the advent of a self‐administered automated 24 hour dietary recall instrument (24HR), developed at the National Cancer Institute (NCI), it is now possible to envision its use in cohort studies investigating the relationships between diet and disease. Understanding that all dietary assessment instruments are subject to measurement error, we compare 3 possible strategies for estimating intake: 1) administering 1–12 24HRs per subject; 2) administering a single food frequency questionnaire (FFQ); and 3) administering a combination of 24HRs and a single FFQ. We used data from the National Cancer Institute's Eating at America's Table Study, which collected 4 24HR, one per season, and an FFQ in a nationally representative sample of 965 U.S. adults. We compared the precision, power and required sample size for the different strategies under the assumption that the 24HR is unbiased for true usual intake. We found that the strategy of 4–6 administrations of the 24HR is sufficient for most nutrients and food groups, and that the combined use of multiple 24HR and FFQ data often provides estimates superior to either alone. In most cases, adding an FFQ to one or more 24HRs improved precision more than adding an additional 24HR. If self‐administered automated 24HRs are to be used in cohort studies, one should consider administering 4–6 24HRs and an FFQ.

Moezzi, A, McDonagh, AM & Cortie, MB 2012, 'Zinc oxide particles: Synthesis, properties and applications', CHEMICAL ENGINEERING JOURNAL, vol. 185, pp. 1-22.
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Zinc oxide powder has traditionally been used as a white pigment and as an additive to rubber. While it has largely been displaced as a pigment in paints, its usage in rubber remains very important. However, the myriad of other practical uses of ZnO are sometimes overlooked, and reviews in the recent scientific literature tend to emphasize high technology applications that do not yet have any commercial reality. Similarly, while some of the low-volume processes used to manufacture ZnO nanostructures have been well covered in the literature, there has been far less reported on the tonnage chemical engineering processes by which most ZnO is actually made. The multiplicity of processes by which ZnO can be produced is a potential source of confusion, however, the process used has a large influence on the properties of the oxide, and hence on its suitability for various applications. Here we provide a contemporary review and analysis of the manufacture of ZnO, and its properties, applications, and future prospects. © 2012 Elsevier B.V.

Moheimani, F, Kim, CHJ, Rahmanto, AS, van Reyk, DM & Davies, MJ 2012, 'Inhibition of lysosomal function in macrophages incubated with elevated glucose concentrations: A potential contributory factor in diabetes-associated atherosclerosis', ATHEROSCLEROSIS, vol. 223, no. 1, pp. 144-151.
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Objective People with diabetes have an elevated risk of atherosclerosis. The accumulation of lipid within macrophage cells in the artery wall is believed to arise via the uptake and subsequent processing of modified low-density lipoproteins (LDL) via the endo-lysosomal system. In this study the effects of prolonged exposure to elevated glucose upon macrophage lysosomal function was examined to determine whether this contributes to modulated protein catabolism. Methods Human monocytes were isolated from white-cell concentrates and differentiated, in vitro, into monocyte-derived macrophages over 11 days in medium containing 530 mmol/L glucose. Murine macrophage-like J774A.1 cells were incubated similarly. Lysosomal cathepsin (B, D, L and S) and acid lipase activities were assessed using fluorogenic substrates; cathepsin protein levels were examined by Western blotting. Lysosomal numbers were examined using the lysomotropic fluorescent dye LysoTracker DND-99, measurement of aryl sulfatase activity, and quantification of lysosome-associated membrane glycoprotein-1 (LAMP-1) by Western blotting. Results Exposure to elevated glucose, but not mannitol, resulted in a concentration-dependent decrease in the activity, and to a lesser extent protein levels, of four lysosomal cathepsins. Acid lipase activity was also significantly reduced. Arysulfatase activity, LAMP-1 levels and lysosomal numbers were also decreased at the highest glucose concentrations, though to a lesser extent.

Mokhadinyana, M, Desset, SL, Williams, DBG & Cole‐Hamilton, DJ 2012, 'Cooperative Ligand Effects in Phase‐Switching Homogeneous Catalysts', Angewandte Chemie International Edition, vol. 51, no. 7, pp. 1648-1652.
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It takes two: Xantphos ligands that contain amidate groups are selective for the linear versus the branched-chain products in the rhodium-catalyzed hydroformylation of 1-octene. However, the catalyst only undergoes CO 2-mediated phase switching in the presence of amidine-substituted triphenylphosphine (see scheme). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molnar, A, Lewis, J, Doble, P, Hansen, G, Prolov, T & Fu, S 2012, 'A rapid and sensitive method for the identification of delta-9-tetrahydrocannabinol in oral fluid by liquid chromatography-tandem mass spectrometry', FORENSIC SCIENCE INTERNATIONAL, vol. 215, no. 1-3, pp. 92-96.
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A fast and sensitive method was developed for detecting delta-9-tetrahydrocannabinol (THC) in oral fluid by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The method is suitable for samples of small volume and low concentration. For method development and validation, neat oral fluid (200μL) spiked with THC and d 3-THC (internal standard) was extracted via liquid-liquid extraction (LLE). The LLE method had an extraction efficiency of 75% with no significant matrix effects observed in either diluted or neat oral fluid samples. LC was performed on a Zorbax Eclipse XDB-C18 Rapid Resolution HT column (2.1mm×50mm, 1.8μm particle size) with positive electrospray ionisation and selected reaction monitoring. The total run time was an efficient 3.5min in isocratic elution mode. The limit of quantification was 1ng/mL and the analysis was linear over the range of 1-500ng/mL with a correlation coefficient of 0.9998. The imprecision (RSD) of the method was 13% and inaccuracy (MRE) was 4%. The method was subsequently applied to two neat oral fluid samples taken from a chronic cannabis smoker. It was also applied to buffer diluted residual oral fluid samples (n=48) collected using the Cozart RapiScan ® system through the Roadside Drug Testing Program (RDTP) in NSW, Australia. A stability study was performed that revealed freezing or refrigerating resulted in comparable decreases in THC recovery from neat oral fluid at the end of two weeks of storage. Storage at room temperature even for one day invoked significant losses and is not recommended. © 2011.

Mondal, AK, Wang, B, Su, D, Wang, Y, Zhang, X & Wang, G 2012, 'Preparation and Enhanced Electrochemical Performance of MnO₂ Nanosheets for Supercapacitors', Journal of the Chinese Chemical Society, vol. 59, no. 10, pp. 1275-1279.
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AbstractMnO2 nanosheets have been synthesized by using a redox reaction of manganese nitrate tetrahydrate and potassium permanganate without any surfactants. The morphology and microstructure of the as‐prepared material were characterized by field emission scanning electron microscopy, transmission electron microscopy and X‐ray diffraction (XRD). Electrochemical performances as electrode materials for supercapacitor were evaluated using cyclic voltammetry and galvanostatic charge‐discharge in 1 M Na2SO4 aqueous electrolyte. It was found that MnO2 nanosheets showed an excellent capacitive behaviour with good cycling stability. The specific capacitance of the MnO2 nanosheet electrode can reach up to 332.8 Fg−1 at a current density of 500 mA/g and a stable cycling performance.

Montgomery, L, Spindler, X, Maynard, P, Lennard, C & Roux, C 2012, 'Pretreatment strategies for the improved cyanoacrylate development of dry latent fingerprints on nonporous surfaces', Journal of Forensic Identification, vol. 62, no. 5, pp. 517-542.
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Cyanoacrylate fuming is a popular technique commonly used by evidence examiners for the development of latent fingermarks on nonporous surfaces. The process involves the preferential formation of hard, white polycyanoacrylate along the ridgelines of the fingerprint as opposed to the substrate background. This preferential deposition results in contrast between the fingerprint and substrate. This contrast may be further enhanced through the use of staining techniques such as rhodamine 6G. Because the cyanoacrylate mechanism is believed to be initiated by fingerprint constituents and catalyzed by moisture, it follows that fingerprints subjected to harsh conditions (e.g., heat, low humidity, or UV light) often produce poorly developed results. This study aimed to further investigate and validate the use of 10% w/v methylamine as a pretreatment strategy to overcome the limitations associated with the cyanoacrylate development of dry fingerprints and to compare the results with those obtained using previously proposed pretreatment solutions. The effectiveness of this treatment was demonstrated on samples similar to those encountered in casework, and scanning electron microscopy (SEM) of the treated fingerprints confirmed the rejuvenation of the dry latent deposits through a qualitative assessment of the polymer morphology.

Moradi, A, Zhand, S, Ghaemi, A, Javid, N & Tabarraei, A 2012, 'Mutations in the S gene region of hepatitis B virus genotype D in Golestan Province-Iran', Virus Genes, vol. 44, no. 3, pp. 382-387.
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Morelato, M, Beavis, A, Ogle, A, Doble, P, Kirkbride, P & Roux, C 2012, 'Screening of gunshot residues using desorption electrospray ionisation-mass spectrometry (DESI-MS)', FORENSIC SCIENCE INTERNATIONAL, vol. 217, no. 1-3, pp. 101-106.
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Several studies have indicated that there are potential environmental sources of particles resembling inorganic primer found in gunshot residues (GSR); as a consequence examiners are reluctant to unambiguously assign the origin of inorganic particles. If organic gunshot residues (OGSR) were found in combination with inorganic particles, the possibility of environmental sources could be potentially eliminated, thereby significantly enhancing the strength of the evidence.Methods have been previously described whereby GSR specimens can be analysed for the presence of OGSR or inorganic GRS (IGSR). However, no methods have been reported that allow the analysis of both OGSR and IGSR on the same specimen.Described in this article is a direct method using desorption electrospray ionisation-mass spectrometry (DESI-MS) for the detection of methyl centralite (MC), ethyl centralite (EC) and diphenylamine (DPA) on adhesive tape GSR stubs typically used for scanning electron microscopy-energy-dispersive X-ray (SEM-EDX) analysis. The optimisation of numerous parameters was conducted using an experimental design. The results indicate that direct analysis of these organic components of GSR is possible although some limitations were also identified.This initial investigation has also indicated that subjecting stubs to DESI analysis does not interfere with subsequent SEM-EDX analysis of primer residues; therefore the technique described herein allows a comprehensive examination of GSR that would be highly probative in the event that both OGSR and IGSR are detected in the same specimen. © 2011 Elsevier Ireland Ltd.

Mueller, T, Aharonovich, I, Wang, Z, Yuan, X, Castelletto, S, Prawer, S & Atatuere, M 2012, 'Phonon-induced dephasing of chromium color centers in diamond', PHYSICAL REVIEW B, vol. 86, no. 19, p. 195210.
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We report on the coherence properties of single photons from chromium-based color centers in diamond. We use field-correlation and spectral line-shape measurements to reveal the interplay between slow spectral wandering and fast dephasing mechanisms as a function of temperature. The zero-phonon transition frequency and its linewidth follow a power-law dependence on temperature, which is consistent with direct electronphonon coupling and phonon-modulated Coulomb coupling to nearby impurities, which are the predominant fast dephasing mechanisms for these centers. Further, the observed reduction in the quantum yield for photon emission as a function of temperature suggests the opening of additional nonradiative channels through thermal activation to higher-energy states and indicates a near-unity quantum efficiency at 4 K.

Mulholland, AR, Thordarson, P, Mensforth, EJ & Langford, SJ 2012, 'Porphyrin dyads linked by a rotatable 3,3′-biphenyl scaffold: a new binding motif for small ditopic molecules', Organic & Biomolecular Chemistry, vol. 10, no. 30, pp. 6045-6045.
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Munasinghe, VS, Stark, D & Ellis, JT 2012, 'New advances in the in-vitro culture of Dientamoeba fragilis', PARASITOLOGY, vol. 139, no. 7, pp. 864-869.
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Dientamoeba fragilis is an intestinal protozoan in humans that is commonly associated with diarrhoea and other gastrointestinal complaints. Studies conducted to investigate the biology of this parasite are limited by methods for in vitro cultivation. The objective of this study was to improve a biphasic culture medium, based on the Loeffler's slope, by further supplementation in order to increase the yield of trophozoites in culture. The current in vitro culture of D. fragilis is a xenic culture with a mix of bacteria. Three different liquid overlays were evaluated including Earle's balanced salt solution (EBSS), PBS and Dulbecco's modified PBS (DPBS), for their ability to support the in vitro growth of D. fragilis trophozoites. Out of these 3 overlays EBSS gave the highest increase in the trophozoite numbers. The effect of supplementation was analysed by supplementing EBSS with ascorbic acid, ferric ammonium citrate, L-cysteine, cholesterol and alpha-lipoic acid and quantification of in vitro growth by cell counts. A new liquid overlay is here described based upon EBSS supplemented with cholesterol and ferric ammonium citrate that, in conjunction with the Loeffler's slope, supports the growth of D. fragilis trophozoites in vitro. This modified overlay supported a 2-fold increase in the numbers of trophozoite in culture from all 4 D. fragilis isolates tested, when compared to a PBS overlay. These advances enable the harvest of a larger number of trophozoites needed for further studies on this parasite.

Murray, B & Phillips, M 2012, 'Temporal introduction patterns of invasive alien plant species to Australia', NeoBiota, vol. 13, pp. 1-14.
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We examined temporal introduction patterns of 132 invasive alien plant species (IAPS) to Australia since European colonisation in 1770. Introductions of IAPS were high during 18101820 (10 species), 1840 1880 (51 species, 38 of these between 1840 and 1860) and 19301940 (9 species). Conspicuously few introductions occurred during 10-year periods directly preceding each introduction peak. Peaks during early European settlement (18101820) and human range expansion across the continent (1840-1860) both coincided with considerable growth in Australias human population. We suggest that population growth during these times increased the likelihood of introduced plant species becoming invasive as a result of increased colonization and propagule pressure. Deliberate introductions of IAPS (104 species) far outnumbered accidental introductions (28 species) and were particularly prominent during early settlement. Cosmopolitan IAPS (25 species) and those native solely to South America (53 species), Africa (27 species) and Asia (19 species) have been introduced deliberately and accidentally to Australia across a broad period of time. A small number of IAPS, native solely to Europe (5 species) and North America (2 species), were all introduced to Australia prior to 1880. These contrasting findings for native range suggest some role for habitat matching, with similar environmental conditions in Australia potentially driving the proliferation of IAPS native to southern-hemisphere regions.

Murray, SA, Garby, T, Hoppenrath, M & Neilan, BA 2012, 'Genetic Diversity, Morphological Uniformity and Polyketide Production in Dinoflagellates (Amphidinium, Dinoflagellata)', PLOS ONE, vol. 7, no. 6, pp. e38253-0.
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Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a 'model' dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of 'cryptic' species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them. © 2012 Murray et al.

Murray, SA, Patterson, DJ & Thessen, AE 2012, 'Transcriptomics and microbial eukaryote diversity: a way forward', TRENDS IN ECOLOGY & EVOLUTION, vol. 27, no. 12, pp. 651-652.
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Recent reviews have pointed out the large proportion of microbial eukaryotic (protist) diversity that has yet to be described, and the enormous challenges that accompany its description [1]. The ~100 000 species [2] of microbial eukaryotes may be significantly underestimated if we continue to discover increasing numbers of cryptic species. Tools such as environmental sequencing, which have been highly successful in revealing novel lineages of uncultured bacteria and archaea, promise to add substantial new data for comparatively little effort [1]. In our opinion, significant challenges, grounded in both biology and the history of study of these organisms, need to be faced before environmental sequencing can unlock our understanding of microbial eukaryotic diversity.

Murray, SA, Wiese, M, Neilan, BA, Orr, RJS, de Salas, M, Brett, S & Hallegraeff, G 2012, 'A reinvestigation of saxitoxin production and sxtA in the 'non-toxic' Alexandrium tamarense Group V clade', HARMFUL ALGAE, vol. 18, no. 1, pp. 96-104.
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The three Alexandrium species A. tamarense, A. fundyense and A. catenella include strains that can be potent producers of the neurotoxin saxitoxin (STX) and its analogues, the causative agents of paralytic shellfish poisoning (PSP). These three species a

Nagata, N, Marriott, D, Harkness, J, Ellis, JT & Stark, D 2012, 'Current treatment options for Dientamoeba fragilis infections', INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE, vol. 2, pp. 204-215.
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Dientamoeba fragilis belongs to the trichomonad group of protozoan parasites and it has been implicated as a cause of gastrointestinal disease with world-wide prevalences ranging from 0.5% to 16%. The majority of patients with dientamoebiasis present with gastrointestinal complaints. Chronic symptoms are common with up to a third of patients exhibiting persistent diarrhoea. Numerous studies have successfully demonstrated parasite clearance, coupled with complete resolution of clinical symptoms following treatment with various antiparasitic compounds. Treatments reported to be successful for dientamoebiasis include carbarsone, diphetarsone, tetracyclines, paromomycin, erythromycin, hydroxyquinolines and the 5-nitroimidazoles, including metronidazole, secnidazole, tinidazole and ornidazole. It is of note that most current treatment data is based only on small number of case reports. No large scale double blind randomised placebo controlled trials testing the efficacy of antimicrobial agents against D. fragilis has been undertaken highlighting the need for further study. In addition there is very little in vitro susceptibility data available for the organism making some current treatment options questionable. The aim of this review is to critically discuss all treatment options currently available for dientamoebiasis.

Nagata, N, Marriott, D, Harkness, J, Ellis, JT & Stark, D 2012, 'In Vitro Susceptibility Testing of Dientamoeba fragilis', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 56, no. 1, pp. 487-494.
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Dientamoeba fragilis is a commonly encountered trichomonad which has been implicated as a cause of gastrointestinal disease in humans. Despite the frequency of reports recording infections with this parasite, little research has been undertaken in terms of antimicrobial susceptibility. The aim of this study was to evaluate the susceptibility of D. fragilis to several commonly used antiparasitic agents: diloxanide furoate, furazolidone, iodoquinol, metronidazole, nitazoxanide, ornidazole, paromomycin, secnidazole, ronidazole, tetracycline, and tinidazole. Antibiotic susceptibility testing was performed on four clinical strains of D. fragilis, designated A, E, M, and V, respectively. Molecular testing followed, and all strains were determined to be genotype 1. The activities of antiprotozoal compounds at concentrations ranging from 2!g/ml to 500!g/ml were determined via cell counts of D. fragilis trophozoites grown in dixenic culture. Minimum lethal concentrations (MLCs) were as follows: ornidazole, 8 to 16 !g/ml; ronidazole, 8 to 16!g/ml; tinidazole, 31!g/ml; metronidazole, 31!g/ml; secnidazole, 31 to 63!g/ml; nitazoxanide, 63 !g/ml; tetracycline, 250!g/ml; furazolidone, 250 to 500!g/ml; iodoquinol, 500!g/ml; paromomycin, 500!g/ml; and diloxanide furoate,>500!g/ml. This is the first study to report the profiles of susceptibility to a wide range of commonly used treatments for clinical isolates of D. fragilis. Our study indicated 5-nitroimidazole derivatives to be the most active compounds in vitro against D. fragilis.

Nelson, LA, Lambkin, CL, Batterham, P, Wallman, JF, Dowton, M, Whiting, MF, Yeates, DK & Cameron, SL 2012, 'Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)', Gene, vol. 511, no. 2, pp. 131-142.
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Niimi, K, Ge, Q, Moir, LM, Ammit, AJ, Trian, T, Burgess, JK, Black, JL & Oliver, BGG 2012, 'β₂-Agonists upregulate PDE4 mRNA but not protein or activity in human airway smooth muscle cells from asthmatic and nonasthmatic volunteers', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 302, no. 3, pp. L334-L342.
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β2-Adrenergic receptor (β2AR) agonists induce airway relaxation via cAMP. Phosphodiesterase (PDE)s degrade and regulate cAMP, and in airway smooth muscle (ASM) cells PDE4D degrades cAMP. Long-acting β2-agonists are now contraindicated as monotherapy for asthma, and increased PDE4D has been speculated to contribute to this phenomenon. In this study we investigated the expression of PDE4D in asthmatic and nonasthmatic ASM cells and its regulation by formoterol and budesonide. Primary ASM cells from people with or without asthma were stimulated with transforming growth factor (TGF)-β1, formoterol, and/or budesonide. PDE4D mRNA was assessed by real-time PCR, or PCR to assess splice variant production. PDE4D protein was assessed by Western blotting, and we investigated the effect of formoterol on cAMP production and PDE activity. Interleukin (IL)-6 was assessed using ELISA. PDE4D mRNA was dose dependently upregulated by formoterol, with a single splice variant, PDE4D5, present. Formoterol did not induce PDE4D protein at time points between 3 to 72 h, whereas it did induce and increase IL-6 secretion. We pretreated cells with actinomycin D and a proteasome inhibitor, MG132, and found no evidence of alterations in mRNA, protein expression, or degradation of PDE4D. Finally PDE activity was not altered by formoterol. This study shows, for the first time, that PDE4D5 is predominantly expressed in human ASM cells from people with and without asthma and that formoterol does not upregulate PDE4D protein production. This leads us to speculate that continual therapy with β2AR agonists is unlikely to cause PDE4-mediated tachyphylaxis.

Niu, N, Liu, T-L, Aharonovich, I, Russell, KJ, Woolf, A, Sadler, TC, El-Ella, HAR, Kappers, MJ, Oliver, RA & Hu, EL 2012, 'A full free spectral range tuning of p-i-n doped gallium nitride microdisk cavity', APPLIED PHYSICS LETTERS, vol. 101, no. 16.
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Nolan, LM, Beatson, SA, Croft, L, Jones, PM, George, AM, Mattick, JS, Turnbull, L & Whitchurch, CB 2012, 'Extragenic suppressor mutations that restore twitching motility to fimL mutants of Pseudomonas aeruginosa are associated with elevated intracellular cyclic AMP levels', MICROBIOLOGYOPEN, vol. 1, no. 4, pp. 490-501.
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Cyclic AMP (cAMP) is a signaling molecule that is involved in the regulation of multiple virulence systems of the opportunistic pathogen Pseudomonas aeruginosa. The intracellular concentration of cAMP in P. aeruginosa cells is tightly controlled at the levels of cAMP synthesis and degradation through regulation of the activity and/or expression of the adenylate cyclases CyaA and CyaB or the cAMP phosphodiesterase CpdA. Interestingly, mutants of fimL, which usually demonstrate defective twitching motility, frequently revert to a wild-type twitching-motility phenotype presumably via the acquisition of an extragenic suppressor mutation(s). In this study, we have characterized five independent fimL twitching-motility revertants and have determined that all have increased intracellular cAMP levels compared with the parent fimL mutant. Whole-genome sequencing revealed that only one of these fimL revertants has acquired a loss-of-function mutation in cpdA that accounts for the elevated levels of intracellular cAMP. As mutation of cpdA did not account for the restoration of twitching motility observed in the other four fimL revertants, these observations suggest that there is at least another, as yet unidentified, site of extragenic suppressor mutation that can cause phenotypic reversion in fimL mutants and modulation of intracellular cAMP levels of P. aeruginosa. Pseudomonas aeruginosa fimL mutants, which usually demonstrate defective twitching motility, frequently revert to a wild-type twitching-motility phenotype presumably via the acquisition of an extragenic suppressor mutation(s). In this study, we have characterized five independent fimL twitching-motility revertants and have determined that all have increased intracellular cAMP levels compared with the parent fimL mutant. Whole-genome sequencing revealed that only one of these fimL revertants has acquired a loss-of-function mutation in cpdA that accounts for the elevated levels of intracellular cAMP. © ...

Nomura, T, Cranfield, CG, Deplazes, E, Owen, DM, Macmillan, A, Battle, AR, Constantine, M, Sokabe, M & Martinac, B 2012, 'Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 109, no. 22, pp. 8770-8775.
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Mechanosensitive (MS) channels of small (MscS) and large (MscL) conductance are the major players in the protection of bacterial cells against hypoosmotic shock. Although a great deal is known about structure and function of these channels, much less is known about how membrane lipids may influence their mechanosensitivity and function. In this study, we use liposome coreconstitution to examine the effects of different types of lipids on MscS and MscL mechano-sensitivity simultaneously using the patch-clamp technique and confocal microscopy. Fluorescence lifetime imaging (FLIM)-FRET microscopy demonstrated that coreconstitution of MscS and MscL led to clustering of these channels causing a significant increase in the MscS activation threshold. Furthermore, the MscL/MscS threshold ratio dramatically decreased in thinner compared with thicker bilayers and upon addition of cholesterol, known to affect the bilayer thickness, stiffness and pressure profile. In contrast, application of micromolar concentrations of lysophosphatidylcholine (LPC) led to an increase of the MscL/MscS threshold ratio. These data suggest that differences in hydrophobic mismatch and bilayer stiffness, change in transbilayer pressure profile, and close proximity of MscL and MscS affect the structural dynamics of both channels to a different extent. Our findings may have far-reaching implications for other types of ion channels and membrane proteins that, like MscL and MscS, may coexist in multiple molecular complexes and, consequently, have their activation characteristics significantly affected by changes in the lipid environment and their proximity to each other.

O'Brien, CJ, Peloquin, JA, Vogt, M, Heinle, M, Gruber, N, Ajani, P, Andruleit, H, Arístegui, J, Beaufort, L, Estrada, M, Karentz, D, Kopczyńska, E, Lee, R, Pritchard, T & Widdicombe, C 2012, 'Global marine plankton functional type biomass distributions: coccolithophores', Earth System Science Data, vol. 5, no. 2, pp. 259-276.
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Abstract. Coccolithophores are calcifying marine phytoplankton of the class Prymnesiophyceae. They are considered to play an import role in the global carbon cycle through the production and export of organic carbon and calcite. We have compiled observations of global coccolithophore abundance from several existing databases as well as individual contributions of published and unpublished datasets. We estimate carbon biomass using standardised conversion methods and provide estimates of uncertainty associated with these values. The database contains 58 384 individual observations at various taxonomic levels. This corresponds to 12 391 observations of total coccolithophore abundance and biomass. The data span a time period of 1929–2008, with observations from all ocean basins and all seasons, and at depths ranging from the surface to 500 m. Highest biomass values are reported in the North Atlantic, with a maximum of 501.7 μg C l−1. Lower values are reported for the Pacific (maximum of 79.4 μg C l−1) and Indian Ocean (up to 178.3 μg C l−1). Coccolithophores are reported across all latitudes in the Northern Hemisphere, from the Equator to 89° N, although biomass values fall below 3 μg C l−1 north of 70° N. In the Southern Hemisphere, biomass values fall rapidly south of 50° S, with only a single non-zero observation south of 60° S. Biomass values show a clear seasonal cycle in the Northern Hemisphere, reaching a maximum in the summer months (June–July). In the Southern Hemisphere the seasonal cycle is less evident, possibly due to a greater proportion of low-latitude data. The original and gridded datasets can be downloaded from Pangaea (http://doi.pangaea.de/10.1594/PANGAEA.785092).

Ormerod, JT & Wand, MP 2012, 'Comment', Technometrics, vol. 54, no. 3, pp. 233-236.
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Ormerod, JT & Wand, MP 2012, 'Gaussian Variational Approximate Inference for Generalized Linear Mixed Models', Journal of Computational and Graphical Statistics, vol. 21, no. 1, pp. 2-17.
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Variational approximation methods have become a mainstay of contemporary machine learning methodology, but currently have little presence in statistics. We devise an effective variational approximation strategy for fitting generalized linear mixed models (GLMMs) appropriate for grouped data. It involves Gaussian approximation to the distributions of random effects vectors, conditional on the responses. We show that Gaussian variational approximation is a relatively simple and natural alternative to Laplace approximation for fast, non-Monte Carlo, GLMM analysis. Numerical studies show Gaussian variational approximation to be very accurate in grouped data GLMM contexts. Finally, we point to some recent theory on consistency of Gaussian variational approximation in this context. Supplemental materials are available online. © 2012 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America.

Orr, RJS, Murray, SA, Stuken, A, Rhodes, L & Jakobsen, KS 2012, 'When Naked Became Armored: An Eight-Gene Phylogeny Reveals Monophyletic Origin of Theca in Dinoflagellates', PLOS ONE, vol. 7, no. 11, pp. e50004-0.
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The dinoflagellates are a diverse lineage of microbial eukaryotes. Dinoflagellate monophyly and their position within the group Alveolata are well established. However, phylogenetic relationships between dinoflagellate orders remain unresolved. To date, only a limited number of dinoflagellate studies have used a broad taxon sample with more than two concatenated markers. This lack of resolution makes it difficult to determine the evolution of major phenotypic characters such as morphological features or toxin production e.g. saxitoxin. Here we present an improved dinoflagellate phylogeny, based on eight genes, with the broadest taxon sampling to date. Fifty-five sequences for eight phylogenetic markers from nuclear and mitochondrial regions were amplified from 13 species, four orders, and concatenated phylogenetic inferences were conducted with orthologous sequences. Phylogenetic resolution is increased with addition of support for the deepest branches, though can be improved yet further. We show for the first time that the characteristic dinoflagellate thecal plates, cellulosic material that is present within the sub-cuticular alveoli, appears to have had a single origin. In addition, the monophyly of most dinoflagellate orders is confirmed: the Dinophysiales, the Gonyaulacales, the Prorocentrales, the Suessiales, and the Syndiniales. Our improved phylogeny, along with results of PCR to detect the sxtA gene in various lineages, allows us to suggest that this gene was probably acquired separately in Gymnodinium and the common ancestor of Alexandrium and Pyrodinium and subsequently lost in some descendent species of Alexandrium. © 2012 Orr et al.

Orwa, JO, Ganesan, K, Newnham, J, Santori, C, Barclay, P, Fu, KMC, Beausoleil, RG, Aharonovich, I, Fairchild, BA, Olivero, P, Greentree, AD & Prawer, S 2012, 'An upper limit on the lateral vacancy diffusion length in diamond', DIAMOND AND RELATED MATERIALS, vol. 24, no. 1, pp. 6-10.
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Ion implantation is widely used to modify the structural, electrical and optical properties of materials. By appropriate masking, this technique can be used to define nano- and micro-structures. However, depending on the type of mask used, experiments have shown that vacancy-related substrate modification can be inferred tens of micrometers away from the edge of the mask used to define the implanted region. This could be due to fast diffusion of vacancies from the implanted area during annealing or to a geometric effect related to ion scattering around the mask edges. For quantum and single-atom devices, stray ion damage can be deleterious and must be minimized. In order to profile the distribution of implantation-induced damage, we have used the nitrogen-vacancy color center as a sensitive marker for vacancy concentration and distribution following MeV He ion implantation into diamond and annealing. Results show that helium atoms implanted through a mask clamped to the diamond surface are scattered underneath the mask to distances in the range of tens of micrometers from the mask edge. Implantation through a lithographically defined and deposited mask, with no spacing between the mask and the substrate, significantly reduces the scattering to = 5 µm but does not eliminate it. These scattering distances are much larger than the theoretically estimated vacancy diffusion distance of ~ 260 nm under similar conditions. This paper shows that diffusion, upon annealing, of vacancies created by ion implantation in diamond, is limited, and the appearance of vacancies many tens of micrometers from the edge of the mask is due to scattering effects

Osabe, K, Kawanabe, T, Sasaki, T, Ishikawa, R, Okazaki, K, Dennis, ES, Kazama, T & Fujimoto, R 2012, 'Multiple Mechanisms and Challenges for the Application of Allopolyploidy in Plants', INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 13, no. 7, pp. 8696-8721.
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An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, ov

Oxborough, K, Moore, CM, Suggett, DJ, Lawson, T, Chan, HG & Geider, RJ 2012, 'Direct estimation of functional PSII reaction center concentration and PSII electron flux on a volume basis: a new approach to the analysis of Fast Repetition Rate fluorometry (FRRf) data', Limnology and Oceanography: Methods, vol. 10, no. 3, pp. 142-154.
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Phytoplankton primary productivity is most commonly measured by 14C assimilation although less direct methods, such as O2 exchange, have also been employed. These methods are invasive, requiring bottle incubation for up to 24 h. As an alternative, Fast Repetition Rate fluorometry (FRRf) has been used, on wide temporal and spatial scales within aquatic systems, to estimate photosystem II (PSII) electron flux per unit volume (JVPSII), which generally correlates well with photosynthetic O2 evolution. A major limitation of using FRRf arises from the need to employ an independent method to determine the concentration of functional photosystem II reaction centers ([RCII]); a requirement that has prevented FRR fluorometers being used, as stand‐alone instruments, for the estimation of electron transport. Within this study, we have taken a new approach to the analysis of FRRf data, based on a simple hypothesis; that under a given set of environmental conditions, the ratio of rate constants for RCII fluorescence emission and photochemistry falls within a narrow range, for all groups of phytoplankton. We present a simple equation, derived from the established FRRf algorithm, for determining [RCII] from dark FRRf data alone. We also describe an entirely new algorithm for estimating JVPSII, which does not require determination of [RCII] and is valid for a heterogeneous model of connectivity among RCIIs. Empirical supporting evidence is presented. These data are derived from FRR measurements across a diverse range of microalgae, in parallel with independent measurements of [RCII]. Possible sources of error, particularly under nutrient stress conditions, are discussed.

Packer, JM, Irish, J, Herbert, BR, Hill, C, Padula, M, Blair, SE, Carter, DA & Harry, EJ 2012, 'Specific non-peroxide antibacterial effect of manuka honey on the Staphylococcus aureus proteome', International Journal of Antimicrobial Agents, vol. 40, no. 1, pp. 43-50.
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Manuka honey, derived from the New Zealand flowering plant Leptospermum scoparium, shows promise as a topical antibacterial agent and effective chronic wound dressing. The aim of this study was to determine the non-peroxide antibacterial effects of this honey on the proteome of the common wound pathogen Staphylococcus aureus. Proteomic analysis was performed on cells treated for a short time with manuka honey compared with the proteome of untreated cells as well as cells treated with a Leptospermum honey sample without antibacterial activity. Treatment with manuka honey resulted in a significant decrease in the bacterial cell growth rate as well as downregulation of ten and upregulation of two proteins. Nine of these proteins were also differentially expressed by cells treated with the inactive Leptospermum honey, but to a lesser degree, and the rate of bacterial growth was not affected. The differentially expressed proteins have roles in ribosomal function, protein synthesis, metabolic processes and transcription. Manuka honey uniquely caused downregulation of two proteins [dihydrolipoamide dehydrogenase (DLD) and elongation factor Tu (EF-Tu)] associated with two of these pathways as well as upregulation of one stress-related protein [cold shock protein C (CspC)]. The proteomic profile following treatment with manuka honey differed from the profiles of other antibacterial agents, indicating a unique mode of action and its potential value as a novel antimicrobial agent. Crown Copyright © 2012 Published by Elsevier B.V. on behalf of International Society of Chemotherapy. All rights reserved.

