Publications

Chuvieco, E & Huete, A 2009, Fundamentals of Satellite Remote Sensing, 1st, CRC/Dekker, Taylor & Francis Informa Group, Boca Raton, Florida USA.

King, E & Walsh, S 2009, Guida pratica all'esame del polso in medicina cinese, Elsevier srl.

Larkum, AWD 2009, A Natural Calling, Springer Netherlands.
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Murray, SA 2009, Diversity and phylogenetics of sand-dwelling dinoflagellates, 1, VDM Verlag, Germany.

Watson, MP, Ben-Nissan, B & West, ST 2009, It is Material - a practical guide to building materials and materials science for construction engineering and design, The Associates E-Press, Australia.

Ajani, PA & Rissik, D 2009, 'Coastal and marine phytoplankton: diversity and ecology' in Suthers, I & Rissik, D (eds), Plankton, A Guide to Their Ecology and Monitoring for Water Quality, CSIRO Publishing, pp. 141-155.

Aumeer-Donovan, S, Lennard, C & Roux, C 2009, 'Friction Ridge Skin: Fingerprint Detection and Recovery Techniques', John Wiley & Sons, Ltd.
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Bergveld, HJ, Danilov, D, Notten, PHL, Pop, V & Regtien, PPL 2009, 'Batteries' in Encyclopedia of Electrochemical Power Sources, pp. 459-477.
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This article gives an overview of available state-of-charge (SoC)-indication methodologies and highlights many related practical implementation issues. First of all, a brief history of the developments in SoC indication is given. The lithium-ion battery technology is briefly discussed as illustration, because battery behavior needs to be understood and taken into account properly to achieve a desired level of accuracy. The focus is on describing the background of behavior that is important to be addressed by the SoC-indication system, such as aging processes. The available SoC-indication methods are classified and advantages and disadvantages are listed. Some examples of practical implementations are given, including important issues to address. As an illustration, a state-of-the-art SoC-indication system for lithium-ion batteries is described at the end of the article.

Bosmans, F, Escoubas, P & Nicholson, GM 2009, 'Spider venom peptides as leads for drug and insecticide design' in de Lima, ME, Pimenta, AMC, Martin-Eauclaire, MF, Zingali, RB & Rochat, H (eds), Animal Toxins: State of the Art. Perspectives In Health and Biotechnology, Editora UFMG, Belo Horizonte, pp. 269-290.
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Spider venoms represent highly complex cocktails of proteins, peptides, neurotransmitters, acylpolyamines and other small molecules employed to subdue and kill their prey or predators. By a process of natural selection, spider venoms have evolved as complex pre-optimized combinatorial peptide libraries, displaying Wide-ranging pharmacological activities.The therapeutic potential of these peptides stems from their highly potent and specific actions to modulate an extensive range of ion channels, receptors, and transporters in vertebrates and invertebrates,as well as their antimicrobial activity. Nevertheless, it is only since the advent of modern analytical technologies that the full potential of this resource is beginning to be exploited for validating novel insecticide targets, and for aiding in the design of novel drugs and bioinsecticides. These techniques have identified that the currently known spider venom pool represents a resource of several million peptides that selectivelytarget specific subtypes ofion channels or receptors. Indeed, some spider toxins are becoming the defining pharmacology for specificsubtypes of ion channels. Furthermore, structure-function studies ofthese molecules are leading not only to the discovery of new molecular tools, but are also providing insight into novel therapeutic approaches for the treatment of cardiovascular diseases, cancer, neuromuscular diseases, pain and to a variety ... of other pathological conditions. Against this background, this review will evaluate peptidic spider toxins as possible lead compounds for new therapeutics and for controlling insect pests. Special attention will be given to their role in the discovery of novel approaches in analgesia and cardiovascular research.

Broom, GM & Macnamara, J 2009, 'Step Four: Evaluating the Program' in Broom, GM (ed), Cutlip & Center's Effective Public Relations - Tenth Edition, Pearson Prentice Hall, United States, pp. 349-377.

Cortie, MB & McDonagh, AM 2009, 'Nanoscience of gold and gold surfaces' in Mohr, F (ed), gold chemistry: applications and future directions in the life sciences, Wiley-VCH, Weinheim, pp. 321-355.

Craddock, MJ, Konstandatos, O & Lennox, KA 2009, 'Some recent developments in the theory of Lie group symmetries for PDEs' in Baswell, AR (ed), Advances in Mathematics Research, Nova Science Publishers, United States of America, pp. 1-40.
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Lie group symmetry methods provide a powerful tool for the analysis of PDEs. Over the last thirty years, considerable progress has been made in the development of this field. In this article, we provide a brief introduction to the method developed by Lie for the systematic computation of symmetries, then move on to a survey of some of the more recent developments. Our focus is on the use of Lie symmetry methods to construct fundamental solutions of partial differential equations of parabolic type. We will show how recent work has uncovered an intriguing connection between Lie symmetry analysis and the theory of integral transforms. Fundamental solutions of families of PDEs which arise in various applications, can be obtained by exploiting this connection. The major applications we give will be in financial mathematics. We will illustrate our results with the problem of pricing a so called zero coupon bond, as well as giving some applications to option pricing. We also discuss some results on group invariant solutions and show how an important PDE in nilpotent harmonic analysis can be studied via its group invariant solutions.

Du Preez, C & Roux, C 2009, 'Tire Impressions', John Wiley & Sons, Ltd.
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Forbes, SL & Dadour, IR 2009, 'The soil environment and forensic entomology' in Byrd, JH & Castner, JL (eds), Forensic Entomology: The Utility of Arthropods in Legal Investigations, CRC Press, United States, pp. 407-426.
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Cadaver decomposition involves complex chemical processes that are readily influenced by surrounding conditions. A body decomposing in an outdoor environment will be affected by ecological conditions such as climate, vegetation, and the soil environment. The soil environment is particularly important, as the process of decomposition can be altered considerably by soil type, pH, moisture, and oxygen content. The type of soil environment will also affect the invertebrate fauna associated with decomposition. As a result, the rate of decomposition will vary for a body decomposing on the soil surface compared to a body decomposing in a burial environment. It is therefore important to consider the effect of the soil environment on entomological evidence collected as part of a forensic investigation. This review will discuss the chemical processes of decomposition and preservation, as well as the effect of the soil environment, and subsequently the insect fauna, on these processes. A better understanding of these processes is imperative in the application of forensic entomology.

Forbes, SL & Nugent, K 2009, 'Dating of anthropological skeletal remains of forensic interest' in Blau, S & Ubelaker, DH (eds), Handbook of Forensic Anthropology and Archaeology: World Archaeological Congress Research Handbooks, Left Coast Press, United States, pp. 164-173.

Gladstone, W 2009, 'Conservation and management of tropical coastal ecosystems' in Nagelkerken, I (ed), Ecological Connectivity among Tropical Coastal Ecosystems, Springer, Dordrecht, the Netherlands, pp. 565-605.
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All major coastal ecosystems in the tropics are being degraded. The problems include losses of biodiversity, reduced ecosystem functions, and costs to coastal human societies. Declines in speciesï½ abundances, and habitat loss and modi?cation are the result of the demands for aquaculture, port construction, trawling, excessive nutrient loads, over?shing and collecting, sedimentation from catchment activities, invasive species, and climate change. A global response to these changes has been conservation and management approaches that aim to reduce, reverse, and prevent unnatural changes and address their underlying causes. Successes in conservation and management are likely when actions are designed to achieve the fundamental ecological goals of ensuring resilience, maintaining ecosystem connectivity, protecting water quality, conserving species-at-risk, conserving representative samples of species and assemblages, and managing at the appropriate spatial scale. Achieving societal aspirations for coastal ecosystems requires that management approaches address the socio-economic aspects of issues and include stakeholder consultation, participation, and education

Gladstone, W 2009, 'Conservation and management of tropical coastal ecosystems' in Ecological Connectivity among Tropical Coastal Ecosystems, pp. 565-605.
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All major coastal ecosystems in the tropics are being degraded. The problems include losses of biodiversity, reduced ecosystem functions, and costs to coastal human societies. Declines in species' abundances, and habitat loss and modification are the result of the demands for aquaculture, port construction, trawling, excessive nutrient loads, overfishing and collecting, sedimentation from catchment activities, invasive species, and climate change. A global response to these changes has been conservation and management approaches that aim to reduce, reverse, and prevent unnatural changes and address their underlying causes. Successes in conservation and management are likely when actions are designed to achieve the fundamental ecological goals of ensuring resilience, maintaining ecosystem connectivity, protecting water quality, conserving species-at-risk, conserving representative samples of species and assemblages, and managing at the appropriate spatial scale. Achieving societal aspirations for coastal ecosystems requires that management approaches address the socio-economic aspects of issues and include stakeholder consultation, participation, and education. Achieving long-term success in conservation and management requires coastal nations to address fundamental issues such as lack of information for management decision-making, population growth and poverty, limited technical and management capacity, poor governance, lack of stakeholder participation, the mismatches between the issue and the geographic scale of management, lack of an ecosystem perspective, ineffective governance and management, and a lack of awareness of the effects of human activities. © 2009 Springer Science+Business Media B.V.

Herbert, BR & Harry, L 2009, 'Difficult proteins' in Sheehan, D & Tyther, R (eds), Two-dimensional electrophoresis protocols, Humana Press, New York, pp. 47-63.
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Labbate, M, Case, RJ & Stokes, H 2009, 'The integron/gene cassette system: an active player in bacterial adaptation' in Gogarten, M, Gogarten, P & Olendzenski, L (eds), Horizontal Gene Transfer, Humana Press, New York, pp. 103-125.
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The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9 % of sequenced bacterial genomes. Overall, gene diversity in cassettes is extraordinarily high suggesting that the integron/gene cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene cassette system highlighting characteristics associated with this system, diversity of elements contained within it and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene cassettes and gene cassette arrays are discussed.

Luong, S & Roux, C 2009, 'Marks or Impressions of Manufactured Items', John Wiley & Sons, Ltd.
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Raymond, JJ, Roux, C & Walsh, SJ 2009, 'Friction Ridge Skin: Interaction between Fingerprint Detection and DNA/Biological Material', John Wiley & Sons, Ltd.
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Rissik, D, van Senden, D, Doherty, M, Ingleton, I, Ajani, PA, Bowling, L, Gibbs, M, Gladstone, M, Kobayashi, T, Suthers, I & Froneman, W 2009, 'Plankton-related water quality issues' in Suthers, I & Rissik, D (eds), Plankton, A Guide to Their Ecology and Monitoring for Water Quality, CSIRO Publishing, pp. 39-72.

Roux, C & Robertson, J 2009, 'Fibers', John Wiley & Sons, Ltd.
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Roux, CP & Robertson, J 2009, 'The Development and Enhancement of Forensic Expertise: Higher Education and In-Service Training' in Fraser, J & Williams, R (eds), Handbook of Forensic Science, Willan, Cullompton, pp. 572-600.

Schlogl, E & Schlogl, L 2009, 'Factor Distributions Implied by Quoted CDO Spreads' in Cont, R (ed), Frontiers in Quantitative Finance, John Wiley and Sons, New Jersey, USA, pp. 217-234.
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Simon, P & Thomas, P 2009, 'Application of Isoconversional Methods for the Processes Occurring in Glassy and Amorphous Materials' in Sestak, J, Holocek, M & Malek, J (eds), Some thermodynamic, structural and behavioral aspects of materials accentuating non-crystalline states, Nymburk, Pilsen, Czech Republic, pp. 248-264.

Stokes, KL, Forbes, SL, Benninger, LA, Carter, DO & Tibbett, M 2009, 'Decomposition studies using animal models in contrasting environments: evidence from temporal changes in soil chemistry and microbial activity' in Ritz, K, Dawson, L & Miller, D (eds), Criminal and Environmental Soil Forensics, Springer, Netherlands, pp. 357-377.
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Traditionally, soil evidence in forensic science has focused predominantly on the transference of soil particles from a victim or suspect and a crime scene. However, a recent increase in forensic taphonomy research has highlighted the potential of soil to provide key information to an investigation involving decomposed remains. A decomposing carcass can release a significant pulse of nutrients into the surrounding soil (gravesoil) resulting in the retention of decomposition products in the soil for a considerable period of time. In order to understand the complex associations between a decomposing carcass and the soil system, research must be conducted in both controlled laboratory environments and outdoor field environments. This chapter discusses two contrasting decomposition studies which aimed to investigate the cadaver/soil interaction. The first study investigated the decomposition of small mouse carcasses buried in soil and was conducted within a controlled laboratory environment in Western Australia. The second study investigated the decomposition of large pig carcasses placed on the soil surface and was conducted in an outdoor field environment in southern Ontario. Both studies investigated a range of decomposition products particularly focusing on carbon-based, nitrogen-based and phosphorus-based compounds as these were considered to offer the most valuable information to address the research questions. The results of both studies provide the opportunity to comment on the effect of carcass size, soil type and decomposition environment on the influx of decomposition products into the soil.

Suggett, DJ & Moore, CM 2009, 'Fluorometry for Biological Sensing' in Encyclopedia of Ocean Sciences, pp. 581-588.
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Light-absorbing pigments cause many marine organisms to naturally fluoresce, a phenomenon whereby light is emitted at a longer wavelength following light absorption at a shorter wavelength. Fluorescence provides a relatively unobtrusive signature of organism abundance and physiology; consequently, a wide variety of fluorescence techniques are now routinely employed in marine biological investigations. Important technological advances throughout the last 20 years have enabled exploration of the taxonomy and physiology of marine organisms with increasing complexity. In particular, the intracellular use of fluorescent tags, molecules, and dyes that covalently bind to sensing biomolecules. However, many such techniques require samples to be removed from nature. Most widespread for assaying biology in situ exploits the fluorescence emitted from chlorophyll a, the predominant light harvesting pigment inherent to all (micro)algae, cyanobacteria, and aquatic vascular plants. Measurements of chlorophyll a fluorescence were introduced in the 1960s to improve estimates of phytoplankton abundance. By the 1990s, this field had evolved to enable the physiology and productivity of primary producers to be examined at scales from the single cell to entire ocean basins. Current remote sensing algorithms concentrate on better describing the relationship between primary productivity and natural fluorescence that is emitted from solar excitation. While several major challenges exist in achieving this goal, such approaches provide great promise for accurately characterizing the role of marine primary productivity during this period of extreme climate change. © 2009 Copyright © 2009 Elsevier Ltd. All rights reserved.

Suggett, DJ & Moore, MC 2009, 'Fluorometry for biological sensing' in Encyclopedia of Ocean Sciences, Springer, Switerland, pp. 87-93.
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© 2009 Elsevier Ltd. Light-absorbing pigments cause many marine organisms to naturally fluoresce, a phenomenon whereby light is emitted at a longer wavelength following light absorption at a shorter wavelength. Fluorescence provides a relatively unobtrusive signature of organism abundance and physiology; consequently, a wide variety of fluorescence techniques are now routinely employed in marine biological investigations. Important technological advances throughout the last 20 years have enabled exploration of the taxonomy and physiology of marine organisms with increasing complexity. In particular, the intracellular use of fluorescent tags, molecules, and dyes that covalently bind to sensing biomolecules. However, many such techniques require samples to be removed from nature. Most widespread for assaying biology in situ exploits the fluorescence emitted from chlorophyll a, the predominant light harvesting pigment inherent to all (micro)algae, cyanobacteria, and aquatic vascular plants. Measurements of chlorophyll a fluorescence were introduced in the 1960s to improve estimates of phytoplankton abundance. By the 1990s, this field had evolved to enable the physiology and productivity of primary producers to be examined at scales from the single cell to entire ocean basins. Current remote sensing algorithms concentrate on better describing the relationship between primary productivity and natural fluorescence that is emitted from solar excitation. While several major challenges exist in achieving this goal, such approaches provide great promise for accurately characterizing the role of marine primary productivity during this period of extreme climate change.

Thomas, P, Heide, KÅ, esták, J, Füglein, EÅ & imon, P 2009, 'Properties of Some Natural Glasses: Australian Opals and Czech Moldavites' in aroslav, ÅEK, Miroslav, HE & JiÅ, ÃML (eds), Some thermodynamic, structural and behavioral aspects of materials accentuating non-crystalline stat, Nymburk, PlzeÅ¿, pp. 200-218.

Upadhyaya, NM & Dennis, ES 2009, 'Rice genomics gateway to future cereal improvement' in Molecular Techniques in Crop Improvement: 2nd Edition, pp. 257-279.
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There is an urgent need to increase world's food production to meet the ever increasing demand. Rice plays a direct role as the cereal feeding half the world's population and as an experimental workhorse. It has the smallest genome among cereals, has remarkable similarities with other cereals in sequence, structure, order and function of genes. Foreign genes can be incorporated into rice with ease by genetic transformation. Rice genetics is also well studied and understood. All these features have made rice a model cereal for functional genomics. With the availability of the near complete genome sequence, the emphasis is not only on understanding the functions of the predicted 35,000-50,000 genes, but also unraveling how these genes interact to control important agronomic traits under different environmental conditions. This chapter covers the genome-wide molecular techniques currently being employed in rice with the ultimate goal of achieving much needed increases in crop productivity. © 2009 Springer Science+Business Media B.V.

Watson, L, Connell, J, Harding, A & Whitchurch, CB 2009, 'Toward using an oxidatively damaged plasmid as an intra- and inter-laboratory standard for ancient DNA studies' in Haslam, M, Robertson, G, Crowther, A, Nugent, S & Kirkwood, L (eds), Archaeological Science Under a Microscope: Studies in Residue and ancient DNA Analysis in Honour of Thomas H. Loy, ANU E Press, Canberra, Australia, pp. 141-150.
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The following paper was originally presented by Dr Thomas H. Loy at the 6th International Conference on Ancient DNA and Associated Biomolecules held in Israel, July 2002. It is included here with editorial and formatting changes with the intention of demonstrating the passion and lateral thinking that underpinned Tomï½s approach to the field of Molecular Archaeology. The paper represents research from three honours projects conducted during the late 1990s and early 2000s. Building a modern model for ancient DNA that could be used during routine procedures was a concept that Tom had long held as an important step forward for the burgeoning discipline. With the equipment and technology that was available at the time, the Damaged Plasmid Model concept was completely viable and worthy of detailed validation. As with all historical accounts, an understanding of more recent developments in molecular techniques and equipment will highlight the need for considerable optimisation of the model before it can be used as an interlaboratory standard for ancient DNA

Acuna Alvarez, L, Exton, D, Timmis, K, Suggett, DJ & Mcgenity, T 2009, 'Characterization Of Marine Isoprene-degrading Communities', Environmental Microbiology, vol. 11, no. 12, pp. 3280-3291.
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P>Isoprene is a volatile and climate-altering hydrocarbon with an atmospheric concentration similar to that of methane. It is well established that marine algae produce isoprene; however, until now there was no specific information about marine isoprene sinks. Here we demonstrate isoprene consumption in samples from temperate and tropical marine and coastal environments, and furthermore show that the most rapid degradation of isoprene coincides with the highest rates of isoprene production in estuarine sediments. Isoprene-degrading enrichment cultures, analysed by denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene and by culturing, were generally dominated by Actinobacteria, but included other groups such as Alphaproteobacteria and Bacteroidetes, previously not known to degrade isoprene. In contrast to specialist methane-oxidizing bacteria, cultivated isoprene degraders were nutritionally versatile, and nearly all of them were able to use n-alkanes as a source of carbon and energy. We therefore tested and showed that the ubiquitous marine hydrocarbon-degrader, Alcanivorax borkumensis, could also degrade isoprene. A mixture of the isolates consumed isoprene emitted from algal cultures, confirming that isoprene can be metabolized at low, environmentally relevant concentrations, and suggesting that, in the absence of spilled petroleum hydrocarbons, algal production of isoprene could maintain viable populations of hydrocarbon-degrading microbes. This discovery of a missing marine sink for isoprene is the first step in obtaining more robust predictions of its flux, and suggests that algal-derived isoprene provides an additional source of carbon for diverse microbes in the oceans.

Aharonovich, I, Castelletto, S, Simpson, DA, Greentree, AD & Prawer, S 2009, 'Photophysics of novel diamond based single photon emitters', Phys Rev A 2010.
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A detailed study of the photophysical properties of several novel color centers in chemical vapor deposition diamond is presented. These emitters show narrow luminescence lines in the near infra-red. Single photon emission was verified with continuous and pulsed excitation with emission rates at saturation in the MHz regime, whilst direct lifetime measurements reveal excited state lifetimes ranging from 1-14 ns. In addition, a number of quantum emitters demonstrate two level behavior with no bunching present in the second order correlation function. An improved method of evaluating the quantum efficiency through the direct measurement of the collection efficiency from two level emitters is presented and discussed. \

Aharonovich, I, Castelletto, S, Simpson, DA, Stacey, A, Mccallum, J, Greentree, AD & Prawer, S 2009, 'Two-level ultrabright single photon emission from diamond nanocrystals', Nano Letters, vol. 9, no. 9, pp. 3191-3195.
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The fabrication of stable ultrabright single photon sources operating at room temperature Is reported. The emitter is based on a color center within a diamond nanocrystal grown on a sapphire substrate by chemical vapor deposition method and exhibits a tw

Aharonovich, I, Santori, C, Fairchild, BA, Orwa, J, Ganesan, K, Fu, KC, Beausoleil, RG, Greentree, AD & Prawer, S 2009, 'Producing optimized ensembles of nitrogen-vacancy color centers for quantum information applications', Journal Of Applied Physics, vol. 106, no. 12.
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Quantum information applications place stringent demands on the development of platforms that can host them. Color centers in diamond have been identified as important media for quantum information processing. Accordingly, the photoluminescence properties of nitrogen-vacancy N-V centers in diamond created by implantation and annealing are studied at cryogenic temperatures below 10 K. We examine high pressure high temperature and chemical vapor deposition synthetic diamonds with varying nitrogen concentration and present an accurate method to estimate the concentration of the N-V centers created by ion implantation. The ion irradiation route produced up to 6 ppm of optically active N-V centers, while nitrogen implantation yielded up to 3 ppm of optically active N-V with 8% conversion efficiency. However, a broadening of the N-V - zero phonon line was observed in all samples. © 200

Aharonovich, I, Zhou, C, Stacey, A, Orwa, J, Castelletto, S, Simpson, D, Greentree, AD, Treussart, F, Roch, J & Prawer, S 2009, 'Enhanced single-photon emission in the near infrared from a diamond color center', Physical Review B, vol. 79, no. 23, pp. 0-0.
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Individual color centers in diamond are promising for near-term quantum technologies including quantum key distribution and metrology. Here we show fabrication of an as-yet uncharacterized nickel-related complex in diamond which has photophysical propert

Ahn, J, Kim, YJ & Wang, G 2009, 'Electrochemical properties of SnO2 nanowires prepared by a simple heat treatment of Sn-Ag alloys', Journal Of Alloys And Compounds, vol. 483, no. 1-2, pp. 422-424.
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One-dimensional (1D) SnO2 nanowires were synthesized by a simple heat treatment of SnAg alloys. The presence of Ag in the alloy and a small amount of impurity oxygen in an inert gas played an important role in the growth of SnO2 nanowires. The oxygen content higher than 1 vol.% in the gas resulted in the formation of fine spherical powders. The Li storage property of nano-sized SnO2 for the spherical and 1D SnO2 was evaluated from the lithium intercalation process in a Li-ion cell. The SnO2 nanowires exhibited a better electrochemical performance as an anode than the spherical powders.

Ahn, J-H, Wang, G & Kim, Y-J 2009, 'Facile synthesis of tin oxide nanofibres', CURRENT APPLIED PHYSICS, vol. 9, no. 2, pp. E176-E179.
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Al-ghazi, Y, Bourot, S, Arioli, T, Dennis, ES & Llewellyn, D 2009, 'Transcript Profiling During Fiber Development Identifies Pathways in Secondary Metabolism and Cell Wall Structure That May Contribute to Cotton Fiber Quality', PLANT AND CELL PHYSIOLOGY, vol. 50, no. 7, pp. 1364-1381.
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A global gene expression profi ling study at different stages of fi ber development was undertaken on two cotton species cultivated for fi ber, Gossypium hirsutum (L.) and G. barbadense (L.). A large proportion of the genome was expressed during both fi ber elongation and subsequent secondary cell wall thickening. There was a major shift in abundance of transcripts for gene regulation, cell organization and metabolism between fi ber elongation and fi ber thickening that was fundamentally similar in both species. Each stage had its own distinctive features represented by specifi c metabolic and regulatory genes, a number of which have been noted previously. Many of the genes expressed in the fi bers were of a similar type and developmental expression to those seen in other fi berproducing plants, indicating a conservation of mechanisms of cell elongation and wall thickening across diverse plant genera. Secondary metabolism and pectin synthesis and modifi cation genes were amongst the most statistically signifi cant differentially expressed categories between the two species during fi ber elongation. The gene profi les of the fi ber thickening stage, however, were almost identical between the two species, suggesting that their different fi nal fi ber quality properties may be established at earlier stages of fi ber development. Expression levels of representative phenylpropanoid and pectin modifi cation genes showed high correlations with specifi c fi ber properties in an inter-specifi c cotton recombinant inbred line (RIL) population, supporting a role in determining fi ber quality.

Al-Qassab, SE, Reichel, MP & Ellis, JT 2009, 'A second generation multiplex PCR for typing strains of Neospora caninum using six DNA targets', Molecular and Cellular Probes, vol. 24, no. 1, pp. 20-26.
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Genetic diversity of Neospora caninum was investigated through a study of repetitive sequences found in the genome of this species. Twenty different loci were studied, and three were identified that varied in repeat content amongst isolates. No relationship was found between the copy number of repetitive sequences present and host type or geographical location from which the isolates were derived. A multiplex PCR assay was developed for multilocus-strain typing using three microsatellites and three minisatellites, based on the polymorphisms found in the repetitive sequences. This study therefore extends knowledge on the repetitive sequences found in the N. caninum genome and the diversity found within the species. It also provides a second generation multiplex assay that can be used to study the biology of N. caninum. In addition, this study included Neospora hughesi (along with other closely related apicomplexans) as controls. The present study shows N. hughesi to be quite distinct from N. caninum in these repetitive sequences, thereby potentially providing a new approach for the differentiation of these two taxa.

Al-Qassab, SE, Reichel, MP, Ivens, A & Ellis, JT 2009, 'Genetic Diversity Amongst Isolates Of Neospora Caninum, And The Development Of A Multiplex Assay For The Detection Of Distinct Strains', Molecular & Cellular Probes, vol. 23, no. 3-4, pp. 132-139.
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Infection with Neospora caninum is regarded as a significant cause of abortion in cattle. Despite the economic impact of this infection, relatively little is known about the biology of this parasite. In this study, mini and microsatellite DNAs were detec

Al-Qassab, SE, Reichel, MP, Su, C, Jenkins, D, Hall, C, Windsor, PA, Dubey, J & Ellis, JT 2009, 'Isolation of Toxoplasma gondii from the brain of a dog in Australia and its biological and molecular characterization', Veterinary Parasitology, vol. 164, no. 2-4, pp. 335-339.
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Toxoplasma gondii was isolated from the brain of a young dog for the ?rst time in Australia. The identity of the parasite was con?rmed by PCR, Western blotting, electron microscopy and cat bioassay. Genotyping of the isolate (TgDgAu1) was determined by PCR-RFLP markers that showed it to be a Type II strain. Western blotting demonstrated the presence of IgM antibodies to T. gondii suggesting the bitch was probably infected during pregnancy and the T. gondii was transmitted to the pups congenitally. We believe this represents the ?rst description of a natural case of congenital transmission of T. gondii in the dog

Ammit, A, Halayko, AJ, Hirst, SJ, Murphy, T & Stewart, A 2009, 'Airways smooth muscle: The next generation', PULMONARY PHARMACOLOGY & THERAPEUTICS, vol. 22, no. 5, pp. 351-352.
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Ammit, AJ, Burgess, JK, Hirst, SJ, Hughes, JM, Kaur, M, Lau, JY & Zuyderduyn, S 2009, 'The effect of asthma therapeutics on signalling and transcriptional regulation of airway smooth muscle function', PULMONARY PHARMACOLOGY & THERAPEUTICS, vol. 22, no. 5, pp. 446-454.
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Apanasovich, TV, Carroll, RJ & Maity, A 2009, 'SIMEX and standard error estimation in semiparametric measurement error models', ELECTRONIC JOURNAL OF STATISTICS, vol. 3, pp. 318-348.
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Arnold, MD & Blaber, MG 2009, 'Optical performance and metallic absorption in nanoplasmonic systems', Optics Express, vol. 17, no. 5, pp. 3835-3847.
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Optical metrics relating to metallic absorption in representative plasmonic systems are surveyed, with a view to developing heuristics for optimizing performance over a range of applications. We use the real part of the permittivity as the independent variable; consider strengths of particle resonances, resolving power of planar lenses, and guiding lengths of planar waveguides; and compare nearly-free-electron metals including Al, Cu, Ag, Au, Li, Na, and K. Whilst the imaginary part of metal permittivity has a strong damping effect, field distribution is equally important and thus factors including geometry, real permittivity and frequency must be considered when selecting a metal. Al performs well at low permittivities (e.g. sphere resonances, superlenses) whereas Au & Ag only perform well at very negative permittivities (shell and rod resonances, LRSPP). The alkali metals perform well overall but present engineering challenges.

Arotsker, L, Siboni, N, Ben-Dov, E, Kramarsky-Winter, E, Loya, Y & Kushmaro, A 2009, 'Vibrio sp as a potentially important member of the Black Band Disease (BBD) consortium in Favia sp corals', FEMS MICROBIOLOGY ECOLOGY, vol. 70, no. 3, pp. 515-524.
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Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2009, 'Formation of Diquinoline Molecular Bricks and Their Assembly into Lattice Inclusion Compounds', CRYSTAL GROWTH & DESIGN, vol. 9, no. 6, pp. 2742-2750.
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Austin, CE, Hare, DJ, Rozelle, A, Robinson, W, Grimm, R & Doble, PA 2009, 'Elemental bio-imaging of calcium phosphate crystal deposits in knee samples from arthritic patients', Metallomics, vol. 1, no. 2, pp. 142-147.
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Laser ablation inductively coupled plasma mass spectrometry (LA ICP-MS) was employed to image deposits of calcium phosphate based crystals in knee cartilage and synovial fluid from arthritic patients. A reaction/collision cell containing hydrogen minimised plasma interferences on calcium and also improved the image quality without significant sensitivity reduction. Areas of high calcium and phosphorus intensities consistent with crystal deposits were observed for both the cartilage and synovial fluid samples. These areas were also characterised by high magnesium and strontium intensities. Distribution patterns of other elements such as copper and sulfur did not correlate with the crystal deposits. Filtered and non-filtered solutions of calcium phosphate crystals grown in synthetic synovial fluid were also imaged as further evidence of crystal deposits. The crystal deposits were detected in the unfiltered Solution, and were absent from the filtered solutions.

Bai, H, Cortie, MB, Maaroof, AI, Dowd, AR, Kealley, CS & Smith, G 2009, 'The preparation of a plasmonically resonant VO2 thermochromic pigment', Nanotechnology, vol. 20, no. 8, pp. 1-9.
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Vanadium dioxide (VO2) undergoes a reversible metal-insulator transition, normally at similar to 68 degrees C. While the properties of continuous semi-transparent coatings of VO2 are well known, there is far less information available concerning the potential use of discrete VO2 nanoparticles as a thermochromic pigment in opaque coatings. Individual VO2 nanoparticles undergo a localized plasmon resonance with near-infrared light at about 1100 nm and this resonance can be switched on and off by simply varying the temperature of the system. Therefore, incorporation of VO2 nanoparticles into a coating system imbues the coating with the ability to self-adaptively modulate its own absorptive efficiency in the near-infrared. Here we examine the magnitude and control of this phenomenon. Prototype coatings are described, made using VO2 powder produced by an improved process. The materials are characterized using calorimetry, x-ray diffraction, high-resolution scanning electron microscopy, transmission electron microscopy, and by measurement of optical properties.

Baird, AH, Bhagooli, R, Ralph, PJ & Takahashi, S 2009, 'Coral bleaching: the role of the host', Trends In Ecology & Evolution, vol. 24, no. 1, pp. 16-20.
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Coral bleaching caused by global warming is one of the major threats to coral reefs. Very recently, research has focused on the possibility of corals switching symbionts as a means of adjusting to accelerating increases in sea surface temperature. Although symbionts are clearly of fundamental importance, many aspects of coral bleaching cannot be readily explained by differences in symbionts among coral species. Here we outline several potential mechanisms by which the host might influence the bleaching response, and conclude that predicting the fate of corals in response to climate change requires both members of the symbiosis to be considered equally.

Baird, MC, Pyne, SG, Ung, AT, Lie, W, Sastraruji, T, Jatisatienr, A, Jatisatienr, C, Dheeranupattana, S, Lowlam, J & Boonchalermkit, S 2009, 'Semisynthesis and Biological Activity of Stemofoline Alkaloids', Journal of Natural Products, vol. 72, no. 4, pp. 679-684.
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The semisynthesis of the Stemona alkaloids (3?R)-stemofolenol (1), (3?S)-stemofolenol (2), methylstemofoline (3), and (3?S)-hydroxystemofoline (5) and the unnatural analogues (11E)-methylstemofoline (15) and 3?R-hydroxystemofoline (11) has been achieved starting from (11Z)-1?,2?-didehydrostemofoline (4). This synthesis allowed, for the first time, access to diastereomerically enriched samples of 1 and 2 and the assignment of their absolute configurations at C-3?. These compounds were obtained in sufficient quantities to allow for their biological testing. In a quantitative assay as AChE inhibitors, (11Z)-1?,2?-didehydrostemofoline (4) and (3?S)-hydroxystemofoline (5) were found to be the most active.

Barard, S, Heeney, M, Chen, L, Colle, M, Shkunov, M, McCulloch, I, Stingelin, N, Philips, M & Kreouzis, T 2009, 'Separate charge transport pathways determined by the time of flight method in bimodal polytriarylamine', JOURNAL OF APPLIED PHYSICS, vol. 105, no. 1.
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Barraud, N, Schleheck, D, Klebensberger, J, Webb, JS, Hassett, DJ, Rice, SA & Kjelleberg, S 2009, 'Nitric Oxide Signaling in Pseudomonas aeruginosa Biofilms Mediates Phosphodiesterase Activity, Decreased Cyclic Di-GMP Levels, and Enhanced Dispersal', JOURNAL OF BACTERIOLOGY, vol. 191, no. 23, pp. 7333-7342.
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Barraud, N, Storey, MV, Moore, ZP, Webb, JS, Rice, SA & Kjelleberg, S 2009, 'Nitric oxide-mediated dispersal in single- and multi-species biofilms of clinically and industrially relevant microorganisms', MICROBIAL BIOTECHNOLOGY, vol. 2, no. 3, pp. 370-378.
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Barrett, BS & Leslie, LM 2009, 'Links between Tropical Cyclone Activity and Madden-Julian Oscillation Phase in the North Atlantic and Northeast Pacific Basins', MONTHLY WEATHER REVIEW, vol. 137, no. 2, pp. 727-744.
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Bartlett, CY, Manua, C, Cinner, J, Sutton, S, Jimmy, R, South, R, Nilson, J & Raina, J 2009, 'Comparison of Outcomes of Permanently Closed and Periodically Harvested Coral Reef Reserves', Conservation Biology, vol. 23, no. 6, pp. 1475-1484.
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In many areas of the developing world, the establishment of permanent marine reserves is inhibited by cultural norms or socioeconomic pressures. Community conserved areas that are periodically harvested are increasingly being implemented as fisheries management tools, but few researchers have empirically compared them with permanently closed reserves. We used a hierarchal control-impact experimental design to compare the abundance and biomass of reef fishes, invertebrates, and substrate composition in periodically harvested and permanent reserves and in openly fished (control sites) of the South Pacific island country of Vanuatu. Fished species had significantly higher biomass in periodically harvested reserves than in adjacent openly fished areas. We did not detect differences in substratum composition between permanent reserves and openly fished areas or between permanent reserves and periodically harvested reserves. Giant clams (tridacnids) and top shells (Trochus niloticus) were vulnerable to periodic harvest, and we suggest that for adequate management of these species, periodically harvested community conservation areas be used in conjunction with other management strategies. Periodic harvest within reserves is an example of adaptive and flexible management that may meet conservation goals and that is suited to the social, economic, and cultural contexts of many coastal communities in the developing world.

Bar-zeev, E, Berman-frank, I, Stambler, N, Vazquez-dominguez, E, Zohary, T, Capuzzo, E, Meeder, E, Suggett, DJ, Iluz, D, Dishon, G & Berman, T 2009, 'Transparent exopolymer particles (TEP) link phytoplankton and bacterial production in the Gulf of Aqaba', Aquatic Microbial Ecology, vol. 56, no. 2-3, pp. 217-225.
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Variations in transparent exopolymer particles (TEP), bacterial biomass production (BP) and primary productivity (PP) were followed over 52 h at a deep water station in the Gulf of Aqaba (Eilat, Israel) during the spring, in April 2008. About 20 h after the start of the study, there was a short (~15 h) but intense storm event that probably caused a nutrient pulse and, subsequently, a brief outgrowth of diatoms in the euphotic layer. Concentrations of TEP and BP ranged from 23 to 228 µg gum xanthan equivalents l1 and from 0.2 to 0.6 µg C l1 h1, respectively. Concentrations of TEP and BP were measured in unfiltered and in GF/C (1.2 µm)-prefiltered samples. Most of the TEP (59 ± 21% of total TEP, mean ± SD) were in the smaller (GF/C-filtered) size fraction (0.41.2 µm); however, after the crash of the diatom bloom, the majority of TEP were in the >1.2 µm size fraction. In the GF/C-filtered fraction, BP averaged 59 ± 12% and 93 ± 5% of total BP in the upper water column and from 300 m, respectively. Significant correlations were observed between TEP and BP, suggesting that active heterotrophic bacteria may have been associated with these particles. During the 3 d of our study, PP and BP in the euphotic zone averaged 480 and 225 mg C m2 d1, respectively, suggesting that about half or more of the primary produced carbon was metabolized by heterotrophic bacteria in the upper water column. Coincident with strong mixing caused by the storm, TEP concentrations decreased in the surface water and increased at depth. We suggest that TEP acted to link carbon flux between the primary producers and heterotrophic bacteria, and that the downward movement of TEP from the upper water layers may be an important process in transferring organic carbon to deeper waters of the Gulf of Aquaba. Sinking TEP could provide not only organic carbon substrates for associated bacteria but also form `hot spots of elevated microbial metabolism and nutrient cycling throughout the water column.

Batenburg-Nguyen, U, Ung, AT & Pyne, SG 2009, 'The synthesis of carbon linked bis-benzylisoquinolines using Mizoroki-Heck and Sonagashira coupling reactions', Tetrahedron, vol. 65, no. 1, pp. 318-327.
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Novel laudanosine dimers in which two laudanosine units are linked at C-2? via a two or three-carbon linker (alkane, alkene or alkyne) have been prepared using palladium-catalysed cross-coupling reactions (MizorokiHeck and Sonagashira reactions). In one example, a second three-carbon linker between the two isoquinoline N-atoms was also present leading to a novel macrocyclic ring system.

Battle, AR, Valenzuela, S, Mechler, A, Nichols, R, Praporski, S, Di Maio, I, Islam, H, Girard-Egrot, AP, Cornell, BA, Prashar, J, Caruso, F, Martin, LL & Martin, DK 2009, 'Novel engineered ion channel provides controllable ion permability for polyelectrolyte microcapsules coated with a lipid membrane', Advanced Functional Materials, vol. 19, pp. 201-208.
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The development of nanostructured microcapsules based on a biomimetic lipid bilayer membrane (BLM) coating of poly(SODIUM STYRENESUFONATE) (pss) /POLY(ALLYLAMINE HYDROCHLORIDE) (pah) POLYELECTROLYTE HOLLOW MICROCAPSULES IS REPORTED

Beagley, KW, Huston, WM, Hansbro, PM & Timms, P 2009, 'Chlamydial Infection of Immune Cells: Altered Function and Implications for Disease', CRITICAL REVIEWS IN IMMUNOLOGY, vol. 29, no. 4, pp. 275-305.
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Bebawy, M, Combes, V, Lee, E, Jaiswal, R, Gong, J, Bonhoure, A & Grau, G 2009, 'Membrane microparticles mediate transfer of P-glycoprotein to drug sensitive cancer cells', Leukemia, vol. 23, no. 9, pp. 1643-1649.
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Multidrug resistance (MDR), a significant impediment to the successful treatment of cancer clinically, has been attributed to the overexpression of P-glycoprotein (P-gp), a plasma membrane multidrug efflux transporter. P-gp maintains sublethal intracellular drug concentrations by virtue of its drug efflux capacity. The cellular regulation of P-gp expression is currently known to occur at either pre- or post-transcriptional levels. In this study, we identify a `non-genetic mechanism whereby microparticles (MPs) serve as vectors in the acquisition and spread of MDR. MPs isolated from drug-resistant cancer cells (VLB100) were co-cultured with drug sensitive cells (CCRFCEM) over a 4 h period to allow for MP binding and P-gp transfer. Presence of P-gp on MPs was established using flow cytometry (FCM) and western blotting. Whole-cell drug accumulation assays using rhodamine 123 and daunorubicin (DNR) were carried out to validate the transfer of functional P-gp after co-culture. We establish that MPs shed in vitro from drug-resistant cancer cells incorporate cell surface P-gp from their donor cells, effectively bind to drug-sensitive recipient cells and transfer functional P-gp to the latter. These findings serve to substantially advance our understanding of the molecular basis for the emergence of MDR in cancer clinically and lead to new treatment strategies which target and inhibit MP mediated transfer of P-gp during the course of treatment.

Becue, A, Moret, S, Champod, C & Margot, P 2009, 'Use of quantum dots in aqueous solution to detect blood fingermarks on non-porous surfaces', FORENSIC SCIENCE INTERNATIONAL, vol. 191, no. 1-3, pp. 36-41.
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Belli, SI, Ferguson, DJ, Katrib, M, Slapetova, I, Mai, K, Slapeta, J, Flowers, SA, Miska, KB, Tomley, FM, Shirley, M, Wallach, M & Smith, NC 2009, 'Conservation of proteins involved in oocyst wall formation in Eimeria maxima, Eimeria tenella and Eimeria acervulina', International Journal For Parasitology, vol. 39, no. 10, pp. 1063-1070.
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Vaccination with proteins from gametocytes of Eimeria maxima protects chickens, via transfer of maternal antibodies, against infection with several species of Eimeria. Antibodies to E. maxima gametocyte proteins recognise proteins in the wall forming bodies of macrogametocytes and oocyst walls of E. maxima, Eimeria tenella and Eimeria acervulina. Homologous genes for two major gametocyte proteins GAM56 and GAM82 were found in E. maxima, E. tenella and E. acervulina. Alignment of the predicted protein sequences of these genes reveals that, as well as sharing regions of tyrosine richness, strong homology exists in their amino-terminal regions, where protective antibodies bind. This study confirms the conservation of the roles of GAM56 and GAM82 in oocyst wall formation and shows that antibodies to gametocyte antigens of E. maxima cross-react with homologous proteins in other species, helping to explain cross-species maternal immunity.

Benson, SJ, Lennard, CJ, Maynard, PJ, Andrews, A, Hill, D & Roux, CP 2009, 'Forensic analysis of explosives using isotope ratio mass spectrometry (IRMS) - Preliminary study on TATP and PETN', Science & Justice, vol. 49, no. 2, pp. 81-86.
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The application of isotopic techniques to investigations requiring the provision of evidence to a Court is limited. The objective of this research was to investigate the application of light stable isotopes and isotope ratio mass spectrometry (IRMS) to solve complex forensic cases by providing a level of discrimination not achievable utilising traditional forensic techniques. Due to the current threat of organic peroxide explosives, such as triacetone triperoxide (TATP), research was undertaken to determine the potential of IRMS to differentiate samples of TATP that had been manufactured utilising different starting materials and/or manufacturing processes. In addition, due to the prevalence of pentaerythritoltetranitrate (PETN) in detonators, detonating cord, and boosters, the potential of the IRMS technique to differentiate PETN samples from different sources was also investigated. Carbon isotope values were measured in fourteen TATP samples, with three definite groups appearing in the initial sample set based on the carbon data alone. Four additional TATP samples (in a second set of samples) were distinguishable utilising the carbon and hydrogen isotopic compositions individually, and also in combination with the oxygen isotope values. The 3D plot of the carbon, oxygen and hydrogen data demonstrated the clear discrimination of the four samples of TATP. The carbon and nitrogen isotope values measured from fifteen PETN samples, allowed samples from different sources to be readily discriminated. This paper demonstrates the successful application of IRMS to the analysis of explosives of forensic interest to assist in discriminating samples from different sources. This research represents a preliminary evaluation of the IRMS technique for the measurement of stable isotope values in TATP and PETN samples, and supports the dedication of resources for a full evaluation of this application in order to achieve Court reportable IRMS results.

Benson, SJ, Lennard, CJ, Maynard, PJ, Hill, D, Andrews, A & Roux, CP 2009, 'Forensic analysis of explosives using isotope ratio mass spectrometry (IRMS) - Discrimination of ammonium nitrate sources', Science & Justice, vol. 49, no. 2, pp. 73-80.
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An evaluation was undertaken to determine if isotope ratio mass spectrometry (IRMS) could assist in the investigation of complex forensic cases by providing a level of discrimination not achievable utilising traditional forensic techniques. The focus of the research was on ammonium nitrate (AN), a common oxidiser used in improvised explosive mixtures. The potential value of IRMS to attribute Australian AN samples to the manufacturing source was demonstrated through the development of a preliminary AN classification scheme based on nitrogen isotopes. Although the discrimination utilising nitrogen isotopes alone was limited and only relevant to samples from the three Australian manufacturers during the evaluated time period, the classification scheme has potential as an investigative aid. Combining oxygen and hydrogen stable isotope values permitted the differentiation of AN prills from three different Australian manufacturers. Samples from five different overseas sources could be differentiated utilising a combination of the nitrogen, oxygen and hydrogen isotope values. Limited differentiation between Australian and overseas prills was achieved for the samples analysed. The comparison of nitrogen isotope values from intact AN prill samples with those from post-blast AN prill residues highlighted that the nitrogen isotopic composition of the prills was not maintained post-blast; hence, limiting the technique to analysis of un-reacted explosive material.

Bhatia, VK, Kealley, CS, Wuhrer, R, Wallwork, K & Cortie, MB 2009, 'Ternary Beta And Gamma Phases In The Al-Au-Cu System At 750 Degrees C', Journal Of Alloys And Compounds, vol. 488, no. 1, pp. 100-107.
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There are many aspects of the phases and phase boundaries of the Al-Au-Cu ternary system that are still unknown. Although a 500 degrees C isothermal section and an 18 karat pseudobinary have been reported, many of the other constitutive relationships wit

Bhatia, VK, Levey, FC, Kealley, CS, Dowd, AR & Cortie, MB 2009, 'The aluminium-copper-gold ternary system', Gold Bulletin, vol. 42, no. 3, pp. 201-208.
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Despite Au, Al and Cu being individually very well-known elements, their ternary phase diagram has not been studied in as much detail as those of many other Au-containing ternaries. Here we review what is known, and consider the prospects for technological exploitation of some of the ternary compositions. The components of greatest interest in Al-Au-Cu may be the P-phases, at least two of which have shape memory properties. Of these, 'Spangold', which has the nominal stoichiometry Au7Cu5Al4, has received some attention for jewellery applications, while the edge compound Cu3Al is a well-known shape memory composition with corresponding specialised industrial uses. The properties of other beta-phase compositions in the system have been scarcely investigated. The system also contains an extensive gamma-phase, Al4AuxCu9-x, where x ranges from 0 to similar to 6.5, and the purple gold phase AuAl2.

Biro, P & Booth, DJ 2009, 'Extreme boldness precedes starvation mortality in six-lined trumpeter (Pelates sexlineatus)', Hydrobiologia, vol. 635, no. 1, pp. 395-398.
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Fishes are often subjected to seasonal and spatial patchiness of food sources. We tested how risk-taking behaviour in the six-lined trumpeter, an estuarine seagrass resident fish, changed with hunger level in a laboratory experiment. When repeatedly offered a risky source of food, well-fed fish did not approach it and all fish survived over a one-month trial. In contrast, fish deprived of all food boldly first approached the risky food source after only a few days without food in some cases, or after many days in other cases, and then continued to approach risky food each time it was presented. Larger individuals were more bold (and had longer starvation endurance) than smaller ones, and after statistically controlling for these size effects, there were consistent individual differences in the propensity to take risks (i.e. boldness). These results show that food-and individual-dependent boldness will together affect vulnerability to predators and influence predation rates when resources become scarce.

Biswas, M, Kwack, H-S, Dang, LS, Henry, MO & McGlynn, E 2009, 'Spatial inhomogeneity of donor bound exciton emission from ZnO nanostructures grown on Si', Nanotechnology, vol. 20, no. 25, pp. 255703-255703.
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Blaber, MG, Arnold, MD & Ford, M 2009, 'Optical properties of intermetallic compounds from first principles calculations: a search for the ideal plasmonic material', Journal Of Physics: Condensed Matter, vol. 21, pp. 144211-144218.
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First principles calculations have been used to predict the optical properties for a range of intermetallic compounds for which little or no experimental optical data are currently available. Density functional theory combined with the random phase approximation is used to calculate the dielectric functions for these compounds. The aim of this work is to investigate how the band edge and plasma frequency vary with composition in order to identify materials with promising plasmonic properties. Towards this end the intermetallic compounds chosen are composed of elements which on their own have reasonable optical properties for plasmonic applications. The position of the band edge relative to the plasma frequency is most favourable in the simple binary compounds formed from the alkali plus noble metals NaAu, KAu and KAg. In particular, for KAu the band edge and plasma frequency occur at almost the same frequency, and hence the imaginary part of the dielectric function is practically zero for frequencies below the plasma frequency. In addition, the plasma frequency in this compound is at relatively low frequency, promising a material with strong plasmon response in the infrared.

Blaber, MG, Arnold, MD & Ford, M 2009, 'Search for the ideal plasmonic nanoshell: the effects of surface scattering and alternatives to gold and silver', Journal of Physical Chemistry C, vol. 113, no. 8, pp. 3041-3045.
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Black, J, Oliver, BG & Roth, M 2009, 'Molecular Mechanisms of Combination Therapy With Inhaled Corticosteroids and Long-Acting beta-Agonists', Chest, vol. 136, no. 4, pp. 1095-1100.
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The treatment of asthma relies on the use of the following two major drug classes: beta(2)-agonists, both short acting and long acting; and corticosteroids (CSs). Although the properties of each drug class are well described, their use in combination del

Blair, S, Cokcetin, N, Harry, L & Carter, D 2009, 'The unusual antibacterial activity of medical-grade Leptospermum honey: antibacterial spectrum, resistance and transcriptome analysis', European Journal of Clinical Microbiology & Infecti..., vol. 28, no. 10, pp. 1199-1208.
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There is an urgent need for new, effective agents in topical wound care, and selected honeys show potential in this regard. Using a medical-grade honey, eight species of problematic wound pathogens, including those with high levels of innate or acquired antibiotic resistance, were killed by 4.0-14.8% honey, which is a concentration that can be maintained in the wound environment. Resistance to honey could not be induced under conditions that rapidly induced resistance to antibiotics. Escherichia coli macroarrays were used to determine the response of bacterial cells to a sub-lethal dose of honey. The pattern of gene expression differed to that reported for other antimicrobial agents, indicating that honey acts in a unique and multifactorial way; 78 (2%) genes were upregulated and 46 (1%) genes were downregulated more than two-fold upon exposure to the medical-grade honey. Most of the upregulated genes clustered into distinct functional regulatory groups, with many involved in stress responses, and the majority of downregulated genes encoded for products involved in protein synthesis. Taken together, these data indicate that honey is an effective topical antimicrobial agent that could help reduce some of the current pressures that are promoting antibiotic resistance.

Bond, D, Dennis, ES, Pogson, B & Finnegan, E 2009, 'Histone Acetylation, VERNALIZATION INSENSITIVE 3, FLOWERING LOCUS C, and the Vernalization Response', Molecular Plant, vol. 2, no. 4, pp. 724-737.
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The quantitative induction of VIN3 by low temperatures is required for PRC2 repression of FLC and promotion of flowering (vernalization) in Arabidopsis. Histone acetylation, a chromatin modification commonly associated with gene transcription, increased on VIN3 chromatin in two spatially and temporally distinct phases in response to low temperatures. During short-term cold exposure, histone H3 acetylation at the transcription start site rapidly increased, implying that it is required for VIN3 induction. Subsequent changes in histone H3 and H4 acetylation occurred following continued VIN3 transcription during prolonged cold exposure. Members of the SAGA-like transcriptional adaptor complex, including the histone acetyltransferase GCN5, which induces expression of the cold acclimation pathway genes, do not regulate VIN3 induction during cold exposure, indicating that the cold acclimation pathway and the cold-induction of VIN3 are regulated by different transcriptional mechanisms. Mutations in the other 11 histone acetyltransferase genes did not affect VIN3 induction. However, nicotinamide, a histone deacetylase inhibitor, induced VIN3 and altered histone acetylation at the VIN3 locus. VIN3 induction was proportional to the length of nicotinamide treatment, which was associated with an early-flowering phenotype and repression of FLC. However, unlike vernalization, the repression of FLC was independent of VIN3 activity. Nicotinamide treatment did not cause a change in the expression of any genes in the autonomous pathway or members of the PRC2 complex, the well characterized repressors of FLC. Our data suggest that FLC is repressed via a novel pathway involving the SIR2 class of histone deacetylases.

Bond, D, Wilson, I, Dennis, ES, Pogson, B & Finnegan, E 2009, 'VERNALIZATION INSENSITIVE 3 (VIN3) is required for the response of Arabidopsis thaliana seedlings exposed to low oxygen conditions', PLANT JOURNAL, vol. 59, no. 4, pp. 576-587.
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VERNALIZATION INSENSITIVE 3 (VIN3), which is required for the vernalization-mediated epigenetic repression of FLOWERING LOCUS C (FLC) in Arabidopsis thaliana, is quantitatively induced in response to low temperatures. We found that hypoxic conditions also induce VIN3 in a quantitative manner but high salt, high temperatures and osmotic stress do not. Inhibition of mitochondrial respiration did not induce VIN3 expression, consistent with the lack of VIN3 induction in response to other stresses that affect the rate of mitochondrial respiration. De novo protein synthesis is required for VIN3 induction during hypoxic conditions; this situation is not the case for VIN3 induction by low temperatures, indicating that different mechanisms act to induce VIN3 expression in response to cold and hypoxic conditions. Without VIN3 activity, fewer seedlings survived following a 72-h period of hypoxic treatment, indicating that VIN3 is required for the survival of Arabidopsis thaliana in response to hypoxic stress. Complementation of the vin3 mutant with a VIN3 transgene restored the wild-type response to low oxygen and confirmed the role of VIN3 in protecting both shoots and roots during low oxygen conditions. Loss of VIN3 protein did not affect the transcriptional regulation of genes known to be important in the response to low oxygen stress, which suggests that there is a novel mechanism to combat hypoxia that involves VIN3. This mechanism is likely to involve chromatin remodelling and may be similar to the role of VIN3 in the epigenetic repression of FLC during the vernalization response.

Bond, DM, Dennis, ES & Finnegan, EJ 2009, 'Hypoxia: A novel function for VIN3', Plant Signaling and Behavior, vol. 4, no. 8, pp. 773-776.
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VERNALIZATION INSENSITIVE 3 (VIN3) encodes a PHD domain chromatin remodelling protein that is induced in response to cold and is required for the establishment of the vernalization response in Arabidopsis thaliana.1 Vernalization is the acquisi- tion of the competence to flower after exposure to prolonged low temperatures, which in Arabidopsis is associated with the epige- netic repression of the floral repressor FLOWERING LOCUS C (FLC).2,3 During vernalization VIN3 binds to the chromatin of the FLC locus,1 and interacts with conserved components of Polycomb-group Repressive Complex 2 (PRC2).4,5 This complex catalyses the tri-methylation of histone H3 lysine 27 (H3K27me3),4,6,7 a repressive chromatin mark that increases at the FLC locus as a result of vernalization.4,7-10 In our recent paper11 we found that VIN3 is also induced by hypoxic condi- tions, and as is the case with low temperatures, induction occurs in a quantitative manner. Our experiments indicated that VIN3 is required for the survival of Arabidopsis seedlings exposed to low oxygen conditions. We suggested that the function of VIN3 during low oxygen conditions is likely to involve the mediation of chromatin modifications at certain loci that help the survival of Arabidopsis in response to prolonged hypoxia. Here we discuss the implications of our observations and hypotheses in terms of epigenetic mechanisms controlling gene regulation in response to hypoxia. © 2009 Landes Bioscience.

Bordas, F, Seassal, C, Dupuy, E, Regreny, P, Gendry, M, Viktorovitch, P, Steel, MJ & Rahmani, A 2009, 'Room temperature low-threshold InAs/InP quantum dot single mode photonic crystal microlasers at 1.5 μm using cavity-confined slow light', Optics Express, vol. 17, no. 7, pp. 5439-5445.
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We have designed, fabricated, and characterized an InP photonic crystal slab structure that supports a cavity-confined slow-light mode, i.e. a bandgap-confined valence band-edge mode. Three dimensional finite difference in time domain calculations predict that this type of structure can support electromagnetic modes with large quality factors and small mode volumes. Moreover these modes are robust with respect to fabrication imperfections. In this paper, we demonstrate room-temperature laser operation at 1.5 ìm of a cavity-confined slow-light mode under pulsed excitation. The gain medium is a single layer of InAs/InP quantum dots. An effective peak pump power threshold of 80 ìW is reported.