Pagan, F, Lim, C, Keglovic, M & McNevin, D 2012, 'Comparison of DNA extraction methods for identification of human remains', Australian Journal of Forensic Sciences, vol. 44, no. 2, pp. 117-127.
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Palee, J, Dheeranupa, S, Jatisatien, A, Wangkarn, S, Mungkornas, P, Pyne, S, Ung, A & Sastraruji, T 2012, 'Influence of Plantlet Age and Different Soilless Culture on Acclimatization of Stemona curtisii Hook.f.', Asian Journal of Plant Sciences, vol. 11, no. 6, pp. 294-299.
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The aim of this experiment was to study the optimal age of Stemona curtisii plantlets for acclimatization. The in vitro shoots of S. curtisii were cultured on Murashige and Skoog solid medium supplemented with 1 mg L-1 naphthalene acetic acid to induce roots. Then, the plantlets from in vitro culture of 4, 8 and 12 week-old were transferred into the soil and their survival rate during the acclimatization process in the greenhouse was investigated. It was found that the 8 week-old plantlets had the highest survival rate of 80%. However, to enhance the survival rate of these plantlets, a soilless culture technique as a possible approach for the acclimatization was considered. Eight week-old plantlets were transferred into either, soil, a hydroponic system (nutrient film technique), coconut fiber or sand. The plantlets which were cultivated in coconut fiber or hydroponic culture showed 100% survival rate with the highest average number of new roots per plant. However, the mean root length of the plantlets grown in hydroponic system was significantly higher than that grown in coconut fiber.

Pant, R, Byrnes, A, Poulton, CG, Li, E, Choi, D-Y, Madden, S, Luther-Davies, B & Eggleton, BJ 2012, 'Photonic-chip-based tunable slow and fast light via stimulated Brillouin scattering', OPTICS LETTERS, vol. 37, no. 5, pp. 969-971.
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We report the first (to our knowledge) demonstration of photonic chip based tunable slow and fast light via stimulated Brillouin scattering. Slow, fast, and negative group velocities were observed in a 7 cm long chalcogenide (As 2S3) rib waveguide with a group index change ranging from ∼ ? 44 to +130, which results in a maximum delay of ∼23 ns at a relatively low gain of ∼23 dB. Demonstration of large tunable delays in a chip scale device opens up applications such as frequency sensing and true-time delay for a phased array antenna, where integration and delays ∼10 ns are highly desirable. © 2012 Optical Society of America.

Park, I, Yoo, J, Kim, B, Adhikari, S, Kim, SK, Yeon, Y, Haynes, CJE, Sutton, JL, Tong, CC, Lynch, VM, Sessler, JL, Gale, PA & Lee, C 2012, 'Oligoether‐Strapped Calix[4]pyrrole: An Ion‐Pair Receptor Displaying Cation‐Dependent Chloride Anion Transport', Chemistry – A European Journal, vol. 18, no. 9, pp. 2514-2523.
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AbstractA ditopic ion‐pair receptor (1), which has tunable cation‐ and anion‐binding sites, has been synthesized and characterized. Spectroscopic analyses provide support for the conclusion that receptor 1 binds fluoride and chloride anions strongly and forms stable 1:1 complexes ([1⋅F]− and [1⋅Cl]−) with appropriately chosen salts of these anions in acetonitrile. When the anion complexes of 1 were treated with alkali metal ions (Li+, Na+, K+, Cs+, as their perchlorate salts), ion‐dependent interactions were observed that were found to depend on both the choice of added cation and the initially complexed anion. In the case of [1⋅F]−, no appreciable interaction with the K+ ion was seen. On the other hand, when this complex was treated with Li+ or Na+ ions, decomplexation of the bound fluoride anion was observed. In contrast to what was seen with Li+, Na+, K+, treating [1⋅F]− with Cs+ ions gave rise to a stable, host‐separated ion‐pair complex, [F⋅1⋅Cs], which contains the Cs+ ion bound in the cup‐like portion of the calix[4]pyrrole. Different complexation behavior was seen in the case of the chloride complex, [1⋅Cl]−. Here, no appreciable interaction was observed with Na+ or K+. In contrast, treating with Li+ produces a tight ion‐pair complex, [1⋅Li⋅Cl], in whic...

Park, JS, Kim, DJ, Park, JW, Ryu, HS, Kim, KW, Wang, GX & Ahn, HJ 2012, 'Evaluation of Sulfur and Multi-Walled Carbon Nanotube Composite Synthesized by Dissolution and Precipitation for Li/S Batteries', Journal of Nanoscience and Nanotechnology, vol. 12, no. 7, pp. 5794-5798.
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An elemental sulfur and multi-walled carbon nanotube (S-MWNT) composite was synthesized by dissolving sulfur in ammonium sul?des and then precipitating on MWNT. Morphology observation by scanning electron microscopy (SEM) con?rmed that S-MWNT product was successfully prepared by incorporating sulfur into MWNT network. Without additional conducting material, the S-MWNT composite cathodes were prepared for electrochemical tests. The properties measured in discharge-charge cycling test showed that the composite had the initial discharge capacity of 1024 mAh g -1, which is about 61% sulfur utilization. However, in the subsequent cycling, the capacities faded. To determine the reason of rapid capacity drop, S-MWNT composite cathodes were compared in the cycling tests with varying three kinds of electrolytes and the cathode was subjected to physical force by rolling. The changes in the cycle performances proved that the deterioration of S-MWNT composite cathodes was not related to the electrolytes but to physical bonding that may not maintain the conducting path between sulfur and MWNT. © 2012 American Scientific Publishers.

Parkinson, KL, Booth, DJ & Lee, JE 2012, 'Validation of otolith daily increment formation for two temperate syngnathid fishes: the pipefishes Stigmatopora argus and Stigmatopora nigra', JOURNAL OF FISH BIOLOGY, vol. 80, no. 3, pp. 698-704.
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Otoliths were used for the first time to successfully validate the age of members of the family Syngnathidae: the spotted pipefish Stigmatopora argus and the wide-bodied pipefish Stigmatopora nigra. Otolith increments were deposited daily in (1) known-age juveniles ranging in age from 0 to 31 days and (2) adults that had been stained with alizarin complexone, and a hatch mark was found on all otoliths which represented day 0. Otolith increment validation will allow development of growth models for S. argus and S. nigra, essential to understanding and managing these exclusive seagrass species. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Paterson, AH, Wendel, JF, Gundlach, H, Guo, H, Jenkins, J, Jin, D, Llewellyn, D, Showmaker, KC, Shu, S, Udall, J, Yoo, M-J, Byers, R, Chen, W, Doron-Faigenboim, A, Duke, MV, Gong, L, Grimwood, J, Grover, C, Grupp, K, Hu, G, Lee, T-H, Li, J, Lin, L, Liu, T, Marler, BS, Page, JT, Roberts, AW, Romanel, E, Sanders, WS, Szadkowski, E, Tan, X, Tang, H, Xu, C, Wang, J, Wang, Z, Zhang, D, Zhang, L, Ashrafi, H, Bedon, F, Bowers, JE, Brubaker, CL, Chee, PW, Das, S, Gingle, AR, Haigler, CH, Harker, D, Hoffmann, LV, Hovav, R, Jones, DC, Lemke, C, Mansoor, S, Rahman, MU, Rainville, LN, Rambani, A, Reddy, UK, Rong, J-K, Saranga, Y, Scheffler, BE, Scheffler, JA, Stelly, DM, Triplett, BA, Van Deynze, A, Vaslin, MFS, Waghmare, VN, Walford, SA, Wright, RJ, Zaki, EA, Zhang, T, Dennis, ES, Mayer, KFX, Peterson, DG, Rokhsar, DS, Wang, X & Schmutz, J 2012, 'Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres', NATURE, vol. 492, no. 7429, pp. 423-+.
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Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five-to sixfold ploidy increase approximately 60million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A t D t (in which t' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups. © 2012 Macmillan Publishers Limited. All rights reserved.

Paul, RG, Elston, MS, Gill, AJ, Marsh, D, Beer, I, Wolmarans, L, Conaglen, JV & Meyer-Rochow, GY 2012, 'Hypercalcaemia due to parathyroid carcinoma presenting in the third trimester of pregnancy', Australian and New Zealand Journal of Obstetrics and Gynaecology, vol. 52, no. 2, pp. 204-207.
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Primary hyperparathyroidism (pHPT) in pregnancy may be associated with significant maternal and fetal morbidity and mortality. Medical management of pHPT in pregnancy is limited, and surgery is the only definitive therapeutic option. The ideal timing for surgery is mid‐second trimester, but surgery may also be safely performed in the third trimester. Delayed parathyroid surgery may result in a hypercalcaemic crisis postpartum owing to loss of active placental calcium transfer. We present a case of parathyroid carcinoma in pregnancy presenting with pre‐eclampsia at 32 weeks’ gestation.

Peng, T, Xie, H, Ding, Y, Wang, W, Li, Z, Jin, D, Tang, Y, Ren, Q & Xi, P 2012, 'CRAFT: Multimodality confocal skin imaging for early cancer diagnosis', JOURNAL OF BIOPHOTONICS, vol. 5, no. 5-6, pp. 469-476.
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Although histological analysis serves as a gold standard to cancer diagnosis, its application on skin cancer detection is largely prohibited due to its invasive nature. To obtain both the structural and pathological information in situ, a Confocal Reflectance/Auto-Fluorescence Tomography (CRAFT) system was established to examine the skin sites in vivo with both reflectance and autofluorescence modes simultaneously. Nude mice skin with cancerous sites and normal skin sites were imaged and compared with the system. The cellular density and reflective intensity in cancerous sites reflects the structural change of the tissue. With the decay coefficient analysis, the corresponding NAD(P)H decay index for cancerous sites is 1.65-fold that of normal sites, leading to a 97.8% of sensitivity and specificity for early cancer diagnosis. The results are verified by the followed histological analysis. Therefore, CRAFT may provide a novel method for the in vivo, non-invasive diagnosis of early cancer. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pérez, A, Zhang, S, Kipnis, V, Freedman, LS & Carroll, RJ 2012, 'Intake_epis_food(): AnRFunction for Fitting a Bivariate Nonlinear Measurement Error Model to Estimate Usual and Energy Intake for Episodically Consumed Foods', Journal of Statistical Software, vol. 46, no. Code Snippet 3, pp. 1-17.
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We consider a Bayesian analysis using WinBUGS to estimate the distribution of usual intake for episodically consumed foods and energy (calories). The model uses measures of nutrition and energy intakes via a food frequency questionnaire (FFQ) along with repeated 24 hour recalls and adjusting covariates. In order to estimate the usual intake of the food, we phrase usual intake in terms of person-specific random effects, along with day-to-day variability in food and energy consumption. Three levels are incorporated in the model. The first level incorporates information about whether an individual in fact reported consumption of a particular food item. The second level incorporates the amount of intake from those individuals who reported consumption of the food, and the third level incorporates the energy intake. Estimates of posterior means of parameters and distributions of usual intakes are obtained by using Markov chain Monte Carlo calculations. This R function reports to users point estimates and credible intervals for parameters in the model, samples from their posterior distribution, samples from the distribution of usual intake and usual energy intake, trace plots of parameters and summary statistics of usual intake, usual energy intake and energy adjusted usual intake.

Pernice, M & Boucher‐Rodoni, R 2012, 'Occurrence of a specific dual symbiosis in the excretory organ of geographically distant Nautiloids populations', Environmental Microbiology Reports, vol. 4, no. 5, pp. 504-511.
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SummaryNautilus is one of the most intriguing of all sea creatures, sharing morphological similarities with the extinct forms of coiled cephalopods that evolved since the Cambrian (542–488 mya). Further, bacterial symbioses found in their excretory organ are of particular interest as they provide a great opportunity to investigate the influence of host–microbe interactions upon the origin and evolution of an innovative nitrogen excretory system. To establish the potential of Nautilus excretory organ as a new symbiotic system, it is, however, necessary to assess the specificity of this symbiosis and whether it is consistent within the different species of present‐day Nautiloids. By addressing the phylogeny and distribution of bacterial symbionts in three Nautilus populations separated by more than 6000 km (N. pompilius from Philippines and Vanuatu, and N. macromphalus from New Caledonia), this study confirms the specificity of this dual symbiosis involving the presence of betaproteobacteria and spirochaete symbionts on a very wide geographical area. Overall, this work sheds further light on Nautiloids excretory organ as an innovative system of interaction between bacteria and cephalopods.

Pernice, M, Meibom, A, Van Den Heuvel, A, Kopp, C, Domart-Coulon, I, Hoegh-Guldberg, O & Dove, S 2012, 'A single-cell view of ammonium assimilation in coral–dinoflagellate symbiosis', The ISME Journal, vol. 6, no. 7, pp. 1314-1324.
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Abstract Assimilation of inorganic nitrogen from nutrient-poor tropical seas is an essential challenge for the endosymbiosis between reef-building corals and dinoflagellates. Despite the clear evidence that reef-building corals can use ammonium as inorganic nitrogen source, the dynamics and precise roles of host and symbionts in this fundamental process remain unclear. Here, we combine high spatial resolution ion microprobe imaging (NanoSIMS) and pulse-chase isotopic labeling in order to track the dynamics of ammonium incorporation within the intact symbiosis between the reef-building coral Acropora aspera and its dinoflagellate symbionts. We demonstrate that both dinoflagellate and animal cells have the capacity to rapidly fix nitrogen from seawater enriched in ammonium (in less than one hour). Further, by establishing the relative strengths of the capability to assimilate nitrogen for each cell compartment, we infer that dinoflagellate symbionts can fix 14 to 23 times more nitrogen than their coral host cells in response to a sudden pulse of ammonium-enriched seawater. Given the importance of nitrogen in cell maintenance, growth and functioning, the capability to fix ammonium from seawater into the symbiotic system may be a key component of coral nutrition. Interestingly, this metabolic response appears to be triggered rapidly by episodic nitrogen availability. The methods and results presented in this study open up for the exploration of dynamics and spatial patterns associated with metabolic activities and nutritional interactions in a multitude of organisms that live in symbiotic relationships.

Petrou, K, Kranz, SA, Doblin, MA & Ralph, PJ 2012, 'PHOTOPHYSIOLOGICAL RESPONSES OF FRAGILARIOPSIS CYLINDRUS (BACILLARIOPHYCEAE) TO NITROGEN DEPLETION AT TWO TEMPERATURES', JOURNAL OF PHYCOLOGY, vol. 48, no. 1, pp. 127-136.
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The photosynthetic efficiency and photoprotective capacity of the sea-ice diatom, Fragilariopsis cylindrus (Grunow) W. Krieg., grown in a matrix of nitrogen repletion and depletion at two different temperatures (-1°C and +6°C) was investigated. Temperature showed no significant effect on photosynthetic efficiency or photoprotection in F. cylindrus. Cultures under nitrogen depletion showed enhanced photoprotective capacity with an increase in nonphotochemical quenching (NPQ) when compared with nitrogen-replete cultures. This phenomenon was achieved at no apparent cost to the photosynthetic efficiency of PSII (F V/F M). Nitrogen depletion yielded a partially reduced electron transport chain in which maximum fluorescence (F M) could only be obtained by adding 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). reoxidation curves showed the presence of Q B nonreducing PSII centers under nitrogen depletion. Fast induction curves (FICs) and electron transport rates (ETRs) revealed slowing of the electrons transferred from the primary (Q A) to the secondary (Q B) quinone electron acceptors of PSII. The data presented show that nitrogen depletion in F. cylindrus leads to the formation of Q B nonreducing PSII centers within the photosystem. On a physiological level, the formation of Q B nonreducing PSII centers in F. cylindrus provides the cell with protection against photoinhibition by facilitating the rapid induction of NPQ. This strategy provides an important ecological advantage, especially during the Antarctic spring, maintaining photosynthetic efficiency under high light and nutrient-limiting conditions. © 2011 Phycological Society of America.

Phillips, ML & Murray, BR 2012, 'Invasiveness in exotic plant species is linked to high seed survival in the soil', EVOLUTIONARY ECOLOGY RESEARCH, vol. 14, no. 1, pp. 83-94.
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Background: Exotic species often do no harm for many generations and then become invasive. The science of invasion ecology seeks to determine the nature or causes of this change. Among the possibilities is that soil-borne fungi play a significant role in reducing the potential for invasiveness in the introduced range. Predictions: The seed survival of invasive species in the soil exceeds that of non-invasives. Seed survival, both in invasives and non-invasives, is higher in the presence of fungicide, but fungicide improves the seed survival of non-invasives more than that of invasives. Methods: A common garden experiment under field conditions to compare seed survival in the soil between invasive and non-invasive exotic plant species. We contrasted seven congeneric pairs of invasive and non-invasive species. The species in each pair originated from the same donor continent, shared similar growth form, habitat occurrence, and residence times in Australia. The addition of fungicide was used as an experimental treatment. Results: Seed survival was significantly higher in invasive species. The addition of fungicide improved seed survival. However, there was also a significant interaction: the fungicide treatment had a significantly stronger effect on the seed survival of non-invasive species. Seed mass differences between congeners did not provide a consistent, significant explanation of seed survival differences. Conclusion: The seeds of invasive species are better equipped to survive in the soil than those of non-invasive species. Moreover, soil-borne fungi play a key role in the lower seed survival of non-invasive species. © 2012 Megan L. Phillips.

Phillips, MR 2012, 'Stability Of InGaN/GaN MQW Luminescence Under Prolonged High Current Injection', Microscopy and Microanalysis, vol. 18, no. S2, pp. 1876-1877.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Piefer, LA, Weeks, BR, Carroll, RJ, Byrne, DH, Ambrus, A & Turner, ND 2012, 'Quercetin and chlorogenic acid affect butyrate excretion, NF‐ κB activity, and cell proliferation in DSS treated rats', The FASEB Journal, vol. 26, no. S1.
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We previously showed quercetin was protective against colon carcinogenesis via inhibition of pro‐inflammatory molecules. The goal of this study was to explore effects of quercetin and chlorogenic acid (CA), stone fruit bioactives, on short chain fatty acid (SCFA) excretion and cell proliferation regulation in a colitis/injury model. Rats (n=63) received diets (basal, 0.05% CA, or 0.45% quercetin) for 3 wk before dextran sodium sulfate (DSS, 3%, 3x, 2 wk separation, n=11/diet) or control (no DSS, n=10/diet) treatments. SCFA concentration and fecal moisture were measured in feces collected pre‐ and post‐DSS treatments and on day 62. Colons were assessed for injury, inflammation, and proliferative index (PI), and mucosal scrapings for NF‐κB activity. DSS increased fecal moisture by 38.7% and SCFA concentration by 139.6% (p<0.0001). Quercetin, a butyrate uptake inhibitor, tended to increase 24 h butyrate excretion in DSS rats relative to basal (p=0.07) and CA (p=0.09). Quercetin and CA diets increased NF‐κB activity and PI (p<0.05) in control rats. Compared to non‐DSS rats, CA decreased NF‐κB activity and PI in DSS rats (p<0.05). Although quercetin and CA affected butyrate excretion, NF‐κB activity, and proliferation, and had no effect on injury, it may be possible these compounds would mitigate injury if given a longer recovery period. Funded by USDA/NIFA 2008‐34402‐19195 and 2009‐34402‐19195.

Pike, DA, Webb, JK & Shine, R 2012, 'Hot mothers, cool eggs: nest-site selection by egg-guarding spiders accommodates conflicting thermal optima', FUNCTIONAL ECOLOGY, vol. 26, no. 2, pp. 469-475.
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In oviparous species providing maternal care, the choice of nest site is crucial for the survival of both the eggs and the mother. Most embryos only develop successfully within a narrow range of incubation conditions, which may differ from the mother's own requirements. How, then, do nest-attending mothers select sites that provide suitable conditions for embryonic development, without compromising their own viability? 3.We investigated nest-site selection in flat-rock spiders, Hemicloea major, a species that guards fixed egg sacs in a thermally challenging environment (under sun-exposed rocks). Females glue egg sacs beneath rocks during late spring and guard their eggs during summer, when temperatures beneath rocks often exceed 50°C. Our field surveys show that spiders laid eggs beneath rocks that were larger and thinner, and thus hotter, than were most available rocks. However, the egg sacs almost invariably were glued to the coolest sites on the substrate beneath a rock, rather than to the (hotter, by about 9°C) underside of the rock. By affixing their egg sacs to the coolest locations beneath the hottest rocks, females ensured that their developing offspring experienced moderate temperatures and avoided lethal extremes and, simultaneously, gave themselves access to much hotter areas (that enhance their feeding and growth rates) under the same rock. This strategy allows mobile adult spiders to actively select higher temperatures than can be tolerated by their embryos, while remaining close enough to their eggs for effective nest guarding. © 2011 The Authors. Functional Ecology © 2011 British Ecological Society.

Pike, DA, Webb, JK & Shine, R 2012, 'Reply to comment on ‘chainsawing for conservation: ecologically informed tree removal for habitat management’', Ecological Management & Restoration, vol. 13, no. 3, pp. e12-e13.
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Poreba, M, McGowan, S, Skinner-Adams, TS, Trenholme, KR, Gardiner, DL, Whisstock, JC, To, J, Salvesen, GS, Dalton, JP & Drag, M 2012, 'Fingerprinting the Substrate Specificity of M1 and M17 Aminopeptidases of Human Malaria, Plasmodium falciparum', PLoS ONE, vol. 7, no. 2, pp. e31938-e31938.
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Background: Plasmodium falciparum, the causative agent of human malaria, expresses two aminopeptidases, PfM1AAP and PfM17LAP, critical to generating a free amino acid pool used by the intraerythrocytic stage of the parasite for proteins synthesis, growth and development. These exopeptidases are potential targets for the development of a new class of anti-malaria drugs. Methodology/Principal Findings: To define the substrate specificity of recombinant forms of these two malaria aminopeptidases we used a new library consisting of 61 fluorogenic substrates derived both from natural and unnatural amino acids. We obtained a detailed substrate fingerprint for recombinant forms of the enzymes revealing that PfM1AAP exhibits a very broad substrate tolerance, capable of efficiently hydrolyzing neutral and basic amino acids, while PfM17LAP has narrower substrate specificity and preferentially cleaves bulky, hydrophobic amino acids. The substrate library was also exploited to profile the activity of the native aminopeptidases in soluble cell lysates of P. falciparum malaria. Conclusions/Significance: This data showed that PfM1AAP and PfM17LAP are responsible for majority of the aminopeptidase activity in these extracts. These studies provide specific substrate and mechanistic information important for understanding the function of these aminopeptidases and could be exploited in the design of new inhibitors to specifically target these for anti-malaria treatment. © 2012 Poreba et al.

Porkovich, AJ, Arnold, MD, Kouzmina, G, Hingley, B & Cortie, MB 2012, 'Calorimetric Sensor for H2O2/H2O Mist Streams', IEEE SENSORS JOURNAL, vol. 12, no. 7, pp. 2392-2398.
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Mist streams comprised of H 2O 2/H 2O droplets are a recent innovation for disinfecting medical equipment, but the availability of a sensor that could monitor the concentration of H 2O 2 applied during the treatment would be desirable. Here we describe a means to obtain a rapid estimation of H 2O 2 concentration in this environment. The proposed sensor is based on a platinum resistance thermometer coated with a layer of MnO 2 catalyst. It may be calibrated to operate either during the mist delivery step of a disinfection cycle, or during the evacuation (drying) phase. Cooling of the sensor surface due to evaporation of H 2O} and effervescence of decomposing H 2O 2 operates against heat generated by the decomposition reaction to produce a well-defined minimum in the temperature. The time and temperature at which this minimum occurs are well correlated, with the H 2O 2 content of the solution used to produce the mist droplets. © 2012 IEEE.

Post, V, Hamidian, M & Hall, RM 2012, 'Antibiotic-resistant Acinetobacter baumannii variants belonging to global clone 1', Journal of Antimicrobial Chemotherapy, vol. 67, no. 4, pp. 1039-1040.
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Poulton, CG, Movchan, AB, Movchan, NV & McPhedran, RC 2012, 'Analytic theory of defects in periodically structured elastic plates', Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 468, no. 2140, pp. 1196-1216.
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We consider the problem of localized flexural waves in thin plates that have periodic structure, consisting of a two-dimensional array of pins or point masses. Changing the properties of the structure at a single point results in a localized mode within the band-gap that is confined to the vicinity of the defect, while changing the properties along an entire line of points results in a waveguide mode. We develop here an analytic theory of these modes and provide semi-analytic expressions for the eigenfrequencies and fields of the point defect states, as well as the dispersion curves of the defect waveguide modes. The theory is based on a derivation of Green's function for the structure, which we present here for the first time. We also consider defects in finite arrays of point masses, and demonstrate the connection between the finite and infinite systems.

Poulton, CG, Pant, R, Byrnes, A, Fan, S, Steel, MJ & Eggleton, BJ 2012, 'Design for broadband on-chip isolator using stimulated Brillouin scattering in dispersion-engineered chalcogenide waveguides', OPTICS EXPRESS, vol. 20, no. 19, pp. 21235-21246.
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We propose a scheme for on-chip isolation in chalcogenide (As 2S3) rib waveguides, in which Stimulated Brillouin Scattering is used to induce non-reciprocal mode conversion within a multi-moded waveguide. The design exploits the idea that a chalcogenide rib buried in a silica matrix acts as waveguide for both light and sound, and can also be designed to be multi-moded for both optical and acoustic waves. The enhanced opto-acoustic coupling allows significant isolation (> 20 dB) within a chip-scale (cm-long) device (< 10 cm). We also show that the bandwidth of this device can be dramatically increased by tuning the dispersion of the waveguide to match the group velocity between optical modes: we find that 20 dB isolation can be extended over a bandwidth of 25 nm. © 2012 Optical Society of America.

Prieto-García, A, Zheng, D, Adachi, R, Xing, W, Lane, WS, Chung, K, Anderson, P, Hansbro, PM, Castells, M & Stevens, RL 2012, 'Mast Cell Restricted Mouse and Human Tryptase·Heparin Complexes Hinder Thrombin-induced Coagulation of Plasma and the Generation of Fibrin by Proteolytically Destroying Fibrinogen', Journal of Biological Chemistry, vol. 287, no. 11, pp. 7834-7844.
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Puill-Stephan, E, Willis, BL, Abrego, D, Raina, J-B & van Oppen, MJH 2012, 'Allorecognition maturation in the broadcast-spawning coral Acropora millepora', Coral Reefs, vol. 31, no. 4, pp. 1019-1028.
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Many sessile marine invertebrates discriminate self from non-self with great precision, but maturation of allorecognition generally takes months to develop in juveniles. Here, we compare the development of allorecognition in full-sibling, half-sibling and non-sibling contact reactions between newly settled juveniles of the broadcast-spawning coral Acropora millepora on the Great Barrier Reef (Australia). Absence of a rejection response showed that A. millepora lacks a mature allorecognition system in the first 2 months post-settlement. From thereon, incompatibilities were observed between juveniles, their level of relatedness (i.e. full-, half- and non-sibling status) governing the rate of allorecognition maturation. All contact reactions between non-siblings resulted in rejections by 3 months post-settlement, whereas the expression of allorecognition took at least 5 months between half-siblings and longer than 13 months for some full-siblings. Approximately 74 % of fused full-siblings ( n = 19) persisted as chimeras at 11 months, thus maturation of allorecognition in this spawning coral appeared to be slower (>13 months) than in brooding corals (~4 months). We hypothesize that late maturation of allorecognition may contribute to flexibility in Symbiodinium uptake in corals with horizontal transmission, and could allow fusions and chimera formation in early ontogeny, which potentially enable rapid size increase through fusion

R. Doddareddy, M, Rawling, T & J. Ammit, A 2012, 'Targeting Mitogen-Activated Protein Kinase Phosphatase-1 (MKP-1): Structure-Based Design of MKP-1 Inhibitors and Upregulators', Current Medicinal Chemistry, vol. 19, no. 2, pp. 163-173.
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Mitogen-activated protein kinase phosphatases (MKPs) are dual specificity protein phosphatases (DUSPs) that dephosphorylate both phospho-tyrosine and phospho-threonine residues on mitogen-activated protein kinases (MAPKs). Because the MAPK family of signalling molecules (phospho-p38 MAPK, c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK)) play essential roles in cell signalling pathways that regulate cell growth and inflammation, controlling MAPK-mediated pathways is a therapeutically attractive strategy. While small molecule MAPK inhibitors have utility, in this review we will focus on exploring the potential of targeting the endogenous MAPK deactivator--MKP-1. Importantly, there is a strong justification for developing both inhibitors and upregulators of MKP-1 because of the diverse roles played by MAPKs in disease: for example, in cancer, MKP-1 inhibitors may prove beneficial, as MKP-1 is overexpressed and is considered responsible for the failure of JNK-driven apoptotic pathways induced by chemotherapeutics; conversely, in inflammatory diseases such as asthma and arthritis, MKP-1 reduces MAPK-mediated signalling and developing novel ligands to upregulate MKP-1 levels would be a therapeutically attractive anti-inflammatory strategy. Thus, in this review we utilise MKP-1 homology modeling to highlight the structural features of MKP-1 inhibitors that permit potent and selective inhibition, and to provide insights into the structural requirements for selective MKP-1 upregulators.

Rahman, MA, Hasegawa, H & Lim, RP 2012, 'Bioaccumulation, biotransformation and trophic transfer of arsenic in the aquatic food chain', ENVIRONMENTAL RESEARCH, vol. 116, pp. 118-135.
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The occurrence, distribution, speciation, and biotransformation of arsenic in aquatic environment (marine and freshwater) have been studied extensively by several research groups during last couple of decades. However, most of those studies have been conducted in marine waters, and the results are available in a number of reviews. Speciation, bioaccumulation, and biotransformation of arsenic in freshwaters have been studied in recent years. Although inorganic arsenic (iAs) species dominates in both marine and freshwaters, it is biotransformed to methyl and organoarsenic species by aquatic organisms. Phytoplankton is considered as a major food source for the organisms of higher trophic levels in the aquatic food chain, and this autotrophic organism plays important role in biotransformation and distribution of arsenic species in the aquatic environment. Bioaccumulation and biotransformation of arsenic by phytoplankton, and trophic transfer of arsenic in marine and freshwater food chains have been important concerns because of possible human health effects of the toxic metalloid from dietary intake. To-date, most of the studies on arsenic biotransformation, speciation, and trophic transfer have focused on marine environments; little is known about these processes in freshwater systems. This article has been reviewed the bioaccumulation, biotransformation, and trophic transfer of arsenic in marine and freshwater food chain. © 2012 Elsevier Inc.

Ramelow, S, Fedrizzi, A, Poppe, A, Langford, NK & Zeilinger, A 2012, 'Polarization-entanglement-conserving frequency conversion of photons', Physical Review A, vol. 85, no. 1.
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Ranjbartoreh, AR & Wang, G 2012, 'Consideration of Bending and Buckling Behaviors of Monolayer and Multilayer Graphene Sheets', Journal of Nanoscience and Nanotechnology, vol. 12, no. 2, pp. 1395-1397.
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Graphene is a two-dimensional carbon based material. Remarkable mechanical, thermal and electrical properties of graphene make it as promising material for advanced applications; nevertheless, majority of its mechanical properties are still unknown. This research investigates buckling and bending behaviors of monolayer and multilayer armchair and zigzag graphene sheets. Bending stiffness, critical buckling force per unit length and critical strain of graphene sheets have been measured by molecular dynamic simulation method. Zigzag graphene sheet shows higher bending stiffness than armchair sheet. Van der Waals interaction between graphene sheets has an improving effect on the stability of middle layers. Cross-linkages reduce the buckling force per unit length and the buckling strain of multi layer graphene sheets. Copyright © 2012 American Scientific Publishers.

Ranjbartoreh, AR & Wang, G 2012, 'Practical Molecular Dynamic Simulation of Monolayer Graphene with Consideration of Structural Defects', Journal of Nanoscience and Nanotechnology, vol. 12, no. 2, pp. 1398-1401.
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Molecular dynamic simulation method has been employed to consider the mechanical properties of pristine and defected armchair and zigzag monolayer graphene sheets under tension and compression. Effects of Stone Wales (SW), Cell deformed (CD) and cell vacancy (CV) defects on ultimate stress and strain of graphene sheets have been considered. Obtained results indicate that zigzag graphene sheet has higher elastic modulus and stiffness than armchair type. Three SW defects have the highest destructive effect on ultimate stress and strain of zigzag graphene sheet while CV defect reveals the highest reducing effect on those of armchair type. Copyright © 2012 American Scientific Publishers.

Ranjbartoreh, AR, Su, D & Wang, G 2012, 'Consideration of Critical Axial Properties of Pristine and Defected Carbon Nanotubes Under Compression', JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, vol. 12, no. 6, pp. 5025-5029.
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Carbon nanotubes are hexagonally configured carbon atoms in cylindrical structures. Exceptionally igh mechanical strength, electrical conductivity, surface area, thermal stability and optical transparency of carbon nanotubes outperformed other known materials in numerous advanced applications. However, their mechanical behaviors under practical loading conditions remain to be demonstrated. This study investigates the critical axial properties of pristine and defected single-and multi-walled carbon nanotubes under axial compression. Molecular dynamics simulation method has been employed to consider the destructive effects of Stone-Wales and atom vacancy defects on mechanical properties of armchair and zigzag carbon nanotubes under compressive loading condition. Armchair carbon nanotube shows higher axial stability than zigzag type. Increase in wall number leads to less susceptibility of multi-walled carbon nanotubes to defects and higher stability of them under axial compression. Atom vacancy defect reveals higher destructive effect than Stone-Wales defect on mechanical properties of carbon nanotubes. Critical axial strain of single-walled arbon nanotube declines by 67% and 26% due to atom vacancy and Stone-Wales defects. Copyright © 2012 American Scientific Publishers. All rights reserved.