Botman, A, Hagen, CW, Li, J, Thiel, BL, Dunn, KA, Mulders, JJ, Randolph, S & Toth, M 2009, 'Electron postgrowth irradiation of platinum-containing nanostructures grown by electron-beam-induced deposition from Pt(PF3)4', Journal of Vacuum Science and Technology B, vol. 27, no. 6, pp. 2759-2763.
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The material grown in a scanning electron microscope by electron beam-induced deposition (EBID) using Pt(PF3)4 precursor is shown to be electron beam sensitive. The effects of deposition time and postgrowth electron irradiation on the microstructure and resistivity of the deposits were assessed by transmission electron microscopy, selected area diffraction, and four-point probe resistivity measurements. The microstructure, notably the platinum nanocrystallite grain size, is shown to evolve with electron fluence in a controllable manner. The resistivity was observed to decrease as a result of postgrowth electron irradiation, with the lowest observed value of 215±15 µO?cm. The authors demonstrate that electron beam-induced changes in microstructure can be caused using electron fluences similar to those used during the course of EBID and suggest that the observed effects can be used to tailor the microstructure and functionality of deposits grown by EBID in situ without breaking vacuum.

Breymann, W, Luthi, D & Platen, E 2009, 'Empirical behavior of a world stock index from intra-day to monthly time scales', The European Physical Journal B, vol. 71, no. 4, pp. 511-522.
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Most of the papers that study the distributional and fractal properties of financial instruments focus on stock prices or foreign exchange rates. This typically leads to mixed results concerning the distributions of log-returns and some multi-fractal properties of exchange rates, stock prices, and regional indices. This paper uses a well diversified world stock index as the central object of analysis. Such index approximates the growth optimal portfolio, which is demonstrated under the benchmark approach, it is the ideal reference unit for studying basic securities. When denominating this world index in units of a given currency, one measures the movements of the currency against the entire market. This provides a least disturbed observation of the currency dynamics. In this manner, one can expect to disentangle, e.g., the superposition of the two currencies involved in an exchange rate. This benchmark approach to the empirical analysis of financial data allows us to establish remarkable stylized facts. Most important is the observation that the repeatedly documented multi-fractal appearance of financial time series is very weak and much less pronounced than the deviation of the mono-scaling properties from Brownian-motion type scaling. The generalized Hurst exponent H(2) assumes typical values between 0.55 and 0.6. Accordingly, autocorrelations of log-returns decay according to a power law, and the quadratic variation vanishes when going to vanishing observation time step size.

Brown, A, Sommerville, DT, Reedy, BJ, Shimmon, R & Tahtouh, M 2009, 'Revisiting the thermal development of latent fingerprints on porous surfaces: new aspects and refinements', Journal of Forensic Sciences, vol. 54, no. 1, pp. 114-121.
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Bruti Liberati, N, Nikitopoulos Sklibosios, C, Platen, E & Schlogl, E 2009, 'Alternative defaultable term structure models', Asia - Pacific Financial Markets, vol. 16, no. 1, pp. 1-31.
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The objective of this paper is to consider defaultable term structure models in a general setting beyond standard risk-neutral models. Using as numeraire the growth optimal portfolio, defaultable interest rate derivatives are priced under the real-world probability measure. Therefore, the existence of an equivalent risk-neutral probability measure is not required. In particular, the real-world dynamics of the instantaneous defaultable forward rates under a jump-diffusion extension of a HJM type framework are derived. Thus, by establishing a modelling framework fully under the real-world probability measure, the challenge of reconciling real-world and risk-neutral probabilities of default is deliberately avoided, which provides significant extra modelling freedom. In addition, for certain volatility specifications, finite dimensional Markovian defaultable term structure models are derived. The paper also demonstrates an alternative defaultable term structure model. It provides tractable expressions for the prices of defaultable derivatives under the assumption of independence between the discounted growth optimal portfolio and the default-adjusted short rate. These expressions are then used in a more general model as control variates for Monte Carlo simulations of credit derivatives.

Buchy, P, Fourment, M, Mardy, S, Sorn, S, Holl, D, Ly, S, Vong, S, Enouf, V, Peiris, JSM & van der Werf, S 2009, 'Molecular Epidemiology of Clade 1 Influenza A Viruses (H5N1), Southern Indochina Peninsula, 2004–2007', Emerging Infectious Diseases, vol. 15, no. 10, pp. 1641-1644.
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Buckle, EC & Booth, DJ 2009, 'Ontogeny of space use and diet of two temperate damselfish species, Parma microlepis and Parma unifasciata', Marine Biology, vol. 156, no. 7, pp. 1497-1505.
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Studies of reef fish herbivory have mainly focused on the impacts and behaviour of adults of tropical species. In this study, the ontogenetic shifts in home range, aggression, feeding rate, diet and gut morphology in juveniles and adults of two temperate territorial damselfishes, Parma microlepis and Parma unifasciata, were determined. Both P. microlepis and P. unifasciata juveniles under 80 mm TL exhibited no aggressive chases towards conspecifics or other species, while above 80 mm TL aggressive chase frequency increased in conjunction with an increase in home range, defended as a territory. Ontogenetic diet shifts, characterised by an increase in herbivory (P. unifasciata: juveniles: 64% plant material, adults: 95% plant material; P. microlepis: juveniles: 43% plant material, adults: 67% plant material) were observed for both species. The ratio of digestive tract length to body length, which often accompanies a switch to herbivory, increased significantly with ontogeny for both species. Compared to tropical confamilial grazers, these temperate damselfish species feeding rates were lower, and they had larger territories which were not as strongly defended (fewer aggressive chases).

Burall, LS, Rodolakis, A, Rekiki, A, Myers, GSA & Bavoil, PM 2009, 'Genomic Analysis of an Attenuated Chlamydia abortus Live Vaccine Strain Reveals Defects in Central Metabolism and Surface Proteins', INFECTION AND IMMUNITY, vol. 77, no. 9, pp. 4161-4167.
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Burgess, J, Ceresa, C, Johnson, S, Kanabar, V, Moir, L, Nguyen, T, Oliver, BG, Schuliga, M & Ward, J 2009, 'Tissue and matrix influences on airway smooth muscle function', Pulmonary Pharmacology & Therapeutics, vol. 22, no. 5, pp. 379-387.
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Asthma is characterized by structural changes in the airways - airway remodelling. These changes include an increase in the bulk of the airway smooth muscle (ASM) and alterations in the profile of extracellular matrix (ECM) proteins in the airway wall. T

Burke, C, Kjelleberg, S & Thomas, T 2009, 'Selective Extraction of Bacterial DNA from the Surfaces of Macroalgae', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 75, no. 1, pp. 252-256.
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Buxton, LJ, Badger, M & Ralph, PJ 2009, 'Effects Of Moderate Heat Stress And Dissolved Inorganic Carbon Concentration On Photosynthesis And Respiration Of Symbiodinium Sp (Dinophyceae) In Culture And In Symbiosis', Journal of Phycology, vol. 45, no. 2, pp. 357-365.
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The influence of temperature and inorganic carbon (C-i) concentration on photosynthesis was examined in whole corals and samples of cultured symbiotic dinoflagellates (Symbiodinium sp.) using combined measurements from a membrane inlet mass spectrometer and chl a fluorometer. In whole corals, O-2 production at 26 degrees C was significantly limited at C-i concentrations below ambient seawater (similar to 2.2 mM). Further additions of C-i up to similar to 10 mM caused no further stimulation of oxygenic photosynthesis. Following exposure to 30 degrees C (2 d), net oxygen production decreased significantly in whole corals, as a result of reduced production of photosynthetically derived oxygen rather than increased host consumption. Whole corals maintained a rate of oxygen evolution around eight times lower than cultured Symbiodinium sp. at inorganic carbon concentrations < 2 mM, but cultures displayed greater levels of photoinhibition following heat treatment (30 degrees C, 2 d). Whole corals and cultured zooxanthellae differed considerably in their responses to C-i concentration and moderate heat stress, demonstrating that cultured Symbiodinium make an incongruous model for those in hospite. Reduced net oxygen evolution, in whole corals, under conditions of low C-i (< 2 mM) has been interpreted in terms of possible sink limitation leading to increased nonphotochemical energy dissipation. The advantages of combined measurement of net gas exchange and fluorometry offered by this method are discussed.

Cadotte, MW, Hamilton, MA & Murray, BR 2009, 'Phylogenetic relatedness and plant invader success across two spatial scales', Diversity And Distributions, vol. 15, no. 3, pp. 481-488.
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Successful invaders often possess similar ecological traits that contribute to success in new regions, and thus under niche conservatism, invader success should be phylogenetically clustered. We asked if the degree to which non-native plant species are phylogenetically related is a predictor of invasion success at two spatial scales. Australia - the whole continent and Royal National Park (south-eastern Australia). We used non-native plant species occupancy in Royal National Park, as well as estimated continental occupancy of these species from herbarium records. We then estimated phylogenetic relationships using molecular data from three gene sequences available on GenBank (matK, rbcL and ITS1). We tested for phylogenetic signals in occupancy using Blomberg's K. Whereas most non-native plants were relatively scarce, there was a strong phylogenetic signal for continental occupancy, driven by the clustering of successful species in Asteraceae, Caryophyllaceae, Poaceae and Solanaceae. However, we failed to detect a phylogenetic signal at the park scale. Our results reveal that at a large spatial scale, invader success is phylogenetically clustered where ecological traits promoting success appear to be shared among close relatives, indicating that phylogenetic relationships can be useful predictors of invasion success at large spatial scales. At a smaller, landscape scale, there was no evidence of phylogenetic clustering of invasion success, and thus, relatedness plays a much reduced role in determining the relative success of invaders.

Campbell, S, Botten, LC, McPhedran, RC & de Sterke, CM 2009, 'Modal method for conical diffraction by slanted lamellar gratings', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, vol. 26, no. 4, pp. 938-948.
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Caprarelli, G & Leitch, EC 2009, 'Volcanic and structural history of the rocks exposed at Pickering Crater (Daedalia Planum, Mars)', Icarus, vol. 202, no. 2, pp. 453-461.
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In the western hemisphere of Mars Amazonian volcanism from Arsia Mons produced the smooth surfaces of Daedalia Planum and masks older rocks. Close to the southern termination of Daedalia Planum basement rocks are exposed in which are preserved craters that escaped or were only partially filled by this most recent volcanism. Pickering Crater is an approximately 130 km diameter crater. The youngest lavas flowed into this crater from Daedalia Planum by way of a NW rim breach, covering its western part. East of a well-defined flow front an older lava sequence with a distinctive platy surface and derived from a more proximal unestablished source to the northeast is exposed. Several units are identified within this sequence on the basis of surface texture, which is more subdued in progressively older rocks. Only local mapping of the flow front boundaries of these units is possible because of incomplete coverage by high resolution imagery. During emplacement of the older lavas a NESW striking en echelon graben system and parallel smaller troughs and dikes formed under inferred regional NWSE extension. A much earlier strike-slip regime pre-dating the lavas exposed in the crater floor is postulated, based on the highly fretted nature of the rim of Pickering Crater and an elongated smaller crater to its northeast, approximately 40 km long in the NESW direction. The rims of these craters contrast with that of a smoother rimmed impact crater in the southeast that was excavated subsequent to strike-slip deformation but prior to the emplacement of platy surfaced lavas.

Carmona, R, Fehr, M & Hinz, J 2009, 'Optimal stochastic control and carbon price formation', SIAM Journal on Control and Optimization, vol. 48, no. 4, pp. 2168-2190.
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To meet the targets of the Kyoto Protocol, the European Union established the European Emission Trading Scheme, a mandatory market for carbon emission allowances. This regulatory framework has introduced a market for emission allowances and created a var

Carroll, R, Maity, A, Mammen, E & Yu, K 2009, 'Efficient Semiparametric Marginal Estimation for the Partially Linear Additive Model for Longitudinal/Clustered Data.', Statistics in biosciences, vol. 1, no. 1, pp. 10-31.
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We consider the efficient estimation of a regression parameter in a partially linear additive nonparametric regression model from repeated measures data when the covariates are multivariate. To date, while there is some literature in the scalar covariate case, the problem has not been addressed in the multivariate additive model case. Ours represents a first contribution in this direction. As part of this work, we first describe the behavior of nonparametric estimators for additive models with repeated measures when the underlying model is not additive. These results are critical when one considers variants of the basic additive model. We apply them to the partially linear additive repeated-measures model, deriving an explicit consistent estimator of the parametric component; if the errors are in addition Gaussian, the estimator is semiparametric efficient. We also apply our basic methods to a unique testing problem that arises in genetic epidemiology; in combination with a projection argument we develop an efficient and easily computed testing scheme. Simulations and an empirical example from nutritional epidemiology illustrate our methods.

Carroll, RJ, Delaigle, A & Hall, P 2009, 'Nonparametric Prediction in Measurement Error Models', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 104, no. 487, pp. 993-1003.
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Carroll, RJ, Delaigle, A & Hall, P 2009, 'Nonparametric Prediction in Measurement Error Models Comment - Rejoinder', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 104, no. 487, pp. 1013-1014.
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Carroll, RJ, Maity, A, Mammen, E & Yu, K 2009, 'Nonparametric additive regression for repeatedly measured data', BIOMETRIKA, vol. 96, no. 2, pp. 383-398.
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Cavanagh, KL, Glover, SA, Price, HL & Schumacher, RR 2009, 'SN2 Substitution Reactions at the Amide Nitrogen in the Anomeric Mutagens, N-Acyloxy-N-alkoxyamides', Australian Journal of Chemistry, vol. 62, no. 7, pp. 700-700.
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N-Acyloxy-N-alkoxyamides 1a are unusual anomeric amides that are pyramidal at the nitrogen because of bis oxyl substitution. Through this configuration, they lose most of their amide character and resemble α-haloketones in reactivity. They are susceptible to SN2 reactions at nitrogen, a process that is responsible for their mutagenic behaviour. Kinetic studies have been carried out with the nucleophile N-methylaniline that show that, like SN2 reactions at carbon centres, the rate constant for SN2 displacement of carboxylate is lowered by branching β to the nitrogen centre, or bulky groups on the alkoxyl side chain. Branching or bulky groups on the carboxylate leaving group, however, do not impact on the rate of substitution, which is mostly controlled by the pKA of the departing carboxylate group. These results are in line with computed properties for the model reaction of ammonia with N-acetoxy-N-methoxyacetamide but are in contrast to the role of steric effects on their mutagenicity.

Chan, C, Beiko, R, Darling, AE & Ragan, M 2009, 'Lateral Transfer Of Genes And Gene Fragments In Prokaryotes', Genome Biology and Evolution, vol. 1, no. NA, pp. 429-438.
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Lateral genetic transfer (LGT) involves the movement of genetic material from one lineage into another and its subsequent incorporation into the new host genome via genetic recombination. Studies in individual taxa have indicated lateral origins for stre

Chan, C, Darling, AE, Beiko, R & Ragan, M 2009, 'Are Protein Domains Modules Of Lateral Genetic Transfer?', PLoS ONE, vol. 4, no. 2, pp. 1-8.
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Background: In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of

Chan, CX, Beiko, RG, Darling, AE & Ragan, MA 2009, 'Lateral Transfer of Genes and Gene Fragments in Prokaryotes', GENOME BIOLOGY AND EVOLUTION, vol. 1, pp. 429-438.
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Chan, CX, Darling, AE, Beiko, RG & Ragan, MA 2009, 'Are protein domains modules of lateral genetic transfer?', PloS one, vol. 4, no. 2, p. e4524.
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BACKGROUND: In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of gene sharing (e.g. lateral gene transfer, LGT), there is little reason to imagine that the units of transfer and recombination correspond to entire, intact genes. Proteins often consist of one or more spatially compact structural regions (domains) which may fold autonomously and which, singly or in combination, confer the protein's specific functions. As LGT is frequent in strongly selective environments and natural selection is based on function, we hypothesized that domains might also serve as modules of genetic transfer, i.e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins. METHODOLOGY/PRINCIPAL FINDINGS: We selected 1,462 orthologous gene sets representing 144 prokaryotic genomes, and applied a rigorous two-stage approach to identify recombination breakpoints within these sequences. Recombination breakpoints are very significantly over-represented in gene sets within which protein domain-encoding regions have been annotated. Within these gene sets, breakpoints significantly avoid the domain-encoding regions (domons), except where these regions constitute most of the sequence length. Recombination breakpoints that fall within longer domons are distributed uniformly at random, but those that fall within shorter domons may show a slight tendency to avoid the domon midpoint. As we find no evidence for differential selection against nucleotide substitutions following the recombination event, any bias against disruption of domains must be a consequence of the recombination event per se. CONCLUSIONS/SIGNIFICANCE: This is the first systematic study relating the units of LGT to structural features at the protein level. Many genes have been int...

Chatterjee, N, Chen, Y-H, Luo, S & Carroll, RJ 2009, 'Analysis of Case-Control Association Studies: SNPs, Imputation and Haplotypes', STATISTICAL SCIENCE, vol. 24, no. 4, pp. 489-502.
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Chaumet, PC & Rahmani, A 2009, 'Coupled-dipole method for magnetic and negative refraction materials', Journal of Quantitative Spectroscopy and Radiative Transfer, vol. 110, no. 1-2, pp. 22-29.
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We present a derivation of the coupled-dipole method, also called discrete dipole approximation, for scatterers with arbitrary dielectric permittivity and magnetic permeability. We discuss the numerical implementation of the method and illustrate its application to magnetic and negative-refraction materials.

Chaumet, PC & Rahmani, A 2009, 'Efficient iterative solution of the discrete dipole approximation for magneto-dielectric scatterers', Optics Letters, vol. 34, no. 7, pp. 917-919.
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The discrete dipole approximation (DDA) has been widely used to study light scattering by nonmagnetic objects. The electric field inside an arbitrary scatterer is found by solving a dense, symmetric, linear system using, in general, an iterative approach. However, when the scatterer has a nonzero magnetic susceptibility, the linear system becomes nonsymmetric, and some of the most commonly used iterative methods fail to work. We study the scattering of light by objects with both electric and magnetic linear responses and discuss the efficiency of several iterative solvers for the nonsymmetric DDA.

Chaumet, PC & Rahmani, A 2009, 'Electromagnetic Force And Torque On Magnetic And Negative-Index Scatterers', Optics Express, vol. 17, no. 4, pp. 2224-2234.
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We derive the analytic expressions of the electromagnetic force and torque on a dipolar particle, with arbitrary dielectric permittivity and magnetic permeability.We then develop a general framework, based on the coupled dipole method, for computing the electromagnetic force and torque experienced by an object with arbitrary shape, dielectric permittivity and magnetic permeability.

Chen, H & Morris, M 2009, 'Differential responses of orexigenic neuropeptides to fasting in offspring of obese mothers', Obesity, vol. 17, no. 7, pp. 1356-1362.
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Maternal obesity due to long-term high-fat diet (HFD) consumption leads to faster growth in offspring during suckling, and increased adiposity at 20 days of age. Decreased expression of the orexigenic neuropeptide Y (NPY) and increased anorexigenic proopiomelanocortin (POMC) mRNA expression were observed in the fed state. However, hunger is the major drive to eat and hypothalamic appetite regulators change in response to meals. Therefore it is important to compare both satiated and fasting states. Female Sprague Dawley rats (8 weeks old) were fed a cafeteria-style HFD (15.33kJ/g) or chow for 5 weeks before mating, with the same diet continuing throughout gestation and lactation. At postnatal day 20, male pups were killed either after overnight fasting or in the fed state. Pups from obese dams were hyperphagic during both pre- and post-weaning periods. Pups from obese dams had higher hypothalamic mRNA expression of POMC and NPY Y1 receptor, but lower hypothalamic melanocortin-4 receptor (MC4R) and its downstream target single-minded gene 1 (Sim1), in the fed state. Overnight fasting reduced circulating glucose, insulin, and leptin and increased hypothalamic NPY Y1 receptor mRNA in pups from both lean and obese dams. Hypothalamic NPY and agouti-related protein were only increased by fasting in pups from obese dams; reductions in MC4R and Sim1 were only seen in pups from lean dams. At weaning, the suppressed orexigenic signals in offspring from obese dams were normalized after overnight fasting, while anorexigenic signaling appeared impaired in these animals. This may contribute to their hyperphagia and faster growth.

Chen, H, Simar, D & Margaret, JM 2009, 'Hypothalamic neuroendocrine circuitry is programmed by maternal obesity: interaction with postnatal nutritional environment', PLoS ONE, vol. 4, no. 7, pp. 1-10.
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Early life nutrition is critical for the development of hypothalamic neurons involved in energy homeostasis. We previously showed that intrauterine and early postnatal overnutrition programmed hypothalamic neurons expressing the appetite stimulator neuropeptide Y (NPY) and suppressor proopiomelanocortin (POMC) in offspring at weaning. However, the long-term effects of such programming and its interactions with post-weaning high-fat-diet (HFD) consumption are unclear.

Chen, Y-H, Chatterjee, N & Carroll, RJ 2009, 'Shrinkage Estimators for Robust and Efficient Inference in Haplotype-Based Case-Control Studies', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 104, no. 485, pp. 220-233.
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Chessman, B, Westhorpe, DP, Mitrovic, S & Hardwick, L 2009, 'Trophic linkages between periphyton and grazing macroinvertebrates in rivers with different levels of catchment development', Hydrobiologia, vol. 625, pp. 135-151.
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In December 1999, domoic acid (DA) a potent neurotoxin, responsible for the syndrome Amnesic Shellfish Poisoning (ASP) was detected for the first time in shellfish harvested in Ireland. Two liquid chromatography (LC) methods were applied to quantify DA in shellfish after sample clean-up using solid-phase extraction (SPE) with strong anion exchange (SAX) cartridges. Toxin detection was achieved using photodiode array ultraviolet (LC-UV) and multiple tandem mass spectrometry (LC-MSn). DA was identified in four species of bivalve shellfish collected along the west and south coastal regions of the Republic of Ireland. The amount of DA that was present in three species was within EU guideline limits for sale of shellfish (20 µg DA/g); mussels (Mytilus edulis), <1.0 µg DA/g; oysters (Crassostrea edulis), <5.0 µg DA/g and razor clams (Ensis siliqua), <0.3 µg DA/g. However, king scallops (Pecten maximus) posed a significant human health hazard with levels up to 240 µg DA/g total tissues. Most scallop samples (55%) contained DA at levels greater than the regulatory limit. The DA levels in the digestive glands of some samples of scallops were among the highest that have ever been recorded (2820 µg DA/g).

Chou, J, Shimmon, R & Ben-Nissan, B 2009, 'Bisphosphonate determination using H-1-NMR spectroscopy for biomedical applications', Journal Of Tissue Engineering And Regenerative Medicine, vol. 3, no. 2, pp. 92-96.
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Bisphosphonate is known to be a very active drug in the treatment of osteoporosis and bone regeneration. A new method has been developed, utilizing nuclear magnetic resonance spectroscopy to identify and measure the amount of bisphosphonate in solution. A standard reference with similar functional group to that of the bisphosphonate was chosen and applied in the experimentation. The results showed that the use of nuclear magnetic resonance spectroscopy (H-1-NMR) in determining the solvent residues of various pharmaceutical drugs has proved to be effective. Unlike chromatography, it is possible to use a universal reference standard as an internal standard assayed by quantitative NMR. Using the same theory, this method is capable of both identifying and quantifying the bisphosphonate in various solutions. This paper is the first publication showing this unique measurement method, which can be used in a range of pharmaceutical and biomedical applications.

Christianson, J, Wilson, I, Llewellyn, D & Dennis, ES 2009, 'The Low-Oxygen-Induced NAC Domain Transcription Factor ANAC102 Affects Viability of Arabidopsis Seeds following Low-Oxygen Treatment', PLANT PHYSIOLOGY, vol. 149, no. 4, pp. 1724-1738.
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Low-oxygen stress imposed by field waterlogging is a serious impediment to plant germination and growth. Plants respond to waterlogging with a complex set of physiological responses regulated at the transcriptional, cellular, and tissue levels. The Arabidopsis (Arabidopsis thaliana) NAC domain-containing gene ANAC102 was shown to be induced under 0.1% oxygen within 30 min in both roots and shoots as well as in 0.1% oxygen-treated germinating seeds. Overexpression of ANAC102 altered the expression of a number of genes, including many previously identified as being low-oxygen responsive. Decreasing ANAC102 expression had no effect on global gene transcription in plants but did alter expression patterns in low-oxygen-stressed seeds. Increasing or decreasing the expression of ANAC102 did not affect adult plant survival of low-oxygen stress. Decreased ANAC102 expression significantly decreased germination efficiency following a 0.1% oxygen treatment, but increased expression had no effect on germination. This protective role during germination appeared to be specific to low-oxygen stress, implicating ANAC102 as an important regulator of seed germination under flooding.

Cinner, JE, McClanahan, TR, Graham, NAJ, Pratchett, MS, Wilson, SK & Raina, J 2009, 'Gear-based fisheries management as a potential adaptive response to climate change and coral mortality', Journal of Applied Ecology, vol. 46, pp. 724-732.
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Clark, C, Kawachi, I, Ryan, LM, Ertel, K, Fay, M & Berkman, L 2009, 'Perceived Neighborhood Safety And Incident Mobility Disability Among Elders: The Hazards Of Poverty', BMC Public Health, vol. 9, no. 162, pp. 0-0.
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Colella, M, Parkinson, A, Evans, T, Lennard, CJ & Roux, CP 2009, 'The recovery of latent fingermarks from evidence exposed to ionizing radiation', Journal of Forensic Sciences, vol. 54, no. 3, pp. 1-8.
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Continual reports of illicit trafficking incidents involving radioactive materials have prompted authorities to consider the likelihood of forensic evidence being exposed to radiation. In this study, we investigated the ability to recover latent fingermark evidence from a variety of substrates that were exposed to ionizing radiation. Fingermarks deposited on common surfaces, including aluminum, glass, office paper, and plastic, were exposed to doses ranging from 1 to 1000 kGy, in an effort to simulate realistic situations where evidence is exposed to significant doses of radiation from sources used in a criminal act. The fingermarks were processed using routine fingermark detection techniques. With the exception of glass and aluminum substrates, radiolysis had a considerable effect on the quality of the developed fingermarks. The damage to ridge characteristics can, in part, be attributed to chemical interactions between the substrate and the components of the fingermark secretions that react with the detection reagents.

Collier, C, Lavery, P, Ralph, PJ & Masini, R 2009, 'Shade-induced response and recovery of the seagrass Posidonia sinuosa', Journal Of Experimental Marine Biology And Ecology, vol. 370, no. 1-2, pp. 89-103.
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The effect of shading on the seagrass Posidonia sinuosa Cambridge et Kuo was investigated to identify mechanisms that prolong its survival during periods of low light and permit its subsequent recovery. We also tested whether the responses were consistent in plants growing at different depths. Shade treatments were low (LS; 70 - 100% of ambient Photosynthetic Photon Flux Density), medium (MS; 12 - 39%) and heavy (HS; 5 - 4%) at the shallow (3 - 4 m) site, whilst the deep (7 - 8 m) site had no HS treatment. HS at the shallow and MS at the deep site were below minimum light requirements (MLR) for the long-term survival of P. sinuoso.

Connan, H, Ray, AS & Thomas, P 2009, 'Comparative Study of Finely Ground Fired Clay Brick and Kaolin Based Fillers in Autoclaved Calcium Silicate Based Building Products', Concrete Forum, vol. 2, no. 1, pp. 25-28.
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The process of hydrothermal curing or autoclaving is particularly well suited to the utilisation of industrial by-products in the production of construction materials as it renders some of these waste materials highly reactive. Research fi ndings have demonstrated that when used in combination with Portland cement (OPC) in the industrially important CaO-Al2O3-SiO2-H2O system, fi nely ground fi red clay brick masonry, an aluminosilica rich waste, is suitable for the production of autoclaved construction materials. Th e use of kaolin clay as a fi ller in the production of these autoclaved calcium silicate based building products is well established. Th is paper presents a comparative study of fi nely ground clay brick industrial waste and kaolin clay used in combination with OPC under autoclaved conditions. Th e observed variations in compressive strength are discussed in the context of the presence of critical phases, which were characterised by microstructural and thermal analytical methods.

Cooper, WA, Kohonen-Corish, MRJ, McCaughan, B, Kennedy, C, Sutherland, RL & Lee, CS 2009, 'Expression and prognostic significance of cyclin B1 and cyclin A in non-small cell lung cancer', HISTOPATHOLOGY, vol. 55, no. 1, pp. 28-36.
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Cortie, M & Rahmani, A 2009, 'Plasmonics' demystified', Australian Physics, vol. 46, no. 2, pp. 42-45.

Cortie, MB, Stokes, NL & McDonagh, AM 2009, 'Plasmon resonance and electric field amplification of crossed gold nanorods', Photonics and Nanostructures: Fundamentals and Applications, vol. 7, no. 3, pp. 143-152.
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Here we explore the unusual plasmon resonances of crossed gold nanorod structures of varying geometries. Using numerical simulations, we show that the resonances of simple rods are hybridized and blue-shifted in the composite structures and that these structures are surrounded by spatially extended and high intensity electric fields. This attribute suggests several potential uses for these shapes, for example as a nano-antenna for the generation of two-photon fluorescence.

Coutts, MJ, Cortie, MB, Ford, M & McDonagh, AM 2009, 'Rapid and Controllable Sintering of Gold Nanoparticle Inks at Room Temperature Using a Chemical Agent', Journal of Physical Chemistry C, vol. 113, no. 4, pp. 1325-1328.
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We show that oxidation of protective thiol ligands and the exothermic reduction of surface area are important factors in the sintering of thiol-stabilized gold nanoparticle films. We also present a chemical treatment to achieve sintering of gold nanoparticles at room temperature. The process is facilitated by the remarkable enthalpy of reaction arising from the reduction of the surface area of the nanoparticles.

Craddock, MJ 2009, 'Fundamental solutions, transition densities and the integration of Lie symmetries', Journal Of Differential Equations, vol. 246, no. 6, pp. 2538-2560.
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In this paper we present some new applications of Lie symmetry analysis to problems in stochastic calculus. The major focus is on using Lie symmetries of parabolic PDEs to obtain fundamental solutions and transition densities. The method we use relies upon the fact that Lie symmetries can be integrated with respect to the group parameter. We obtain new results which show that for PDEs with nontrivial Lie symmetry algebras, the Lie symmetries naturally yield Fourier and Laplace transforms of fundamental solutions, and we derive explicit formulas for such transforms in terms of the coefficients of the PDE.

Craddock, MJ & Lennox, KA 2009, 'The Calculation Of Expectations For Classes Of Diffusion Processes By Lie Symmetry Methods', Annals Of Applied Probability, vol. 19, no. 1, pp. 127-157.
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This paper uses Lie symmetry methods to calculate certain expectations for a large class of Ito diffusions. We show that if the problem has sufficient symmetry, then the problem of computing functionals of the form E-x(e(-lambda Xt-f0tg(Xs)ds)) can be reduced to evaluating a single integral of known functions. Given a drift f we determine the functions g for which the corresponding functional can be calculated by symmetry. Conversely, given g, we can determine precisely those drifts f for which the transition density and the functional may be computed by symmetry. Many examples are presented to illustrate the method.

D'Agata, V, Tiralongo, A, Castorina, A, Leggio, GM, Micale, V, Carnazza, ML & Drago, F 2009, 'Parkin Expression Profile in Dopamine D3 Receptor Knock-Out Mice Brains', NEUROCHEMICAL RESEARCH, vol. 34, no. 2, pp. 327-332.
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Dalton, JP, Brindley, PJ, Donnelly, SM & Robinson, MW 2009, 'The enigmatic asparaginyl endopeptidase of helminth parasites', Trends In Parasitology, vol. 25, no. 2, pp. 59-61.
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The clan CD cysteine protease of Schistosoma mansoni (SmAE, also known as Sm32 or schistosome legumain) is an asparaginyl endopeptidase that cleaves C-terminal to asparaginyl (Asn) residues. The enzyme was considered to function in the hydrolytic degradation of host haemoglobin within the parasite gut 1 B. Götz and M.Q. Klinkert, Expression and partial characterization of a cathepsin B-like enzyme (Sm31) and a proposed `haemoglobinase (Sm32) from Schistosoma mansoni, Biochem. J. 290 (1993), pp. 801806. View Record in Scopus | Cited By in Scopus (26)[1]. However, Dalton and Brindley [2] proposed that the primary role of the enzyme was the trans-processing and activation of other schistosome proteases after noting that zymogens of clan AA aspartic proteases (cathepsin D) and clan CA cysteine proteases (cathepsins L, F, B1 and C) each possessed an asparaginyl-endopeptidase-cleavage site at the juncture between the prosegment and mature enzyme domain. Prosegment removal by trans-processing exposes the active site of the mature enzyme to enable entry of haemoglobin substrate. Cytochemistry revealed that schistosome asparaginyl endopeptidase is expressed in the gastrodermis surrounding the gut lumen, the same locality as the haemoglobin-degrading enzymes. Sajid et al. [3] provided support for this trans-processing hypothesis by showing that a recombinant S. mansoni asparaginyl endopeptidase could convert the zymogen of schistosome cathepsin B1 to a mature enzyme in vitro. Delcroix et al. [4] also showed that 20% of cathepsin B activity was lost when the expression of asparaginyl endopeptidase of three-week-old male and female schistosomes was knocked down using RNA interference (RNAi).

Daniel, R, Sanchez, JJ, Nassif, N, Hernandez, A & Walsh, SJ 2009, 'Partial forensic validation of a 16plex SNP assay for the inference of biogeographical ancestry', Forensic Science International: Genetics Supplement Series, vol. 2, pp. 477-478.
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A partial forensic validation study demonstrated the suitability of an ancestry informative 16 locus SNP assay to forensic casework.

Davis, TE, Ollendick, TH & Öst, LG 2009, 'Intensive Treatment of Specific Phobias in Children and Adolescents', Cognitive and Behavioral Practice, vol. 16, no. 3, pp. 294-303.
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One-session treatment (OST), a variant of cognitive-behavioral therapy, combines graduated in vivo exposure, participant modeling, reinforcement, psychoeducation, cognitive challenges, and skills training in an intensive treatment model. Treatment is maximized to one 3-hour session. In this paper, we review the application of OST for specific phobia in youth and highlight practical matters related to OST and its use in a clinical setting. We also briefly review results of treatment outcome studies and suggest future directions for clinical research and practice. We conclude that OST is an efficient and efficacious treatment. © 2009.

de Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 2009, 'Efficient coupling into slow light photonic crystal waveguide without transition region: role of evanescent modes', Optics Express, vol. 17, no. 20, pp. 17338-17343.
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We show that efficient coupling between fast and slow photonic crystal waveguide modes is possible, provided that there exist strong evanescent modes to match the waveguide fields across the interface. Evanescent modes are required when the propagating modes have substantially different modal fields, which occurs, for example, when coupling an index-guided mode and a gap-guided mode.

Dean, D, Bruno, WJ, Wan, R, Gomes, JP, Devignot, S, Mehari, T, de Vries, HJC, Morre, SA, Myers, G, Read, TD & Spratt, BG 2009, 'Predicting Phenotype and Emerging Strains among Chlamydia trachomatis Infections', EMERGING INFECTIOUS DISEASES, vol. 15, no. 9, pp. 1385-1394.
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Delaigle, A, Fan, J & Carroll, RJ 2009, 'A Design-Adaptive Local Polynomial Estimator for the Errors-in-Variables Problem', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 104, no. 485, pp. 348-359.
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Dematte, JA, Huete, A, Ferreira, LG, Nanni, MR & Fiorio, PR 2009, 'Methodology for bare soil detection and discrimination by Landsat TM image', The Open Remote Sensing Journal, vol. 2, no. 1, pp. 24-35.
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The objective of this work was to develop and test a remote sensing technique to determine bare soils with pixel information from satellite images. The methodology was tested and improved on a 2,805 km2 area located in the state of São Paulo, Brazil. The pixel data from a Landsat-5/TM image was transformed into reflectances. 294 pixels were evaluated by five factors simultaneously and included the following: color composition image; vegetation index; soil brightness information (soil line concept), and a comparison between spectral curve of the pixel with spectral patterns of soils. A validation procedure was based on the discriminate analysis for the real soil related with each pixel. For this, a soil map was overlaid onto the image, and the pixels were related to its respective soil class. Soil brightness variations were readily observed in the spectral curves and in red-NIR features and corresponded to differences in texture and particle size as well in iron and organic matter content. Although qualitative, the observation of color composition was useful for pixel identification. The soil line concept was very useful as it presented a high R2 coefficient (0.90). Comparison between ground level soil spectral curves with satellite information could assist on the evaluation of the real format of the curves. Discriminate analysis indicated a 99.3% correct classification of the soils. Field work validation indicated 90% significance. The present method could help researchers acquire valuable information (i.e., soil attributes quantification), when soil data must be acquired from satellite images.

Deng, W, Drozdowicz-Tomsia, K, Jin, D & Goldys, EM 2009, 'Enhanced Flow Cytometry-Based Bead Immunoassays Using Metal Nanostructures', ANALYTICAL CHEMISTRY, vol. 81, no. 17, pp. 7248-7255.
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Dennis, ES & Peacock, WJ 2009, 'Vernalization in cereals', Journal of Biology, vol. 8, no. 6.
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How vernalization - exposure to a period of cold - induces flowering in Arabidopsis has been intensively investigated at the genetic and moleular levels. Recent papers, including one in BMC Plant Biology, shed light on changes in gene regulation that occur on vernalization in cereals. © 2009 BioMed Central Ltd.

Didelot, X, Darling, AE & Falush, D 2009, 'Inferring Genomic Flux In Bacteria', Genome Research, vol. 19, no. 2, pp. 306-317.
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Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular, pathogenicity. Comparative genomics has the potential to elucida

Dison, W, Elder, M, Riley, TR & Young, R 2009, 'The Dehn function of Stallings’ group', Geometric and Functional Analysis, vol. 19, pp. 406-422.
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Djordjevic, SP, Cain, A, Evershed, NJ, Falconer, L, Levings, RS, Lightfoot, D & Hall, RM 2009, 'Emergence and evolution of multiply antibiotic-resistant Salmonella enterica Serovar paratyphi B D-Tartrate-Utilizing strains containing SG11', Antimicrobial agents and chemotherapy, vol. 53, no. 6, pp. 2319-2326.
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The first Australian isolate of Salmonella enterica serovar Paratyphi B D-tartrate-utilizing (dT+) that is resistant to ampicillin, chloramphenicol, florfenicol, streptomycin, spectinomycin, sulfonamides, and tetracycline (ApCmFlSmSpSuTc) and contains SGI1 was isolated from a patient with gastroenteritis in early 1995. This is the earliest reported isolation globally. The incidence of infections caused by these SGI1-containing multiply antibiotic-resistant S. enterica serovar Paratyphi B dT+ strains increased during the next few years and occurred sporadically in all states of Australia. Several molecular criteria were used to show that the early isolates are very closely related to one another and to strains isolated during the following few years and in 2000 and 2003 from home aquariums and their owners. Early isolates from travelers returning from Indonesia shared the same features. Thus, they appear to represent a true clone arising from a single cell that acquired SGI1. Some minor differences in the resistance profiles and molecular profiles also were observed, indicating the ongoing evolution of the clone, and phage type differences were common, indicating that this is not a useful epidemiological marker over time. Three isolates from 1995, 1998, and 1999 contained a complete sul1 gene but were susceptible to sulfamethoxazole due to a point mutation that creates a premature termination codon.

Doege, J, Fehr, M, Hinz, J, Luthi, H & Wilhelm, M 2009, 'Risk management in power markets: The Hedging value of production flexibility', European Journal Of Operational Research, vol. 199, no. 3, pp. 936-943.
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Since the 1990s power markets are being restructured worldwide and nowadays electrical power is traded as a commodity. The liberalization and with it the uncertainty in gas, fuel and electrical power prices requires an effective management of production

Dondrup, M, Albaum, SP, Griebel, T, Henckel, K, Juenemann, S, Kahlke, T, Kleindt, CK, Kuester, H, Linke, B, Mertens, D, Mittard-Runte, V, Neuweger, H, Runte, KJ, Tauch, A, Tille, F, Puehler, A & Goesmann, A 2009, 'EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data', BMC BIOINFORMATICS, vol. 10.
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Dooley, AH & Golodets, VY 2009, 'The geometric dimension of an equivalence relation and finite extensions of countable groups', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 29, pp. 1789-1814.
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Dooley, AH & Mortiss, G 2009, 'On the critical dimensions of product odometers', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 29, pp. 475-485.
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Dossou, KB, Poulton, CG, Botten, LC, Mahmoodian, S, McPhedran, RC & de Sterke, CM 2009, 'Modes of symmetric composite defects in two-dimensional photonic crystals', PHYSICAL REVIEW A, vol. 80, no. 1.
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Duggin, IG & Bell, SD 2009, 'Termination structures in the Escherichia coli chromosome replication fork trap', Journal of Molecular Biology, vol. 387, no. 3, pp. 532-539.
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The Escherichia coli chromosome contains two opposed sets of unidirectional DNA replication pause (Ter) sites that, according to the replication fork trap theory, control the termination of chromosome replication by restricting replication fork fusion to the terminus region. In contrast, a recent hypothesis suggested that termination occurs at the dif locus instead. Using twodimensional agarose gel electrophoresis, we examined DNA replication intermediates at the Ter sites and at dif in wild-type cells. Two definitive signatures of site-specific terminationspecific replication fork arrest and converging replication forkswere clearly detected at Ter sites, but not at dif. We also detected a significant pause during the latter stages of replication fork convergence at Ter sites. Quantification of fork pausing at the Ter sites in both their native chromosomal context and the plasmid context further supported the fork trap model.

Dunlop, RA, Brunk, U & Rodgers, K 2009, 'Oxidized proteins: Mechanisms of removal and consequences of accumulation', IUBMB Life, vol. 61, no. 5, pp. 522-527.
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Elevated levels of oxidized proteins are reported in diseased tissue from age-related pathologies such as atherosclerosis, neurodegenerative disorders, and cataract. Unlike the precise mechanisms that exist For the repair of nucleic acids, lipids, and ca

Duong, T, Koch, I & Wand, M 2009, 'Highest density difference region estimation with application to flow cytometric data', Biometrical Journal, vol. 51, no. 3, pp. 504-521.
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Motivated by the needs of scientists using flow cytometry, we study the problem of estimating the region where two multivariate samples differ in density. We call this problem highest density difference region estimation and recognise it as a two-sample analogue of highest density region or excess set estimation. Flow cytometry samples are typically in the order of 10 000 and 100 000 and with dimension ranging from about 3 to 20. The industry standard for the problem being studied is called Frequency Difference Gating, due to Roederer and Hardy (2001). After couching the problem in a formal statistical framework we devise an alternative estimator that draws upon recent statistical developments such as patient rule induction methods. Improved performance is illustrated in simulations. While motivated by flow cytometry, the methodology is suitable for general multivariate random samples where density difference regions are of interest

Duval, L, Nerrienet, E, Rousset, D, Mba, SAS, Houze, S, Fourment, M, Le Bras, J, Robert, V & Ariey, F 2009, 'Chimpanzee Malaria Parasites Related to Plasmodium ovale in Africa', PLOS ONE, vol. 4, no. 5.
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Duxbury, Z, Schliep, MT, Ritchie, RJ, Larkum, A & Chen, M 2009, 'Chromatic photoacclimation extends utilisable photosynthetically active radiation in the chlorophyll d-containing cyanobacterium, Acaryochloris marina', Photosynthesis Research, vol. 101, no. 1, pp. 69-75.
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Chromatic photoacclimation and photosynthesis were examined in two strains of Acaryochloris marina (MBIC11017 and CCMEE5410) and in Synechococcus PCC7942. Acaryochloris contains Chl d, which has an absorption peak at ca 710 nm in vivo. Cultures were grown in one of the three wavelengths (525 nm, 625 nm and 720 nm) of light from narrow-band photodiodes to determine the effects on pigment composition, growth rate and photosynthesis: no growth occurred in 525 nm light. Synechococcus did not grow in 720 nm light because Chl a does not absorb effectively at this long wavelength. Acaryochloris did grow in 720 nm light, although strain MBIC11017 showed a decrease in phycobilins over time. Both Synechococcus and Acaryochloris MBIC11017 showed a dramatic increase in phycobilin content when grown in 625 nm light. Acaryochloris CCMEE5410, which lacks phycobilins, would not grow satisfactorily under 625 nm light. The cells adjusted their pigment composition in response to the light spectral conditions under which they were grown. Photoacclimation and the Q (y) peak of Chl d could be understood in terms of the ecological niche of Acaryochloris, i.e. habitats enriched in near infrared radiation.

Esteban-marcos, A, Darling, AE & Ragan, M 2009, 'Seevolution: Visualizing Chromosome Evolution', Bioinformatics, vol. 25, no. 7, pp. 960-961.
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Genome evolution underpins all of biology, yet its principles can be difficult to communicate to the non-specialist. To facilitate broader understanding of genome evolution, we have designed an interactive 3D environment that enables visualization of div

Evershed, NJ, Levings, RS, Wilson, NL, Djordjevic, SP & Hall, RM 2009, 'Unusual class 1 integron-associated gene cassette configuration found in IncA/C plasmids from Salmonella enterica', Antimicrobial agents and chemotherapy, vol. 53, no. 6, pp. 2640-2642.
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IncA/C plasmids carrying an unusual cassette configuration in a class 1 integron and five further shared resistance genes, aacC4, aphA1, hph, sul2, and tetA(D) were found in Salmonella enterica serovars Senftenberg and Ohio. A deletion formed using a short region of homology in the 5' conserved segment and the orfF cassette created an array with only part of orfF followed by the aadA2 cassette. The IncA/C plasmids were not recoverable by conjugation, but additional conjugative resistance plasmids were present in some strains.

Fahnenstiel, G, Hong, Y, Millie, D, Doblin, MA, Johengen, T & Reid, D 2009, 'Marine dinoflagellate cysts in the ballast tank sediments of ships entering the Laurentian Great Lakes', Verhandlungen Internationale Verein Limnology, vol. 30, no. 7, pp. 1035-1038.

Faille, D, Combes, V, Mitchell, AJ, Fontaine, A, Juhan-Vague, I, Alessi, M-C, Chimini, G, Fusai, T & Grau, GE 2009, 'Platelet microparticles: a new player in malaria parasite cytoadherence to human brain endothelium', FASEB JOURNAL, vol. 23, no. 10, pp. 3449-3458.
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Faille, D, El-Assaad, F, Alessi, M-C, Fusai, T, Combes, V & Grau, GE 2009, 'Platelet-endothelial cell interactions in cerebral malaria: The end of a cordial understanding', THROMBOSIS AND HAEMOSTASIS, vol. 102, no. 6, pp. 1093-1102.
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Farrell, G, Larter, C, Hou, JY, Zhang, RH, Yeh, MM, Williams, J, Pena, A, Francisco, R, Osvath, SR, Brooling, J, Teoh, N & Sedger, LM 2009, 'Apoptosis in experimental NASH is associated with p53 activation and TRAIL receptor expression.', Journal of Gastroenterology and Hepatology, vol. 24, no. 3, pp. 443-452.
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Background and Aims: We examined extrinsic and intrinsic (endogenous) mitochondrial apoptosis pathways in experimental non-alcoholic steatohepatitis (NASH). Methods: To assess extrinsic pathways, we measured hepatic expression of death-inducing cytokine receptors (tumor necrosis factor-a-receptor (TNF-R)1, TNF-R2, Fas, and TNFa-related apoptosis-inducing ligand-receptor (TRAIL-R) mRNA, TUNEL, caspase 3 activation, liver injury and liver pathology in mice fed a methionine and choline deficient (MCD) diet. For endogenous stress pathways, we determined serum insulin-like growth factor-1 (IGF-1), hepatic p53, Bcl-XL, tBid and p21 expression. Results: Methionine and choline deficient feeding increased alanine aminotransferase (ALT) and apoptosis from day 10, without increases in TNF-R1, TNF-R2, and Fas. However, murine TRAIL receptors, particularly decoyTRAIL-R1/TNFRSFH23 and Killer/DR5 mRNA increased. MCD feeding enhanced hepatic p53 expression, corresponding to ~50% fall in serum IGF-1, decreased Bcl-XL, enhanced Bid cleavage to tBid, and up-regulation of p21. Nutritional restitution experiments showed that correcting either methionine or choline deficiency suppressed liver inflammation (extrinsic pathway), but failed to correct apoptosis, IGF-1 or p53. Conclusions: Methionine and choline deficiency lower IGF-1 to de-repress p53 during induction of steatohepatitis. The p53 induced by nutritional stress is biologically active in mediating mitochondrial cell death pathways, but may also be responsible for TRAIL receptor expression, thereby linking intrinsic and exogenous apoptosis pathways in NASH.

Figueira, WF, Biro, P, Booth, DJ & Valenzuela Davie, VC 2009, 'Performance of tropical fish recruiting to temperate habitats: role of ambient temperature and implications of climate change', Marine Ecology-Progress Series, vol. 384, no. 0, pp. 231-239.
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The warming of coastal oceans due to climate change is increasing the overwinter survival of tropical fishes transported to temperate latitudes by ocean currents. However, the processes governing early post-arrival mortality are complex and can result in minimum threshold temperatures for overwinter survival, which are greater than those predicted based upon physiological temperature tolerances alone. This 3.5 mo laboratory study monitored the early performance of a tropical damselfish Abudefduf vaigiensis that occurs commonly during austral summer along the SE Australian coast, under nominal summer and winter water temperatures, and compares results with a co-occurring year-round resident of the same family, Parma microlepis. Survivorship, feeding rate, growth and burst swimming ability (as a measure of predator escape ability) were all reduced for the tropical species at winter water temperatures compared to those in summer, whereas the temperate species experienced no mortality and only feeding rate was reduced at colder temperatures. These results suggest that observed minimum threshold survival temperatures may be greater than predicted by physiology alone, due to lowered food intake combined with increased predation risk (a longer time at vulnerable sizes and reduced escape ability). Overwinter survival is a significant hurdle in pole-ward range expansions of tropical fishes, and a better understanding of its complex processes will allow for more accurate predictions of changes in biodiversity as coastal ocean temperatures continue to increase due to climate change.

Filipovic, D & Platen, E 2009, 'Consistent Market Extensions Under the Benchmark Approach', Mathematical Finance, vol. 19, no. 1, pp. 41-52.
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The existence of the growth optimal portfolio (GOP), also known as the Kelly portfolio, is vital for a financial market to be meaningful. The GOP, if it exists, is uniquely determined by the market parameters of the primary security accounts. However, markets may develop and new security accounts become tradable. What happens to the GOP if the original market is extended? In this paper we provide a complete characterization of market extensions which are consistent with the existence of a GOP. We show that a three fund separation theorem applies for the extended GOP. This includes, in particular, the introduction of a locally risk free security, the savings account. We give necessary and sufficient conditions for a consistent exogenous specification of the prevailing short rates.

Fisher, JB, Mahli, Y, Bonal, D, da Rocha, HR, Araujo, AC, Gamo, M, Goulden, ML, Hirano, T, Huete, A, Kondo, H, Kumagai, T, Loescher, HW, Miller, SD, Nobre, AD, Nouvellon, Y, Oberbauer, SF, Panuthai, S, Roupsard, O, Saleska, SR, Tanaka, K, Tanaka, N, Tu, KP & von Randow, C 2009, 'The land-atmosphere water flux in the tropics', Global Change Biology, vol. 15, no. 11, pp. 2694-2714.
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Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from O decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370 mm yr-1, but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr-1) is considered in discussion on the use of flux data to validate and interpolate models.

Flerchinger, GN, Xaio, W, Marks, D, Sauer, TJ & Yu, Q 2009, 'Comparison of algorithms for incoming atmospheric long-wave radiation', Water resources research, vol. 45, pp. 1-13.
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While numerous algorithms exist for predicting incident atmospheric long-wave radiation under clear (L clr ) and cloudy skies, few comparisons have been published to assess the accuracy of the different algorithms. Virtually no comparisons have been made for both clear and cloudy skies across multiple sites. This study evaluates the accuracy of 13 algorithms for predicting incident long-wave radiation under clear skies, ten cloud correction algorithms, and four algorithms for all-sky conditions using data from 21 sites across North America and China.

Flerchinger, GN, Xiao, W, Sauer, TJ & Yu, Q 2009, 'Simulation of within-canopy radiation exchange', NJAS Wageningen Journal of Life Sciences, vol. 57, no. 1 Special Issue, pp. 5-15.
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Radiation exchange at the surface plays a critical role in the sui face energy balance, plant microclimate, and plant growth. The ability to simulate the surface energy balance and the microclimate within the plant canopy is contingent upon simulation of the surface radiation exchange. A validation and modification exercise of the Simultaneous Heat and Water (SHAW) model was conducted for simulating the sui face short-wave and long-wave radiation exchange over and within wheat, maize and soya bean plant canopies using data collected at Yucheng in the North China Plain and neat Ames. Iowa Whereas model testing was limited to monocultures and mixed canopies of green and senesced leaves, methodologies were developed for simulating short-wave and long-wave radiation fluxes applicable to a multi-species, multi-layer plant canopy Although the original SHAW model slightly under predicted reflected solar radiation with a mean bias en or (MBE) of -5 to -10 W m(-2), one would conclude that the simulations were quite reasonable if within-canopy measurements were not available However, within-canopy short-wave radiation was considerably under estimated (MBE of approximately -20 W m(-2)) by the original SHAW model Additionally, leaf temperatures tended to be overpredicted (MBE = +0 76 degrees C) near the top of the canopy and underpredicted near the bottom (MBE = -1 12 degrees C) Modification to the SHAW model reduced MBE of above canopy reflected radiation to -1 to -6 W m(-2) and within-canopy radiation simulations to approximately -6 W m(-2). bias in leaf temperature was reduced to less than 0 4 degrees C Model modifications resulted in essentially no change in simulated evapotranspiration lot wheat. 4.5% lower for maize and 1% higher for soya bean.

Ford, M, Russo, S & Gale, JD 2009, 'Proceedings of the International Conference on Nanoscience and Nanotechnology (Melbourne, 25-29 February 2008) PREFACE', Journal Of Physics: Condensed Matter, vol. 21, no. 14, p. 140301.
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The International Conference on Nanoscience and Nanotechnology is held bi-annually in Australia, supported by the Australian Research Council and Australian Nanotechnology Network. The purpose of the conference is to provide a forum for discussion about all aspects of nanoscience and nanotechnology, to enable young Australian researchers a chance to meet and engage with leading global scientists in the field, and to set up the exchange mechanisms and collaborations that will enable the field to continue to develop and flourish.

Forno, E, Onderdonk, AB, McCracken, J, Litonjua, AA, Laskey, D, Delaney, ML, DuBois, AM, Gold, DR, Ryan, LM, Weiss, ST & Celedon, JC 2009, 'Diversity of the Gut Microbiota and Eczema in Infants', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, vol. 179.

Fronzi, M, Piccinin, S, Delley, B, Traversa, E & Stampfl, C 2009, 'Water adsorption on the stoichiometric and reduced CeO2(111) surface: a first-principles investigation', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 11, no. 40, pp. 9188-9199.
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Fry, D, Mcsporran, K, Ellis, JT & Harvey, C 2009, 'Protozoal Hepatitis Associated With Immunosuppressive Therapy In A Dog', Journal Of Veterinary Internal Medicine, vol. 23, no. 2, pp. 366-368.
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Fu, WJ, Mallick, B & Carroll, RJ 2009, 'Why do we observe misclassification errors smaller than the Bayes error?', JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION, vol. 79, no. 5, pp. 717-722.
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Fukuyama, S, Nakano, T, Matsumoto, T, Oliver, BG, Burgess, J, Moriwaki, A, Tanaka, K, Kubo, M, Hoshino, T, Tanaka, H, Mckenzie, A, Matsumoto, K, Aizawa, H, Nakanishi, Y, Yoshimura, A, Black, J & Inoue, H 2009, 'Pulmonary Suppressor of Cytokine Signaling-1 Induced by IL-13 Regulates Allergic Asthma Phenotype', American Journal Of Respiratory And Critical Care Medicine, vol. 179, no. 11, pp. 992-998.
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Rationale: Th2 cytokines play an important role in allergic diseases. These cytokines activate signal transduction pathways, including Janus kinase/signal transducer and activator of transcription (STAT) signaling. Although the suppressor of cytokine sig

Gentle, AR, Smith, G & Maaroof, AI 2009, 'Frequency And Percolation Dependence Of The Observed Phase Transition In Nanostructured And Doped Vo2 Thin Films', Journal of Nanophotonics, vol. 3, no. 031505, pp. 1-15.
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The response to applied electric fields of vanadium dioxide thin films above and below the phase transition depends on the size of grains if below ~200nm across, and on aluminum doping above a critical concentration. Tc drops as doping level increases, but does not depend on grain size. The observed phase transition undergoes a remarkable qualitative shift as the applied field goes from optical to low frequencies. The expected insulator to metal transition is found at optical frequencies, but at low frequencies an insulator-to-insulator transition occurs. Optical switching at both T < Tc and T > Tc is nearly independent of doping level and grain size. In contrast dc properties in both phases are sensitive to both factors. The band gaps from optical and dc data differ, and densities of states change with doping level. Such behaviour can arise if there is a transient phase change. The way doping and grain size can support such a phase is discussed. Only individual nanograins need to switch phases coherently to explain data, not the whole sample. Resistance as a function of composition across the transition was derived using effective medium compositional analysis of optical data in the hysteresis zone. The percolation thresholds are not at the usual Tc values.