Raviraj, V, Zhang, H, Chien, H-Y, Cole, L, Thompson, EW & Soon, L 2012, 'Dormant but migratory tumour cells in desmoplastic stroma of invasive ductal carcinomas', Clinical & Experimental Metastasis, vol. 29, no. 3, pp. 273-292.
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Rawling, T, McDonagh, AM, Tattam, B & Murray, M 2012, 'Synthesis of unsymmetrical biaryl ureas from N-carbamoylimidazoles: kinetics and application', Tetrahedron, vol. 68, no. 30, pp. 6065-6070.
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N-Carbamoylimidazoles dissociate in solution to yield imidazole and an isocyanate that may be reacted with another aryl amine to form an unsymmetrical biaryl urea. This paper investigates the reaction kinetics and the influence of electron withdrawing/do

Reid, S, Johnson, L, Woodland, N & Marks, DC 2012, 'Pathogen reduction treatment of buffy coat platelet concentrates in additive solution induces proapoptotic signaling', TRANSFUSION, vol. 52, no. 10, pp. 2094-2103.
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BACKGROUND: Pathogen reduction technology (PRT) can potentially reduce the risk of transfusion-transmitted infections. However, PRT treatment of platelet (PLT) concentrates also results in reduced PLT quality and increased markers of apoptosis during storage. The aim of this study was to investigate changes to the expression and activation of proteins involved in apoptosis signaling. STUDY DESIGN AND METHODS: Samples from riboflavin and ultraviolet light PRT-treated and untreated (control) buffy coat-derived PCs in 70% SSP+ and 30% plasma were taken on Days 1, 5, and 7 of storage. Phosphatidylserine (PS) exposure, expression of Bcl-2 family proteins, cytochrome c release, and cleavage of caspase-3 and caspase-3 substrates were analyzed using flow cytometry and Western blotting. RESULTS: Compared to untreated controls, markers of apoptosis signaling were increased after PRT and subsequent storage. PS exposure on the PLT outer membrane was significantly higher after PRT on Days 5 and 7 of storage (p < 0.05). Expression of proapoptotic Bak and Bax was higher after PRT and subsequent storage. Cytochrome c release and caspase-3 cleavage were also greater and occurred earlier in the PRT-treated PLTs. The cleavage of caspase-3 substrates gelsolin and ROCK I were also increased after PRT, compared to untreated controls. CONCLUSIONS: This study demonstrated an increase in proapoptotic signaling during PLT storage, which was exacerbated by PRT. Many of these differences emerged outside the current 5-day storage period. These changes may not currently influence PLT transfusion quality, but will need to be carefully evaluated when considering extending PLT storage beyond 5 days. © 2012 American Association of Blood Banks.

Reim, KF, Nunn, J, Jin, X-M, Michelberger, PS, Champion, TFM, England, DG, Lee, KC, Kolthammer, WS, Langford, NK & Walmsley, IA 2012, 'Multipulse Addressing of a Raman Quantum Memory: Configurable Beam Splitting and Efficient Readout', Physical Review Letters, vol. 108, no. 26.
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Reimers, JR & Cai, Z-L 2012, 'Hydrogen bonding and reactivity of water to azines in their S-1 (n,pi*) electronic excited states in the gas phase and in solution', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 14, no. 25, pp. 8791-8802.
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A unified picture is presented of water interacting with pyridine, pyridazine, pyrimidine, and pyrazine on the S 1 manifold in both gas-phase dimers and in aqueous solution. As (n,π*) excitation to the S 1 state removes electrons from the ground-state hydrogen bond, this analysis provides fundamental understanding of excited-state hydrogen bonding. Traditional interpretations view the excitation as simply breaking hydrogen bonds to form dissociated molecular products, but reactive processes such as photohydrolysis and excited-state proton coupled electron transfer (PCET) are also possible. Here we review studies performed using equations-of-motion coupled-cluster theory (EOM-CCSD), multireference perturbation theory (CASPT2), time-dependent density-functional theory (TD-DFT), and excited-state Monte Carlo liquid simulations, adding new results from symmetry-adapted-cluster configuration interaction (SAC-CI) and TD-DFT calculations. Invariably, gas-phase molecular dimers are identified as stable local minima on the S 1 surface with energies less than those for dissociated molecular products. Lower-energy biradical PCET minima are also identified that could lead to ground-state recombination and hence molecular dissociation, dissociation into radicals or ions, or hydration reactions leading to ring cleavage. For pyridine.water, the calculated barriers to PCET are low, suggesting that this mechanism is responsible for fluorescence quenching of pyridine.water at low energies rather than accepted higher-energy Dewar-benzene based 'channel three' process. Owing to (n,π*) excitation localization, much higher reaction barriers are predicted for the diazines, facilitating fluorescence in aqueous solution and predicting that the as yet unobserved fluorescence from pyridazine.water and pyrimidine.water should be observable. Liquid simulations based on the assumption that the solvent equilibrates on the fluorescence timescale quantitatively reproduce the observed s...

Rice, SA, van den Akker, B, Pomati, F & Roser, D 2012, 'A risk assessment of Pseudomonas aeruginosa in swimming pools: a review', Journal of Water and Health, vol. 10, no. 2, pp. 181-196.
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Despite routine monitoring and disinfection, treated swimming pools are frequently contaminated with the opportunistic pathogen Pseudomonas aeruginosa, which can represent a significant public health threat. This review was undertaken to identify the current understanding of risk factors associated with pool operation with respect to P. aeruginosa. The ecology and factors that promote growth of P. aeruginosa in the pool environment are complex and dynamic and so we applied a systematic risk assessment approach to integrate existing data, with the aim to improve pool management and safety. Sources of P. aeruginosa, types of infections, dose responses, routes of transmission, as well as the efficacy of current disinfectant treatments were reviewed. This review also highlights the critical knowledge gaps that are required for a more robust, quantitative risk assessment of P. aeruginosa. Quantitative risk management strategies have been successfully applied to drinking water systems and should similarly be amenable to developing a better understanding of the risk posed by P. aeruginosa in swimming pools.

Richman, MB & Leslie, LM 2012, 'Adaptive Machine Learning Approaches to Seasonal Prediction of Tropical Cyclones', Procedia Computer Science, vol. 12, pp. 276-281.
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Tropical cyclones (TCs) are devastating phenomena that cause loss of life and catastrophic damage, owing to destructive winds, flooding rains and coastal inundation from storm surges. Accurate seasonal predictions of TC frequency and intensity are required, with a lead-time appropriate for preemptive action. Current schemes rely on linear statistics to generate forecasts of the TC activity for an upcoming season. Such techniques employ a suite of intercorrelated predictors; however, the relationships between predictors and TCs violate assumptions of standard prediction techniques. We extend tradition linear approaches, implementing support vector regression (SVR) models. Multiple linear regression (MLR) is used to create a baseline to assess SVR performance. Nine predictors for each calendar month (108 total) were inputs to MLR. MLR equations were unstable, owing to collinearity, requiring variable selection. Stepwise multiple regression was used to select a subset of three attributes adaptive to specific climatological variability. The R2 for the MLR testing data was 0.182. The SVR model used the same predictors with a radial basis function kernel to extend the traditional linear approach. Results of that model had an R2 of 0.255 (∼ 40% improvement over linear model). Refinement of the SVR to include the Quasi-Biennial Oscillation (QBO) improved the SVR predictions dramatically with an R2 of 0.564 (∼ 121% improvement over SVR without QBO). © 2012 Published by Elsevier B.V.

Ritchie, LE, Carroll, R, Weeks, B, Rooney, L & Turner, ND 2012, 'Novel sorghum brans containing bioactive compounds alter the production of microbial secondary metabolites in response to a DSS‐induced chronic inflammatory state', The FASEB Journal, vol. 26, no. S1.
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We have shown that black bran containing bioactives reduces colonic injury and NF‐κB activity with chronic inflammation, which may result from altered microbiota and short chain fatty acids (SCFA e.g., butyrate). Rats (n=80) were fed diets with 6% fiber from cellulose (C), or bran from black (B), sumac (S), or high tannin (HT) sorghum (anthocyanins, condensed tannins, or both, respectively). Ten rats in each diet received 3% dextran sulfate sodium (DSS) three times to stimulate inflammation. Feces were collected pre and post DSS to assess SCFA. On day 63, colon tissue was collected to determine injury and gene expression. After DSS, butyrate concentrations were higher (p<0.0001) with C and B (19.7 and 22.6) compared to S and HT (8.5 and 14.1). SCFA transporter (MCT1 and Slc5a8) expression was upregulated in C, S or HT DSS rats (avg 35, 48, and 12%) and downregulated in B DSS rats (avg 18%) compared to controls. In DSS rats, butyrate excretion, as a percent of total SCFA, was elevated with B (23%) compared to C, S or HT (19, 9, 15%). Thus, with chronic inflammation, there was an inverse relationship between the direction of transporter expression change and butyrate excretion. To determine the implications of the diet effects on butyrate and SCFA transporter levels in chronic inflammation, it will be necessary to evaluate proliferation and apoptosis. Funding: United Sorghum Checkoff Board Roo31A‐09.

Ritchie, RJ & Larkum, AWD 2012, 'Modelling photosynthesis in shallow algal production ponds', PHOTOSYNTHETICA, vol. 50, no. 4, pp. 481-500.
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Shallow ponds with rapidly photosynthesising cyanobacteria or eukaryotic algae are used for growing biotechnology feedstock and have been proposed for biofuel production but a credible model to predict the productivity of a column of phytoplankton in suc

Robinson, MW, Alvarado, R, To, J, Hutchinson, AT, Dowdell, SN, Lund, M, Turnbull, L, Whitchurch, CB, O'Brien, BA, Dalton, JP & Donnelly, S 2012, 'A helminth cathelicidin-like protein suppresses antigen processing and presentation in macrophages via inhibition of lysosomal vATPase', FASEB JOURNAL, vol. 26, no. 11, pp. 4614-4627.
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We previously reported the identification of a novel family of immunomodulatory proteins, termed helminth defense molecules (HDMs), that are secreted by medically important trematode parasites. Since HDMs share biochemical, structural, and functional characteristics with mammalian cathelicidin-like host defense peptides (HDPs), we proposed that HDMs modulate the immune response via molecular mimicry of host molecules. In the present study, we report the mechanism by which HDMs influence the function of macrophages. We show that the HDM secreted by Fasciola hepatica (FhHDM-1) binds to macrophage plasma membrane lipid rafts via selective interaction with phospholipids and/or cholesterol before being internalized by endocytosis. Following internalization, FhHDM-1 is rapidly processed by lysosomal cathepsin L to release a short C-terminal peptide (containing a conserved amphipathic helix that is a key to HDM function), which then prevents the acidification of the endolysosomal compartments by inhibiting vacuolar ATPase activity. The resulting endolysosomal alkalization impedes macrophage antigen processing and prevents the transport of peptides to the cell surface in conjunction with MHC class II for presentation to CD4+ T cells. Thus, we have elucidated a novel mechanism by which helminth pathogens alter innate immune cell function to assist their survival in the host.

Robinson, MW, Hutchinson, AT & Donnelly, S 2012, 'Antimicrobial peptides: utility players in innate immunity', FRONTIERS IN IMMUNOLOGY, vol. 3, no. OCT.
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Roczen, M, Schade, M, Malguth, E, Callsen, G, Barthel, T, Gref, O, Toefflinger, JA, Schoepke, A, Schmidt, M, Leipner, HS, Ruske, F, Phillips, MR, Hoffmann, A, Korte, L & Rech, B 2012, 'Structural investigations of silicon nanostructures grown by self-organized island formation for photovoltaic applications', APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING, vol. 108, no. 3, pp. 719-726.
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The self-organized growth of crystalline silicon nanodots and their structural characteristics are investigated. For the nanodot synthesis, thin amorphous silicon (a-Si) layers with different thicknesses have been deposited onto the ultrathin (2 nm) oxidized (111) surface of Si wafers by electron beam evaporation under ultrahigh vacuum conditions. The solid phase crystallization of the initial layer is induced by a subsequent in situ annealing step at 700°C, which leads to the dewetting of the initial a-Si layer. This process results in the self-organized formation of highly crystalline Si nanodot islands. Scanning electron microscopy confirms that size, shape, and planar distribution of the nanodots depend on the thickness of the initial a-Si layer. Cross-sectional investigations reveal a single-crystalline structure of the nanodots. This characteristic is observed as long as the thickness of the initial a-Si layer remains under a certain threshold triggering coalescence. The underlying ultra-thin oxide is not structurally affected by the dewetting process. Furthermore, a method for the fabrication of close-packed stacks of nanodots is presented, in which each nanodot is covered by a 2 nm thick SiO 2 shell. The chemical composition of these ensembles exhibits an abrupt Si/SiO 2 interface with a low amount of suboxides. A minority charge carrier lifetime of 18 μs inside of the nanodots is determined. © 2012 Springer-Verlag.

Rodgers, KJ & Jackson, CL 2012, 'Aneurysm prevention: keep the cat out of the bag', CARDIOVASCULAR RESEARCH, vol. 96, no. 3, pp. 350-351.
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Rodrigues, CDA & Harry, EJ 2012, 'The Min System and Nucleoid Occlusion Are Not Required for Identifying the Division Site in Bacillus subtilis but Ensure Its Efficient Utilization', PLoS Genetics, vol. 8, no. 3, pp. e1002561-e1002561.
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Precise temporal and spatial control of cell division is essential for progeny survival. The current general view is that precise positioning of the division site at midcell in rod-shaped bacteria is a result of the combined action of the Min system and nucleoid (chromosome) occlusion. Both systems prevent assembly of the cytokinetic Z ring at inappropriate places in the cell, restricting Z rings to the correct site at midcell. Here we show that in the bacterium Bacillus subtilis Z rings are positioned precisely at midcell in the complete absence of both these systems, revealing the existence of a mechanism independent of Min and nucleoid occlusion that identifies midcell in this organism. We further show that Z ring assembly at midcell is delayed in the absence of Min and Noc proteins, while at the same time FtsZ accumulates at other potential division sites. This suggests that a major role for Min and Noc is to ensure efficient utilization of the midcell division site by preventing Z ring assembly at potential division sites, including the cell poles. Our data lead us to propose a model in which spatial regulation of division in B. subtilis involves identification of the division site at midcell that requires Min and nucleoid occlusion to ensure efficient Z ring assembly there and only there, at the right time in the cell cycle. © 2012 Rodrigues, Harry.

Roelke, DL, Spatharis, S & Mitrovic, SM 2012, 'A new hydrology: effects on ecosystem form and functioning', Canadian Journal of Fisheries and Aquatic Sciences, vol. 69, no. 8, pp. 1377-1379.
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Water cycles are changing because of human population growth and climate change. Such changes will affect fundamental system-level characteristics that in turn will greatly influence ecosystem form and functioning. Here, a collection of papers is offered that furthers our understanding of cause and effect relationships between altered hydrology and various ecosystem properties. Combined, these papers address issues related to inflows, connectivity, and circulation and vertical mixing. In regards to altered inflows, this collection of papers addresses how seagrass bed communities, incidence of some haptophyte harmful algal blooms, and biodiversity of intermittently flowing streams might respond. These papers also address factors that influence connectivity in wetlands, and in the case of a lake and its neighboring wetland, how connectivity between systems can profoundly affect ecosystem form and functioning. Finally, the effects of altered circulation and vertical mixing are addressed as they relate to the spread of some cyanobacteria blooms to higher latitudes. The reader of this collection of papers gains a better appreciation of how ecosystem form and functioning is influenced by hydrologic processes and can conclude that there is a need for continued research in this area to better understand the impacts of human population growth and climate change.

Rong, Y, Qin, X, Jin, D, Lou, W, Wu, L, Wang, D, Wu, W, Ni, X, Mao, Z, Kuang, T, Zang, YQ & Qin, X 2012, 'A phase I pilot trial of MUC1-peptide-pulsed dendritic cells in the treatment of advanced pancreatic cancer', Clinical and Experimental Medicine, vol. 12, no. 3, pp. 173-180.
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Ronquist, F, Teslenko, M, van der Mark, P, Ayres, DL, Darling, A, Höhna, S, Larget, B, Liu, L, Suchard, MA & Huelsenbeck, JP 2012, 'MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space', Systematic Biology, vol. 61, no. 3, pp. 539-542.
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software. © 2012 The Author(s).

Roudnew, B, Seymour, JR, Jeffries, TC, Lavery, TJ, Smith, RJ & Mitchell, JG 2012, 'Bacterial and Virus-Like Particle Abundances in Purged and Unpurged Groundwater Depth Profiles', GROUND WATER MONITORING AND REMEDIATION, vol. 32, no. 4, pp. 72-77.
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Bacteria and viruses are ubiquitous in subterranean aquatic habitats. Bacterial abundance is known to vary with depth in aquifers; however, whether viral abundance varies with depth is less well known. Here we use flow cytometry (FCM) to enumerate bacteria and virus-like particles (VLP) from groundwater depth profiles. Groundwater samples were obtained from a set of nested piezometers from depths of 15, 30, 45, 60, 80, and 90?m and bacteria and VLP abundances were determined in purged aquifer water and unpurged water at each slot depth. Mean bacterial abundance (cells?/?mL) was not significantly different in unpurged water (3.2?×?105) compared to purged water (1.4?×?105); however, mean VLP abundance (particles?/?mL) was significantly greater in unpurged water (4.4?×?105) compared to purged water (2.3?×?105). Purged water was used to investigate the aquifer depth profile and bacterial and VLP abundances were observed to vary significantly between depths. The virus-bacteria ratio was determined and was observed to steadily increase with depth. Overall, our data indicate the dynamic nature of bacterial and viral abundances in subsurface environments which should be considered when designing groundwater microbial sampling methodologies.

Roux, C, Crispino, F & Ribaux, O 2012, 'From Forensics to Forensic Science', Current Issues in Criminal Justice, vol. 24, no. 1, pp. 7-24.
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Saerbeck, T, Klose, F, Le Brun, AP, Füzi, J, Brule, A, Nelson, A, Holt, SA & James, M 2012, 'Invited Article: Polarization “Down Under”: The polarized time-of-flight neutron reflectometer PLATYPUS', Review of Scientific Instruments, vol. 83, no. 8, pp. 081301-081301.
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This review presents the implementation and full characterization of the polarization equipment of the time-of-flight neutron reflectometer PLATYPUS at the Australian Nuclear Science and Technology Organisation (ANSTO). The functionality and efficiency of individual components are evaluated and found to maintain a high neutron beam polarization with a maximum of 99.3% through polarizing Fe/Si supermirrors. Neutron spin-flippers with efficiencies of 99.7% give full control over the incident and scattered neutron spin direction over the whole wavelength spectrum available in the instrument. The first scientific experiments illustrate data correction mechanisms for finite polarizations and reveal an extraordinarily high reproducibility for measuring magnetic thin film samples. The setup is now fully commissioned and available for users through the neutron beam proposal system of the Bragg Institute at ANSTO.

Salter, PS, Jesacher, A, Spring, JB, Metcalf, BJ, Thomas-Peter, N, Simmonds, RD, Langford, NK, Walmsley, IA & Booth, MJ 2012, 'Adaptive slit beam shaping for direct laser written waveguides', Optics Letters, vol. 37, no. 4, pp. 470-470.
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Sambrook, MR, Hiscock, JR, Cook, A, Green, AC, Holden, I, Vincent, JC & Gale, PA 2012, 'Hydrogen bond-mediated recognition of the chemical warfare agent soman (GD)', Chemical Communications, vol. 48, no. 45, pp. 5605-5605.
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Sastraruji, K, Sastraruji, T, Ung, AT, Griffith, R, Jatisatienr, A & Pyne, SG 2012, 'Synthesis of stemofoline analogues as acetylcholinesterase inhibitors', TETRAHEDRON, vol. 68, no. 35, pp. 7103-7115.
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Thirty-two new stemofoline analogues were prepared from didehydrostemofoline for studies as AChE inhibitors. C-3 Side-chain modified amino, carbamate, triazole and oxazole stemofoline derivatives were prepared. In general the amine derivatives were found to be stronger inhibitors of AChE than their alcohol analogues that we previously reported. Compounds 5 and 26, with small C-3 side-chain substituents, were two of the most active inhibitors. Preliminary molecular docking studies suggested that these compounds may inhibit AChE by binding horizontally along the passage of the active-site gorge and block access to acetylcholine.

Sastraruji, T, Pyne, SG & Ung, AT 2012, 'ChemInform Abstract: Oxidation of Acyclic Alkenes and Allyl and Benzyl Ethers with DIB/t‐BuOOH/Mg(OAc)₂.', ChemInform, vol. 43, no. 26, pp. no-no.
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AbstractThe ethers (VIII) and (XII) can be chemoselectively oxidized in the presence of a terminal alkene.

Sastraruji, T, Pyne, SG & Ung, AT 2012, 'Oxidation of acyclic alkenes and allyl and benzyl ethers with DIB/t-BuOOH/Mg(OAc)(2)', TETRAHEDRON, vol. 68, no. 2, pp. 598-602.
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Oxidation of (11Z)-1',2'-didehydrostemofoline with DIB/TBHP/Mg(OAc)(2)center dot 4H(2)O resulted in oxidative cleavage of the C-11-C-12 double bond instead of the desired allylic oxidation of the 1-butenyl side chain. Stemofoline gave a similar result. The oxidation of more simple terminal alkenes was regioselective and gave vinyl ketones while allyl and benzyl ethers gave acrylate and benzoate esters, respectively. Allyl and benzyl ethers could be chemoselectively oxidized in the presence of a terminal alkene or benzyl group. Oxidation of an internal alkene was poorly regioselective, in contrast to the oxidation of 1-substituted cyclohexenes.

Schartner, EP, Jin, D, Ebendorff-Heidepriem, H, Piper, JA, Lu, Z & Monro, TM 2012, 'Lanthanide upconversion within microstructured optical fibers: improved detection limits for sensing and the demonstration of a new tool for nanocrystal characterization', Nanoscale, vol. 4, no. 23, pp. 7448-7448.
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We investigate a powerful new sensing platform based on the excitation of upconversion luminescence from NaYF4:Yb/Er nanocrystals loaded in solution within a suspended-core microstructured optical fiber. We demonstrate a substantial improvement in the detection limit that can be achieved in a suspended-core fiber sensor for solution-based measurements using these nanocrystals as an alternative to more traditional fluorophores, with sensing of concentrations as low as 660 fM demonstrated compared with the 10 pM obtained using quantum dots. This nanocrystal loaded suspended core fiber platform also forms the basis for a novel and robust nanoscale spectrometry device capable of capturing power-dependent spectra over a large dynamic range from 103 W cm-2 to 106 W cm-2 using a laser diode. This serves as a useful tool to study the multiple energy levels of rare earth luminescent nano-materials, allowing the two sharp emission bands to be studied in detail over a large dynamic range of excitation powers. Thus, in addition to demonstrating a highly sensitive dip sensor, we have devised a powerful new approach for characterizing upconversion nanoparticles. © 2012 The Royal Society of Chemistry.

Scheurer, MS, Arnold, MD, Setiadi, J & Ford, MJ 2012, 'Damping of Plasmons of Closely Coupled Sphere Chains Due to Disordered Gaps', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 116, no. 1, pp. 1335-1343.
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The damping of plasmons due to structural disorder may have important practical consequences. Here, we use spherical harmonic expansions to quantify the damping of plasmons of ensembles of closely coupled sphere chains with moderately disordered gaps. We show that the quadratic shift of average resonance position due to disorder is maintained in the transition from weak to close coupling, but the sensitivity to disorder increases. Further, we find that although the main peak is most often damped and broadened by disorder, it is possible for the optical extinction of disordered gold chains to increase slightly due to red-skew into a region with more favorable metal properties. © 2011 American Chemical Society.

Schiek, R, Solntsev, AS & Neshev, DN 2012, 'Temporal dynamics of all-optical switching in quadratic nonlinear directional couplers', Applied Physics Letters, vol. 100, no. 11, pp. 111117-111117.
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We study the temporal dynamics of all-optical switching in nonlinear directional couplers in periodically poled lithium niobate. The characteristic features of such switching, including asymmetric pulse break-up and back-switching were measured in full agreement with the theoretical predictions. Based on the time-resolved measurement of intensity-dependent switching, finally the theoretically long-known continuous-wave switching curve has experimentally been confirmed.

Scott, NE, Nothaft, H, Edwards, AVG, Labbate, M, Djordjevic, SP, Larsen, MR, Szymanski, CM & Cordwell, SJ 2012, 'Modification of the Campylobacter jejuni N-Linked Glycan by EptC Protein-mediated Addition of Phosphoethanolamine', Journal of Biological Chemistry, vol. 287, no. 35, pp. 29384-29396.
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Campylobacter jejuni is the major worldwide cause of bacterial gastroenteritis. C. jejuni possesses an extensive repertoire of carbohydrate structures that decorate both protein and non-protein surface-exposed structures. An N-linked glycosylation system encoded by the pgl gene cluster mediates the synthesis of a rigidly conserved heptasaccharide that is attached to protein substrates or released as free oligosaccharide in the periplasm. Removal of N-glycosylation results in reduced virulence and impeded host cell attachment. Since the N-glycan is conserved, the N-glycosylation system is also an attractive option for glyco-engineering recombinant vaccines in Escherichia coli. To determine whether non-canonical N-glycans are present in C. jejuni, we utilized high throughput glycoproteomics to characterize C. jejuni JHH1and identified 93 glycosylation sites, including 34 not previously reported. Interrogation of these data allowed the identification of a phosphoethanolamine (pEtN)-modified variant of the N-glycan that was attached to multiple proteins. The pEtN moiety was attached to the terminal GalNAc of the canonical N-glycan. Deletion of the pEtN transferase eptC removed all evidence of the pEtN-glycan but did not globally influence protein reactivity to patient sera, whereas deletion of the pglB oligosaccharyltransferase significantly reduced reactivity. Transfer of eptC and the pgl gene cluster to E. coli confirmed the addition of the pEtN-glycan to a target C. jejuni protein. Significantly reduced, yet above background levels of pEtN-glycan were also observed in E. coli not expressing eptC, suggesting that endogenous E. coli pEtN transferases can mediate the addition of pEtN to N-glycans. The addition of pEtN must be considered in the context of glycoengineering and may alter C. jejuni glycan-mediated structure-function interactions. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.

Seymour, JR, Doblin, MA, Jeffries, TC, Brown, MV, Newton, K, Ralph, PJ, Baird, M & Mitchell, JG 2012, 'Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current', ENVIRONMENTAL MICROBIOLOGY REPORTS, vol. 4, no. 5, pp. 548-555.
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Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the samples, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to 'warm-water' ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Seymour, LM, Jenkins, C, Deutscher, AT, Raymond, BBA, Padula, MP, Tacchi, JL, Bogema, DR, Eamens, GJ, Woolley, LK, Dixon, NE, Walker, MJ & Djordjevic, SP 2012, 'Mhp182 (P102) binds fibronectin and contributes to the recruitment of plasmin(ogen) to the Mycoplasma hyopneumoniae cell surface', CELLULAR MICROBIOLOGY, vol. 14, no. 1, pp. 81-94.
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Mycoplasma hyopneumoniae is a major, economically damaging respiratory pathogen. Although M. hyopneumoniae cells bind plasminogen, the identification of plasminogen-binding surface proteins and the biological ramifications of acquiring plasminogen requires further investigation. mhp182 encodes a highly expressed 102kDa protein (P102) that undergoes proteolytic processing to generate surface-located N-terminal 60kDa (P60) and C-terminal 42kDa (P42) proteins of unknown function. We show that recombinant P102 (rP102) binds plasminogen at physiologically relevant concentrations (K D~76nM) increasing the susceptibility of plasmin(ogen) to activation by tissue-specific plasminogen activator (tPA). Recombinant proteins constructed to mimic P60 (rP60) and P42 (rP42) also bound plasminogen at physiologically significant levels. M. hyopneumoniae surface-bound plasminogen was activated by tPA and is able to degrade fibrinogen, demonstrating the biological functionality of M. hyopneumoniae-bound plasmin(ogen) upon activation. Plasmin(ogen) was readily detected in porcine ciliated airways and plasmin levels were consistently higher in bronchoalveolar lavage fluid from M. hyopneumoniae-infected animals. Additionally, rP102 and rP42 bind fibronectin with K Ds of 26 and 33nM respectively and recombinant P102 proteins promote adherence to porcine kidney epithelial-like cells. The multifunctional binding ability of P102 and activation of M. hyopneumoniae-sequestered plasmin(ogen) by an exogenous activator suggests P102 plays an important role in virulence. © 2011 Blackwell Publishing Ltd.

Shafer, CM, Mercer, AE, Richman, MB, Leslie, LM & Doswell, CA 2012, 'An Assessment of Areal Coverage of Severe Weather Parameters for Severe Weather Outbreak Diagnosis', Weather and Forecasting, vol. 27, no. 4, pp. 809-831.
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Abstract The areal extent of severe weather parameters favorable for significant severe weather is evaluated as a means of identifying major severe weather outbreaks. The first areal coverage method uses kernel density estimation (KDE) to identify severe weather outbreak locations. A selected severe weather parameter value is computed at each grid point within the region identified by KDE. The average, median, or sum value is used to diagnose the event’s severity. The second areal coverage method finds the largest contiguous region where a severe weather parameter exceeds a specified threshold that intersects the KDE region. The severe weather parameter values at grid points within the parameter exceedance region are computed, with the average, median, or sum value used to diagnose the event’s severity. A total of 4057 severe weather outbreaks from 1979 to 2008 are analyzed. An event is considered a major outbreak if it exceeds a selected ranking index score (developed in previous work), and is a minor event otherwise. The areal coverage method is also compared to Storm Prediction Center (SPC) day-1 convective outlooks from 2003 to 2008. Comparisons of the SPC forecasts and areal coverage diagnoses indicate the areal coverage methods have similar skill to SPC convective outlooks in discriminating major and minor severe weather outbreaks. Despite a seemingly large sample size, the rare-events nature of the dataset leads to sample size sensitivities. Nevertheless, the findings of this study suggest that areal coverage should be tested in a forecasting environment as a means of providing guidance in future outbreak scenarios.

Shi, X, Tong, Cao, Wen, Guo, Shen & Wang 2012, 'Enhancing the specificity and efficiency of polymerase chain reaction using polyethyleneimine-based derivatives and hybrid nanocomposites', International Journal of Nanomedicine, vol. 7, pp. 1069-1069.
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Shimoni, O, Postma, A, Yan, Y, Scott, AM, Heath, JK, Nice, EC, Zelikin, AN & Caruso, F 2012, 'Macromolecule Functionalization of Disulfide-Bonded Polymer Hydrogel Capsules and Cancer Cell Targeting', ACS Nano, vol. 6, no. 2, pp. 1463-1472.
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We present a generic and versatile method for functionalization of disulfide-stabilized PMA hydrogel capsules (HCs) with macromolecules, including a number of specific antibodies to cancer cells. Functionalization was achieved by reversible addition-fragmentation chain transfer (RAFT) polymerization of poly(N-vinyl pyrrolidone) (PVPON), which introduced biorelevant heterotelechelic end groups (thiol and amine) to the polymer chain. The PVPON with heterotelechelic end groups was conjugated to the outermost layer of PMA HCs through the thiol groups and reacted with biotin via the amine groups to generate PMA/PVPON biotin HCs. On the basis of the high specific interaction and high affinity between biotin and avidin, and its derivates, such as NeutrAvidin (NAv), we functionalized the PMA HCs with biotinylated antibodies. We demonstrate significantly enhanced cellular binding and internalization of the antibody (Ab)-functionalized capsules compared with control human immunoglobulin (IgG)-functionalized capsules, suggesting these capsules can specifically interact with cells through antibody/antigen recognition. We anticipate that the versatility of the functionalization approach reported in this study will assist in targeted therapeutic delivery applications. © 2012 American Chemical Society.

Shine, R, Webb, JK, Lane, A & Mason, RT 2012, 'Familiarity with a female does not affect a male's courtship intensity in garter snakes Thamnophis sirtalis parietalis', CURRENT ZOOLOGY, vol. 58, no. 6, pp. 805-811.
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In many animal species, males direct more intense courtship towards females they have not previously encountered, than towards females with which they have previously mated. To test the factors responsible for this 'Coolidge Effect', we need studies on a wide range of taxa-including those with mating systems in which we would not expect (based on current theory) that such an effect would be evident. The Coolidge Effect has been documented in several lizard species, but has not been looked for (and would not be expected) in snakes. We conducted experimental trials with red-sided garter snakes Thamnophis sirtalis pa-rietalis at a communal den in Manitoba, to see whether previous exposure to a female (either courting, or courting plus mating) modified male mate choice or courtship intensity. In keeping with prediction from theory (but contrary to an early anecdotal re-port), male garter snakes did not modify their courtship behaviour based upon their familiarity (or lack thereof) with a specific female. At least in large courting aggregations, male snakes may maximize their fitness by basing mate-choice upon immediate attributes of the female (body size, condition, mated status) and the intensity of competition (numbers and sizes of rival males) rather than information derived from previous sexual encounters. © 2012 Current Zoology.

Siboni, N, Abrego, D, Seneca, F, Motti, CA, Andreakis, N, Tebben, J, Blackall, LL & Harder, T 2012, 'Using Bacterial Extract along with Differential Gene Expression in Acropora millepora Larvae to Decouple the Processes of Attachment and Metamorphosis', PLOS ONE, vol. 7, no. 5.
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Siboni, N, Ben-Dov, E, Sivan, A & Kushmaro, A 2012, 'Geographic Specific Coral-Associated Ammonia-Oxidizing Archaea in the Northern Gulf of Eilat (Red Sea)', MICROBIAL ECOLOGY, vol. 64, no. 1, pp. 18-24.
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Simar, D, Chen, H, Lambert, K, Mercier, J & Morris, MJ 2012, 'Interaction between maternal obesity and post-natal over-nutrition on skeletal muscle metabolism', Nutrition, Metabolism and Cardiovascular Diseases, vol. 22, no. 3, pp. 269-276.
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Background and aims: Maternal obesity and post-natal over-nutrition play an important role in programming glucose and lipid metabolism later in life. The aim of this study was to decipher the contributions of maternal obesity and post-natal over-nutrition on glucose and lipid metabolism in skeletal muscle. Method and results: Male offspring of Sprague Dawley rat mothers fed either chow or high fat diet (HFD) for 5 weeks prior to mating were subsequently fed either chow or HFD until 18 weeks of age. Collection of plasma and skeletal muscle was performed at weaning (20 days) and 18 weeks. At weaning, offspring from obese mothers showed increased body weight, plasma insulin and lactate concentrations associated with reduced skeletal muscle glucose transporter 4 (GLUT4) and increased monocarboxylate transporter 1 (MCT1) protein. In 18-week old offspring, post-weaning HFD further exacerbated the elevated body weight caused by maternal obesity. Surprisingly this additive effect on body weight was not reflected in plasma glucose, insulin, lactate and MCT1; these markers were only increased by post-weaning HFD consumption. However, an additive effect of maternal obesity and post-weaning HFD led to decreased muscle GLUT4 levels, as well as mRNA levels of carnitine palmitoyl transferase-1, myogenic differentiation protein and myogenin. Conclusion: Post-weaning HFD exerted an additive effect to that of maternal obesity on body weight and skeletal muscle markers of glucose and lipid metabolism but not on plasma glucose and insulin levels, suggesting that maternal obesity and post-natal over-nutrition impair skeletal muscle function via different mechanisms. © 2010 Elsevier B.V.