George, AM, Jones, PM & Middleton, P 2009, 'Cystic fibrosis infections: treatment strategies and prospects', FEMS Microbiology Letters, vol. 300, no. 2, pp. 153-164.
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Pseudomonas aeruginosa and Burkholderia cepacia are the two major Gram-negative rods that colonize/infect the lungs of patients with cystic fibrosis (CF). These organisms may cause progressive respiratory failure, although occasionally more rapid infections result in the 'Cepacia' syndrome. Many antibiotics have been used against Pseudomonas and Burkholderia, but once chronic colonization has been established, eradication of these organisms is rare. Drug therapy for CF patients is compromised by a number of bacterial factors that render the infectious agents resistant to antibiotics, including efflux pumps that remove antibiotics, lack of penetration of antibiotics into bacterial biofilms, and changes in the cell envelope that reduce the permeability of antibiotics. Any combination of these mechanisms increases the likelihood of bacterial survival. Therefore, combinations of antibiotics or of antibiotic and nonantibiotic compounds are currently being tested against Pseudomonas and Burkholderia. However, progress has been slow, with only occasional combinations showing promise for the eradication of persistent Gram-negative rods in the airways of CF patients. This review will summarize the current knowledge of CF infections and speculate on potential future pathways to treat these chronic infections.

Ghilarducci, T, Nell, E, Mittnik, S, Platen, E, Semmler, W & Chappe, R 2009, 'Memorandum on A new financial architecture and new regulations', Investigacion Economica, vol. 68, no. 267, pp. 147-161.
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Gillings, M, Labbate, M, Sajjad, A, Giguère, N, Holley, MP & Stokes, H 2009, 'Mobilization of a Tn402-Like Class 1 Integron with a Novel Cassette Array via Flanking Miniature Inverted-Repeat Transposable Element-Like Structures', Applied and Environmental Microbiology, vol. 75, no. 18, pp. 6002-6004.
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A Tn402-like class 1 integron was recovered from a prawn-associated bacterium. One of its cassettes included methionine sulfoxide reductase genes, the first example of such genes being captured by an integron. The integron was flanked by direct repeats that resemble miniature inverted-repeat transposable element equences. Excision of the integron by homologous ecombination through these sequences was demonstrated.

Godlewski, M, Wojcik-Glodowska, A, Guziewicz, E, Yatsunenko, S, Zakrzewski, A, Dumont, Y, Chikoidze, E & Phillips, M 2009, 'Optical properties of manganese doped wide band gap ZnS and ZnO', Optical Materials, vol. 31, pp. 1768-1771.
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Optical properties of ZnMnO layers grown at low temperature by Atomic Layer Deposition and Metalorganic Vapor Phase Epitaxy are discussed and compared to results obtained for ZnMnS samples. Present results suggest a double valence of Mn ions in ZnO lattice. Strong absorption, with onset at about 2.1 eV, is tentatively related to Mn 2+ to 3+ photoionization. Mechanism of emission deactivation in ZnMnO is discussed and is explained by the processes following the assumed Mn 2+ to 3+ recharging.

Gorrie, CA, Waite, ME & Rogers, LJ 2009, 'Correlations Between Hand Preference and Cortical Thickness in the Secondary Somatosensory (SII) Cortex of the Common Marmoset, Callithrix jacchus (vol 122, pg 1343, 2008)', BEHAVIORAL NEUROSCIENCE, vol. 123, no. 2, pp. 468-III.

Gottardo, R, Brinkman, RR, Luta, G, Luta, G & Wand, MP 2009, 'Recent bioinformatics advances in the analysis of high throughput flow cytometry data.', Advances in bioinformatics, p. 461763.
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Gou, X, Li, R, Wang, G, Chen, Z & Wexler, D 2009, 'Room-temperature solution synthesis of Bi2O3 nanowires for gas sensing application', NANOTECHNOLOGY, vol. 20, no. 49.
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Green, PJ & Mortera, J 2009, 'Sensitivity of inferences in forensic genetics to assumptions about founding genes', Annals of Applied Statistics, vol. 3, no. 2, pp. 731-763.
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Many forensic genetics problems can be handled using structured systems of discrete variables, for which Bayesian networks offer an appealing practical modeling framework, and allow inferences to be computed by probability propagation methods. However, w

Greenup, A, Peacock, J, Dennis, ES & Trevaskis, B 2009, 'The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals', ANNALS OF BOTANY, vol. 103, no. 8, pp. 1165-1172.
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In arabidopsis (Arabidopsis thaliana), FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) play key roles in regulating seasonal flowering-responses to synchronize flowering with optimal conditions. FT is a promoter of flowering activated by long days and

Gribben, PE, Wright, JT, O'Connor, W, Doblin, MA, Eyre, B & Steinberg, P 2009, 'Reduced performance of native infauna following recruitment to a habitat-forming invasive marine alga', Oecologia, vol. 158, no. 4, pp. 733-745.
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Despite well-documented negative impacts of invasive species on native biota, evidence for the facilitation of native organisms, particularly by habitat-forming invasive species, is increasing. However, most of these studies are conducted at the population or community level, and we know little about the individual fitness consequences of recruitment to habitat-forming invasive species and, consequently, whether recruitment to these habitats is adaptive. We determined the consequences of recruitment to the invasive green alga Caulerpa taxifolia on the native soft-sediment bivalve Anadara trapezia and nearby unvegetated sediment. Initially, we documented the growth and survivorship of A. trapezia following a natural recruitment event, to which recruitment to C. taxifolia was very high. After 12 months, few clams remained in either habitat, and those that remained showed little growth. Experimental manipulations of recruits demonstrated that all performance measures (survivorship, growth and condition) were significantly reduced in C. taxifolia sediments compared to unvegetated sediments. Exploration of potential mechanisms responsible for the reduced performance in C. taxifolia sediments showed that water flow and water column dissolved oxygen (DO) were significantly reduced under the canopy of C. taxifolia and that sediment anoxia was significantly higher and sediment sulphides greater in C. taxifolia sediments. However, phytoplankton abundance (an indicator of food supply) was significantly higher in C. taxifolia sediments than in unvegetated ones. Our results demonstrate that recruitment of native species to habitat-forming invasive species can reduce growth, condition and survivorship and that studies conducted at the community level may lead to erroneous conclusions about the impacts of invaders and should include studies on life-history traits, particularly juveniles.

Grujic, T, Kuhlmey, B, de Sterke, CM & Poulton, CG 2009, 'Modelling of photonic crystal fiber based on layered inclusions', Journal of the Optical Society of America B: Optical ..., vol. 26, no. 10, pp. 1852-1861.
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Photonic crystal fibers often consist of rotationally symmetric inclusions in an otherwise uniform background medium. The band diagrams and modes of such structures can be efficiently calculated using geometry-specific methods that exploit this rotational symmetry. Until now, these have only been applied to fibers in which the inclusions are circular and have a uniform refractive index. Here, we generalize this to arbitrary rotationally symmetric inclusions using a transfer matrix approach, and we implement this approach in an approximate scalar method, which is valid for low-index contrasts and in the rigorous Rayleigh multipole method. We apply the methods to structures incorporating inclusions with graded refractive indices and to structures incorporating metal rings.

Gueidan, C, Savic, S, Thues, H, Roux, C, Keller, C, Tibell, L, Prieto, M, Heiomarsson, S, Breuss, O, Orange, A, Froberg, L, Wynns, AA, Navarro-Rosines, P, Krzewicka, B, Pykaelae, J, Grube, M & Lutzoni, F 2009, 'Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: recent progress and remaining challenges', TAXON, vol. 58, no. 1, pp. 184-208.
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Guha, S, Ryan, LM & Morara, M 2009, 'Gauss-Seidel Estimation Of Generalized Linear Mixed Models With Application To Poisson Modeling Of Spatially Varying Disease Rates', Journal of Computational and Graphical Statistics, vol. 18, no. 4, pp. 818-837.
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Generalized linear mixed models (GLMMs) are often fit by computational procedures such as penalized quasi-likelihood (PQL). Special cases of GLMMs are generalized linear models (GLMs), which are often fit using algorithms like iterative weighted least sq

Gunawan, C, Teoh, WY, Marquis, CP, Lifia, J & Amal, R 2009, 'Reversible Antimicrobial Photoswitching in Nanosilver', SMALL, vol. 5, no. 3, pp. 341-344.
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Ha, S, Sukhorukov, AA, Dossou, KB, Botten, LC, de Sterke, CM & Kivshar, Y 2009, 'Bloch-Mode Extraction From Near-Field Data In Periodic Waveguides', Optics Letters, vol. 34, no. 24, pp. 3776-3778.
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We demonstrate that the spatial profiles of both propagating and evanescent Bloch modes in a periodic structure can be extracted from a single measurement of an electric field at the specified optical wavelength. We develop a systematic extraction proced

Haapkyla, J, Seymour, AS, Barneah, O, Brickner, I, Hennige, S, Suggett, DJ & Smith, D 2009, 'Association of Waminoa sp. (Acoela) with corals in the Wakatobi Marine Park, South-East Sulawesi, Indonesia', Marine Biology, vol. 156, no. 5, pp. 1021-1027.
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This is the first quantitative study on the prevalence of epizoic Waminoa sp. acoel worms and their association with corals in the Wakatobi Marine National Park (WMNP), South-East Sulawesi, Indonesia. Three replicate transects were laid on the reef crest

Hagge, DA, Saunders, BM, Ebenezer, GJ, Ray, NA, Marks, VT, Britton, WJ, Krahenbuhl, JL & Adams, LB 2009, 'Lymphotoxin-alpha and TNF Have Essential but Independent Roles in the Evolution of the Granulomatous Response in Experimental Leprosy', AMERICAN JOURNAL OF PATHOLOGY, vol. 174, no. 4, pp. 1379-1389.
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Hahn, MA, McDonnell, J & Marsh, DJ 2009, 'The effect of disease-associated HRPT2 mutations on splicing', JOURNAL OF ENDOCRINOLOGY, vol. 201, no. 3, pp. 387-396.
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Hamidian, M, Tajbakhsh, M, Walther-Rasmussen, J & Zali, M-R 2009, 'Emergence of Extended-Spectrum beta-Lactamases in Clinical Isolates of Salmonella enterica in Tehran, Iran', JAPANESE JOURNAL OF INFECTIOUS DISEASES, vol. 62, no. 5, pp. 368-371.

Hanen, C & Zinder, Y 2009, 'The worst-case analysis of the Garey-Johnson algorithm', Journal Of Scheduling, vol. 12, no. 4, pp. 389-400.
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The Garey-Johnson algorithm is a well known polynomial-time algorithm constructing an optimal schedule for the maximum lateness problem with unit execution time tasks, two parallel identical processors, precedence constraints and release times. The paper is concerned with the worst-case analysis of a generalization of the Garey-Johnson algorithm to the case of arbitrary number of processors. In contrast to other algorithms for the maximum lateness problem, the tight performance guarantee for the even number of processors differs from the tight performance guarantee for the odd number of processors.

Hare, D, Bishop, D, Austin, C & Doble, P 2009, 'The answer is elemental', Biochemist, vol. 31, no. 1, p. 46.
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Trace elements play a key role in a wide range of biological processes. A full understanding of those processes requires a knowledge not only of the genomics and proteomics of the organism, but also the distribution and concentration of trace elements. A new application of inductively coupled plasma mass spectrometry (ICP-MS) provides the capability to directly visualize trace elements in soft tissue, offering the promise of improved diagnosis and monitoring of disease. © 2009 The Biochemical Society.

Hare, DJ, Haarburger, D, Austin, CE, Fryer, FI, Grimm, R, Reedy, BJ, Scolyer, RA, Thompson, JF & Doble, PA 2009, 'Elemental bio-imaging of melanoma in lymph node biopsies', The Analyst, vol. 134, no. 3, pp. 450-453.
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The spatial distribution of trace elements in human lymph nodes partially infiltrated by melanoma cells was determined by elemental bio-imaging. Imaging of 31P within the nodal capsule and normal lymph node tissue showed a clear demarcation of the tumour boundary, with a significant decrease in relative 31P concentration within the tumour. The location of the tumour boundary was confirmed by haematoxylin and eosin staining of serial sections and observation by light microscopy. Further enhancement of the tumour boundary was achieved by imaging the 31P/34S ratio. 31P/66Zn ratio images showed a decreasing ratio beyond the tumour boundary that extended into peritumour normal lymph node tissue.

Hare, DJ, Reedy, BJ, Grimm, R, Wilkins, S, Volitakis, I, George, JL, Cherny, R, Bush, A, Finkelstein, D & Doble, PA 2009, 'Quantitative elemental bio-imaging of Mn, Fe, Cu and Zn in 6-hydroxydopamine induced Parkinsonism mouse models', metallomics, vol. 1, no. 1, pp. 53-58.
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This study demonstrates the application of quantitative elemental bio-imaging for the determination of the distribution Cu, Mn, Fe and Zn in Parkinsonism mouse model brains. Elevated concentrations of these metals within the substantia nigra (SN) are suspected to play a role on the development of Parkinsons disease. Elemental bio-imaging employs laser ablation inductively coupled mass spectrometry (LA-ICP-MS) to construct images of trace element distribution. Quantitative data was produced by ablating the standard tissue sections and recording the mean signal intensity calibrated against multi level matrix matched tissue standards. The concentrations of Fe within the substantia nigra of the lesioned animals increased significantly when compared against control animals. Furthermore, the data was compared against solution nebulisation ICP-MS in which the whole substantia nigra was excised. The trends were the same for both methods; however the elemental bio-imaging method returned significantly higher concentrations. This was caused by dilution from inclusion of surrounding tissue of the SN during the excision procedure.

Harris, N, Arnold, MD, Blaber, MG & Ford, M 2009, 'Plasmonic resonances of closely coupled gold nanosphere chains', Journal of Physical Chemistry C, vol. 113, no. 7, pp. 2784-2791.
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The optical properties of an ordered array of gold nanospheres have been calculated using the T-matrix method in the regime where the near-fields of the particles are strongly coupled. The array consists of a one-dimensional chain of spheres of 15 nm diameter where the number of spheres in the chain and interparticle spacing is varied. Calculations have been performed with chains up to 150 particles in length and with an interparticle spacing between 0.5 and 30 nm. Incident light polarized along the axis of the chain (longitudinal) and perpendicular (transverse) to it are considered, and in the latter case for wavevectors along and perpendicular to the chain axis. For fixed chain length the longitudinal plasmon resonance red shifts, relative to the resonance of an isolated sphere, as the interparticle spacing is reduced. The shift in the plasmon resonance does not appear to follow an exponential dependence upon gap size for these extended arrays of particles. The peak shift is inversely proportional to the distance, a result that is consistent with the van der Waals attraction between two spheres at short range, which also varies as 1/d. The transverse plasmon resonance shifts in the opposite direction as the interparticle gap is reduced; this shift is considerably smaller and approaches 500 nm as the gap tends to zero. Increasing the number of particles in the chain for a fixed gap has a similar effect on the longitudinal and transverse plasmon. In this case, however, the longitudinal plasmon tends toward an asymptotic value with increasing chain length, with the asymptotic value determined by the interparticle spacing. Here, the approach to the asymptote is exponential with a characteristic length of approximately two particles, at small interparticle spacings. This approach to an asymptote as the chain length becomes infinite has been verified in a finite element calculation with periodic boundary conditions.

Hart, J, Yanosky, J, Puett, R, Ryan, LM, Dockery, D, Smith, T, Garshick, E & Laden, F 2009, 'Spatial Modeling Of Pm10 And No2 In The Continental United States, 1985-2000', Environmental Health Perspectives, vol. 117, no. 11, pp. 1690-1696.
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Background: Epidemiologic studies of air pollution have demonstrated a link between long-term air pollution exposures and mortality. However, many have been limited to city-specific average pollution measures or spatial or land-use regression exposure models in small geographic areas. Objectives: Our objective was to develop nationwide models of annual exposure to particulate matter < 10 Êm in diameter (PM10) and nitrogen dioxide during 1985.2000. Methods: We used generalized additive models (GAMs) to predict annual levels of the pollutants using smooth spatial surfaces of available monitoring data and geographic information system. derived covariates. Model performance was determined using a cross-validation (CV) procedure with 10% of the data. We also compared the results of these models with a commonly used spatial interpolation, inverse distance weighting. Results: For PM10, distance to road, elevation, proportion of low-intensity residential, highintensity residential, and industrial, commercial, or transportation land use within 1 km were all statistically significant predictors of measured PM10 (model R2 = 0.49, CV R2 = 0.55). Distance to road, population density, elevation, land use, and distance to and emissions of the nearest nitrogen oxides.emitting power plant were all statistically significant predictors of measured NO2 (model R2 = 0.88, CV R2 = 0.90). The GAMs performed better overall than the inverse distance models, with higher CV R2 and higher precision. Conclusions: These models provide reasonably accurate and unbiased estimates of annual exposures for PM10 and NO2. This approach provides the spatial and temporal variability necessary to describe exposure in studies assessing the health effects of chronic air pollution.

Hauser, V, Howlett, C & Matthews, C 2009, 'The Place of Indigenous Knowledge in Tertiary Science Education: A Case Study of Canadian Practices in Indigenising the Curriculum', Australian Journal of Indigenous Education, vol. 38, no. S1, pp. 46-58.
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In Australia, Indigenising the curriculum is increasingly acknowledged as a possible avenue for addressing Indigenous under-representation in tertiary science education in a culturally appropriate and relevant manner. While no Australian university has implemented such a program, there is much to be learnt about the inherent complexities of Indigenising curriculum before it is pursued. In Canada, however, innovative university programs have been implemented that imbed Indigenous knowledge into the curriculum. This paper details key findings from research that sought to learn from Canadian practices in Indigenising tertiary science curriculum, by exploring the practices and experiences of two Canadian programs: Trent University's Indigenous Environmental Studies program, and Cape Breton University's Integrative Science program. © 2009, Cambridge University Press. All rights reserved.

Haynes, L, Arzey, E, Bell, C, Buchanan, N, Burgess, G, Cronan, V, Dickason, C, Field, H, Gibbs, S, Hansbro, PM, Hollingsworth, T, Hurt, AC, Kirkland, P, McCracken, H, O'Connor, J, Tracey, J, Wallner, J, Warner, S, Woods, R & Bunn, C 2009, 'Australian surveillance for avian influenza viruses in wild birds between July 2005 and June 2007', AUSTRALIAN VETERINARY JOURNAL, vol. 87, no. 7, pp. 266-272.
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Hazard, D, Becue, A, Moret, S, Drapel, V, Milon, MP, Dobler, A, Pun, KM, Jung, B, Comment, S, Jolliet, F & Mizrahi, S 2009, 'Detect and recognise', Revue Internationale de Criminologie et de Police Technique et Scientifique, vol. 62, no. 2, pp. 17-36.
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The detection of relevant traces, not always visible, is the challenge that systematically confronts the scientist attending a scene of investigation: infinitesimal traces may form the pattern of papillary ridges or may help extract a DNA profile. Searches are oriented when an odour may lead towards remnants of a flammable product on a fire scene, when relevant digital traces are extracted from gigantic masses of data or when testing specifically if a person has consumed a product. The project directed towards the simultaneous increase in the detection capability of latent traces and the recognition of what may better explain a presence or an action necessarily combines both the development of new techniques and their integration in a global approach of the investigative field, whose foundations remain to be consolidated.

Heinz, E, Tischler, P, Rattei, T, Myers, G, Wagner, M & Horn, M 2009, 'Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae', BMC Genomics, vol. 10.
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Background: Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using Escherichia coli (positive control) and Bacillus subtilis (negative control), and applied it to five chlamydial species; Chlamydia trachomatis, Chlamydia muridarum, Chlamydia (a.k.a. Chlamydophila) pneumoniae, Chlamydia (a.k.a. Chlamydophila) caviae, and Protochlamydia amoebophila.Results: In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition.Conclusion: This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP http://www.microbial-ecology.net/pcomp and might provide future guidance in the quest for anti-chlamydial vaccines. © 2009 Heinz et al; licensee BioMed Central Ltd.

Hemming, M, Fieg, S, Peacock, J, Dennis, ES & Trevaskis, B 2009, 'Regions associated with repression of the barley (Hordeum vulgare) VERNALIZATION1 gene are not required for cold induction', Molecular Genetics and Genomics, vol. 282, no. 2, pp. 107-117.
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Activity of the VERNALIZATION1 (VRN1) gene is required for Xowering in temperate cereals such as wheat and barley. In varieties that require prolonged exposure to cold to Xower (vernalization), VRN1 is expressed at low levels and is induced by vernalization to trigger Xowering. In other varieties, deletions or insertions in the Wrst intron of the VRN1 gene are associated with increased VRN1 expression in the absence of cold treatment, reducing or eliminating the requirement for vernalization. To characterize natural variation in VRN1, the Wrst intron of the barley (Hordeum vulgare) VRN1 gene (HvVRN1) was assayed for deletions or insertions in a collection of 1,000 barleys from diverse geographical regions. Ten alleles of HvVRN1 containing deletions or insertions in the Wrst intron were identiWed, including three alleles that have not been described previously. DiVerent HvVRN1 alleles were associated with diVering levels of HvVRN1 expression in nonvernalized plants and with diVerent Xowering behaviour. Using overlapping deletions, we delineated regions in the HvVRN1 Wrst intron that are associated with low levels of HvVRN1 expression in non-vernalized plants. Deletion of these intronic regions does not prevent induction of HvVRN1 by cold or the maintenance of increased HvVRN1 expression following cold treatment. We suggest that regions within the Wrst intron of HvVRN1 are required to maintain low levels of HvVRN1 expression prior to winter but act independently of the regulatory mechanisms that mediate induction of HvVRN1 by cold during winter.

Hennige, SJ, Suggett, DJ, Warner, ME, McDougall, KE & Smith, DJ 2009, 'Photobiology of Symbiodinium revisited: bio-physical and bio-optical signatures', Coral Reefs, vol. 28, no. 1, pp. 179-195.
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Light is often the most abundant resource within the nutrient-poor waters surrounding coral reefs. Consequently, zooxanthellae (Symbiodinium spp.) must continually photoacclimate to optimise productivity and ensure coral success. In situ coral photobiolo

Hernaman, V, Probert, PK & Robbins, WD 2009, 'Trophic ecology of coral reef gobies: interspecific, ontogenetic, and seasonal comparison of diet and feeding intensity', MARINE BIOLOGY, vol. 156, no. 3, pp. 317-330.
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Hill, R, Ulstrup, K & Ralph, PJ 2009, 'Temperature Induced Changes In Thylakoid Membrane Thermostability Of Cultured, Freshly Isolated, And Expelled Zooxanthellae From Scleractinian Corals', Bulletin of Marine Science, vol. 85, no. 3, pp. 223-244.
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Coral bleaching events are characterized by a dysfunction between the cnidarian coral host and the symbiotic dinoflagellate algae, known as zooxanthellae (genus Symbiodinium). Elevated temperature and intense light induce coral bleaching, where zooxanthellae are expelled from the host tissue. The primary cellular process in zooxanthellae which leads to coral bleaching is unresolved, and here, we investigated the sensitivity of the thylakoid membrane in a Symbiodinium culture and in genetically identified freshly isolated and expelled Symbiodinium cells. The fluorescence-temperature curve technique was used to measure the critical temperature (Tc) at which irreversible damage to the thylakoid membrane occurred. The accuracy of this technique was confirmed through the collection of scanning transmission electron micrographs which demonstrated the clear relationship between Tc and thylakoid membrane degradation. Analysis of 10 coral species with a diverse range of genetically distinct Symbiodinium communities showed a decline in Tc from summer to winter. A Symbiodinium culture and fragments of Pocillopora damicornis (Linnaeus, 1758) were exposed to a series of light and temperature treatments, where Tc increased from approximately 37 °C to 42 °C upon exposure to elevated temperature. Under bleaching conditions, the thermostability of the thylakoid membrane increased within 4 hrs by 5.1 °C, to a temperature far above bleaching thresholds, in both freshly isolated and photosynthetically competent zooxanthellae expelled from P. damicornis under these conditions. It is demonstrated that the thermostability of the thylakoid membrane increases in cultured, freshly isolated, and expelled zooxanthellae exposed to bleaching stress, suggesting it is not the primary site of impact during coral bleaching events.

Howell, VM, Gill, A, Clarkson, A, Nelson, AE, Dunne, R, Delbridge, LW, Robinson, BG, Teh, BT, Gimm, O & Marsh, DJ 2009, 'Accuracy of Combined Protein Gene Product 9.5 and Parafibromin Markers for Immunohistochemical Diagnosis of Parathyroid Carcinoma', JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, vol. 94, no. 2, pp. 434-441.
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Huang, K, Filarsky, M, Padula, M, Raftery, MJ, Herbert, BR & Wilkins, MR 2009, 'Micropreparative fractionation of the complexome by blue native continuous elution electrophoresis.', Proteomics, vol. 9, no. 9, pp. 2494-2502.
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The large-scale analysis of protein complexes is an emerging challenge in the field of proteomics. Currently, there are few methods available for the fractionation of protein complexes that are compatible with downstream proteomic techniques. Here, we describe the technique of blue native continuous elution electrophoresis (BN-CEE). It combines the features of blue native PAGE (BN-PAGE) and continuous elution electrophoresis (CEE), generating liquid-phase fractions of protein complexes of up to 800 kDa. The resulting complexes can be further analysed by BN-PAGE, by SDS-PAGE and/or by MS. This can help define the constituent proteins of many complexes and their stoichiometry. As BN-CEE is also micropreparative, with a capacity to separate milligram quantities of protein complexes, it will assist the study of proteins of lower abundance. In this regard, the acrylamide concentration and elution rate during separation can be controlled to help `zoom in on particular high mass regions and thus complexes of interest. We illustrate the utility of the technique in the analysis of Saccharomyces cerevisiae cellular lysate.

Huang, YC, Solntsev, AS, Wang, TD & Hsu, WW 2009, 'Generation of fs laser pulses from a ps pulse-pumped optical parametric amplifier with a beat-wave seed signal', OPTICS COMMUNICATIONS, vol. 282, no. 11, pp. 2250-2254.
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Huttunen, JE, Dawson, M, Roux, CP & Robertson, J 2009, 'Physical Evidence In Drug Intelligence Part 3: Supercritical Fluid Extraction-High Performance Liquid Chromatography Of Packaging Tapes', Australian Journal of Forensic Sciences, vol. 41, no. 1, pp. 63-72.
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It may be desirable to compare samples of packaging tape or identify their specific brand and/or model based on analytical results. Such information may, for example, be used to infer or refute hypotheses of common origin for separately seized packages o

Inocent, G, Bertrand, PMJ, Honore, FK, Odette, Z, Salome, N, Valery, C, Georges, GE & Henri, AZP 2009, 'Physiopathologic Factors Resulting in Poor Outcome in Childhood Severe Malaria in Cameroon', PEDIATRIC INFECTIOUS DISEASE JOURNAL, vol. 28, no. 12, pp. 1081-1084.
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Jafari, F, Hamidian, M, Rezadehbashi, M, Doyle, M, Salmanzadeh-ahrabi, S, Derakhshan, F & Zali, MR 2009, 'Prevalence and antimicrobial resistance of diarrheagenic Escherichia coli and Shigella species associated with acute diarrhea in Tehran, Iran', Canadian Journal of Infectious Diseases and Medical Microbiology, vol. 20, no. 3.
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A study was performed to determine the prevalence and antimicrobial resistance of Shigella species and diarrheagenic Escherichia coli isolates cultured from patients with acute diarrhea in Tehran, Iran. Between May 2003 and May 2005, 1120 diarrheal specimens were collected and assayed for bacterial enteropathogens by conventional and molecular methods. Etiological agents were isolated from 564 (50.3%) specimens, and included 305 (54%) E coli, 157 (27.8%) Shigella species, and 102 (18%) from other genera of bacteria. The predominant E coli was Shiga toxin-producing E coli (105 isolates [34.5%]) and the predominant Shigella serotype was Shigella sonnei (88 isolates [56.1%]). A high rate of antibiotic resistance was observed among E coli, with 40 of 53 (75.5%) Shiga toxin-producing E coli isolates resistant to amoxicillin and tetracycline, and eight (5.2%) E coli isolates resistant to more than six antibiotics. Most Shigella isolates were resistant to tetracycline (95%) and trimethoprim- sulfamethoxazole (91.7%), with greatest antibiotic resistance observed among S sonnei (53 of 88 [60.2%] isolates). Antibiotic resistance is widespread in diarrheagenic E coli and Shigella in children with acute diarrhea in Tehran, Iran; hence, updated strategies for appropriate use of antimicrobial agents in Iran are needed. ©2009 Pulsus Group Inc. All rights reserved.

Jambou, R, El-Assaad, F, Combes, V & Grau, GE 2009, 'Citicoline (CDP-choline): What role in the treatment of complications of infectious diseases', INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, vol. 41, no. 7, pp. 1467-1470.
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Jiang, X, Waterland, M, Blackwell, L, Wu, Y, Jayasundera, KP & Partridge, A 2009, 'Sensitive determination of estriol-16-glucuronide using surface plasmon resonance sensing', STEROIDS, vol. 74, no. 10-11, pp. 819-824.
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Jin, D, Piper, JA, Leif, RC, Yang, S, Ferrari, BC, Yuan, J, Wang, G, Vallarino, LM & Williams, JW 2009, 'Time-gated flow cytometry: an ultra-high selectivity method to recover ultra-rare-event mu-targets in high-background biosamples', JOURNAL OF BIOMEDICAL OPTICS, vol. 14, no. 2.
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Johnson, F, Padmadas, S & Brown, JJ 2009, 'On the Spatial Inequalities of Institutional Versus Home Births in Ghana: A Multilevel Analysis', Journal of Community Health, vol. 34, no. 1, pp. 64-72.
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Spatial inequalities related to the choice of delivery care have not been studied systematically in Sub-Saharan Africa where maternal and perinatal health outcomes continue to worsen despite a range of safe motherhood interventions. Using retrospective d

Jones, AC, Arns, CH, Hutmacher, DW, Milthorpe, BK, Sheppard, AP & Knackstedt, M 2009, 'The correlation of pore morphology, interconnectivity and physical properties of 3D ceramic scaffolds with bone ingrowth', Biomaterials, vol. 30, no. 7, pp. 1440-1451.
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In the design of tissue engineering scaffolds, design parameters including pore size, shape and interconnectivity, mechanical properties and transport properties should be optimized to maximize successful inducement of bone ingrowth. In this paper we describe a 3D micro-CT and pore partitioning study to derive pore scale parameters including pore radius distribution, accessible radius, throat radius, and connectivity over the pore space of the tissue engineered constructs. These pore scale descriptors are correlated to bone ingrowth into the scaffolds. Quantitative and visual comparisons show a strong correlation between the local accessible pore radius and bone ingrowth; for well connected samples a cutoff accessible pore radius of similar to 100 mu M is observed for ingrowth. The elastic properties of different types of scaffolds are simulated and can be described by standard cellular solids theory: (E/E(0))-(rho/rho(s))(n). Hydraulic conductance and diffusive properties are calculated; results are consistent with the concept of a threshold conductance for bone ingrowth. Simple simulations of local flow velocity and local shear stress show no correlation to in vivo bone ingrowth patterns. These results demonstrate a potential for 3D imaging and analysis to define relevant pore scale morphological and physical properties within scaffolds and to provide evidence for correlations between pore scale descriptors, physical properties and bone ingrowth.

Jones, PM & George, AM 2009, 'Opening of the ADP-bound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle', Proteins-Structure Function And Bioinformatics, vol. 75, no. 2, pp. 387-396.
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ABC transporters are ubiquitous, ATP-dependent transmembrane pumps. The mechanism by which ATP hydrolysis in the nucleotide-binding domain (NBD) effects conformational changes in the transmembrane domain that lead to allocrite translocation remains largely unknown. A possible aspect of this mechanism was suggested by previous molecular dynamics simulations of the MJ0796 NBD dimer, which revealed a novel, nucleotide-dependent intrasubunit conformational change involving the relative rotation of the helical and catalytic subdomains. Here, we find that in four of five simulations of the ADP/ATP-bound dimer, the relative rotation of the helical and catalytic subdomains in the ADP-bound monomer results in opening of the ADP-bound active site, probably sufficient or close to sufficient to allow nucleotide exchange. We also observe that in all five simulations of the ADP/ATP-bound dimer, the intimate contact of the LSGGQ signature sequence with the ATP gamma-phosphate is weakened by the intrasubunit conformational change within the ADP-bound monomer. We discuss how these results support a constant contact model for the function of the NBD dimer in contrast to switch models, in which the NBDs are proposed to fully disassociate during the catalytic cycle.

Jones, PM, O'Mara, M & George, AM 2009, 'ABC transporters: A riddle wrapped in a mystery inside an enigma', Trends in Biochemical Sciences, vol. 34, no. 10, pp. 520-531.
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ATP-binding cassette (ABC) transporters form one of the largest and most ancient of protein families. ABC transporters couple hydrolysis of ATP to vectorial translocation of diverse substrates across cellular membranes. Many human ABC transporters are medically important in causing, for example, multidrug resistance to cytotoxic drugs. Seven complete prokaryotic structures and one eukaryotic structure have been solved for transporters from 2002 to date, and a wealth of research is being conducted on and around these structures to resolve the mechanistic conundrum of how these transporters couple ATP hydrolysis in cytosolic domains to substrate translocation through the transmembrane pore. Many questions remained unanswered about this mechanism, despite a plethora of data and a number of interesting and controversial models.

Jonkers, W, Rodrigues, CDA & Rep, M 2009, 'Impaired Colonization and Infection of Tomato Roots by the Delta frp1 Mutant of Fusarium oxysporum Correlates with Reduced CWDE Gene Expression', MOLECULAR PLANT-MICROBE INTERACTIONS, vol. 22, no. 5, pp. 507-518.
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Joss, MJ, Koenig, JE, Labbate, M, Polz, MF, Gillings, M, Stokes, H, Doolittle, WF & Boucher, Y 2009, 'ACID: annotation of cassette and integron data', BMC Bioinformatics, vol. 10, no. 118, pp. 1-9.
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Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms.

Kabakova, IV, Corcoran, B, Bolger, JA, de Sterke, CM & Eggleton, BJ 2009, 'All-optical self-switching in optimized phase-shifted fiber Bragg grating', OPTICS EXPRESS, vol. 17, no. 7, pp. 5083-5088.
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Kamal, M, Tan, Y, Seale, JP & Qu, X 2009, 'Targeting Buche-Inflammatory Pathway By Sk0506 To Manage Type 2 Diabetes And Alzheimer Disease', Neurochemical Research, vol. 34, no. 12, pp. 2163-2169.
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Type 2 diabetes mellitus (T2DM) and Alzheimers disease (AD) affect a large percent of the population worldwide. Experimental studies have revealed that T2DM and AD share several molecular processes that underlie their respective degenerative pathology. Based on this information, we quantified TNF-?, IL-6 levels, serum glucose, serum triglyceride, hepatic triglyceride, serum AST, serum ALT and butyrylcholinesterase (BuChE) in various rat tissues. HFD was fed to rats resulting in increased body weight, fasting blood glucose, IL-6, TNF-? levels, hepatic triglyceride, serum AST, serum ALT and BuChE. SK0506 treatment significantly prevented weight gain induced by HFD feeding. SK0506, but not Rosiglitazone, significantly reduced serum and hepatic triglycerides levels. Treatment with SK0506 also ameliorated elevated levels of both inflammatory markers (TNF-? and IL-6) and serum liver enzymes (ALT and AST) significantly in HFD fed rats. BuChE activity also reduced in skeletal muscle and adipose tissues of rats treated by SK0506. In conclusion, current study has opened new potential avenues towards research for management of T2DM and AD by Chinese herbal extracts, SK0506.

Kealley, CS, Cortie, MB, Maaroof, AI & Xu, X 2009, 'The versatile colour gamut of coatings of plasmonic metal nanoparticles', Physical Chemistry Chemical Physics, vol. 11, no. 28, pp. 5897-5902.
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We have investigated the colour gamut of coatings produced by the growth of plasmonically-active coatings of cap-shaped Au or Ag nanoparticles on a transparent substrate. The control of colour and spectral selectivity that can be obtained by the manipulation of the rates of nucleation and growth were explored using a combination of experiment and calculation. In our experimental work the Au nanoparticles were grown in situ using a wet chemical electroless plating technique while the Ag nanoparticles were produced by physical vapour deposition. The optical properties were numerically simulated using the discrete dipole approximation. The resulting measured or calculated transmission spectra were mapped to the CIE L-a*-b* colour space. The aspect ratio of the nanoparticles was the primary factor in determining the colours in both cases. However, increasing the nucleation rate of the particles resulted in them becoming more closely packed, which also red-shifted the optical extinction peak of the structure due to interactions of their near-fields. This caused an enhancement in the blue component of the transmitted light. Coatings of Ag particles had a significantly wider and brighter colour gamut than those of Au.

Kelehear, C, Webb, JK & Shine, R 2009, 'Rhabdias pseudosphaerocephala infection in Bufo marinus: lung nematodes reduce viability of metamorph cane toads', Parasitology, vol. 136, no. 8, pp. 919-927.
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Cane toads (Bufo marinus) were introduced to Australia in 1935 and have since spread widely over the continent, generating concern regarding ecological impacts on native predators. Most Australian cane toad populations are infected with lung nematodes Rhabdias pseudosphaerocephala, a parasite endemic to New World (native-range) cane toad populations; presumably introduced to Australia with its toad host. Considering the high intensities and prevalence reached by this parasite in Australian toad populations, and public ardour for developing a control plan for the invasive host species, the lack of experimental studies on this host-parasite system is surprising. To investigate the extent to which this lungworm influences cane toad viability, we experimentally infected metamorph toads (the smallest and presumably most vulnerable terrestrial phase of the anuran life cycle) with the helminth. Infected toads exhibited reduced survival and growth rates, impaired locomotor performance (both speed and endurance), and reduced prey intake. In summary, R. pseudosphaerocephala can substantially reduce the viability of metamorph cane toads.

Khare, S, Chaudhary, K, Bissonnette, M & Carroll, R 2009, 'Aberrant crypt foci in colon cancer epidemiology.', Methods in molecular biology (Clifton, N.J.), vol. 472, pp. 373-386.
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Colonic carcinogenesis is characterized by progressive accumulations of genetic and epigenetic derangements. These molecular events are accompanied by histological changes that progress from mild cryptal architectural abnormalities in small adenomas to eventual invasive cancers. The transition steps from normal colonic epithelium to small adenomas are little understood. In experimental models of colonic carcinogenesis aberrant crypt foci (ACF), collections of abnormal appearing colonic crypts, are the earliest detectable abnormality and precede adenomas. Whether in fact ACF are precursors of colon cancer, however, remains controversial. Recent advances in magnification chromoendoscopy now allow these lesions to be identified in vivo and their natural history ascertained. While increasing lines of evidence suggest that dysplastic ACF harbor a malignant potential, there are few prospective studies to confirm causal relationships and supporting epidemiological studies are scarce. It would be very useful, for example, to clarify the relationship of ACF incidence to established risks for colon cancer, including age, smoking, sedentary lifestyle, and Western diets. In experimental animal models, carcinogens dose-dependently increase ACF, whereas most chemopreventive agents reduce ACF incidence or growth. In humans, however, few agents have been validated to be chemopreventive of colon cancer. It remains unproven, therefore, whether human ACF could be used as reliable surrogate markers of efficacy of chemopreventive agents. If these lesions could be used as reliable biomarkers of colon cancer risk and their reductions as predictors of effective chemopreventive agents, metrics to quantify ACF could greatly facilitate the study of colonic carcinogenesis and chemoprevention.

Kile, M, Hoffman, E, Hsueh, Y, Afroz, S, Quamruzzaman, Q, Rahman, M, Mahiuddin, G, Ryan, LM & Christiani, D 2009, 'Variability In Biomarkers Of Arsenic Exposure And Metabolism In Adults Over Time', Environmental Health Perspectives, vol. 117, no. 3, pp. 455-460.
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OBJECTIVES: To characterize inter- and intraindividual variability in IUAs in healthy individuals. METHODS: In a longitudinal study conducted in Bangladesh, we collected water and spot urine samples from 196 participants every 3 months for 2 years. Water arsenic (As) was measured by inductively coupled plasma-mass spectrometry and urinary As [arsenite, arsenate, monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA)] were detected using high-performance liquid chromatography-hydride-generated atomic absorption spectrometry. We used linear mixed-effects models to compute variance components and evaluate the association between UAs and selected factors. RESULTS: The concentrations of IUAs were fairly reproducible within individuals, with intraclass correlation coefficients (ICCs) of 0.41, 0.35, 0.47, and 0.49 for inorganic As (InAs), MMA, DMA, and total urinary As (TUA). However, when expressed as a ratio, the percent InAs (%InAs), %MMA, and %DMA were poorly reproducible within individuals, with ICCs of 0.16, 0.16, and 0.17, respectively. Arsenic metabolism was significantly associated with sex, exposure, age, smoking, chewing betel nut, urinary creatinine, and season. Specificity and sensitivity analyses showed that a single urine sample adequately classified a participant's urinary As profile as high or low, but TUA had only moderate specificity for correctly classifying drinking water exposures. CONCLUSIONS: Epidemiologic studies should use both urinary As concentrations and the relative proportion of UAs to minimize measurement error and to facilitate interpretation of factors that influence As metabolism.

Kim, HS, Kim, WS, Gu, HB & Wang, G 2009, 'Electrochemical performance of SnPO4-coated LiNi1/3Mn1/3Co1/3O2 cathode materials', Journal of New Materials for Electrochemical Systems, vol. 12, no. 4, pp. 171-238.
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A Sn phosphate was successfully coated to the surface of LiNi1/3Co1/3Mn1/3O2 particles using a new method we developed. The elements Sn and P were observed to be uniformly distributed on the surface of the LiNi1/3Co1/3Mn1/3O2. After the Sn phosphate coating, the onset temperature shifted up to about 250 oC, and the exothermic value also decreased to 116.3 J/g, i.e. the thermal stability of the material was enhanced. The rate capability of the 1 wt% Sn phosphate-coated LiNi1/3Co1/3Mn1/3O2 materials was enhanced at room temperature and 60 oC. However, a 3 wt% Sn phosphate coating degraded the electrochemical performance. The 1 wt% Sn phosphate-coated material showed improved cycle performance compared to that of the bare material at room temperature and 60 oC. It is believed that the oxide coating layer prevented direct contact with the organic electrolyte.

Kim, JK, Xiao, H, Tan, Y, Wang, Z, Seale, JP & Qu, X 2009, 'The Effects And Mechanism Of Saponins Of Panax Notoginseng On Glucose Metabolism In 3T3-L1 Cells', The American Journal of Chinese Medicine, vol. 37, no. 6, pp. 1179-1189.
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This study was carried out to determine the effect of saponins of Panax notoginseng (SPN), a naturally occurring cardiovascular agent, on: (1) glucose uptake, (2) GLUT4 translocation and (3) glycogen synthesis in 3T3-L1 adipocytes. Electrospray ionization-Mass spectrometry (ESI-MS) was used to determine the structural characterization of the major active components of SPN. 3T3-L1 adipocytes were cultured and treated with 100 nM insulin alone or with 10, 50 and 100 ?g/ml of SPN. [3H]2-deoxyglucose glucose uptake, GLUT4 immunofluorescence imaging and glycogen synthesis assay were carried out to determine the effects of SPN on glucose metabolism. Under insulin stimulation, SPN significantly increased glucose uptake in a dose-dependent manner; 50 ?g/ml of SPN increased glucose uptake by 64% (p < 0.001). Immunofluorescence imaging and analysis have revealed that 50 and 100 ?g/ml of SPN increased GLUT4 in the plasma membrane by 3-fold and 6-fold respectively (p < 0.001). Furthermore, the incorporation of D-[U-14C] glucose into glycogen was enhanced by 53% in 3T3-L1 cells treated with 100 ?g/ml of SPN (p < 0.01 vs. insulin stimulation alone). SPN, a naturally occurring agent used to treat ischemic cardio-cerebral vascular disease in China, enhanced insulin-stimulated glucose uptake and glycogen synthesis in adipocytes. The results of this study indicate that SPN may have a therapeutic potential for hyperglycaemia in type 2 diabetes.

Kipnis, V, Midthune, D, Buckman, DW, Dodd, KW, Guenther, PM, Krebs-Smith, SM, Subar, AF, Tooze, JA, Carroll, RJ & Freedman, LS 2009, 'Modeling Data with Excess Zeros and Measurement Error: Application to Evaluating Relationships between Episodically Consumed Foods and Health Outcomes', BIOMETRICS, vol. 65, no. 4, pp. 1003-1010.
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Klein, J-M, Henault, M, Roux, C, Bultel, Y & Georges, S 2009, 'Direct methane solid oxide fuel cell working by gradual internal steam reforming: Analysis of operation', JOURNAL OF POWER SOURCES, vol. 193, no. 1, pp. 331-337.
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Konstantinov, K, Wang, G, Lao, ZJ & Liu, HK 2009, 'Nanostructured metal oxides as electrode materials for electrochemical capacitors', Journal of Nanoscience & Nanotechnology, vol. 9, no. 2, pp. 1263-1267.
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In this study, nanostructured transition metal oxides, such as Co3O4, NiO and MnO2 were comprehensively studied and reported as promising electrode materials for electrochemical capacitors. The materials have been obtained by solution or spray solution techniques, which are cost-effective and promising for industry application. All materials feature a large specific surface area, which can reach up to 270 m2/g. The high surface area is a compulsory condition for high capacitance. The best MnO2 materials yielded up to 406 F/g.

Krimmer, D, Loseli, M, Hughes, JM, Oliver, BG, Moir, LM, Hunt, NH, Black, JL & Burgess, JK 2009, 'CD40 and OX40 ligand are differentially regulated on asthmatic airway smooth muscle', Allergy, vol. 64, no. 7, pp. 1074-1082.
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Background: CD40 and OX40 Ligand (OX40L) are cell-surface molecules expressed on airway smooth muscle (ASM) that can enhance inflammatory cell activation and survival. The aim of this study was to examine the effect of tumour necrosis factor-alpha (TNF-a) and interferon-gamma (IFN-?) on ASM CD40 and OX40L expression. Methods: CD40 and OX40L expression on human ASM cells from asthmatic and nonasthmatic donors following stimulation with TNF-a and/or IFN-? was measured using cell-surface enzyme-linked immunosorbent assay (ELISA) and flow cytometry. Involvement of signalling pathway was investigated with pharmacological inhibitors. Soluble TNF receptor levels were quantified by ELISA. Results: Interferon-? and TNF-a synergistically increased CD40 expression to a greater extent on asthmatic than on nonasthmatic ASM. In contrast, IFN-? reduced TNF-a-induced OX40L expression to a similar extent in both cell types. TNF-a and IFN-? induced CD40 via nuclear factor-?B (NF-?B) and signal transducer and activator of transcription-3 in both cell types and modulated OX40L via NF-?B and c-Jun N terminal kinase in nonasthmatic cells. Similar effects on the induction of OX40L in asthmatic cells were seen with NF-?B, but these were not statistically significant. The reduced OX40L expression with TNF-a and IFN-? involved extracellular regulated kinase 1/2 activation. Conclusion: Asthmatic ASM may modulate airway inflammation locally by increasing CD40 and OX40L expression in response to cytokines. IFN-? may regulate ASM pro-inflammatory actions by differentially modulating ASM CD40 and OX40L expression.

Kropinski, AM, Borodovsky, M, Carver, TJ, Cerdeño-Tárraga, AM, Darling, A, Lomsadze, A, Mahadevan, P, Stothard, P, Seto, D, Van Domselaar, G & Wishart, DS 2009, 'In silico identification of genes in bacteriophage DNA.', Methods in molecular biology (Clifton, N.J.), vol. 502, pp. 57-89.
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One of the most satisfying aspects of a genome sequencing project is the identification of the genes contained within it.These are of two types: those which encode tRNAs and those which produce proteins. After a general introduction on the properties of protein-encoding genes and the utility of the Basic Local Alignment Search Tool (BLASTX) to identify genes through homologs, a variety of tools are discussed by their creators. These include for genome annotation: GeneMark, Artemis, and BASys; and, for genome comparisons: Artemis Comparison Tool (ACT), Mauve, CoreGenes, and GeneOrder.

Labbate, M, Case, RJ & Stokes, HW 2009, 'The integron/gene cassette system: an active player in bacterial adaptation.', Methods in molecular biology (Clifton, N.J.), vol. 532, pp. 103-125.
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The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9% of sequenced bacterial genomes. Overall, gene diversity in cassettes is extraordinarily high, suggesting that the integron/gene cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene cassette system highlighting characteristics associated with this system, diversity of elements contained within it, and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene cassettes and gene cassette arrays are discussed.

Lamb, PJ, Leslie, LM, Timmer, RP & Speer, MS 2009, 'Multidecadal variability of Eastern Australian dust and Northern New Zealand sunshine: Associations with Pacific climate system', JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, vol. 114.
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Lanyon, BP & Langford, NK 2009, 'Experimentally generating and tuning robust entanglement between photonic qubits', NEW JOURNAL OF PHYSICS, vol. 11.
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Lapine, M 2009, 'Tunable metamaterials: the key step to practical application', SPIE Newsroom.
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Lapine, M, Powell, D, Gorkunov, M, Shadrivov, I, Marques, R & Kivshar, Y 2009, 'Structural tunability in metamaterials', APPLIED PHYSICS LETTERS, vol. 95, no. 8.
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Lauro, FM, McDougald, D, Thomas, T, Williams, TJ, Egan, S, Rice, S, DeMaere, MZ, Ting, L, Ertan, H, Johnson, J, Ferriera, S, Lapidus, A, Anderson, I, Kyrpides, N, Munk, AC, Detter, C, Han, CS, Brown, MV, Robb, FT, Kjelleberg, S & Cavicchioli, R 2009, 'The genomic basis of trophic strategy in marine bacteria', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 106, no. 37, pp. 15527-15533.
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Lawrence, FJ, Botten, LC, Dossou, KB, de Sterke, CM & McPhedran, RC 2009, 'Impedance of square and triangular lattice photonic crystals', PHYSICAL REVIEW A, vol. 80, no. 2.
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Le Gac, G, Rahmani, A, Seassal, C, Picard, E, Hadji, E & Callard, S 2009, 'Tuning Of An Active Photonic Crystal Cavity By An Hybrid Silica/Silicon Near-Field Probe', Optics Express, vol. 17, no. 24, pp. 21672-21679.
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The influence of a near-field tip on the spectral characteristics of a resonant mode of an active photonic crystal micro-cavity was investigated. The wavelength shift of the mode was theoretically and experimentally demonstrated and evaluated as a function of the nature and the position of the tip above the cavity. Experiment showed that the shift induced is ten times higher with a Si-coated silica probe than with a bare silica tip: a shift until 2 nm was reached with Si-coated tip whereas the shift with bare silica tip is in the range of the tenth of nanometer, for wavelengths around 1,55 ìm.

Lee, ETC, Wong, FWS & Lim, CED 2009, 'A Modified Technique of LAVH with the Biswas Uterovaginal Elevator', Journal of Minimally Invasive Gynecology, vol. 16, no. 6, pp. 755-760.
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This was a review of 512 consecutive cases of laparoscopic-assisted vaginal hysterectomy (LAVH) for benign gynecologic conditions with the Biswas uterovaginal elevator (BUVE) from February 2003 through June 2008. A single operator, using the BUVE and a standard surgical protocol, performed all hysterectomies. Variables analysis included patient demographics, operative times, uterine weight, hospital stay, intraoperative blood loss, and intraoperative and postoperative complications. LAVH was successfully performed for all patients. The median operative time was 70.07 minutes, range 35 to 250 minutes. The median uterine weight was 301.97 g (range 43-1690 g). The median estimated blood loss was 118.19 mL (range 5-1600 mL). The median length of hospital stay was 1.38 days (range 1-6 days). The overall complication rate was 6.25%. No case sustained injury to the ureter or major vessels or required conversion. LAVH with the BUVE eliminates the need for laparotomy in performing hysterectomies for benign gynecologic disorders. The BUVE can achieve a full range of uterine manipulation. It allows safe and easy dissection of the bladder and precise colpotomy through simultaneous uterine elevation and delineation of vaginal fornices. Prevention of ureteric injury is made possible by moving the surgical field away from the ureter. The technique described can be used to handle a wide variety of diseases and situations and has been shown to be safe, fast, easy to learn, and reproducible and carries few complications. © 2009 AAGL.

Lee, JH & Zaslawski, CJ 2009, 'Blinding in Clinical Trials', Australian Journal of Acupuncture and Chinese Medicine, vol. 4, no. 2, pp. 32-33.
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Blinding is an important design feature to control bias in randomised controlled trials. Placebos that are improperly formulated or implemented may introduce bias into a trial, thereby making the reporting and success of blinding inadequate.

Leif, RC, Yang, S, Jin, D, Piper, J, Vallarino, LM, Williams, JW & Zucker, RM 2009, 'Calibration beads containing luminescent lanthanide ion complexes', JOURNAL OF BIOMEDICAL OPTICS, vol. 14, no. 2.
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Leong, G, Gorrie, C, Ng, K, Rutkowski, S & Waite, P 2009, 'Electrical perceptual threshold testing: A validation study', Journal Of Spinal Cord Medicine, vol. 32, no. 2, pp. 140-146.
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Background/Objective: To investigate inter-rater and intra-rater reliability of electrical perceptual threshold (EPT) testing in assessing somatosensory function in healthy volunteers. Study Design: Prospective experimental. Setting: Hospital-based spina

Lessard, BD, Wallman, JF & Dowton, M 2009, 'Incorrect report of cryptic species within Chrysomya rufifacies (Diptera : Calliphoridae)', INVERTEBRATE SYSTEMATICS, vol. 23, no. 6, pp. 507-514.
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Li, L, Yu, Q, Su, Z & van der Tol, C 2009, 'A simple method using climatic variables to estimate canopy temperature, sensible and latent heat fluxes in a winter wheat field on the North China Plain', Hydrological Processes, vol. 23, no. 5, pp. 665-674.
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Estimation of evapotranspiration from a crop field is of great importance for detecting crop water status and proper irrigation scheduling. The Penman-Monteith equation is widely viewed as the best method to estimate evapotranspiration but it requires canopy resistance, which is very difficult to determine in practice. This paper presents a simple method simplified from the Penman-Monteith equation for estimating canopy temperature (Tc). The proposed method is a biophysically-sound extended version of that proposed by Todorovic. The estimated canopy temperature is used to calculate sensible heat flux, and then latent heat flux is calculated as the residual of the surface energy balance. An eddy covariance (EC) system and an infrared thermometer (IRT) were installed in an irrigated winter wheat field on the North China Plain in 2004 and 2005, to measure Tc, and sensible and latent heat fluxes were used to test the modified Todorovic model (MTD). The results indicate that the original Todorovic model (TD) severely underestimates Tc and sensible heat flux, and hence severely overestimates the latent heat flux. However, the MTD model has good capability for estimating Tc, and gives acceptable results for latent heat flux at both half-hourly and daily scales. The MTD model results also agreed well with the evapotranspiration calculated from the measured Tc.

Lim, CED, Wilkinson, JM, Wong, WSF & Cheng, NCL 2009, 'Effect of Acupuncture on Induction of Labor', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 15, no. 11, pp. 1209-1214.
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Lim, CED, Yii, MF, Cheng, NCL & Chow, YKM 2009, 'The role of micronutrients in pregnancy', Australian Family Physician, vol. 38, no. 12, pp. 980-984.
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Background: The antenatal shared care model has become increasingly popular among Australian women as the preferred mode of pregnancy care. General practitioners are often asked by their pregnant women patients about the nutrients needed during pregnancy. Objective: This article discusses the role of various micronutrients and trace elements needed in pregnancy, and provides daily intake recommendations of these nutrients as a reference point. Discussion: Much attention has been given to micronutrients such as folate and iron, but less regard to other trace elements that are also important in pregnancy. Encouraging a balanced diet and ensuring the adequacy of these micronutrients is essential for minimising pregnancy complications. However, GPs should also be aware of the maximum level of recommended intakes and any possible adverse effects.

Lim, D & Wong, F 2009, 'Syndrome X', JOURNAL OF COMPLEMENTARY MEDICINE, vol. 8, no. 6, pp. 39-40.

Lim, D, Wong, F & Wong, V 2009, 'Menopausal syndrome', JOURNAL OF COMPLEMENTARY MEDICINE, vol. 8, no. 2, pp. 55-57.

Lim, DCE, Cheng, LNC & Wong, FWS 2009, 'Could it be Henoch-Schönlein purpura?', Australian Family Physician, vol. 38, no. 5, pp. 321-324.
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Background: Henoch-Schönlein purpura is the most common form of systemic vasculitis in the paediatric setting with 90% of cases occuring in childhood. Although diagnosis in the primary care setting may be difficult, it is vital in order to avoid significant complications. Objective: This article outlines the pathogenesis, clinical manifestations and classification of Henoch-Schönlein purpura and details evidence based investigations and management. Discussion: Henoch-Schönlein purpura is a self limiting disease characterised by a tetrad of clinical manifestations that vary in occurrence and order of presentation. There is no single diagnostic test to confirm Henoch-Schönlein purpura; diagnosis depends on recognition of clinical manifestations. Management usually occurs in the ambulatory setting and is mainly supportive. Priorities include symptom relief and preventive therapy to reduce the risk of complications. Further trials to clarify the role of glucocorticosteroids are needed before a definitive role for steroids in the management of Henoch-Schönlein purpura can be established.