Simpson, SL, Yverneau, H, Cremazy, A, Jarolimek, CV, Price, HL & Jolley, DF 2012, 'DGT-Induced Copper Flux Predicts Bioaccumulation and Toxicity to Bivalves in Sediments with Varying Properties', Environmental Science & Technology, vol. 46, no. 16, pp. 9038-9046.
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Sinetova, MA, Červený, J, Zavřel, T & Nedbal, L 2012, 'On the dynamics and constraints of batch culture growth of the cyanobacterium Cyanothece sp. ATCC 51142', Journal of Biotechnology, vol. 162, no. 1, pp. 148-155.
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Sinutok, S, Hill, R, Doblin, MA, Kuhl, M & Ralph, PJ 2012, 'Microenvironmental changes support evidence of photosynthesis and calcification inhibition in Halimeda under ocean acidification and warming', CORAL REEFS, vol. 31, no. 4, pp. 1201-1213.
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The effects of elevated CO 2 and temperature on photosynthesis and calcification of two important calcifying reef algae (Halimedamacroloba and Halimeda cylindracea) were investigated with O 2 microsensors and chlorophyll a fluorometry through a combination of two pCO 2 (400 and 1,200 µatm) and two temperature treatments (28 and 32 °C) equivalent to the present and predicted conditions during the 2100 austral summer. Combined exposure to pCO 2 and elevated temperature impaired calcification and photosynthesis in the two Halimeda species due to changes in the microenvironment around the algal segments and a reduction in physiological performance. There were no significant changes in controls over the 5-week experiment, but there was a 50-70 % decrease in photochemical efficiency (maximum quantum yield), a 70-80 % decrease in O 2 production and a threefold reduction in calcification rate in the elevated CO 2 and high temperature treatment. Calcification in these species is closely coupled with photosynthesis, such that a decrease in photosynthetic efficiency leads to a decrease in calcification. Although pH seems to be the main factor affecting Halimeda species, heat stress also has an impact on their photosystem II photochemical efficiency. There was a strong combined effect of elevated CO 2 and temperature in both species, where exposure to elevated CO 2 or temperature alone decreased photosynthesis and calcification, but exposure to both elevated CO 2 and temperature caused a greater decline in photosynthesis and calcification than in each stress individually. Our study shows that ocean acidification and ocean warming are drivers of calcification and photosynthesis inhibition in Halimeda. Predicted climate change scenarios for 2100 would therefore severely affect the fitness of Halimeda, which can result in a strongly reduced production of carbonate sediments on coral reefs under such changed climate conditions.

Skoog, K, Söderström, B, Widengren, J, von Heijne, G & Daley, DO 2012, 'Sequential Closure of the Cytoplasm and Then the Periplasm during Cell Division in Escherichia coli', Journal of Bacteriology, vol. 194, no. 3, pp. 584-586.
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ABSTRACT To visualize the latter stages of cell division in live Escherichia coli , we have carried out fluorescence recovery after photobleaching (FRAP) on 121 cells expressing cytoplasmic green fluorescent protein and periplasmic mCherry. Our data show conclusively that the cytoplasm is sealed prior to the periplasm during the division event.

Smale, DA, Barnes, DKA, Barnes, RSK, Smith, DJ & Suggett, DJ 2012, 'Spatial variability in the structure of intertidal crab and gastropod assemblages within the Seychelles Archipelago (Indian Ocean)', Journal of Sea Research, vol. 69, pp. 8-15.
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Tropical nearshore ecosystems represent global hotspots of marine biodiversity and endemism but are often poorly understood and impacted by human activities. The Seychelles Archipelago (Western Indian Ocean) sustains a wealth of marine life, much of which is threatened by rapid development associated with tourism and climate change. Six marine parks exist within the Archipelago, but their biodiversity value and ecological health are poorly known, especially with regards to non-fish and coral species. Here we investigate spatial patterns of littoral biodiversity on 6 islands, 5 of which were granitic and within marine parks, including the first surveys of Curieuse and Ile Cocos. Our surveys formed a nested sampling design, to facilitate an examination of variability in species richness, faunal abundance, taxonomic distinctness and assemblage composition at multiple spatial scales, from islands (>. 100. s. km) to quadrats (metres). We identified (mostly to species) and enumerated two target taxa, brachyuran decapod crustaceans and gastropod molluscs, and recorded over 8300 individuals belonging to over 150 species. Crabs and gastropods exhibited different patterns of spatial variability, as crab assemblages were generally more distinct between islands, while gastropod assemblages were markedly variable at the smallest spatial scales of 'patch' and 'quadrat'. Intertidal biodiversity was greatest on Curieuse Island and least at Desroches, the latter was being the only coral atoll we surveyed and thereby differing in its geological and ecological context. We discuss likely drivers of these biodiversity patterns and highlight urgently-needed research directions. Our assessment of the status of poorly-known invertebrate assemblages across the Seychelles will complement more extensive surveys of coral and fish assemblages and, in doing so, provide a useful baseline for monitoring the effects of key stressors in the region, such as coastal development and climat...

Smith, GB 2012, 'Green nanophotonics', JOURNAL OF NANOPHOTONICS, vol. 6, no. 1, pp. 1-19.
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Nanotechnology, in particular nanophotonics, is proving essential to achieving green outcomes of sustainability and renewable energy at the production scales needed. Nanomaterials enable optimization of optical, opto-electrical, and thermal responses. Optical harmonization of material responses to environmental energy flows involves large changes in spectral response over limited wavelength bands and 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 economical and have 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 advantages have arisen in this work such as the savings and environmental benefits of cool roofs extending beyond the more obvious benefit of reduced heat flows from the roof into the building. We explore some of the likely elements involved in harmonizing nature and technology with applications of nanophotonics to reduce the use of energy in buildings. © 2012 Society of Photo-Optical Instrumentation Engineers.

Smith, GB, Aguilar, JLC, Gentle, AR & Chen, D 2012, 'Multi-parameter sensitivity analysis: A design methodology applied to energy efficiency in temperate climate houses', ENERGY AND BUILDINGS, vol. 55, pp. 668-673.
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Quantified sensitivities of heating and cooling loads to different variables that influence heat gain and loss in a building provides a valuable basis for energy efficient design, especially in temperate climate zones where particular parameter settings

Smith, MJA, McPhedran, RC, Poulton, CG & Meylan, MH 2012, 'Negative refraction and dispersion phenomena in platonic clusters', Waves in Random and Complex Media, vol. 22, no. 4, pp. 435-458.
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We consider the problem of Gaussian beam scattering by finite arrays of pinned points, or platonic clusters, in a thin elastic plate governed by the biharmonic plate equation. Integral representations for Gaussian incident beams are constructed and numerically evaluated to demonstrate the different behaviours exhibited by these finite arrays. We show that it is possible to extend the scattering theory from infinite arrays of pinned points to these finite crystals, which exhibit the predicted behaviour well. Analytical expressions for the photonic superprism parameters p, q and r, which are measures for dispersion inside the crystal, are also derived for the pinned plate problem here. We demonstrate the existence of negative refraction, beam splitting, Rayleigh anomalies, internal reflection, and near-trapping on the first band surface, giving examples for each of these behaviours. © 2012 Taylor and Francis Group, LLC.

Smith, RJ, Jeffries, TC, Roudnew, B, Fitch, AJ, Seymour, JR, Delpin, MW, Newton, K, Brown, MH & Mitchell, JG 2012, 'Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems', ENVIRONMENTAL MICROBIOLOGY, vol. 14, no. 1, pp. 240-253.
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A metagenomic analysis of two aquifer systems located under a dairy farming region was performed to examine to what extent the composition and function of microbial communities varies between confined and surface-influenced unconfined groundwater ecosystems. A fundamental shift in taxa was seen with an overrepresentation of Rhodospirillales, Rhodocyclales, Chlorobia and Circovirus in the unconfined aquifer, while Deltaproteobacteria and Clostridiales were overrepresented in the confined aquifer. A relative overrepresentation of metabolic processes including antibiotic resistance (beta-lactamase genes), lactose and glucose utilization and DNA replication were observed in the unconfined aquifer, while flagella production, phosphate metabolism and starch uptake pathways were all overrepresented in the confined aquifer. These differences were likely driven by differences in the nutrient status and extent of exposure to contaminants of the two groundwater systems. However, when compared with freshwater, ocean, sediment and animal gut metagenomes, the unconfined and confined aquifers were taxonomically and metabolically more similar to each other than to any other environment. This suggests that intrinsic features of groundwater ecosystems, including low oxygen levels and a lack of sunlight, have provided specific niches for evolution to create unique microbial communities. Obtaining a broader understanding of the structure and function of microbial communities inhabiting different groundwater systems is particularly important given the increased need for managing groundwater reserves of potable water.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 2012, 'Spontaneous Parametric Down-Conversion and Quantum Walks in Arrays of Quadratic Nonlinear Waveguides', Physical Review Letters, vol. 108, no. 2.
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Song, Z, Anissimov, YG, Zhao, J, Nechaev, AV, Nadort, A, Jin, D, Prow, TW, Roberts, MS & Zvyagin, AV 2012, 'Background free imaging of upconversion nanoparticle distribution in human skin', Journal of Biomedical Optics, vol. 18, no. 6, pp. 061215-061215.
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Widespread applications of nanotechnology materials have raised safety concerns due to their possible penetration through skin and concomitant uptake in the organism. This calls for systematic study of nanoparticle transport kinetics in skin, where high-resolution optical imaging approaches are often preferred. We report on application of emerging luminescence nanomaterial, called upconversion nanoparticles (UCNPs), to optical imaging in skin that results in complete suppression of background due to the excitation light back-scattering and biological tissue autofluorescence. Freshly excised intact and microneedle-treated human skin samples were topically coated with oil formulation of UCNPs and optically imaged. In the first case, 8-and 32-nm UCNPs stayed at the topmost layer of the intact skin, stratum corneum. In the second case, 8-nm nanoparticles were found localized at indentations made by the microneedle spreading in dermis very slowly (estimated diffusion coefficient, Dnp=3-7×10-12 cm2·s-1). The maximum possible UCNP-imaging contrast was attained by suppressing the background level to that of the electronic noise, which was estimated to be superior in comparison with the existing optical labels. © 2013 SPIE.

Stark, D, Roberts, T, Marriott, D, Harkness, J & Ellis, JT 2012, 'Detection and Transmission of Dientamoeba fragilis from Environmental and Household Samples', AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, vol. 86, no. 2, pp. 233-236.
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Dientamoeba fragilis is a commonly occurring pathogenic protozoan often detected at higher rates in stool samples than Giardia intestinalis. However, little is known about its life cycle and mode of transmission. A total of 210 environmental and household samples were examined for the presence of D. fragilis by culture and polymerase chain reaction. Of 100 environmental samples, D. fragilis was detected only in untreated sewage. In the household samples D. fragilis was detected in 30% of household contacts tested and was not detected in any domestic pets. This study provides evidence that environmental transmission of D. fragilis is unlikely and that pets played no role in transmission of the disease in this study. Direct transmission from infected persons is the most likely mode of transmission for D. fragilis. The study also highlights the need for household contacts to be screened, given the propensity of close contacts to become infected with the organism.

Starkey, MR, Kim, RY, Beckett, EL, Schilter, HC, Shim, D, Essilfie, A-T, Nguyen, DH, Beagley, KW, Mattes, J, Mackay, CR, Horvat, JC & Hansbro, PM 2012, 'Chlamydia muridarum Lung Infection in Infants Alters Hematopoietic Cells to Promote Allergic Airway Disease in Mice', PLoS ONE, vol. 7, no. 8, pp. e42588-e42588.
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Background: Viral and bacterial respiratory tract infections in early-life are linked to the development of allergic airway inflammation and asthma. However, the mechanisms involved are not well understood. We have previously shown that neonatal and infant, but not adult, chlamydial lung infections in mice permanently alter inflammatory phenotype and physiology to increase the severity of allergic airway disease by increasing lung interleukin (IL)-13 expression, mucus hyper-secretion and airway hyper-responsiveness. This occurred through different mechanisms with infection at different ages. Neonatal infection suppressed inflammatory responses but enhanced systemic dendritic cell:T-cell IL-13 release and induced permanent alterations in lung structure (i.e., increased the size of alveoli). Infant infection enhanced inflammatory responses but had no effect on lung structure. Here we investigated the role of hematopoietic cells in these processes using bone marrow chimera studies. Methodology/Principal Findings: Neonatal (<24-hours-old), infant (3-weeks-old) and adult (6-weeks-old) mice were infected with C. muridarum. Nine weeks after infection bone marrow was collected and transferred into recipient age-matched irradiated naïve mice. Allergic airway disease was induced (8 weeks after adoptive transfer) by sensitization and challenge with ovalbumin. Reconstitution of irradiated naïve mice with bone marrow from mice infected as neonates resulted in the suppression of the hallmark features of allergic airway disease including mucus hyper-secretion and airway hyper-responsiveness, which was associated with decreased IL-13 levels in the lung. In stark contrast, reconstitution with bone marrow from mice infected as infants increased the severity of allergic airway disease by increasing T helper type-2 cell cytokine release (IL-5 and IL-13), mucus hyper-secretion, airway hyper-responsiveness and IL-13 levels in the lung. Reconstitution with bone marrow from in...

Stelzer-Braid, S, Johal, H, Skilbeck, K, Steller, A, Alsubie, H, Tovey, E, Van Asperen, P, McKay, K & Rawlinson, WD 2012, 'Detection of viral and bacterial respiratory pathogens in patients with cystic fibrosis', Journal of Virological Methods, vol. 186, no. 1-2, pp. 109-112.
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Stocker, R & Seymour, JR 2012, 'Ecology and Physics of Bacterial Chemotaxis in the Ocean', MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, vol. 76, no. 4, pp. 792-812.
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Summary: Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as high performance compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean.

Stokes, HW, Martinez, E, Chowdhury, PR & Djordjevic, S 2012, 'Class 1 integron-associated spread of resistance regions in Pseudomonas aeruginosa: plasmid or chromosomal platforms?', JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, vol. 67, no. 7, pp. 1799-1800.
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Multidrug-resistant Pseudomonas aeruginosa infections are a growing clinical problem. Of particular concern is the range of b-lactamase genes associated with this species. If the spread of resistance is to be controlled, it is critical that researchers have a good understanding of the mechanisms by which resistance genes are spread. In the Enterobacteriaceae, the role of plasmids in the lateral gene transfer (LGT) of resistance is extensive. However, many clinical isolates of Gram-negative bacteria also commonly carry additional syntenic blocks of DNA as part of the chromosome that are lineage specific within a species and are known as genomic islands.

Stokes, N, Cortie, MB, Davis, TJ & McDonagh, AM 2012, 'Plasmon Resonances in V-Shaped Gold Nanostructures', PLASMONICS, vol. 7, no. 2, pp. 235-243.
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Using numerical simulations, we examine the change in plasmon resonance behavior in gold nanorod structures that have a V shape. The reduction in symmetry compared to linear rods causes two different longitudinal-type resonances to appear in a single structure, and the relative intensity and hybridization of these can be controlled by varying the angle of the arms of the 'V.' The resonances may also be selectively excited by controlling the polarization of the incident light, thereby providing a convenient way to control a nanoscale optical electric field using far-field parameters. For example, the wavelength at which a strong resonance occurs in the V-shaped structures studied can be switched between 630 and 900 nm by a 90° rotation of the polarization of the incident light. Due to the symmetry of the targets, there will be three types of special near-field location; a location at which the electric field intensity is enhanced by either resonance, a location at which the electric field intensity is enhanced by the 630 nm resonance but not by the 890 nm resonance, and a location at which the electric field intensity is enhanced by the 890 nm resonance but not by the 630 nm one. © 2011 Springer Science+Business Media, LLC.

Strauss, MP, Liew, ATF, Turnbull, L, Whitchurch, CB, Monahan, LG & Harry, EJ 2012, '3D-SIM Super Resolution Microscopy Reveals a Bead-Like Arrangement for FtsZ and the Division Machinery: Implications for Triggering Cytokinesis', PLOS BIOLOGY, vol. 10, no. 9, p. e1001389.
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FtsZ is a tubulin-like GTPase that is the major cytoskeletal protein in bacterial cell division. It polymerizes into a ring, called the Z ring, at the division site and acts as a scaffold to recruit other division proteins to this site as well as providing a contractile force for cytokinesis. To understand how FtsZ performs these functions, the in vivo architecture of the Z ring needs to be established, as well as how this structure constricts to enable cytokinesis. Conventional wide-field fluorescence microscopy depicts the Z ring as a continuous structure of uniform density. Here we use a form of super resolution microscopy, known as 3D-structured illumination microscopy (3D-SIM), to examine the architecture of the Z ring in cells of two Gram-positive organisms that have different cell shapes: the rod-shaped Bacillus subtilis and the coccoid Staphylococcus aureus. We show that in both organisms the Z ring is composed of a heterogeneous distribution of FtsZ. In addition, gaps of fluorescence were evident, which suggest that it is a discontinuous structure. Time-lapse studies using an advanced form of fast live 3D-SIM (Blaze) support a model of FtsZ localization within the Z ring that is dynamic and remains distributed in a heterogeneous manner. However, FtsZ dynamics alone do not trigger the constriction of the Z ring to allow cytokinesis. Lastly, we visualize other components of the divisome and show that they also adopt a bead-like localization pattern at the future division site. Our data lead us to propose that FtsZ guides the divisome to adopt a similar localization pattern to ensure Z ring constriction only proceeds following the assembly of a mature divisome. © 2012 Strauss et al.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, McPhedran, RC & de Sterke, CM 2012, 'Nanowire array photovoltaics: Radial disorder versus design for optimal efficiency', APPLIED PHYSICS LETTERS, vol. 101, no. 17, pp. 173902-1-173902-5.
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Solar cell designs based on disordered nanostructures tend to have higher efficiencies than structures with uniform absorbers, though the reason is poorly understood. To resolve this, we use a semi-analytic approach to determine the physical mechanism leading to enhanced efficiency in arrays containing nanowires with a variety of radii. We use our findings to systematically design arrays that outperform randomly composed structures. An ultimate efficiency of 23.75 is achieved with an array containing 30 silicon, an increase of almost 10 over a homogeneous film of equal thickness. © 2012 American Institute of Physics.

Su, D, Ford, M & Wang, G 2012, 'Mesoporous NiO crystals with dominantly exposed {110} reactive facets for ultrafast lithium storage', Scientific Reports, vol. 2, no. 1, p. 924.
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Faceted crystals with exposed highly reactive planes have attracted intensive investigations for applications such as hydrogen production, enhanced catalytic activity, and electrochemical energy storage and conversion. Herein, we report the synthesis of mesoporous NiO crystals with dominantly exposed {110} reactive facets by the thermal conversion of hexagonal Ni(OH)2 nanoplatelets. When applied as anode materials in lithium-ion batteries, mesoporous NiO crystals exhibit a high reversible lithium storage capacity of 700 mAh g-1 at 1 C rate in 100 cycles and an excellent cyclability. In particular, the dominantly exposed {110} reactive facets and mesoporous nanostructure of NiO crystals lead to ultrafast lithium storage, which mimics the high power delivery of supercapacitors.

Su, D, Horvat, J, Munroe, P, Ahn, H, Ranjbartoreh, AR & Wang, G 2012, 'ChemInform Abstract: Polyhedral Magnetite Nanocrystals with Multiple Facets: Facile Synthesis, Structural Modelling, Magnetic Properties and Application for High Capacity Lithium Storage.', ChemInform, vol. 43, no. 16, pp. no-no.
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AbstractPolyhedral Fe3O4 nanocrystals with multiple facets are hydrothermally synthesized from an aqueous solution of FeSO4, Fe(NO3)3, and LiOH (autoclave, 180 °C, 2 h).

Su, D, Horvat, J, Munroe, P, Ahn, H, Ranjbartoreh, AR & Wang, G 2012, 'Polyhedral Magnetite Nanocrystals with Multiple Facets: Facile Synthesis, Structural Modelling, Magnetic Properties and Application for High Capacity Lithium Storage', Chemistry – A European Journal, vol. 18, no. 2, pp. 488-497.
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AbstractPolyhedral magnetite nanocrystals with multiple facets were synthesised by a low temperature hydrothermal method. Atomistic simulation and calculations on surface attachment energy successfully predicted the polyhedral structure of magnetite nanocrystals with multiple facets. X‐ray diffraction, field emission scanning electron microscopy, and high resolution transmission microscopy confirmed the crystal structure of magnetite, which is consistent with the theoretical modelling. The magnetic property measurements show the superspin glass state of the polyhedral nanocrystals, which could originate from the nanometer size of individual single crystals. When applied as an anode material in lithium ion cells, magnetite nanocrystals demonstrated an outstanding electrochemical performance with a high lithium storage capacity, a satisfactory cyclability, and an excellent high rate capacity.

Su, D, Kim, H, Kim, W & Wang, G 2012, 'ChemInform Abstract: Mesoporous Nickel Oxide Nanowires: Hydrothermal Synthesis, Characterization and Applications for Lithium‐Ion Batteries and Supercapacitors with Superior Performance.', ChemInform, vol. 43, no. 38, pp. no-no.
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AbstractMesoporous NiO nanowires are prepared from aqueous solutions containing NiCl2, K2C2O4, and ethylene glycol (autoclave, 220 °C, 12 h).

Su, D, Kim, H, Kim, W & Wang, G 2012, 'Mesoporous Nickel Oxide Nanowires: Hydrothermal Synthesis, Characterisation and Applications for Lithium‐Ion Batteries and Supercapacitors with Superior Performance', Chemistry – A European Journal, vol. 18, no. 26, pp. 8224-8229.
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AbstractMesoporous nickel oxide nanowires were synthesized by a hydrothermal reaction and subsequent annealing at 400 °C. The porous one‐dimensional nanostructures were analysed by field‐emission SEM, high‐resolution TEM and N2 adsorption/desorption isotherm measurements. When applied as the anode material in lithium‐ion batteries, the as‐prepared mesoporous nickel oxide nanowires demonstrated outstanding electrochemical performance with high lithium storage capacity, satisfactory cyclability and an excellent rate capacity. They also exhibited a high specific capacitance of 348 F g−1 as electrodes in supercapacitors.

Su, D, Kim, H-S, Kim, W-S & Wang, G 2012, 'Synthesis of tuneable porous hematites (α-Fe2O3) for gas sensing and lithium storage in lithium ion batteries', Microporous and Mesoporous Materials, vol. 149, no. 1, pp. 36-45.
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Tuneable porous α-Fe2O3 materials were prepared by using a selective etching method. The structure and morphology of the as-prepared porous hematites have been systematically characterised by X-ray diffraction, field emission scanning electron microscope, and transmission electron microscope. We found that the pore size and pore volume can be controlled by adjusting the etching time during the synthesis process. The porous hematites have been applied for gas sensing and lithium storage in lithium ion cells. The porous α-Fe2O3 materials demonstrated a reversible lithium storage capacity of 1269 mAh/g. When used as a sensing material in gas sensors, porous α-Fe2O3 exhibited a superior sensitivity towards toxic and flammable gases. © 2011 Elsevier Inc. All rights reserved.

Suggett, DJ, Hall‐Spencer, JM, Rodolfo‐Metalpa, R, Boatman, TG, Payton, R, Tye Pettay, D, Johnson, VR, Warner, ME & Lawson, T 2012, 'Sea anemones may thrive in a high CO₂ world', Global Change Biology, vol. 18, no. 10, pp. 3015-3025.
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AbstractIncreased seawater pCO2, and in turn ‘ocean acidification’ (OA), is predicted to profoundly impact marine ecosystem diversity and function this century. Much research has already focussed on calcifying reef‐forming corals (Class: Anthozoa) that appear particularly susceptible to OA via reduced net calcification. However, here we show that OA‐like conditions can simultaneously enhance the ecological success of non‐calcifying anthozoans, which not only play key ecological and biogeochemical roles in present day benthic ecosystems but also represent a model organism should calcifying anthozoans exist as less calcified (soft‐bodied) forms in future oceans. Increased growth (abundance and size) of the sea anemone (Anemonia viridis) population was observed along a natural CO2 gradient at Vulcano, Italy. Both gross photosynthesis (PG) and respiration (R) increased with pCO2 indicating that the increased growth was, at least in part, fuelled by bottom up (CO2 stimulation) of metabolism. The increase of PG outweighed that of R and the genetic identity of the symbiotic microalgae (Symbiodinium spp.) remained unchanged (type A19) suggesting proximity to the vent site relieved CO2 limitation of the anemones' symbiotic microalgal population. Our observations of enhanced productivity with pCO2, which are consistent with previous reports for some calcifying corals, convey an increase in fitness that may enable non‐calcifying anthozoans to thrive in future environments, i.e. higher seawater pCO2. Understanding how CO2

Suggett, DJ, Kikuchi, RKP, Oliveira, MDM, Spanó, S, Carvalho, R & Smith, DJ 2012, 'Photobiology of corals from Brazil’s near-shore marginal reefs of Abrolhos', Marine Biology, vol. 159, no. 7, pp. 1461-1473.
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Coral communities were examined from highly turbid near-shore marginal reefs of Abrolhos (Brazil) to test a paradigm previously developed from observations in clear water reefs; specifically, that coral photobiological properties follow a highly conserved linear relationship with optical depth (ζ) via preferential 'non-photochemical' over 'photochemical' dissipation of absorbed light energy. PAM flourometry in situ was used to examine the photobiology of the most dominant coral species throughout the platform surfaces and bases of Abrolhos' characteristic 'chapeirões' reef framework; however, none of the species consistently adhered to the 'clear water paradigm'. PAM measurements further demonstrated that species conformed to two different strategies of non-photochemical energy dissipation: transient but relatively rapid for the two closely related endemic species (Mussismilia braziliensis and Mussismilia harttii) as opposed to more persistent for Montastrea cavernosa, Porites astreoides and Siderastrea stellata. Further experiments demonstrated that tolerance to anomalous stress amongst species did not correspond with the non-photochemical energy dissipation strategy present but was consistent with the relative dominance of species within the chapeirões coral communities. © 2012 Springer-Verlag.

Sun, B, Liu, H, Munroe, P, Ahn, H & Wang, G 2012, 'Nanocomposites of CoO and a mesoporous carbon (CMK-3) as a high performance cathode catalyst for lithium-oxygen batteries', NANO RESEARCH, vol. 5, no. 7, pp. 460-469.
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A nanocomposite of CoO and a mesoporous carbon (CMK-3) has been studied as a cathode catalyst for lithium-oxygen batteries in alkyl carbonate electrolytes. The morphology and structure of the as-prepared nanocomposite were characterized by field emission scanning electron microscopy, transmission electron microscopy and high resolution transmission electron microscopy. The electrochemical properties of the mesoporous CoO/CMK-3 nanocomposite as a cathode catalyst in lithium-oxygen batteries were studied using galvanostatic charge-discharge methods. The reaction products on the cathode were analyzed by Fourier transform infrared spectroscopy. The CoO/CMK-3 nanocomposite exhibited better capacity retention than bare mesoporous CMK-3 carbon, Super-P carbon or CoO/Super-P nanocomposite. The synergistic effects arising from the combination of CoO nanoparticles and the mesoporous carbon nanoarchitecture may be responsible for the optimum catalytic performance in lithium-oxygen batteries. © 2012 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

Sun, B, Wang, B, Su, D, Xiao, L, Ahn, H & Wang, G 2012, 'Graphene nanosheets as cathode catalysts for lithium-air batteries with an enhanced electrochemical performance', CARBON, vol. 50, no. 2, pp. 727-733.
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Graphene nanosheets have been investigated as cathode catalysts for lithium-air batteries with alkyl carbonate electrolyte. Field emission scanning electron microscopy, transmission electron microscope and Raman spectroscopy have confirmed the high quality of the as-prepared graphene nanosheets and the surface analysis has identified the mesoporous characteristic of graphene nanosheets. The electrochemical properties of graphene nanosheets as cathode catalysts in lithium-air batteries were evaluated by a galvanostatic charge/discharge testing. The reaction products on the graphene nanosheets cathode were analyzed by X-ray diffraction and Fourier transform infrared spectroscopy. The graphene nanosheet electrodes exhibited a much better cycling stability and lower overpotential than that of the Vulcan XC-72 carbon. This work demonstrated that graphene nanosheets could be an efficient catalyst for lithium-air batteries. © 2011 Elsevier Ltd. All rights reserved.

Suthers, B, Hansbro, P, Thambar, S, McEvoy, M, Peel, R & Attia, J 2012, 'Pneumococcal vaccination may induce anti-oxidized low-density lipoprotein antibodies that have potentially protective effects against cardiovascular disease', Vaccine, vol. 30, no. 27, pp. 3983-3985.
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Suurbach, JH, McGowan, EM, Simpson, A, Tran, N & Martiniello-Wilks, R 2012, 'A unique bioluminescent prostate cancer mouse model for the evaluation of stem-cell based gene therapy', JOURNAL OF TISSUE ENGINEERING AND REGENERATIVE MEDICINE, vol. 6, pp. 288-288.

Suwarno, SR, Chen, X, Chong, TH, Puspitasari, VL, McDougald, D, Cohen, Y, Rice, SA & Fane, AG 2012, 'The impact of flux and spacers on biofilm development on reverse osmosis membranes', Journal of Membrane Science, vol. 405-406, pp. 219-232.
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Tan, X, Khalil, N, Tesarik, C, Vanapalli, K, Yaputra, V, Alkhouri, H, Oliver, BGG, Armour, CL & Hughes, JM 2012, 'Th1 cytokine-induced syndecan-4 shedding by airway smooth muscle cells is dependent on mitogen-activated protein kinases', AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY, vol. 302, no. 7, pp. 1700-1710.
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In asthma, airway smooth muscle (ASM) chemokine secretion can induce mast cell recruitment into the airways. The functions of the mast cell chemoattractant CXCL10, and other chemokines, are regulated by binding to heparan sulphates such as syndecan-4. This study is the first demonstration that airway smooth muscle cells (ASMC) from people with and without asthma express and shed syndecan-4 under basal conditions. Syndecan-4 shedding was enhanced by stimulation for 24 h with the Th1 cytokines interleukin-1β (IL-1β) or tumor necrosis factor-α (TNF-α), but not interferon-γ (IFNγ), nor the Th2 cytokines IL-4 and IL-13. ASMC stimulation with IL-1β, TNF-α, and IFNγ (cytomix) induced the highest level of syndecan-4 shedding. Nonasthmatic and asthmatic ASM cell-associated syndecan-4 protein expression was also increased by TNF-α or cytomix at 4-8 h, with the highest levels detected in cytomix-stimulated asthmatic cells. Cell-associated syndecan- 4 levels were decreased by 24 h, whereas shedding remained elevated at 24 h, consistent with newly synthesized syndecan-4 being shed. Inhibition of ASMC matrix metalloproteinase-2 did not prevent syndecan-4 shedding, whereas inhibition of ERK MAPK activation reduced shedding from cytomix-stimulated ASMC. Although ERK inhibition had no effect on syndecan-4 mRNA levels stimulated by cytomix, it did cause an increase in cell-associated syndecan-4 levels, consistent with the shedding being inhibited. In conclusion, ASMC produce and shed syndecan-4 and although this is increased by the Th1 cytokines, the MAPK ERK only regulates shedding. ASMC syndecan-4 production during Th1 inflammatory conditions may regulate chemokine activity and mast cell recruitment to the ASM in asthma. © 2012 the American Physiological Society.

Tekwe, CD, Carroll, RJ & Dabney, AR 2012, 'Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data', Bioinformatics, vol. 28, no. 15, pp. 1998-2003.
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Abstract Motivation: Protein abundance in quantitative proteomics is often based on observed spectral features derived from liquid chromatography mass spectrometry (LC-MS) or LC-MS/MS experiments. Peak intensities are largely non–normal in distribution. Furthermore, LC-MS-based proteomics 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 and accelerated failure time-model with log-normal, log-logistic and Weibull distributions were used to detect any differentially expressed proteins. The statistical operating characteristics of each method are explored using both real and simulated datasets. Results: Survival methods generally have greater statistical power than standard differential expression methods when the proportion of missing protein level data is 5% or more. In particular, the AFT models we consider consistently achieve greater statistical power than standard testing procedures, with the discrepancy widening with increasing missingness in the proportions. Availability: The testing procedures discussed in this article can all be performed using readily available software such as R. The R codes are provided as supplemental materials. Contact:  ctekwe@stat.tamu.edu

Tekwe, CD, Lei, J, Yao, K, Li, X, Rezaei, R, Dahanayaka, S, Meininger, CJ, Carroll, RJ, Bazer, FW & Wu, G 2012, 'Oral administration of interferon‐τ reduces adiposity in Zucker diabetic fatty rats', The FASEB Journal, vol. 26, no. S1.
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The Zucker diabetic fatty (ZDF) rat spontaneously develops type‐2 diabetes at 7 to 8 weeks of age. This study tested the hypothesis that oral administration of Interferon‐ô (IFNT) reduces obesity and delay the onset of diabetes in ZDF rats. Beginning at 4 weeks of age, 18 male ZDF rats were fed a Purina 5008 diet and received drinking water containing 0, 330 and 660 ng IFNT/100 mL (n=6/group), providing 0, 4 and 8 μg IFNT/kg BW per day. At 12 weeks of age, rats were euthanized to obtain tissues. Water or food intake did not differ (P > 0.05) among the three groups of rats. Compared to the control group, oral administration of 8 μg IFNT/kg BW per day reduced (P < 0.05) the body weight of the rats by 6.2%, the onset of diabetes by 8.5 days, concentrations of branched‐chain amino acids by 28%, and white adipose tissue by 40%, while increasing (P < 0.05) brown adipose tissue (BAT) in the interscapular region by 46%. Oral administration of 8 μg IFNT/kg BW per day enhanced (P < 0.05): 1) glucose oxidation in the liver, BAT, and white adipose tissue; 2) oleate oxidation in the liver, gastrocnemius muscle and BAT; and 3) leucine transamination in skeletal muscle. None of the measured variables differed (P > 0.05) between the rats receiving oral administration of 0 and 4 μg IFNT/kg BW per day. Our results indicate that IFNT at 8 μg IFNT/kg BW per day reduced obesity and improved the metabolic profile in ZDF rats. (Supported by AHA and NIH grants)

Tekwe, CD, Lei, J, Yao, K, Li, X, Rezaei, R, Dahanayaka, S, Meininger, CJ, Carroll, RJ, Bazer, FW & Wu, G 2012, 'Oral administration of L‐leucine reduces nitric oxide synthesis by endothelial cells of rats', The FASEB Journal, vol. 26, no. S1.
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High concentrations of branched‐chain amino acids in plasma are commonly associated with endothelial dysfunction in obese humans and animals. This study tested the hypothesis that elevated levels of leucine in plasma can reduce nitric oxide (NO) synthesis by endothelial cells (EC). Beginning at 19 weeks of age, male Sprague‐Dawley rats were fed a semi‐purified diet containing a normal fat content and received drinking water containing either 1% L‐leucine or 0.68% L‐alanine (isonitrogenous control) (n=8/group). Twenty‐four‐hour whole‐body energy expenditure of rats was determined every 4 weeks using Oxymas (an open circuit calorimeter, Columbus Instruments, Ohio). At 31 weeks of age, rats were euthanized to obtain tissues. Oral administration of leucine increased (P < 0.01) concentrations of leucine in plasma by 35%, but did not affect (P > 0.05) water consumption (25 mL/kg BW per day), food intake, body weight, skeletal muscle weight, white adipose tissue weight, or whole‐body heat production. Leucine administration enhanced (P < 0.05) glutamine:fructose‐6‐phosphate transaminase activity and decreased (P < 0.05) NO synthesis in EC and whole‐body insulin sensitivity. These novel results indicate that elevated concentrations of leucine promote glucosamine synthesis and reduce NO production by EC, contributing to increased risk for cardiovascular disease. (Supported by AHA and NIH grants).