Lim, DCE, Xue, CC, Wong, FWS, O'Sullivan, AJ & Jian, PL 2009, 'Acupuncture for polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, no. 2.
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Liu, H, Wang, G, Park, J, Wang, J, Liu, H & Zhang, C 2009, 'Electrochemical performance of alpha-Fe2O3 nanorods as anode material for lithium-ion cells', Electrochimica Acta, vol. 54, no. 6, pp. 1733-1736.
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Alpha-Fe2O3 nanorods were synthesized by a facile hydrothermal method. The as-prepared alpha-Fe2O3 nanorods have a high quality crystalline nanostructure with diameters in the range of 6080 nm and lengths extending from 300 to 500 nm. The crystal structure of the alpha-Fe2O3 nanorods was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The alpha-Fe2O3 nanorod anodes exhibit a stable specific capacity of 800 mAh/g. This indicates significantly improved electrochemical performance in lithium-ion cells, compared to that of commercial microcrystalline alpha-Fe2O3 powders.

Liu, H, Wexler, D & Wang, G 2009, 'One-pot facile synthesis of iron oxide nanowires as high capacity anode materials for lithium ion batteries', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 487, no. 1-2, pp. L24-L27.
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Lobo, G, Waite, KA, Planchon, P, Todd, R, Nassif, N & Eng, C 2009, 'Germline and somatic cancer-associated mutations in the ATP-binding motifs of PTEN influence its subcellular localization and tumor suppressive function', Human Molecular Genetics, vol. 18, no. 15, pp. 2851-2862.
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Germline and somatic PTEN mutations are found in Cowden syndrome (CS) and multiple sporadic malignancies, respectively. PTEN function appears to be modulated by subcellular compartmentalization, and mislocalization may affect function. We have shown that cellular ATP levels affect nuclear PTEN levels. Here, we examined the ATP-binding capabilities of PTEN and functional consequences, relevant to cancer-associated mutations. PTEN mutation analysis of CS patients and sporadic colorectal carcinomas and comparative aminoacid analysis were utilized to identify mutations in ATP-binding motifs. The ability of wild-type (WT) or mutant PTEN to bind ATP was assessed by ATP-agarose-binding assays. Subcellular fractionation, western blotting, confocal microscopy and growth assays were used to determine relative nuclear-cytoplasmic localization and function. Somatic colorectal carcinoma-derived PTEN missense mutations were associated with nuclear mislocalization. These mutations altered cellular proliferation, apoptosis and anchorage-dependent growth. Examination of PTEN's amino acid sequence revealed these mutations resided in previously undescribed ATP-binding motifs (c.60-73; c.122-136). In contrast to WT PTEN, both cancer-associated somatic and germline-derived PTEN missense mutations, which lie within the ATP-binding motifs, result in mutant PTEN that does not bind ATP efficiently. We also show that CS patients with germline ATP-binding motif-mutations had nuclear PTEN mislocalization. Of four unrelated patients with functional germline ATP-binding domain mutations, all three female patients had breast cancers. Germline and somatic mutations within PTEN's ATP-binding domain play important pathogenic roles in both heritable and sporadic carcinogenesis by PTEN nuclear mislocalization resulting in altered signaling and growth. Manipulation of ATP may represent novel therapies in tumors with such PTEN alterations.

Lord, MS, Pasqui, D, Barbucci, R & Milthorpe, BK 2009, 'Protein adsorption on derivatives of hyaluronic acid and subsequent cellular response', Journal of Biomedical Materials Research Part A, vol. 91A, no. 3, pp. 635-646.
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The modulation of biological interactions with artificial surfaces is a vital aspect of biomaterials research. Serum protein adsorption onto photoreactive hyaluronic acid (Hyal-N3) and its sulfated derivative (HyalS-N3) was analyzed to determine extent of protein interaction and protein conformation as well as subsequent cell adhesion. There were no significant (p < 0.01) differences in the amount of protein adsorbed to the two polymers; however, proteins were found to be more loosely bound on HyalS-N3 compared with Hyal-N3. Fibronectin was adsorbed onto HyalS-N3 in such an orientation as to allow the availability of the cell binding region, while there was more restricted access to this region on fibronectin adsorbed onto Hyal-N3. This was confirmed by reduced cell adhesion on fibronectin precoated Hyal-N3 compared with fibronectin precoated HyalS-N3. Minimal cell adhesion was observed on albumin and serum precoated Hyal-N3. The quartz crystal microbalance confirmed that specific cell-surface interactions were experienced by cells interacting with the fibronectin precoated polymers and serum precoated HyalS-N3

Lowther, J, Robinson, MW, Donnelly, SM, Xu, W, Stack, CM, Matthews, J & Dalton, JP 2009, 'The Importance of pH in Regulating the Function of the Fasciola hepatica Cathepsin L1 Cysteine Protease', Plos Neglected Tropical Diseases, vol. 3, no. 1, pp. 1-11.
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The helminth parasite Fasciola hepatica secretes cathepsin L cysteine proteases to invade its host, migrate through tissues and digest haemoglobin, its main source of amino acids. Here we investigated the importance of pH in regulating the activity and functions of the major cathepsin L protease FheCL1. The slightly acidic pH of the parasite gut facilitates the auto-catalytic activation of FheCL1 from its inactive proFheCL1 zymogen; this process was similar to 40-fold faster at pH 4.5 than at pH 7.0. Active mature FheCL1 is very stable at acidic and neutral conditions ( the enzyme retained similar to 45% activity when incubated at 37 degrees C and pH 4.5 for 10 days) and displayed a broad pH range for activity peptide substrates and the protein ovalbumin, peaking between pH 5.5 and pH 7.0. This pH profile likely reflects the need for FheCL1 to function both in the parasite gut and in the host tissues. FheCL1, however, could not cleave its natural substrate Hb in the pH range pH 5.5 and pH 7.0; digestion occurred only at pH <= 4.5, which coincided with pH-induced dissociation of the Hb tetramer. Our studies indicate that the acidic pH of the parasite relaxes the Hb structure, making it susceptible to proteolysis by FheCL1. This process is enhanced by glutathione (GSH), the main reducing agent contained in red blood cells. Using mass spectrometry, we show that FheCL1 can degrade Hb to small peptides, predominantly of 4-14 residues, but cannot release free amino acids. Therefore, we suggest that Hb degradation is not completed in the gut lumen but that the resulting peptides are absorbed by the gut epithelial cells for further processing by intracellular di- and amino-peptidases to free amino acids that are distributed through the parasite tissue for protein anabolism.

Luo, M, Platten, D, Chaudhury, A, Peacock, J & Dennis, ES 2009, 'Expression, Imprinting, and Evolution of Rice Homologs of the Polycomb Group Genes', Molecular Plant, vol. 2, no. 4, pp. 711-723.
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Polycomb group proteins (PcG) play important roles in epigenetic regulation of gene expression. Some core PcG proteins, such as Enhancer of Zeste (E(z)), Suppressor of Zeste (12) (Su(z)12), and Extra Sex Combs (ESC), are conserved in plants. The rice genome contains two E(z)-like genes, OsiEZ1 and OsCLF, two homologs of Su(z)12, OsEMF2a and OsEMF2b, and two ESC-like genes, OsFIE1 and OsFIE2. OsFIE1 is expressed only in endosperm; the maternal copy is expressed while the paternal copy is not active. Other rice PcG genes are expressed in a wide range of tissues and are not imprinted in the endosperm. The two E(z)-like genes appear to have duplicated before the separation of the dicots and monocots; the two homologs of Su(z)12 possibly duplicated during the evolution of the Gramineae and the two ESClike genes are likely to have duplicated in the ancestor of the grasses. No homologs of the Arabidopsis seed-expressed PcG genes MEA and FIS2 were identified in the rice genome. We have isolated T-DNA insertion lines in the rice homologs of three PcG genes. There is no autonomous endosperm development in these T-DNA insertion lines. One line with a T-DNA insertion in OsEMF2b displays pleiotropic phenotypes including altered flowering time and abnormal flower organs, suggesting important roles in rice development for this gene.

Luo, X, Lim, CED, Huang, C, Wu, J, Wong, WSF & Cheng, NCL 2009, 'Heterotopic pregnancy following in vitro fertilization and embryo transfer: 12 cases report', Archives of Gynecology and Obstetrics, vol. 280, no. 2, pp. 325-329.
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Objective: To evaluate the incidence, predisposing factors, early diagnosis and treatment options of heterotopic pregnancy (HP) following in vitro fertilization and embryo transfer (IVF-ET) procedure. Methods: A retrospective review study was performed to identify the HP cases after IVF-ET at the Reproductive Centre in Guangdong Women and Children's Hospital in China between the years of 2002-2007. Results: Twelve out of 1,476 pregnancies (0.81%) were diagnosed for HP, of which nine patients elected for exploratory salpingectomy, two patients received selective fetal reduction by embryo aspiration under ultrasound guidance, and one patient opted for expectant treatment. Postoperatively, four intrauterine pregnancies were continued to develop until term while two were delivered at 35 weeks of gestation. The achievement ratio of continuous pregnancy was 66.7% (6/9). Conclusion: The incidence of HP is increasing due to the widespread use of assisted reproductive technology. An early transvaginal sonography performed by experienced radiologist/radiographer is considered to be essential and beneficial in establishing early diagnosis of HP. Both salpingectomy and selective fetal reduction by embryo aspiration can be administered as one of the effective therapies for HP with the optimal outcome of intrauterine pregnancy. © 2009 Springer-Verlag.

Lutherborrow, M, Appavoo, M, Simpson, AM & Tuch, BE 2009, 'Gene expression profiling of HUH7-ins Lack of a granulogenic function for Chromogranin A', Islets, vol. 1, no. 1, pp. 60-72.
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Previously, the insulin producing liver cell line HUH7-ins has been shown to synthesize, store and secrete insulin in response to glucose via secretory granules. The current study characterized the gene expression profile of HUH7-ins with the aim to identify changes possibly involved in the formation of granules. Additionally, experiments were conducted to determine the influence of chromograninA (egA) on secretory granule biogenesis (5GB) in HUH7-ins. Expression of 165 genes were significantly changed in HUH7-ins, though interestingly the majority of secretory granule associated genes, such as the chromogranins were unchanged. egA was over-expressed in glucose unresponsive HUH7-ins cells to test whether egA played a role in 5GB and would restore the regulated secretory phenotype. Over expression affected neither the storage nor regulated secretion of insulin. These data suggest that 5GB may by regulated at a post-transcriptional level with no evidence to indicate that egA regulates SGB in the cell line HUH7-ins.

Lutherborrow, MA, Appavoo, M, Simpson, AM & Tuch, BE 2009, 'Gene expression profiling of HUH7-ins: lack of a granulogenic function for chromogranin A.', Islets, vol. 1, no. 1, pp. 62-74.
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Previously, the insulin producing liver cell line HUH7-ins has been shown to synthesize, store and secrete insulin in response to glucose via secretory granules. The current study characterized the gene expression profile of HUH7-ins with the aim to identify changes possibly involved in the formation of granules. Additionally, experiments were conducted to determine the influence of chromogranin A (CgA) on secretory granule biogenesis (SGB) in HUH7-ins. Expression of 165 genes were significantly changed in HUH7-ins,though interestingly the majority of secretory granule associated genes, such as the chromogranins were unchanged. CgA was over-expressed in glucose unresponsive HUH7-ins cells to test whether CgA played a role in SGB and would restore the regulated secretory phenotype. Over-expression affected neither the storage nor regulated secretion of insulin. These data suggest that SGB may by regulated at a post-transcriptional level with no evidence to indicate that CgA regulates SGB in the cell line HUH7-ins.

Maaroof, AI, Cortie, MB, Harris, N & Wieczorek, L 2009, 'Mie and Bragg plasmons in subwavelength silver semi-shells', Small, vol. 4, no. 12, pp. 2292-2299.
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Machado, A, Wu, Y, Yang, Y, Llewellyn, D & Dennis, ES 2009, 'The MYB transcription factor GhMYB25 regulates early fibre and trichome development', PLANT JOURNAL, vol. 59, no. 1, pp. 52-62.
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Little is still known about the developmental control of the long seed coat trichomes of cotton (Gossypium hirsutum L.). In Arabidopsis, leaf trichome initiation is regulated by a group of well-defined transcription factors that includes MYB and homeodomain types. Many MYBs are expressed in fibres, but their roles in fibre development remain unclear. We analysed the function of one MYB transcription factor, GhMYB25, identified from transcriptome comparisons between wild-type and fibreless cotton mutants. A GhMYB25 promoter-GUS construct in transgenic cotton was expressed in the epidermis of ovules, developing fibre initials and fibres, in the trichomes of a number of tissues including leaves, stems and petals, as well as in the anthers, pollen and the epidermal layers of roots and root initials, but not in root hairs. Cotton is an allotetraploid with two very similar GhMYB25 genes that were silenced by a single RNAi construct. GhMYB25-silenced cotton showed alterations in the timing of rapid fibre elongation, resulting in short fibres, dramatic reductions in trichomes on other parts of the plant, and reductions in seed production. Reciprocal crosses between transgenic and nontransgenic plants indicated that pollen and ovule viability per se were not disrupted. Ectopic over-expression of GhMYB25 had more subtle impacts, with increases in cotton fibre initiation and leaf trichome number. High expression appeared to adversely affect fertility. Our results provide convincing evidence for a role of GhMYB25, like other MIXTA-like MYBS, in regulating specialized outgrowths of epidermal cells, including, in this case, cotton fibres.

Macnamara, J 2009, 'Public relations in the interactive age: New practices, not just new media', Asia Pacific Public Relations Journal, vol. 10, pp. 1-16.
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An analysis of public relations practice through content analysis of 10 media spokesperson training programs, reporting evidence of a 'control paradigm' of communication, with focus on "control" and "managing" messages and the media, and lack of two-way interactive communication.

MacNamara, S & Burrage, K 2009, 'Krylov and steady-state techniques for the solution of the chemical master equation for the mitogen-activated protein kinase cascade', Numerical Algorithms, vol. 51, no. 3, pp. 281-307.
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Models of chemical kinetics in which some reactions are much faster than others are often treated by a type of quasi-steady-state approximation (QSSA). The total QSSA (tQSSA) was introduced for models of Michaelis-Menten enzyme kinetics and shown to be valid over a wider parameter regime than the usual QSSA. Here, we extend the tQSSA to the Mitogen-Activated Protein Kinase Cascade, an important signaling system in cell biochemistry. These approximations were first developed in a deterministic setting, but here we also describe how to incorporate this approximation into the discrete and stochastic framework of the Chemical Master Equation (CME). The CME gives rise to a large-scale matrix exponential that can be solved by Krylov methods in combination with operator splitting and the tQSSA. © 2008 Springer Science+Business Media, LLC.

Mahmoodian, S, McPhedran, RC, de Sterke, CM, Dossou, KB, Poulton, CG & Botten, LC 2009, 'Single and coupled degenerate defect modes in two-dimensional photonic crystal band gaps', PHYSICAL REVIEW A, vol. 79, no. 1.
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Mahmoodian, S, Poulton, CG, Dossou, KB, McPhedran, RC, Botten, LC & de Sterke, CM 2009, 'Modes of shallow photonic crystal waveguides: semi-analytic treatment', Optics Express, vol. 17, no. 22, pp. 19629-19643.
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We investigate the formation of photonic crystal waveguide (PCW) modes within the framework of perturbation theory. We derive a differential equation governing the envelope of PCW modes constructed from weak perturbations using an effective mass formulation based on the Luttinger-Kohn method from solid-state physics. The solution of this equation gives the frequency of the mode and its field. The differential equation lends itself to simple analytic approximations which reduce the problem to that of solving slab waveguide modes. By using this model, we demonstrate that the nature of the projected band structure and corresponding Bloch functions are central to the behaviour of PCW modes. With this understanding, we explain why the odd mode in a hexagonal PCW spans the entire Brillouin zone while the even mode is cut off.

Mai, K, Sharman, PA, Walker, RA, Katrib, M, De Souza, D, McConville, M, Wallach, M, Belli, SI, Ferguson, DJ & Smith, NC 2009, 'Oocyst wall formation and composition in coccidian parasites', Memorias do Instituto Oswaldo Cruz, vol. 104, no. 2, pp. 281-289.
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The oocyst wall of coccidian parasites is a robust structure that is resistant to a variety of environmental and chemical insults. This resilience allows oocysts to survive for long periods, facilitating transmission from host to host. The wall is bilayered and is formed by the sequential release of the contents of two specialized organelles - wall forming body 1 and wall forming body 2 - found in the macrogametocyte stage of Coccidia. The oocyst wall is over 90% protein but few of these proteins have been studied. One group is cysteine-rich and may be presumed to crosslink via disulphide bridges, though this is yet to be investigated. Another group of wall proteins is rich in tyrosine. These proteins, which range in size from 8-31 kDa, are derived from larger precursors of 56 and 82 kDa found in the wall forming bodies. Proteases may catalyze processing of the precursors into tyrosine-rich peptides, which are then oxidatively crosslinked in a reaction catalyzed by peroxidases. In support of this hypothesis, the oocyst wall has high levels of dityrosine bonds. These dityrosine crosslinked proteins may provide a structural matrix for assembly of the oocyst wall and contribute to its resilience.

Maity, A, Carroll, RJ, Mammen, E & Chatterjee, N 2009, 'Testing in semiparametric models with interaction, with applications to gene-environment interactions', JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, vol. 71, pp. 75-96.
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Manso-Silvan, L, Vilei, EM, Sachse, K, Djordjevic, SP, Thiaucourt, F & Frey, J 2009, 'Mycoplasma leachii sp. nob. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and reclassification of Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides sbusp. capri', International Journal of Systematic and Evolutionary Microbiology, vol. 59, pp. 1353-1358.
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The Mycoplasma mycoides cluster consists of six pathogenic mycoplasmas causing disease in ruminants, which share many genotypic and phenotypic traits. The M. mycoides cluster comprises five recognized taxa: Mycoplasma mycoides subsp. mycoides Small Colony (MmmSC), M. mycoides subsp. mycoides Large Colony (MmmLC), M. mycoides subsp. capri (Mmc), Mycoplasma capricolum subsp. capricolum (Mcc) and M. capricolum subsp. capripneumoniae (Mccp). The group of strains known as Mycoplasma sp. bovine group 7 of Leach (MBG7) has remained unassigned, due to conflicting data obtained by different classification methods. In the present paper, all available data, including recent phylogenetic analyses, have been reviewed, resulting in a proposal for an emended taxonomy of this cluster: (i) the MBG7 strains, although related phylogenetically to M. capricolum, hold sufficient characteristic traits to be assigned as a separate species, i.e. Mycoplasma leachii sp. nov. (type strain, PG50T = N29T = NCTC 10133T = DSM 21131T); (ii) MmmLC and Mmc, which can only be distinguished by serological methods and are related more distantly to MmmSC, should be combined into a single subspecies, i.e. Mycoplasma mycoides subsp. capri, leaving M. mycoides subsp. mycoides (MmmSC) as the exclusive designation for the agent of contagious bovine pleuropneumonia. A taxonomic description of M. leachii sp. nov. and emended descriptions of M. mycoides subsp. mycoides and M. mycoides subsp. capri are presented. As a result of these emendments, the M. mycoides cluster will hereafter be composed of five taxa comprising three subclusters, which correspond to the M. mycoides subspecies, the M. capricolum subspecies and the novel species M. leachii.

Mantri, VA, Thakur, MC, Kumar, M, Reddy, CRK & Jha, B 2009, 'The carpospore culture of industrially important red alga Gracilaria dura (Gracilariales, Rhodophyta)', AQUACULTURE, vol. 297, no. 1-4, pp. 85-90.
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Maric, S, Donnelly, SM, Robinson, MW, Skinner-Adams, TS, Trenholme, K, Gardiner, D, Dalton, JP, Stack, CM & Lowther, J 2009, 'The M17 Leucine Aminopeptidase of the Malaria Parasite Plasmodium falciparum: Importance of Active Site Metal Ions in the Binding of Substrates and Inhibitors', Biochemistry, vol. 48, no. 23, pp. 5435-5439.
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The M17 leucine aminopeptidase of the intraerythrocytic stages of the malaria parasite Plasmodium falciparum (PfLAP) plays it role in releasing amino acids from host hemoglobin that are used for parasite protein synthesis, growth, and development. This enzyme represents a target at which new antimalarials Could be designed since metalloaminopeptidase inhibitors prevent the growth of the parasites in vitro and in vivo. A study on the metal ion binding characteristics of recombinant P. falciparum M17 leucine aminopeptidase (rPfLAP) shows that the active site of this exopeptidase contains two metal-binding sites, a readily exchangeable site (site 1) and a tight binding site (site 2). The enzyme retains activity when the metal ion is removed from site 1, while removal of metal ions from both sites results in an inactive apoenzyme that cannot be reactivated by the addition of divalent metal cations. The metal Ion at site I is readily exchangeable with several divalent metal ions and displays a preference in the order of preference Zn2+ > Mn2+ > Co2+ > Mg2+. While it is likely that native PfLAP contains a Zn2+ in site 2, the metal ion located in site 1 may be dependent on the type and concentration of metal ions in the cytosolic compartment of the parasite. Importantly, the type of metal ion present at site 1 influences not only the catalytic efficiency of the enzyme for peptide Substrates but also the mode of binding by bestatin, a metal-chelating inhibitor of M17 aminopeptidases with antimalarial activity.

Martelli, C, Canning, J, Reimers, JR, Sintic, M, Stocks, D, Khoury, T & Crossley, M 2009, 'Evanescent-Field Spectroscopy Using Structured Optical Fibers: Detection Of Charge-Transfer At The Porphyrin-Silica Interface', Journal of the American Chemical Society, vol. 131, no. 8, pp. 2925-2933.
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The fabrication of porphyrin thin films derived from dichloro[5,10,15,20-tetra(heptyl)porphyrinato]tin(IV) [Cl-Sn(THP)-Cl] in the holes of photonic crystal fibers over 90 cm in length is described. Evanescent field spectroscopy (EFS) is used to investigate the interfacial properties of the films, with the high surface optical intensity and the long path length combining to produce significant absorption. By comparison with results obtained for similar films formed from Cl-Sn(THP)-Cl inside fused-silica cuvettes and on glass slides, the film is shown to be chemisorbed as a surface Si-O-Sn(THP)-X (X = Cl or OH) species. In addition to the usual porphyrin Q and Soret bands, new absorptions in the in-fiber films are observed by EFS at 445 nm and between 660-930 nm. The 660-930 nm band is interpreted as a porphyrin to silicon charge-transfer transition and postulated to arise following chemisorption at mechanical-strain induced defect sites on the silica surface. Such defect sites are caused by the optical fiber production process and are less prevalent on other glass surfaces. EFS within optical fibers therefore offers new ways for understanding interface phenomena such as surface adsorbates on glass. Such understanding will benefit all devices that exploit interface phenomena, both in optical fibers and other integrated waveguide forms. They may be directly exploited to create ultrasensitive molecular detectors and could yield novel photonic devices.

Martinez, JG, Huang, JZ, Burghardt, RC, Barhoumi, R & Carroll, RJ 2009, 'USE OF MULTIPLE SINGULAR VALUE DECOMPOSITIONS TO ANALYZE COMPLEX INTRACELLULAR CALCIUM ION SIGNALS', ANNALS OF APPLIED STATISTICS, vol. 3, no. 4, pp. 1467-1492.
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Martinez, JG, Huang, JZ, Burghardt, RC, Barhoumi, R & Carroll, RJ 2009, 'Use of multiple singular value decompositions to analyze complex intracellular calcium ion signals', Annals of Applied Statistics, vol. 3, no. 4, pp. 1467-1492.
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We compare calcium ion signaling (Ca2+) between two exposures; the data are present as movies, or, more prosaically, time series of images. This paper describes novel uses of singular value decompositions (SVD) and weighted versions of them (WSVD) to extract the signals from such movies, in a way that is semi-automatic and tuned closely to the actual data and their many complexities. These complexities include the following. First, the images themselves are of no interest: all interest focuses on the behavior of individual cells across time, and thus, the cells need to be segmented in an automated manner. Second, the cells themselves have 100+ pixels, so that they form 100+ curves measured over time, so that data compression is required to extract the features of these curves. Third, some of the pixels in some of the cells are subject to image saturation due to bit depth limits, and this saturation needs to be accounted for if one is to normalize the images in a reasonably unbiased manner. Finally, the Ca2+ signals have oscillations or waves that vary with time and these signals need to be extracted. Thus, our aim is to show how to use multiple weighted and standard singular value decompositions to detect, extract and clarify the Ca2+ signals. Our signal extraction methods then lead to simple although finely focused statistical methods to compare Ca2+ signals across experimental conditions. © Institute of Mathematical Statistics, 2009.

Maslovskaya, O, Brown, JJ & Padmadas, S 2009, 'Disentangling the complex association between female genital cutting and HIV among Kenyan women', Journal of Biosocial Science, vol. 41, no. 6, pp. 815-830.
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Female genital cutting (FGC) is a widespread cultural practice in Africa and the Middle East, with a number of potential adverse health consequences for women. It was hypothesized by Kun (1997) that FGC increases the risk of HIV transmission through a nu

Matic, J, Terry, TD, Bockel, DV, Maddocks, T, Tinworth, D, Jennings, MP, Djordjevic, SP & Walker, M 2009, 'Development of Non-antibiotic-resistant, Chromosomally based, constitutive and inducible expression systems for aroA-Attenuated Salmonella enterica Serovar Typhimurium', Infection And Immunity, vol. 77, no. 5, pp. 1817-1826.
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Live-vaccine delivery systems expressing two model antigens from Mycoplasma hyopneumoniae, F2P97 (Adh) and NrdF, were constructed using Salmonella enterica serovar Typhimurium aroA (STM-1), and immunogenicity in mice was evaluated. Recombinant plasmid-based expression (PBE) and chromosomally based expression (CBE) systems were constructed. The PBE system was formed by cloning both antigen genes into pJLA507 to create an operon downstream of temperature-inducible promoters. Constitutive CBE was achieved using a promoter-trapping technique whereby the promoterless operon was stably integrated into the chromosome of STM-1, and the expression of antigens was assessed. The chromosomal position of the operon was mapped in four clones. Inducible CBE was obtained by using the in vivo-induced sspA promoter and recombining the expression construct into aroD. Dual expression of the antigens was detected in all systems, with PBE producing much larger quantities of both antigens. The stability of antigen expression after in vivo passage was 100% for all CBE strains recovered. PBE and CBE strains were selected for comparison in a vaccination trial. The vaccine strains were delivered orally into mice, and significant systemic immunoglobulin M (IgM) and IgG responses against both antigens were detected among all CBE groups. No significant immune response was detected using PBE strains. Expression of recombinant antigens in S. enterica serovar Typhimurium aroA from chromosomally located strong promoters without the use of antibiotic resistance markers is a reliable and effective method of inducing a significant immune response.

Matthews, Z, PADMADAS, SS, Hutter, I, McEachran, J & Brown, JJ 2009, 'Does early childbearing and a sterilization-focused family planning programme in India fuel population growth?', Demographic Research, vol. 20, pp. 693-720.
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Recent stagnation in the reduction of infant mortality in India can arguably be attributed to early child bearing practices and the lack of progress in lengthening birth intervals. Meanwhile, family planning efforts have been particularly successful in the southern states such as Andhra Pradesh, although family limitation is almost exclusively by means of sterilisation at increasingly younger ages. This paper examines the population impact of the unprecedented convergence of early childbearing trajectories in India and quantifies the potential implications stemming from the neglect of strategies that encourage delaying and spacing of births. The effects of adopting a `later, longer and fewer family planning strategy are compared with the continuation of fertility concentrated in the younger age groups. Results from the cohort component population projections suggest that a policy encouraging later marriage and birth spacing would achieve a future total population which is about 52 million less in 2050 than if the current early fertility trajectory is continued.

Maynard, PJ, Jenkins, J, Edey, C, Payne, GL, Lennard, CJ, McDonagh, AM & Roux, CP 2009, 'Near infrared imaging for the improved detection of fingermarks on difficult surfaces', Australian Journal of Forensic Sciences, vol. 41, no. 1, pp. 43-62.
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The near infrared spectral region offers advantages over the visible region in the detection of latent fingermarks due to increased contrast and decreased background luminescence. In this work, a chemical imaging system was used to image latent fingermarks in the near-infrared (NIR) region. A variety of porous, non-porous and semi-porous surfaces were tested using standard chemical and physical enhancement techniques. NIR dyes were also used to enhance latent marks. Both absorption and luminescence properties of the treated marks were examined over the spectral range 650-1100 nm. Significant NIR absorption was found for ninhydrin, iodine/benzoflavone, physical developer, and powdering. NIR luminescence emission was found for DFO, ninhydrin with zinc salt post treatment, 1,2-indanedione and genipin. Significant NIR luminescence emission was found for cyanoacrylate fuming followed by staining with NIR dyes. In addition, metal oxide powders coated with NIR dyes were able to enhance fingermarks on a patterned and highly luminescent surface.

Mbere-Nguyen, U, Ung, AT & Pyne, SG 2009, 'The synthesis of carbon-linked bisbenzylisoquinolines via ruthenium- mediated olefin-metathesis', Tetrahedron, vol. 65, no. 31, pp. 5990-6000.
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Novel laudanosine dinners in which two laudanosine units are linked at C-2' via a two and four-carbon linker have been prepared using ruthenium-mediated olefin-metathesis. In addition, a second four-carbon linker between the two isoquinoline N-atoms was also present leading to a novel macrocyclic ring system. Five of these compounds showed higher cytostatic activity on three cancer cell lines than thalicarpine.

Mccracken, J, Schwartz, J, Bruce, N, Mittleman, M, Ryan, LM & Smith, K 2009, 'Combining Individual- And Group-level Exposure Information Child Carbon Monoxide In The Guatemala Woodstove Randomized Control Trial', Epidemiology, vol. 20, no. 1, pp. 127-136.
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Background: Epidemiology frequently relies on surrogates of long-term exposures, often either individual-level short-term measurements or group-level based on long-term characteristics of subjects and their environment. Whereas individual-level measures

McDonagh, L, Thornton, C, Wallman, JF & Stevens, JR 2009, 'Development of an antigen-based rapid diagnostic test for the identification of blowfly (Calliphoridae) species of forensic significance', FORENSIC SCIENCE INTERNATIONAL-GENETICS, vol. 3, no. 3, pp. 162-165.
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McGowan, S, Porter, CJ, Lowther, J, Stack, CM, Golding, SJ, Skinner-Adams, TS, Trenholme, K, Teuscher, F, Donnelly, SM, Grembecka, J, Mucha, A, Kafarski, P, DeGori, R, Buckle, AM, Gardiner, D, Whisstock, J & Dalton, JP 2009, 'Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase', Proceedings Of The National Academy Of Sciences Of The United States Of America, vol. 106, no. 8, pp. 2537-2542.
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Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in >2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH2]Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.

McGrath, KC, Li, X, Puranik, R, Liong, E, Tan, J, Dy, V, Dibartolo, B, Barter, P, Rye, K & Heather, AK 2009, 'Role of 3 beta-hydroxysteroid-delta 24 reductase in mediating antiinflammatory effects of high-density lipoproteins in endothelial cells', Arteriosclerosis Thrombosis And Vascular Biology, vol. 29, no. 6, pp. 877-882.
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Objective-The purpose of this study was to investigate the ability of high-density lipoproteins (HDLs) to upregulate genes with the potential to protect against inflammation in endothelial cells. Methods and Results-Human coronary artery endothelial cell

Mckemmish, L, Reimers, JR, Mckenzie, R, Mark, A & Hush, N 2009, 'Penrose-Hameroff Orchestrated Objective-Reduction Proposal For Human Consciousness Is Not Biologically Feasible', Physical Review E, vol. 80, no. 2.
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Penrose and Hameroff have argued that the conventional models of a brain function based on neural networks alone cannot account for human consciousness, claiming that quantum-computation elements are also required. Specifically, in their Orchestrated Objective Reduction (Orch OR) model [R. Penrose and S. R. Hameroff, J. Conscious. Stud. 2, 99 (1995)], it is postulated that microtubules act as quantum processing units, with individual tubulin dimers forming the computational elements. This model requires that the tubulin is able to switch between alternative conformational states in a coherent manner, and that this process be rapid on the physiological time scale. Here, the biological feasibility of the Orch OR proposal is examined in light of recent experimental studies on microtubule assembly and dynamics. It is shown that the tubulins do not possess essential properties required for the Orch OR proposal, as originally proposed, to hold. Further, we consider also recent progress in the understanding of the long-lived coherent motions in biological systems, a feature critical to Orch OR, and show that no reformation of the proposal based on known physical paradigms could lead to quantum computing within microtubules. Hence, the Orch OR model is not a feasible explanation of the origin of consciousness.

McKemmish, LK, Reimers, JR, McKenzie, RH, Mark, AE & Hush, NS 2009, 'Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible.', Physical review. E, Statistical, nonlinear, and soft matter physics, vol. 80, no. 2 Pt 1, p. 021912.
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Penrose and Hameroff have argued that the conventional models of a brain function based on neural networks alone cannot account for human consciousness, claiming that quantum-computation elements are also required. Specifically, in their Orchestrated Objective Reduction (Orch OR) model [R. Penrose and S. R. Hameroff, J. Conscious. Stud. 2, 99 (1995)], it is postulated that microtubules act as quantum processing units, with individual tubulin dimers forming the computational elements. This model requires that the tubulin is able to switch between alternative conformational states in a coherent manner, and that this process be rapid on the physiological time scale. Here, the biological feasibility of the Orch OR proposal is examined in light of recent experimental studies on microtubule assembly and dynamics. It is shown that the tubulins do not possess essential properties required for the Orch OR proposal, as originally proposed, to hold. Further, we consider also recent progress in the understanding of the long-lived coherent motions in biological systems, a feature critical to Orch OR, and show that no reformation of the proposal based on known physical paradigms could lead to quantum computing within microtubules. Hence, the Orch OR model is not a feasible explanation of the origin of consciousness.

McPhedran, RC, Nicorovici, NA, Botten, LC & Milton, GW 2009, 'Cloaking by plasmonic resonance among systems of particles: cooperation or combat?', Comptes Rendus Physique, vol. 10, no. 5, pp. 391-399.
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We study quasistatic cloaking by the mechanism of plasmonic resonance, for systems of coated cylinders. Our focus is on the nature of the resonant cloaking interaction: whether systems of particles can be made to cooperate in cloaking a polarizable particle from an applied uniform field. We show that in fact if the cloaking regions of the systems of particles overlap, then they tend to interact in a fashion detrimental to their cloaking of the polarizable particle. If the cloaking regions touch but do not overlap, then the system of particles can cloak a larger region than each would in isolation.

Meeker, J, Missmer, S, Altshul, L, Vitonis, A, Ryan, LM, Cramer, D & Hauser, R 2009, 'Serum And Follicular Fluid Organochlorine Concentrations Among Women Undergoing Assisted Reproduction Technologies', Environmental health, vol. 8, no. 32, pp. 1-10.
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Mercer, AE, Shafer, CM, Doswell, CA, Leslie, LM & Richman, MB 2009, 'Objective Classification of Tornadic and Nontornadic Severe Weather Outbreaks', MONTHLY WEATHER REVIEW, vol. 137, no. 12, pp. 4355-4368.
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Meyer-Rochow, GY, Smith, JM, Richardson, A-L, Marsh, DJ, Sidhu, SB, Robinson, BG & Benn, DE 2009, 'Denaturing High Performance Liquid Chromatography Detection of SDHB, SDHD, and VHL Germline Mutations in Pheochromocytoma', JOURNAL OF SURGICAL RESEARCH, vol. 157, no. 1, pp. 55-62.
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Miklos, I & Darling, AE 2009, 'Efficient Sampling Of Parsimonious Inversion Histories With Application To Genome Rearrangement In Yersinia', Genome Biology and Evolution, vol. 1, no. NA, pp. 153-164.
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Inversions are among the most common mutations acting on the order and orientation of genes in a genome, and polynomial-time algorithms exist to obtain a minimal length series of inversions that transform one genome arrangement to another. However, the m

Miller, CM, Boulter, N, Ikin, RJ & Smith, NC 2009, 'The immunobiology of the innate response to Toxoplasma gondii', International Journal For Parasitology, vol. 39, no. 1, pp. 23-39.
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Toxoplasma gondii is a unique intracellular parasite. It can infect a variety of cells in virtually all warm-blooded animals. It has a worldwide distribution and, overall, around one-third of people are seropositive for the parasite, with essentially the entire human population being at risk of infection. For most people, T. gondii causes asymptomatic infection but the parasite can cause serious disease in the immunocompromised and, if contracted for the first time during pregnancy, can cause spontaneous abortion or congenital defects, which have a substantial emotional, social and economic impact. Toxoplasma gondii provokes one of the most potent innate, pro-inflammatory responses of all infectious disease agents. It is also a supreme manipulator of the immune response so that innate immunity to T. gondii is a delicate balance between the parasite and its host involving a coordinated series of cellular interactions involving enterocytes, neutrophils, dendritic cells, macrophages and natural killer cells. Underpinning these interactions is the regulation of complex molecular reactions involving Toll-like receptors, activation of signalling pathways, cytokine production and activation of anti-microbial effector mechanisms including generation of reactive nitrogen and oxygen intermediates.

Miller, CM, Smith, NC, Ikin, RJ, Boulter, N, Dalton, JP & Donnelly, SM 2009, 'Immunological interactions between 2common pathogens, the Th1-inducing protozoan Toxoplasma gondii and the Th2-inducing helminth Fasciola hepatica', PLoS ONE, vol. 4, no. 5, pp. 1-10.
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The nature of the immune response to infection is dependent on the type of infecting organism. Intracellular organisms such as Toxoplasma gondii stimulate a Th1-driven response associated with production of IL-12, IFN-?, nitric oxide and IgG2a antibodies and classical activation of macrophages. In contrast, extracellular helminths such as Fasciola hepatica induce Th2 responses characterised by the production of IL-4, IL-5, IL-10 and IgG1 antibodies and alternative activation of macrophages. As co-infections with these types of parasites commonly exist in the field it is relevant to examine how the various facets of the immune responses induced by each may influence or counter-regulate that of the other.

Miller, CMD, Smith, NC, Ikin, RJ, Boulter, NR, Dalton, JP & Donnelly, S 2009, 'Immunological interactions between 2 common pathogens, Th1-inducing protozoan Toxoplasma gondii and the Th2-inducing helminth Fasciola hepatica.', PloS one, vol. 4, no. 5, p. e5692.
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Background

The nature of the immune response to infection is dependent on the type of infecting organism. Intracellular organisms such as Toxoplasma gondii stimulate a Th1-driven response associated with production of IL-12, IFN-gamma, nitric oxide and IgG2a antibodies and classical activation of macrophages. In contrast, extracellular helminths such as Fasciola hepatica induce Th2 responses characterised by the production of IL-4, IL-5, IL-10 and IgG1 antibodies and alternative activation of macrophages. As co-infections with these types of parasites commonly exist in the field it is relevant to examine how the various facets of the immune responses induced by each may influence or counter-regulate that of the other.

Principal findings

Regardless, of whether F. hepatica infection preceded or succeeded T. gondii infection, there was little impact on the production of the Th1 cytokines IL-12, IFN-gamma or on the development of classically-activated macrophages induced by T. gondii. By contrast, the production of helminth-specific Th2 cytokines, such as IL-4 and IL-5, was suppressed by infection with T. gondii. Additionally, the recruitment and alternative activation of macrophages by F. hepatica was blocked or reversed by subsequent infection with T. gondii. The clinical symptoms of toxoplasmosis and the survival rate of infected mice were not significantly altered by the helminth.

Conclusions

Despite previous studies showing that F. hepatica suppressed the classical activation of macrophages and the Th1-driven responses of mice to bystander microbial infection, as well as reduced their ability to reject these, here we found that the potent immune responses to T. gondii were capable of suppressing the responses to helminth infection. Clearly, the outcome of particular infections in polyparasitoses depends on the means and potency by which each pathogen controls the immune response.

Milthorpe, BK 2009, 'In Vitro Adsorption of Tear Proteins to Hydroxyethyl Methacrylate-Based Contact Lens Materials', Eye and Contact Lens: Science and Clinical Practice, vol. 35, no. 6, pp. 320-328.
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Investigations of polymer interactions in single protein solutions is a necessary step in the elucidation of in vivo early binding events during protein deposition on hydroxyethyl methacrylate-based contact lens materials. Quantity and tenacity of binding of significant tear components to groups I and IV contact lenses was assessed. Competitive binding by these components was also examined. METHODS: Adsorption on FDA groups I and IV hydrogel lenses was monitored using I-labeled protein. Lenses were incubated in increasing concentrations of radiolabeled single species proteins in solution. For competition experiments, concentration of each radiolabeled protein was held constant and the adsorption/sorption challenged with increasing concentrations of nonlabeled proteins. Lenses were soaked in phosphate-buffered saline to determine desorption. RESULTS: Group IV lenses bound large amounts of lysozyme, whereas group I lenses bound highest amounts of albumin. Albumin binding to both lens types was relatively strong and could not be competed from binding by other proteins lysozyme, lactoferrin, and mucin. Mucin at high concentrations tended to positively cooperate with the binding of lactoferrin and albumin to all lenses. CONCLUSIONS: Binding of proteins to hydroxyethyl methacrylate-based hydrogel lens surfaces is affected by charge and polymer components, and perhaps manufacturing processes. Albumin binds strongly to lens surfaces, and this may play an adverse role during contact lens wear.

Mittnik, S, Nell, E, Platen, E, Semmler, W & Chappe, R 2009, 'Financial market meltdown and a need for new financial regulations', METU Studies in Development, vol. 36, no. 1, pp. 253-269.
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The financial crisis, triggered by the subprime and real estate crisis in the US, has become global It is deeply rooted in a decade-long misuse of the financial market for rent-seeking. The financial industry has largely abandoned Its role as a service industry, supposedly charging reasonable fees for the services of spreading risk and allocating capital and credit. Instead it provides a market for speculation, corporate control - mergers and acquisitions -: and a casino for bettmg on or hedging practically any kind of risk - the derivatives market.

Miura, T & Huete, A 2009, 'Performance of Three Reflectance Calibration Methods for Airborne Hyperspectral Spectrometer Data', Sensors, vol. 9, no. 2, pp. 794-813.
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In this study, the performances and accuracies of three methods for converting airborne hyperspectral spectrometer data to reflectance factors were characterized and compared. The reflectance mode (RM) method, which calibrates a spectrometer against a white reference panel prior to mounting on an aircraft, resulted in spectral reflectance retrievals that were biased and distorted. The magnitudes of these bias errors and distortions varied significantly, depending on time of day and length of the flight campaign. The linear-interpolation (LI) method, which converts airborne spectrometer data by taking a ratio of linearly-interpolated reference values from the preflight and postflight reference panel readings, resulted in precise, but inaccurate reflectance retrievals. These reflectance spectra were not distorted, but were subject to bias errors of varying magnitudes dependent on the flight duration length. The continuous panel (CP) method uses a multi-band radiometer to obtain continuous measurements over a reference panel throughout the flight campaign, in order to adjust the magnitudes of the linear-interpolated reference values from the preflight and post-flight reference panel readings. Airborne hyperspectral reflectance retrievals obtained using this method were found to be the most accurate and reliable reflectance calibration method.

Miyakis, S, van Hal, SJ, Barratt, J, Stark, D, Marriott, D & Harkness, J 2009, 'Absence of human Bocavirus in bronchoalveolar lavage fluid of lung transplant patients', JOURNAL OF CLINICAL VIROLOGY, vol. 44, no. 2, pp. 179-180.
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Mobli, M, de Araujo, AD, Lambert, LK, Pierens, GK, Windley, MJ, Nicholson, GM, Alewood, PF & King, GF 2009, 'Direct Visualisation of Disulfide Bonds through Diselenide Proxies Using 77Se NMR Spectroscopy', Angewandte Chemie-international Edition, vol. 48, no. 49, pp. 9312-9314.
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Se-ing is believing: Many proteins are cross-braced by disulfide bonds that frequently play key roles in protein structure, folding, and function. Unfortunately, the methods available for assignment of disulfide-bond connectivities in proteins are technically difficult and prone to misinterpretation. Now disulfide bond connectivities in native proteins can be visualized directly using 77Se NMR spectroscopy.

Mohr, R, Voss, B, Schliep, MT, Kurz, T, Maldener, I, Adams, DG, Larkum, A, Chen, M & Hess, WR 2009, 'A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris', ISME Journal, vol. 4, no. 11, pp. 1456-1469.
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Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (23 degrees 26' 31.2 '' S, 151 degrees 54' 50.4 '' E). The 16S ribosomal RNA is 2% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371 965 nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms.

Moles, A, Wright, IA, Pitman, AJ, Murray, B & Westoby, M 2009, 'Is there a latitudinal gradient in seed production?', Ecography, vol. 32, no. 1, pp. 78-82.
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We compiled data from seed rain studies at 33 sites from around the world to determine whether the greater mean seed mass of tropical plants is associated with production of fewer seeds per square meter of ground. We found no significant linear relationship between latitude and annual seed rain density, but found some evidence for a mid-latitude peak in seed rain density (quadratic relationship, p=0.018; R-2=0.23). Combining seed rain data with seed mass data suggests that vegetation at the equator produces between 19 and 128 times more total mass of seed per year than does vegetation at 60 degrees. This gradient in seed production would far outweigh the doubling in net primary productivity (NPP) over the same range of latitudes. Thus, our (admittedly small) dataset suggests that tropical vegetation allocates a much greater proportion of NPP to reproduction. This raises two important questions for the future: 1) why might tropical vegetation commit more energy to seed production than vegetation further from the equator? 2) What aspect of plant growth might receive proportionally less energy in tropical ecosystems?

Monahan, LG, Robinson, A & Harry, L 2009, 'Lateral Ftsz Association And The Assembly Of The Cytokinetic Z Ring In Bacteria', Molecular Microbiology, vol. 74, no. 4, pp. 1004-1017.
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Cell division in bacteria is facilitated by a polymeric ring structure, the Z ring, composed of tubulin-like FtsZ protofilaments. Recently it has been shown that in Bacillus subtilis, the Z ring forms through the cell cycle-mediated remodelling of a helical FtsZ polymer. To investigate how this occurs in vivo, we have exploited a unique temperature-sensitive strain of B. subtilis expressing the mutant protein FtsZ(Ts1). FtsZ(Ts1) is unable to complete Z ring assembly at 49°C, becoming trapped at an intermediate stage in the helix-to-ring progression. To determine why this is the case, we used a combination of methods to identify the specific defect of the FtsZ(Ts1) protein in vivo. Our results indicate that while FtsZ(Ts1) is able to polymerize normally into protofilaments, it is defective in the ability to support lateral associations between these filaments at high temperatures. This strongly suggests that lateral FtsZ association plays a crucial role in the polymer transitions that lead to the formation of the Z ring in the cell. In addition, we show that the FtsZ-binding protein ZapA, when overproduced, can rescue the FtsZ(Ts1) defect in vivo. This suggests that ZapA functions to promote the helix-to-ring transition of FtsZ by stimulating lateral FtsZ association.

Moody, SJ, Phillips, MR & Toth, M 2009, 'Assessment of SEM Image Quality using 1D Power Spectral Density Estimation', MICROSCOPY AND MICROANALYSIS, vol. 15, pp. 48-49.
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Moore, C, Mills, M, Achterberg, E, Geider, R, Laroche, J, Lucas, M, Mcdonagh, E, Pan, X, Poulton, A, Rijkenberg, M, Suggett, DJ, Ussher, S & Woodward, E 2009, 'Large-scale Distribution Of Atlantic Nitrogen Fixation Controlled By Iron Availability', Nature Geoscience, vol. 2, no. 12, pp. 867-871.
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Oceanic fixed-nitrogen concentrations are controlled by the balance between nitrogen fixation and denitrification(1-4). A number of factors, including iron limitation(5-7), can restrict nitrogen fixation, introducing the potential for decoupling of nitrogen inputs and losses(2,5,8). Such decoupling could significantly affect the oceanic fixed-nitrogen inventory and consequently the biological component of ocean carbon storage and hence air-sea partitioning of carbon dioxide(2,5,8,9). However, the extent to which nutrients limit nitrogen fixation in the global ocean is uncertain. Here, we examined rates of nitrogen fixation and nutrient concentrations in the surfacewaters of the Atlantic Ocean along a north-south 10,000 km transect during October and November 2005. We show that rates of nitrogen fixation were markedly higher in the North Atlantic compared with the South Atlantic Ocean. Across the two basins, nitrogen fixation was positively correlated with dissolved iron and negatively correlated with dissolved phosphorus concentrations. We conclude that inter-basin differences in nitrogen fixation are controlled by iron supply rather than phosphorus availability. Analysis of the nutrient content of deep waters suggests that the fixed nitrogen enters North Atlantic Deep Water. Our study thus supports the suggestion that iron significantly influences nitrogen fixation(5), and that subsequent interactions with ocean circulation patterns contribute to the decoupling of nitrogen fixation and loss(2,4,8).

Moore, CP, Blaikie, RJ & Arnold, MD 2009, 'An improved transfer-matrix model for optical superlenses', Optics Express, vol. 17, no. 16, pp. 14260-14269.
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The use of transfer-matrix analyses for characterizing planar optical superlensing systems is studied here, and the simple model of the planar superlens as an isolated imaging element is shown to be defective in certain situations. These defects arise due to neglected interactions between the superlens and the spatially varying shadow masks that are normally used as scattering objects for imaging, and which are held in near-field proximity to the superlenses. An extended model is proposed that improves the accuracy of the transfer-matrix analysis, without adding significant complexity, by approximating the reflections from the shadow mask by those from a uniform metal layer. Results obtained using both forms of the transfer matrix model are compared to finite element models and two example superlenses, one with a silver monolayer and the other with three silver sublayers, are characterized. The modified transfer matrix model gives much better agreement in both cases.

Moriya, S, Kawai, Y, Kaji, S, Smith, AC, Harry, L & Errington, J 2009, 'Effects of oriC relocation on control of replication initiation in Bacillus subtilis', Microbiology-uk, vol. 155, pp. 3070-3082.
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In bacteria, DNA replication initiation is tightly regulated in order to coordinate chromosome replication with cell growth. In Escherichia coli, positive factors and negative regulatory mechanisms playing important roles in the strict control of DNA replication initiation have been reported. However, it remains unclear how bacterial cells recognize the right time for replication initiation during the cell cycle. In the Gram-positive bacterium Bacillus subtilis, much less is known about the regulation of replication initiation, specifically, regarding negative control mechanisms which ensure replication initiation only once per cell cycle. Here we report that replication initiation was greatly enhanced in strains that had the origin of replication (oriC) relocated to various loci on the chromosome. When oriC was relocated to new loci further than 250 kb counterclockwise from the native locus, replication initiation became asynchronous and earlier than in the wild-type cells. In two oriC-relocated strains (oriC at argG or pnbA, 257 degrees or 300 degrees on the 360 degrees chromosome map, respectively), DnaA levels were higher than in the wild-type but not enough to cause earlier initiation of replication. Our results suggest that the initiation capacity of replication is accumulated well before the actual time of initiation, and its release may be suppressed by a unique DNA structure formed near the native oriC locus.

Morris, M & Chen, H 2009, 'Established maternal obesity in the rat reprograms hypothalamic appetite regulators and leptin signaling at birth', International Journal of Obesity, vol. 33, no. 1, pp. 115-122.
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Objective:Key appetite regulators and their receptors are already present in the fetal hypothalamus, and may respond to hormones such as leptin. Intrauterine food restriction or hyperglycemia can reprogram these circuits, possibly predisposing individuals to adverse health outcomes in adulthood. Given the global obesity epidemic, maternal overweight and obesity is becoming more prevalent. Earlier, we observed rapid growth of pups from obese dams during the suckling period. However, it is unclear whether this is because of alterations in leptin and hypothalamic appetite regulators at birth.Design:Female SpragueDawley rats were fed palatable high-fat diet (HFD) or chow for 5 weeks to induce obesity before mating. The same diet continued during gestation. At day 1, after birth, plasma and hypothalamus were collected from male and female pups.Measurements:Body weight and organ mass were recorded. Leptin and insulin levels were measured in the plasma by radioimmunoassay. Hypothalamic mRNA expression of neuropeptide-Y (NPY), pro-opiomelanocortin, leptin receptor and its downstream signal, STAT3 (signal transducer and activator of transcription 3), were measured using real-time PCR.Results:Body and organ weights of pups from obese dams were similar to those from lean dams, across both genders. However, plasma leptin levels were significantly lower in offspring from obese dams (male: 0.53±0.13 vs 1.05±0.21 ng ml^-1; female: 0.33±0.09 vs 2.12±0.57 ng ml^-1, respectively; both P<0.05).

Movchan, NV, McPhedran, RC, Movchan, AB & Poulton, CG 2009, 'Wave scattering by platonic grating stacks', Proceedings Of The Royal Society A-Mathematical ..., vol. 465, no. 2111, pp. 3383-3400.
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We address the problem of scattering of flexural waves obeying the biharmonic equation by a stack of a finite number of gratings. We express the solution of the scattering problem for a single grating in terms of reflection and transmission matrices, incorporating the effects of both propagating and evanescent incident waves. The plane wave expansion coefficients above and below the grating are linked to multipole coefficients within the grating using the grating sums and the Rayleigh identities. We derive the recurrence procedure giving the reflection and transmission matrices of the stack in terms of those of individual layers. Trapped waves between a pair of gratings are investigated.

Mungkornasawakul, P, Chaiyong, S, Sastraruji, T, Jatisatienr, A, Jatisatienr, C, Pyne, SG, Ung, AT, Korth, J & Lie, W 2009, 'Alkaloids from the Roots of Stemona aphylla', Journal of Natural Products, vol. 72, no. 5, pp. 848-851.
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Three known compounds, stemofoline (1), (2'S)-hydroxystemofoline (2), and (11Z)-1',2'-didehydrostemofoline (3), along with two new alkaloids, stemaphylline (4) and stemaphylline-N-oxide (5), have been isolated from a root extract of Stemona aphylla. The structures of these alkaloids were determined on the basis of their spectroscopic data. The analysis of the crude dichloromethane extract by GC-MS in the EIMS mode showed the presence of alkaloids 1-4, the alkaloid 11, and stilbostemin R (12). The crude dichloromethane extract and 4 were tested for their comparative biological activities. The results of their acetylcholinesterase (AChE) inhibitory activities showed that the crude extract had higher activity than that of 4. The insecticidal properties of the crude extract and 4, using a topical application, showed that 4 had an activity similar to the positive control, methomyl, whereas the crude extract had much lower activity. Their antimicrobial activity against Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, Pseudomonas auruginosa ATCC 27853, and Candida albicans ATCC 90028 was weak (MIC 62.5-125 ?g/mL, MBC 125-250 ?g/mL, MFC 125 ?g/mL) but much higher than that of the crude extract.

Mungkornasawakul, P, Pyne, SG, Ung, AT, Jatisatienr, A & Willis, AC 2009, 'Stemofoline ethyl acetate solvate', Acta Crystallographica Section E: Structure Reports Online, vol. 65, no. 8.
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Crystals of the title compound, C22H29NO 5·C4H8O2, {[systematic name: (2R,3R,5R,5aS,6R,8aR,9S)-(5Z)-5-[3-butyl-tetra-hydro-6-methyl-2,5-methano-4,3, 8a-[1]propan-yl[3]yl-idene-furo[3,2-f][1,4]oxazepin-7(5H)-yl-idene] -4-meth-oxy-3-methyl-furan-2(5H)-one ethyl acetate solvate} were isolated from the root extracts of Stemona aphylla (Stemonaceae). The structure closely resembles those of stemofoline derivatives which have previously been reported. Inter-molecular contacts are observed between some C-bonded H atoms and nearby O atoms, perhaps indicating weak inter-actions which could influence the packing of species within the unit cell. © 2009 Mungkornasawakul et al.

Murray, B, Baker, AC & Robson, TC 2009, 'Impacts of the replacement of native woodland with exotic pine plantations on leaf-litter invertebrate assemblages: a test of a novel framework', International Journal of Ecology, vol. 2009, no. 49035, pp. 1-6.
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We present an empirical comparison of invertebrate community sturcture between aereras of undisturbed native eucalypt woodland and areas that have been cleared and replaced with plantations of exotic radiata pine (Pinus radiata). Implementation of a novel conceptual framework revealed that both insect (in autumn) and arachnid (in winter) assemblages demonstrated inhibition in response to the pine plantations.

Murray, SA, Ip, CL, Moore, R, Nagahama, Y & Fukuyo, Y 2009, 'Are prorocentroid dinoflagellates monophyletic? A study of 25 species based on nuclear and mitochondrial genes', Protist, vol. 160, no. 2, pp. 245-264.
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The dinoflagellate sub-class Prorocentrophycidae has a distinct morphology, lacking the typical dinoflagellate cell structure of a clear cingulum and sulcus. It includes species that produce the toxin okadaic acid. Despite its uniqueness, the group has been found polyphyletic in some previous molecular phylogenetic studies. We have re-investigated the phylogeny of this sub-class by culturing and sequencing new strains, comparing sequences from three genes, the mitochondrial cytochrome c oxidase subunit 1 ( cox 1) and the nuclear large and small subunit rRNA (LSU and SSU) encoding genes. We analyzed sequences from twenty-five named and two still undescribed species of Prorocentrophycidae. We used newly recognized features of the secondary structure to align regions of the LSU rRNA. The phylogeny based on cox 1 provided the most well-supported tree and showed strong support for the monophyly of prorocentroid dinoflagellates, while the LSU phylogeny was inconclusive. As in previous studies, phylogeny based on SSU shows the group to appear paraphyletic, however, support values were low. Two strongly supported sub-clades were consistently identified. Benthic and planktonic modes appear to have evolved on multiple occasions within both clades of Prorocentriphycidae. The capability to synthesize toxins appears to have arisen early in prorocentroid evolution and, in particular, okadaic acid synthesis is present in some, but not all, members of Clade 2. The D2a region of the LSU rRNA appears to have developed a deletion in three definable steps during prorocentroid evolution. While the phylogenies inferred from the three genes were not congruent, our results give reserved support to the monophyly of the group.

Murray, SA, O'Connor, WA, Alvin, A, Mihali, TK, Kalaitzis, J & Neilan, BA 2009, 'Differential accumulation of paralytic shellfish toxins from Alexandrium minutum in the pearl oyster, Pinctada imbricata', Toxicon, vol. 54, no. 3, pp. 217-223.
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To investigate the potential for differential accumulation of paralytic shellfish toxins (PSTs) in various tissues of the akoya pearl oyster, Pinctada imbricata, two feeding trials were carried out using the PST-producing dinoflagellate, Alexandrium minu

Murrihy, RC, Byrne, M & Gonsalvez, C 2009, 'Testing an empirically derived mental health training model featuring small groups, distributed practice and patient discussion', Medical Education, vol. 43, no. 2, pp. 140-145.
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Internationally, family doctors seeking to enhance their skills in evidence-based mental health treatment are attending brief training workshops, despite clear evidence in the literature that short-term, massed formats are not likely to improve skills in this complex area. Reviews of the educational literature suggest that an optimal model of training would incorporate distributed practice techniques; repeated practice over a lengthy time period, small-group interactive learning, mentoring relationships, skills-based training and an ongoing discussion of actual patients. This study investigates the potential role of group-based training incorporating multiple aspects of good pedagogy for training doctors in basic competencies in brief cognitive behaviour therapy (BCBT). Six groups of family doctors (n = 32) completed eight 2-hour sessions of BCBT group training over a 6-month period. A baseline control design was utilised with pre- and post-training measures of doctors' BCBT skills, knowledge and engagement in BCBT treatment. Family doctors' knowledge, skills in and actual use of BCBT with patients improved significantly over the course of training compared with the control period. This research demonstrates preliminary support for the efficacy of an empirically derived group training model for family doctors. Brief CBT group-based training could prove to be an effective and viable model for future doctor training.

Myers, GSA, Mathews, SA, Eppinger, M, Mitchell, C, O'Brien, KK, White, OR, Benahmed, F, Brunham, RC, Read, TD, Ravel, J, Bavoil, PM & Timms, P 2009, 'Evidence that Human Chlamydia pneumoniae Was Zoonotically Acquired', JOURNAL OF BACTERIOLOGY, vol. 191, no. 23, pp. 7225-7233.
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Naumann, U & Wand, M 2009, 'Automation in high-content flow cytometry screening', Cytometry, vol. 75, no. 9, pp. 789-797.
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High-content flow cytometric screening (FC-HCS) is a 21st Century technology that combines robotic fluid handling, flow cytometric instrumentation, and bioinformatics software, so that relatively large numbers of flow cytometric samples can be processed and analysed in a short period of time. We revisit a recent application of FC-HCS to the problem of cellular signature definition for acute graft-versus-host-disease. Our focus is on automation of the data processing steps using recent advances in statistical methodology. We demonstrate that effective results, on par with those obtained via manual processing, can be achieved using our automatic techniques. Such automation of FC-HCS has the potential to drastically improve diagnosis and biomarker identification.

Nelson, LA, Dowton, M & Wallman, JF 2009, 'Thermal attributes of Chrysomya species', ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, vol. 133, no. 3, pp. 260-275.
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Ng, PR, Tahtouh, M, Walker, S & Reedy, BJ 2009, 'Detection of illicit substances in fingerprints by infrared spectral imaging', Analytical and Bioanalytical Chemistry, vol. 394, no. 8, pp. 2039-2048.
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FTIR and Raman spectral imaging can be used to simultaneously image a latent fingerprint and detect exogenous substances deposited within it. These substances might include drugs of abuse or traces of explosives or gunshot residue. In this work, spectral searching algorithms were tested for their efficacy in finding targeted substances deposited within fingerprints. "Reverse" library searching, where a large number of possibly poor-quality spectra from a spectral image are searched against a small number of high-quality reference spectra, poses problems for common search algorithms as they are usually implemented. Out of a range of algorithms which included conventional Euclidean distance searching, the spectral angle mapper (SAM) and correlation algorithms gave the best results when used with second-derivative image and reference spectra. All methods tested gave poorer performances with first derivative and undifferentiated spectra. In a search against a caffeine reference, the SAM and correlation methods were able to correctly rank a set of 40 confirmed but poor-quality caffeine spectra at the top of a dataset which also contained 4,096 spectra from an image of an uncontaminated latent fingerprint. These methods also successfully and individually detected aspirin, diazepam and caffeine that had been deposited together in another fingerprint, and they did not indicate any of these substances as a match in a search for another substance which was known not to be present. The SAM was used to successfully locate explosive components in fingerprints deposited on silicon windows. The potential of other spectral searching algorithms used in the field of remote sensing is considered, and the applicability of the methods tested in this work to other modes of spectral imaging is discussed.

Nordin, A & Roux, C 2009, 'Proposal 1861 to conserve Aspicilia farinosa: author correction', MYCOTAXON, vol. 110, pp. 493-493.

Notter, SJ, Stuart, BH, Rowe, RR & Langlois, NE 2009, 'The initial changes of fat deposits during the decomposition of human and pig remains', Journal of Forensic Sciences, vol. 54, no. 1, pp. 195-201.
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The early stages of adipocere formation in both pig and human adipose tissue in aqueous environments have been investigated. The aims were to determine the short-term changes occurring to fat deposits during decomposition and to ascertain the suitability of pigs as models for human decomposition. Subcutaneous adipose tissue from both species after immersion in distilled water for up to six months was compared using Fourier transform infrared spectroscopy, gas chromatography-mass spectrometry and inductively coupled plasma-mass spectrometry. Changes associated with decomposition were observed, but no adipocere was formed during the initial month of decomposition for either tissue type. Early-stage adipocere formation in pig samples during later months was detected. The variable time courses for adipose tissue decomposition were attributed to differences in the distribution of total fatty acids between species. Variations in the amount of sodium, potassium, calcium, and magnesium were also detected between species. The study shows that differences in total fatty acid composition between species need to be considered when interpreting results from experimental decomposition studies using pigs as human body analogs.

Novikov, A 2009, 'On Distributions Of First Passage Times And Optimal Stopping Of Ar(1) Sequences', Theory of Probability and its Applications, vol. 53, no. 3, pp. 419-429.
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Sufficient conditions for the exponential boundedness of first passage times of autoregressive (AR(1)) sequences are derived in this paper. An identity involving the mean of the first passage time is obtained. Further, this identity is used for finding a logarithmic asymptotic of the mean of the first passage time of Gaussian AR(1)-sequences from a strip. Accuracy of the asymptotic approximation is illustrated by Monte Carlo simulations. A corrected approximation is suggested to improve accuracy of the approximation. An explicit formula is derived for the generating function of the first passage time for the case of AR(1)-sequences generated by an innovation with the exponential distribution. The latter formula is used to study an optimal stopping problem.

Novikov, A 2009, 'Some remarks on distributions and expectation of exit times of AR(1) sequences', Teoriya Veroyatnostei i ee Primeneniya, vol. 53, no. 3, pp. 459-471.

Nowak, D, Florek, M, Kwiatek, W, Lekki, J, Chevallier, P, Hacura, A, Wrzalik, R, Ben-Nissan, B, Van Grieken, R & Kuczumow, A 2009, 'Morphology and the chemical make-up of the inorganic components of black corals', Materials Science and Engineering C, vol. 29, no. 3, pp. 1029-1038.
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Black corals (Cnidaria, Antipatharia) from three different sources were investigated with the aim of detecting inorganic components and their morphology. In general, the skeleton of black corals was composed of the chitin fibrils admixed with peptides and the chitin presence was confirmed by the X-ray diffraction (XRD), Fourier Transformed Infrared Spectrometry (FTIR) and microRaman Microscopy, the latter giving the opportunity of tracing single fibrils and their location. The composition and concentrations of the inorganic components of the black corals were measured, using a scanning electron microprobe and micro-Particle Induced X-ray Emission (mu-PIXE). The application of such instruments enabled the estimation of the constituent distributions in a microscale. The mapping option was the most useful technique of making analyses in these studies, just to reveal the composition of chamber-like cells. Analysis of the morphology and microstructure showed that there were three distinct regions within the coral: a core and the cells encircled with adjacent interface gluing strips. The majority of the elements analyzed were selectively distributed and segregated in a striking way in mentioned distinctive zones of the skeleton and it was detected for the first time. The core area was characterized by the relatively elevated concentrations of Ca. The measurements gave extremely clear images of the distribution of particular elements in the skeletal tissue, with I, Ca, K and Fe much more concentrated in the gluing zones, while C, N, Na and Mg present in the interiors of particular skeletal cells. The distribution of some elements (Mg, Fe) and some compounds (chitin) and functional groups (S-S, C-I) allows differentiating the biological and mechanical functions of particular fragments of the rods

Oliver, S, Finnegan, E, Dennis, ES, Peacock, J & Trevaskis, B 2009, 'Vernalization-induced flowering in cereals is associated with changes in histone methylation at the VERNALIZATION1 gene', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 106, no. 20, pp. 8386-8391.
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Prolonged exposure to low temperatures (vernalization) accelerates the transition to reproductive growth in many plant species, including the model plant Arabidopsis thaliana and the economically important cereal crops, wheat and barley. Vernalization-in

Ollendick, TH, Jarrett, MA, Wolff, JC & Scarpa, A 2009, 'Reactive and proactive aggression: Cross-informant agreement and the clinical utility of different informants', Journal of Psychopathology and Behavioral Assessment, vol. 31, no. 1, pp. 51-59.
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The current study examined cross-informant agreement and clinical utility of parent and teacher ratings of reactive and proactive aggression (two functions of aggression) in the prediction of aggressive and rule-breaking behavior (two forms of aggressive behavior) in a clinically-heterogeneous referred sample. Reactive and proactive measures were significantly related to one another within informant. Furthermore, the reactive and proactive measures of aggression were significantly related across informants and resulted in differential predictions of emotion-focused aggressive and goal-directed rule-breaking behaviors in home and school settings. Both reactive and proactive functions of aggression predicted aggressive acts that were more emotion-focused, whereas only the proactive function of aggression predicted instrumental acts of aggression. The current findings suggest that setting-specific reports of functions and forms of aggressive behavior are valuable and that it may be premature to abandon the reactive and proactive aggression distinction. © 2008 Springer Science+Business Media, LLC.

Ollendick, TH, Öst, LG, Reuterskiöld, L, Costa, N, Cederlund, R, Sirbu, C, Davis, TE & Jarrett, MA 2009, 'One-Session Treatment of Specific Phobias in Youth: A Randomized Clinical Trial in the United States and Sweden', Journal of Consulting and Clinical Psychology, vol. 77, no. 3, pp. 504-516.
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One hundred and ninety-six youth, ages 7-16, who fulfilled Diagnostic and Statistical Manual of Mental Disorders (4th ed.) criteria for various specific phobias were randomized to a one-session exposure treatment, education support treatment, or a wait list control group. After the waiting period, the wait list participants were offered treatment and, if interested, rerandomized to 1 of the 2 active treatments. The phobias were assessed with semistructured diagnostic interviews, clinician severity ratings, and behavioral avoidance tests, whereas fears, general anxiety, depression, and behavior problems were assessed with self- and parent report measures. Assessments were completed pretreatment, posttreatment, and at 6 months following treatment. Results showed that both treatment conditions were superior to the wait list control condition and that 1-session exposure treatment was superior to education support treatment on clinician ratings of phobic severity, percentage of participants who were diagnosis free, child ratings of anxiety during the behavioral avoidance test, and treatment satisfaction as reported by the youth and their parents. There were no differences on self-report measures. Treatment effects were maintained at follow-up. Implications of these findings are discussed. © 2009 American Psychological Association.

Owen, M, Ryan, LM & Holmes, L 2009, 'Effects Of Retinoic Acid On Dominant Bemimelia Expression In Mice', Birth Defects Research Part A: Clinical and Molecular Teratology, vol. 85, no. 1, pp. 36-41.
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BACKGROUND: Dominant hemimelia (Dh) is an autosomal dominant mutation that arose spontaneously in mice. Dh animals are asplenic and they exhibit asymmetric hindlimb defects in association with reduced numbers of lumbar vertebrae. These defects suggest that Dh acts early in embryonic development to affect patterning of the anterior-posterior (A-P) and left-right axes. This study was undertaken to determine whether retinoic acid (RA), which is involved in A-P patterning and coordination of bilaterally synchronized somitogenesis, affects phenotypic expression of the Dh gene. METHODS: Thirty-four pregnant females were given, by oral intubation, a single dose of 50 or 75 mg all-trans RA per kilogram body weight at GD 9, 10, or 11. The pregnant females were then euthanized at GD 18 and fetuses removed by cesarean section. A total of 326 fetuses were identified by phenotype and linked DNA and their skeletons were analyzed. RESULTS: There was a differential effect of RA on the axial skeleton and hindlimb of Dh/+ mice as compared to their wild-type littermates. Dose- and stage-specific effects on sternebrae and vertebrae were observed. CONCLUSIONS: The effects of RA dosing on numbers of sternebrae and vertebrae suggest that Dh embryos have a primary defect in retinoid-mediated A-P patterning. Dosing with RA may produce the observed effects on phenotypic expression of Dh/+ by indirectly or directly modifying an already existing altered Hox expression pattern. As the relationship between axial patterning and the asymmetric limb is unknown, Dh is an important model for studying this relationship. Birth Defects Research (Part A) 85:36-41, 2009,

p, S, merfort, I, Hughes, MJ, Oliver, BG, Tamm, M & Roth, M 2009, 'Dimethylfumarate inhibits NFkB function at multiple levels to limit airway smooth muscle cell cytokine secretion', American Journal of Physiology - Lung Cellular and Molecular Physiology, vol. 297, no. 2, pp. 326-339.
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The antipsoriatic dimethylfumarate (DMF) has been anecdotically reported to reduce asthma symptoms and to improve quality of life of asthma patients. DMF decreases the expression of proinflammatory mediators by inhibiting the transcription factor NF-?B and might therefore be of interest for the therapy of inflammatory lung diseases. In this study, we determined the effect of DMF on platelet-derived growth factor (PDGF)-BB- and TNFa-induced asthma-relevant cytokines and NF-?B activation by primary human asthmatic and nonasthmatic airway smooth muscle cells (ASMC). Confluent nonasthmatic and asthmatic ASMC were incubated with DMF (0.1100 µM) and/or dexamethasone (0.00010.1 µM), NF-?B p65 siRNA (100 nM), the NF-?B inhibitor helenalin (1 µM) before stimulation with PDGF-BB or TNFa (10 ng/ml). Cytokine release was measured by ELISA. NF-?B, mitogen and stress-activated kinase (MSK-1), and CREB activation was determined by immunoblotting and EMSA. TNFa-induced eotaxin, RANTES, and IL-6 as well as PDGF-BB-induced IL-6 expression was inhibited by DMF and by dexamethasone from asthmatic and nonasthmatic ASMC, but the combination of both drugs showed no glucocorticoid sparing effect in either of the two groups. NF-?B p65 siRNA and/or the NF-?B inhibitor helenalin reduced PDGF-BB- and TNFa-induced cytokine expression, suggesting the involvement of NF-?B signaling. DMF inhibited TNFa-induced NF-?B p65 phosphorylation, NF-?B nuclear entry, and NF-?B-DNA complex formation, whereas PDGF-BB appeared not to activate NF-?B within 60 min. Both stimuli induced the phosphorylation of MSK-1, NF-?B p65 at Ser276, and CREB, and all were inhibited by DMF. These data suggest that DMF downregulates cytokine secretion not only by inhibiting NF-?B but a wider range of NF-?B-linked signaling proteins, which may explain its potential beneficial effect in asthma.

Padula, M 2009, 'Challenges, current status and future perspectives of proteomics in improving understanding, diagnosis and treatment of vascular disease', European Journal of Vascular and Endovascular Surgery, vol. 38, pp. 346-355.
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Park, J, Shen, X & Wang, G 2009, 'Solvothermal synthesis and gas-sensing performance of Co3O4 hollow nanospheres', Sensors and Actuators B: Chemical, vol. 136, no. 2, pp. 494-498.
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Co3O4 hollow nanospheres with a diameter of 200300 nm were synthesized by a surfactant-assisted solvothermal method. X-ray diffraction and Raman spectrum measurements demonstrate that the products are pure face-centered cubic Co3O4. Transmission electron microscopy and selected area electron diffraction analyses reveal that the walls of Co3O4 hollow nanospheres have a uniform thickness of not, vert, similar40 nm and are constructed by an oriented aggregation of Co3O4 nanocrystals. The optical absorption properties of the Co3O4 hollow nanospheres were investigated by UVvis spectroscopy and the results indicate that the Co3O4 hollow nanospheres are semiconducting with direct band gaps of 2.23, 1.25 and 1.00 eV. The gas-sensing performance of the as-prepared Co3O4 hollow nanospheres was investigated towards a series of typical organic solvents and fuels. The Co3O4 hollow nanospheres show good sensing performances towards toluene and acetone vapors with rapid response and high sensitivity at low operating temperature.

Parlati, C, Colombo, P, Buttini, F, Young, PM, Adi, H, Ammit, AJ & Traini, D 2009, 'Pulmonary Spray Dried Powders of Tobramycin Containing Sodium Stearate to Improve Aerosolization Efficiency', PHARMACEUTICAL RESEARCH, vol. 26, no. 5, pp. 1084-1092.
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Pearce, ND & Wand, M 2009, 'Explicit connections between longitudinal data analysis and kernel machines', Electronic Journal of Statistics, vol. 3, pp. 797-823.
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Two areas of research longitudinal data analysis and kernel machines have large, but mostly distinct, literatures. This article shows explicitly that both fields have much in common with each other. In particular, many popular longitudinal data fitting procedures are special types of kernel machines. These connections have the potential to provide fruitful cross-fertilization between longitudinal data analytic and kernel machine methodology

Perez-Wurfl, I, Hao, X, Gentle, A, Kim, D-H, Conibeer, G & Green, MA 2009, 'Si nanocrystal p-i-n diodes fabricated on quartz substrates for third generation solar cell applications', APPLIED PHYSICS LETTERS, vol. 95, no. 15.
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Pernice, M, Boucher, J, Boucher-Rodoni, R, Joannot, P & Bustamante, P 2009, 'Comparative bioaccumulation of trace elements between Nautilus pompilius and Nautilus macromphalus (Cephalopoda: Nautiloidea) from Vanuatu and New Caledonia', ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, vol. 72, no. 2, pp. 365-371.
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Petocz, G, Rangits, G, Shaw, M, de Bod, H, Williams, DBG & Kollar, L 2009, 'Platinum complexes of malonate-derived monodentate phosphines and their application in the highly chemo- and regioselective hydroformylation of styrene', JOURNAL OF ORGANOMETALLIC CHEMISTRY, vol. 694, no. 2, pp. 219-222.
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Petrou, K, Doblin, M, Hassler, C & Ralph, P 2009, 'MULTIPLE STRESSORS ON ANTARCTIC MICROALGAE IMPACTS OF SEASONAL FREEZING AND MELTING OF SEA-ICE', PHYCOLOGIA, vol. 48, no. 4, pp. 106-106.

Phillips, M, Drouin, D, Moody, SJ & Ton-That, C 2009, 'Imaging Fundamental Electronic Excitations at High Spatial Resolution Using Scanning Cathodoluminescence Microscopy', Microscopy & Microanalysis, vol. 15, no. S2, pp. 670-671.
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Phipps, S, Hansbro, N, Lam, CE, Foo, SY, Matthaei, KI & Foster, PS 2009, 'Allergic sensitization is enhanced in early life through toll-like receptor 7 activation', Clinical and Experimental Allergy, vol. 39, no. 12, pp. 1920-1928.
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Background Prospective cohort studies suggest that children hospitalized in early life with severe infections are significantly more likely to develop recurrent wheezing and asthma. Objective Using an inhalational mouse model of allergic airways inflammation, we sought to determine the effect of viral and bacterial-associated molecular patterns on the magnitude of the allergic inflammatory response and whether this effect was age dependent. Methods BALB/c mice were sensitized by intranasal administration of endotoxinlow ovalbumin (OVA) in the absence or presence of viral single-stranded (ss)RNA, lipoteichoic acid or flagellin as neonates (within the first 24 h of life) or as weanlings (4 weeks of age). Mice were challenged four times with OVA at 6 weeks of age and end-points (bronchoalveolar lavage cytology, histology, antigen-specific T and B cell responses) determined at 7 weeks of age. Results Inhalational sensitization (<24 h or 4 weeks of age) and challenge with OVA induced a mild allergic inflammatory response in the airways as indicated by increased numbers of eosinophils and mucus cells, elevated serum OVA-specific IgG1, and production of T helper 2 (Th2) cytokines. Mice sensitized to endotoxinlow OVA at birth in the presence of ssRNA or lipoteichoic acid, but not flagellin, showed an increase in the numbers of airway and tissue eosinophils, mucus producing cells and antigen-specific production of IL-13 as compared with mice exposed only to endotoxinlow OVA. By contrast, all three TLR ligands failed to increase the magnitude of OVA-induced allergic inflammation in mice sensitized as weanlings. Conclusions Recognition of distinct microbial-associated patterns in early life may preferentially promote the de novo differentiation of bystander, antigen-specific CD4+ T cells toward a Th2 phenotype, and promote an asthma-like phenotype upon cognate antigen exposure in later life. © 2009 Blackwell Publishing Ltd.

Pickett, J, Och, D & Leitch, EC 2009, 'Devonian Marine Invertebrate fossils from the Port Macquarie Block, New South Wales', Proceedings Of The Linnean Society Of New South Wales, vol. 130, pp. 193-217.

Pinlaor, P, Kaewpitoon, N, Laha, T, Sripa, B, Kaewkes, S, Morales, ME, Mann, VH, Parriott, SK, Suttiprapa, S, Robinson, MW, To, J, Dalton, JP, Loukas, A & Brindley, PJ 2009, 'Cathepsin F Cysteine Protease of the Human Liver Fluke, Opisthorchis viverrini', PLOS NEGLECTED TROPICAL DISEASES, vol. 3, no. 3.
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Pissuwan, D, Valenzuela, S & Cortie, MB 2009, 'Prospects for Gold Nanorod Particles in Diagnostic and Therapeutic Applications', Biotechnology & Genetic Engineering Reviews, vol. 25, pp. 93-112.
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Rod-shaped gold nanoparticles ('nanorods') have recently attracted widespread attention due to their unique optical properties and facile synthesis. In particular, they can support a longtudinal surface plasmon, which results in suspensions of themhaving a strong extinction peak in the upper visible or near-infrared parts of the spectrum. The position of this peak can be readily tuned by controlling the shape of the rods. In addition, the surface of the nanorods can be functionalised by a very wide variety of molecules. This has led to interest in their use as selctive biomarkers in biodiagnostics or for selective targeting in photothermal therapeutics. Here we review the recent advances in the use of gold nanoparticles in these applications. additionally the information available regarding their biocompatibility in discussed.

Pissuwan, D, Valenzuela, S, Miller, CM, Killingsworth, MC & Cortie, MB 2009, 'Destruction and Control of Toxoplasma gondii Tachyzoites Using Gold Nanosphere / Antibody Conjugates', Small, vol. 5, no. 9, pp. 1030-1034.
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The protozoan parasiteToxoplasma gondii can be selectively targeted and photothermally destroyed by gold nanosphere/antibody conjugates (see image). The optical response of the nanospheres within the tissue window is shifted and enhanced by aggregation. Attachment of the conjugates alone, even without plasmonic heating, lowers the infectivity of the organism.

Platen, E & Rendek, RJ 2009, 'Exact scenario simulation for selected multi-dimensional stochastic processes', Communications on Stochastic Analysis, vol. 3, no. 3, pp. 443-465.
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Accurate scenario simulation methods for solutions of multi - dimensional stochastic differential equations find application in stochastic analysis, the statistics of stochastic processes and many other areas, for instance, in finance. Various discrete time simulation methods have been developed over the years. However, the simulation of solutions of some stochastic differential equations can be problematic due to systematic errors and numerical instabilities. Therefore, it is valuable to identify multi-dimensional stochastic differential equations with solutions that can be simulated exactly. This avoids several of the theoretical and practical problems encountered by those simulation methods that use discrete time approximations. This paper provides a survey of methods for the exact simulation of paths of some multidimensional solutions of stochastic differential equations including Ornstein- Uhlenbeck, square root, squared Bessel, Wishart and L´evy type processes.

Porntip, P, Kaewpitoon, N, Laha, T, Sripa, B, Kaewkes, S, Morales, ME, Mann, VH, Parriott, SK, Suttiprapa, S, Robinson, MW, To, J, Dalton, JP, Loukas, AC & Brindley, PJ 2009, 'Cathepsin F cysteine protease of the human liver fluke, Opisthorchis viverrini', Plos Neglected Tropical Diseases, vol. 3, no. 3, pp. 1-15.
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The liver fluke Opisthorchis viverrini is classified as a class I carcinogen due to the association between cholangiocarcinoma and chronic O. viverrini infection. During its feeding activity within the bile duct, the parasite secretes several cathepsin F cysteine proteases that may induce or contribute to the pathologies associated with hepatobiliary abnormalities.

Potter, C, Klooster, S, Huete, A, Genovese, V, Bustamante, M, Guimaraes, FL, Cosme, DOJR & Zepp, R 2009, 'Terrestrial carbon sinks in the Brazilian Amazon and Cerrado region predicted from MODIS satellite data and ecosystem modeling', Biogeosciences, vol. 6, pp. 937-945.
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A simulation model based on satellite observations of monthly vegetation cover from the Moderate Resolution Imaging Spectroradiometer (MODIS) was used to estimate monthly carbon fluxes in terrestrial ecosystems of Brazilian Amazon and Cerrado re- gions over the period 2000â2004. Net ecosystem production (NEP) flux for atmospheric CO2 in the region for these years was estimated. Consistently high carbon sink fluxes in terrestrial ecosystems on a yearly basis were found in the western portions of the states of Acre and RondËonia and the northern portions of the state of Par ´ a. These areas were not significantly impacted by the 2002â2003 El NiËno event in terms of net annual carbon gains. Areas of the region that show periodically high carbon source fluxes from terrestrial ecosystems to the atmosphere on yearly basis were found throughout the state of MaranhËao and the southern portions of the state of Amazonas. As demonstrated though tower site comparisons, NEP modeled with monthly MODIS Enhanced Vegetation Index (EVI) inputs closely resembles the mea sured seasonal carbon fluxes at the LBA Tapajos tower site. Modeling results suggest that the capacity for use of MODIS Enhanced Vegetation Index (EVI) data to predict seasonal uptake rates of CO2 in Amazon forests and Cerrado woodlands is strong.

Powter, DM & Gladstone, W 2009, 'Habitat-mediated use of space by juvenile and mating adult Port Jackson sharks, Heterodontus portusjacksoni, in Eastern Australia', Pacific Science, vol. 63, no. 1, pp. 1-14.
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Studies of spatial ecology of demersal sharks are critical to understanding the significance of habitat variation; however, limited information exists. Spatial ecology of adult Heterodontus portusjacksoni was studied at three locations on the central and southern coast of New South Wales, Australia, from January 2002 to December 2005. Juveniles within a nursery area were studied from December 2002 to December 2005. Tag-recapture, day and night underwater visual census, and acoustic tagging were used. Adults returned annually to the same coastal breeding reefs for up to four consecutive years. Individual juveniles resided within a sea-grass nursery area for at least 2 yr and were not uniformly distributed throughout the nursery. Adult females often sheltered in aggregations in gutters as a male avoidance strategy, and both sexes utilized the sand/reef interface in the absence of gutters. Juveniles aggregated infrequently due to absence of habitat features that mediated aggregation. Acoustic tracks of adults revealed periods of inactivity up to 27 hr. Juveniles spent significant amounts of time inactive, punctuated with short bouts of swimming. Juveniles utilized moderate activity spaces (3,510-583,990 m^sup 2^) centered over a core area of the sea-grass bed but also ranged over much larger areas of the bay. Use of space by H. portusjacksoni is strongly influenced by habitat characteristics throughout its life history.

Pringle, RM, Syfert, M, Webb, JK & Shine, R 2009, 'Quantifying historical changes in habitat availability for endangered species: use of pixel- and object-based remote sensing', Journal Of Applied Ecology, vol. 46, no. 3, pp. 544-553.
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Establishing medium- to long-term trends in habitat availability for endangered species is important for determining the causes of historical population declines and for designing effective management plans. For some animal species, relative habitat availability can be estimated using time series of aerial photographs, but the limited information in old black-and-white images makes it challenging to estimate accurately at large spatial scales. Australia's most endangered snake, the broad-headed snake Hoplocephalus bungaroides, requires unshaded, exfoliated sandstone rocks for shelter. Using digitized aerial photographs of four sites from 1941 and 1971, and a Quickbird satellite image from 2006, we estimated the trend in habitat availability for a well-studied population of H. bungaroides in New South Wales. We did this using both traditional, pixel-based classifications and a more recently developed object-based approach.

Quevrain, E, Domart-Coulon, I, Pernice, M & Bourguet-Kondracki, M-L 2009, 'Novel natural parabens produced by a Microbulbifer bacterium in its calcareous sponge host Leuconia nivea', ENVIRONMENTAL MICROBIOLOGY, vol. 11, no. 6, pp. 1527-1539.
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Raina, J, Tapiolas, DM, Willis, BL & Bourne, DG 2009, 'Coral-associated bacteria and their role in the biogeochemical cycling of sulfur', Applied and Environmental Microbiology, vol. 75, no. 11, pp. 3492-3501.
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Marine bacteria play a central role in the degradation of dimethylsulfoniopropionate (DMSP) to dimethyl sulfide (DMS) and acrylic acid, DMS being critical to cloud formation and thereby cooling effects on the climate. High concentrations of DMSP and DMS have been reported in scleractinian coral tissues although, to date, there have been no investigations into the influence of these organic sulfur compounds on coralassociated bacteria. Two coral species, Montipora aequituberculata and Acropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera, Roseobacter, Spongiobacter, Vibrio, and Alteromonas, which were isolated on media with either DMSP or DMS as the sole carbon source, comprised the majority of clones retrieved from coral mucus and tissue 16S rRNA gene clone libraries. Clones affiliated with Roseobacter sp. constituted 28% of the M. aequituberculata tissue libraries, while 59% of the clones from the A. millepora libraries were affiliated with sequences related to the Spongiobacter genus. Vibrio spp. were commonly isolated from DMS and acrylic acid enrichments and were also present in 16S rRNA gene libraries from coral mucus, suggesting that under ¿normal¿ environmental conditions, they are a natural component of coral-associated communities. Genes homologous to dddD, and dddL, previously implicated in DMSP degradation, were also characterized from isolated strains, confirming that bacteria associated with corals have the potential to metabolize this sulfur compound when present in coral tissues. Our results demonstrate that DMSP, DMS, and acrylic acid potentially act as nutrient sources for coral-associated bacteria and that these sulfur compounds are likely to play a role in structuring bacterial communities in corals, with important consequences for the health of both corals and coral reef ecosystems.

Raja, S, Thomas, P, Stuart, BH, Guerbois, JL & O'Brien, C 2009, 'The estimation of pig bone age for forensic application using thermogravimetric analysis', Journal Of Thermal Analysis And Calorimetry, vol. 98, no. 1, pp. 173-176.
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An accurate means of determining bone age is a goal for forensic scientists. In this study, thermogravimetric analysis (TGA) has been used to examine pig bone specimens of different post-mortem age. Analysis of bone in both air and nitrogen atmospheres reveals a decrease in total mass loss as the bones age. Two mass loss steps due to the decomposition of the organic bone components were observed and show decreasing trends with age for decomposition in an air atmosphere. In a nitrogen atmosphere the decomposition was observed to be more complex and age dependence of the mass loss for each step was not identified. The TGA data, however, demonstrates the potential of the technique as a means of estimating post-mortem age of forensic bone specimens.

Ramelow, S, Ratschbacher, L, Fedrizzi, A, Langford, NK & Zeilinger, A 2009, 'Discrete Tunable Color Entanglement', PHYSICAL REVIEW LETTERS, vol. 103, no. 25.
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Ramsay, HA, Leslie, LM & Kepert, JD 2009, 'A High-Resolution Simulation of Asymmetries in Severe Southern Hemisphere Tropical Cyclone Larry (2006)', MONTHLY WEATHER REVIEW, vol. 137, no. 12, pp. 4171-4187.
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Ramsey, KH, Sigar, IM, Schripsema, JH, Denman, CJ, Bowlin, AK, Myers, GAS & Rank, RG 2009, 'Strain and Virulence Diversity in the Mouse Pathogen Chlamydia muridarum', INFECTION AND IMMUNITY, vol. 77, no. 8, pp. 3284-3293.
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Ranjbartoreh, A & Wang, G 2009, 'Bending stability of inner and outer tubes of double-walled carbon nanotube', International Journal of Nanoscience, vol. 8, no. 1-2, pp. 9-13.
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This paper considers the effects of bending moment on the structure of double-walled carbon nanotube (DWCNT). Two types of DWCNTs with almost the same aspect ratio (length/radius) are selected; also continuum modeling is utilized to study the bending stability of inner and outer tubes. As a result of the van der Waals interaction between adjacent tubes the critical bending moment of inner tube is higher than this moment of outer tube which is indicated from the obtained results of this research; thus, achieving higher reliability in nanostructures, the critical bending moment of outer tube should be taken into account.

RANJBARTOREH, AR & WANG, G 2009, 'BENDING STABILITY OF INNER AND OUTER TUBES OF DOUBLE-WALLED CARBON NANOTUBE', International Journal of Nanoscience, vol. 08, no. 01n02, pp. 9-13.
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This paper considers the effects of bending moment on the structure of double-walled carbon nanotube (DWCNT). Two types of DWCNTs with almost the same aspect ratio (length/radius) are selected; also continuum modeling is utilized to study the bending stability of inner and outer tubes. As a result of the van der Waals interaction between adjacent tubes the critical bending moment of inner tube is higher than this moment of outer tube which is indicated from the obtained results of this research; thus, achieving higher reliability in nanostructures, the critical bending moment of outer tube should be taken into account.

Rasoulouniriana, D, Siboni, N, Ben-Dov, E, Kramarsky-Winter, E, Loya, Y & Kushmaro, A 2009, 'Pseudoscillatoria coralii gen. nov., sp nov., a cyanobacterium associated with coral black band disease (BBD)', DISEASES OF AQUATIC ORGANISMS, vol. 87, no. 1-2, pp. 91-96.
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Rawling, T, Austin, CE, Buchholz, F, Colbran, SB & McDonagh, AM 2009, 'Ruthenium Phthalocyanine-Bipyridyl Dyads as Sensitisers for Dye-Sensitised Solar Cells: Dye Coverage versus Molecular Efficiency', Inorganic Chemistry, vol. 48, no. 7, pp. 3215-3227.
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The application of ruthenium phthalocyanine complexes as sensitizing dyes in dye-sensitized solar cells (DSCs) is explored. Four monomeric complexes are reported which vary in peripheral substitution and axial ligand anchoring groups. Sensitizing dyes containing two ruthenium centers are also presented. These dyads, which contain ruthenium phthalocyanine and bipyridyl chromophores, were prepared using a protection/deprotection strategy that allows for convenient purification. DSCs fabricated using the phthalocyanine complexes and dyads were less efficient than those incorporating a standard DSC dye. However, on the basis of the number of molecules bound to the TiO2 electrode surfaces, several of the new complexes were more efficient at pholocurrent generation. The results highlight the importance of molecular size, and thus the dye coverage of the electrode surface in the design of new sensitizing dyes.

Rawling, T, Austin, CE, Hare, DJ, Doble, PA, Zareie, HM & McDonagh, AM 2009, 'Thin films of Ruthenium Phthalocyanine complexes', Nano Research, vol. 2, pp. 678-687.
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Four new ruthenium phthalocyanine complexes bearing axial ligands with thioacetate groups that facilitate thin film formation on gold surfaces are presented. Scanning tunnelling microscopy (STM) images and surface coverage data obtained by solution inductively coupled plasma mass spectrometry (ICP-MS) experiments show that peripheral and axial ligand substituents on the complexes have a significant effect on their surface coverage. A laser ablation ICP-MS technique that provides information about thin films across macro-sized areas is described here for the first time. Using the technique, the maximum surface coverage of a ruthenium phthalocyanine complex was found to occur within one minute of gold substrate immersion in the complexcontaining solution.

Raymond, JJ, Van Oorschot, R, Gunn, PR, Walsh, SJ & Roux, CP 2009, 'Trace DNA success rates relating to volume crime offences', Forensic Science International: Genetics Supplement Series, vol. 2, no. 1, pp. 136-137.
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In this study, 252 trace DNA samples (from handled surfaces) from 201 burglary, robbery and drugs cases were compiled to assess success rates and to interpret the value of trace DNA evidence in volume crime investigations. The average amount of DNA recovered from the trace DNA samples collected was 1.7 ng. Full or major (12 or more alleles) profiles were recovered from 14% of samples. Samples from firearms and burglary points of entry were the least successful. Mixtures were recovered from 21% of samples, presenting a case for the collection of more elimination profiles to enable more samples to be used for database purposes. The research highlighted the difficulties in collecting data relating to the success rates of samples. Computerised automation of this process would be extremely beneficial in the assistance of policy development, method application, training, and investigative usefulness.

Raymond, JJ, Van Oorschot, R, Gunn, PR, Walsh, SJ & Roux, CP 2009, 'Trace evidence characteristics of DNA: A preliminary investigation of the persistence of DNA at crime scenes', Forensic Science International: Genetics, vol. 4, no. 1, pp. 26-33.
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The successful recovery of trace or contact DNA is highly variable. It is seemingly dependent on a wide range of factors, from the characteristics of the donor, substrate and environment, to the delay between contact and recovery. There is limited research on the extent of the effect these factors have on trace DNA analysis. This study investigated the persistence of trace DNA on surfaces relevant to the investigation of burglary and robbery offences. The study aimed to limit the number of variables involved to solely determine the effect of time on DNA recovery. Given that it is difficult to control the quantity of DNA deposited during a hand contact, human buffy coat and DNA control solution were chosen as an alternative to give a more accurate measure of quantity. Set volumes of these solutions were deposited onto outdoor surfaces (window frames and vinyl material to mimic burglary and `bag snatch offences) and sterile glass slides stored in a closed environment in the laboratory, for use as a control. Trace DNA casework data was also scrutinised to assess the effect of time on DNA recovery from real samples. The amount of DNA recovered from buffy coat on the outdoor surfaces declined by approximately half over two weeks, to a negligible amount after six weeks. Profiles could not be obtained after two weeks. The samples stored in the laboratory were more robust, and full profiles were obtained after six weeks, the longest time period tested in these experiments. It is possible that profiles may be obtained from older samples when kept in similarly favourable conditions.

Raymond, JJ, Van Oorschot, R, Walsh, SJ, Roux, CP & Gunn, PR 2009, 'Trace DNA and street robbery: A criminalistic approach to DNA evidence', Forensic Science International: Genetics Supplement Series, vol. 2, no. 1, pp. 544-546.
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It is now routine to detect trace DNA from handled objects, and with such low quantities of DNA the principles of criminalistics are now more relevant to biological evidence. This study aimed to provide data into the abundance, transfer and persistence of trace DNA, in a particular crime scenariostreet robbery. Items commonly stolen during a robbery (handbags and wallets) were swabbed to determine the background levels of DNA present. The likelihood of DNA transferring onto wallets during and after a robbery was investigated, as was the amount of handling time needed for the offender's DNA to become a major component in the recovered profile. A significant amount of DNA was recovered from wallets and bags in regular use, including small amounts of non-owner DNA. This indicates that background DNA may interfere with the recovery of offenders DNA. Profiles recovered from wallets stolen in a simulated robbery were in the majority mixtures, however the robber was a major component of the mixture or a single source profile in 40% of the profiles. The findings demonstrate that background data on the trace evidence characteristics of DNA will aid its interpretation and presentation in criminal trials.

Reichel, MP & Ellis, JT 2009, 'Neospora caninum--how close are we to development of an efficacious vaccine that prevents abortion in cattle?', International Journal For Parasitology, vol. 39, no. 11, pp. 1173-1187.
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Neospora caninum is a protozoan parasite that causes abortion in cattle around the world. Although the clinical signs of disease in both dogs and cattle have now been recognised for over 20 years, treatment and control options are still limited, despite the availability of a commercial vaccine in some countries of the world. The case for an efficacious vaccine has not been convincingly waged by farmers, veterinarians and other members of the agricultural and rural communities. In recent times, however, economic modelling has been used to estimate the industry losses due to Neospora-associated abortion, providing, in turn, the business case for forms of control for this parasite, including the development of vaccines. In this review, we document progress in all areas of the vaccine development pipeline, including live, killed and recombinant forms and the animal models available for vaccine evaluation. In addition, we summarise the main outcomes on the economics of Neospora control and suggest that the current boom in the global dairy industry increases the specific need for a vaccine against N. caninum-associated abortion.

Reimers, JR, Lee, SH, Larsen, AG, Kotani, H, Ohkubo, K, Fukuzumi, S & Crossley, MJ 2009, 'The nature of long-lived photo-induced charge separation in ferrocene-porphyrin-fullerene molecules', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 238.

Reimers, JR, Mckemmish, L, Mckenzie, R, Mark, A & Hush, N 2009, 'Weak, Strong, And Coherent Regimes Of Frohlich Condensation And Their Applications To Terahertz Medicine And Quantum Consciousness', Proceedings of The National Academy of Sciences of the United States of America, vol. 106, no. 11, pp. 4219-4224.
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In 1968, Frohlich showed that a driven set of oscillators can condense with nearly all of the supplied energy activating the vibrational mode of lowest frequency. This is a remarkable property usually compared with Bose-Einstein condensation, superconductivity, lasing, and other unique phenomena involving macroscopic quantum coherence. However, despite intense research, no unambiguous example has been documented. We determine the most likely experimental signatures of Frohlich condensation and show that they are significant features remote from the extraordinary properties normally envisaged. Frohlich condensates are classified into 3 types: weak condensates in which profound effects on chemical kinetics are possible, strong condensates in which an extremely large amount of energy is channeled into 1 vibrational mode, and coherent condensates in which this energy is placed in a single quantum state. Coherent condensates are shown to involve extremely large energies, to not be produced by the Wu-Austin dynamical Hamiltonian that provides the simplest depiction of Frohlich condensates formed using mechanically supplied energy, and to be extremely fragile. They are inaccessible in a biological environment. Hence the Penrose-Hameroff orchestrated objective-reduction model and related theories for cognitive function that embody coherent Frohlich condensation as an essential element are untenable. Weak condensates, however, may have profound effects on chemical and enzyme kinetics, and may be produced from biochemical energy or from radio frequency, microwave, or terahertz radiation. Pokorny's observed 8.085-MHz microtubulin resonance is identified as a possible candidate, with microwave reactors (green chemistry) and terahertz medicine appearing as other feasible sources.

Ren, D, Wang, J, Fu, R, Karoly, DJ, Hong, Y, Leslie, LM, Fu, C & Huang, G 2009, 'Mudslide-caused ecosystem degradation following Wenchuan earthquake 2008', GEOPHYSICAL RESEARCH LETTERS, vol. 36.
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Rice, SA, Tan, CH, Mikkelsen, PJ, Kung, V, Woo, J, Tay, M, Hauser, A, McDougald, D, Webb, JS & Kjelleberg, S 2009, 'The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage', ISME JOURNAL, vol. 3, no. 3, pp. 271-282.
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Ridwan, S, Thompson, RS, Jap, B, Lal, S & Fischer, P 2009, 'Single Channel Wireless EEG: Proposed Application in Train Drivers', African Journal of Information & Communication Te..., vol. 5, no. 2, pp. 1-10.
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Electroencephalography (EEG) can be used as an indicator of fatigue. Several studies have shown that slow wave brain activities, delta (0-4 Hz) and theta (4- 8 Hz), increase as an individual becomes fatigued, while the fast brain activities, alpha (8-13 Hz) and beta (13-35 Hz), decrease. However, an EEG is a complex piece of equipment that is generally used in laboratory based studies. In order to develop a fatigue countermeasure device for train drivers using EEG, there is a need for a simple and wireless EEG monitor. This paper explains the development of a single channel wireless EEG device

Ridwan, SD, Thompson, R, Jap, BT, Lal, SK & Fischer, P 2009, 'Single Channel Wireless EEG: Proposed Application in Train Drivers', African Journal of Information & Communication Technology, vol. 5, no. 2.
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Electroencephalography (EEG) can be used as an indicator of fatigue. Several studies have shown that slow wave brain activities, delta (0-4 Hz) and theta (4- 8 Hz), increase as an individual becomes fatigued, while the fast brain activities, alpha (8-13 Hz) and beta (13-35 Hz), decrease. However, an EEG is a complex piece of equipment that is generally used in laboratory based studies. In order to develop a fatigue countermeasure device for train drivers using EEG, there is a need for a simple and wireless EEG monitor. This paper explains the development of a single channel wireless EEG device.

Rissman, A, Mau, B, Biehl, B, Darling, AE, Glasner, J & Perna, N 2009, 'Reordering Contigs Of Draft Genomes Using The Mauve Aligner', Bioinformatics, vol. 25, no. 16, pp. 2071-2073.
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Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel application of the Mauve aligner and viewer provides an automated reorde

Robertson, J & McNevin, D 2009, 'Book Reviews', Australian Journal of Forensic Sciences, vol. 41, no. 1, pp. 81-84.
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Robinson, MW, Menon, R, Donnelly, SM, Dalton, JP & Ranganathan, S 2009, 'An Integrated Transcriptomics And Proteomics Analysis Of The Secretome Of The Helminth Pathogen Fasciola Hepatica Proteins Associated With Invasion And Infection Of The Mammalian Host', Molecular & Cellular Proteomics, vol. 8, no. 8, pp. 1891-1907.
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To infect their mammalian hosts, Fasciola hepatica larvae must penetrate and traverse the intestinal wall of the duodenum, move through the peritoneum, and penetrate the liver. After migrating through and feeding on the liver, causing extensive tissue damage, the parasites move to their final niche in the bile ducts where they mature and produce eggs. Here we integrated a transcriptomics and proteomics approach to profile Fasciola secretory proteins that are involved in host-pathogen interactions and to correlate changes in their expression with the migration of the parasite. Prediction of F. hepatica secretory proteins from 14,031 expressed sequence tags (ESTs) available from the Wellcome Trust Sanger Centre using the semiautomated EST2Secretome pipeline showed that the major components of adult parasite secretions are proteolytic enzymes including cathepsin L, cathepsin B, and asparaginyl endopeptidase cysteine proteases as well as novel trypsin-like serine proteases and carboxypeptidases. Proteomics analysis of proteins secreted by infective larvae, immature flukes, and adult F. hepatica showed that these proteases are developmentally regulated and correlate with the passage of the parasite through host tissues and its encounters with different host macromolecules. Proteases such as FhCL3 and cathepsin B have specific functions in larvae activation and intestinal wall penetration, whereas FhCL1, FhCL2, and FhCL5 are required for liver penetration and tissue and blood feeding. Besides proteases, the parasites secrete an array of antioxidants that are also highly regulated according to their migration through host tissues. However, whereas the proteases of F. hepatica are secreted into the parasite gut via a classical endoplasmic reticulum/Golgi pathway, we speculate that the antioxidants, which all lack a signal sequence, are released via a non-classical trans-tegumental pathway.

Robson, TC, Baker, AC & Murray, B 2009, 'Differences in leaf-litter invertebrate assemblages between radiata pine plantations and neighbouring native eucalypt woodland', Austral Ecology, vol. 34, no. 4, pp. 368-376.
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We investigated the structure, composition and environmental correlates of leaf-litter invertebrate assemblages in Pinus radiata plantations and in neighbouring native eucalypt woodland in the Jenolan Caves Karst Conservation Reserve, south-east Australia. Invertebrate assemblages of plantations were compared with remnant eucalypt woodland located well away from the influence of plantations to determine the direct effects of plantations as a result of habitat-replacement with a non-native plantation species. We also included in our comparisons edge habitat of eucalypt woodland located immediately adjacent to plantations. This unique edge habitat is exposed to the intrusion of large volumes of pine leaf-litter from plantations, which has the potential to affect indirectly invertebrate assemblages of surrounding woodland. We found that species richness of invertebrates was significantly lower in pine plantations compared with remnant eucalypt woodland. There was a complete absence of species from 12 invertebrate orders that were found in surrounding eucalypt woodland. A rich and abundant native plant understorey that provides increased habitat heterogeneity is the most likely explanation for the richer invertebrate assemblage found in remnant eucalypt woodland. The total abundance of all invertebrate taxa in pine plantations in winter was significantly higher than in remnant eucalypt woodland, pine-litter edges and pine-free edges. Plantations were characterized by particularly high abundances of species in two orders, Acari and Collembola. High abundances of acarine and collembolan species in plantations were associated with a decompositional environment represented by comparatively higher moisture contents and higher C : N ratios of both leaf-litter and soil, higher soil conductivity and lower soil pH.

Rodgers, K, Ford, J & Brunk, U 2009, 'Heat shock proteins: Keys to healthy ageing?', Redox Report, vol. 14, no. 4, pp. 147-153.
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Organisms produce reactive species throughout their lives, and this may result in damage to proteins and other biological molecules. Oxidatively damaged proteins are normally selectively degraded and replaced, but this process appears to be less efficien

Roger, E & Ramp, D 2009, 'Incorporating habitat use in models of fauna fatalities on roads', Diversity And Distributions, vol. 15, no. 2, pp. 222-231.
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To highlight the benefit of using habitat use to improve the accuracy of predictive road fatality models. The Snowy Mountains Highway in southern New South Wales, Australia. A binary logistic regression model was constructed using wombat fatality presenc

Roy Chowdhury, P, Merlino, J, Labbate, M, Cheong, EY, Gottlieb, T & Stokes, H 2009, 'Tn6060, a Transposon from a Genomic Island in a Pseudomonas aeruginosa Clinical Isolate That Includes Two Class 1 Integrons', Antimicrobial agents and chemotherapy, vol. 53, no. 12, pp. 5294-5296.
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A 25,441-bp transposon was recovered from a Pseudomonas aeruginosa clinical isolate. While the transposition module was >99% identical to sequence of Tn1403, the element had been subject to rearrangements, with two In70.2-like class 1 integrons inserted into it in an unusual "tail-to-tail" configuration. One cassette array was the same as that in In70.2; however, the second was different, generating a transposon that collectively includes six resistance cassettes.

Ruffieux, Y & Green, PJ 2009, 'Alignment of multiple configurations using hierarchical models', Journal Of Computational And Graphical Statistics, vol. 18, no. 3, pp. 756-773.
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We describe a method for aligning multiple unlabeled configurations simultaneously, Specifically. we extend the two-con figuration matching approach of Green and Mardia (2006) to the multiple configuration setting. Our approach is based on the introducti

Ruppert, D, Wand, M & Carroll, RJ 2009, 'Semiparametric regression during 2003-2007', Electronic Journal of Statistics, vol. 3, no. 1, pp. 1193-1256.
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Semiparametric regression is a fusion between parametric regression and nonparametric regression that integrates low-rank penalized splines, mixed model and hierarchical Bayesian methodology thus allowing more streamlined handling of longitudinal and spatial correlation. We review progress in the field over the five-year period between 2003 and 2007. We find semiparametric regression to be a vibrant field with substantial involvement and activity, continual enhancement and widespread application.

Rutlidge, HT & Reedy, BJ 2009, 'Classification of heterogeneous solids using infrared hyperspectral imaging', Applied Spectrocopy, vol. 63, no. 2, pp. 172-179.
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Methods were explored for the classification of heterogeneous powder mixtures using Fourier transform infrared (FT-IR) hyperspectral image data. The images collected were non-congruent, meaning that samples of the same mixture do not have the same spatial arrangements of their components in their images. In order to classify such images on a one-image-per-object basis, dimension reduction was carried out so as to produce a score or feature vector for each image that preserved information about the heterogeneity of the sample. These feature vectors were then classified using discriminant analysis (DA) or soft independent modeling of class analogy (SIMCA). The most successful approach was the use of a median-interquartile range "super-spectrum" as the feature vector representing each image; using principal component analysis (PCA) DA classification, 87.5% of training samples were correctly classified using leave-one-out cross-validation, and 100% of a test set were correctly classified. This compares with 52.5% and 72%, respectively, when single-point spectra were used to classify the samples.

Ryan, L 2009, 'Spatial Epidemiology Some Pitfalls and Opportunities', EPIDEMIOLOGY, vol. 20, no. 2, pp. 242-244.
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Sabir, MI, Xu, X & Li, L 2009, 'A review on biodegradable polymeric materials for bone tissue engineering applications', Journal of Materials Science, vol. 44, pp. 5713-5724.
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Salama, RO, Traini, D, Chan, H-K, Sung, A, Ammit, AJ & Young, PM 2009, 'Preparation and Evaluation of Controlled Release Microparticles for Respiratory Protein Therapy', JOURNAL OF PHARMACEUTICAL SCIENCES, vol. 98, no. 8, pp. 2709-2717.
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Sameer, A-EI, Amany, GM, Abdela, AA & Fadel, SA 2009, 'CYP2C19 genotypes in a population of healthy volunteers and in children with hematological malignancies in Gaza Strip.', The Canadian journal of clinical pharmacology = Journal canadien de pharmacologie clinique, vol. 16, no. 1, pp. e156-e162.
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Cytochrome P450 2C19 (CYP2C19) participates in the metabolism of many clinically important drugs and xenobiotic compounds. Genetic polymorphisms of the CYP2C19 gene are described to have possible effect on drug treatment and increasing susceptibility to carcinogenic substances. The aim of this study was to determine the frequencies of the common polymorphic CYP2C19 alleles (CYP2C19*2 and CYP2C19*3) in Gaza Strip population and to investigate their association with occurrence of childhood hematological malignancies as compared to healthy subjects.The polymorphism of CYP2C19 was analyzed by PCR-RFLP. DNA was extracted from blood samples obtained from 52 previously diagnosed hematological malignancy children and 200 normal subjects.In the patient group the frequencies of CYP2C19*2 and CYP2C19*3 were 9.62% and 0.96%, respectively; while in the control group the respective frequencies were 5.75% and 3%. There is no significant difference between the healthy and the patient groups in terms of the frequencies of CYP2C19*2 and CYP2C19*3. The genotyping analysis showed the following results: 15.39% (1*/2*), 1.92% (1*/3*), 1.92% (2*/2*) and 80.77% (1*/1*) in the patients, while in the normal subjects the distribution of CYP2C19*1/*1, *1/*2, *1/*3, *2/*2, *2/*3 and *3/*3 genotypes were 86.5, 6.5, 3, 1.5, 2, and 0.5 %, respectively.There is no significant association between the CYP2C19 polymorphism and the occurrence of the childhood hematological malignancies. The distribution of CYP2C19*2 in the Gaza Strip population is lower than that in Caucasians, Africans and the Asian populations. The CYP2C19*3 allele, which was not reported in the Caucasian populations, is present in 3% of the Gaza Strip population. Further studies are needed to investigate the role of other CYPs' polymorphisms in our patient group.

Sanchez, B, Budtz-jorgensen, E & Ryan, LM 2009, 'An Estimating Equations Approach To Fitting Latent Exposure Models With Longitudinal Health Outcomes', Annals of Applied Statistics, vol. 3, no. 2, pp. 830-856.
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The analysis of data arising from environmental health studies which collect a large number of measures of exposure can benefit from using latent variable models to summarize exposure information. However, difficulties with estimation of model parameters may arise since existing fitting procedures for linear latent variable models require correctly specified residual variance structures for unbiased estimation of regression parameters quantifying the association between (latent) exposure and health outcomes. We propose an estimating equations approach for latent exposure models with longitudinal health outcomes which is robust to misspecification of the outcome variance. We show that compared to maximum likelihood, the loss of efficiency of the proposed method is relatively small when the model is correctly specified. The proposed equations formalize the ad-hoc regression on factor scores procedure, and generalize regression calibration. We propose two weighting schemes for the equations, and compare their efficiency. We apply this method to a study of the effects of in-utero lead exposure on child development.

Sanchez, BN, Houseman, EA & Ryan, LM 2009, 'Residual-Based Diagnostics for Structural Equation Models', BIOMETRICS, vol. 65, no. 1, pp. 104-115.
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Saraireh, S, Smith, P, King, B, Reimers, JR, Wallace, B & Crossley, M 2009, 'Norbornadiene-Based Molecules For Functionalizing The Si(001) Surface', Journal of Physical Chemistry C, vol. 113, no. 36, pp. 16094-16103.
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One of the fundamental requirements in the development of silicon-based molecular electronic devices is the ability to attach organic molecules to silicon surfaces to form well-defined structures that are stable and possess specific characteristics. Previous work has shown that, although norbornadiene (NBE) forms very stable structures on the Si(001) surface with its apex CH(2) group pointing outward from the surface, these structures cannot be resolved in scanning tunneling microscopy. In this paper, we report the results of density functional theory calculations of the interaction with the Si(001) surface of 7-trifluoroacetoxy-norbornadiene (7-TFA-NBE) in which a hydrogen atom of the apex CH(2) group is substituted by the trifluoroacetoxy OC(O)CF(3) group. This molecule is shown to form very stable structures with the trifluoroacetoxy group sitting well above the surface. Moreover, in contrast to NBE, we find that the different 7-TFA-NBE chemisorption structures should be distinguishable in high-resolution scanning tunneling microscopy experiments. This raises the exciting possibility of employing norbornadiene-based molecules with appropriately chosen functional groups to create molecular structures on Si(001) that are stable and experimentally distinguishable and yield the requisite atomic and electronic properties.