Tekwe, CD, Lei, J, Yao, K, Li, X, Rezaei, R, Dahanayaka, S, Meininger, CJ, Carroll, RJ, Bazer, FW & Wu, G 2012, 'Oral administration of α‐ketoglutarate or interferon‐τ reduces adiposity in diet‐induced obese rats', The FASEB Journal, vol. 26, no. S1.
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Obesity is a risk factor for many chronic diseases, including hypertension, type‐2 diabetes, and cancer. High levels of branched‐chain amino acids (BCAA) in plasma are commonly associated with endothelial dysfunction in obesity. This study tested the hypothesis that dietary supplementation with á‐ketoglutarate (AKG) or interferon‐ô (IFNT) may stimulate BCAA catabolism in tissues, thereby reducing the circulating levels of BCAA and increasing NO synthesis by EC. Beginning at 4 wk of age, male Sprague‐Dawley rats were fed a low‐fat (LF) or high‐fat (HF) diet for 15 wk. At 19 wk of age, lean or obese rats continued to be fed their respective diets and received drinking water containing either 0 or 1% AKG, or 80 μg IFNT/100 mL (n=8/group). At 31 wk of age, rats were euthanized to obtain tissues. Water consumption (25 mL/kg BW per day) or food intake did not differ among the three groups of rats. Oral administration of AKG (250 mg/kg BW per day) or IFNT (20 μg/kg BW per day) reduced (P<0.05) concentrations of BCAA in plasma, adiposity, and glutamine: fructose‐6‐phosphate transaminase activity in EC, and enhanced (P<0.05) whole‐body insulin sensitivity and NO synthesis by EC, in LF and HF rats. AKG administration reduced (P<0.05) body weights of LF and HF rats, as did IFNT on LF rats. These results indicate that AKG or IFNT can reduce adiposity and increase NO production by EC in diet‐induced obese rats. (Supported by AHA and NIH grants).

Teng, Y, Zhou, J, Lin, G, Hua, J, Zeng, H, Zhou, S & Qiu, J 2012, 'Ultrafast modification of elements distribution and local luminescence properties in glass', Journal of Non-Crystalline Solids, vol. 358, no. 9, pp. 1185-1189.
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The success in construction of three-dimensional micro optical components or devices inside transparent materials is highly dependent on the ability to modify materials’ local structure. Especially, the realization of space-selective manipulation of element distribution is highly desirable since most of optical parameters such as refractive index and luminescence are closely related to element distribution. Up to present, the only way to control selective element distribution is local melting of glass. Here, we reported, for the first time to our knowledge, the success in realization of space-selective manipulation of element distribution in glassy state region (i.e., un-melted region) inside glass with the irradiation of high repetition rate femtosecond laser. Confocal fluorescence spectra and micro-Raman spectra show that the luminescence distribution of Cu+ ions and the glass network structure can be controlled with femtosecond laser irradiation, revealing the potential applications of this technique in the fabrication of functional waveguides and integrated optical devices.

Teng, Y, Zhou, J, Lin, G, Luo, F, Zhou, S & Qiu, J 2012, 'Recent Research Progress on Femtosecond Laser Induced Microstructures in Glasses', International Journal of Optomechatronics, vol. 6, no. 2, pp. 179-187.
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Thessen, AE, Patterson, DJ & Murray, SA 2012, 'The Taxonomic Significance of Species That Have Only Been Observed Once: The Genus Gymnodinium (Dinoflagellata) as an Example', PLOS ONE, vol. 7, no. 8, pp. e44015-0.
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Thorburn, AN, Foster, PS, Gibson, PG & Hansbro, PM 2012, 'Components of Streptococcus pneumoniae Suppress Allergic Airways Disease and NKT Cells by Inducing Regulatory T Cells', The Journal of Immunology, vol. 188, no. 9, pp. 4611-4620.
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Abstract Asthma is an allergic airways disease (AAD) caused by dysregulated immune responses and characterized by eosinophilic inflammation, mucus hypersecretion, and airway hyperresponsiveness (AHR). NKT cells have been shown to contribute to AHR in some mouse models. Conversely, regulatory T cells (Tregs) control aberrant immune responses and maintain homeostasis. Recent evidence suggests that Streptococcus pneumoniae induces Tregs that have potential to be harnessed therapeutically for asthma. In this study, mouse models of AAD were used to identify the S. pneumoniae components that have suppressive properties, and the mechanisms underlying suppression were investigated. We tested the suppressive capacity of type-3-polysaccharide (T3P), isolated cell walls, pneumolysoid (Ply) and CpG. When coadministered, T3P + Ply suppressed the development of: eosinophilic inflammation, Th2 cytokine release, mucus hypersecretion, and AHR. Importantly, T3P + Ply also attenuated features of AAD when administered during established disease. We show that NKT cells contributed to the development of AAD and also were suppressed by T3P + Ply treatment. Furthermore, adoptive transfer of NKT cells induced AHR, which also could be reversed by T3P + Ply. T3P + Ply-induced Tregs were essential for the suppression of NKT cells and AAD, which was demonstrated by Treg depletion. Collectively, our results show that the S. pneumoniae components T3P + Ply suppress AAD through the induction of Tregs that blocked the activity of NKT cells. These data suggest that S. pneumoniae components may have potential as a therapeutic strategy for the suppression of allergic asthma through the induction of Tregs and suppression of NKT cells.

Tian, H, Li, B, Zhu, J, Wang, H, Li, Y, Xu, J, Wang, J, Wang, W, Sun, Z, Liu, W, Huang, X, Yan, X, Wang, Q, Yao, X & Tang, Y 2012, 'Two selective fluorescent chemosensors for cadmium ions in 99% aqueous solution: the end group effect on the selectivity, DFT calculations and biological applications', Dalton Trans., vol. 41, no. 7, pp. 2060-2065.
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Tian, L, Dai, Z, Zhang, L, Zhang, R, Ye, Z, Wu, J, Jin, D & Yuan, J 2012, 'Preparation and time-gated luminescence bioimaging applications of long wavelength-excited silica-encapsulated europium nanoparticles', Nanoscale, vol. 4, no. 11, pp. 3551-3551.
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Silica-encapsulated luminescent lanthanide nanoparticles have shown great potential as biolabels for various time-gated luminescence bio-detections in recent years. The main problem of these nano-biolabels is their short excitation wavelengths within the UV region. In this work, a new type of silica-encapsulated luminescent europium nanoparticle, with a wide excitation range from UV to visible light in aqueous solutions, has been prepared using a conjugate of (3-isocyanatopropyl)triethoxysilane bound to a visible light-excited Eu 3+ complex, 2,6-bis(1′,1′,1′, 2′,2′,3′,3′-heptafluoro-4′,6′-hexanedion- 6′-yl)-dibenzothiophene-Eu 3+-2-(N,N-diethylanilin-4-yl)-4,6- bis(pyrazol-1-yl)-1,3,5-triazine (IPTES-BHHD-Eu 3+-BPT conjugate), as a functionalized precursor. The nanoparticles, which are prepared by the copolymerization of the IPTES-BHHD-Eu 3+-BPT conjugate, tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane in a water-in-oil reverse microemulsion consisting of Triton X-100, n-octanol, cyclohexane and water in the presence of aqueous ammonia, are monodisperse, spherical and uniform in size. Their diameter is 42 ± 3 nm and they are strongly luminescent with a wide excitation range from UV to ∼475 nm and a long luminescence lifetime of 346 μs. The nanoparticles were successfully used for streptavidin labeling and the time-gated luminescence imaging detection of two environmental pathogens, cryptosporidium muris and cryptosporidium parvium, in water samples. The results demonstrated the practical utility of the new nanoparticles as visible light-excited biolabels for time-gated luminescence bioassay applications. © 2012 The Royal Society of Chemistry.

Toddo, S, Söderström, B, Palombo, I, von Heijne, G, Nørholm, MHH & Daley, DO 2012, 'Application of split‐green fluorescent protein for topology mapping membrane proteins in Escherichia coli', Protein Science, vol. 21, no. 10, pp. 1571-1576.
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AbstractA topology map of a membrane protein defines the location of transmembrane helices and the orientation of soluble domains relative to the membrane. In the absence of a high‐resolution structure, a topology map is an essential guide for studying structure–function relationships. Although these maps can be predicted directly from amino acid sequence, the predictions are more accurate if combined with experimental data, which are usually obtained by fusing a reporter protein to the C‐terminus of the protein. However, as reporter proteins are large, they cannot be used to report on the cytoplasmic/periplasmic location of the N‐terminus of a protein. Here, we show that the bimolecular split‐green fluorescent protein complementation system can overcome this limitation and can be used to determine the location of both the N‐ and C‐termini of inner membrane proteins in Escherichia coli.

Ton-That, C, Foley, M, Phillips, MR, Tsuzuki, T & Smith, Z 2012, 'Correlation between the structural and optical properties of Mn-doped ZnO nanoparticles', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 522, pp. 114-117.
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The crystallographic and optical properties of Mn-doped ZnO nanoparticles prepared by a sol-gel process have been investigated by X-ray diffraction, UV-visible absorption spectroscopy and cathodoluminescence microanalysis. X-ray diffraction reveals that the nanoparticles have hexagonal wurtzite crystal structure, with the lattice constants along the a- and c-axes increasing with increasing Mn concentration from 0 to 2.4 at%. For all Mn concentrations in this range, the nanoparticles are essentially free of native point defects so that they exhibit only band-edge luminescence. The optical bandgap and band-edge emission energies for Mn-doped ZnO were found to increase in proportion to the lattice constants. The direct correlation between the bandgap and crystal structure suggests that the band-edge optical properties of Mn-doped ZnO is predominantly influenced by the amount of Mn atoms substituting Zn on the lattice sites. © 2012 Elsevier B.V. All rights reserved.

Ton-That, C, Weston, L & Phillips, MR 2012, 'Characteristics of point defects in the green luminescence from Zn- and O-rich ZnO', PHYSICAL REVIEW B, vol. 86, no. 11, pp. 1-5.
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Cathodoluminescence spectra have been measured to determine the characteristics of ubiquitous green luminescence (GL) in nonstoichiometric zinc oxide (ZnO). Zn- and O-rich ZnO were found to exhibit characteristic emissions at 2.53 eV [full width at half-maximum (FWHM) 340 meV] and 2.30 eV (FWHM 450 meV), respectively. Hydrogen was used to probe the physical nature of GL centers. The Zn-rich GL is enhanced upon H incorporation, whereas the O-rich GL is completely quenched as its underlying acceptor-like V Zn centers are passivated by H. The GL emission bands each exhibit remarkably different excitation-power dependencies. The Zn-rich GL follows a close to linear relationship with excitation power, while the O-rich GL exhibits a square-root dependence. Calculations based on bimolecular recombination equations show the defect concentration in Zn-rich ZnO is three orders of magnitude greater than that in O-rich ZnO, indicating V O is more readily formed than V Zn in thermochemical treatments of ZnO. © 2012 American Physical Society.

Trevitt, AJ, Reimers, JR, Clarke, RJ & Vandenberg, JI 2012, 'BIOPHYSCHEM2011: A Joint Meeting of the Australian Society for Biophysics and the RACI Physical Chemistry Division Foreword', AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 65, no. 5, pp. 439-441.
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Tritt, A, Eisen, JA, Facciotti, MT & Darling, AE 2012, 'An Integrated Pipeline for de Novo Assembly of Microbial Genomes', PLOS ONE, vol. 7, no. 9, pp. 1-9.
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Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron's Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the other assembly algorithm. In particular, the assemblies produced by A5 exhibit 50% or more reduction in broken protein coding sequences relative to SOAPdenovo assemblies. The A5 pipeline can also assemble Illumina sequence data from libraries constructed by the Nextera (transposon-catalyzed) protocol, which have markedly different characteristics to mechanically sheared libraries. Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage. © 2012 Tritt et al.

Uzair, B, Tabassum, S, Rasheed, M & Rehman, SF 2012, 'Exploring Marine Cyanobacteria for Lead Compounds of Pharmaceutical Importance', The Scientific World Journal, vol. 2012, pp. 1-10.
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The Ocean, which is called the “mother of origin of life,” is also the source of structurally unique natural products that are mainly accumulated in living organisms. Cyanobacteria are photosynthetic prokaryotes used as food by humans. They are excellent source of vitamins and proteins vital for life. Several of these compounds show pharmacological activities and are helpful for the invention and discovery of bioactive compounds, primarily for deadly diseases like cancer, acquired immunodeficiency syndrome (AIDS), arthritis, and so forth, while other compounds have been developed as analgesics or to treat inflammation, and so forth. They produce a large variety of bioactive compounds, including substances with anticancer and antiviral activity, UV protectants, specific inhibitors of enzymes, and potent hepatotoxins and neurotoxins. Many cyanobacteria produce compounds with potent biological activities. This paper aims to showcase the structural diversity of marine cyanobacterial secondary metabolites with a comprehensive coverage of alkaloids and other applications of cyanobacteria.

van Dongen-Vogels, V, Seymour, JR, Middleton, JF, Mitchell, JG & Seuront, L 2012, 'Shifts in picophytoplankton community structure influenced by changing upwelling conditions', ESTUARINE COASTAL AND SHELF SCIENCE, vol. 109, pp. 81-90.
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The influence of upwelling events on the structure of picophytoplankton communities was assessed at the annual scale from a station within the South Australian shelf region. In this region, local (wind) and global (La Niña/El NiñoSouthern Oscillation) hydroclimatic conditions affect the development of upwelling over the austral summer. Using flow cytometry, changes in picophytoplankton community structure were investigated in relation to the properties of the water column when the nature and strength of upwelling event differed for the upwelling seasons of 2008, 2009, and 2010. In 2008, strong upwelling favorable southeasterlies were responsible for extensive upwelling and the dominance of picoeukaryotes. Alternatively, in 2009, the observed dominance of Prochlorococcus reflected the presence of oligotrophic conditions whilst southeasterlies were replaced by downwelling favorable north-westerlies that likely prohibited the full development of upwelling. In 2010, whilst southeasterlies remained relatively weak, particularly cold and low saline upwelled waters indicated enhanced upwelling events. This weak local wind field together with the occurrence of El Niño explained the observation of shallow upwelled waters below the warm surface layer and subsequent enhanced stratification. These conditions led to the dominance of Synechococcus in surface and fluorescence maximum depths, but of Prochlorococcus in bottom upwelled waters. The tight association between upwelling and stratification, i.e. whether upwelled waters reach shallower depths and/or mix with those of the surface as a result of variable climatic conditions, was suggested as the process driving the vertical heterogeneity of picophytoplankton populations. This study brings valuable information for changing picophytoplankton community structure with potential future changing hydroclimatic forcing.

Van Lent, S, Piet, JR, Beeckman, D, van der Ende, A, Van Nieuwerburgh, F, Bavoil, P, Myers, G, Vanrompay, D & Pannekoek, Y 2012, 'Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains', Journal of Bacteriology, vol. 194, no. 24, pp. 6930-6931.
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ABSTRACT Chlamydia psittaci primarily infects birds, but zoonotic transmission occurs in people in close contact with infected birds. The clinical outcome ranges from inapparent disease to pneumonia. Here we report the genome sequences of all 9 Chlamydia psittaci genotype reference strains.

Van Ly, D, Burgess, JK, Brock, TG, Lee, TH, Black, JL & Oliver, BGG 2012, 'Prostaglandins but not leukotrienes alter extracellular matrix protein deposition and cytokine release in primary human airway smooth muscle cells and fibroblasts', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 303, no. 3, pp. L239-L250.
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Eicosanoids are lipid-signaling mediators released by many cells in response to various stimuli. Increasing evidence suggests that eicosanoids such as leukotrienes and prostaglandins (PGs) may directly mediate remodeling. In this study, we assessed whether these substances could alter extracellular matrix (ECM) proteins and the inflammatory profiles of primary human airway smooth muscle cells (ASM) and fibroblasts. PGE2decreased both fibronectin and tenascin C in fibroblasts but only fibronectin in ASM. PGD2decreased both fibronectin and tenascin C in both ASM and fibroblasts, whereas PGF2αhad no effect on ECM deposition. The selective PGI2analog, MRE-269, decreased fibronectin but not tenascin C in both cell types. All the PGs increased IL-6 and IL-8 release in a dose-dependent manner in ASM and fibroblasts. Changes in ECM deposition and cytokine release induced by prostaglandins in both ASM and fibroblasts were independent of an effect on cell number. Neither the acute nor repeated stimulation with leukotrienes had an effect on the deposition of ECM proteins or cytokine release from ASM or fibroblasts. We concluded that, collectively, these results provide evidence that PGs may contribute to ECM remodeling to a greater extent than leukotrienes in airway cells.

Verhoeven, MPC, Kelaher, BP, Bishop, MJ & Ralph, PJ 2012, 'Epiphyte grazing enhances productivity of remnant seagrass patches', AUSTRAL ECOLOGY, vol. 37, no. 8, pp. 885-892.
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Anthropogenic nutrient enrichment is increasingly modifying community structure and ecosystem functioning in terrestrial and aquatic ecosystems. In marine ecosystems, the paradigm is that nutrient enrichment leads to a decline of seagrasses by stimulatin

Voyer, M, Gladstone, W & Goodall, H 2012, 'Methods of social assessment in Marine Protected Area planning: Is public participation enough?', MARINE POLICY, vol. 36, no. 2, pp. 432-439.
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Addressing social and economic considerations is crucial to the success of Marine Protected Area (MPA) planning and management. Ineffective social assessment can alienate local communities and under- mine the success of existing and future MPAs. It is rare to critique the success of methods used currently to incorporate social and economic considerations into MPA planning. Three Australian MPA planning processes covering three states and incorporating federal and state jurisdictions are reviewed in order to determine how potential social impacts were assessed and considered. These case studies indicate that Social Impact Assessment (SIA) is under-developed in Australian MPA planning. Assessments rely heavily on public participation and economic modelling as surrogates for dedicated SIA and are followed commonly by attitudinal surveys to gauge public opinion on the MPA after its establishment. The emergence of issues around public perception of the value of MPAs indicates the failure of some of these proposals to adequately consider social factors in planning and management. This perception may have potential implications for the long term success of individual MPAs. It may also compromise Australia's ability to meet international commitments for MPA targets to gazette at least 10% of all its marine habitats as MPAs. Indeed, this is demonstrated in two of the three case studies where social and economic arguments against MPAs have been used to delay or block the future expansion of the MPA network.

Walford, S-A, Wu, Y, Llewellyn, DJ & Dennis, ES 2012, 'Epidermal cell differentiation in cotton mediated by the homeodomain leucine zipper gene, GhHD-1', PLANT JOURNAL, vol. 71, no. 3, pp. 464-478.
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Gossypium hirsutum L. (cotton) fibres are specialized trichomes a few centimetres in length that grow from the seed coat. Few genes directly involved in the differentiation of these epidermal cells have been identified. These include GhMYB25-like and GhMYB25, two related MYB transcription factors that regulate fibre cell initiation and expansion. We have also identified a putative homeodomain leucine zipper (HD-ZIP) transcription factor, GhHD-1, expressed in trichomes and early fibres that might play a role in cotton fibre initiation. Here, we characterize GhHD-1 homoeologues from tetraploid G. hirsutum and show, using reporter constructs and quantitative real-time PCR (qRT-PCR), that they are expressed predominantly in epidermal tissues during early fibre development, and in other tissues bearing epidermal trichomes. Silencing of GhHD-1 reduced trichome formation and delayed the timing of fibre initiation. Constitutive overexpression of GhHD-1 increased the number of fibres initiating on the seed, but did not affect leaf trichomes. Expression of GhHD-1 in cotton silenced for different fibre MYBs suggest that in ovules it acts downstream of GhMYB25-like, but is unaffected in GhMYB25- or GhMYB109-silenced plants. Microarray analysis of silencing and overexpression lines of GhHD-1 indicated that it potentially regulates the levels of ethylene and reactive oxidation species (ROS) through a WRKY transcription factor and calcium-signalling pathway genes to activate downstream genes necessary for cell expansion and elongation. © 2012 CSIRO.

Wand, MP & Ormerod, JT 2012, 'Continued fraction enhancement of Bayesian computing', Stat, vol. 1, no. 1, pp. 31-41.
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The agéd number theoretic concept of continued fractions can enhance certain Bayesian computations. The crux of this claim is due to continued fraction representations of numerically challenging special function ratios that arise in Bayesian computing. Continued fraction approximation via Lentz's Algorithm often leads to efficient and stable computation of such quantities. Copyright © 2012 John Wiley & Sons, Ltd.

Wang, B, Li, K, Su, D, Ahn, H & Wang, G 2012, 'Superior Electrochemical Performance of Sulfur/Graphene Nanocomposite Material for High‐Capacity Lithium–Sulfur Batteries', Chemistry – An Asian Journal, vol. 7, no. 7, pp. 1637-1643.
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AbstractSulfur/graphene nanocomposite material has been prepared by incorporating sulfur into the graphene frameworks through a melting process. Field‐emission scanning electron microscope analysis shows a homogeneous distribution of sulfur in the graphene nanosheet matrix. The sulfur/graphene nanocomposite exhibits a super‐high lithium‐storage capacity of 1580 mAh g−1 and a satisfactory cycling performance in lithium–sulfur cells. The enhancement of the reversible capacity and cycle life could be attributed to the flexible graphene nanosheet matrix, which acts as a conducting medium and a physical buffer to cushion the volume change of sulfur during the lithiation and delithiation process. Graphene‐based nanocomposites can significantly improve the electrochemical performance of lithium–sulfur batteries.

Wang, B, Park, J, Su, D, Wang, C, Ahn, H & Wang, G 2012, 'Solvothermal synthesis of CoS2–graphene nanocomposite material for high-performance supercapacitors', Journal of Materials Chemistry, vol. 22, no. 31, pp. 15750-15750.
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A CoS 2-graphene nanocomposite was prepared by a facile solvothermal method. FESEM and TEM analyses have confirmed that CoS 2 nanoparticles with sizes of 5-15 nm are densely anchored on graphene nanosheets. The as-prepared nanocomposite was electrochemically tested as an electrode material for supercapacitors. The CoS 2-graphene nanocomposite exhibited specific capacitances of 314 F g -1 in the aqueous electrolyte and 141 F g -1 in the organic electrolyte at a current rate of 0.5 A g -1 with excellent cycling stability. The electrochemical performance of the nanocomposite has been significantly improved, compared to bare graphene nanosheets and CoS 2 nanoparticles. This could be credited to the 3D nanoarchitecture, in which CoS 2 nanoparticles were sandwiched between graphene nanosheets, and the additional electrochemical contribution of the decorated CoS 2 nanoparticles. © 2012 The Royal Society of Chemistry.

Wang, B, Su, D, Park, J, Ahn, H & Wang, G 2012, 'Graphene-supported SnO2 nanoparticles prepared by a solvothermal approach for an enhanced electrochemical performance in lithium-ion batteries', Nanoscale Research Letters, vol. 7, no. 1, pp. 1-10.
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SnO2 nanoparticles were dispersed on graphene nanosheets through a solvothermal approach using ethylene glycol as the solvent. The uniform distribution of SnO2 nanoparticles on graphene nanosheets has been confirmed by scanning electron microscopy and transmission electron microscopy. The particle size of SnO2 was determined to be around 5 nm. The assynthesized SnO2/graphene nanocomposite exhibited an enhanced electrochemical performance in lithium-ion batteries, compared with bare graphene nanosheets and bare SnO2 nanoparticles. The SnO2/graphene nanocomposite electrode delivered a reversible lithium storage capacity of 830 mAh g-1 and a stable cyclability up to 100 cycles. The excellent electrochemical properties of this graphene-supported nanocomposite could be attributed to the insertion of nanoparticles between graphene nanolayers and the optimized nanoparticles distribution on graphene nanosheets. © 2012 Wang et al.

Wang, J, Wu, J, Chen, Y, Wang, H, Li, Y, Liu, W, Tian, H, Zhang, T, Xu, J & Tang, Y 2012, 'A small-molecular europium complex with anion sensing sensitivity', Dalton Transactions, vol. 41, no. 41, pp. 12936-12936.
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Wang, JJJ 2012, 'On asymmetric generalised t stochastic volatility models', Mathematics and Computers in Simulation, vol. 82, no. 11, pp. 2079-2095.
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In stochastic volatility (SV) models, asset returns conditional on the latent volatility are usually assumed to have a normal, Student-t or exponential power (EP) distribution. An earlier study uses a generalised t (GT) distribution for the conditional returns and the results indicate that the GT distribution provides a better model fit to the Australian Dollar/Japanese Yen daily exchange rate than the Student-t distribution. In fact, the GT family nests a number of well-known distributions including the commonly used normal, Student-t and EP distributions. This paper extends the SV model with a GT distribution by incorporating general volatility asymmetry. We compare the empirical performance of nested distributions of the GT distribution as well as different volatility asymmetry specifications. The new asymmetric GT SV models are estimated using the Bayesian Markov chain Monte Carlo (MCMC) method to obtain parameter and log-volatility estimates. By using daily returns from the Standard and Poors (S&P) 500 index, we investigate the effects of the specification of error distributions as well as volatility asymmetry on parameter and volatility estimates. Results show that the choice of error distributions has a major influence on volatility estimation only when volatility asymmetry is not accounted for. © 2012 IMACS. Published by Elsevier B.V. All rights reserved.

Wang, Q, Yu, JH, Kim, JS, Kim, KW, Wang, G, Ahn, JH, Kang, Y & Ahn, HJ 2012, 'Electrochemical properties of all solid Li/Ni3S2 cells using polymer electrolyte based on star-shaped siloxane acrylate cross-linker', Journal of Ceramic Processing Research, vol. 13, no. SPL. ISS.2, pp. S398-S402.
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All solid Li/Ni3S2 cells were assembled with a novel solid polymer electrolyte cured via in-situ chemical cross-linking with siloxane acrylate. Several ether plasticizers with various chain lengths were used to optimize the cycling property of Li/ Ni3S2 cell. The Li/ Ni3S2 cell containing the Triethylene glycol dimethyl ether as plasticizer show optimum first charging-discharge and cycling performance, that capacity still maintain 413.32 mAh/g after 20 cycles.

Wang, Y, Park, J, Sun, B, Ahn, H & Wang, G 2012, 'ChemInform Abstract: Wintersweet‐Flower‐Like CoFe₂O₄/MWCNTs Hybrid Material for High‐Capacity Reversible Lithium Storage.', ChemInform, vol. 43, no. 51, pp. no-no.
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AbstractCoFe2O4/multiwalled carbon nanotubes hybrid materials are hydrothermally synthesized from mixtures of FeCl3, CoCl2, multiwalled carbon nanotubes, ethylene glycol, diethylenetriamine, and KOH solution (autoclave, 180 °C, 10 h).

Wang, Y, Park, J, Sun, B, Ahn, H & Wang, G 2012, 'Wintersweet-Flower-Like CoFe2O4/MWCNTs Hybrid Material for High-Capacity Reversible Lithium Storage', CHEMISTRY-AN ASIAN JOURNAL, vol. 7, no. 8, pp. 1940-1946.
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CoFe 2O 4/multiwalled carbon nanotubes (MWCNTs) hybrid materials were synthesized by a hydrothermal method. Field emission scanning electron microscopy and transmission electron microscopy analysis confirmed the morphology of the as-prepared hybrid material resembling wintersweet flower 'buds on branches', in which CoFe 2O 4 nanoclusters, consisting of nanocrystals with a size of 5-10 nm, are anchored along carbon nanotubes. When applied as an anode material in lithium ion batteries, the CoFe 2O 4/MWCNTs hybrid material exhibited a high performance for reversible lithium storage. In particular, the hybrid anode material delivered reversible lithium storage capacities of 809, 765, 539, and 359 mAhg -1 at current densities of 180, 450, 900, and 1800 mAg -1, respectively. The superior performance of CoFe 2O 4/MWCNTs hybrid materials could be ascribed to the synergistic pinning effect of the wintersweet-flower-like nanoarchitecture. This strategy could also be applied to synthesize other metal oxide/CNTs hybrid materials as high-capacity anode materials for lithium ion batteries. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wang, Y, Su, D, Ung, A, Ahn, J-H & Wang, G 2012, 'Hollow CoFe₂O₄nanospheres as a high capacity anode material for lithium ion batteries', Nanotechnology, vol. 23, no. 5, pp. 055402-055402.
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Hollow structured CoFe 2O 4 nanospheres were synthesized by a hydrothermal method. The uniform hollow nanosphere architecture of the as-prepared CoFe 2O 4 has been confirmed by field emission scanning electron microscopy and transmission electron microscopy analysis, which give an outer diameter of 200300nm and a wall thickness of about 100nm. CoFe 2O 4 nanospheres exhibited a high reversible capacity of 1266mAhg 1 with an excellent capacity retention of 93.6% over 50 cycles and an improved rate capability. CoFe 2O 4 could be a promising high capacity anode material for lithium ion batteries. © 2012 IOP Publishing Ltd.

Wangpraseurt, D, Larkum, AWD, Ralph, PJ & Kuehl, M 2012, 'Light gradients and optical microniches in coral tissues', FRONTIERS IN MICROBIOLOGY, vol. 3, no. 316, pp. 1-9.
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Light quantity and quality are among the most important factors determining the physiology and stress response of zooxanthellate corals. Yet, almost nothing is known about the light ?eld that Symbiodinium experiences within their coral host, and the basic optical properties of coral tissue are unknown. We used scalar irradiance microprobes to characterize vertical and lateral light gradients within and across tissues of several coral species. Our results revealed the presence of steep light gradients with photosynthetically available radiation decreasing by about one order of magnitude from the tissue surface to the coral skeleton. Surface scalar irradiance was consistently higher over polyp tissue than over coenosarc tissue in faviid corals. Coral bleaching increased surface scalar irradiance by ~150% (between 500 and 700 nm) relative to a healthy coral. Photosynthesis peaked around 300 µm within the tissue, which corresponded to a zone exhibiting strongest depletion of scalar irradiance. Deeper coral tissue layers, e.g., ~1000 µm into aboral polyp tissues, harbor optical microniches, where only ~10% of the incident irradiance remains. We conclude that the optical microenvironment of corals exhibits strong lateral and vertical gradients of scalar irradiance, which are affected by both tissue and skeleton optical properties. Our results imply that zooxanthellae populations inhabit a strongly heterogeneous light environment and highlight the presence of different optical microniches in corals; an important ?nding for understanding the photobiology, stress response, as well as the phenotypic and genotypic plasticity of coral symbionts.

Ward, R & Carroll, RJ 2012, 'Testing Hardy-Weinberg equilibrium with a simple root-mean-square statistic', Biostatistics, vol. 15, no. 1, pp. 74-86.
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We provide evidence that a root-mean-square test of goodness-of-fit can besignificantly more powerful than state-of-the-art exact tests in detectingdeviations from Hardy-Weinberg equilibrium. Unlike Pearson's chi-square test,the log--likelihood-ratio test, and Fisher's exact test, which are sensitive torelative discrepancies between genotypic frequencies, the root-mean-square testis sensitive to absolute discrepancies. This can increase statistical power, aswe demonstrate using benchmark datasets and through asymptotic analysis. Withthe aid of computers, exact P-values for the root-mean-square statistic can becalculated eeffortlessly, and can be easily implemented using the author'sfreely available code.

Webb, G, Miller, P & Peters, B 2012, 'Pyriproxyfen for the Control of Australian Salt-Marsh Mosquito, Aedes vigilax', Journal of the American Mosquito Control Association, vol. 28, no. 1, pp. 50-52.
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The efficacy of pyriproxyfen against the Australian salt-marsh mosquito, Aedes vigilax, was examined in 2 laboratory and 1 semi-field study using both technical grade and formulated products. In a doseresponse study, the median emergence inhibition (EI 50) and EI95 values were determined to be 0.019 and 0.076 ppb, respectively, for pyriproxyfen technical grade, 0.021 and 0.092 ppb for a microencapsulated formulation (Sumilarv® 90CS), and 0.054 and 0.236 ppb for the formulated s-methoprene product, Altosid™ Liquid Larvicide. A further laboratory comparison of the microencapsulated formulation of pyriproxyfen and Altosid, at the nominal field rate for Altosid, showed that both products provided 100% emergence inhibition and this was confirmed in a semi-field study, which also included a granular formulation of pyriproxyfen (Sumilarv 0.5G). © 2012 by The American Mosquito Control Association, Inc.