Sasani, S, Hemming, M, Oliver, S, Greenup, A, Tavakkol-afshari, R, Mahfoozi, S, Poustini, K, Sharifi, H, Dennis, ES, Peacock, J & Trevaskis, B 2009, 'The influence of vernalization and daylength on expression of flowering-time genes in the shoot apex and leaves of barley (Hordeum vulgare).', JOURNAL OF EXPERIMENTAL BOTANY, vol. 60, no. 7, pp. 2169-2178.
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Responses to prolonged low-temperature treatment of imbibed seeds (vernalization) were examined in barley (Hordeum vulgare). These occurred in two phases: the perception of prolonged cold, which occurred gradually at low temperatures, and the acceleration of reproductive development, which occurred after vernalization. Expression of the VERNALIZATION1 gene (HvVRN1) increased gradually in germinating seedlings during vernalization, both at the shoot apex and in the developing leaves. This occurred in darkness, independently of VERNALIZATION2 (HvVRN2), consistent with the hypothesis that expression of HvVRN1 is induced by prolonged cold independently of daylength flowering-response pathways. After vernalization, expression of HvVRN1 was maintained in the shoot apex and leaves. This was associated with accelerated inflorescence initiation and with down-regulation of HvVRN2 in the leaves. The largest determinant of HvVRN1 expression levels in vernalized plants was the length of seed vernalization treatment. Daylength did not influence HvVRN1 expression levels in shoot apices and typically did not affect expression in leaves. In the leaves of plants that had experienced a saturating seed vernalization treatment, expression of HvVRN1 was higher in long days, however. HvFT1 was expressed in the leaves of these plants in long days, which might account for the elevated HvVRN1 expression. Long-day up-regulation of HvVRN1 was not required for inflorescence initiation, but might accelerate subsequent stages of inflorescence development. Similar responses to seed vernalization were also observed in wheat (Triticum aestivum). These data support the hypothesis that VRN1 is induced by cold during winter to promote spring flowering in vernalization-responsive cereals.

Sastraruji, K, Pyne, SG, Ung, AT, Mungkornasawakul, P, Lie, W & Jatisatienr, A 2009, 'Structural Revision of Stemoburkilline from an E-Alkene to a Z-Alkene', Journal of Natural Products, vol. 72, no. 2, pp. 316-318.
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Semisynthesis studies starting from (11Z)-1?,2?-didehydrostemofoline (4) indicated that the known Stemona alkaloid stemoburkilline is the Z-isomer and not the E-isomer as initially reported. The semisynthesis involved conversion of (11Z)-1?,2?-didehydrostemofoline (4) to 11(S),12(S)-dihydrostemofoline (3) followed by a stereoselective base-catalyzed ring-opening reaction to give (Z)-stemoburkilline (8). The same product was obtained using a similar synthetic protocol starting from isostemofoline (6) via a based-catalyzed ring-opening reaction of 11(S),12(R)-dihydrostemofoline (1). A re-examination of the crude root extracts of Stemona burkillii Prain and further NOE studies established stemoburkilline as the Z-isomer

Scanlan, DJ, Ostrowski, M, Mazard, S, Dufresne, A, Garczarek, L, Hess, WR, Post, AF, Hagemann, M, Paulsen, I & Partensky, F 2009, 'Ecological Genomics of Marine Picocyanobacteria', MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, vol. 73, no. 2, pp. 249-+.
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Schleheck, D, Barraud, N, Klebensberger, J, Webb, JS, McDougald, D, Rice, SA & Kjelleberg, S 2009, 'Pseudomonas aeruginosa PAO1 Preferentially Grows as Aggregates in Liquid Batch Cultures and Disperses upon Starvation', PLOS ONE, vol. 4, no. 5.
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Schwefel, HG & Poulton, CG 2009, 'An improved method for calculating resonances of multiple dielectric disks arbitrarily positioned in the plane', Optics Express, vol. 17, no. 15, pp. 13178-13186.
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We present a numerically improved multipole formulation for the calculation of resonances of multiple disks located at arbitrary positions in a 2-d plane, and suitable for the accurate computation of the resonances of large numbers of disks and of high-wavenumber eigenstates. Using a simple reformulation of the field expansions and boundary conditions, we are able to transform the multipole formalism into a linear eigenvalue problem, for which fast and accurate methods are available. Observing that the motion of the eigenvalues in the complex plane is analytic with respect to a two parameter family, we present a numerical algorithm to compute a range of multiple-disk resonances and field distributions using only two diagonalizations. This method can be applied to photonic molecules, photonic crystals, photonic crystal fibers, and random lasers.

Scott, NE, Bogema, D, Connolly, AM, Falconer, L, Djordjevic, SP & Cordwell, SJ 2009, 'Mass spectrometric characterisation of the surface-associated 42 kDa lipoprotein JIpA as a Glycosylated antigen in strains of Campylobacter jejuni', Journal Of Proteome Research, vol. 8, no. 10, pp. 4654-4664.
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Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world. Immunoproteomics highlighted a 42-45 kDa antigen that comigrated on two-dimensional (2-DE) gels with the C. jejuni major outer membrane protein (MOMP). Predictive analysis revealed two candidates for the identity of the antigen, the most likely of which was the surface-associated lipoprotein, JlpA. Recombinant JlpA (rJlpA) reacted with patient sera, confirming that JlpA is antigenic. Polyclonal antibodies raised against rJlpA reacted against 3 JlpA mass variants from multiple C. jejuni. These variants differed by approximately 1.5 kDa, suggesting the presence of the N-linked C. jejuni glycan on two sites. Soybean agglutinin affinity and 2-DE purified 2 JlpA glycoforms (43.5 and 45 kDa). Their identities were confirmed using mass spectrometry following trypsin digest. Glycopeptides within JlpA variants were identified by proteinase-K digestion, graphite micropurification and MS-MS. Sites of glycosylation were confirmed as asparagines 107 and 146, both of which are flanked by the N-linked sequon. Sequence analysis confirmed that the N146 sequon is conserved in all C. jejuni genomes examined to date, while the N107 sequon is absent in the reference strain NCTC 11168. Western blotting confirmed the presence of only a single JlpA glycoform in both virulent (O) and avirulent (GS) isolates of NCTC 11168. MS analysis showed that JlpA exists as 3 discrete forms, unmodified, glycosylated at N146, and glycosylated at both N146/107, suggesting glycan addition at N146 is necessary for N107 glycosylation. Glycine extracts and Western blotting revealed that doubly glycosylated JlpA was the predominant form on the C. jejuni JHH1 surface; however, glycosylation is not required for antigenicity. This is the first study to identify N-linked glycosylation of a surface-exposed C. jejuni virulence factor and to show strain variation in glycosylation sites.

Seebacher, F, Murray, SA & Else, PL 2009, 'Thermal acclimation and regulation of metabolism in a reptile (Crocodylus porosus): the importance of transcriptional mechanisms and membrane composition', Physiological and Biochemical Zoology, vol. 82, no. 6, pp. 766-775.
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Energy metabolism is fundamental for animal fitness because it fuels locomotion, growth, and reproduction. Mitochondrial capacities often acclimate to compensate for negative thermodynamic effects. Our aim was to determine the importance of transcriptional regulation and membrane fatty acid composition in modulating oxidative capacities at body temperatures selected in a cold and a warm environment by a reptile (Crocodylus porosus). In the cool environment (mean selected T(b) = 21 degrees C), mRNA concentrations of the transcription factor peroxisome proliferator-activated receptor gamma (PPAR gamma) and its coactivator PPAR gamma coactivator 1 alpha (PGC-1 alpha), as well as of the cytochrome c oxidase (COX) subunits COX1 and COX5, were significantly higher in the liver but not in skeletal muscle compared with animals in the warm environment (mean selected T(b) = 29 degrees C). F(O)F(1)-ATPase subunit alpha mRNA concentrations were significantly higher in both muscle and the liver in the cool animals. A positive relationship between PGC-1 alpha and PPAR gamma mRNA concentrations, with an indicator of mitochondrial density (16S rRNA) in muscle and COX and F(O)F(1)-ATPase subunit alpha mRNA concentrations in liver, suggest that these proteins regulate quantity increases of mitochondria during acclimation. The percent saturated fatty acids in liver membranes of cool animals was significantly lower, and the n3 fatty acid content was significantly higher, compared with in warm animals. The n3 fatty acid content was positively related to COX enzyme activity in the liver, and there was a negative relationship between n7 fatty acid content and COX activity in muscle. Hence, metabolic acclimation is mediated by both transcriptional regulation and membrane fatty acid composition. The importance of PGC-1 alpha and PPAR gamma in a reptile indicate that the mechanisms that regulate metabolism are conserved among vertebrates.

Segele, ZT, Lamb, PJ & Leslie, LM 2009, 'Large-scale atmospheric circulation and global sea surface temperature associations with horn of Africa June-September rainfall', International Journal of Climatology, vol. 29, no. 8, pp. 1075-1100.
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This study uses correlation, regression, and composite analyses for the period 1970-1999 to explore the relationships between the June-September rainfall in the Horn of Africa (especially Ethiopian) and large-scale regional atmospheric circulation patterns across Africa and the Atlantic and Indian Oceans, and global sea surface temperature (SST) anomalies. Abundant rainfall in the Horn of Africa is associated with enhanced westerlies across western and central Africa. These westerlies are produced by a stronger north-east directed mean sea level pressure (MSLP) gradient resulting from MSLP intensification over the Gulf of Guinea and deepening of the monsoon trough across the Arabian Peninsula. This is reflected by a strong correlation (-0.71) between 5-day (pentad) Ethiopian rainfall and the Gulf of Guinea minus the Arabian Peninsula MSLP difference. This correlation decreases to -0.39 when the seasonal cycles are removed from both time series. A wet Horn of Africa monsoon is also associated with deep moist air extending up to mid-troposphere and large water vapour transport convergence across much of Ethiopia, a strong Somali low-level jet, and a strong tropical easterly jet (TEJ). Although there are large changes in TEJ strength, the position of the jet axis shows little variation between wet and dry events. Associated with the TEJ, the strongest upper level divergence occurs at 100 hPa, where the raw/de-seasonalized zonal wind speed correlates negatively (-0.71/-0.23) with the corresponding Ethiopian rainfall at the pentad time-scale. Furthermore, SSTs over the equatorial Pacific, Indian, and southern Atlantic Oceans correlate strongly with contemporary Ethiopian summer rainfall. In general, Ethiopian rainfall is suppressed during El Niño and enhanced during La Niña. This identification and documentation of the regional atmospheric circulation patterns and global SST anomalies directly linked to rainfall variability over Ethiopia/Horn of Africa, are crucial fo...

Segele, ZT, Lamb, PJ & Leslie, LM 2009, 'Seasonal-to-Interannual Variability of Ethiopia/Horn of Africa Monsoon. Part I: Associations of Wavelet-Filtered Large-Scale Atmospheric Circulation and Global Sea Surface Temperature', JOURNAL OF CLIMATE, vol. 22, no. 12, pp. 3396-3421.
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Segele, ZT, Leslie, LM & Lamb, PJ 2009, 'Evaluation and adaptation of a regional climate model for the Horn of Africa: rainfall climatology and interannual variability', INTERNATIONAL JOURNAL OF CLIMATOLOGY, vol. 29, no. 1, pp. 47-65.
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Sentuerk, D, Nguyen, DV, Tassone, F, Hagerman, RJ, Carroll, RJ & Hagerman, PJ 2009, 'Covariate Adjusted Correlation Analysis with Application to FMR1 Premutation Female Carrier Data', BIOMETRICS, vol. 65, no. 3, pp. 781-792.
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Seuront, L, Leterme, SC, Seymour, JR, Mitchell, JG, Ashcroft, D, Noble, W, Thomson, PG, Davidson, AT, van den Enden, R, Scott, FJ, Wright, SW, Schapira, M, Chapperon, C & Cribb, N 2009, 'Role of microbial and phytoplanktonic communities in the control of seawater viscosity off East Antarctica (30-80° E)', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 57, no. 9-10, pp. 877-886.
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Despite the long-standing belief that seawater viscosity is driven by temperature and salinity, biologically increased seawater viscosity has repeatedly been reported in relation to phytoplankton exudates in shallow, productive coastal waters. Here, seawater viscosity was investigated in relation to microbial and phytoplanktonic communities off the coast of East Antarctica along latitudinal transects located between 30°E and 80°E in sub-surface waters and at the deep chlorophyll maximum (DCM). The physical component of seawater viscosity observed along each transects ranged from 1.80 to 1.95 cP, while the actual seawater viscosity ranged from 1.85 to 3.69 cP. This resulted in biologically increased seawater viscosity reaching up to 84.9% in sub-surface waters and 77.6% at the DCM. Significant positive correlations were found between elevated seawater viscosity and (i) bacterial abundance in sub-surface waters and (ii) chlorophyll a concentration and the abundance of flow cytometrically-defined auto- and heterotrophic protists at the DCM. Among the 12 groups and 108 species of protists identified under light microscopy, dinoflagellates and more specifically Alexandrium tamarense and Prorocentrum sp. were the main contributors to the patterns observed for elevated seawater viscosity. Our observations, which generalised the link previously identified between seawater viscosity and phytoplankton composition and standing stock to the Southern Ocean, are the first demonstration of increases in seawater viscosity linked to marine bacterial communities, and suggest that the microbially-increased viscosity might quantitatively be at least as important as the one related to phytoplankton secretion.

Seymour, JR, Ahmed, T & Stocker, R 2009, 'Bacterial chemotaxis towards the extracellular products of the toxic phytoplankton Heterosigma akashiwo', Journal Of Plankton Research, vol. 31, no. 12, pp. 1557-1561.
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Marine bacteria exhibit positive chemotactic responses to the extracellular exudates of the toxic phytoplankton Heterosigma akashiwo. In the environment, this will support bacteriaalgae associations with potential implications for harmful algal bloom dynamics.

Seymour, JR, Marcos & Stocker, R 2009, 'Resource Patch Formation and Exploitation throughout the Marine Microbial Food Web', AMERICAN NATURALIST, vol. 173, no. 1, pp. E15-E29.
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Shafer, CM, Mercer, AE, Doswell, CA, Richman, MB & Leslie, LM 2009, 'Evaluation of WRF Forecasts of Tornadic and Nontornadic Outbreaks When Initialized with Synoptic-Scale Input', MONTHLY WEATHER REVIEW, vol. 137, no. 4, pp. 1250-1271.
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Sheldon, CC, Finnegan, E, Peacock, J & Dennis, ES 2009, 'Mechanisms of gene repression by vernalization in Arabidopsis', PLANT JOURNAL, vol. 59, no. 3, pp. 488-498.
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P>FLOWERING LOCUS C (FLC) is a major regulator of flowering time in Arabidopsis. Repression of FLC occurs in response to prolonged cold exposure (vernalization) and is associated with an enrichment of the repressive histone modification trimethylated H3

Shen, X, Wang, G & Wexler, D 2009, 'Large-scale synthesis and gas sensing application of vertically aligned and double-sided tungsten oxide nanorod arrays', Sensors and Actuators B: Chemical, vol. 143, no. 1, pp. 325-332.
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Large-scale vertically aligned and double-sided Co-doped hexagonal tungsten oxide nanorod arrays have been successfully synthesized by a facile hydrothermal method without using any template, catalyst, or substrate. Scanning electron microscopy and transmission electron microscopy analyses reveal an interesting three-order hierarchical nanostructure from small, single-crystalline nanorods via nanorod bundles to double-sided nanorod arrays. The optical absorption properties of the Co-doped WO3 samples were investigated by ultravioletvisible spectroscopy, and the results indicate that the Co-doped WO3 nanostructures are semiconducting with direct band gaps of 2.26 eV and 2.77 eV. The gas sensing performance of the as-prepared Co-doped WO3 double-sided nanorod arrays was tested towards a series of typical organic solvents and fuels. The sample shows excellent gas sensing performance towards 1-butanol vapor, with rapid response and high sensitivity. We propose that the double-sided nanorod arrays are formed from urchin-like microspheres via a self-assembly and fusion process. This new synthesis strategy could be extended to prepare other well-aligned nanorod arrays for many functional applications.

Shiraev, T, Chen, H & Morris, MJ 2009, 'Differential effects of restricted versus unlimited high-fat feeding in rats on fat mass, plasma hormones and brain appetite regulators', Journal of Neuroendocrinology, vol. 21, no. 7, pp. 602-609.
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The rapid rise in obesity has been linked to altered food consumption patterns. There is increasing evidence that, in addition to total energy intake, the macronutrient composition of the diet may influence the development of obesity. The present study aimed to examine the impact of high dietary fat content, under both isocaloric and hypercaloric conditions, compared with a low fat diet, on adiposity, glucose and lipid metabolism, and brain appetite regulators in rats. Male Sprague-Dawley rats were exposed to one of three diets: control (14% fat), ad lib high-fat palatable (HFD, 35% fat) or high-fat palatable restricted (HFD-R, matched to the energy intake of control) and were killed in the fasting state 11 weeks later. Body weight was increased by 28% in unrestricted HFD fed rats, with an almost tripling of caloric intake and fat mass (P < 0.001) and double the plasma triglycerides of controls. Glucose intolerance and increased insulin levels were observed. HFD-R animals calorie matched to control had double their fat mass, plasma insulin and triglycerides (P < 0.05). Only ad lib consumption of the HFD increased the hypothalamic mRNA expression of the appetite-regulating peptides, neuropeptide Y and pro-opiomelanocortin. Although restricted consumption of palatable HFD had no significant impact on hypothalamic appetite regulators or body weight, it increased adiposity and circulating triglycerides, suggesting that the proportion of dietary fat, independent of caloric intake, affects fat deposition and the metabolic profile.

Shiryaev, AN & Novikov, A 2009, 'On a stochastic version of the trading rule 'Buy and Hold'', Statistics and Decision, vol. 26, no. 4, pp. 289-302.
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The paper deals with the problem of finding an optimal one-time rebalancing strategy assuming that in the BlackâScholes model the drift term of the stock may change its value spontaneously at some random non-observable (hidden) time. The problem is studied on a finite time interval under two criteria of optimality (logarithmic and linear). The methods of the paper are based on the results for the quickest detection of drift change for Brownian motion.

Shokri, MR & Gladstone, W 2009, 'Higher taxa are effective surrogates for species in the selection of conservation reserves in estuaries', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 19, no. 6, pp. 626-636.
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1. The lack of information about marine biodiversity is problematic for the selection of conservation reserves that aim to protect representative samples of biodiversity. A number of surrogate measures for biodiversity have been suggested as a potential solution to this problem. 2. The present study tested the effectiveness of using higher taxa of macroinvertebrates as a surrogate for species-level identification to depict spatial variation in species richness and assemblage variation and to select conservation reserves in one estuary in south-east Australia. 3. Spatial patterns of richness and assemblage variation for species were significantly correlated with patterns defined from genera, families, orders, classes, and phyla with a decline in the magnitude of correlation coefficients from finer to coarser resolutions. A network of reserves selected to include representatives of all phyla, classes, orders, families and genera coincidentally included 54%, 61.7%, 75%, 92.6%, 98.8% species in 8.3%, 13.9%, 17.7%, 44.4% and 58.3% of grid cells, respectively. However, only reserves selected for genera, families and orders performed significantly better than random selection. 4. Percentage of species represented by orders, families and genera in a realistic level of available grid cells for conservation (i.e. 13.9%) were very close ranging between 70 and 73.5%. A factor diminishing the performance of order as surrogate for species richness was related to the difficulty of identifying many macroinvertebrates to the order level. Therefore, it is concluded that genus- and family-level identification is an effective surrogate for species-level identification for conservation planning in estuaries. Copyright © 2008 John Wiley & Sons, Ltd.

Shokri, MR, Gladstone, W & Jelbart, J 2009, 'The effectiveness of seahorses and pipefish (Pisces: Syngnathidae) as a flagship group to evaluate the conservation value of estuarine seagrass beds', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 19, no. 5, pp. 588-595.
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1. Syngnathids (Pisces, Syngnathidae: seahorses and pipefish) were investigated for their use as a flagship group to evaluate the conservation value of estuarine seagrass beds in estuaries in south-east Australia. Some species of syngnathids are listed internationally as vulnerable or endangered, and they are a charismatic group of fish that attracts a high level of public support and sympathy. Syngnathids are also protected in several states of Australia. Conservation of syngnathids might provide coincidental benefits to other species that share their habitats. 2. The effectiveness of syngnathids as a flagship group was assessed by (1) testing for correlations with other fish in species richness, density, assemblage variation, and summed irreplaceability value, and (2) determining the number of species of all other fish coincidentally captured in marine protected areas (MPAs) selected for syngnathids. The study was undertaken in a single estuary (scale: tens of square kilometres) and across multiple estuaries (scale: hundreds of square kilometres). 3. Densities of syngnathids and other fish were correlated only at the scale of multiple estuaries. Species richness and summed irreplaceability of syngnathids and other fish were not spatially correlated. Spatial variations in assemblages of syngnathids and other fish were correlated. MPAs selected for syngnathids included more non-syngnathid species than a random selection of locations. 4. This study provides evidence that ranking the conservation value of seagrass beds on the basis of the density and assemblage variation of syngnathids, and selecting MPAs to represent syngnathid species, will simultaneously benefit other fish. Synganthids are therefore regarded as a useful flagship group for conservation planning.

Shokri, MR, Gladstone, W & Kepert, A 2009, 'Annelids, arthropods or molluscs are suiable as surrogate taxa for selecting conservation reserves in estuaries', Biodiversity and conservation, vol. 18, no. 5, pp. 1117-1130.
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The urgent need to conserve aquatic biodiversity and the lack of spatial data on biodiversity has motivated conservation planners and researchers to search for more readily obtainable information that could be used as proxies or surrogates. The surrogate taxon approach shows promise in some aquatic environments (e.g. intertidal) but not others (e.g. coral reefs, temperate rocky reefs). Estuaries are transitional environments at the landsea junction with a unique biodiversity, but are the most threatened of aquatic environments because of high levels of human use. The comparatively small numbers of conservation reserves means that estuarine biodiversity is poorly protected. Selecting additional conservation reserves within estuaries would be facilitated by the identification of a suitable surrogate that could be used in conservation planning. In one estuary in Southeast Australia, we evaluated separately the effectiveness of annelids, arthropods, and molluscs as surrogates for predicting the species richness, abundance, assemblage variation, and summed irreplaceability of other species and for coincidentally representing other species in networks of conservation reserves selected for each surrogate. Spatial patterns in the species richness and assemblage variation (but not summed irreplaceability) of each surrogate were significantly correlated with the spatial patterns of other species.

Siboni, N, Martinez, S, Abelson, A, Sivan, A & Kushmaro, A 2009, 'Conditioning film and initial biofilm formation on electrochemical CaCO3 deposition on a metallic net in the marine environment', BIOFOULING, vol. 25, no. 7, pp. 675-683.
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Siyushev, P, Jacques, V, Aharonovich, I, Kaiser, F, Muller, T, Lombez, L, Atature, M, Castelletto, S, Prawer, S, Jelezko, F & Wrachtrup, J 2009, 'Low-temperature optical characterization of a near-infrared single-photon emitter in nanodiamonds', New Journal of Physics, vol. 11.
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In this paper, we study the optical properties of single defects emitting in the near infrared (NIR) in nanodiamonds at liquid helium temperature. The nanodiamonds are synthesized using a microwave chemical vapor deposition method followed by nickel implantation and annealing. We show that single defects exhibit several striking features at cryogenic temperature: the photoluminescence is strongly concentrated into a sharp zero-phonon line (ZPL) in the NIR, the radiative lifetime is in the nanosecond range and the emission is linearly polarized. The spectral stability of the defects is then investigated. An optical resonance linewidth of 4 GHz is measured using resonant excitation on the ZPL. Although Fourier-transform-limited emission is not achieved, our results show that it might be possible to use consecutive photons emitted in the NIR by single defects in diamond nanocrystals to perform two photon interference experiments, which are at the heart of linear quantum computing protocols.

Smagghe, B, Hoy, J, Percifield, R, Kundu, S, Hargrove, M, Sarath, G, Hilbert, J, Watts, R, Dennis, ES, Peacock, J, Dewilde, S, Moens, L, Blouin, G, Olson, J & Appleby, C 2009, 'Correlations Between Oxygen Affinity and Sequence Classifications of Plant Hemoglobins', Biopolymers, vol. 91, no. 12, pp. 1083-1096.
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Smallwood, AG, Thomas, P, Ray, AS & Simon, P 2009, 'Application of a Fickian model of diffusion to the dehydration of graded specimens of a precious Australian sedimentary opal derived from Coober Pedy', Journal Of Thermal Analysis And Calorimetry, vol. 97, no. 2, pp. 685-688.
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A model developed for the estimation of the diffusion coefficient based on Fickian diffusion is applied to the dehydration of a Coober Pedy white play of colour (precious) opal using thermogravimetric analysis (TG). The model was originally applied to bulk and powdered opal (opal with no bulk). In this paper the opal was graded prior to TG analysis. The diffusion coefficient was calculated and is reported up to the critical point of water.

Smith, G 2009, 'Amplified radiative cooling via optimised combinations of aperture geometry and spectral emittance profiles of surfaces and the atmosphere', Solar Energy Materials And Solar Cells, vol. 93, no. 9, pp. 1696-1701.
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Net thermal radiation cooling, from surfaces at sub-ambient temperatures, to the night sky is amplified if the aperture to the sky is partially blocked with heat mirrors. The temperature at which radiation loss stagnates (the effective sky temperature) falls continuously as the aperture closes and is derived in terms of the aperture size and the spectral properties and temperatures of the atmosphere and of the emitting surface. Cooling surfaces must have high absorptance between 7.9 mu m and 13 mu m where the atmosphere is most transparent. The best response for the remainder of the Planck radiation spectrum surprisingly switches between two spectral extremes at a temperature which falls as the aperture gets smaller. A perfect absorber is best above this switch, while surfaces which reflect all of this radiation are best below it. A simple formula is presented for the cross-over temperature as a function of aperture size. With known material properties plus representative non-radiative heat gains a high emittance surface is generally better except when heat mirrors are not used. A known high emittance roof paint at 10 degrees C below ambient, under a 45 degrees aperture lined with shiny aluminium, can achieve a net output power near 135W m(-2) under a clear sky.

Smith, G 2009, 'Guest editorial, Nanostructured Thin Films', Journal of Nanophotonics, vol. 3, no. NA, pp. 1-4.
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Nanostructured thin films (NSTF) are providing enormous scope for advances in optical, electronic and optoelectronic engineering and underpinning key developments in nanoscience. From a scientific perspective they embody numerous challenges and opportunities: covering concepts, models, growth, structure and characterization. Emerging technologies which depend on NSTF include photonics and plasmonics for information processing and communications; semiconductor and molecular electronics; display and lighting; single molecule bio-sensing, proteomics, advanced medical therapies, diagnostics and imaging; large scale, low cost approaches to energy efficiency, renewable energy and energy storage; and material surfaces which are durable, self-repair, self-clean, and have the ability to sense, change color, and to modulate reflectance, transmittance or thermal emittance.

Song, C, Ye, Z, Wang, G, Jin, D, Yuan, J, Guan, Y & Piper, J 2009, 'Preparation and time-gated luminescence bioimaging application of ruthenium complex covalently bound silica nanoparticles', TALANTA, vol. 79, no. 1, pp. 103-108.
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Sotirchos, IM, Hudson, AL, Ellis, JT & Davey, MW 2009, 'A unique thioredoxin of the parasitic nematode Haemonchus contortus with glutaredoxin activity', Free Radical Biology and Medicine, vol. 46, no. 5, pp. 579-585.
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The dependency of parasites on the cellular redox systems has led to their investigation as novel drug targets. Defence against oxidative damage is through the thioredoxin and glutathione systems. The classic thioredoxin is identified by the active site Cys-Gly-Pro-Cys (CGPC). Here we describe the identification of a unique thioredoxin in the parasitic nematode, Haemonchus contortus. This thioredoxin-related protein, termed HcTrx5, has an arginine in its active site (Cys-Arg-Ser-Cys; CRSC) that is not found in any other organism. Recombinant HcTrx5 was able to reduce the disulfide bond in insulin, and be regenerated by mammalian thioredoxin reductase with a Km 2.19 ± 1.5 µM, similar to the classic thioredoxins. However, it was also able to reduce insulin when glutathione and glutathione reductase replaced the thioredoxin reductase. When coupled with H. contortus peroxiredoxin, HcTrx5 was active using either the thioredoxin reductase or the glutathione and glutathione reductase. HcTrx5 is expressed through the life cycle, with highest expression in the adult stage. The unique activity of this thioredoxin makes it a potential drug target for the control of this parasite.

Speer, MS, Wiles, P & Pepler, A 2009, 'Low pressure systems off the New South Wales coast and associated hazardous weather: Establishment of a database', Australian Meteorological and Oceanographic Journal, vol. 58, no. 1, pp. 29-39.
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The New South Wales (NSW) coast is subject to heavy rain, strong wind and large waves resulting from low pressure systems over the adjacent Tasman Sea that develop from a variety of synoptic and mesoscale mechanisms. A database of these maritime lows and their impacts has been developed in the NSW Climate Services Centre of the Bureau of Meteorology. The database currently extends back to 1970 and includes data on rainfall amounts, with wind speed and significant wave height data still to be added. The database events were classified into six synoptic types based on the mean sea level pressure synoptic pattern in which the lows formed. The six types are: inland trough lows (30 per cent), easterly trough lows (14 per cent), and ex-tropical cyclones (4 per cent), all of which originate in the subtropical or tropical easterlies; and, lows forming on a wave on a front (37 per cent) decaying front lows (12 per cent) and lows in the westerlies (3 per cent), the latter two of which originate from mid-latitude low pressure systems or fronts in the westerlies. Since 1970, only inland trough lows have shown a significant increase in frequency which is consistent with a slight increase in spring rainfall in an area over northeast NSW over the same period. In contrast, there has been a decrease in ex-tropical cyclone numbers impacting the NSW coast since 1970, which is consistent with a decrease in summer rainfall generally along the NSW coast. The development of the database is ongoing but it is planned to extend it back in time to further investigate the relationship between maritime low pressure development and NSW coastal rainfall trends.

Spindler, X, Stoilovic, M, Lennard, C & Lennard, A 2009, 'Spectral variations for reaction products formed between different amino acids and latent fingermark detection reagents on a range of cellulose-based substrates', Journal of Forensic Identification, vol. 59, no. 3, pp. 308-324.
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Ninhydrin, 1,2-indanedione, 1,2-indanedione-zinc, and l,8-diazafluoren-9- one (DFO) are reagents used worldwide for latent fingermark detection on paper substrates. Although research groups have concentrated on optimization studies and improvements in reagent formulations, mechanistic studies and comparisons against the different amino acid constituents in eccrine secretions are rare in the literature. It is known from studies undertaken in different geographic areas that these reagents produce varied results on different paper substrates under different environmental conditions; however, such observations have not been quantified. In this study, ninhydrin, indanedione, indanedione-zinc, and DFO reagents have been used to enhance deposits of nine major amino acids on three types of cellulose-based media: ashless filter paper, 10% recycled copy paper, and cellulose-coated TLC plates. Absorption and luminescence spectra were recorded for the resulting reaction products. The results provide some insight into the activity of these fingermark detection reagents with respect to the different amino acids present in eccrine deposits. References.

Stacey, A, Aharonovich, I, Prawer, S & Butler, JE 2009, 'Controlled synthesis of high quality micro/nano-diamonds by microwave plasma chemical vapor deposition', Diamond and Related Materials, vol. 18, no. 1, pp. 51-55.
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Diamond containing engineered color centers is rapidly becoming a medium of choice for quantum information applications. Many of the dramatic recent results in this field have been demonstrated in diamond nano-crystals. Here we demonstrate controlled syn

Stark, DJ, Barratt, JL, Ellis, JT, Harkness, JL & Marriott, DJ 2009, 'Repeated Dientamoeba fragilis infections: a case report of two families from Sydney, Australia', Infectious Disease Reports, vol. 1, no. e4, pp. 7-9.
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We report cases of two unrelated families who both presented with recurrent Dientamoeba fragilis infections. Subsequent antimicrobial therapy resulted in the clearance of D. fragilis and total resolution of gastrointestinal symptoms in both families. This report highlights the potentially recurrent nature of D. fragilis infections and the need for laboratories to routinely test for this organism.

Stark, DJ, Barratt, JL, Van Hal, SJ, Marriott, DJ, Harkness, JL & Ellis, JT 2009, 'Clinical significance of enteric protozoa in the immunosuppressed human population', Clinical Microbiology Reviews, vol. 22, no. 4, pp. 634-650.
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Globally, the number of immunosuppressed people increases each year, with the human immunodeficiency virus (HIV) pandemic continuing to spread unabated in many parts of the world. Immunosuppression may also occur in malnourished persons, patients undergoing chemotherapy for malignancy, and those receiving immunosuppressive therapy. Components of the immune system can be functionally or genetically abnormal as a result of acquired (e.g., caused by HIV infection, lymphoma, or high-dose steroids or other immunosuppressive medications) or congenital illnesses, with more than 120 congenital immunodeficiencies described to date that either affect humoral immunity or compromise T-cell function. All individuals affected by immunosuppression are at risk of infection by opportunistic parasites (such as the microsporidia) as well as those more commonly associated with gastrointestinal disease (such as Giardia). The outcome of infection by enteric protozoan parasites is dependent on absolute CD4+ cell counts, with lower counts being associated with more severe disease, more atypical disease, and a greater risk of disseminated disease. This review summarizes our current state of knowledge on the significance of enteric parasitic protozoa as a cause of disease in immunosuppressed persons and also provides guidance on recent advances in diagnosis and therapy for the control of these important parasites.

Stark, DJ, Van Hal, SJ, Barratt, JL, Ellis, JT, Marriott, DJ & Harkness, JL 2009, 'Limited genetic diversity among genotypes of Enterocytozoon bieneusi strains Isolated from HIV-Infected patients from Sydney, Australia', Journal of Medical Microbiology, vol. 58, no. 3, pp. 355-357.
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Microsporidia are intracellular parasites, with over 1200 species belonging to 143 genera described to date. They are opportunistic pathogens in humans and can cause chronic diarrhoea in immunosuppressed patients. Both Enterocytozoon bieneusi and Encephalitozoon intestinalis cause intestinal disease, with Enterocytozoon bieneusi more commonly identified in patients with human immunodeficiency virus (HIV) infection. In this study, intestinal microsporidial clinical isolates from patients in Sydney, Australia, were genotyped. All specimens were from HIV-infected men with low CD4(+) T-cell counts (<100 cells mm(-3)). Genotyping of the internal transcribed spacer regions of the rRNA gene showed the presence of only one genotype, the anthroponotic Enterocytozoon bieneusi genotype B strain. This study thus highlighted the limited genetic diversity among Australian Enterocytozoon bieneusi isolates, and it is hypothesized that, due to the reduced incidence of microsporidia. and the subsequent reduction in the human reservoir of the anthroponotic genotype B, locally acquired intestinal microsporidiosis will rarely be seen in HIV-infected persons undergoing highly active antiretroviral therapy in the future in Australia.

Staudenmayer, J, Lake, EE & Wand, M 2009, 'Robustness for general design mixed models using the t-distribution', Statistical Modelling, vol. 9, no. 3, pp. 235-255.
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The t-distribution allows the incorporation of outlier robustness into statistical models while retaining the elegance of likelihood-based inference. In this paper, we develop and implement a linear mixed model for the general design of the linear mixed model using the univariate t-distribution. This general design allows a considerably richer class of models to be fit than is possible with existing methods. Included in this class are semi-parametric regression and smoothing and spatial models.

Stelzer-braid, S, Oliver, BG, Blazey, A, Argent, E, Newsome, T, Rawlinson, W & Tovey, E 2009, 'Exhalation of Respiratory Viruses by Breathing, Coughing, and Talking', Journal of Medical Virology, vol. 81, no. 9, pp. 1674-1679.
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There is a lack of quantitative information about the generation of virus aerosols by infected subjects. The exhaled aerosols generated by coughing, talking, and breathing were sampled in 50 subjects using a novel mask, and analyzed using PCR for nine re

Stephens, RS, Myers, G, Eppinger, M & Bavoil, PM 2009, 'Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved', FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY, vol. 55, no. 2, pp. 115-119.
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Stokes, KL, Forbes, SL & Tibbett, M 2009, 'Freezing skeletal muscle tissue does not affect its decomposition in soil: Evidence from temporal changes in tissue mass, microbial activity and soil chemistry based on excised samples', Forensic Science International, vol. 183, no. 1-3, pp. 6-13.
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The study of decaying organisms and death assemblages is referred to as forensic taphonomy, or more simply the study of graves. This field is dominated by the fields of entomology, anthropology and archaeology. Forensic taphonomy also includes the study

Stratford, P, Lal, S & Meara, A 2009, 'Neurophysiology of therapeutic alliance', Gestalt Journal of Australia and New Zealand, vol. 5, no. 2, pp. 19-47.
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Currently no studies exist on assessing neurophysiological correlates, especially brain activity, during therapeutic alliance (TA) between client and therapist. The aims of this study were to assess electroencephalography (EEG) activity in the client with symptomatic anxiety throughout therapy during moments of high TA established using SCR measurements from both client and therapist. Fifteen clients aged, 48 ± 9.4 years (males: n=7, females: n=8) underwent six (S1-S6), weekly 1-hour psychotherapy sessions (90 hours of repeated measures). For the duration of therapy the frontal site remained active while the occipital site `went to sleep. During high TA the parietal cortex - the `seat of imagination, was active. The parietal cortex appears to be highly active when processing trauma as the client develops cognitive and emotional insight. The temporal site reflected accessing emotional memory with high alpha and beta activity. Heart-rate (HR) and anxiety levels decreased over time.

Strom, D, Ralph, PJ & Stauber, JL 2009, 'Development of a Toxicity Identification Evaluation Protocol Using Chlorophyll-a Fluorescence in a Marine Microalga', Archives Of Environmental Contamination And Toxic..., vol. 56, no. 1, pp. 30-38.
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Growth inhibition bioassays with the microalga Nitzschia closterium have recently been applied in marine Toxicity Identification Evaluation (TIE) testing. However, the 48-h test duration can result in substantial loss of toxicants over time, which might lead to an underestimation of the sample toxicity. Although shorter-term microalgal bioassays can minimize such losses, there are few bioassays available and none are adapted for marine TIE testing. The acute (5-min) chlorophyll-a fluorescence bioassay is one alternative; however, this bioassay was developed for detecting herbicides in freshwater aquatic systems and its suitability for marine TIE testing was not known. In this study, a chlorophyll-a fluorescence bioassay using the marine microalga Isochrysis galbana was able to detect contaminants other than herbicides at environmentally relevant concentrations and tolerated the physical and chemical manipulations needed for a Phase I TIE. Phase I TIE procedures were successfully developed using this chlorophyll-a fluorescence bioassay and used to identify all classes of contaminants present in a synthetic mixture of known chemical composition. In addition, TIEs with both the acute fluorescence bioassay and the standard growth inhibition bioassay identified the same classes of toxicants in a sample of an unknown complex effluent. Even though the acute chlorophyll-a fluorescence end point was less sensitive than the chronic cell division end point, TIEs with the chlorophyll-a fluorescence bioassay provided a rapid and attractive alternative to longer-duration bioassays.

Suggett, DJ, MacIntyre, HL, Kana, TM & Geider, RJ 2009, 'Comparing electron transport with gas exchange:parameterising exchange rates between alternative photosynthetic currencies for eukaryotic phytoplankton', Aquatic Microbial Ecology, vol. 56, no. 2-3, pp. 147-162.
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Estimates of aquatic primary productivity derived from in situ active chl a fluorescence have rapidly gained popularity over the past 2 decades. This trend has been driven primarily by the need to improve upon `conventional carbon (C) uptake- or oxygen (O2) evolution-based productivity estimates that require water samples to be incubated ex situ. Unlike the conventional approaches to measuring productivity, chlorophyll fluorescence measurements inherently describe only the activity of photosystem II (PSII) in the light reactions; thus, the photosynthetic `currency of the fluorescence based approach is an electron turnover rate for PSII (ETRPSII). A photosynthetic currency of electrons has limited ecological relevance but can be converted to a currency of carbon if an `exchange rate, i.e. a value or factor of equivalence for any single time point, is applied. We used fast repetition rate fluorometry (FRRf), mass inlet membrane spectrometry (MIMS) and 14C uptake to determine ETRPSII, gross and net O2 evolution and C fixation measured simultaneously for 6 microalgal species and for different steady-state growth conditions. Quantifying the PSII reaction centre (RCII) concentration and the spectral dependency of the effective absorption cross section yielded an FRRf approach that provided a robust estimate of the ETRPSII and gross O2 evolution for all species and conditions tested; however, the ETRPSII exceeded carbon dioxide (CO2) uptake by a factor of ~5.4 to 11.6. At least 3 species exhibited substantial light-dependent O2 cycling to account for ~40 to 60% of the difference between the ETRPSII and CO2 uptake. The highly variable nature of the ETRPSII:CO2 uptake `exchange rate observed here highlights the need for future studies that rely on active fluorescence to examine aquatic productivity to focus towards a systematic description of how electrons are coupled to C fixation in nature

Suggett, DJ, Moore, CM, Hickman, AE & Geider, RJ 2009, 'Interpretation of fast repetition rate (FRR) fluorescence: signatures of phytoplankton community structure versus physiological state', Marine Ecology Progress Series, vol. 376, pp. 1-19.
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Introduction of active chlorophyll a fluorescence protocols, in particular fast repetition rate (FRR) fluorometry, to oceanography and limnology 15 yr ago has enabled rapid assessment of photosynthetic physiology in situ. The FRR protocol generates simultaneous measurements of Photosystem II (PSII) effective absorption cross sections (termed sPSII) and photochemical efficiency (termed Fv/Fm). Both Fv/Fm and sPSII measurements have been utilised to examine the effects of physiological stress on the photosynthetic apparatus of phytoplankton in an ever growing number of fluorescence-based studies. However, it is now becoming clearer that in situ values of Fv/Fm and sPSII also contain taxonomic information. Here, we present a synthesis of previously unpublished and published data, which show that Fv/Fm and sPSII vary principally with broad-scale changes in community structure. These patterns observed in situ conform to trends observed in laboratory-grown cultures of a range of phytoplankton taxa. The magnitudes of variability in Fv/Fm and sPSII driven by changes in phytoplankton community structure often exceed that induced by nutrient limitation (as determined from controlled nutrient addition experiments). An exception to this general trend occurs in high-nutrient, low-chlorophyll a (HNLC) regions, where strong phenotypic changes in Fv/Fm and sPSII have been repeatedly demonstrated on relief of iron limitation. Overall, FRR fluorescence measurements of both Fv/Fm and sPSII in natural populations represent a combination of the taxonomic `signature (values of Fv/Fm and sPSII determined by the taxa present) within the phytoplankton community that is further modified according to the (photo-) physiological status. As such, fluorescence-based investigations of mixed populations must account for potential variations in phytoplankton community structure before interpretations of physiological status are made.

Summerhayes, SA, Bishop, M, Leigh, A & Kelaher, BP 2009, 'Effects of oyster death and shell disarticulation on associated communities of epibiota', Journal of Experimental Marine Biology and Ecology, vol. 379, no. 1-2, pp. 60-67.
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Oyster mortality and subsequent degradation of shell matrices may influence associated epibiota by modifying processes of filtration and biodeposition and by changing habitat structure. In the Hawkesbury River, NSW, Australia, QX disease devastated aquaculture populations of the native Sydney rock oyster, Saccostrea glomerata, and threatened wild populations. To ascertain effects of this oyster mortality on associated epibiota, we compared epifaunal communities occupying 100% oyster shell cover among 5 sites along the estuary, ranging from 25 ppt salinity and live oyster density of 96 ± 13 m- 2, to 32 ppt salinity and live oyster density of 3187 ± 233 m- 2. Epifaunal richness was greatest closest to the estuarine mouth, where live oyster abundance was greatest. Epifaunal abundance, by contrast, generally increased with distance upstream, as oyster matrices were increasingly dominated by the shells of dead oysters. To ascertain the role of live and dead oysters as habitat providers, we carried out a manipulative experiment to test the hypothesis that the epifaunal assemblages that settle over a 4 month period will significantly differ among constructed matrices comprised of live, whole dead and/or degraded (single valve) oysters. Treatments containing a component of single valves, which increase the availability of interstitial spaces and provide greater surface area for attachment, supported the greatest numbers of epibiota. Matrices comprised solely of live oysters supported fewest species and numbers of organisms. Results demonstrate that death and degradation of oysters alter the structure of associated communities, even where 100% cover of shell matrix is maintained. These results have important ramifications for management strategies and retaining estuarine biodiversity in the event that disease such as QX causes local oyster extinctions.

Sun, H, Huang, J, Huete, A, Peng, D & Zhang, F 2009, 'Mapping paddy rice in China with multi-date MODIS data', Zhejiang University Journal (Science A): applied physics and engineering, vol. 10, no. 10, pp. 1509-1522.
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The objective of this study was to obtain spatial distribution maps of paddy rice fields using multi-date moderate-resolution imaging spectroradiometer (MODIS) data in China. Paddy rice fields were extracted by identifying the unique characteristic of high soil moisture in the flooding and transplanting period with improved algorithms based on rice growth calendar regionalization. The characteristic could be reflected by the enhanced vegetation index (EVI) and the land surface water index (LSWI) derived from MODIS sensor data. Algorithms for single, early, and late rice identification were obtained from selected typical test sites. The algorithms could not only separate early rice and late rice planted in the same fields, but also reduce the uncertainties. The areal accuracy of the MODIS-derived results was validated by comparison with agricultural statistics, and the spatial matching was examined by ETM+ (enhanced thematic mapper plus) images in a test region. Major factors that might cause errors, such as the coarse spatial resolution and noises in the MODIS data, were discussed. Although not suitable for monitoring the inter-annual variations due to some inevitable factors, the MODIS-derived results were useful for obtaining spatial distribution maps of paddy rice on a large scale, and they might provide reference for further studies

Sun, Y, Carroll, RJ & Li, D 2009, 'Semiparametric estimation of fixed-effects panel data varying coefficient models', Advances in Econometrics, vol. 25, pp. 101-129.
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We consider the problem of estimating a varying coefficient panel data model with fixed-effects (FE) using a local linear regression approach. Unlike first-differenced estimator, our proposed estimator removes FE using kernel-based weights. This results a one-step estimator without using the backfitting technique. The computed estimator is shown to be asymptotically normally distributed. A modified least-squared cross-validatory method is used to select the optimal bandwidth automatically. Moreover, we propose a test statistic for testing the null hypothesis of a random-effects varying coefficient panel data model against an FE one. Monte Carlo simulations show that our proposed estimator and test statistic have satisfactory finite sample performance.

Sung, ZR, Furner, I, Yadegari, R, Pikaard, C, Wagner, D, Michaels, S & Dennis, L 2009, 'Erratum: Editorial (Molecular Plant (2009) 2:4 (553) DOI: 10.1093/mp/ssp035)', Molecular Plant, vol. 2, no. 5, p. 1123.
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Sung, ZR, Furner, I, Yadgari, R, Pikaard, C, Wagner, D, Michaels, S & Dennis, L 2009, 'Molecular Plant: Editorial', Molecular Plant, vol. 2, no. 4, p. 553.
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Sutherland, DL 2009, 'Microbial mat communities in response to recent changes in the physiochemical environment of the meltwater ponds on the McMurdo Ice Shelf, Antarctica', POLAR BIOLOGY, vol. 32, no. 7, pp. 1023-1032.
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Sutherland, DL & Hawes, I 2009, 'Annual growth layers as proxies of past growth conditions for benthic microbial mats in a perennially ice-covered Antarctic lake', FEMS MICROBIOLOGY ECOLOGY, vol. 67, no. 2, pp. 279-292.
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Syaifudin, ARM, Jayasundera, KP & Mukhopadhyay, SC 2009, 'A low cost novel sensing system for detection of dangerous marine biotoxins in seafood', SENSORS AND ACTUATORS B-CHEMICAL, vol. 137, no. 1, pp. 67-75.
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Tamanini, E, Katewa, A, Sedger, LM, Todd, M & Watkinson, M 2009, 'A Synthetically Simple, Click-Generated Cyclam-Based Zinc(II) Sensor', Inorganic Chemistry, vol. 48, no. 1, pp. 319-324.
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A cyclam-based macrocyclic sensor has been prepared using synthetically simple "click" chemistry to link a fluorophore to the macrocyclic receptor. This sensor shows high selectivity for Zn(II) over a range of other metals, providing a significant enhancement of fluorescence intensity over a wide pH range. As such, this is the first cyclam-based sensor demonstrated to be selective for Zn(II) and is the first example of a triazole being used as a coordinating ligand on an azamacrocycle, The sensor can access biologically available zinc in mammalian cells, sensing the Zn(II) flux that exists during apoptotic cell death.

Thomas, A & Green, PJ 2009, 'Enumerating the decomposable neighbors of a decomposable graph under a simple perturbation scheme', Computational Statistics & Data Analysis, vol. 53, no. 4, pp. 1232-1238.
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Given a decomposable graph, we characterize and enumerate the set of pairs of vertices whose connection or disconnection results in a new graph that is also decomposable. We discuss the relevance of these results to Markov chain Monte Carlo methods that

Thomas, A & Green, PJ 2009, 'Enumerating The Junction Trees Of A Decomposable Graph', Journal of Computational and Graphical Statistics, vol. 18, no. 4, pp. 930-940.
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We derive methods for enumerating the distinct junction tree representations for any given decomposable graph. We discuss the relevance of the method to estimating conditional independence graphs of graphical models and give an algorithm that, given a ju

Thompson, AM, Dunlop, RA, Dean, R & Rodgers, K 2009, 'Evidence that DOPA-derivatives are generated after L-DOPA incorporation into proteins by mammalian cells', Journal Of Adhesion, vol. 85, no. 9, pp. 561-575.
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The adhesive and cohesive properties of the amino acid L-3,4-dihydroxyphenylalanine (DOPA) have been widely explored as a potential material for adhesion, based, among other things, on the biological system of blue mussel extracellular byssal threads and

Thompson, PA, Baird, ME, Ingleton, T & Doblin, MA 2009, 'Long-term changes in temperate Australian coastal waters: implications for phytoplankton', Marine Ecology Progress Series, vol. 394, pp. 1-19.
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A ~60 yr physical and chemical data set from 4 coastal stations around Australia plus remotely sensed SeaWiFS and phytoplankton taxonomic data were used to evaluate the temporal and spatial variation in phytoplankton ecology. The most consistent trend observed at all stations was a long-term increase in surface salinity of ~0.003 ± 0.0008 psu yr1. All stations showed positive trends in temperature, with the fastest surface warming (0.0202°C yr1 over 60 yr) in the western Tasman Sea. Long-term trends in warming and stratification were more evident in some months and were not well characterized by annual averages. There was no general pattern of increasing stratification (0 to 50 m); only some stations and a few months showed significant changes. Long-term trends in surface nitrate and phosphate concentrations were either not significant (3 instances) or positive (5 instances) and were up to 6.1 nM phosphate yr1. A pronounced decline in silicate was evident at the 3 east coast stations, with concentrations falling by as much as 58 nM yr1 over the last ~30 yr. The western Tasman Sea experienced a ~50% decline in the growth rate and biomass of the spring bloom from 1997 to 2007, while other sites showed significant temporal variability in chlorophyll a that was associated with the Southern Oscillation Index (SOI). Diatoms tended to dominate the microplankton, especially during periods of low stratification. In conclusion, the physical, chemical and biological properties of Australian temperate waters have changed considerably over the last 60 yr in response to variation in the SOI and the strengthening East Australian Current.

Thorburn, AN, Hansbro, PM & Gibson, PG 2009, 'Pneumococcal vaccines for allergic airways diseases', EXPERT OPINION ON BIOLOGICAL THERAPY, vol. 9, no. 5, pp. 621-629.
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Tileli, V, Knowles, W, Toth, M & Thiel, BL 2009, 'Noise characteristics of the gas ionization cascade used in low vacuum scanning electron microscopy', Journal Of Applied Physics, vol. 106, no. 1, pp. 0-0.
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The noise characteristics of gas cascade amplified electron signals in low vacuum scanning electron microscopy (LVSEM) are described and analyzed. We derive expressions for each component contributing to the total noise culminating in a predictive, quantitative model that can be used for optimization of LVSEM operating parameters. Signal and noise behavior is characterized experimentally and used to validate the model. Under most operating conditions, the noise is dominated by the excess noise generated in the gas amplification cascade. At high gains, the excess noise increases proportionally with gain such that the signal-to-noise ratio is constant. The effects of several instrument operating parameters, including working distance, gas pressure, beam current, and detector bias, are condensed and presented in the form of a master curve.

Timmins, M, Thomas-hall, S, Darling, AE, Zhang, E, Hankamer, B, Marx, U & Schenk, P 2009, 'Phylogenetic And Molecular Analysis Of Hydrogen-producing Green Algae', Journal Of Experimental Botany, vol. 60, no. 6, pp. 1691-1702.
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A select set of microalgae are reported to be able to catalyse photobiological H(2) production from water. Based on the model organism Chlamydomonas reinhardtii, a method was developed for the screening of naturally occurring H(2)-producing microalgae. B

Tomljenovic-Hanic, S, Rahmani, A, Steel, MJ & de Sterke, M 2009, 'Comparison of the sensitivity of air and dielectric modes in photonic crystal slab sensors', Optics Express, vol. 17, no. 17, pp. 14552-14557.
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Optical cavities provide a route to sensing through the shift of the optical resonant peak. However, effective sensing with optical cavities requires the optimization of the modal quality factor, Q, and the field overlap with the sample, f. For a photonic crystal slab (PCS) this figure of merit, M = fQ, involves two competing effects. The air modes usually have large f but small Q, whereas the dielectric modes have high-Q and small f. We compare the sensitivity of air and dielectric modes for different PCS cavity designs and account for loss associated with absorption by the sensed sample or its host liquid. We find that optimizing Q at the expense of f is the most beneficial strategy, and modes deriving from the dielectric bands are thus preferred.

Tong, X, Li, J, Yu, Q & Qin, Z 2009, 'Ecosystem water use efficiency in an irrigated cropland in the North China Plain', Journal Of Hydrology, vol. 374, no. 3-4, pp. 329-337.
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The eddy covariance technique and the cuvette method were used to investigate water use efficiency in an irrigated winter wheat (Triticum asetivum L.)/summer maize (Zea mays L.) rotation system in the North China Plain. The results show that ecosystem water use efficiency (WUEe) changed diurnally and season, ally. Daily maximal WUEe appeared in the morning. WUEe generally peaked in late April in wheat field and in late July/early August in maize field. From 2003 to 2006, seasonal mean WUEe was 6.7-7.4 mg CO2 g(-1) H2O for wheat and 8.4-12.1 mg CO2 g(-1) H2O for maize. WUEe was much lower than canopy water use efficiency (WUEc) under small leaf area index (LAI) but very close to WUEc under large LAI. With the increase in LAI, WUEe enlarged rapidly under low LAI but slowly when LAI was higher than one. WUEe was greater on the cloudy days than on the sunny days. Under the same solar radiation, WUEe was higher in the morning than in the afternoon. The ratio of internal to ambient CO2 partial pressure (Ci/Ca) decreased significantly with the increase in photosynthetically active radiation (PAR) when PAR was lower than the critical values (around 500 and 1000 mu mol m(-2) s(-1) for wheat and maize, respectively). Beyond critical PAR, C-i/C-a was approximately constant at 0.69 for wheat and 0.42 for maize Therefore., when LAI and solar radiation was large enough, WUEe has negative correlation with vapor pressure deficit in both of irrigated wheat and maize fields.

Toth, M, Lobo, CJ, Lysaght, MJ, Vladar, AE & Postek, MT 2009, 'Contamination-free imaging by electron induced carbon volatilization in environmental scanning electron microscopy', Journal Of Applied Physics, vol. 106, pp. 034306-034306.
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Many ultraviolet, x-ray and charged particle beam techniques are inhibited by the growth of carbonaceous films caused by cross linking of hydrocarbon contaminant adsorbates. In electron microscopy, such films obscure surface features and reduce resolution. We demonstrate how resolution degradation can be alleviated using a H2O environment via gas mediated, electron beam induced carbon volatilization, a process that competes with film growth. Net behavior is a function of electron flux, which provides control over growth kinetics during imaging. Under optimized conditions, film growth can be eliminated, removing contamination as a factor limiting image information content and resolution.

Treangen, T, Darling, AE, Achaz, G, Ragan, M, Messeguer, X & Rocha, E 2009, 'A Novel Heuristic For Local Multiple Alignment Of Interspersed DNA Repeats', IEEE-acm Transactions On Computational Biology And Bioinformatics, vol. 6, no. 2, pp. 180-189.
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Pairwise local sequence alignment methods have been the prevailing technique to identify homologous nucleotides between related species. However, existing methods that identify and align all homologous nucleotides in one or more genomes have suffered fro

Tsolis, RM, Seshadri, R, Santos, RL, Sangari, FJ, Garcia Lobo, JM, de Jong, MF, Ren, Q, Myers, G, Brinkac, LM, Nelson, WC, DeBoy, RT, Angiuoli, S, Khouri, H, Dimitrov, G, Robinson, JR, Mulligan, S, Walker, RL, Elzer, PE, Hassan, KA & Paulsen, IT 2009, 'Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism', PLOS ONE, vol. 4, no. 5.
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Turner, ND, Paulhill, KJ, Warren, CA, Davidson, LA, Chapkin, RS, Lupton, JR, Carroll, RJ & Wang, N 2009, 'Quercetin Suppresses Early Colon Carcinogenesis Partly through Inhibition of Inflammatory Mediators', II INTERNATIONAL SYMPOSIUM ON HUMAN HEALTH EFFECTS OF FRUITS AND VEGETABLES: FAVHEALTH 2007, vol. 841, pp. 237-241.

Ujvari, B, Wallman, JF, Madsen, T, Whelan, M & Hulbert, AJ 2009, 'Experimental studies of blowfly (Calliphora stygia) longevity: A little dietary fat is beneficial but too much is detrimental', COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, vol. 154, no. 3, pp. 383-388.
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Van Belle, LE, Carter, DO & Forbes, SL 2009, 'Measurement of ninhydrin reactive nitrogen influx into gravesoil during aboveground and belowground carcass (Sus domesticus) decomposition', Forensic Science International, vol. 193, no. 1-3, pp. 37-41.
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Carcass decomposition results in the release of nitrogenous compounds into associated soil. The current study investigated the release of ninhydrin reactive nitrogen (NRN) following burial (similar to 40 cm depth) and decomposition on the soil surface. A

van Hal, SJ, Gilgado, F, Doyle, T, Barratt, J, Stark, D, Meyer, W & Harkness, J 2009, 'Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 47, no. 6, pp. 1818-1823.
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Varlow, M, Wuthrich, V, Murrihy, R, Rémond, L, Tuqiri, R, van Kessel, J, Wheatley, A, Dedousis-Wallace, A & Kidman, A 2009, 'Stress literacy in Australian adolescents', Youth Studies Australia, vol. 28, no. 4, pp. 29-34.
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Stress literacy is a term that refers to knowledge about stress and stress management techniques. Levels of stress literacy were examined in more than nine hundred Australian adolescents by providing a short stress-management education session and assessing stress literacy using a pre-post survey design. It was found that while adolescents had a reasonable knowledge of the symptoms of stress and effective stress management techniques, the likelihood of adolescents seeking help for stress or using these stress management techniques was low. The implications of these findings are discussed.

Vessalas, K, Ray, AS, Thomas, P, Guerbois, JL, Joyce, PA & Haggman, J 2009, 'Pozzolanic reactivity of the supplementary cementitious material pitchstone fines by thermogravimetric analysis', Journal Of Thermal Analysis And Calorimetry, vol. 97, no. 1, pp. 71-76.
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Thermogravimetric (TG) analysis was applied to the characterisation of the pozzolanic reaction in mortars containing the supplementary cementitious materials (SCMs) pitchstone fines (PF) and fly ash (FA) as partial replacements for Portland cement (PC). TG analysis was used to determine the proportion of calcium hydroxide (CH) present from the hydration of the PC based on the dehydroxylation of the CH present in the blended PC-SCM mortars. The consumption of CH indicated that both SCMs underwent the pozzolanic reaction and that PF was found to compare favourably in its pozzolanic reactivity of FA, the industry and globally accepted standard artificial pozzolan.

Vessalas, K, Ray, AS, Thomas, P, Sri Ravindrarajah, R, Joyce, PA & Haggman, J 2009, 'Pitchstone Fines - A New Naturally Occuring Pozzolan from North Queensland', Concrete Forum, vol. 2, no. 1, pp. 11-15.
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Global warming presents an ever-challenging battle to humankind, as emissions arising from industrially produced gteenhouse gases are predicted to alter the long-term climatic patterns of earth. Harmful environmental emissions arising during the manufactute of Portland cements (C) can be effectively reduced by incorporating siliceous-aluminous based supplementary cementitious materials (SCMs), as partial cement replacements. In Australia, mined pitchstone fines (PF), derived as waste material from expandable perlire production, area viable SCM for reducing cement consumption using an eco-friendly approach. This paper reports on the results of an experimental investigation into the pozzolanic activity of PP. Up to 40% cement was replaced with PF in mortar mixes. In addition, PP was used to partially replace sand. Strength activity index (SM) values for PP were evaluated using accelerated 28-day compressive strengths for all PP substitution levels, with flows and wet densities of mortar mixes reported.

Vessalas, K, Ray, AS, Thomas, P, Sri Ravindrarajah, R, Joyce, PA & Haggman, J 2009, 'Pitchstone fines pozzolanic activity assessment as partial Portland cement (PC) replacements', Journal of Australasian Ceramic Society, vol. 44, no. 1, pp. 7-12.
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Mined pitchstone fines (PF), derived as a waste by-product from expandable perlite production in Australia, are a viable, environmentally friendly aluminosilicate supplementary cementitious material (SCM) suitable for partial Portland cement (PC) replacement, thus reducing greenhouse gas emissions resulting from PC manufacture. This paper reports on the findings of pozzolanic activity exhibited at 10%, 20% and 40% replacement levels of PC, through compressive strength determinations of mortar after 1, 7 and 28 days ageing, using strength activity index (SAI) criteria. Additionally, flows and wet densities have been examined using a polycarboxylic based high-range water-reducing admixture (HRWRA) superplasticiser and fixed water content relative to cementitious material present for all PF substitution levels.

Wallach, A, Murray, B & O'neill, A 2009, 'Can threatened species survive where the top predator is absent?', Biological Conservation, vol. 142, no. 1, pp. 43-52.
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Top predators have been described as highly interactive keystone species. Their decline has been linked to secondary extinctions and their increase has been linked to ecological restoration. Several authors have recently argued that the dingo Canis lupus dingo is another example of a top predator that maintains mesopredators and generalist herbivores at low and stable numbers, thereby increasing biodiversity and productivity. Due to the sensitivity of many Australian species to introduced mesopredators and herbivores, the top predator hypothesis predicts that threatened species will not survive where dingoes are rare or absent. However, several threatened species have survived inside the Dingo Barrier Fence (DBF). We present a new view on the survival of the yellow-footed rock-wallaby Petrogale xanthopus xanthopus and the malleefowl Leipoa ocellata inside the DBF where the dingo is considered very rare, or in areas where the dingo is believed to have been eradicated several decades ago. We found that dingoes co-occurred with both threatened species. Dingoes were present at all wallaby colonies surveyed and occurred throughout their range. The most common predator detected in areas inhabited by the wallabies was in fact the dingo, and we found no significant difference between dingo abundance inside compared to outside the DBF. Malleefowl nests were found to be scent marked by dingoes at the three sites that we surveyed, despite these sites being close to human settlement and sheep farms, and in small and fragmented patches of wilderness. These findings provide further evidence for an association between the presence of dingoes and the survival of threatened species, which is in agreement with the top predator hypothesis.

Wallach, AD & O'neill, AJ 2009, 'Artificial water points: Hotspots of extinction or biodiversity?', BIOLOGICAL CONSERVATION, vol. 142, no. 7, pp. 1253-1254.
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Wallach, AD & O'Neill, AJ 2009, 'Threatened species indicate hot-spots of top-down regulation', Animal Biodiversity and Conservation, vol. 32, no. 2, pp. 127-133.

Wallach, AD, Inbar, M & Shanas, U 2009, 'Roe deer and decapitated Anemone flowers', ISRAEL JOURNAL OF PLANT SCIENCES, vol. 57, no. 1-2, pp. 103-106.
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Wallach, AD, Ritchie, EG, Read, J & O'Neill, AJ 2009, 'More than Mere Numbers: The Impact of Lethal Control on the Social Stability of a Top-Order Predator', PLOS ONE, vol. 4, no. 9.
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Walsh, SP, King, EJ & Simpson, G 2009, 'Pulse Diagnosis: An Introductory Guide for the Experienced Practitioner', The Journal of Chinese Medicine, vol. 89, pp. 5-12.
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Pulse diagnosis is widely regarded as a core component of the diagnostic framework of Chinese medicine. Such regard for pulse diagnosis is founded on the premise that pulse assessment is a clinically reliable diagnostic method. The validity of the pulse as a diagnostic tool tends to be founded on its historical roots in antiquity; because pulse diagnosis has been in use for so long, its validity is rarely questioned. Such uncritical acceptance of the information provided by classical texts (and reiterated in contemporary literature) has left the pedagogical framework for the use of pulse diagnosis compromised, and subsequently its reliability as a diagnostic tool is questionable. In many cases, the information available for practitioners is either ambiguous, lacking clear instruction on the use of pulse diagnosis, or contradictory, with different authors holding opposing views. This paper aims to clarify some of the problems associated with the use of pulse diagnosis in a modern context, and to encourage practitioners to identify misconceptions regarding pulse diagnosis, thus facilitating its use as a reliable diagnostic tool in contemporary clinical practice.

Walters, SN, Donnelly, S, Robinson, M, Dalton, J & Grey, ST 2009, 'Identification of novel parasite-derived compounds that promote long-term islet allograft survival', XENOTRANSPLANTATION, vol. 16, no. 5, pp. 402-402.

Wand, M 2009, 'Semiparametric regression and graphical models', Australian & New Zealand Journal of Statistics, vol. 51, no. 1, pp. 9-41.
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Semiparametric regression models that use spline basis functions with penalization have graphical model representations. This link is more powerful than previously established mixed model representations of semiparametric regression, as a larger class of models can be accommodated. Complications such as missingness and measurement error are more naturally handled within the graphical model architecture. Directed acyclic graphs, also known as Bayesian networks, play a prominent role. Graphical model-based Bayesian `inference engines, such as bugs and vibes, facilitate fitting and inference. Underlying these are Markov chain Monte Carlo schemes and recent developments in variational approximation theory and methodology

Wang, B, Konstantinov, K, Wexler, D, Liu, H & Wang, G 2009, 'Synthesis of nanosized vanadium pentoxide/carbon composites by spray pyrolysis for electrochemical capacitor application', Electrochimica Acta, vol. 54, no. 5, pp. 1420-1425.
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Nanostructured vanadium pentoxide/carbon (V2O5/carbon) composite powders with enhanced specific capacitance were synthesized by the spray pyrolysis technique. Electrochemical properties were examined by the cyclic voltammetry technique. Following analysis of powders sprayed at different temperatures, composite powders obtained at an optimum temperature of 450 °C yielded a maximum specific capacitance of 295 F g-1 in 2 M KCl electrolyte at a 5-mV s-1 scan rate. The weight percentage of carbon-related species was 2.7 wt% in this V2O5/carbon composite, as detected by thermogravimetric analysis (TGA) and confirmed by transmission electron microscope energy dispersive spectroscopy (TEM-EDS) analysis. Following initial X-ray diffraction (XRD) characterization, scanning electron microscope (SEM), TEM and high-resolution TEM (HRTEM) imaging revealed a specific morphology of spherical shell agglomerates of V2O5 nanorods and nanoribbons, with each shell comprising a network of these one- and two-dimensional nanoparticles in an amorphous carbon matrix. The V2O5 network was not fully dense, and the majority of the nanorod sizes were in the range of 50150 nm, with additional long nanoribbons extending from the outsides of the spherical shells. The specific surface area was 18 m2 g-1 for the composite powders, and the pore size distribution revealed that the majority of pores had diameters in the range of 4050 Å, which was relatively larger than the pore diameters obtained at 500 °C and would be beneficial for electrochemical performance. The enhancement of the specific capacitance in V2O5/carbon composites was attributed to the distribution of amorphous carbon throughout the V2O5 and the particular open nanostructure.

Wang, G, Park, JS & Park, MS 2009, 'Growth, characterisation and technological applications of semiconductor SnO(2) nanotubes and In(2)O(3) nanowires', Journal of Nanoscience & Nanotechnology, vol. 9, no. 2, pp. 1144-1147.
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Tin dioxide nanotubes (200 nm in diameter) were synthesised by the sol-gel template method. The gas sensitivity of SnO2 nanotubes has been investigated. Due to the small grain size and large amount of grain boundary, SnO2 nanotubes demonstrated good sensitivity in sensing ethanol gas and had an ability to detect ammonia gas without any doping or surface modification. In2O3 semiconductor nanowires were synthesized efficiently by the chemical vapor deposition method through carbon thermal reduction. The diameter, length and morphologies of In2O3 nanowires can be varied by controlling the synthetic conditions. The In2O3 nanowires were characterised by field emission scanning electron microscopy (FE-SEM) and high resolution transmission electron microscopy (HRTEM). The application of In2O3 nanowires for gas sensors was tested.

Wang, G, Shen, X & Yao, J 2009, 'One-dimensional nanostructures as electrode materials for lithium-ion batteries with improved electrochemical performance', Journal of Power Sources, vol. 189, no. 1, pp. 543-546.
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One-dimensional (1D) nanosize electrode materials of lithium iron phosphate (LiFePO4) nanowires and Co3O4carbon nanotube composites were synthesized by the hydrothermal method. The as-prepared 1D nanostructures were structurally characterized by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. We tested the electrochemical properties of LiFePO4 nanowires as cathode and Co3O4carbon nanotubes as anode in lithium-ion cells, via cyclic voltammetry and galvanostatic charge/discharge cycling. LiFePO4 nanorod cathode demonstrated a stable performance over 70 cycles, with a remained specific capacity of 140 mAh g-1. Nanocrystalline Co3O4carbon nanotube composite anode exhibited a reversible lithium storage capacity of 510 mAh g-1 over 50 cycles. 1D nanostructured electrode materials showed strong potential for lithium-ion batteries due to their good electrochemical performance.

Wang, G, Shen, X, Horvat, J, Wang, B, Liu, H, Wexler, D & Yao, J 2009, 'Hydrothermal synthesis and optical, magnetic, and supercapacitance properties of nanoporous cobalt oxide nanorods', Journal of Physical Chemistry C, vol. 113, no. 11, pp. 4357-4361.
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Nanoporous cobalt oxide nanorods were synthesized by a hydrothermal method. Transmission electron microscopy analysis showed that the individual Co3O4 nanorods have a nanoporous structure, consisting of the textured aggregations of nanocrystals. Optical properties of Co3O4 nanorods were characterized by Raman and UV-vis spectroscopy. Magnetic property measurement shows that Co3O4 nanorods have a low Nel transition temperature of 35 K. We observed quite significant exchange bias for nanoporous Co3O4 nanorods, indicating the existence of magnetic coupling between the nanocrystals in Co3O4 nanorods. When applied as electrode materials in supercapacitors, Co3O4 demonstrated a high capacitance of 280 F/g.

Wang, G, Shen, X, Wang, B, Yao, J & Park, J 2009, 'Synthesis and characterisation of hydrophilic and organophilic graphene nanosheets', Carbon, vol. 47, no. 5, pp. 1359-1364.
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Hydrophilic graphene nanosheets were rapidly synthesized by reacting graphene oxide nanosheets with poly(sodium 4-styrene sulfonate) and simultaneously reducing by hydrazine hydrate under hydrothermal conditions. Organophilic graphene nanosheets were prepared by reacting with octadecylamine and reduction by hydroquinone through a reflux process. Ultravioletvisible spectroscopy and Fourier transform infrared spectroscopy measurements confirmed the attachment of organic molecules to the graphene nanosheets to achieve hydrophilic and organophilic affinity. X-ray diffraction, Raman spectroscopy, and transmission electron microscopy analysis indicated that the crystal structure of the graphene nanosheets was maintained intact after chemical functionalisation.

Wang, G, Shen, X, Yao, J & Park, J 2009, 'Graphene nanosheets for enhanced lithium storage in lithium ion batteries', Carbon, vol. 47, no. 8, pp. 2049-2053.
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Graphene nanosheets were synthesized in large quantities using a chemical approach. Field emission electron microscope observation revealed that loose graphene nanosheets agglomerated and crumpled naturally into shapes resembling flower-petals. High resolution transmission electron microscope analysis, Raman spectroscopy and ultravioletvisible spectroscopy measurements confirmed the graphitic crystalline structure of the graphene nanosheets. The nanosheets exhibited an enhanced lithium storage capacity as anodes in lithium-ion cells and good cyclic performance.

Wang, G, Shen, X, Yao, J, Wexler, D & Ahn, J 2009, 'Hydrothermal synthesis of carbon nanotube/cobalt oxide core-shell one-dimensional nanocomposite and application as an anode material for lithium-ion batteries', Electrochemistry Communications, vol. 11, no. 3, pp. 546-549.
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Carbon nanotube/cobalt oxide core-shell one-dimensional nanostructures were prepared via a hydrothermal synthesis method, in which nanosize cobalt oxide crystals were homogeneously coated on the surface of carbon nanotubes. The morphologies and crystal structures of the as-prepared core-shell nanocomposites were analysed by X-ray diffraction, field emission gun scanning electron microscopy, and transmission electron microscopy. When applied as anodes in lithium-ion cells, carbon nanotube/cobalt oxide core-shell nanostructures exhibited an initial lithium storage capacity of 1250 mAh/g and a stable capacity of 530 mAh/g over 100 cycles. The good electrochemical performance could be attributed to the nanocrystalline cobalt oxide and the unique core-shell one-dimensional nanostructures.

Wang, G, Wang, B, Park, J, Wang, Y, Sun, B & Yao, J 2009, 'Highly efficient and large-scale synthesis of graphene by electrolytic exfoliation', Carbon, vol. 47, no. 14, pp. 3242-3246.
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Highly efficient and large-scale synthesis of graphene from graphite was produced by electrolytic exfoliation using poly(sodium-4-styrenesulfonate) as an effective electrolyte. Scanning and transmission electron microscopy, and atomic force microscopy confirmed the existence of monolayer graphene sheets and stacks containing a few graphene sheets. Raman spectroscopy demonstrated that the as-prepared graphene sheets have low defect content. Based on the measurement of FTIR spectra, the edge-to-face interaction (?? interaction) between the graphene surface and aromatic rings of poly(sodium-4-styrenesulfonate) could be primarily responsible for producing exfoliation of the graphite electrode to graphene during electrolysis. In contrast to micromechanical exfoliation, electrolytic exfoliation can be scaled up for large-scale and continuous graphene production.

Wang, G, Wang, B, Park, J, Yang, J, Shen, X & Yao, J 2009, 'Synthesis of enhanced hydrophilic and hydrophobic graphene oxide nanosheets by a solvothermal method', Carbon, vol. 47, no. 1, pp. 68-72.
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We report that the hydrophilic affinity of graphene oxide nanosheets can be significantly increased by reacting with allylamine. High resolution transmission electron microscopy and electron diffraction analysis confirmed that the graphene oxide nanosheets were amorphous in structure. Hydrophobic graphene oxide nanosheets were also prepared via functionalising with phenylisocynate (C6H5NCO) through a solvothermal synthesis process. Hydrophobic graphene oxide nanosheets can be used as additives in polymer-based composites and other functional applications.

Wang, G, Wang, B, Wang, X, Park, J, Dou, SX, Ahn, H & Kim, K 2009, 'Sn/graphene nanocomposite with 3D architecture for enhanced reversible lithium storage in lithium ion batteries', Journal of Materials Chemistry, vol. 19, no. 44, pp. 8378-8384.
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A general strategy has been demonstrated to achieve optimum electrochemical performance by constructing 3D nanocomposite architecture with the combination of nanosize Sn particles and graphene nanosheets. In the first step, the lithium storage properties of graphene have been investigated by first principles calculations. The results show that lithium can be stably stored on both sides of graphene sheets (LiC3), inducing in a theoretical capacity of 744 mAh/g. In the second step, a synthetic approach has been designed to prepare Sn/graphene nanocomposite with 3D architecture, in which Sn nanoparticles act as a spacer to effectively separate graphene nanosheets. FESEM and TEM analysis revealed the homogeneous distribution of Sn nanoparticles (25 nm) in graphene nanosheet matrix. Cyclic voltammetry measurement has proved the highly reversible nature of the reaction between Li+ and Sn/graphene nanocomposite. The 3D nanoarchitecture gives the Sn/graphene nanocomposite electrode an enhanced electrochemical performance. This strategy can be extended to prepare other anode and cathode materials for advanced energy storage and conversion devices such as lithium ion batteries, supercapacitors, and fuel cells.

Wang, J, Chou, SL, Liu, H, Wang, G, Zhang, C, Chew, SY & Liu, H 2009, 'Highly flexible and bendable free-standing thin film polymer for battery application', Materials Letters, vol. 63, no. 27, pp. 2352-2354.
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Highly flexible and bendable free-standing polypyrrole (PPy) films were prepared using the electrochemical polymerization method. The paper-like films are soft, lightweight, mechanically robust, and highly electrically conductive. The morphologies and electrochemical behaviour of the free-standing pure PPy films were affected by the electrochemical polymerization conditions. The free-standing films show promise as cathodes for flexible and bendable batteries

Wang, M & Dennis, ES 2009, 'SPT5-like, a new component in plant RdDM', EMBO REPORTS, vol. 10, no. 6, pp. 573-575.
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Plant DNA is extensively methylated at cytosine residues; however, unlike in animals, the methylation occurs not only at CG sites but also at CNG and CHHin which H represents A, C or Tsites. A significant proportion (~30%) of this cytosine methylation in Arabidopsis is dependent on the RNA-silencing pathway known as RNA-directed DNA methylation (RdDM; Matzke et al, 2009). RdDM has a crucial role in silencing retrotransposons and endogenous repeats, thereby maintaining genome stability. It probably also has a role in regulating the transcriptional activities of plant genes that contain, or are adjacent to, transposons or repetitive elements, many of which might have a role in stress responses. In addition, RdDM is required for the maintenance and systemic transmission of post-transcriptional gene silencing in plants (Brosnan et al, 2007; Eamens et al, 2008), presumably by causing modification of the transgene DNA that is necessary for producing secondary small-interfering RNAs (siRNAs; Daxinger et al, 2009). The existence of RdDM was initially demonstrated using exogenous viral RNAs (Wassenegger et al, 1994; Jones et al, 1999), and was subsequently shown to be mediated by 24-nucleotide (nt) siRNAs, which form the predominant population of endogenous small RNAs (Kasschau et al, 2007; Mosher et al, 2008). siRNAs can also be generated by viruses and transgenes in plants to direct RdDM (Mette et al, 2000; Wang et al, 2001).

Wang, X, Zeng, Z, Ahn, H & Wang, G 2009, 'First-principles study on the enhancement of lithium storage capacity in boron doped graphene', APPLIED PHYSICS LETTERS, vol. 95, no. 18.
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Wang, Y, Chi, Q, Hush, N, Reimers, JR, Zhang, J & Ulstrup, J 2009, 'Scanning Tunneling Microscopic Observation Of Adatom-Mediated Motifs On Gold-Thiol Self-Assembled Monolayers At High Coverage', Journal Of Physical Chemistry C, vol. 113, no. 45, pp. 19601-19608.
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Self-assembled monolayers (SAMs) formed by chemisorption of a branched-chain alkanethiol, 2-methyl-1-propanethiol, on Au(111) surfaces were Studied by in situ scanning tunneling microscopy (STM) under electrochemical potential control and analyzed using extensive density functional theory (DFF) calculations. The SAM forms in the unusual (8 x root 3)-4 superlattice, producing a very complex STM image. Seventy possible structures were considered for the SAM, with the calculated lowest-energy configuration in fact predicting the details of the unusual observed STM image. The most stable structure involves two R-S-Au-S-R adatom-mediated motifs per surface cell, with steric-induced variations in the adsorbate alignment inducing the observed STM image contrasts. Observed pits covering 5.6 +/- 0.5% of the SAM surface are consistent with this structure. These results provide the missing link from the structural motifs observed on Surfaces at low coverage and on gold nanoparticles to the observed spectroscopic properties of high-coverage SAMs formed by methanethiol. However, the significant role attributed to intermolecular steric packing effects suggests a lack of generality for the adatom-mediated motif at high coverage.

Wang, Y, Li, Y, Wu, Z & Murray, B 2009, 'Insular shifts and trade-offs in life-history traits in pond frogs in the Zhoushan Archipelago, China', Journal Of Zoology, vol. 278, no. 1, pp. 65-73.
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Island and mainland populations of animal species often differ strikingly in life-history traits such as clutch size, egg size, total reproductive effort and body size. However, despite widespread recognition of insular shifts in these life-history traits in birds, mammals and reptiles, there have been no reports of such life-history shifts in amphibians. Furthermore, most studies have focused on one specific life-history trait without explicit consideration of coordinated evolution among these intimately linked life-history traits, and thus the relationships among these traits are poorly studied. Here we provide the first evidence of insular shifts and trade-offs in a coordinated suite of life-history traits for an amphibian species, the pond frog Rana nigromaculata. Life-history data were collected from eight islands in the Zhoushan Archipelago and neighboring mainland China. We found consistent, significant shifts in all life-history traits between mainland and island populations. Island populations had smaller clutch sizes, larger egg sizes, larger female body size and invested less in total reproductive effort than mainland populations. Significant negative relationships were found between egg size and clutch size and between egg size and total reproductive effort among frog populations after controlling for the effects of body size. Therefore, decreased reproductive effort and clutch size, larger egg size and body size in pond frogs on islands were selected through trade-offs as an overall life-history strategy. Our findings contribute to the formation of a broad, repeatable ecological generality for insular shifts in life-history traits across a range of terrestrial vertebrate taxa.

Wang, Y, Ma, Y & Carroll, RJ 2009, 'Variance estimation in the analysis of microarray data', JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, vol. 71, pp. 425-445.
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Ward, J, Gilmore, SR, Robertson, J & Peakall, R 2009, 'A Grass Molecular Identification System for Forensic Botany: A Critical Evaluation of the Strengths and Limitations', JOURNAL OF FORENSIC SCIENCES, vol. 54, no. 6, pp. 1254-1260.
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Warren, CA, Paulhill, KJ, Davidson, LA, Lupton, JR, Taddeo, SS, Hong, MY, Carroll, RJ, Chapkin, RS & Turner, ND 2009, 'Quercetin May Suppress Rat Aberrant Crypt Foci Formation by Suppressing Inflammatory Mediators That Influence Proliferation and Apoptosis', JOURNAL OF NUTRITION, vol. 139, no. 1, pp. 101-105.
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Warren, CA, Paulhill, KJ, Davidson, LA, Lupton, JR, Taddeo, SS, Hong, MY, Carroll, RJ, Chapkin, RS & Turner, ND 2009, 'Quercetin may suppress rat aberrant crypt foci formation by suppressing inflammatory mediators that influence proliferation and apoptosis (vol 139, pg 101, 2009)', JOURNAL OF NUTRITION, vol. 139, no. 4, pp. 792-792.
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Webb, JK, Du, WG, Pike, DA & Shine, R 2009, 'Chemical cues from both dangerous and nondangerous snakes elicit antipredator behaviours from a nocturnal lizard', Animal Behaviour, vol. 77, no. 6, pp. 1471-1478.
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Many prey species use chemical cues to detect predators. According to the threat sensitivity hypothesis, prey should match the intensity of their antipredator behaviour to the degree of threat posed by the predator. Several species of lizards display antipredator behaviours in the presence of snake chemical cues, but how species specific are these responses? In Australia, most snake species eat lizards, and are therefore potentially dangerous. Hence, we predicted that lizards should display generalized rather than species-specific antipredator behaviours. To test this prediction, we quantified the behavioural responses of velvet geckos, Oedura lesueurii, to chemical cues from five species of elapid snakes that are syntopic with velvet geckos but differ in their degree of danger. These five snake species included two nocturnal ambush foragers that eat geckos (broad-headed snake Hoplocephalus bungaroides, and death adder, Acanthophis antarcticus), two active foragers that eat skinks (but rarely eat geckos) and that differ in their activity times (nocturnal small-eyed snake, Cryptophis nigrescens, and diurnal whip snake, Demansia psammophis), and a nocturnal nonthreatening species that feeds entirely on blind snakes (bandy-bandy, Vermicella annulata). Geckos showed similar antisnake behaviours (tail waving, tail vibration), and a similar intensity of responses (reducing activity, freezing), to chemical cues from all five snake species, even though the snakes differed in their degree of danger and foraging modes. Our results suggest that velvet geckos display generalized antipredator responses to chemicals from elapid snakes, rather than responding in a graded fashion depending upon the degree of threat posed by a particular snake species.

Webb, JK, Pringle, RM & Shine, R 2009, 'Intraguild predation, thermoregulation, and microhabitat selection by snakes', Behavioral Ecology, vol. 20, no. 2, pp. 271-277.
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Intraguild (IG) predation, the killing and eating of potential competitors, can be a powerful force within faunal assemblages. If both the IG predator and its prey prefer similar microhabitats in spatially structured environments, avoidance of the predator may relegate IG prey to suboptimal habitats. In southeastern Australia, the broad-headed snake (Hoplocephalus bungaroides) is an endangered species sympatric with the small-eyed snake (Cryptophis nigrescens), an abundant and geographically widespread species known to eat other snakes. Both of these nocturnal ectotherms shelter diurnally beneath thermally distinctive "hot rocks," which are in limited supply. When selecting shelter sites, broad-headed snakes thus face a trade-off between predation risk and habitat quality. In laboratory experiments, we allowed broad-headed snakes to choose between retreat sites differing in thermal regimes, in scent cues from predators, and in the actual presence of the predator. Broad-headed snakes displayed an aversion to sites with live predators and predator scent, yet nonetheless frequently selected those sites to obtain thermal benefits. In trials with live predators, adult broad-headed snakes shared hot rocks with small-eyed snakes, but most juveniles did not; data from a 16-year field study likewise suggest that broad-headed snakes only cohabit with small-eyed snakes if the two snakes are similar in body size. Our results suggest that thermoregulatory considerations are sufficient to prompt juvenile (but not adult) broad-headed snakes to risk IG predation, emphasizing the importance of microhabitat quality and body size in mediating IG predator-prey interactions.

Webb, RR, Doble, PA & Dawson, M 2009, 'Optimisation of HPLC gradient separations using artificial neural networks (ANNs): Application to benzodiazepines in post-mortem samples', Journal Of Chromatography B-Analytical Technologi..., vol. 877, no. 7, pp. 615-620.
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Artificial neural networks (ANNs) were used in conjunction with an experimental design to optimise a gradient HPLC separation of nine benzodiazepines. Using the best performing ANN, the optimum conditions predicted were 25 mM formate buffer (pH 2.8), 10% MeOH, acetonitrile (ACN) gradient 0-15 min, 6.5-48.5%. The error associated with the prediction of retention times and peak widths under these conditions was less than 5% for six of the nine analytes. The optimised method, with limits of detection (LODs) in the range of 0.0057-0.023 mu g/mL and recoveries between 58% and 92%, was successfully applied to authentic post-mortem samples. This method represents a more flexible and convenient means for optimising gradient elution separations using ANNs than has been previously reported.

Weckmann, M, Trian, T & Oliver, BGG 2009, 'Reconstruction is not renovation - The role of remodeling in asthma', Journal of Asthma and Allergy, no. 2, pp. 33-42.
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The chronicity of asthma results not only in persistent lung inflammation but also in changes in structure and composition of this vital organ. These changes are most commonly referred to as remodeling, and include epithelial dysplasia, angiogenesis, changes in the extracellular matrix and increased smooth muscle mass. In this review we summarize recent findings on the contribution of remodeling to the pathological phenotype of asthma. We discuss how and why current treatment (such as corticosteroids) options fail to adequately treat remodeling. © 2009 Weckmann et al, publisher and licensee Dove Medical Press Ltd.

Wei, Y & Carroll, RJ 2009, 'Quantile Regression With Measurement Error', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 104, no. 487, pp. 1129-1143.
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Weuve, J, Korrick, S, Weisskopf, M, Ryan, LM, Schwartz, J, Nie, H, Grodstein, F & Hu, H 2009, 'Cumulative Exposure To Lead In Relation To Cognitive Function In Older Women', Environmental Health Perspectives, vol. 117, no. 4, pp. 574-580.
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BACKGROUND: Recent data indicate that chronic low-level exposure to lead is associated with accelerated declines in cognition in older age, but this has not been examined in women. OBJECTIVE: We examined biomarkers of lead exposure in relation to performance on a battery of cognitive tests among older women. METHODS: Patella and tibia bone lead-measures of cumulative exposure over many years-and blood lead, a measure of recent exposure, were assessed in 587 women 47-74 years of age. We assessed their cognitive function 5 years later using validated telephone interviews. RESULTS: Mean +/- SD lead levels in tibia, patella, and blood were 10.5 +/- 9.7 mu g/g bone, 12.6 +/- 11.6 mu g/g bone, and 2.9 +/- 1.9 mu g/dL, respectively, consistent with community-level exposures. In multivariable-adjusted analyses of all cognitive tests combined, levels of all three lead biomarkers were associated with worse cognitive performance. The association between bone lead and letter fluency score differed dramatically from the other bone lead-cognitive score associations, and exclusion of this particular score from the combined analyses strengthened the associations between bone lead and cognitive performance. Results were statistically significant only for tibia lead: one SD increase in tibia lead corresponded to a 0.051-unit lower standardized summary cognitive score (95% confidence interval: -0.099 to -0.003; P = 0.04), similar to the difference in cognitive scores we observed between women who were 3 years apart in age. CONCLUSIONS: These findings suggest that cumulative exposure to lead, even at low levels experienced in community settings, may have adverse consequences for women's cognition in older age.

Wheatley, A, Murrihy, R, van Kessel, J, Wuthrich, V, Rémond, L, Tiqiri, R, Dadds, M & Kidman, A 2009, 'Aggression management training for youth in behaviour schools: A quasi-experimental study', Youth Studies Australia, vol. 28, no. 1, pp. 29-36.
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A 16-week, bi-weekly, cognitive behavioural therapy (CBT)-based aggression management training course was conducted with a limited sample of behavioural school students in New South Wales. Attendance, withdrawal and suspension rates over the training period were compared to those of a control period. Parent and teacher feedback, assessed at pre- and post-training, delivered preliminary information on disruptive behaviours and peer relations, Results revealed mixed findings with some improvements indisruptive behaviours, suspensions and withdrawals over the training period, Further research is needed to replicate these findings with a larger group of students.

White, SW, Ollendick, T, Scahill, L, Oswald, D & Albano, AM 2009, 'Preliminary Efficacy of a Cognitive-Behavioral Treatment Program for Anxious Youth with Autism Spectrum Disorders', JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS, vol. 39, no. 12, pp. 1652-1662.
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White, SW, Oswald, D, Ollendick, T & Scahill, L 2009, 'Anxiety in children and adolescents with autism spectrum disorders', CLINICAL PSYCHOLOGY REVIEW, vol. 29, no. 3, pp. 216-229.
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Whiting, MJ, Webb, JK & Keogh, JS 2009, 'Flat lizard female mimics use sexual deception in visual but not chemical signals', Proceedings Of The Royal Society B-biological Sciences, vol. 276, no. 1662, pp. 1585-1591.
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Understanding what constrains signalling and maintains signal honesty is a central theme in animal communication. Clear cases of dishonest signalling, and the conditions under which they are used, represent an important avenue for improved understanding of animal communication systems. Female mimicry, when certain males take on the appearance of females, is most commonly a male alternative reproductive tactic that is condition-dependent. A number of adaptive explanations for female mimicry have been proposed including avoiding the costs of aggression, gaining an advantage in combat, sneaking copulations with females on the territories of other males, gaining physiological benefits and minimizing the risk of predation. Previous studies of female mimicry have focused on a single mode of communication, although most animals communicate using multiple signals. Male Augrabies flat lizards adopt alternative reproductive tactics in which some males (she-males) mimic the visual appearance of females. We experimentally tested in a wild population whether she-males are able to mimic females using both visual and chemical signals. We tested chemical recognition in the field by removing scent and relabelling females and she-males with either male or female scent. At a distance, typical males (he-males) could not distinguish she-males from females using visual signals, but during close encounters, he-males correctly determined the gender of she-males using chemical signals. She-males are therefore able to deceive he-males using visual but not chemical signals. To effectively deceive he-males, she-males avoid close contact with he-males during which chemical cues would reveal their deceit. This strategy is probably adaptive, because he-males are aggressive and territorial; by mimicking females, she-males are able to move about freely and gain access to females on the territories of resident males.

Williams, DBG & Cullen, A 2009, 'Al(OTf)(3)-Mediated Epoxide Ring-Opening Reactions: Toward Piperazine-Derived Physiologically Active Products', JOURNAL OF ORGANIC CHEMISTRY, vol. 74, no. 24, pp. 9509-9512.
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Williams, DBG & Netshiozwi, TE 2009, 'Synthesis and characterisation of severely hindered P-OR compounds', TETRAHEDRON, vol. 65, no. 48, pp. 9973-9982.
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Williams, DBG, Caddy, J, Blann, K, Grove, JJC & Holzapfel, CW 2009, 'Chiral Cyclobutanols and Cyclopentane Dimers via Samarium(II) Iodide Induced Keto-Olefin Cyclisations of Carbohydrate-Derived Unsaturated Ketones', SYNTHESIS-STUTTGART, no. 12, pp. 2009-2014.
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Williams, DBG, Evans, SJ, de Bod, H, Mokhadinyana, MS & Hughes, T 2009, 'Directed ortho Metallation Chemistry and Phosphine Synthesis: New Ligands for the Suzuki-Miyaura Reaction', SYNTHESIS-STUTTGART, no. 18, pp. 3106-3112.
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Williams, DBG, Sibiya, MS, van Heerden, PS, Kirk, M & Harris, R 2009, 'Verkade super base-catalysed transesterification of propylene carbonate with methanol to co-produce dimethyl carbonate and propylene glycol', JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL, vol. 304, no. 1-2, pp. 147-152.
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Wilton, J, Jenkins, C, Cordwell, SJ, Falconer, L, Minion, F, Oneal, D, Djordjevic, MA, Connolly, AM, Barchia, I, Walker, MJ & Djordjevic, SP 2009, 'Mhp493 (P216) is a proteolytically processed, cilium and heparin binding protein of Mycoplasma hyopneumoniae', Molecular Microbiology, vol. 71, no. 3, pp. 566-582.
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Mycoplasma hyopneumoniae induces respiratory disease in swine by colonizing cilia causing ciliostasis, cilial loss and epithelial cell death. Heparin binds to M. hyopneumoniae cells in a dose-dependent manner and blocks its ability to adhere to porcine cilia. We show here that Mhp493 (P216), a paralogue of the cilium adhesin P97 (Mhp183), is cleaved between amino acids 1040 and 1089 generating surface-accessible, heparin-binding proteins P120 and P85. Antiphosphoserine antibodies recognized P85 in 2-D immunoblotting studies and TiO2 chromatography of trypsin digests of P85 isolated a single peptide with an m/z of 917.3. A phosphoserine residue in the tryptic peptide (90)VSELpSFR(96) (position 94 in P85) was identified by MALDI-MS/MS. Polyhistidine fusion proteins (F1(P216), F2(P216), F3(P216)) spanning Mhp493 bound heparin with biologically significant Kd values, and heparin, fucoidan and mucin inhibited this interaction. Latex beads coated with F1(P216), F2(P216) and F3(P216) adhered to and entered porcine kidney epithelial-like (PK15) cell monolayers. Microtitre plate-based assays showed that sequences within P120 and P85 bind to porcine cilia and are recognized by serum antibodies elicited during infection by M. hyopneumoniae. Mhp493 contributes significantly to the surface architecture of M. hyopneumoniae and is the first cilium adhesin to be described that lacks an R1 cilium-binding domain.

Wohlthat, S, Kirchner, T & Reimers, JR 2009, 'N-Silylamine Junctions For Molecular Wires To Gold: The Effect Of Binding Atom Hybridization On The Electronic Transmission', Journal Of Physical Chemistry C, vol. 113, no. 47, pp. 20458-20462.
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In molecular conduction studies, amine groups are often used as linkers between molecules and gold surfaces. We demonstrate using density functional theory (DFT) that N-silyl substitution of 1,4-benzenediamine (BDA) produces a highly polarizable junction with a conductance and electrostatic profile that depends strongly on the local hybridization. In BDA itself, a forced change in hybridization from sp(3) to sp(2) is predicted to increase the conductivity by an order of magnitude. N-silyl Substitution is shown to make this effect accessible while maintaining a 5-fold conductance ratio and Sufficient binding strength to allow junctions to spontaneously assemble. Hence N-silylamines are predicted to form useful, externally controllable molecular junctions.

Wong, FWS, Lin, L & Lim, DCE 2009, 'Drug and herb interactions: Searching the web', Australian Family Physician, vol. 38, no. 8, pp. 627-633.
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Background: Australian patients spend large sums of money on complementary medicine and therapy each year. General practitioners are often asked questions about whether prescribed medications will interact with complementary medications. What current internet resources can be accessed to assist in answering these questions? Objective: This article looks at current internet resources that can assist GPs to answer patient questions about interactions between prescribed and complementary medicines. Discussion: Many of the websites found in this study provided limited information and limited searchability. We found seven webistes out of 100 that met our selection criteria. A web portal, with risk categorisation of mild, moderate and severe for drug-herb interactions, can assist doctors in clinical decision making. Maximum benefits could be obtained by working corroboratively with the Therapeutic Goods Administration.

Wong, VCK, Lim, CED, Luo, X & Wong, WSF 2009, 'Current alternative and complementary therapies used in menopause', GYNECOLOGICAL ENDOCRINOLOGY, vol. 25, no. 3, pp. 166-174.
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Wright, AR, Wang, G, Xu, W, Zeng, Z & Zhang, C 2009, 'The spin-orbit interaction enhanced terahertz absorption in graphene around the K point', Microelectronics Journal, vol. 40, no. 4-5, pp. 857-859.
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We present a quantitative analysis on the effect of the spinorbit interaction in the optical absorption of ?-electrons in graphene. It has been shown that the optical absorption amplitude of graphene around the K point in the Brillouin zone has a node in the two-dimensional Brillouin zone of honeycomb lattice. We calculated the k-dependent absorption matrix by taking into account the finite spinorbit interaction in graphene. It was found that the spinorbit interaction lifts the nodes in the absorption matrix. Furthermore, in the terahertz frequency regime, the spinorbit interaction can significantly enhance the optical absorption in graphene, by up to 100%.

Wu, H, Wexler, D & Wang, G 2009, 'PtxNi alloy nanoparticles as cathode catalyst for PEM fuel cells with enhanced catalytic activity', Journal Of Alloys And Compounds, vol. 488, no. 1, pp. 195-198.
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A series of PtxNi/C (x = 13) nanoparticle catalysts were prepared using a chemical reduction method, where the aim was to reduce the Pt loading and maintain high catalytic reactivity towards the oxygen reduction reaction. The catalysts were characterized by X-ray diffraction, field emission scanning electron microscopy, and transmission electron microscopy. The electrochemical performance of the PtxNi/C alloy catalysts was evaluated by cyclic voltammetry, steady-state measurements, and chronoamperometric testing. We found that the catalytic reactivity of Pt catalysts towards oxygen reduction can be maintained or even enhanced by partially replacing platinum with nickel.

Wu, J, Ye, Z, Wang, G, Jin, D, Yuan, J, Guan, Y & Piper, J 2009, 'Visible-light-sensitized highly luminescent europium nanoparticles: preparation and application for time-gated luminescence bioimaging', JOURNAL OF MATERIALS CHEMISTRY, vol. 19, no. 9, pp. 1258-1264.
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Yamaji, N, Little, MJ, Nishio, H, Billen, B, Villegas, E, Nishiuchi, Y, Tytgat, J, Nicholson, GM & Corzo, G 2009, 'Synthesis, Solution Structure, And Phylum Selectivity Of A Spider Delta-Toxin That Slows Inactivation Of Specific Voltage-Gated Sodium Channel Subtypes', Journal Of Biological Chemistry, vol. 284, no. 36, pp. 24568-24582.
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Magi 4, now renamed ?-hexatoxin-Mg1a, is a 43-residue neurotoxic peptide from the venom of the hexathelid Japanese funnel-web spider (Macrothele gigas) with homology to ?-hexatoxins from Australian funnel-web spiders. It binds with high affinity to receptor site 3 on insect voltage-gated sodium (NaV) channels but, unlike ?-hexatoxins, does not compete for the related site 3 in rat brain despite being previously shown to be lethal by intracranial injection. To elucidate differences in NaV channel selectivity, we have undertaken the first characterization of a peptide toxin on a broad range of mammalian and insect NaV channel subtypes showing that ?-hexatoxin-Mg1a selectively slows channel inactivation of mammalian NaV1.1, NaV1.3, and NaV1.6 but more importantly shows higher affinity for insect NaV1 (para) channels. Consequently, ?-hexatoxin-Mg1a induces tonic repetitive firing of nerve impulses in insect neurons accompanied by plateau potentials. In addition, we have chemically synthesized and folded ?-hexatoxin-Mg1a, ascertained the bonding pattern of the four disulfides, and determined its three-dimensional solution structure using NMR spectroscopy. Despite modest sequence homology, we show that key residues important for the activity of scorpion ?-toxins and ?-hexatoxins are distributed in a topologically similar manner in ?-hexatoxin-Mg1a. However, subtle differences in the toxin surfaces are important for the novel selectivity of ?-hexatoxin-Mg1a for certain mammalian and insect NaV channel subtypes. As such, ?-hexatoxin-Mg1a provides us with a specific tool with which to study channel structure and function and determinants for phylum- and tissue-specific activity.

Yang, J, Wang, G, Liu, H, Park, J & Cheng, X 2009, 'Controlled synthesis and characterization of ZnSe nanostructures via a solvothermal approach in a mixed solution', Materials Chemistry And Physics, vol. 115, no. 1, pp. 204-208.
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In the present study, ZnSe nanostructures with complex morphologies and different phase structures were synthesized via a solvothermal approach using a mixed solution of triethylenetetramine (TETA) and de-ionized water (DIW). It was found that the phase and morphology of the as-prepared products could be controlled by changing the volume ratio of TETA to DIW. Metastable ZnSe nanoflowers with layered structure could be obtained from pure TETA, which can be transformed to the wurtzite structure after heat-treating at 500 °C in Ar atmosphere. With the addition of DIW, the morphology changed from flowers to spheres, and when the volume ratio of TETA to DIW was 1:1, loose spheres composed of nanoparticles were obtained. Variation of the TETA content in the mixed solvent also allows controlling of the crystallographic phase of ZnSe (wurtzite or zinc blende). Both the as-prepared products and the annealed powders were systematically characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared absorbance spectroscopy (FTIR), thermogravimetric analysis (TGA), and ultravioletvisible (UVvis) spectroscopy methods.

Yang, Z, Ding, G, Cai, H, Xu, X, Wang, H & Zhao, X 2009, 'Analysis and elimination of the 'skip contact' phenomenon in an inertial micro-switch for prolonging its contact time', JOURNAL OF MICROMECHANICS AND MICROENGINEERING, vol. 19, no. 4.
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Yao, J, Park, JS, Konstantinov, K, Wang, G, Ahn, J & Liu, HK 2009, 'Electrochemical performance of nanocrystalline SnO2-carbon nanotube composites as anode in lithium-ion cells', Journal of Nanoscience & Nanotechnology, vol. 9, no. 2, pp. 1474-1478.
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SnO2-carbon nanotube composites were prepared by chemical treatment of tin chloride salt mixed with carbon nanotubes, followed by heat-treatment at high temperature. Nanosize SnO2 particles were formed and embedded in a carbon nanotube matrix. TEM and HRTEM observation confirmed the homogeneous distribution of SnO2 nanoparticles. SnO2-carbon nanotube anodes demonstrated high lithium storage capacity and stable cyclability, which could be attributed to the nanosize SnO2 crystals and the formation of carbon nanotube networks in the electrode.

Yao, J, Shen, X, Wang, B, Liu, H & Wang, G 2009, 'In situ chemical synthesis of SnO(2)-graphene nanocomposite as anode materials for lithium-ion batteries', Electrochemistry Communications, vol. 11, pp. 1849-1852.
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An in situ chemical synthesis approach has been developed to prepare SnO2graphene nanocomposite. Field emission scanning electron microscopy and transmission electron microscopy observation revealed the homogeneous distribution of SnO2 nanoparticles (46 nm in size) on graphene matrix. The electrochemical reactivities of the SnO2graphene nanocomposite as anode material were measured by cyclic voltammetry and galvanostatic charge/discharge cycling. The as-synthesized SnO2graphene nanocomposite exhibited a reversible lithium storage capacity of 765 mAh/g in the first cycle and an enhanced cyclability, which can be ascribed to 3D architecture of the SnO2graphene nanocomposite.

Yii, MF, Lim, CED, Luo, X, Wong, WSF, Cheng, NCL & Zhan, X 2009, 'Polycystic ovarian syndrome in adolescence', Gynecological Endocrinology, vol. 25, no. 10, pp. 634-639.
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Background.Polycystic ovarian syndrome PCOS, which is a common endocrinopathy seen not only in adult women but also in female adolescents nowadays, is associated with reproductive, metabolic and cardiovascular problems. Objective.This article aims to review the current evidence on managing PCOS in adolescence. In addition, the pathophysiology, risk factors, clinical presentations and existing diagnostic criteria of PCOS will also be discussed. Discussion.Certain risk factors are available to assist the clinicians to identify adolescents at risk of PCOS as the signs can be masked by the normal physiological changes during puberty. It is important to screen and diagnose adolescent PCOS in order to prevent the development of future infertility, type II diabetes mellitus, cardiovascular disease, and even endometrial cancer. Lifestyle modification is of the greatest benefit for adolescents in terms of management, with the condition that full support is available from both the clinicians and their families. The psychological impact of PCOS also constitutes a major concern in adolescent PCOS. © 2009 Informa UK Ltd All rights reserved.

Yoshioka, H, Miura, T, Dematte, JA, Batchily, K & Huete, A 2009, 'Derivation of soil line influence on two-band vegetation indices and vegetation isolines', Remote Sensing, vol. 1, no. 4, pp. 842-857.
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This paper introduces derivations of soil line influences on two-band vegetation indices (VIs) and vegetation isolines in the red and near infra-red reflectance space. Soil line variations are described as changes in the soil line parameters (slope and offset) and the red reflectance of the soil surface. A general form of a VI model equation written as a ratio of two linear functions (e.g., NDVI and SAVI) was assumed. It was found that relative VI variations can be approximated by a linear combination of the three soil parameters. The derived expressions imply the possibility of estimating and correcting for soil-induced bias errors in VIs and their derived biophysical parameters, caused by the assumption of a general soil line, through the use of external data sources such as regional soil maps.

Yung, PY, Burke, C, Lewis, M, Egan, S, Kjelleberg, S & Thomas, T 2009, 'Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion', NUCLEIC ACIDS RESEARCH, vol. 37, no. 21.
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Zhang, F, Li, Y, Guo, ZP & Murray, B 2009, 'Climate warming and reproduction in Chinese alligators', Animal Conservation, vol. 12, no. 2, pp. 128-137.
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The Chinese alligator Alligator sinensis is a critically endangered species endemic to China, and one of the most endangered crocodilian species in the world. Like many other reptiles, important aspects of alligator biology such as foraging, timing of hibernation, breeding and the sex ratio of offspring are all affected by temperature variation. We examined the effects of long-term temperature change on oviposition dates and clutch sizes of the Chinese alligator in a semi-natural facility in southern China. Our study focused on two captive generations including an old breeding generation captured from the wild and a generation composed of their F1 offspring. Median oviposition date shifted to earlier in the year and mean clutch size was larger for both generations as the monthly mean air temperature in April increased over the 19 years of data collection. We observed a mean advance in oviposition date of 10 days for the old breeding generation from 1987 to 2005 and 8 days for both generations from 1991 to 2005. Correspondingly, clutch sizes for the two generations also increased during this period. There were no differences in median oviposition dates and clutch sizes between the two generations from 1991 to 2005. Our results suggest that Chinese alligators have responded to increasing global temperatures. Our findings also suggest that recent increasing global temperatures have the potential to have a substantial effect on Chinese alligator populations in the wild, thus prompting an urgent need for field monitoring of the effects of global warming on this endangered alligator species.

Zhang, J, Li, T, Zhou, L, Tang, L, Xu, L, Wu, T & Lim, DCE 2009, 'Chinese herbal medicine for subfertile women with polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, no. 1.
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Zhao, HY, Zheng, W, Meng, ZX, Zhou, HM, Xu, XX, Li, Z & Zheng, YF 2009, 'Bioelectrochemistry of hemoglobin immobilized on a sodium alginate-multiwall carbon nanotubes composite film', Biosensors and Bioelectronics, vol. 24, pp. 2352-2357.
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Zhou, J, Zhuang, Y, Ye, S, Teng, Y, Lin, G, Zhu, B, Xie, J & Qiu, J 2009, 'Broadband downconversion based infrared quantum cutting by cooperative energy transfer from Eu2+ to Yb3+ in glasses', Applied Physics Letters, vol. 95, no. 14.
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Zhu, B, Zhang, Q, Zhang, Y, Tao, Z, Clegg, J, Reimers, JR, Lindoy, L & Wei, G 2009, 'Polymeric Di- And Discrete Trinuclear Silver(I) Assemblies Incorporating Gamma-Carbon Bonded, Neutral Acetylacetone-Imine Motifs Assembled From Racemic And Diastereopure N,N '-Bis(Acetylacetone)Cyclohexanediimine Units', Dalton Transactions, vol. -, no. 25, pp. 4896-4900.
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Diastereopure (1R,2R)-N,N'-bis(acetylacetone)cyclohexanedi-imine L(1) and its corresponding (1R,2R)L(1)/(1S,2S)L(2) enantiomeric mixture react with AgNO(3) to yield the unusual coordination polymer [Ag(2)(L(1))(L(2))(NO(3))(2)](n) (1) and the unique trimetallic discrete species {[Ag(3)(L(1))(3)(mu(3)-O,O,O-NO(3))(H(2)O)(3)](2)(NO(3))}(NO(3))(3)center dot 8.5H(2)O (2) which incorporates a symmetrical mu(3)-bridging nitrato group that gives rise to a C(3)-symmetric triskelion motif; both species also feature gamma-carbon eta(1) aryl-like coordination of neutral bridging acetylacetone-imine units to the respective Ag(I) centres.

Zhuang, Y, Kendrick, MJ, Teng, Y, Zhou, J, Ye, S, Liu, X, Lin, G, Ruan, J & Qiu, J 2009, 'Broadband downconversion from oxygen-deficient centers to Yb3+ in germanate glasses', Journal of the Optical Society of America B: Optical Physics, vol. 26, no. 11, pp. 2185-2188.
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Zilberg, E, Xu, Z, Burton, D, Karrar, M & Lal, S 2009, 'Statistical validation of physiological indicators for non-invasive and hybrid driver drowsiness detection system', African Journal of Information & Communication Te..., vol. 5, no. 2, pp. 1-9.
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A hybrid system for detecting driver drowsiness was examined by using piezofilm movement sensors integrated into the car seat, seat belt and steering wheel. Statistical associations between increase in the driver drowsiness and the non-invasive and conventional physiological indicators were investigated. Statistically significant associations were established for the analysed physiological indicators car seat movement magnitude and (electroencephalogram) EEG alpha band power percentage. All of the associastions were physiologically plausible with increase in probability of drowsiness associated with increases in the EEG alpha band power percentage and reduction in the seat movement magnitude. Adding a non-invasive measure such as seat movement magnitude to any combination of the EEG derived physiological predictors always resulted in improvement of associations. These findings can serve as a foundation for designing the vehicle-based fatigue countermeasure device as well as highlight potential difficulties and limitations of detection algorithm for such devices.

Alkhouri, H, Roth, M, Oliver, B, Armour, CL & Hughes, JM 2009, 'Role of C/EBP-Isoforms in IP-10 and IL-6 Production by Human Airway Smooth Muscle Cells.', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Al-Sohaily, S, Currey, N, Henderson, C, Leong, R, Biankin, A, Warusavitarne, J & Kohonen-Corish, M 2009, 'Methylation of the 'mutated in colorectal cancer' gene correlates with poorer short term survival in patients with colorectal cancer', JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY-BLACKWELL PUBLISHING, INC, pp. A245-A245.

Al-Sohaily, S, Henderson, C, Leong, R, Biankin, A, Kohonen-Corish, M & Warusavitarne, J 2009, 'Prognostic role of vascular endothelial growth factor in colorectal cancer', JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY-BLACKWELL PUBLISHING, INC, pp. A246-A246.

Armstrong, C, Lal, S, Kavanagh, D & Rossiter, P 2009, 'SmartData project: Game Consoles as a computing platform for in-the-field biomedical data management', BROADBANDCOM 2009 - Selected Papers on Broadband Communication, Information Technology and Biomedical Applications, pp. 381-386.
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Biomedical research increasingly requires for testing be conducted outside the lab, in the field such as the participants home or work environment. This type of research requires semi-autonomous computer systems that collect such data and send it back to the lab for processing and dissemination. A key aspect of this type of research is the selection of the required software and hardware components. These systems need to be reliable, allow considerable customizability and be readily accessible but also able to be locked down. In this paper we develop a set of requirements for the hardware and software for such a system. We then utilise these requirements to evaluate the use of game consoles as a hardware platform in comparison to other hardware choices.

Arnold, MD & Smith, G 2009, 'Comparisons of enhanced absorption in closely-coupled grating-mirror and random particle-mirror systems', Proceeding of the SPIE 7404, SPIE, San Diego, USA, pp. 1-8.
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The grating-mirror geometry is a particularly rich plasmonic system due to the coupling of localized and global modes, and it is applicable to negative index materials, plasmonic imaging, and spectral filters. Recently absorption in sub-percolative films was found to be greatly enhanced by the addition of a mirror - a situation that is also reasonably modeled by a grating-mirror geometry. A great deal of attention has been focused on the coupling of barely-sub-wavelength periodic grating modes to surface plasmon polaritons that exhibit sharp spectral features. In contrast, island films have only quasi-periodicity at a few tens of nanometers, and produce broader spectral features, suggesting the influence of localized surface plasmons. In this work we examine how absorption is affected by variations in geometry of grating-mirror systems, to identify basic physics for future investigations of particle-mirror systems.