Weckmann, M, Moir, LM, Heckman, CA, Black, JL, Oliver, BG & Burgess, JK 2012, 'Lamstatin - a novel inhibitor of lymphangiogenesis derived from collagen IV', JOURNAL OF CELLULAR AND MOLECULAR MEDICINE, vol. 16, no. 12, pp. 3062-3073.
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The lymphatic system is essential for the maintenance of tissue homeostasis and immunity. Its dysfunction in disease (such as lymphangioleiomyomatosis) can lead to chylous effusions, oedema or dissemination of malignant cells. Collagen IV has six α chains, of which some of the non-collagenous-1 domains have endogenous anti-angiogenic properties, however, little is known about specific endogenous anti-lymphangiogenic characteristics. In this study we sought to investigate the expression levels of collagen IV non-collagenous-1 domains in lung tissue of patients with and without lymphangioleiomyomatosis to explore the hypothesis that a member of the collagen IV family, specifically the non-collagenous domain-1 of α5, which we named lamstatin, has anti-lymphangiogenic properties. Levels of lamstatin detected by immunohistochemistry were decreased in lungs of lymphangioleiomyomatosis patients. We produced recombinant lamstatin in an E.coli expression system and synthesized a 17-amino acid peptide from a theoretically identified, active region (CP17) and tested their effects in vitro and in vivo. Recombinant lamstatin and CP17 inhibited proliferation, migration and cord formation of human microvascular lung lymphatic endothelial cells, in vitro. Furthermore, lamstatin and CP17 decreased complexity and dysplasia of the tumour-associated lymphatic network in a lung adenocarcinoma xenograft mouse model. In this study we identified a novel, direct inhibitor of lymphangiogenesis, derived from collagen IV. This may prove useful for exploring new avenues of treatment for lymphangioleiomyomatosis and metastasis via the lymphatic system in general. © 2012 The Authors Journal of Cellular and Molecular Medicine © 2012 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Wei, J, Carroll, RJ, Harden, KK & Wu, G 2012, 'Comparisons of treatment means when factors do not interact in two-factorial studies', Amino Acids, vol. 42, no. 5, pp. 2031-2035.
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Scientists in the fields of nutrition and other biological sciences often design factorial studies to test the hypotheses of interest and importance. In the case of two-factorial studies, it is widely recognized that the analysis of factor effects is generally based on treatment means when the interaction of the factors is statistically significant, and involves multiple comparisons of treatment means. However, when the two factors do not interact, a common understanding among biologists is that comparisons among treatment means cannot or should not be made. Here, we bring this misconception into the attention of researchers. Additionally, we indicate what kind of comparisons among the treatment means can be performed when there is a nonsignificant interaction among two factors. Such information should be useful in analyzing the experimental data and drawing meaningful conclusions. © Springer-Verlag 2011.

Wei, Y, Ma, Y & Carroll, RJ 2012, 'Multiple imputation in quantile regression', Biometrika, vol. 99, no. 2, pp. 423-438.
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We propose a multiple imputation estimator for parameter estimation in a quantile regression model when some covariates are missing at random. The estimation procedure fully utilizes the entire dataset to achieve increased efficiency, and the resulting coefficient estimators are root-n consistent and asymptotically normal. To protect against possible model misspecification, we further propose a shrinkage estimator, which automatically adjusts for possible bias. The finite sample performance of our estimator is investigated in a simulation study. Finally, we apply our methodology to part of the Eating at American's Table Study data, investigating the association between two measures of dietary intake. 2012 Biometrika Trust2012 © 2012 Biometrika Trust.

Wertheim, JO, Fourment, M & Kosakovsky Pond, SL 2012, 'Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy', Molecular Biology and Evolution, vol. 29, no. 2, pp. 451-456.
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Westgeest, KB, de Graaf, M, Fourment, M, Bestebroer, TM, van Beek, R, Spronken, MIJ, de Jong, JC, Rimmelzwaan, GF, Russell, CA, Osterhaus, ADME, Smith, GJD, Smith, DJ & Fouchier, RAM 2012, 'Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution', Journal of General Virology, vol. 93, no. 9, pp. 1996-2007.
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Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA). In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371–376, 2004) from its introduction in humans in 1968 until 2003. The current study focused on the genetic evolution of NA and compared it with HA using the dataset of Smith and colleagues, updated to the epidemic of the 2009/2010 season. Phylogenetic trees and genetic maps were constructed to visualize the genetic evolution of NA and HA. The results revealed multiple reassortment events over the years. Overall rates of evolutionary change were lower for NA than for HA1 at the nucleotide level. Selection pressures were estimated, revealing an abundance of negatively selected sites and sparse positively selected sites. The differences found between the evolution of NA and HA1 warrant further analysis of the evolution of NA at the phenotypic level, as has been done previously for HA.

Westhorpe, DP & Mitrovic, SM 2012, 'Dissolved organic carbon mobilisation in relation to variable discharges and environmental flows in a highly regulated lowland river', Marine and Freshwater Research, vol. 63, no. 12, pp. 1218-1218.
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The relationships between discharge and dissolved organic carbon (DOC) have been extensively studied in rainfall runoff-driven stream systems. Less is known about discharge and DOC relationships in river systems dependent on floodplain inundation. We examined DOC dynamics and mobilisation over low discharge periods and several larger discharge events in the highly regulated lowland Namoi River, Australia. Stable isotope signatures (δ13C) of various water-column fractions (e.g. 200 µm, fine particulate organic matter) were used to determine the sources of DOC. DOC concentrations over low discharge periods were fairly similar among sites and ranged between 5 and 10 mg L–1. Concentrations during a high-discharge event increased substantially with a mean of 20.4 mg L–1 and a maximum of 44 mg L–1. Significant positive linear relationships were found between DOC concentrations and discharge (P < 0.001, r2 = 0.45). The 13C composition of DOC sampled across the three sites (e.g. –26.2‰) suggests a mixture of terrestrial and aquatic sources, with little downstream variation; however, we would envisage that during periods of high discharge allochthonous sources would dominate. Environmental flows (that are ecologically beneficial, potentially reversing changes brought about by flow regulation) have been allocated to the river, with the intention to increase the amount of DOC delivered to the river. The relationship between DOC and discharge was used to estimate DOC loads to the river under different modelled flow-management scenarios, including without environmental flow, with environmental flow, and simulated natural (low development) flow. On the basis of the modelling results, environmental flows should increase the amount of allochthonous DOC transported within the river in years with moderate and large flow events. Years with low flows did not deliver large loads of allochthonous DOC. The present results showed the potential variability in DOC d...

Westhorpe, DP, Mitrovic, SM & Woodward, KB 2012, 'Diel variation of dissolved organic carbon during large flow events in a lowland river', Limnologica, vol. 42, no. 3, pp. 220-226.
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Diel variation in dissolved organic carbon (DOC) within lotic systems has been reported on numerous occasions. However, to our knowledge there has been no published work on diel DOC variation within lowland rivers during high flow events. We sampled DOC

Weston, L, Ton-That, C & Phillips, MR 2012, 'Doping properties of hydrogen in ZnO', JOURNAL OF MATERIALS RESEARCH, vol. 27, no. 17, pp. 2220-2224.
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The doping properties and stability of hydrogen in zinc oxide (ZnO) crystals have been investigated by cathodoluminescence (CL) spectroscopy. Hydrogen incorporation was achieved by hydrogen plasma at 200 °C. The ZnO near-band-edge (NBE) peak is dramatically enhanced, while the green emission at 2.4 eV is quenched with increasing hydrogen incorporation. These effects are attributed to hydrogen passivating green luminescence centers, which are most likely negatively charged zinc vacancy defects. E-beam irradiation of H-doped ZnO crystals by an intense electron beam with μW power reverses the hydrogen doping process. This effect is ascribed to the dissociation of H-related defects, formation of Chidden H2, and electromigration of H + under the influence of the local trapped charge-induced electric field. These results highlight the potential to modify the local luminescent properties of ZnO by e-beam irradiation. © 2012 Materials Research Society.

Weyermann, C, Bucher, L, Majcherczyk, P, Mazzella, W, Roux, C & Esseiva, P 2012, 'Statistical discrimination of black gel pen inks analysed by laser desorption/ionization mass spectrometry', FORENSIC SCIENCE INTERNATIONAL, vol. 217, no. 1-3, pp. 127-133.
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Pearson correlation coefficients were applied for the objective comparison of 30 black gel pen inks analysed by laser desorption ionization mass spectrometry (LDI-MS). The mass spectra were obtained for ink lines directly on paper using positive and nega

Williams, DBG & Bredenkamp, T 2012, 'Pd/Al(OTf)₃ Catalyzed Methoxycarbonylation: On the Importance of Counterions and the Acid Source', ChemCatChem, vol. 4, no. 2, pp. 206-208.
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Williams, DBG, Sibiya, MS & van Heerden, PS 2012, 'Efficient hydroalkoxylation of alkenes to generate octane-boosting ethers using recyclable metal triflates and highly active metal triflate/Brønsted acid-assisted catalysts', Fuel Processing Technology, vol. 94, no. 1, pp. 75-79.
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gem-Disubstituted alkenes are directly and readily etherified with alcohols using Al(OTf) 3 and Zr(OTf) 4 as recyclable Lewis acid catalysts. In contrast, primary or secondary alkene analogues were inert under these conditions, enabling excellent chemoselectivity. Lanthanide triflates are inactive as catalysts for such reactions, as is phosphoric acid. But a combination of these two otherwise inactive entities led to an 'assisted acidity' scenario that saw significant unmatched catalyst activity. All catalysts of this study are recyclable a number of times without loss of activity. © 2011 Elsevier B.V. All rights reserved.

Wilson, KG & Ralph, PJ 2012, 'Laboratory testing protocol for the impact of dispersed petrochemicals on seagrass', MARINE POLLUTION BULLETIN, vol. 64, no. 11, pp. 2421-2427.
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To improve the effectiveness of oil spill mitigation, we developed a rapid, logistically simple protocol to detect petrochemical stress on seagrass. Sections of leaf blades from Zostera muelleri subsp. capricorni were exposed to the water accommodated fraction (WAF) of non-dispersed and dispersed Tapis crude oil and fuel oil (IFO-380) for 5. h. Photosynthetic health was monitored by assessing changes in effective quantum yield of photosystem II (ΔF/Fm') and chlorophyll a pigment concentrations. Loss of total petroleum hydrocarbons (TPH) was measured using an oil-in-water fluorometer, whilst GC-MS analyses quantified the hydrocarbon components within each treatment. Few significant differences were detected in the chlorophyll a pigment analyses; however, ΔF/Fm' appeared sensitive to petrochemical exposure. Dispersing both types of oil resulted in a substantial increase in the TPH of the WAF and was generally correlated with a greater physiological impact to the seagrass health, compared with the oil alone. © 2012 Elsevier Ltd.

Wittmann, B, Ramelow, S, Steinlechner, F, Langford, NK, Brunner, N, Wiseman, HM, Ursin, R & Zeilinger, A 2012, 'Loophole-free Einstein–Podolsky–Rosen experiment via quantum steering', New Journal of Physics, vol. 14, no. 5, pp. 053030-053030.
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Woo, JKK, Webb, JS, Kirov, SM, Kjelleberg, S & Rice, SA 2012, 'Biofilm dispersal cells of a cystic fibrosisPseudomonas aeruginosaisolate exhibit variability in functional traits likely to contribute to persistent infection', FEMS Immunology & Medical Microbiology, vol. 66, no. 2, pp. 251-264.
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Wood, M, Maynard, P, Spindler, X, Lennard, C & Roux, C 2012, 'Visualization of Latent Fingermarks Using an Aptamer-Based Reagent', ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, vol. 51, no. 49, pp. 12272-12274.
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Wood, M, Maynard, P, Spindler, X, Lennard, C & Roux, C 2012, 'Visualization of Latent Fingermarks Using an Aptamer‐Based Reagent', Angewandte Chemie, vol. 124, no. 49, pp. 12438-12440.
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Don't touch! Aptamers selected against lysozyme are transformed into aptamer-based reagents, with which latent fingermarks can be developed with high selectivity and sensitivity. The design of aptamers targeting components of latent fingermarks opens up a new range of detection methods that previously have not been explored.

Woolnough, C, Wang, Y, Kan, CY, Morris, JM, Tasevski, V & Ashton, AW 2012, 'Source of angiopoietin-2 in the sera of women during pregnancy', Microvascular Research, vol. 84, no. 3, pp. 367-374.
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Placental development requires coordinated angiogenesis regulated by multiple factors including angiopoietins. Previously we demonstrated that the concentration of angiopoietin-2 (Ang-2) in the sera of women rises markedly in pregnancy in early gestation

Wu, H, Wexler, D, Wang, G & Liu, H 2012, 'Cocore–Ptshell nanoparticles as cathode catalyst for PEM fuel cells', Journal of Solid State Electrochemistry, vol. 16, no. 3, pp. 1105-1110.
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Nanoscale Co core-Pt shell particles were successfully synthesized based on a successive reduction strategy. The as-prepared core-shell nanoparticles were characterized by X-ray diffraction, energy-dispersive X-ray spectroscopy, transmission electron microscope, and electrochemical methods. It was found that the catalytic reactivity of Co core-Pt shell/C catalysts toward oxygen reduction was enhanced. It is believed that the prepared Co core-Pt shell/C nanoparticles could be promising for cathode catalysis in proton exchange membrane fuel cells with much reduced Pt content, but significantly increased catalytic activity. © Springer-Verlag 2011.

Wu, Y, Guan, S & Wang, G 2012, 'Preface', Pure and Applied Chemistry, vol. 84, no. 12.
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Wynne, O, Horvat, JC, Smith, R, Hansbro, PM, Clifton, VL & Hodgson, DM 2012, 'Effect of neonatal respiratory infection on adult BALB/c hippocampal glucocorticoid and mineralocorticoid receptors', Developmental Psychobiology, vol. 54, no. 5, pp. 568-575.
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AbstractThe current study investigated the effects of neonatal infection with Chlamydia muridarum bacteria on glucocorticoid (GR) and mineralocorticoid (MR) receptors in the adult mouse hippocampus. In male adults infected at birth, circulating corticosterone was significantly increased when compared to same sex controls; while neonatal infection resulted in female adults with significantly increased GR mRNA compared to same sex controls. When comparing males and females after neonatal infection, males had significantly less GR protein than females. Interestingly, after control treatment, males had significantly more GR mRNA, MR mRNA, and GR protein with significantly lower corticosterone than females. Neonatal respiratory infection significantly impacts adult hippocampal GR and MR, and circulating corticosterone in a sex‐specific manner potentially altering stress responsivity. © 2011 Wiley Periodicals,Inc. Dev Psychobiol 54: 568–575, 2012.

Xiang, X, Gui, H, King, NJC, Cole, L, Wang, H, Xie, Q & Bao, S 2012, 'IL‐22 and non‐ELR‐CXC chemokine expression in chronic hepatitis B virus‐infected liver', Immunology & Cell Biology, vol. 90, no. 6, pp. 611-619.
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Hepatitis B virus infection is still a major global health problem, despite decades of research. Interleukin (IL)‐22 induces acute phase reactants and chemokines, favors anti‐microbial defence and protects tissues from damage. IL‐22 is important in chronic skin inflammation, but its role in chronic hepatitis B (CHB) is unclear. This study explores the association between intra‐hepatic IL‐22 expression, its relevant associated cytokines and the severity of liver inflammation/fibrosis in CHB patients. IL‐22, IL‐17, IL‐10, IL‐6, non‐ELR‐CXC chemokines (CXCL‐9, CXCL‐10, CXCL‐11), fibroblast growth factors and Kupffer cell (KC) numbers were measured in patients with CHB (n=65), acute hepatitis B (AHB; n=4), chronic hepatitis C (CHC; n=14) and non‐viral hepatitis (n=23), using immunohistochemistry. Expression of IL‐22, IL‐17, IL‐10, IL‐6, non‐ELR‐CXC chemokines and number of KCs in liver tissues were substantially higher in AHB patients than others. In CHB patients, the expression of IL‐22, IL‐6, CXCL‐9 and CXCL‐10 were significantly higher with alanine aminotransferase (ALT) levels ⩽twice the upper limit of normal (ULN), compared with those with ALT levels >twice the ULN, whereas IL‐10 and IL‐17 showed a reverse pattern. IL‐22 was inversely (P<0.01), but IL‐17 was positively (P<0.05), correlated with the histological activity index) in these patients, and a significant negative correlation between the fibrosis stage and IL‐22 or non‐ELR‐CXC chemokines was observed. Furthermore, immunofluorescent labeling demonstrated a close spatial association of IL‐22, CXCL‐9, ‐10 or ‐11 in the CHB liver. We speculate that IL‐22 and non‐ELR‐CXC chemokines synergistically may provide protection in liver inflammation/fibrosis during CHB infection.

Xiao, H & Fu, S 2012, 'A Sensitive Gas Chromatography-Mass Spectrometry Method for the Determination of Patulin in Apple Juice', JOURNAL OF AOAC INTERNATIONAL, vol. 95, no. 6, pp. 1709-1712.
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A simple and sensitive GC/MS method was developed for the detection of patulin in apple juice. The method utilized a common laboratory chemical, 3-nitrobenzyl alcohol, as an internal standard. The calibration curve, ranging from 5 to 100 µg/L, showed good linearity with a correlation coefficient of 0.999. The LOD and LOQ were 2 and 5 µg/L, respectively. The significant advantage of the method was removal of the need for in-house synthesis of appropriate internal standards as reported by other researchers. The method also eliminated the need for careful sample preparation procedures, as outlined in some AOAC methods in which no internal standard was utilized. The streamlined extraction process and the improved sensitivity warrant the developed method to be a useful alternative for drug testing laboratories, especially those with large specimen volume and throughput to determine patulin levels in apple juice.

Xiao, L, Lao, W-G, Tan, Y & Qu, X 2012, 'In Vitro Investigation of Anti-Diabetic Effect of Taxus cuspidate Extracts by Ultrasound Assisted Method', The American Journal of Chinese Medicine, vol. 40, no. 06, pp. 1205-1215.
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Extracting active components from Chinese medicinal herbs efficiently is a key step in the investigation of their pharmacological effects and modes of action. In this project, we compared the ultrasound-assisted method and the conventional solvent method for extracting the active compound of Taxus cuspidate (dong bei hong dou shan). Through the analysis of various extractions with a quadruple time-of-fight (Q-TOF) LC/MS, we demonstrated that the ultrasound-assisted method reduced solvent consumption and had shorter extraction time, while the extraction yields of the active compound (taxol) were equivalent to or even higher than those obtained with the conventional solvent extraction method. Through the comparison of Taxus cuspidate extracts (TCEs) with different concentrations of acetone and ethanol, we proved that 50% ethanol was an optimal solvent for extracting taxol from Taxus cuspidate. Based on traditional Chinese medicine (TCM) literature, we further determined whether TCEs possess antidiabetic effects by testing glucose uptake in 3T3-L1 adipocytes treated with TCEs from Taxus cuspidate bark and twigs under insulin stimulation (100 nM). The results showed that neither taxol (10 μg/ml) nor TCEs (1 and 0.1 mg/ml) changed glucose uptake significantly compared with insulin alone. This study demonstrated that the ultrasound-assisted method with 50% ethanol is a highly efficient approach for extracting Taxus cuspidate, which may be applicable for extraction of other Chinese medicinal herbs. Extracts of Taxus cuspidate bark and twigs had no effect on insulin stimulated-glucose uptake in vitro. This result conflicts with the description in TCM literature. Further in vivo study to clarify Taxus cuspidate's metabolic actions is necessary.

Xu, J, Jia, L, Ma, Y, Liu, X, Tian, H, Liu, W & Tang, Y 2012, 'Novel lanthanide hybrid functional materials for high performance luminescence application: The relationship between structures and photophysical behaviors', Materials Chemistry and Physics, vol. 136, no. 1, pp. 112-119.
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Xu, X, Li, WX, Zhang, Y, De Silva, KSB, Kim, JH & Choi, S 2012, 'The Effects of Graphene Doping on the In-Field J(c) of MgB2 Wires', JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, vol. 12, no. 2, pp. 1402-1405.
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Yang, M, Kumar, RK, Hansbro, PM & Foster, PS 2012, 'Emerging roles of pulmonary macrophages in driving the development of severe asthma', Journal of Leukocyte Biology, vol. 91, no. 4, pp. 557-569.
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ABSTRACTAsthma is recognized as a heterogeneous disorder, although in most patients, the clinical manifestations are effectively managed with established combination therapies. However, 5–10% of asthmatics have severe asthma, which does not respond to treatment, and these patients account for &gt;50% of asthma-related healthcare costs. New investigations into the pathogenesis of glucocorticoid resistance in severe asthma indicate that pulmonary macrophages may play central roles in promoting airway inflammation, particularly in asthma that is resistant to steroid therapy. Importantly, factors that are linked to the activation of pulmonary macrophages may contribute to glucocorticoid resistance and severe asthma. Here, we review recent advances in understanding the roles of pulmonary macrophages in the mechanisms of glucocorticoid resistance and the pathogenesis of severe asthma. We discuss the role of macrophage phenotype, infection, IFN-γ, LPS, associated signaling pathways, TNF-α, MIF, and other macrophage-associated factors. Understanding the pathogenesis of steroid-resistant severe asthma will contribute to the identification of optimal therapeutic strategies for the effective management of the disease.

Yi, GY, Ma, Y & Carroll, RJ 2012, 'A functional generalized method of moments approach for longitudinal studies with missing responses and covariate measurement error', Biometrika, vol. 99, no. 1, pp. 151-165.
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Abstract Covariate measurement error and missing responses are typical features in longitudinal data analysis. There has been extensive research on either covariate measurement error or missing responses, but relatively little work has been done to address both simultaneously. In this paper, we propose a simple method for the marginal analysis of longitudinal data with time-varying covariates, some of which are measured with error, while the response is subject to missingness. Our method has a number of appealing properties: assumptions on the model are minimal, with none needed about the distribution of the mismeasured covariate; implementation is straightforward and its applicability is broad. We provide both theoretical justification and numerical results.

Yin, L, Fristedt, R, Herdean, A, Solymosi, K, Bertrand, M, Andersson, MX, Mamedov, F, Vener, AV, Schoefs, B & Spetea, C 2012, 'Photosystem II Function and Dynamics in Three Widely Used Arabidopsis thaliana Accessions', PLoS ONE, vol. 7, no. 9, pp. e46206-e46206.
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Yin, S, Li, L, Yang, Y & Reimers, JR 2012, 'Challenges for the Accurate Simulation of Anisotropic Charge Mobilities through Organic Molecular Crystals: The beta Phase of mer-Tris(8-hydroxyquinolinato)aluminum(III) (Alq3) Crystal', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 116, no. 28, pp. 14826-14836.
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Quantitative agreement has been found between observed and calculated charge mobilities through organic conductors, despite the use of many assumptions in the calculations, including: the relative strength of the intermolecular electronic coupling to the reorganization energy driving charge localization, the treatment of site variability in the material, the involvement of tunneling processes during charge hopping between sites, the use of weak-coupling-based perturbation theory to determine hopping rates, the residence times for charges on sites, the effect of the large field strengths used in experimental studies, the general appropriateness of simple one-dimensional diffusion modeling approaches, and the involvement of molecular excited states of the ions. We investigate the impact of these assumptions, concluding that all may be very significant. In some cases, methodological options are considered, and optimum procedures are determined, showing that (i) the use of Koopmans' theorem to estimate intermolecular couplings in solids is problematic and (ii) the correct expression for the residence lifetime of a charge on a crystal site. These conclusions are drawn from simulations of anisotropic charge mobilities through the β phase of mer-tris(8- hydroxyquinolinato)aluminum(III) (Alq3) crystal, a material commonly used in OLED applications. Calculations are compared that determine mobilities at finite applied field from drift velocities through either semianalytical solutions of the master equation or else kinetic Monte Carlo simulations, as well as those that determine mobilities from multidimensional diffusion coefficients at zero field by Monte Carlo and those that analytically solve simplified one-dimensional diffusion models. For crystalline Alq3 itself, the calculations predict electron mobilities that are 4-6 orders of magnitude larger than those predicted by similar methods for amorphous Alq3, in agreement with experimental findings. This work v...

York, PH, Kelaher, BP, Booth, DJ & Bishop, MJ 2012, 'Trophic responses to nutrient enrichment in a temperate seagrass food chain', MARINE ECOLOGY PROGRESS SERIES, vol. 449, pp. 291-296.
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Simple ecological models that predict trophic responses to bottom-up forcing are valuable tools for ecosystem managers. Traditionally, theoretical ecologists have used resource-dependent functional responses to explain the modification of food chains exposed to bottom-up perturbations. These models predict alternating positive, negative and zero responses at each trophic level. More recently, ratio-dependent functional response models that predict proportional increases at each level have challenged this paradigm. The present study tested the predictions of the 2 hypotheses empirically by comparing the relative biomasses of 4 trophic levels of an estuarine seagrass food chain in relatively undisturbed, low-nutrient catchments and 'developed' catchments subjected to a prolonged period of nutrient enrichment. We found that nutrient-enriched sites had significantly greater biomass of both epiphytic algae and grazing invertebrates; however, the bottom- up forcing of nutrients was attenuated at higher trophic levels (occupied by juvenile and piscivorous fish), with no significant effect of catchment development. This disconnect in the upward cascade of energy may be due to a number of possible reasons including high levels of diversity and omnivory, trophic subsidy within the system or the strength or nature of perturbations. Although the predictions of both hypotheses failed to hold across all trophic groups, ratio dependence was prevalent at the lower levels of the food chain, which has implications for catchment management. © 2012 Inter-Research.

Younger, JS, Booth, DJ & Kurniawan, K 2012, 'Sustainable development – the East Bali poverty project', Proceedings of the Institution of Civil Engineers - Municipal Engineer, vol. 165, no. 1, pp. 43-58.
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Sustainable development is an essential objective for all governments, whether tasked with leading a fully industrialised country or grappling with the challenges faced by developing countries. Efforts to deal with some of the major issues of the world that have loomed over the past few decades such as water and sanitation and poverty, the scale of which has primarily resulted from very large population growth over the past half century, have generally failed. This is particularly noticeable in the fast industrialising countries of Asia and in parts of Africa. In more recent times, it has been recognised that resolution of poverty problems really only succeed if the people requiring assistance are directly and fully embraced in the solutions needed, along with the approaches and procedures adopted to tackle the problems. In this paper, details are presented of the approach taken to respond to the aspirations of a desperately poor community of 15 000 in a remote area of Bali, Indonesia, with difficult access, and raise it to a situation of sustainable development. In the beginning the elders of the community prioritised education for their children as a means of providing for a better future. Before the children could respond properly, serious health issues had to be addressed, and this meant taking a long-term and holistic view with a matching schedule of parallel infrastructure and social programmes, and full participation of the community. This privately funded integrated development is now in its eleventh year, and the many challenges and solutions to achieve sustainable development are described. The project provides many lessons for adaptation, and is already providing selective assistance elsewhere.

Yu, J-H, Park, J-W, Wang, Q, Ryu, H-S, Kim, K-W, Ahn, J-H, Kang, Y, Wang, G & Ahn, H-J 2012, 'Electrochemical properties of all solid state Li/S battery', Materials Research Bulletin, vol. 47, no. 10, pp. 2827-2829.
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All-solid-state lithium/sulfur (Li/S) battery is prepared using siloxane cross-linked network solid electrolyte at room temperature. The solid electrolytes show high ionic conductivity and good electrochemical stability with lithium and sulfur. In the first discharge curve, all-solid-state Li/S battery shows three plateau potential regions of 2.4 V, 2.12 V and 2.00 V, respectively. The battery shows the first discharge capacity of 1044 mAh g -1-sulfur at room temperature. This first discharge capacity rapidly decreases in 4th cycle and remains at 512 mAh g -1-sulfur after 10 cycles. © 2012 Elsevier Ltd. All rights reserved.

Yunusa, IAM, Loganathan, P, Nissanka, SP, Manoharan, V, Burchett, MD, Skilbeck, CG & Eamus, D 2012, 'Application of Coal Fly Ash in Agriculture: A Strategic Perspective', CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY, vol. 42, no. 6, pp. 559-600.
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Copyright © 2012 Crown copyright. Fly ash is a major waste of coal-power generation and its management is a major environmental and economic challenge, and it will become even more critical with a projected increase in the reliance on coal for power generation. The authors discuss how the unique physicochemical properties of ash can be strategically employed to ameliorate acidity and sodicity, and physical and fertility constraints, in agricultural soils. They show that with careful selection of ash type and methods and rates of application, mutually compatible with the soil and crop type, the often reported phytotoxicity due to high concentrations of certain trace metals can be avoided while maintaining the quality of produce and minimizing risk to the environment. Specific examples are presented to demonstrate where it is economical to use fly ash as a low-cost alternative to certain fertilizers and liming materials on farms. The authors also propose criteria for the selection of ash and for regulatory parameters that would ensure the safe and routine utilization of ash in plant production systems.

Zhang, L, Wang, M, Wang, C, Hu, X & Wang, G 2012, 'Label-free impedimetric immunosensor for sensitive detection of 2,4-dichlorophenoxybutyric acid (2,4-DB) in soybean', Talanta, vol. 101, pp. 226-232.
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Electrochemical impedance immunosensor, with its high sensitivity from electrochemical impedance analysis and ideal specificity from the immunoassay, is increasingly used in the detection of a kind of phenoxy acid herbicides which is 2,4-Dichlorophenoxybutyric acid (2,4-DB). In this experiment, synthetic 2,4-DB antibodies were immobilized on the electrode by the crosslinking of l-Cysteine/glutaraldehyde, and 2,4-DB were measured by the increase of electron-transfer resistance when the immune reaction occurred, with Fe(CN) 63-/Fe(CN)64- as the probe. Under optimal conditions, the change of resistance is in a linear relationship with the logarithm of the concentration in the range of 1.0×10 -7-1.0×10-3 g/L (R=0.994) with the detection limit of 1.0×10-7 g/L (0.1 ppb). This method bears such merits as simplicity in operation, high sensitivity, wide linear range, specificity, reproducibility and good stability. The actual soybean samples were analyzed with the recovery of 82.8%-102.3%. © 2012 Elsevier B.V. All rights reserved.

Zhang, L, Wang, Y, Ye, Z, Jin, D & Yuan, J 2012, 'New Class of Tetradentate β-Diketonate-Europium Complexes That Can Be Covalently Bound to Proteins for Time-Gated Fluorometric Application', Bioconjugate Chemistry, vol. 23, no. 6, pp. 1244-1251.
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Luminescent lanthanide complexes that can be covalently bound to proteins have shown great utility as biolabels for highly sensitive time-gated luminescence bioassays in clinical diagnostics and biotechnology discoveries. In this work, three new tetradentate β-diketonate-europium complexes that can be covalently bound to proteins to display strong and long-lived Eu 3+ luminescence, 1,2-bis[4′-(1″,1″,1″, 2″,2″,3″,3″-heptafluoro-4″,6″-hexanedion- 6″-yl)-benzyl]-4-chlorosulfobenzene-Eu3+ (BHHBCB-Eu 3+), 1,2-bis[4′-(1″,1″,1″,2″,2″- pentafluoro-3″,5″-pentanedion-5″-yl)-benzyl] -4-chlorosulfobenzene-Eu3+ (BPPBCB-Eu3+), and 1,2-bis[4′-(1″,1″,1″-trifluoro-2″, 4″-butanedion-4″-yl)-benzyl]-4-chlorosulfobenzene-Eu3+ (BTBBCB-Eu3+), have been designed and synthesized as biolabels for time-gated luminescence bioassay applications. The luminescence spectroscopy characterizations of the aqueous solutions of three complex-bound bovine serum albumin reveal that BHHBCB-Eu3+ has the strongest luminescence with the largest quantum yield (40%) and longest luminescence lifetime (0.52 ms) among the complexes, which is superior to the other currently available europium biolabels. The BHHBCB-Eu3+-labeled streptavidin was prepared and used for both the time-gated luminescence immunoassay of human prostate specific antigen and the time-gated luminescence microscopy imaging of a pathogenic microorganism Cryptosporidium muris. The results demonstrated the practical utility of the new Eu3+ complex-based biolabel for time-gated luminescence bioassay applications. (Chemical Equation Presented) © 2012 American Chemical Society.

Zhang, R, Ye, Z, Yin, Y, Wang, G, Jin, D, Yuan, J & Piper, JA 2012, 'Developing Red-Emissive Ruthenium(II) Complex-Based Luminescent Probes for Cellular Imaging', Bioconjugate Chemistry, vol. 23, no. 4, pp. 725-733.
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(Figure Presented) Ruthenium(II) complexes have rich photophysical attributes, which enable novel design of responsive luminescence probes to selectively quantify biochemical analytes. In this work, we developed a systematic series of Ru(II)- bipyrindine complex derivatives, [Ru(bpy) 3-n(DNP-bpy) n](PF 6) 2 (n = 1, 2, 3; bpy, 2,2′-bipyridine; DNP-bpy, 4-(4-(2,4- dinitrophenoxy)phenyl)-2, 2′-bipyridine), as luminescent probes for highly selective and sensitive detection of thiophenol in aqueous solutions. The specific reaction between the probes and thiophenol triggers the cleavage of the electron acceptor group, 2,4-dinitrophenyl, eliminating the photoinduced electron transfer (PET) process, so that the luminescence of on-state complexes, [Ru(bpy) 3-n(HP-bpy) n] 2+ (n = 1, 2, 3; HP-bpy, 4-(4-hydroxyphenyl)-2,2′- bipyridine), is turned on. We found that the complex [Ru(bpy)(DNP-bpy) 2] 2+ remarkably enhanced the on-to-off contrast ratio compared to the other two (37.8 compared to 21 and 18.7). This reveals a new strategy to obtain the best Ru(II) complex luminescence probe via the most asymmetric structure. Moreover, we demonstrated the practical utility of the complex as a cell-membrane permeable probe for quantitative luminescence imaging of the dynamic intracellular process of thiophenol in living cells. The results suggest that the new probe could be a very useful tool for luminescence imaging analysis of the toxic thiophenol in intact cells. © 2012 American Chemical Society.

Zhang, W, Zhang, R, Zhang, J, Ye, Z, Jin, D & Yuan, J 2012, 'Photoluminescent and electrochemiluminescent dual-signaling probe for bio-thiols based on a ruthenium(II) complex', Analytica Chimica Acta, vol. 740, pp. 80-87.
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Photoluminescence (PL) and electrochemiluminescence (ECL) detection techniques are highly sensitive and widely used methods for clinical diagnostics and analytical biotechnology. In this work, a unique ruthenium(II) complex, [Ru(bpy)2(DNBSO-bpy)](PF6)2 (bpy: 2,2'-bipyridine; DNBSO-bpy: 2,4-dinitrobenzenesulfonate of 4-(4-hydroxyphenyl)-2,2'-bipyridine), has been designed and synthesized as a highly sensitive and selective PL and ECL dual-signaling probe for the recognition and detection of bio-thiols in aqueous media. As a thiol-responsive probe, the complex can specifically and rapidly react with bio-thiols in aqueous solutions to yield a bipyridine-Ru(II) complex derivative, [Ru(bpy)2(HP-bpy)]2+ (HP-bpy: 4-(4-hydroxyphenyl)-2,2'-bipyridine), accompanied by the remarkable PL and ECL enhancements. The complex was used as a probe for the PL and ECL detections of cysteine (Cys) and glutathione (GSH) in aqueous solutions. The dose-dependent PL and ECL enhancements showed good linear relationships against the Cys/GSH concentrations with the detection limits at nano-molar concentration level. Moreover, the complex-loaded HeLa cells were prepared for PL imaging of the endogenous intracellular thiols. The results demonstrated the practical utility of the complex as a cell-membrane permeable probe for PL imaging detection of bio-thiols in living cells. © 2012 Elsevier B.V..

Zhao, C, Liu, C, Xia, J, Zhang, Y, Yu, Q & Eamus, D 2012, 'Recognition of key regions for restoration of phytoplankton communities in the Huai River basin, China', JOURNAL OF HYDROLOGY, vol. 420, pp. 292-300.
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Healthy phytoplankton communities are the basis of healthy water ecosystems, and form the foundation of many freshwater food webs. Globally many freshwater ecosystems are degraded because of intensive human activities, so water ecosystem restoration is a

Zhao, Z, Eamus, D, Yu, Q, Li, Y, Yang, H & Li, J 2012, 'Climate constraints on growth and recruitment patterns of Abies faxoniana over altitudinal gradients in the Wanglang Natural Reserve, eastern Tibetan Plateau', AUSTRALIAN JOURNAL OF BOTANY, vol. 60, no. 7, pp. 602-614.
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The radial growth and recruitment patterns of trees in subalpine areas are subject to the influence of changing environmental conditions associated with changes in elevation. To investigate responses of fir radial growth and recruitment to climate factors at different elevations, tree-ring width chronologies and age structures of Abies faxoniana were developed from five sampling sites at ∼28003300m elevation on the north-western and south-eastern aspects in the Wanglang Natural Reserve on the eastern edge of Tibetan Plateau. Statistical characteristics of the chronologies indicated that expressed population signal and signal-to-noise ratio increased with increasing elevation in the north-western aspect; the reverse was observed on the south-eastern aspect. Correlation analysis between chronologies and climate variables showed that fir radial growth was negatively correlated with previous growing season mean temperatures and was positively correlated with January precipitation in all plots. The amount of precipitation in the growing season (June and July) greatly influenced radial growth in the two lower sites of both the aspects. The three plots on the north-western aspect were characterised by significant rates of tree recruitment in the past five decades. There were multi-decadal periods of heightened recruitment over the past three centuries in the two south-eastern plots. Widespread disturbances after 1920s were not observed in any plots and the infrequent small-scale disturbances that occurred were not the main factors influencing recent recruitment in any plots. Correlation analysis between recruitment residuals and climate variables showed that fir seedling recruitment in the north-western aspect plots was mainly controlled by springsummer temperatures. But recruitment was greatly restricted by competition with dense bamboos and other tree species in the south-eastern aspect. Overall, previous August mean temperature and January precipitation wer...

Zhou, J, Teng, Y, Ye, S, Lin, G & Qiu, J 2012, 'A discussion on spectral modification from visible to near-infrared based on energy transfer for silicon solar cells', Optical Materials, vol. 34, no. 5, pp. 901-905.
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We report on spectral modification from visible to near-infrared (NIR) in Pr3+ and Yb3+ codoped oxyfluoride glass for c-Si solar cell. The excitation and emission spectra indicate the energy transfer from Pr3+ to Yb3+. The theoretical quantum efficiency is calculated based on the fluorescent lifetime and has reached more than 150%. However, the external quantum efficiency (EQE) of the Pr3+ and Yb3+ codoped glass covered on silicon solar cell is decreased compared to that of the host glass. The reasons of the negative effect of spectral modification on EQE are discussed and analyzed.

Zhou, J, Teng, Y, Zhou, S & Qiu, J 2012, 'Quantum Cutting in Luminescent Glasses and Glass Ceramics', International Journal of Applied Glass Science, vol. 3, no. 4, pp. 299-308.
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In the last decade, revolutions in photonic material design and large‐area nanostructure fabrication have given researchers and technologists tools to enable a new era of ultrahigh‐efficiency photovoltaics. Quantum cutting has received much attention as a potential approach to enhance the photovoltaic conversion efficiency of solar cell in the recent decades. In this article, we review the phenomena, mechanisms, and design of the quantum cutting processes, focusing on the promising applications of the transparent glasses and glass ceramic materials as the down‐converter of solar spectrum. We discuss the gaps between the current theoretical analysis and the practical applications of the quantum‐cutting materials. To concave the negative effects of using the quantum‐cutting materials as a down‐converter on the front surface of the solar cell, much attention should be given to the choice of material and improvement of the material properties as well as the integration of photonic nanostructures and circuits on the solar cell.

Zuccala, ES, Gout, AM, Dekiwadia, C, Marapana, DS, Angrisano, F, Turnbull, L, Riglar, DT, Rogers, KL, Whitchurch, CB, Ralph, SA, Speed, TP & Baum, J 2012, 'Subcompartmentalisation of Proteins in the Rhoptries Correlates with Ordered Events of Erythrocyte Invasion by the Blood Stage Malaria Parasite', PLOS ONE, vol. 7, no. 9, p. e46160.
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Host cell infection by apicomplexan parasites plays an essential role in lifecycle progression for these obligate intracellular pathogens. For most species, including the etiological agents of malaria and toxoplasmosis, infection requires active host-cell invasion dependent on formation of a tight junction - the organising interface between parasite and host cell during entry. Formation of this structure is not, however, shared across all Apicomplexa or indeed all parasite lifecycle stages. Here, using an in silico integrative genomic search and endogenous gene-tagging strategy, we sought to characterise proteins that function specifically during junction-dependent invasion, a class of proteins we term invasins to distinguish them from adhesins that function in species specific host-cell recognition. High-definition imaging of tagged Plasmodium falciparum invasins localised proteins to multiple cellular compartments of the blood stage merozoite. This includes several that localise to distinct subcompartments within the rhoptries. While originating from the same organelle, however, each has very different dynamics during invasion. Apical Sushi Protein and Rhoptry Neck protein 2 release early, following the junction, whilst a novel rhoptry protein PFF0645c releases only after invasion is complete. This supports the idea that organisation of proteins within a secretory organelle determines the order and destination of protein secretion and provides a localisation-based classification strategy for predicting invasin function during apicomplexan parasite invasion. © 2012 Zuccala et al.

Ajani, P 1970, 'How green is my ocean? Phytoplankton biodiversity in the coastal waters of New South Wales. Climate Futures Postgraduate Forum 2012, Macquarie University', P.
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Invited Oral Presentation

Ajani, P 1970, 'Microalgal diversity in the coastal waters of New South Wales (Invited Oral Presentation). UNESCO/Intergovernmental Oceanographic Commissions 10th Advanced Phytoplankton Course: Taxonomy and Systematics 2012, Denmark'.
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Invited Oral Presentation

Ajani, PA 1970, 'All Things Oysters', Oyster Farmer Workshops, Australia.
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Invited Oral Presentation

Alahyarizadeh, G, Aghajani, H, Mahmodi, H, Rahmani, R & Hassan, Z 1970, 'Effects of structure parameters on time response and power-current characteristics of InGaN/GaN single quantum well laser by solving rate equations', 2012 International Conference on Enabling Science and Nanotechnology, 2012 International Conference on Enabling Science and Nanotechnology (ESciNano), IEEE, pp. 1-2.
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Alkhouri, H, Wai-Shing, M, Krimmer, D, Oliver, B, Armour, C & Hughes, JM 1970, 'The effects of human lung mast cell products on the synthetic functions of lung fibroblasts', EUROPEAN RESPIRATORY JOURNAL, EUROPEAN RESPIRATORY SOC JOURNALS LTD.

Al-Zubaydi, AYT, Dartnall, J & Dowd, A 1970, 'Design, Construction and Calibration of an Instrument for Measuring the Production of Chilled Water by the Combined Effects of Evaporation and Night Sky Radiation', Volume 7: Fluids and Heat Transfer, Parts A, B, C, and D, ASME 2012 International Mechanical Engineering Congress and Exposition, American Society of Mechanical Engineers, Houston, Texas, USA, pp. 1523-1532.
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This paper presents the design and mathematical modeling of thermal radiator panels to be used primarily to measure night sky radiation from dry and wet coated surfaces. Three panels may be used in conjunction as a combined measuring system. One panel consists of an upper dry surface coated aluminum sheet laminated to an ethylene vinyl acetate foam backing block having a pattern of parallel flow water channels and header channels milled into its mating surface prior to lamination to the aluminum sheet. This configuration provides a fin and channel radiator instrument whereby circulating water may be used to measure the heat loss from this panel to night sky radiation. In a second configuration, the surface of a panel without buried water channels but otherwise identical may be wetted in order to study and compare the night sky radiation from its wet surface. In this case, the measuring water is circulated over the upper face of this panel. In a third configuration, water is sprayed onto the surface of the second panel (or a similar panel) so that an evaporative cooling effect is gained in addition to the radiation effect. Initial TRNSYS simulations for the performance of all three configurations are presented and it is planned to use the panels as calibrated instruments for discriminating between the cooling effects of night sky radiation and evaporation.

Angus, K, Thomas, P, Vessalas, K & Ray, A 1970, 'Investigation of ground flint glass as a supplementary cementitious material in autoclaved lime-silica binders', From Materials to Structures: Advancement Through Innovation - Proceedings of the 22nd Australasian Conference on the Mechanics of Structures and Materials, ACMSM 2012, Australasian Conference on the Mechanics of Structures and Materials, CRC Press, Sydney, Australia, pp. 247-249.
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A potential application for the use of cullet glass is as a supplementary cementitious material (SCM). Cullet is a ground soda-lime-silica glass waste that has the potential to react with calcium hydroxide (CH) produced as a secondary product from the hydration of Portland cement (PC) in forming principal calciumsilicate- hydrate (C-S-H) strengthening phases. Additionally, the relatively high sodium content of the glass has the potential to act as precursor for the activation of aluminosilicates such as fly ash (FA). This paper investigates this potential by using these wastes in autoclaved hydrated lime CH-silica systems. Compressive strengths of autoclaved compacted cylinders were evaluated and the results demonstrate that the addition of ground glass provides higher strength, when used as a partial silica substitute, and aids in the activation of FA. © 2013 Taylor & Francis Group.

Bruti Liberati, N & Platen, E 1970, 'On weak predictor-corrector schemes for jump-diffusion processes in finance', Topics in Numerical Methods for Finance: Proceedings in Mathematics and Statistics, Numerical Methods for Finance Conference, Springer, Limerick, Ireland, pp. 1-12.
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Event-driven uncertainties such as corporate defaults, operational failures, or central bank announcements are important elements in the modeling of financial quantities. Therefore, stochastic differential equations (SDEs) of jumpdiffusion type are often used in finance. We consider in this paper weak discrete time approximations of jump-diffusion SDEs which are appropriate for problems such as derivative pricing and the evaluation of risk measures. We present regular and jump-adapted predictorcorrector schemes with first and second order of weak convergence. The regular schemes are constructed on regular time discretizations that do not include jump times, while the jump-adapted schemes are based on time discretizations that include all jump times. A numerical analysis of the accuracy of these schemes when applied to the jump-diffusion Merton model is provided.

Büttner, TFS, Kabakova, IV, Hudson, DD, Pant, R, Li, E & Eggleton, BJ 1970, 'Multi-wavelength Gratings formed via cascaded Stimulated Brillouin Scattering', Optics Express, Optica Publishing Group, pp. 26434-26434.
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Byrnes, A, Pant, R, Poulton, CG, Li, E, Choi, D-Y, Madden, S, Luther-Davies, B, Eggleton, BJ & IEEE 1970, 'On-chip, Tunable, Narrow-Bandpass Microwave Photonic Filter Using Stimulated Brillouin Scattering (SBS)', 2012 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Lasers and Electro-Optics (CLEO), IEEE, San Jose, CA.

Campbell, LT, Simonin, AR, Padula, MP, Harry, E, Herbert, BR & Carter, DA 1970, 'The fungal secretome and virulence: Analysis of the proteins secreted by Cryptococcus gattii strains with different virulence profiles', MYCOSES, WILEY-BLACKWELL, pp. 163-163.

Chartrand, KM, Rasheed, M, Petrou, K & Ralph, PJ 1970, 'Establishing tropical seagrass light requirements in a dynamic port environment', Proceedings of the 12th International Coral Reef Symposium, Cairns, Australia, 9-13 July 2012, International Coral Reef Symposium, ReefBase, Cairns.
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Tropical seagrasses inhabit naturally turbid waters with dynamic light environments and variable water quality in coastal waters adjacent to the Great Barrier Reef. Large tidal fluxes amplify the magnitude of these conditions with extreme high and low light over relatively short time scales (i.e. hours). Large port developments in the region have the potential to confound the complex relationships between seagrass physiology and this dynamic light field with the onset of dredging and their associated turbid plumes. Understanding the capacity for seagrasses to respond to changes in the quantity and quality of the light environment will allow for prediction of how seagrass species and populations will tolerate changes in light attenuation that may occur during dredging. We present a strategy for determining seasonal-specific light requirements for an intertidal tropical seagrass community in a port environment. Locally relevant light requirements are established by describing the relationships among photosynthetic inputs and losses, tidal exposure, shifts in spectral light quality, seasonality and the capacity to utilise below ground carbon reserves. The outcomes of the study provide guidelines for a mitigation strategy that is focused on maintaining critical windows of light to support seagrass growth and the longer term survival of these productive coastal ecosystems.

Chen, Q, Peng, C, Wen, S-H & Shi, X-Y 1970, 'Synthesis and Characterization of Multifunctional Dendrimer-based Organic/Inorganic Hybrid Nanoparticles for Dual Mode CT/MR Imaging Applications', 2012 INTERNATIONAL FORUM ON BIOMEDICAL TEXTILE MATERIALS, PROCEEDINGS, International Forum on Biomedical Textile Materials (IFBMTM), DONGHUA UNIV PRESS, Donghua Univ, Shanghai, PEOPLES R CHINA, pp. 7-11.

Chong, HS, Campbell, LT, Padula, M, Harry, E, Hill, C, Li, S, Herbert, B, Wilkins, MR & Carter, DA 1970, 'The dynamic response of Cryptococcus gattii cells to fluconazole: a time-course analysis of the proteome and interactome', MYCOSES, WILEY-BLACKWELL, pp. 115-116.

Clementson, L, Gusmao, FM, Oubelkheir, K, ajani, P, Richardson, A & Steven, A 1970, 'Phytoplankton community composition in Moreton Bay after the January 2011 Brisbane floods', Coast to Coasts - Australia's National Coastal Conference 2012, Australia National Coastal Conference, Australian Coastal Councils Association Inc.
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Poster Presentation

Cornell, BA, Alkhamici, H, Brown, L, Carne, S, Goodchild, SC, Richards, R & Valenzuela, SM 1970, 'Ion Channel Proteins that Spontaneously Insert into Lipid Bilayer Membranes: An Impedance Spectroscopy Study Employing Tethered Membranes', BIOPHYSICAL JOURNAL, 56th Annual Meeting of the Biophysical-Society, CELL PRESS, San Diego, CA, pp. 682A-683A.
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Cranfield, CG, Deplazes, E, MacMillan, A, Owen, D, Nomura, T, Constantine, M, Corry, B & Martinac, B 1970, 'Clustering of the Mechanosensitive Ion Channels of Large and Small Conductance MscL and MscS - a FRET-Flim Study', BIOPHYSICAL JOURNAL, 56th Annual Meeting of the Biophysical-Society, CELL PRESS, San Diego, CA, pp. 120A-120A.
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Deplazes, E, Jayatilaka, D, Louhivuori, M, Marrink, S-J & Corry, B 1970, 'A Model of the Open Pore MscL Based on Experimental Data and Restrained Coarse Grained Simulations', Biophysical Journal, Elsevier BV, pp. 121a-122a.
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Faiz, A, Tjin, G, Harkness, LM, Oliver, B, Black, JL & Burgess, JK 1970, 'Secreted Cathepsin H Activity Is Regulated By Corticosteroids And May Affect Airway Remodelling In Asthma', A68. TISSUE REMODELING IN THE LUNG, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A2147-A2147.
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Freeman, LM, Koh, B, Edwards, J & Zaslawski, CJ 1970, 'Defining Alternative Medicine in the Context of Athletic Performance and the Spirit of Sports: D(etermination), O(bservance), P(ermissibility) or E(ducation', Proceedings International Conference on Sports and Society, 3rd International Conference on Sports and Society, Common Ground, Cambridge, UK.

Ge, Q, Krimmer, D, Chen, L, Burgess, JK, Black, J & Oliver, BG 1970, 'Cigarette Smoke Induces A Distinct Fibrotic Signature In Bronchial Epithelial Cells', A64. LOCAL AND SYSTEMIC EFFECTS OF SMOKE EXPOSURE, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A2021-A2021.
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Ge, Q, Krimmer, D, Chen, L, Burgess, JK, Black, JL & Oliver, BG 1970, 'CIGARETTE SMOKE INDUCES A DISTINCT FIBROTIC SIGNATURE IN BRONCHIAL EPITHELIAL CELLS IN COMPARISON TO TGFB', RESPIROLOGY, WILEY-BLACKWELL, pp. 30-30.

Gerrits, T, Thomas-Peter, N, Gates, JC, Lita, AE, Metcalf, BJ, Calkins, B, Tomlin, NA, Fox, AE, Lamas Linares, A, Spring, JB, Langford, NK, Mirin, RP, Smith, PGR, Walmsley, IA & Nam, SW 1970, 'On-chip, photon-number-resolving, telecom-band detectors for scalable photonic information processing', Optics InfoBase Conference Papers.
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We demonstrate an integrated photon-number resolving detector, operating in the telecom band at 1550 nm, employing an evanescently coupled design that allows the detector to be placed at arbitrary locations within a planar optical circuit. Up to 5 photons are resolved in the guided optical mode via absorption from the evanescent field into a tungsten transition-edge sensor. The detection efficiency of the absorbing tungsten region is 7.2 %. © OSA 2012.

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 1970, 'On-chip, photon-number-resolving, telecom-band detectors for scalable photonic information processing', 2012 Conference on Lasers and Electro-Optics, CLEO 2012.
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We demonstrate an integrated photon-number resolving detector, operating in the telecom band at 1550 nm, employing an evanescently coupled design that allows the detector to be placed at arbitrary locations within a planar optical circuit. Up to 5 photons are resolved in the guided optical mode via absorption from the evanescent field into a tungsten transition-edge sensor. The detection efficiency of the absorbing tungsten region is 7.2 %. © 2012 OSA.

Godecke, E, Rai, T, Ciccone, NA, Granger, AS, West, D, Cream, A, Cartwright, J & Hankey, G 1970, 'European Stroke Conference. 21st Conference, Lisbon, May 2012: Abstract e-Book', Cerebrovascular Diseases, European Stroke Conference, S. Karger AG, Lisbon, Portugal, pp. 1-2.
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URL: http://content.karger.com/ProdukteDB/miscArchiv/CED_2012_033_s_2/index.html#/1/

Gräfe, M, Solntsev, AS, Keil, R, Tünnermann, A, Nolte, S, Szameit, A, Sukhorukov, AA & Kivshar, YS 1970, 'Classical optical simulation of Bi-photon generation in quadratic waveguide arrays', Optics InfoBase Conference Papers, Conference on Lasers and Electro-Optics (CLEO), IEEE, San Jose, CA.
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We suggest and demonstrate experimentally that evolution of classical light can simulate bi-photon generation through spontaneous parametric downconversion and correlated quantum walks in waveguide arrays, including violation of Bell's inequality. © 2012 OSA.

Gräfe, M, Solntsev, AS, Keil, R, Tünnermann, A, Nolte, S, Szameit, A, Sukhorukov, AA & Kivshar, YS 1970, 'Classical optical simulation of bi-photon generation in quadratic waveguide arrays', CLEO: Applications and Technology, CLEO_AT 2012.
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We suggest and demonstrate experimentally that evolution of classicallight can simulate bi-photon generation through spontaneous parametric downconversion and correlated quantum walks in waveguide arrays, including violation of Bell's inequality. © 2011 Optical Society of America.

Gräfe, M, Solntsev, AS, Keil, R, Tünnermann, A, Nolte, S, Szameit, A, Sukhorukov, AA & Kivshar, YS 1970, 'Classical Optical Simulation of Bi-Photon Generation in Quadratic Waveguide Arrays', Conference on Lasers and Electro-Optics 2012, CLEO: Applications and Technology, OSA, pp. JW4A.104-JW4A.104.
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We suggest and demonstrate experimentally that evolution of classicallight can simulate bi-photon generation through spontaneous parametric downconversion and correlated quantum walks in waveguide arrays, including violation of Bell's inequality. © 2011 Optical Society of America.

Gräfe, M, Solntsev, AS, Keil, R, Tünnermann, A, Nolte, S, Szameit, A, Sukhorukov, AA & Kivshar, YS 1970, 'Classical Optical Simulation of Bi-Photon Generation in Quadratic Waveguide Arrays', Advanced Photonics Congress, Nonlinear Photonics, OSA, pp. NW2D.2-NW2D.2.
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We suggest and demonstrate experimentally that evolution of classical light can simulate bi-photon generation through spontaneous parametric downconversion and correlated quantum walks in waveguide arrays, including violation of Bell's inequality. © 2011 Optical Society of America.

Greentree, AD, Henderson, MR, Gibson, BC, Ebendorff-Heidepriem, H, Kuan, K, Afshar, S, Orwa, JO, Aharonovich, I, Karle, TJ, Tomljenovic-Hanic, S, Prawer, S, Monro, TM & IEEE 1970, 'Diamond in glass, a new platform for quantum photonics', 2012 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Lasers and Electro-Optics, IEEE, San Jose, CA, USA.
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Diamond color centers represent one of the most important frontiers for room-temperature solid-state quantum devices. Here we show the incorporation of fluorescent diamond nanoparticles into tellurite glass optical fibers. This system offers a new platform for quantum sensing and robust single photon collection and distribution. © 2012 OSA.

Gu, H, Stuckey, PJ & Wallace, MG 1970, 'Maximising the Net Present Value of Large Resource-Constrained Projects', Principles and Practice of Constraint Programming - CP 2012, International Conference on Principles and Practice of Constraint Programming, Springer Berlin Heidelberg, Québec City, QC, Canada, pp. 767-781.
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Gu, H, Wallace, Mark.G. & Stuckey, Peter.J. 1970, 'An improved Lagrangian relaxation method for maximising the net present value of large resource-constrained projects', The 20th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2012), International Symposium on the Mathematical Theory of Networks and Systems, Melbourne, Victoria.

Hahn, MA, Dickson, K-A, Jackson, S, Clarkson, A, Gill, AJ & Marsh, DJ 1970, 'Abstract 2167: The tumor suppressor CDC73/parafibromin is required for the maintenance of histone 2B monoubiquitination both in vitro and in vivo', Cancer Research, Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL, American Association for Cancer Research (AACR), pp. 2167-2167.
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Abstract CDC73 (cell division cycle 73), also known as parafibromin, is a ubiquitously expressed tumor suppressor that is mutated in the germline of patients with the familial disorder Hyperparathyroidism Jaw Tumor syndrome, as well as somatically mutated in sporadic parathyroid cancer. Furthermore, CDC73 has been implicated in breast, gastric, renal and colorectal tumorigenesis. CDC73 is a member of the PAF1 (RNA polymerase II-associated factor 1) transcriptional complex (PAF1c), along with PAF1, CTR9, LEO1, and SKI8. Consistent with roles in transcription, CDC73 is localized to the nucleus, and has also been reported in the nucleolus. This tumor suppressor has been shown to function as a negative regulator of cell cycle progression and to promote apoptosis, as well as have a role in the regulation of 3′ processing of histone mRNA. We used CDC73 as bait in a yeast two-hybrid assay and identified the E3 ubiquitin ligase ring finger proteins RNF20 and RNF40 as CDC73 binding partners. RNF20 and RNF40 exist in a heterodimeric complex that functions to monoubiquitinate histone H2B at lysine 120 (H2B-K120). Monoubiquitination of H2B-K120 is associated with transcription in undamaged cells, is induced after DNA damage, and has a role in the maintenance of replication-dependent histone mRNA 3′ - end processing. We have confirmed the interaction of CDC73 with both RNF20 and RNF40 in mammalian cells by co-immunoprecipitation of overexpressed and endogenous proteins from human embryonic kidney (HEK293) cells. Down-regulation of endogenous CDC73 by siRNA in HEK293 cells and the breast cancer cell line MCF7 led to a significant reduction of monoubiquitinated H2B-K120. Furthermore, in a series of eleven parathyroid carcinomas harboring mutations in CDC73 that led to loss of nuclear CDC73, monoubiquitinated H2B-K120 was either absent or significantly reduced relative to benign parathyroid tumors that expressed nuclear C...

Hansbro, PM, Horvat, JC, Essilfie, A-T, Kim, RYH, Starkey, MR, Mayall, JR, Beckett, EL & Foster, PS 1970, 'Efficacy Of Antibiotic-Based Therapeutic Strategies For The Treatment Of Infection-Induced, Steroid-Resistant Allergic Airways Disease', B37. NEW INSIGHTS INTO ASTHMA AND COPD TREATMENT, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A2863-A2863.
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Harkness, LM, Ashton, A, Oliver, B & Burgess, JK 1970, 'The Anti-Angiogenic Function Of Tumstatin In The Asthmatic Lung', A108. AIRWAYS HYPERRESPONSIVENESS: CAUSES AND TREATMENTS, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A2410-A2410.
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Harkness, LM, Ashton, AW, Oliver, BG & Burgess, JK 1970, 'TSANZ Poster Abstracts', Respirology, Wiley, pp. 42-87.
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Horvat, JC, Essilfie, A-T, Kim, RY, Mayall, JR, Starkey, MR, Beckett, EL, Foster, PS & Hansbro, PM 1970, 'EFFICACY OF ANTIBIOTIC-BASED THERAPEUTIC STRATEGIES FOR THE TREATMENT OF INFECTION-INDUCED, STEROID-RESISTANT ALLERGIC AIRWAYS DISEASE', RESPIROLOGY, WILEY-BLACKWELL, pp. 27-27.

Howell, VM, Dickson, K-A, Kan, CWS, Hahn, MA & Marsh, DJ 1970, 'Abstract 3150: miR-100 in ovarian cancer cell lines', Cancer Research, Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL, American Association for Cancer Research (AACR), pp. 3150-3150.
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Abstract MicroRNA (miRNA), small non-coding RNA sequences that regulate gene expression, have the potential to function as tumor suppressors or oncogenes. To determine the contribution of miRNA to ovarian oncogenesis this project sought to identify dysregulated miRNA and their targets in ovarian cancer cell lines. miRNA expression profiling was performed on 6 serous epithelial ovarian cancer (SEOC) cell lines and normal ovarian surface epithelial (OSE) cells. miRNAs differentially expressed between SEOC and OSEs were selected for further analyses and candidate target genes identified by prediction algorithms. miRNA expression was restored by transient transfection of miRNA mimics or stable transduction of lentiviral vectors expressing miRNA precursors. The effects on the expression of 2 predicted targets, SMARCA5 and FRAP1, were investigated using a luciferase reporter system, quantitative RT-PCR (qPCR) and immunoblotting. The effect of miRs on cellular proliferation was also explored. Expression profiling identified miR-100 as having &gt;5-fold lower expression in SEOC vs OSE cells. Seed sequences or binding sites for miR-100 were identified in the 3′UTRs of SMARCA5 and FRAP1. Using a luciferase expression system in OVCAR-3 cells, a miR-100 mimic repressed expression of SMARCA5 3′UTR by 40 % (p&lt;0.0001), and FRAP1 3′UTR by 30% (p&lt;0.0005). No effect of the mimic was observed when the predicted miR-100 binding sites in each gene's 3′UTR were mutated. Stable transduction of OV202 cells with pre-miR-100 resulted in a 3-5 fold increase in miR-100 expression. This stably transduced SEOC cell line showed decreased cellular proliferation, and repressed transcript and protein levels of SMARCA5/SNF2H and FRAP1/mTOR compared with the cell line transduced with the empty lentiviral vector. We identified miR-100 as a modulator of cellular proliferation in OV202 cells, possibly through regulation of SNF...

Howes, J, Ralph, P, Stuart, B & Gardner, S 1970, 'Biochemical energy balance of the coral symbiosis using vibrational spectroscopy', 12th International Coral Reef Symposium, Cairns.

Hsu, A, Parsons, K, Barr, I, Hansbro, P & Wark, PAB 1970, 'DEFICIENT ANTIVIRAL RESPONSES TO INFLUENZA IN PRIMARY BRONCHIAL EPITHELIAL CELLS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE', RESPIROLOGY, WILEY-BLACKWELL, pp. 24-24.

Hsu, S-H, Paoletti, C, Torres, M, Ritchie, RJ, Larkum, AWD & Grillet, C 1970, 'Light transmission of the marine diatom Coscinodiscus wailesii', SPIE Proceedings, SPIE Smart Structures and Materials + Nondestructive Evaluation and Health Monitoring, SPIE, San Diego, United States, pp. 1-8.
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The results of a detailed investigation of light transmission behavior of a centric marine diatom species Coscinodiscus wailesii are reported. We measured 3-dimentional intensity distributions of both broadband and monochromatic light transmitted through individual valves of the diatom in air and water. Cross-sectional intensity profiles of transmitted light indicates valves of C. wailesii can concentrate light into certain regions. At a distance from the valve shorter than its diameter, light intensities close to the optical axis are relatively higher than those in the surrounds; at a longer distance, transmitted light intensities display ring-shaped profiles. The distance showing this light concentration characteristic becomes shorter as the wavelength of incoming light goes up. These results may offer insight into the understanding of biological functions of diatom frustules' intricate structures and inspire new optical biomimetic applications.

Huyang, G, Canning, J, Bishop, D, McDonagh, A & Crossley, MJ 1970, 'An evaluation of the distribution of metal ions in otherwise uniform titania sol-gel layers designed for optical sensing using laser ablation inductive coupled plasma mass spectroscopy', SPIE Proceedings, OFS2012 22nd International Conference on Optical Fiber Sensor, SPIE, Beijing, China.
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Free-base porphyrins are bound to titania sol-gel layers deposited on glass slides. The porphyrin-containing titania layers show the UV-VIS spectra of the porphyrin and are found to be uniformly and evenly distributed. By addition of a metal salt to the titania layer, it was possible to metallate the free-base porphyrin within and change the UV-VIS absorbance of the porphyrin. The metalloporphyrins based on Cu and Zn ions could be detected by laser ablation inductive coupled plasma mass spectroscopy (LA-ICP-MS). Aggregation of metals is observed indicating that metal ions are also attaching directly to the titania. In samples where already metalized porphyrins are used little or no aggregation is observed, indicating that the titania sol gel is non-uniform in its affinity for metal ions. © 2012 SPIE.

Jaffar, J, Tan, X, Black, JL, Oliver, BG, Argraves, WS, Twal, WO & Burgess, JK 1970, 'The Release Of Soluble Fibulin-1 From Airway Epithelial Cells Is Increased By Transforming Growth Factor Beta', D108. OUT OF CONTROL: PROLIFERATIVE AND FIBROTIC REMODELING OF THE LUNG, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A6684-A6684.
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Jaffar, J, Tan, X, Black, JL, Oliver, BG, Argraves, WS, Twal, WO & Burgess, JK 1970, 'TRANSFORMING GROWTH FACTOR BETA INCREASES THE RELEASE OF SOLUBLE FIBULIN-1 FROM AIRWAY EPITHELIAL CELLS', RESPIROLOGY, WILEY-BLACKWELL, pp. 42-42.

Jaffar, J, Tan, X, Black, JL, Oliver, BG, Corte, T, Wolters, P, Argraves, WS, Twal, WO & Burgess, JK 1970, 'The Serum Level Of Fibulin-1 Is Elevated In Idiopathic Pulmonary Fibrosis', C103. PATHOGENESIS, BIOMARKERS, AND RISK FACTORS FOR INTERSTITIAL LUNG DISEASE: FROM BENCH TO BEDSIDE, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A5173-A5173.
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James, PR, Van Ly, D, Hansbro, PM, Burgess, JK, Black, JL & Oliver, B 1970, 'Phosphodiesterase-4 Enzyme Inhibitors Do Not Affect Rhinovirus Induced Cytokine Release Or Replication', D35. PHOSPHODIESTERASE INHIBITORS AS THERAPEUTICS FOR LUNG DISEASES, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A5702-A5702.
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Jennings, EM, Morris, JS, Carroll, RJ, Manyam, GC & Baladandayuthapani, V 1970, 'Hierarchical Bayesian methods for integration of various types of genomics data', Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), IEEE, pp. 5-8.
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Kan, C, Hahn, M, Cowley, M, Kaplan, W, Howell, V & Marsh, D 1970, '517 Genomic Instability is a Hallmark Feature of Serous Epithelial Ovarian Cancer and May Contribute to MicroRNA Dysregulation', European Journal of Cancer, Elsevier BV, pp. S123-S123.
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Keely, S, Baird, A, Kominsky, D, McNamee, EN, Hansbro, PM, Shalwitz, RA & Colgan, SP 1970, 'Immune modulation by prolyl hydroxylase inhibition contributes to the prevention of endotoxemia in a murine model of inflammatory bowel disease.', The FASEB Journal, Experimental Biology Meeting, Wiley, San Diego, CA.
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Hypoxia‐inducible factor (HIF) prolyl hydroxylation inhibition (PHDi) has been shown to reduce mucosal disease severity in murine models of colitis at several levels of clinical and biochemical scoring. However, little is known about PHDi influence on systemic immune function during mucosal inflammation. Induction of TNBS colitis leads to an early pyrogenic response (fever), followed by a cryogenic response (hypothermia) due to bacteremia. We hypothesized that PHDi modulates systemic immune responses to bacteremia, associated with colitis. TNBS colitis mice, were treated with AKB‐4924, a HIF‐1 isoform‐predominant PHD inhibitor. AKB‐4924 treatment led to significantly reduced weight loss and disease activity, compared to vehicle. AKB‐4924 groups were pyrogenic, but did not become cryogenic. AKB‐4924 augmented epithelial barrier function and led to a 50‐fold reduction in serum endotoxin during colitis. AKB‐4924 modulated cytokines involved in pyrogenesis and cryogenesis, significantly reducing serum levels of IL‐1β (2‐fold), IL‐6 (17‐fold) and TNF‐α (3‐fold), while increasing IL‐10 (2‐fold). Neutrophils exhibited increased phagocytotic capacity and reduced TNF‐α expression (2‐fold) with AKB‐4924 pretreatment. Together, these results suggest that AKB‐4924 may prevent TNBS colitis induced endotoxemia on a multifactorial level, through previously unappreciated systemic mechanisms.

Kehr, B, Reinert, K & Darling, AE 1970, 'Hidden breakpoints in genome alignments', WABI, Workshop on Algorithms in Bioinformatics (WABI), Springer, Ljubljana, Slovenia,, pp. 391-403.
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During the course of evolution, an organism's genome can undergo changes thataffect the large-scale structure of the genome. These changes include genegain, loss, duplication, chromosome fusion, fission, and rearrangement. Whengene gain and loss occurs in addition to other types of rearrangement,breakpoints of rearrangement can exist that are only detectable by comparisonof three or more genomes. An arbitrarily large number of these 'hidden'breakpoints can exist among genomes that exhibit no rearrangements in pairwisecomparisons. We present an extension of the multichromosomal breakpoint median problem togenomes that have undergone gene gain and loss. We then demonstrate that themedian distance among three genomes can be used to calculate a lower bound onthe number of hidden breakpoints present. We provide an implementation of thiscalculation including the median distance, along with some practicalimprovements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints insimulated data sets under a wide range of evolutionary scenarios. Wedemonstrate that in simulations the hidden breakpoint counts depend strongly onrelative rates of inversion and gene gain/loss. Finally we apply currentmultiple genome aligners to the simulated genomes, and show that all alignersintroduce a high degree of error in hidden breakpoint counts, and that thiserror grows with evolutionary distance in the simulation. Our results suggestthat hidden breakpoint error may be pervasive in genome alignments.

Leif, RC, Yang, S, Lu, Y, Jin, D & Chambers, S 1970, 'A cost-effective analog method to produce time-gated luminescence images', SPIE Proceedings, SPIE BiOS, SPIE, San Francisco, California, United States, pp. 82250Z-82250Z.
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Time-gated luminescence images were obtained by analog summation of a series of sequential images that were obtained with a cooled modified interline CCD camera, and a fluorescence microscope modified to use a UV LED for illumination. The interline CCD camera obtains an analog sum of a multi-frame image by not reading out the storage line after each frame is acquired; instead, the charges from the acquisition pixels are transferred to the storage pixels, which adds them to those previously stored; subsequently, the sum of the images is readout from the storage pixels and digitized. The length of the exposure is limited by the capacity of the storage pixels and the rate of generation of background (noise). Previously, the quality of the images obtained with the room temperature camera was degraded by the buildup of thermal noise. The interline transfer, electronically shuttered, cooled astronomy CCD camera, which was modified for analog summation rapidly produced low noise images; yet permitted long exposures. The past problems with lanthanide dyes of low extinction coefficients and equipment cost have now been solved. © 2012 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

Liu, Y, Xie, H, Alonas, E, Santangelo, PJ, Jin, D & Xi, P 1970, 'CW STED nanoscopy with a Ti:Sapphire oscillator', SPIE Proceedings, Photonics Asia, SPIE, Beijing, China, pp. 85531B-85531B.
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Fluorescence microscopy has become an essential tool to study biological molecules, pathways and events in living cells, tissues and animals. Meanwhile, the conventional optical microscopy is limited by the wavelength of the light. Even the most advanced confocal microscopy or multiphoton microscopy can only yield optical resolution approaching the diffraction limit of ~200 nm. This is still larger than many subcellular structures, which are too small to be resolved in detail. These limitations have driven the development of super-resolution optical imaging methodologies over the past decade. The stimulated emission depletion (STED) microscopy was the first and most direct approach to overcoming the diffraction limit for far-field nanoscopy. Typically, the excitation focus is overlapped by an intense doughnut-shaped spot to instantly de-excite markers from their fluorescent state to the ground state by stimulated emission. This effectively eliminates the periphery of the Point Spread Function (PSF), resulting in a narrower focal region, or super-resolution. Scanning a sharpened spot through the specimen renders images with sub-diffraction resolution. Multi-color STED imaging can present important structural and functional information for protein-protein interaction. In this work, we presented a dual color, synchronization-free STED stimulated emission depletion (STED) microscopy with a Ti:Sapphire oscillator. The excitation wavelengths were 532nm and 635nm, respectively. With pump power of 4.6 W and sample irradiance of 310 mW, we achieved super-resolution as high as 71 nm. We also imaged 200 nm nanospheres as well as all three cytoskeletal elements (microtubules, intermediate filaments, and actin filaments), clearly demonstrating the super-resolution resolving power over conventional diffraction limited imaging. It also allowed us to discover that, Dylight 650, exhibits improved performance over ATTO647N, a fluorophore frequently used in STED. Furtherm...

Lu, J, Whitchurch, C, Turnbull, L, Carter, D, Schlothauer, R & Harry, L 1970, 'THE THERAPEUTIC USE OF HONEY ON CHRONIC WOUND INFECTIONS', WOUND REPAIR AND REGENERATION, pp. A73-A73.

Ma, X, Huete, A, Yu, Q, Davies, K & Coupe, NR 1970, 'MONITORING SPATIAL PATTERNS OF VEGETATION PHENOLOGY IN AN AUSTRALIAN TROPICAL TRANSECT USING MODIS EVI', XXII ISPRS CONGRESS, TECHNICAL COMMISSION VIII, XXII International Society for Photogrammetry & Remote Sensing Congress., ISPRS Society, Melbourne, Australia, pp. 271-276.
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Phenology is receiving increasing interest in the area of climate change and vegetation adaptation to climate. The phenology of a landscape can be used as a key parameter in land surface models and dynamic global vegetation models to more accurately simulate carbon, water and energy exchanges between land cover and atmosphere. However, the characterisation of phenology is lacking in tropical savannas which cover more than 30% of global land area, and are highly vulnerable to climate change. The objective of this study is to investigate the spatial pattern of vegetation phenology along the Northern Australia Tropical Transect (NATT) where the major biomes are wet and dry tropical savannas. For this analysis we used more than 11 years Moderate Resolution Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI) product from 2000 to 2011. Eight phenological metrics were derived: Start of Season (SOS), End of Season (EOS), Length of Season (LOS), Maximum EVI (MaxG), Minimum EVI (MinG), annual amplitude (AMP), large integral (LIG), and small integral (SIG) were generated for each year and each pixel. Our results showed there are significant spatial patterns and considerable interannual variations of vegetation phenology along the NATT study area. Generally speaking, vegetation growing season started and ended earlier in the north, and started and ended later in the south, resulting in a southward decrease of growing season length (LOS). Vegetation productivity, which was represented by annual integral EVI (LIG), showed a significant descending trend from the northern part of NATT to the southern part. Segmented regression analysis showed that there exists a distinguishable breakpoint along the latitudinal gradient, at least in terms of annual minimum EVI (EVI), which is located between 18.84"S to 20.04"S.

Mahmodi, H, Hashim, MR & Allahyarzadeh, G 1970, 'Design and study of a GeSn-SiGeSn single quantum well structure for infrared photodetection', 2012 International Conference on Enabling Science and Nanotechnology, 2012 International Conference on Enabling Science and Nanotechnology (ESciNano), IEEE, pp. 1-2.
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Mueller, P, Turnbull, L, Schlothauer, R, Whitchurch, C & Harry, E 1970, 'NEW ZEALAND MANUKA HONEY HELPS HUMAN KERATINOCYTES TO SURVIVE IN PRESENCE OF S-AUREUS', WOUND REPAIR AND REGENERATION, WILEY-BLACKWELL, pp. A75-A75.

Ng, C, Raingeard, D, Chan, A, Steinberg, P & McDougald, D 1970, 'qPCR detection of hepto- and neuro- cyanotoxins in a Singaporean reservoir system', Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, European Society for Comparative Physiology and Biochemistry, Elsevier BV, pp. S26-S26.
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Ng, HY, Oliver, BG, Burgess, JK, Krymskaya, VP, Black, JL & Moir, LM 1970, 'Collagen IV α5 (Lamstatin) Decreases Proliferation And Migration Of Lymphangioleiomyomatosis (LAM)–Cell Like TSC2-Negative Mouse Embryonic Fibroblasts', D108. OUT OF CONTROL: PROLIFERATIVE AND FIBROTIC REMODELING OF THE LUNG, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A6692-A6692.
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Ng, HY, Oliver, BGG, Burgess, JK, Krymskaya, VP, Black, JL & Moir, LM 1970, 'PROLIFERATION AND MIGRATION OF TSC2-NULL MOUSE EMBRYONIC FIBROBLASTS IS INHIBITED BY THE NC1 DOMAIN OF COLLAGEN IV A5 (LAMSTATIN)', RESPIROLOGY, WILEY-BLACKWELL, pp. 53-53.

Nunn, J, Langford, NK, Champion, T, Sprague, MR, Michelberger, PS, Lee, KC, Jin, XM, England, D, Kolthammer, WS & Walmsley, IA 1970, 'Synchronizing single photons with quantum memories', 2012 Conference on Lasers and Electro-Optics, CLEO 2012.
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Without deterministic single photon sources, multiphoton rates fall exponentially with the number of photons required, making practical photonics unfeasible. We show how quantum memories improve multiphoton rates by many orders of magnitude. © 2012 OSA.

Nunn, J, Langford, NK, Champion, T, Sprague, MR, Michelberger, PS, Lee, KC, Jin, XM, England, D, Kolthammer, WS & Walmsley, IA 1970, 'Synchronizing single photons with quantum memories', CLEO: Applications and Technology, CLEO_AT 2012.
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Without deterministic single photon sources, multiphoton rates fall exponentially with the number of photons required, making practical photonics unfeasible. We show how quantum memories improve multiphoton rates by many orders of magnitude. copy; 2011 Optical Society of America.

Nunn, J, Langford, NK, Champion, T, Sprague, MR, Michelberger, PS, Lee, KC, Jin, XM, England, D, Kolthammer, WS & Walmsley, IA 1970, 'Synchronizing single photons with quantum memories', CLEO: Applications and Technology, CLEO_AT 2012.
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Without deterministic single photon sources, multiphoton rates fall exponentially with the number of photons required, making practical photonics unfeasible. We show how quantum memories improve multiphoton rates by many orders of magnitude. copy; 2011 Optical Society of America.

Nunn, J, Langford, NK, Champion, T, Sprague, MR, Michelberger, PS, Lee, KC, Jin, XM, England, D, Steven Kolthammer, W & Walmsley, IA 1970, 'Synchronizing single photons with quantum memories', Optics InfoBase Conference Papers.
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Without deterministic single photon sources, multiphoton rates fall exponentially with the number of photons required, making practical photonics unfeasible. We show how quantum memories improve multiphoton rates by many orders of magnitude. © 2011 Optical Society of America.

Pant, R, Byrnes, A, Li, E, Choi, D-Y, Poulton, CG, Fan, S, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'Photonic chip based tunable and dynamically reconfigurable microwave photonic filter using stimulated Brillouin scattering', Advanced Photonics Congress, Bragg Gratings, Photosensitivity, and Poling in Glass Waveguides, OSA, pp. JW4D.5-JW4D.5.
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Pant, R, Byrnes, A, Poulton, CG, Li, E, Choi, D-Y, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'On-chip slow and fast light using stimulated Brillouin scattering', Advanced Photonics Congress, Integrated Photonics Research, Silicon and Nanophotonics, OSA, Colorado Springs, Colorado United States, pp. ITu3C.2-ITu3C.2.
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We report the first demonstration of on-chip SBS slow and fast light using stimulated Brillouin scattering. Slow (~2307 km/s), fast and negative (~-6818 km/s) group velocities were observed in a 7cm long chalcogenide waveguide. © 2012 OSA.

Pant, R, Byrnes, A, Poulton, CG, Li, E, Choi, D-Y, Madden, S, Luther-Davies, B, Eggleton, BJ & IEEE 1970, 'Photonic chip based tunable slow and fast light via stimulated Brillouin scattering', 2012 CONFERENCE ON LASERS AND ELECTRO-OPTICS (CLEO), Conference on Nonlinear Optics and Applications VI, SPIE-INT SOC OPTICAL ENGINEERING, Brussels, BELGIUM.
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Peng, T, Xie, H, Ding, Y, Lu, Y, Jin, D & Xi, P 1970, 'LOSOM: Phase Relief Imaging Can Be Achieved with Confocal System', OPTICS IN HEALTH CARE AND BIOMEDICAL OPTICS V, Optics in Health Care and Biomedical Optics, SPIE, Beijing, China.
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We reported recently that laser oblique scanning optical microscopy (LOSOM) is able to obtain a relief image in transparent sample directly. To optimize the performance of LOSOM, the parameters such as numerical aperture, the distance between the specimen and the fluorescent medium and the pinhole size are investigated in this work. A beam blocker is introduced in light path which enhances dramatically the visualization of local phase difference. © Copyright SPIE.

Peng, T, Xie, H, Ding, Y, Wang, W, Li, Z, Jin, D, Tang, Y, Ren, Q & Xi, P 1970, 'Confocal Reflectance/Auto-Fluorescence Tomograpy (CRAFT) for Early Skin Cancer Diagnosis', Biomedical Optics and 3-D Imaging, Biomedical Optics, OSA, pp. BTu3A.48-BTu3A.48.
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Histopathological analysis has been the gold standard of conventional cancer diagnosis for decades, which is based on the structural and/or biochemical change of the cancerous sites, through biopsy. However, due to cosmetic reasons, the biopsy procedure has to be limited. In this work, we report the noninvasive, in situ, 3-D optical diagnostic method for "virtual biopsy". To obtain simultaneously the structural and pathological information, a multimodality Confocal Reflectance/Auto-Fluorescence Tomography (CRAFT) system was established. Nude mice skin with cancerous sites and normal skin sites were compared with the system. The cellular density and reflective intensity in cancerous sites reflects the structural alteration of the tissue. The corresponding NAD(P)H decay index for cancerous sites is 2.45-fold that of normal sites, leading to a clearly separation of the cancerous sites with the healthy control sites. The results are verified by the followed histological analysis. Therefore, CRAFT may provide a novel method for the in vivo, non-invasive diagnosis of early cancer. © 2012.

Plank, M, Kaiko, G, Luck, H, Li, J, Mattes, J, Hansbro, P & Foster, PS 1970, 'THE ROLE OF MICRORNAS IN CD4 T CELL FUNCTION', RESPIROLOGY, WILEY-BLACKWELL, pp. 51-51.

Plank, MW, Kaiko, GE, Tay, HL, Mattes, J, Hansbro, PM & Foster, PS 1970, 'The Role Of MicroRNAs In CD4+ T Cell Function', C71. MAJOR IMPACT OF MICRO-RNA FUNCTION, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A4988-A4988.
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Platen, E 1970, 'Benchmarked risk minimization', The Art of Finance 2012 FIRN Annual Conference, Hobart, Tasmania.

Platen, E 1970, 'Benchmarked risk minimization in incomplete markets', The Sixth Bachelier Colloquium on Mathematical Finance and Stochastic Calculus, Metabief, France.

Platen, E 1970, 'Numerical solution of SDEs', Seminar Presentation, Ecole Centrale, Paris, France.

Platen, E 1970, 'Numerical solution of stochastic differential equations with jumps in finance', Tenth International Conference on Monte Carlo and Quasi-Monte Carlo Methods in Scientific Computing, Sydney Australia.

Platen, E & Rendek, R 1970, 'The Affine Nature of Aggregate Wealth Dynamics', 7th Bachelier Colloquium on Mathematical Finance and Stochastic Calculus, Metabief, France.
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The paper derives a parsimonious two-component affine diffusion model for a world stock index to capture the dynamics of aggregate wealth. The observable state variables of the model are the normalized index and the inverse of the stochastic market activity, both modeled as square root processes. The square root process in market activity time for the normalized aggregate wealth emerges from the affine nature of aggregate wealth dynamics, which will be derived under basic assumptions and does not contain any parameters that have to be estimated. The proposed model employs only three well interpretable structural parameters, which determine the market activity dynamics, and three initial parameters. It is driven by the continuous, nondiversifiable uncertainty of the market and no other source of uncertainty. The model, to be valid over long time periods, needs to be formulated in a general financial modeling framework beyond the classical no-arbitrage paradigm. It reproduces a list of major stylized empirical facts, including Student-t distributed log-returns and typical volatility properties. Robust methods for fitting and simulating this model are demonstrated.

Raingeard, D, Ng, C, Seow, WY, Jinyu, BC, Guest, J, Steinberg, P & McDougald, D 1970, 'Evolution from Bacteria to Mammalia of selected marker genes involved in energy metabolism and stress responses: Bioinformatic approach and applications in coral reef ecology', Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 28th Congress of the New European-Society-for-Comparative-Physiology-and-Biochemistry (ESCPB) on Cellular and Molecular Mechanisms for Physiological Adaptation to Multiple Stress, Elsevier BV, Bilbao, SPAIN, pp. S29-S29.
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Reim, KF, Nunn, J, Jin, XM, Michelberger, PS, Champion, TFM, England, DG, Lee, KC, Langford, NK & Walmsley, IA 1970, 'Multi-pulse addressing of a Raman quantum memory: Configurable beam splitting and efficient readout', 2012 Conference on Lasers and Electro-Optics, CLEO 2012.
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We address an optical quantum memory with multiple pulses, enabling unit efficiency readout and programmable beam splitting. The resulting coherent processor with built-in storage is universal for scalable photonic quantum information processing. © 2012 OSA.

Reim, KF, Nunn, J, Jin, XM, Michelberger, PS, Champion, TFM, England, DG, Lee, KC, Langford, NK & Walmsley, IA 1970, 'Multi-pulse addressing of a Raman quantum memory: Configurable beam splitting and efficient readout', Optics InfoBase Conference Papers.
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We address an optical quantum memory with multiple pulses, enabling unit efficiency readout and programmable beam splitting. The resulting coherent processor with built-in storage is universal for scalable photonic quantum information processing. © 2012 Optical Society of America.

Saad, S, Chen, H, Al-Odat, I, Killingsworth, M & Pollock, CA 1970, 'RENAL DISORDERS INDUCED BY MATERNAL SMOKING', NEPHROLOGY, WILEY-BLACKWELL, pp. 54-54.

Saad, S, Chen, H, Pollock, CA & Wong, MG 1970, 'MATERNAL OBESITY RELATED RENAL INJURY IN MOTHER AND OFFSPRING IS MEDIATED THROUGH DOWN REGULATION OF RENAL FARNESOID X RECEPTOR (FXR) EXPRESSION', NEPHROLOGY, WILEY-BLACKWELL, pp. 59-60.

Schartner, EP, Jin, D, Ebendorff-Heidepriem, H, Piper, JA & Monro, TM 1970, 'Lanthanide upconversion nanocrystals within microstructured optical fibres; a sensitive platform for biosensing and a new tool for nanocrystal characterisation', SPIE Proceedings, Asia Pacific Optical Sensors Conference, SPIE, Sydney, Australia, pp. 83512Q-83512Q.
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We investigate a powerful new sensing platform based on upconversion luminescence in NaYF4: Yb/Er nanocrystals loaded inside a suspended-core microstructured optical fibre. The use of a NIR source enables autofluorescence from the glass to be reduced compared to using visible sources for excitation of fluorescence. We demonstrate a substantial improvement in the detection limit that can be achieved in a suspended-core fibre sensor, with detection limits as low as 660 fM achieved. This is a factor of 15× better than the best results previously reported using Quantum dots in a similar fibre. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

Schulte, EF, Cooper, KA, Phillips, M & Shinde, SL 1970, 'Characterization of a novel fluxless surface preparation process for die interconnect bonding', 2012 IEEE 62nd Electronic Components and Technology Conference, 2012 IEEE 62nd Electronic Components and Technology Conference (ECTC), IEEE, San Diego, CA, USA, pp. 26-30.
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For applications such as 3D integration, flip chip, and other die interconnection processes, a variety of metals is used to form an electrical and mechanical bond between the two components. Native oxides, however, quickly form on many of the common bond materials, hindering the integrity of the joint and adversely affecting long-term reliability. A new method has been developed to reduce these surface oxides and passivate the exposed metal surfaces against re-oxidation. Avoiding the use of acids or the possible exposure to hot electrons, ions and highly energetic atoms of conventional vacuum plasma, the developed and tested processing is carried out in atmospheric ambient to remove native oxides from solders and contact metals, enabling consistent bonding at modest temperatures and bond forces. The processing approach has been applied to a variety of metal and alloy surfaces, with bonding pursued over a range of forces and temperatures. Analysis of treated and untreated surfaces will also be presented, including SEM images and surface analysis techniques such as laser ellipsometry. Finally, physical bonding results will demonstrate the efficacy of the proposed atmospheric surface preparation approach, lowering the temperatures and bond forces required to achieve effective joining between component parts. © 2012 IEEE.

See, HV, Simpson, JL, Hansbro, PM & Wark, PAB 1970, 'STABLE COPD PATIENTS HAVE LESS RHINOVIRUS-INDUCED INTRACELLULAR INNATE CYTOKINES DETECTED IN PBMCS COMPARED TO HEALTHY ADULTS', RESPIROLOGY, WILEY-BLACKWELL, pp. 64-64.

Sklibosios Nikitopoulos, C & Platen, E 1970, 'Alternative Term Structure Models for Reviewing Expectations Puzzles', Research Paper Number, World Finance Conference, Rhodes, Greece.

Slobozhanyuk, AP, Filonov, DS, Lapine, M, Belov, PA, Shadrivov, IV, Kivshar, YS & IEEE 1970, 'Nonlinear Spiral Metamaterials', 2012 IEEE ANTENNAS AND PROPAGATION SOCIETY INTERNATIONAL SYMPOSIUM (APSURSI), IEEE Antennas-and-Propagation-Society International Symposium (APSURSI), IEEE, Chicago, IL, USA.
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We investigate nonlinear behavior of metamaterial element, where responses of a different nature are intrinsically coupled through its structure. We provide an experimental demonstration of the electromagnetically induced compression of the metamaterials elements, which leads to a remarkable shift of the resonance frequency. We believe that these results are useful for the future development of nonlinear and tunable metamaterials. © 2012 IEEE.

Solntsev, AS & Sukhorukov, AA 1970, 'Combined frequency conversion and pulse compression in nonlinear tapered waveguides', Optics Letters, Optica Publishing Group, pp. 446-446.
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Solntsev, AS, Clark, AS, Setzpfandt, F, Collins, MJ, Xiong, C, Wu, A, Eilenberger, F, Schreiber, A, Katzschmann, F, Schiek, R, Sohler, W, Mitchell, A, Silberhorn, C, Eggleton, BJ, Pertsch, T, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Simultaneous Photon-Pair Generation and Quantum Walks in a Waveguide Array', Frontiers in Optics 2012/Laser Science XXVIII, Frontiers in Optics, OSA, pp. FTu4D.2-FTu4D.2.
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We demonstrate experimentally simultaneous photon-pair generation and quantum walks in a PPLN waveguide array where the output photon correlations can be controlled by varying the pump laser wavelength, switching from classical to quantum statistics. © OSA 2012.

Solntsev, AS, Setzpfandt, F, Eilenberger, F, Wu, CW, Neshev, DN, Sukhorukov, AA, Pertsch, T & Kivshar, YS 1970, 'Observation of spontaneous parametric down-conversion in quadratic nonlinear waveguide arrays', Optics InfoBase Conference Papers, Conference on Lasers and Electro-Optics (CLEO), IEEE, San Jose, CA.
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We characterize experimentally the process of bi-photons generation through spontaneous parametric down-conversion in LiNbO3 waveguide arrays. We demonstrate the formation of unique spatial-spectral distribution of photons and its dependence on phasematching conditions. © 2012 Optical Society of America.

Solntsev, AS, Setzpfandt, F, Eilenberger, F, Wu, CW, Neshev, DN, Sukhorukov, AA, Pertsch, T & Kivshar, YS 1970, 'Observation of spontaneous parametric down-conversion in quadratic nonlinear waveguide arrays', Advanced Photonics Congress, Nonlinear Photonics, OSA, pp. NTu4D.2-NTu4D.2.
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We characterize experimentally the process of bi-photons generation through spontaneous parametric down-conversion in LiNbO3 waveguide arrays. We demonstrate the formation of unique spatial-spectral distribution of photons and its dependence on phasematching conditions. © 2012 Optical Society of America.

Solntsev, AS, Setzpfandt, F, Wu, A, Neshev, DN, Sukhorukov, AA, Kivshar, YS & Pertsch, T 1970, 'Observation of spontaneous parametric down conversion in LiNbO3 waveguide arrays', CLEO: Applications and Technology, CLEO_AT 2012.
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We study experimentally the process of bi-photon generation through spontaneous parametric down-conversion in waveguide arrays. We show the formation of a unique spatial-spectral photon pattern and its dependence on the phase-matching conditions. © 2011 Optical Society of America.

Solntsev, AS, Setzpfandt, F, Wu, A, Neshev, DN, Sukhorukov, AA, Kivshar, YS & Pertsch, T 1970, 'Observation of spontaneous parametric down conversion in LiNbO3 waveguide arrays', Conference on Lasers and Electro-Optics 2012, CLEO: Applications and Technology, OSA, pp. JW4A.113-JW4A.113.
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We study experimentally the process of bi-photon generation through spontaneous parametric down-conversion in waveguide arrays. We show the formation of a unique spatial-spectral photon pattern and its dependence on the phase-matching conditions. © 2011 Optical Society of America.

Solntsev, AS, Setzpfandtc, F, Wu, A, Neshev, DN, Sukhorukov, AA, Kivshar, YS & Pertsch, T 1970, 'Observation of spontaneous parametric down conversion in LiNbO3 waveguide arrays', Optics InfoBase Conference Papers.
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We study experimentally the process of bi-photon generation through spontaneous parametric down-conversion in waveguide arrays. We show the formation of a unique spatial-spectral photon pattern and its dependence on the phase-matching conditions. © 2011 Optical Society of America.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Generation of photon pairs in cubic nonlinear waveguide arrays', Optics InfoBase Conference Papers.
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We analyze the quantum statistics of photon pair generation through spontaneous four-wave mixing in nonlinear waveguide arrays and predict pump power-controlled transition between bunching and anti-bunching correlations due to self-focusing of the pump beam. © 2012 Optical Society of America.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Generation of Photon Pairs in Cubic Nonlinear Waveguide Arrays', Advanced Photonics Congress, Nonlinear Photonics, OSA, pp. NTh2A.7-NTh2A.7.
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We analyze the quantum statistics of photon pair generation through spontaneous four-wave mixing in nonlinear waveguide arrays and predict pump power-controlled transition between bunching and anti-bunching correlations due to self-focusing of the pump beam. © 2012 Optical Society of America.

Solntsev, AS, Sukhorukov, AA, Neshev, DN & Kivshar, YS 1970, 'Photon-pair generation in arrays of cubic nonlinear waveguides', Optics Express, Optica Publishing Group, pp. 27441-27441.
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Sprague, MR, Lee, KC, Sussman, BJ, Nunn, J, Langford, NK, Jin, XM, Champion, T, Michelberger, P, Reim, KF, England, D, Jaksch, D & Walmsley, IA 1970, 'Entangling the motion of diamonds at room temperature', 2012 Conference on Lasers and Electro-Optics, CLEO 2012.
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We demonstrate entanglement between the vibrational mode of two macroscopic, spatially-separated diamonds at room temperature with ultrashort pulses and a far-off-resonant Raman interaction. © 2012 OSA.

Sprague, MR, Lee, KC, Sussman, BJ, Nunn, J, Langford, NK, Jin, XM, Champion, T, Michelberger, P, Reim, KF, England, D, Jaksch, D & Walmsley, IA 1970, 'Entangling the motion of diamonds at room temperature', Optics InfoBase Conference Papers.
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We demonstrate entanglement between the vibrational mode of two macroscopic, spatially-separated diamonds at room temperature with ultrashort pulses and a far-off-resonant Raman interaction. © 2012 Optical Society of America.

Starkey, M, Kim, R, Horvat, J, Essilfie, A-T, Beagley, K, Mattes, J, Foster, P & Hansbro, P 1970, 'Constitutive IL-13 promotes respiratory chlamydial infection and infection-induced chronic airway hyper-responsiveness (175.18)', The Journal of Immunology, 99th Annual Meeting of the American-Association-of-Immunologists, The American Association of Immunologists, Boston, MA, pp. 175.18-175.18.
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Abstract We have previously shown that chlamydial lung infections in early-life drive the development of chronic airway hyper-responsiveness (AHR). To elucidate the mechanisms involved, we used a murine model of chlamydial lung infection, to investigate the influence of IL-13 on infection and infection-induced AHR. Infected IL-13-/- mice had less severe infection, reduced inflammation (neutrophils, dendritic cells, macrophages and T cells), less mucus secreting cells (MSCs) in the airways and attenuated AHR. More severe infection in wild-type (WT) mice was associated with the development of alternatively activated macrophages (increased Arg-1, FIZZ-1 and Ym-1), which were suppressed in IL-13-/- mice. Surprisingly, infection of WT mice did not induce any detectable increase in IL-13 expression. However, infection decreased the level of the IL-13 decoy receptor (IL-13Rα2), which may allow constitutive IL-13 to signal. Interestingly, reconstitution of IL-13 in IL-13-/- mice restored infection-induced inflammation and MSC formation, but not AHR. Furthermore, infection-induced inflammation and mucus were Stat-6-independent, whilst infection-induced AHR was dependent upon Stat-6. Thus, early-life respiratory chlamydial infection results in decreased decoy receptor expression, which allows constitutive IL-13 to signal and promote more severe infection, which drives the development of chronic AHR that persists into adulthood.

Starkey, MR, Kim, RY, Horvat, JC, Essilfie, AT, Beagley, KW, Mattes, J, Foster, PS & Hansbro, PM 1970, 'CONSTITUTIVE IL-13 PROMOTES RESPIRATORY CHLAMYDIAL INFECTION-INDUCED CHRONIC AIRWAY HYPERRESPONSIVENESS', RESPIROLOGY, WILEY-BLACKWELL, pp. 84-84.

Stifter, SA, Fung, K, Horvat, J, Hansbro, P, de Weerd, NA & Hertzog, PJ 1970, 'Expression, purification and biological characterisation of a novel type I interferon, IFN epsilon', IMMUNOLOGY, European Congress of Immunology, WILEY-BLACKWELL, Glasgow, SCOTLAND, pp. 248-248.

Stuart, BH, Notter, SJ, Selvalatchmanan, J & Fu, S 1970, 'The influence of water chemistry on the formation of adipocere', 21st International Symposium on the Forensic Sciences Abstracts, 21st International Symposium on the Forensic Sciences.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, McPhedran, RC & de Sterke, CM 1970, 'Disorder in Silicon Nanowire Arrays for Photovoltaic Applications.', Frontiers in Optics 2012/Laser Science XXVIII, Frontiers in Optics, OSA, pp. FTu4B.3-FTu4B.3.
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We study the effect of non-uniform radii on the optical absorption of silicon nanowire arrays. Whilst previous studies have shown that radius disorder can increase the efficiency, the mechanism is unclear. To elucidate this we study structures with a small supercell, forming a regular nanowire array with two distinct radii. We find that these arrays have new electromagnetic resonances, not present in arrays with uniform radii, leading to increased absorption. © OSA 2012.

Sukhorukov, AA, Solntsev, AS, Kruk, SS, Neshev, DN & Kivshar, YS 1970, 'Nonlinear coupled-mode theory for periodic waveguides and metamaterials with loss and gain', AIP Conference Proceedings, THE FIFTH INTERNATIONAL WORKSHOP ON THEORETICAL AND COMPUTATIONAL NANO-PHOTONICS: TaCoNa-Photonics 2012, AIP, Bad Honnef, GERMANY, pp. 80-82.
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Tay, HL, Kaiko, GE, Plank, MW, Mattes, J, Hansbro, PM & Foster, PS 1970, 'MIRNAS REGULATE BACTERIAL INFECTION IN LUNGS', RESPIROLOGY, WILEY-BLACKWELL, pp. 33-33.

Tjin, G, Faiz, A, Harkness, L, Oliver, BGG, Black, JL & Burgess, JK 1970, 'EXPRESSION AND ROLE OF CATHEPSINS IN ASTHMATIC AIRWAYS', RESPIROLOGY, WILEY-BLACKWELL, pp. 14-14.

Van Ly, D, Crossett, B, Burgess, JK, Black, JL & Oliver, BG 1970, 'Epithelial Derived Lipids Result In Rhinovirus Induced '2 Adrenoceptor Desensitization', A37. LIPIDS IN LUNG DISEASES, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A1433-A1433.
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Van Ly, D, Crossett, B, Burgess, JK, Black, JL & Oliver, BG 1970, 'EPITHELIAL DERIVED LIPIDS RESULT IN RHINOVIRUS INDUCED B-2 ADRENOCEPTOR DESENSITIZATION', RESPIROLOGY, WILEY-BLACKWELL, pp. 24-24.

Van Ly, D, Trian, T, Burgess, JK, Black, JL & Oliver, BG 1970, 'PROSTAGLANDINS HAVE VARIABLE INDUCTION OF CAMP AND HETROLOGOUS beta(2) ADRENOCEPTOR DESENSITIZATION', RESPIROLOGY, WILEY-BLACKWELL, pp. 43-43.

Van Ly, D, Trian, T, Burgess, JK, Black, JL & Oliver, BG 1970, 'Prostaglandins Have Variable Induction Of CAMP And Hetrologus '2 Adrenoceptor Desensitization', C30. THE ROLE OF THE SMOOTH MUSCLE CELL IN AIRWAY DISEASE, American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California, American Thoracic Society, pp. A4139-A4139.
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Blount, C, Cummings, D, Mayer Pinto, M & Pernice, M 2012, Bimonthly Coral Monitoring Report: Dredging Report 1 − Ichthys Nearshore Environmental Monitoring Program, no. 1, pp. 1-94, Sydney.

Leigh, A 2012, 'Experiencing the Landscape: essential training for environmental scientists', The Conversation.
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Article about field-based learning in environmental science at UTS

Murray, BR 2012, 'Book review: Fifty Years of Invasion Ecology: The Legacy of Charles Elton', Wiley, p. e43.