Asatryan, AA, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC & de Sterke, CM 2009, 'The local density of states of metamaterial photonic crystals', Conference on Lasers and Electro-Optics/The International Quantum Electronics Conference (IQEC), Optical Society of America, Baltimore, USA, pp. 1-2.
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We study the local density of states (LDOS) of photonic crystals made with metamaterial inclusions and show that the introduction of metamaterial components substantially widens and deepens band gaps in comparison with normal photonic crystals.

Asatryan, AA, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC & de Sterke, CM 2009, 'The local density of states of metamaterial photonic crystals', 2009 CONFERENCE ON LASERS AND ELECTRO-OPTICS AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2009), VOLS 1-5, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 2531-+.

Asatryan, AA, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC & De Sterke, CM 2009, 'The local density of states of metamaterial photonic crystals', Optics InfoBase Conference Papers.
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We study the local density of states (LDOS) of photonic crystals made with metamaterial inclusions and show that the introduction of metamaterial components substantially widens and deepens band gaps in comparison with normal photonic crystals. © 2009 Optical Society of America.

Asatryan, AA, Gredeskul, S, Botten, LC, Byrne, MA, Freilikher, VD, Shadrivov, I, McPhedran, RC & Kivshar, YS 2010, 'Transmission and Localization of Classical Waves in Weakly', Progress in Electromagnetics Research Symposium, PIERS (Invited Presentation), Electromagnetic Academy, Xi'an China, pp. 651-651.
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We study the transmission and localization of classical waves in one-dimensional disordered structures composed of alternating layers of left- and right-handed materials (mixed stacks) and compare them to the structures composed of di®erent layers of the same material (homogeneous stacks). For weakly scattering layers, we have developed an e®ective analytical approach and have calculated the transmission length within a wide region of the input parame- ters. This enables us to describe in a uni¯ed way the localized and ballistic regimes as well as the crossover between them. It is shown that if both refractive index and layer thickness are random, in the long-wavelength range, mixed and homogeneous stacks demonstrate di®erent dependencies of the transmission length on the wavelength in localized regime, as well as di®erent structures of ballistic regimes. While in the ultra-long wavelength range normal random dielectric samples transmit light as an e®ectively uniform medium, the transmission length in mixed stacks is always a strongly °uctuating quantity. In mixed stacks with only refractive-index disorder, the Ander- son localization is substantially suppressed, the localization length grows with wavelength much faster, the crossover region becomes essentially wider, and the transmission resonances appear in much longer stacks, than in the general case. E®ects of absorption on the one-dimensional trans- port and localization has also been studied, both analytically and numerically. Speci¯cally, it is shown that the crossover region is particularly sensitive to losses, so that even small absorption suppresses noticeably the oscillations of the transmission length in the frequency domain. All our theoretical predictions are in an excellent agreement with the results of numerical simulations.

Blaikie, RJ, Moore, CP & Arnold, MD 2009, 'Improved analytical models for single- and multi-layer silver superlenses', Materials Research Society Symposium Proceedings 1182, Materials Research Society Symposium Proceedings 1182, Materials Research Society, San Francisco, USA, pp. 1-11.
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Spatial-frequency transfer functions are regularly used to model the imaging performance of near-field `superlensï½ systems. However, these do not account for interactions between the object that is being imaged and the superlens itself. As the imaging in these systems is in the near field, such interactions are important to consider if accurate performance estimates are to be obtained. We present here a simple analytical modification that can be made to the transfer function to account for near-field interactions for objects consisting of small apertures in otherwise-continuous metal screens. The modified transfer functions are evaluated by comparison with full-field finite-element simulations for representative single-layer and multilayer silver superlenses, and good agreement is found.

Boyce, A, Wilson, F, Chen, H, Gibson, K, Lumbers, E & Morris, M 2009, 'Differential Regulation of the Intrarenal Resin-Angiotensin System by Maternal Obesity and Postnatal Overnutrition', REPRODUCTIVE SCIENCES, 56th Annual Meeting of the Society-for-Gynecologic-Investigation, SAGE PUBLICATIONS INC, Glasgow, SCOTLAND, pp. 135A-135A.

Bruti Liberati, N & Platen, E 2009, 'Strong Predictor-Corrector Euler Methods for Stochastic Differential Equations', X Workshop on Quantitative Finance to the Memory of Nicola Bruti-Liberati, Milan, Italy.

Bruti Liberati, N, Nikitopoulos Sklibosios, C, Platen, E & Schlogl, E 2009, 'Alternative defaultable term structure models', X Workshop on Quantitative Finance to the Memory of Nicola Bruti-Liberati, Milan, Italy.

Chan, JH, Shimmon, R, Spindler, X, Maynard, PJ, Lennard, CJ, Roux, CP & Stuart, BH 2009, 'Investigation into isatin and 1,4-anthraquinones as fingerprint detection reagents on porous surfaces', UTS Faculty of Science Research Day Book of Abstracts, UTS Faculty of Science Research Day, pp. 1-1.

Cho, Y, Turner, ND, Taddeo, SS, Davidson, LA, Wang, N, Vannucci, M, Carroll, RJ, Chapkin, RS & Lupton, JR 2009, 'Chemoprotective fish oil/pectin diets temporally alter gene expression profiles in exfoliated colonocytes', FASEB JOURNAL, FEDERATION AMER SOC EXP BIOL.

Dauly, C, Escoubas, P, Nicholson, GM, King, GF & Hornshaw, M 2009, 'Nanoscale characterization of spider venom peptides by high resolution LC-MS/MS analysis', Bremen, Germany.

de Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 2009, 'Direct, efficient coupling into slow light photonic crystal waveguide: Role of evanescent modes', Optics InfoBase Conference Papers.
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Efficient coupling between fast and slow PC waveguide modes is possible if strong evanescent modes are needed to match the fields across the interface. This occurs when the propagating modes have substantially different modal fields. © 2009 Optical Society of America.

de Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 2009, 'Direct, efficient coupling into slow light photonic crystal waveguide: Role of evanescent modes', Optics InfoBase Conference Papers.
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Efficient coupling between fast and slow PC waveguide modes is possible if strong evanescent modes are needed to match the fields across the interface. This occurs when the propagating modes have substantially different modal fields. © 2009 Optical Society of America.

De Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 2009, 'Role of evanescent modes in direct, efficient coupling into slow light photonic crystal waveguides', Optics InfoBase Conference Papers.
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The assumption that coupling into slow PC waveguide modes is inefficient is shown to be incorrect. Efficient coupling is possible, provided strong evanescent modes are present to match fields at the interface with fast medium. © 2009 Optical Society of America.

De Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 2009, 'Role of evanescent modes in direct, efficient coupling into slow light photonic crystal waveguides', 2009 Asia Communications and Photonics Conference and Exhibition, ACP 2009.
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The assumption that coupling into slow PC waveguide modes is inefficient is shown to be incorrect. Efficient coupling is possible, provided strong evanescent modes are present to match fields at the interface with fast medium. © 2009 Optical Society of America.

De Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 2009, 'Role of evanescent modes in direct, efficient coupling into slow light photonic crystal waveguides', Optics InfoBase Conference Papers.
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The assumption that coupling into slow PC waveguide modes is inefficient is shown to be incorrect. Efficient coupling is possible, provided strong evanescent modes are present to match fields at the interface with fast medium. © 2009 Optical Society of America.

Deviese, T, Colombini, M, Regert, M, Stuart, BH & Guerbois, JL 2009, 'TG-MS analysis of archaeological bone from burials of the late Roman period', Medicta 2009 Book of Abstracts, 9th Mediterranean Conference on Calorimetry and Thermal Analysis, Marseille.

Doblin, MA, Ralph, PJ, Oubelkheir, K, Hassler, CS, Suthers, I & Thompson, P 2009, 'Using IMOS to bridge the gap between direct measurements of marine primary production and models', Adelaide, Australia.

Freeman, LM, Koh, B, Jonson, PT & Zaslawski, CJ 2009, 'Athletes healthcarebehaviour: an ethnographers conumdrum', Proceedings of 4th Annual International Ethnography Symposium, University of Liverpool, Liverpool England.

Freeman, LM, White, D & Zaslawski, CJ 2009, 'Emergent practitioners of CHinese Medicine: an ethnographic inquiry into medical thought', Proceedings of 4th Annual International Ethnography Symposium, University of Liverpool, Liverpool England.

Freitas, RM, Shimabukuro, YE, Rosa, RR & Huete, A 2009, 'FRACTION IMAGES DERIVED FROM EO-1 HYPERION MULTITEMPORAL DATA FOR DRY SEASON GREEN UP ANALYSIS IN TAPAJOS NATIONAL FOREST, BRAZILIAN AMAZONIA', 2009 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM, VOLS 1-5, IEEE International Geoscience and Remote Sensing Symposium, IEEE, Cape Town, SOUTH AFRICA, pp. 3395-+.
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Fu, KMC, Santori, C, Barclay, PE, Meyer, N, Holm, AM, Aharonovich, I, Prawer, S & Beausoleil, RG 2009, 'Optical coupling of nitrogen-vacancy centers in diamond to GaP waveguides', Optics InfoBase Conference Papers.
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In this work NV coupling to GaP waveguides on a diamond surface is demonstrated. The NV-waveguide coupling strength and waveguide loss are measured. This approach may be useful for NV-based quantum information processing. © 2008 Optical Society of America.

Fu, K-MC, Santori, C, Barclay, PE, Meyer, N, Holm, AM, Aharonovich, I, Prawer, S & Beausoleil, RG 2009, 'Optical coupling of nitrogen-vacancy centers in diamond to GaP waveguides', 2009 CONFERENCE ON LASERS AND ELECTRO-OPTICS AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2009), VOLS 1-5, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 2050-+.

Fu, KMC, Santori, C, Barclay, PE, Meyer, N, Holm, AM, Aharonovicli, I, Prawer, S & Beausoleil, RG 2009, 'Photonic structures for QIP in diamond', Proceedings of SPIE - The International Society for Optical Engineering.
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We observe the coupling of nitrogen-vacancy centers in single-crystal diamond to GaP waveguides on the diamond surface. We describe the fabrication procedure and characterize the waveguide performance. Our results indicate that the GaP/diamond hybrid system is a promising system for coupling nitrogen-vacancies to optical microstructures for quantum information processing and sensing applications. © 2009 SPIE.

Fung, KY, Cumming, H, Mangan, N, Stifter, S, Horvat, J, Hansbro, P & Hertzog, PJ 2009, 'Characterisation of a novel, constitutive cytokine that regulates mucosal immunity in the reproductive tract', CYTOKINE, Tri-Society Annual Conference of the International-Cytokine-Society/International-Society-of-Interferon-and-Cytokine-Research/Society-of-Leukocyte-Biology, ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, Lisbon, PORTUGAL, pp. 89-89.
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Ge, Q, Oliver, BGG, Moir, LM, Lau, EMT, Black, JL & Burgess, JK 2009, 'TGF-beta 1 Induction of Fibronectin in Human Bronchial Epithelial Cells Is Smad-2/3 Dependent', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Gracanin, M, Rodgers, KJ, Hawkins, CL & Davies, MJ 2009, 'Amino Acids, Peptide and Protein Hydroperoxides, and their Decomposition Products, Modify the Activity of the 26S Proteasome', FREE RADICAL BIOLOGY AND MEDICINE, 16th Annual Meeting of the Society-for-Free-Radical-Biology-and-Medicine, ELSEVIER SCIENCE INC, San Francisco, CA, pp. S121-S121.

Gunning, SJ, Maggio, FJ, Windley, MJ, Valenzuela, S, King, GF & Nicholson, GM 2009, 'Janus-faced atracotoxins are specific blockers of invertebrate KCa channels', 34th Congress of the Federation of European Biochemical Societies, Prague, Czech Republic.

Hansbro, PM, Essilfie, AT, Simpson, JL, Dunkley, ML & Gibson, PG 2009, 'Haemophilus influenzae Induces Features of Neutrophilic Asthma.', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Hansbro, PM, Starkey, MR, Horyat, JC, Kim, RY, Phipps, S, Gibson, PG & Foster, PS 2009, 'Early life chlamydial infection enhances allergic airways disease through age-dependent differences in immunopathology', JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS.

Hansbro, PM, Thorburn, AN, Foster, PS & Gibson, PG 2009, 'Streptococcus pneumoniae vaccine, Prevenar, utilises Tregs to suppress Asthma', JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS.

Hansbro, PM, Thorburn, AN, O'Sullivan, BJ, Thomas, R, Foster, PS & Gibson, PG 2009, 'Prevenar Suppresses Allergic Airways Disease through the Induction of Regulatory T Cells', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Heather, AK, Li, XH, Bartusch, M, Dy, V, Liong, EC, McGrath, KC & Tan, JTM 2009, 'DHCR24 is a negative regulator of NF-B and chronic inflammation in human endothelial cells.', Arteriosclerosis, Thrombosis, and Vascular Biology, You have accessArteriosclerosis, Thrombosis, and Vascular Biology Annual Conference, American Heart Association, pp. E27-E28.
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Hess, L, Ratana, P, Huete, A, Potter, C & Melack, J 2009, 'USE OF MODIS ENHANCED VEGETATION INDEX TO DETECT SEASONAL PATTERNS OF LEAF PHENOLOGY IN CENTRAL AMAZON VARZEA FOREST', 2009 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM, VOLS 1-5, IEEE International Geoscience and Remote Sensing Symposium, IEEE, Cape Town, SOUTH AFRICA, pp. 3387-+.
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Horvat, JC, Starkey, MR, Beagley, KW, Gibsoo, PG, Foster, PS & Hansbro, PM 2009, 'Chlamydial respiratory infection predisposes to neutrophil dominated allergic airways disease (AAD)', JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS.

Horvat, JC, Starkey, MR, Beagley, KW, Preston, JA, Gibson, PG, Foster, PS & Hansbro, PM 2009, 'Neutrophil Influx during Chlamydial Lung Infection Determines the Phenotype of Allergic Airways Disease (AAD)', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Gilbert, J, Roudnew, B, Smith, R, Seuront, L & Mitchell, J 2009, 'Taxonomic clustering of microbial metagenomes in the Coorong lagoon system', Adelaide, Australia.

Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Roudnew, B, Smith, R, Seuront, L & Mitchell, JG 2009, 'Functional metagenomics of sediment microbial communities from a hypersaline coastal lagoon', Adelaide, Australia.

Kabakova, IV, Corcoran, B, Bolger, JA, de Sterke, CM & Eggleton, BJ 2009, 'All-Optical Self-Switching in an Optimized Fiber Bragg Grating with a pi Phase Shift', 2009 CONFERENCE ON LASERS AND ELECTRO-OPTICS AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2009), VOLS 1-5, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 956-957.

Kabakova, IV, Corcoran, B, Bolger, JA, De Sterke, CM & Eggleton, BJ 2009, 'All-optical self-switching in an optimized fiber Bragg grating with a π phase shift', 2009 Conference on Lasers and Electro-Optics and 2009 Conference on Quantum Electronics and Laser Science Conference, CLEO/QELS 2009.
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We experimentally demonstrate all-optical self-switching of sub-nanosecond pulses in a fiber grating with a π phase-shift, which acts as a cavity, enhancing the intensity. At 1.5 kW peak power the transmission increases by 4.2 dB. ©2009 Optical Society of America.

Karrar, M, Zilberg, E, Xu, ZM, Burton, D & Lal, S 2009, 'Comparing statistical associations between driver drowsiness and EEG alpha bursts based on the spectral and EEG and morphological techniques of EEG analysis', BROADBANDCOM 2009 - Selected Papers on Broadband Communication, Information Technology and Biomedical Applications, pp. 399-404.
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A driver drowsiness detection analysis was performed on the electroencephalography data collected from 40 non-professional drivers undergoing a driving simulation task. A statistical comparison between two different EEG analysis methods was carried out to determine which method had a greater association with drowsiness. First, the statistical association between the alpha component of the EEG and the video-based driver drowsiness rating level was examined, and then the statistical association between the alpha bursts and the driver drowsiness level was examined. From the results it was shown that both spectral and alpha burst analysis methods showed a significant association with drowsiness, however, the alpha burst method exhibited the strongest association with the video-based drowsiness ratings.

Kau, D, Tang, S, Karpov, IV, Dodge, R, Klehn, B, Kalb, JA, Strand, J, Diaz, A, Leung, N, Wu, J, Lee, S, Langtry, T, Chang, KW, Papagianni, C, Lee, J, Hirst, J, Erra, S, Flores, E, Righos, N, Castro, H & Spadini, G 2009, 'A stackable cross point phase change memory', Technical Digest - International Electron Devices Meeting, IEDM.
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A novel scalable and stackable nonvolatile memory technology suitable for building fast and dense memory devices is discussed. The memory cell is built by layering a storage element and a selector. The storage element is a Phase Change Memory (PCM) cell [1] and the selector is an Ovonic Threshold Switch (OTS) [2]. The vertically integrated memory cell of one PCM and one OTS (PCMS) is embedded in a true cross point array. Arrays are stacked on top of CMOS circuits for decoding, sensing and logic functions. A RESET speed of 9 nsec and endurance of 106 cycles are achieved. One volt of dynamic range delineating SET vs. RESET is also demonstrated. © 2009 IEEE.

Kavanagh, D, Lal, S, Santhakumar, V & Rossiter, P 2009, 'Wireless reaction time measurement device for field studies of arousal', BROADBANDCOM 2009 - Selected Papers on Broadband Communication, Information Technology and Biomedical Applications, pp. 355-360.
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This paper describes the application of wireless technology for acquisition of data from home environments, mobile vehicles and laboratories for monitoring ongoing changes in the individuals reaction times (RT). A small-hand-held device based on TMote [1] technology was selected as the platform for development of a RT monitoring system. A number of communication protocols were investigated to overcome the consequences of using wireless technology, for example, latency issues, loss of data, etc. The results are discussed from the perspective of our planned future directions for the application and improvement of the RT device.

Kim, H, Turner, ND, Taddeo, SS, Davidson, LA, Wang, N, Vannucci, M, Chapkin, RS, Carroll, RJ & Lupton, JR 2009, 'A fish oil/pectin diet suppresses radiation-enhanced colon carcinogenesis via down-regulation of the beta-catenin signaling pathway', FASEB JOURNAL, FEDERATION AMER SOC EXP BIOL.

Koelsch, M, Mallak, R, Graham, GG, Rees, MD, Milligan, MK, Newsham, DW, Nguyen, LQ, Kettle, AJ, Scott, K, Ziegler, JB, Kajer, T, Fu, S, Hawkins, CL & Davies, MJ 2009, 'Acetaminophen (Paracetamol) Inhibits the Formation of Myeloperoxidase-Derived Oxidants and Biological Damage at Therapeutically-Achievable Concentrations', FREE RADICAL BIOLOGY AND MEDICINE, 16th Annual Meeting of the Society-for-Free-Radical-Biology-and-Medicine, ELSEVIER SCIENCE INC, San Francisco, CA, pp. S139-S140.

Krimmer, DI, Burgess, JK, Black, JL & Oliver, BGG 2009, 'Cigarette Smoke Exposure Upregulates the Production of Extracellular Matrixd Proteins from Lung Fibroblasts.', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Kuo, C, Johnston, SL, King, NJC, Wark, P, Lim, S, Burgess, JK, Black, JL & Oliver, BG 2009, 'Effect of Rhinovirus on Primary Bronchial Epithelial Cells and Fibroblast Extracellular Matrix Deposition and Migration', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Lau, JY, Gervasio, OL, Oliver, BG, Black, JL, Williams, C, Wilton, SD & Burgess, JK 2009, 'Interaction of Fibulin-1 and Fibronectin in Asthma', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Lau, JY, Oliver, BG, Baraket, M, Wilton, SD, Williams, C, Black, JL & Burgess, JK 2009, 'Fibulin-1: Expression and Function in Asthma', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Lavery, TJ, Roudnew, B, Seymour, JR, Mitchell, JG, Seuront, L & Smetacek, V 2009, 'Whales: A net sink or source of carbon to the atmosphere?', Adelaide, Australia.

Lawrence, FJ, Botten, LC, Dossou, KB & De Sterke, CM 2009, 'Impedance of square and hexagonal photonic crystals', 2009 Conference on Lasers and Electro-Optics and 2009 Conference on Quantum Electronics and Laser Science Conference, CLEO/QELS 2009.
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We rigorously define an impedance for photonic crystals, which generally needs to be a matrix. We use it to design a two-layer anti-reflection coating for a frequency where the bulk crystal reflects over 50%. ©2009 Optical Society of America.

Lawrence, FJ, Botten, LC, Dossou, KB & de Sterke, CM 2009, 'Impedance of Square and Hexagonal Photonic Crystals', 2009 CONFERENCE ON LASERS AND ELECTRO-OPTICS AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2009), VOLS 1-5, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 2539-+.

Lawrence, FJ, Botten, LC, Dossou, KB & Martijn De Sterke, C 2009, 'Impedance of square and hexagonal photonic crystals', Optics InfoBase Conference Papers.
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We rigorously define an impedance for photonic crystals, which generally needs to be a matrix. We use it to design a two-layer anti-reflection coating for a frequency where the bulk crystal reflects over 50%. © 2009 Optical Society of America.

Lawrence, FJ, Botten, LC, Dossou, KB & Martijn De Sterke, C 2009, 'Impedance of square and hexagonal photonic crystals', Optics InfoBase Conference Papers.
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We rigorously define an impedance for photonic crystals, which generally needs to be a matrix. We use it to design a two-layer anti-reflection coating for a frequency where the bulk crystal reflects over 50%. © 2009 Optical Society of America.

Lee, MW, Grillet, C, Poulton, CG, Monat, C, Smith, CLC, Maegi, E, Freeman, D, Madden, S, Luther-Davies, B & Eggleton, BJ 2009, 'An Expanded -Space Evanescent Coupling Technique for Characterizing Photonic Crystal Waveguides', 2009 CONFERENCE ON LASERS AND ELECTRO-OPTICS AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2009), VOLS 1-5, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 1325-+.

Lee, MW, Grillet, C, Poulton, CG, Monat, C, Smith, CLC, Mägi, E, Freeman, D, Madden, S, Luther-Davies, B & Eggleton, BJ 2009, 'An expanded k-space evanescent coupling technique for characterizing photonic crystal waveguides', 2009 Conference on Lasers and Electro-Optics and 2009 Conference on Quantum Electronics and Laser Science Conference, CLEO/QELS 2009.
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We demonstrate an expanded k-space evanescent coupling technique for characterizing the dispersion and loss of photonic crystal waveguides (PCWG) by measuring the Fabry-Pérot spectrum of a closed waveguide using a highly curved taper. ©2009 Optical Society of America.

Lewis, KC, Wuhrer, R, Ben-Nissan, B, Valenzuela, S & Moran, K 2009, 'X-ray mapping of minerals incorporated into liposomes', Microscopy and Microanalysis 2009, Microscopy and Microanalysis 2009, Cambridge University Press, Richmond, Virginia, USA, pp. 908-909.
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Liposomes are spherical particles in an aqueous medium formed by a lipid bilayer enclosing an aqueous compartment. They have been long considered as a potential delivery device in the medical and pharmaceutical industries due to their ability to encapsulate different compounds, as the lipids form into liposomes. The ability of these liposomes to be stored in the body, and to be taken up by cells, makes them ideal for drug delivery. They can also potentially increase the efficiency of supplements, particularly those with no accumulation toxicity.

Macnamara, J 2009, 'Australian federal government online public consultation trials: Local learnings in e-democracy', Communication, Creativity and Global Citizenship: Refereed Proceedings of the Australian and New Zealand Communication Association Conference 2009, Australian New Zealand Communications Association Annual Conference, Queensland University of Technology, Brisbane, pp. 1006-1023.
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After its landslide victory in the 2007 Australian Federal election which was widely described as the YouTube election, the Rudd Labor government launched a series of trial public consultation blogs in 2008 as part of a commitment to e-democracy through the use of interactive Web 2.0 communication applications. At the same time, Barack Obama swept into power in the United States aided by Web 2.0 media including text messaging, blogs, YouTube, Twitter, and social networks such as Facebook which gained unprecedented levels of online political engagement. While e-democracy and e-government have been emerging concepts in many countries over more than a decade, these two experiences provide new information on the successes and challenges of online citizenship. This paper reports key findings of research into the Australian governments 2008 and early 2009 e-democracy efforts and compares these with US e-democracy initiatives including the Barack Obama presidential campaign and recent international research findings.

Macnamara, J 2009, 'Media as practice 2.0: Towards a historical and integrated reconceptualisation of media', Australian Media Traditions 6th Biennial Conference: Internationalising Media History: From Australia to the World, University of Sydney, Sydney.
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This paper argues that focusing on 'media as practice', as proposed by Nick Couldry (2004) reconceptualises media in a historical context and escapes the narrow framework of mass media theory which focuses on particular technologies of production and distribution, and accumulation and maintenance of mass audiences. Whereas other approaches to studying media focussed on political economy, media effects, texts, or audiences tend to narrowly examine either media production, distribution or consumption, a media as practice approach examines media as complex interrelated and integrated practices of production, distribution and consumption and affords understanding of media today which include citizen media and social media in which 'prosumers' or 'produsers' engage alongside traditional content producers and distributors.

Mohd. Syaifudin, AR, Jayasundera, KP & Mukhopadhyay, SC 2009, 'A novel planar interdigital sensor based sensing and instrumentation for detection of dangerous contaminated chemical in seafood', 2009 IEEE Intrumentation and Measurement Technology Conference, I2MTC 2009, pp. 701-706.
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A novel planar interdigital sensor based sensing and instrumentation system has been developed for detection of dangerous contaminated chemicals in seafood. Three novel interdigital sensors have been designed and fabricated. The sensors were designed with different configurations and analyses of all sensors were conducted from the experiments in order to select the best sensor for further analysis with domoic acid. Initial studies were conducted with Proline which is structurally close related to our target molecule, domoic acid. The changes in sensor sensitivity were analysed with mussels before and after adding the proline. The presence of proline on the mussel surface and also inside the mussel was very clearly detected by the sensor. Further experiment was conducted with small amount of domoic acid (0.5 μg to 5.0 μg) and it was found that Sensor-1 was able to detect approximately 12.6 μg/g of DA in mussel meat. Results of the effect of water and different concentration of domoic acid were also carried out and presented. Threshold levels of sensor's sensitivity with different mussel thickness were established. The outcomes from the experiments have shown that novel interdigital sensing system has the potential to be one of the options to assess the quality of seafood products for in-situ monitoring. © 2009 IEEE.

Moir, LM, Poniris, MH, Santa, T, Burgess, JK, Oliver, BGG & Black, JL 2009, 'Doxycycline May Modulate Lymphangioleiomyomatosis (LAM) Cell Function In Vitro.', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Moulton, BD, Chen, J, Croucher, G, Lal, S, Lawrence, EM, Mahendran, L & Varis, AP 2009, 'Ambulatory Health Monitoring and Remote Sensing Systems to be used by Outpatients and Elders at Home: User-Related Design Considerations', 2009 11th IEEE International Conference on e-Health Networking, Applications & Services, International Conference on e-Health Networking, Applications & Services, IEEE International Conference, Sydney, Australia, pp. 48-53.
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Recent developments have seen increased interest in the effect of end-user attributes on the in-practice effectiveness of systems that detect incapacitating falls and trauma at home. It is hoped that consideration and evaluation of such issues will ultimately result in long-term benefits including earlier crisis detection and response, reduced hospital admissions, and improved quality of life for relatively large groups of people. Key concerns include the needs and capabilities of end-users, the ability to nominate who is to be alerted, security, privacy, interface design and system failures. It is concluded that particularly relevant avenues for further research include end-user characteristics, interface design and peer-to-peer components.

Newton, K, Jeffries, TC, Seymour, JR, Leterme, S, Mitchell, J & Seuront, L 2009, 'Impact of salinity on viral morphological diversity', Adelaide, Australia.

Nicholson, GM, Escoubas, P, Dauly, C & King, GF 2009, 'Spider venoms for novel therapeutics: from Venomics to drug candidates', 16th World Congress on Animal, Plant and Microbial Toxins, Recife Brazil.

Nicholson, GM, Gunning, SJ, Windley, MJ, Maggio, FJ, Valenzuela, S & King, GF 2009, 'Defining the lethal ion channel targets of insecticidal spider toxins', 16th World Congress on Animal, Plant and Microbial Toxins.

Notter, SJ, Stuart, BH, Dent, BB & Forbes, SL 2009, 'The effect of water environment on adipocere formation', 4th Mediterranean Academy of Forensic Sciences Meeting Abstracts, 4th Mediterranean Academy of Forensic Sciences Meeting, Antalya, pp. 1-1.

Notter, SJ, Stuart, BH, Dent, BB & Forbes, SL 2009, 'The effect of water environment on adipocere formation', UTS Faculty of Science Research Day Book of Abstracts, UTS Faculty of Science Research Day.

Notter, SJ, Stuart, BH, Langlois, NE & Dent, BB 2009, 'Adipocere formation in aqueous environments', 21st Congress of the International Academy of Legal Medicine Abstracts, Congress of the International Academy of Legal Medicine, Lisbon.

Oliver, B, Orpez, T, Lopez-Madrona, JC, Suardiaz, M, Lopez-Gomez, C, Nevado-Alcaide, IA, Maldonado-Sanchez, R, Marin, C & Fernandez, O 2009, 'Influence of prolonged interferon-beta therapy on genes involved in its signalling pathway in different peripheral blood mononuclear subpopulations from patients with multiple sclerosis', MULTIPLE SCLEROSIS, 25th Congress of the European-Committee-for-Treatment-and-Research-in-Multiple-Sclerosis, SAGE PUBLICATIONS LTD, Dusseldorf, GERMANY, pp. S185-S185.

Paulhill, KJ, Taddeo, SS, Davidson, LA, Carroll, RJ, Chapkin, RS, Lupton, JR & Turner, ND 2009, 'Dietary lipid source alters quercetin effects on antioxidant enzyme/phase I and II gene expression in rat colon', FASEB JOURNAL, FEDERATION AMER SOC EXP BIOL.

Petrou, K, Doblin, MA, Hassler, CS & Ralph, PJ 2009, 'Multiple stressors on the sea ice diatom Fragilariopsis cylindrus - photophysiological impacts of seasonal freezing and melting of sea ice', Japan.

Platen, E 2009, 'A benchmark approach beyond semi-martingales', Workshop on Non-Semi-Martingale Modelling in Finance, Helsinki, Finland.

Platen, E 1970, 'A benchmark approach to quantitative finance', Workshop at Enterprise Risk Management Symposium, Chicago, USA.

Platen, E 2009, 'A Variance Reduction Technique Based on Integral Representations', Seminar Presentation, Fraunhofer Institute and the University of Kaiserslauten, Kaiserslauten, Germany.

Platen, E 2009, 'Asset markets and monetary policy', Seminar Presentation, Imperial College, London, London, UK.

Platen, E 2009, 'Asset markets and monetary policy', Seminar Presentation, Technical University Munich, Munich, Germany.

Platen, E 2009, 'Asset markets and monetary policy', Seminar Presentation, University of Lugano, Lugano, Switzerland.

Platen, E 2009, 'Numerical solution of stochastic differential equations with jumps in finance', Seminar Presentation, University of Oxford, Oxford, UK.

Platen, E 2009, 'On interest rate term structure modeling under the benchmark approach', 4th General Conference on Advanced Mathematical Methods in Finance, Alesund, Norway.

Platen, E 2009, 'On interest rate term structure modeling under the benchmark approach', Seminar Presentation, Humboldt University, Berlin, Germany.

Platen, E 1970, 'Quantitative methods - Computing and numerical methods', Workshop, Ajou University, Korea.

Platen, E 1970, 'Valuing guaranteed minimum death benefit options in variable annuities under a benchmark approach', Enterprise Risk Management Symposium, Chicago, USA.

Poulton, CG, Mahmoodian, S, Dossou, KB, McPhedran, RC, Botten, LC & de Sterke, CM 2009, 'Semi-analytical models for resonant states near photonic crystal band edges', THEORETICAL AND COMPUTATIONAL NANOPHOTONICS (TACONA-PHOTONICS 2009), 2nd International Workshop on Theoretical and Computational Nanophotonics (TaCoNa-Photonics 2009), AMER INST PHYSICS, Bad Honnef, GERMANY, pp. 78-+.

Raja, S, Stuart, BH & Thomas, P 2009, 'The development of analytical techniques for the determination of forensic bone age', 5th European Academy of Forensic Science Conference Book of Abstracts, 5th European Academy of Forensic Science Conference, Glasgow, pp. 1-1.

Raja, S, Stuart, BH, Thomas, P & Howes, JM 2009, 'The development of analytical techniques for the determination of forensic bone age', UTS Faculty of Science Research Day Book of Abstracts, UTS Faculty of Science Research Day.

Raja, S, Thomas, P & Stuart, BH 2009, 'A study of storage conditions and treatments for forensic bone specimens using thermogravimetric analysis', Medicta 2009 Book of Abstracts, 9th Mediterranean Conference on Calorimetry and Thermal Analysis, Marseille.

Raja, S, Thomas, P, Stuart, BH & O'Brien, C 2009, 'Pyrolysis gas chromatography - mass spectrometry analysis for the estimation of pig bone age', 21st Congress of the International Academy of Legal Medicine Abstracts, Congress of the International Academy of Legal Medicine, Lisbon.

Ramelow, S, Ratschbache, L, Fedrizzi, A, Langford, NK & Zeilinger, A 2009, 'Discrete, tunable color-entanglement', Optics InfoBase Conference Papers.

Ramelow, S, Ratschbache, L, Fedrizzi, A, Langford, NK & Zeilinger, A 2009, 'Discrete, tunable color-entanglement', CLEO/Europe - EQEC 2009 - European Conference on Lasers and Electro-Optics and the European Quantum Electronics Conference.
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Ray, AS, Connan, H, Liu, B & Thomas, P 2009, 'Alumina-Silica Rich Clay Brick Waste In Hydrothermally Treated Cement-Based Construction Products', Proceedings of the 34th Conference on Our World In Concrete & Structures, Conference On Our World In Concrete & Structures, CI-Premier Conference Organisation, Singapore, Singapore, pp. 289-296.
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An urgent need for creative, sustainable approaches, which minimise the environmental impact of conventional Portland Cement (PC) -based construction materials, is recognised throughout the world. In recent years intensive research has been directed to the use of alumino-silicate materials to produce blended PC. The reduction of CO2 emissions, through the minimisation of PC consumption in the manufacture of PC-based construction products, and utilisation of industrial byproducts, to limit environmental impact, are the principal drivers of this worldwide activity. A number of supplementary cementitious materials (SCMs) containing alumina and silica such as fly ash, granulated blast furnace slag and silica fume are well known additives for the production of blended PCs due to their pozzolanic properties. The potential of other by-products such as those from the construction and demolition industry are less known however, even though they represent an excellent source of reactive alumina and silica-rich material. This paper deals with fired clay bricks (CB), generated as a waste product from construction and demolition activities, and their value as an additive in the manufacture of PC-based construction products. The research findings reported in this paper are from laboratory scale experiments conducted under hydrothermal conditions in an autoclave where fmely ground Cl3 waste was incorporated in the mixes. From a combination of analytical techniques including X-ray Diffraction, Differential Thermal Analysis, Scanning Electron Microscopy and solid-state Nuclear Magnetic Resonance, it was established that the aluminosilicate phase in the fired clay bricks promoted the development of the tobermorite, the principal binder in most calcium silicate products under hydrothermal conditions. The use of CB waste as a cement replacement for the manufacture of these products was also demonstrated as a viable option.

Santhakumar, V, Lal, S, Kavanagh, D & Rossiter, P 2009, 'Centralised data collection point for multiple Wireless Mesh Networks', BROADBANDCOM 2009 - Selected Papers on Broadband Communication, Information Technology and Biomedical Applications, pp. 203-208.
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Wireless sensor devices are cost effective environment monitoring systems which have the ability to continuously monitor the surrounding environment and log data. However due to their design, limited battery and storage capacity [1] an aggregation point is necessary to store any continuous stream of data for secure and permanent use. This paper looks at using a centralised data aggregation point to collect data from multiple remote mesh networks for analysis utilising low-end hardware to communicate over a secure network.

Schlogl, E 2009, 'Quantitative finance before and after the crisis', Seminar Presentation, Sim Corp, Sydney, Australia.

Schulte, J, Roger, J, Zhang, F, Yates, B, Bridgeman, A & Lidbury, B 2009, 'Language difficulties in first year Science - an interim report', UniServe Science Proceedings 2009, UniServe Science, UniServe, University of Sydney, Sydney, pp. 139-145.

Schulte, J, Zhang, F, Lidbury, B, Bridgeman, A, Rodgers, J & Yates, B 2009, 'Embedding high impact education practices in 1st year science: outcomes and future directions', UniServe Science Proceedings, UniServe Science, UniServe, The University of Sydney, Sydney.

Schulte, J, Zhang, F, Lidbury, B, Bridgeman, A, Yates, B & Rodger, J 2009, 'Embedding in-discipline language support for first year students in the sciences', AUSTRALIAN ASSOCIATION FOR RESEARCH IN EDUCATION Conference 2009 (AARE 2009), AUSTRALIAN ASSOCIATION FOR RESEARCH IN EDUCATION, Canberra, pp. 1-20.
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This paper reports on a project which aims at addressing the need to cater for the language needs of a diverse student body (both domestic and international student body) by embedding strategic approaches to learning and teaching in first year sciences in tertiary education. These strategies consist of active learning skills which are widely used in language learning. The disciplines covered by the project are Biology, Chemistry and Physics and involves the University of Canberra (UC), University of Sydney (USyd), University of Tasmania (UTAS), University of Technology, Sydney (UTS) and University of Newcastle (Newcastle) in Australia. This project is funded by the Australian Learning and Teaching Council (ALTC). The paper discusses the background to the study and reports on results on the language difficulties faced by first year science student cohorts from data collected in 2008 as well as qualitative data was also collected on 2008 students’ attitudes towards online science learning. It will also report on the results on the implementation of the learning strategies at UTS and UTAS in Physics and Chemistry disciplines in 2009. Keywords: First year science teaching, role of language in science teaching, active learning skills

Seidel, P, Merfort, I, Hughes, JM, Oliver, BGG, Tamm, M & Roth, M 2009, 'Dimethylfumarate Modulates Chemokine Expression in Airway Smooth Muscle Cells: Role of Heme-Oxygenase and NF-kappa B', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Sevastyanov, S, Lin, B & Hwang, FJ 2009, 'Makespan minimization in parallel flow shops', The 9th Workshop on Models and Algorithms for Planning and Scheduling Problems (MAPSP 2009), MAPSP, Abbey Rolduc.

Seymour, JR 2009, 'Cascading resource patch exploitation in a heterogeneous microbial seascape', Adelaide, Australia.

Sieveking, DP, Lim, P, Chow, RW, Dunn, LL, Bao, S, McGrath, KC, Heather, AK, Handelsman, DJ, Celermajer, DS & Ng, MK 2009, 'A Sex-Specific Role for Androgens in Angiogenesis', CIRCULATION, 82nd Scientific Session of the American-Heart-Association, LIPPINCOTT WILLIAMS & WILKINS, Orlando, FL, pp. S1140-S1140.

Siglekow, N, Pangon, L, Musgrove, EA & Kohonen-Corish, M 2009, 'Biological function of the mutated in colorectal cancer (MCC) gene', JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY, pp. A241-A241.

Sinutok, S, Hill, R & Ralph, PJ 2009, 'The effect of light intensity on photosynthetic efficiency and calcification in three reef building species of Halimeda', ASPAB 2009 Conference, Townsville, Australia.
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Calcareous green algae from the genus Halimeda are widely distributed in tropical and subtropical marine environments. Halimeda is important as a carbonate sediment producer, as a source of food for herbivores, as a phototroph, and as a provider of shelter and nursery ground for invertebrates on coral reefs. Halimeda cylindracea, H. macroloba, and H. opuntia collected from the intertidal zone at Heron Island reef in the southern Great Barrier Reef of Australia were maintained in flow-through seawater tanks under three different irradiances (50, 400 and 900 µmol photon m-2 s-1) for a 4 day period. Measures of photosynthetic efficiency were investigated using Pulse Amplitude Modulated (PAM) fluorometry and chlorophyll concentrations (a and b) were determined after 4 days on an apical lobe of the thallus. Growth and calcification were examined by staining the thallus with Alizarin Red-S solution. Pigmentation, growth, and calcification were found to be independent of irradiance, remaining constant over time between treatments, except for chlorophyll a in H. cylindracea which was higher in low light than in higher light treatments. The results indicate that each species responded differently under the high light treatment at midday, with H. cylindracea and H. macroloba showing a reduction in photochemical quenching (Y(II)), indicating downregulation in photosynthetic efficiency. This was mirrored by an increase in non-regulated energy dissipation yield of PSII (Y(NO)), suggesting that photoinhibition was occurring. In comparison to this species, H. opuntia showed no changes in Y(II) and Y(NO) while H. macroloba showed higher Y(II) and lower Y(NO) only in the morning and the evening. Non-photochemical quenching yield (Y(NPQ)) was low in all treatments and in all three species which may indicate a low potential for photoprotection mechanisms in these algae. However, further investigation is required which run over an extended period of time and between seasons.

Smith, GB & Gentle, AR 2009, 'Angular selectivity: impact on optimised coatings for night sky radiative cooling', Proc SPIE 2009, 7404, SPIE Nanostructured Thin Films II, SPIE, San Diego CA USA, pp. 19-27.
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To achieve strong net thermal radiation emission from surfaces whose temperature is at or below ambient it is important to have high absorptance between 7.9 μm to 13 μm where the atmosphere is most transparent. Outside of this band the atmosphere behaves like a black body emitter and hence at these wavelengths net radiant heat loss is normally not possible at sub-ambient temperatures. It becomes possible using two types of angular selectivity, which also improve emission between 7.9 μm to 13 μm. One is coating based, and one uses external heat mirrors. In the latter low emittance mirrors replace the higher emitting segments of the atmosphere. The coating’s net gain is a result of its reflectance rise countering the atmosphere’s drop in transparency as ray angles to the zenith approach the horizontal. These ideas are examined in the context of experimental data on coatings which rely on nanostructure to largely limit their spectral absorption to the atmosphere’s transparent band. The angular selective coating becomes possible in two multilayer types (a) one nano-layer is strongly reflective (b) one layer has much higher index than the other. Type (a) materials as nanoparticles provide surface phonon resonance in the desired absorption band.

Sollod, B, Gunning, SJ, Wen, S, Gentz, MC, Nicholson, GM & King, GK 2009, 'A dual-target, self-synergizing ion channel toxin from spider venom', 16th World Congress on Animal, Plant and Microbial Toxins, Canberra, ACT.

Stuart, BH 2009, 'The development and application of flexible-learning science textbooks', UTS Teaching and Learning Forum Abstracts, UTS Teaching and Learning Forum.

Sutherland, D, Spigel, B, Plew, D, Norton, N & Howard-Williams, C 2009, 'Limiting nutrients of phytoplankton growth in the Upper Waitaki lakes', Development workshop for the Upper Waitaki Catchment, Canterbury, New Zealand.

Syaifudin, ARM, Yunus, MA, Mukhopadhyay, SC & Jayasundera, KP 2009, 'A Novel Planar Interdigital Sensor for Environmental Monitoring', 2009 IEEE SENSORS, VOLS 1-3, 8th IEEE Conference on Sensors, IEEE, Christchurch, NEW ZEALAND, pp. 105-+.

Tomljenovic-Hanic, S, Rahmani, A, Steel, MJ & de Sterke, CM 2009, 'Photonic Crystal Cavities for Sensing: Dielectric Modes versus Air Modes', 2009 CONFERENCE ON LASERS AND ELECTRO-OPTICS AND QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2009), VOLS 1-5, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 3175-3176.

Tomljenovic-Hanic, S, Rahmani, A, Steel, MJ & De Sterke, CM 2009, 'Photonic crystal cavities for sensing: Dielectric modes versus air modes', 2009 Conference on Lasers and Electro-Optics and 2009 Conference on Quantum Electronics and Laser Science Conference, CLEO/QELS 2009.
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Effective sensing with photonic crystal cavities requires optimization of modal quality factor and field overlap. For several unrelated cavities, we find the quality factor dominates, so that dielectric modes are strongly favored over air modes. ©2009 IEEE.

Tomljenovic-Hanic, S, Rahmani, A, Steel, MJ & Martijn de Sterke, C 2009, 'Photonic crystal cavities for sensing: Dielectric modes versus air modes', Optics InfoBase Conference Papers.
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Effective sensing with photonic crystal cavities requires optimization of modal quality factor and field overlap. For several unrelated cavities, we find the quality factor dominates, so that dielectric modes are strongly favored over air modes. © 2009 OSA.

Tovey, ER, Ng, DSY, Stelzer-Braid, S, Rawlinson, WD & Oliver, BG 2009, 'Children With Asthma And No URTI, More Commonly Have Rhinovirus In Their Exhaled Breath, Than In Mucous (Retracted article. See vol. 127, pg. 551, 2011)', JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, 65th Annual Meeting of the American-Academy-of-Allergy-Asthma-and-Immunology, MOSBY-ELSEVIER, Washington, DC, pp. S171-S171.
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Trian, T, Moir, LM, Burgess, JK, Black, JL, Reddel, H, Oliver, BG & McParland, B 2009, 'RHINOVIRUS-Induced Exacerbations of Asthma - How Is the b2-Adrenoceptor Implicated?', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Vallotton, P, Sun, C, Wang, D, Ranganathan, P, Turnbull, L & Whitchurch, CB 2009, 'Segmentation and tracking of individual Pseudomonas aeruginosa bacteria in dense populations of motile cells', Proceedings of Image and Vision Computing New Zealand 2009, Image and Vision Computing Conference, IEEE, Wellington, NZ, pp. 221-225.
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The dynamics of individual bacteria underlies the manifestation of complex multicellular behaviours such as biofilm development and colony expansion. High resolution movies of expanding bacterial colonies reveal intriguing patterns of cell motions. A quantitative understanding of the observed behaviour in relation to the bacterias own motile apparatus and to hydrodynamic forces requires that bacteria be identified and tracked over time. This represents a demanding undertaking as their size is close to the diffraction limit; they are very close to each other; and a typical image may contain over a thousand cells. Here, we describe the approach that we have developed to segment individual bacteria and track them in high resolution phase contrast microscopy movies. We report that over 99% of nonoverlapping bacteria could be segmented correctly using mathematical morphology, and we present preliminary results that exploit this new capability.

Vessalas, K, Ray, AS, Thomas, P, Joyce, PA & Haggman, J 2009, 'Assessment of chemical durability of pitchstone fines in Portland cement blended mortars', Concrete Solutions 09: Adding value in changing climates - Proceedings of the 24th Biennial Conference of the Concrete Institute of Australia, Concrete Solutions 09: Adding value in changing climates - 24th Biennial Conference of the Concrete Institute of Australia, Concrete Institute of Australia, Sydney, Australia, pp. 1-9.
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The use of supplementary cementitious materials (SCMs) as partial replacement of Portland cement (PC) is an effective way of reducing the consumption of PC. This investigation is aimed at assessing some chemical durability aspects of PC-SCM blended mortars containing pitchstone fines (PF) and fly ash (FA) at 20% and 40% replacement levels of PC. Hardened mortar cubes containing these two pozzolanic SCMs and a control mortar containing 100% PC were prepared and pre-aged in lime-saturated water for 28-days. These specimens were then immersed into 1M solution of sodium sulphate (Na2SO4) and their mass and pH recorded after 28-days and 56-days. Specimens were also immersed in deionised water as a control environment for comparison of mass change and pH. In the case of PF, data from 1M Na2SO4 immersion demonstrate increasing substitution rate provides lower mass gain. In contrast, increasing replacement rate of PC by FA in 1M Na2SO4 demonstrates higher mass gain comparable to 100% PC.

Wang, E, Chen, C & Yu, Q 2009, 'Modeling the response of wheat and maize productivity to climate variability and irrigation in the North China Plain.', Interfacing Modelling and Simulation with Mathematical and Computational Sciences, Australia, Cairns, pp. 2742-2748.
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The North China Plain (NCP) is the largest agricultural production area in China, accounting for about 50% of wheat and 30% of maize grain production in China, with a dominant wheat-maize double cropping system. Due to the concentrated summer monsoon rainfall and inter-annual climate variability, irrigation is required to support the high productivity of the wheat-maize system, especially for the wheat crop and in the northern part of the plain, where excessive use of ground- and surface water for irrigation has caused rapid decline of groundwater tables and severe reduction of available surface water from the Yellow River. The productivity of the double cropping system and its reliance on decreasing water supplies under the variable climate need to be assessed. There is still a lack of systematic studies on how the productivity of the wheat-maize system could respond to different levels of reduced irrigation water supply.

Wark, PAB, Hsu, A & Hansbro, P 2009, 'Innate immune response of bronchial epithelial cells to infection with influenza', JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS.

Wark, PAB, See, HV, Simpson, JL, Forbes, RL & Hansbro, P 2009, 'Peripheral blood monocytes (PBMCs) display innate antiviral response to rhinovirus (RV) infected bronchial epithelial cells', JOURNAL OF IMMUNOLOGY, AMER ASSOC IMMUNOLOGISTS.

Yamaji, N, Little, MJ, Nishio, H, Villegas, E, Billen, B, Tytgat, J, Nicholson, GM & Corzo, G 2009, 'Synthesis, solution structure and phyla-specificity of a spider δ-toxin that slows inactivation of specific voltage-gated sodium channel subtypes', 16th World Congress on Animal, Plant and Microbial Toxins, Recife Brazil.

Zinder, Y & Walker, SJ 2009, 'Scheduling flexible multiprocessor tasks on parallel machines', 9th Workshop on Models and Algorithms for Planning and Scheduling Problems, Workshop on Models and Algorithms for Planning and Scheduling Problems, Abbey Rolduc, Netherlands, pp. 23-25.
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We consider the following scheduling problem. A ?nite set of tasks (jobs, operations) N = {1, 2, . . . , n} is to be processed on m > 1 identical parallel machines (processors). The processing of tasks begins at time t = 0. Each machine can process only one task at a time. The order in which tasks can be processed is restricted by a transitive, antire?exive and antisymmetric relation on N, called precedence constraints. If task j precedes task g, denoted j ? g, t h e n task g can not be processed until task j has been completed. In order to be completed, a task j requires pj units of processing time. At di?erent points in time a task may be processed by a di?erent number of machines. The maximum number of machines which can process task j simultaneously is 1 = uj = m. The number of machines processing a task can change at any point in time without penalty

de Winton, M, Jellyman, D, Sutherland, D & Walsh, J 2009, A review of the potential to re-establish macrophyte beds in Te Waihora (Lake Ellesmere), Hamilton.

Hallegraeff, GM, Beardall, J, Brett, S, Doblin, MA, Hosja, W, de Salas, M & Thompson, P www.oceanclimatechange.org.au 2009, Marine climate change in Australia: Impacts and adaptation responses: Phytoplankton, pp. 1-10, Australia.

Hudson, N, Hickey, C, Nagals, J, Sutherland, D & Wells, R 2009, Joint venture discharge consent renewal – assessment of effects on the Tarawera River: Water Quality and aquatic plants, Hamilton.

Norton, N, Spigel, B, Sutherland, DL, Trolle, D & Plew, D 2009, Lake Benmore Water Quality: a modelling method to assist with assessments of nutrient loadings., Christchurch, NZ.

Salas, M, Cheal, A, Lough, J, McKinnon, D, Meekan, M, Sweatman, H, Coleman, M, Chambers, L, Dunlop, N, Church, J, Dowdney, J, Feng, M, Griffiths, S, Hobday, A, Matear, R, Poloczanska, E, Richardson, A, Ridgway, K, Risbey, J, Thompson, P, Thresher, R, Weller, E, Saintilan, N, Wilson, S, Lenanton, R, Hosja, W, Moore, P, Wernberg, T, Marshall, D, Connolly, R, Hill, K, Congdon, B, Devney, C, Fuentes, M, Graham, N, Hamann, M, Kingsford, M, Munday, P, Pratchett, M, Sheaves, M, Beardall, J, Brett, S, Waschka, M, Dann, P, Edgar, G, Swadling, K, Connell, S, Russell, B, Ward, T, Lukoschek, V, McGregor, S, Jenkins, G, Campbell, A, Steinberg, P, Anthony, K, Lovelock, C, Skilleter, G, Figueira, WF, Booth, DJ, Doblin, MA, Davidson, J, Holbrook, N, Howard, W, Kendrick, G & Smale, D NCCARF Publication 2009, Report Card of Marine Climate Change for Australia, pp. 1-2, Australia.

Sutherland, D & Edwards, T 2009, Weed surveillance of four Canterbury High Country Lakes and the Ecological Condition of Lakes Ohau and Alexandrina using LakeSPI, Christchurch.

Sutherland, D, Kelly, G, Dumas, J, Spigel, B & Norton, N 2009, Water quality parameters in the Upper Waitaki Basin December 2008 – April 2009, Christchurch.

Sutherland, DL 2009, Effects of MTAD on Te Waiwai Lagoon, Southland - Statement of Evidence, Christchurch, NZ.

Sutherland, DL 2009, Effects of the proposed MTAD on the water quality and aquatic ecology in the Southern Lakes, Statement of Evidence, Christchurch, NZ.

Breymann, W, Lüthi, D & Platen, E 2009, 'Empirical behavior of a world stock index from intra-day to monthly time scales', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 251 Abstract: Inspired by the theoretically oriented dynamic analysis of moving average rules in Chiarella, He and Hommes (CHH) (2006a) model, this paper conducts a dynamic analysis of a microstructure model of continuous double auctions in which the probability of heterogeneous agents to trade is determined by the rules of either fundamentalists mean-reverting to the fundamental or chartists choosing moving average rules based their relative performance. With such a realistic market microstructure, the model is able not only to obtain the results of the CHH model but also to characterise most of the stylized facts including the power-law behaviour of volatility. The results seem to suggest that a comprehensive explanation of several statistical properties of returns is possible in a framework where both behavioral traits and realistic microstructure have a role.

Bruti Liberati, N, Nikitopoulos Sklibosios, C, Platen, E & Schlogl, E 2009, 'Alternative Defaultable Term Structure Models', Quantitative Finance Research Paper Series.
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The objective of this paper is to consider defaultable term structure models in a general setting beyond standard risk-neutral models. Using as numeraire the growth optimal portfolio, defaultable interest rate derivatives are priced under the real-world probability measure. Therefore, the existence of an equivalent risk-neutral probability measure is not required. In particular, the real-world dynamics of the instantaneous defaultable forward rates under a jump-diffusion extension of a HJM type framework are derived. Thus, by establishing a modelling framework fully under the real-world probability measure, the challenge of reconciling real-world and risk-neutral probabilities of default is deliberately avoided, which provides significant extra modelling freedom. In addition, for certain volatility specifications, finite dimensional Markovian defaultable term structure models are derived. The paper also demonstrates an alternative defaultable term structure model. It provides tractable expressions for the prices of defaultable derivatives under the assumption of independence between the discounted growth optimal portfolio and the default-adjusted short rate. These expressions are then used in a more general model as control variates for Monte Carlo simulations of credit derivatives.

Craddock, MJ & Platen, E 2009, 'On explicit probability laws for classes of scalar diffusions', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 246 Abstract: This paper uses Lie symmetry group methods to obtain transition probability densities for scalar diffusions, where the diffusion coefficient is given by a power law. We will show that if the drift of the diffusion satisfies a certain family of Riccati equations, then it is possible to compute a generalized Laplace transform of the transition density for the process. Various explicit examples are provided. We also obtain fundamental solutions of the Kolmogorov forward equation for diffusions, which do not correspond to transition probability densities.

Hinz, J & Novikov, A 2009, 'On fair pricing of emission-related derivatives', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 257 Abstract: The climate rescue is on the top of many agendas. In thisc ontext, emission trading schemes are considered as promising tools. The regulatory framework of an emission trading scheme introduces a market for emission allowances and creates need for risk management by appropriate financial contracts. In this work, we address logical principles underlying their valuation.

Hulley, H & Platen, E 2009, 'A visual criterion for identifying Ito diffusions as martingalesor strict local martingales', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 263 Abstract: It is often important, in applications of stochastic calculus to financial modelling, to know whether a given local martingale is a martingale or a strict local martingale. We address this problem in the context of a time-homogenous diffusion process with a finite lower boundary, presented as the solution of a driftless stochastic differential equation. Our main theorem demonstrates that the question of whether or not this process is a martingale may be decided simply by examining the slope of a certain increasing function. Further results establish the connection between our theorem and other results in the literature, while a number of examples are provided to illustrate the use of our criterion.

Ignatieva, K & Platen, E 2009, 'Modelling co-movements and tail dependency in the international stock market via copulae', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 265 Abstract: This paper examines international equity market co-movements using time-varying copulae. We examine distributions from the class of Symmetric Generalized Hyperbolic (SGH) distributions for modelling univariate marginals of equity index returns. We show based on the goodness-of-fit testing that the SGH class outperforms the normal distribution, and that the Student-t assumption o nmarginals leads to the best performance, and thus, can be used to fit multivariate copula for the joint distribution of equity index returns. We show in our study that the Student-t copula is not only superior to the Gaussian copula, where the dependence structure relates to the multivariate normal distribution, but also out performs some alternative mixture copula models which allow to reï¬ect asymmetric dependencies in the tails of the distribution. The Student-t copula with Student-t marginals allows to model realistically simultaneous co-movements and to capture taild ependency in the equity index returns. From the point of view of risk management, it is a good candidate for modelling the returns arising in an international equity index portfolio where the extreme losses are known to have a tendency to occur simultaneously. We apply copulae to the estimation of the Value-at-Risk and the Expected Shortfall, and show that the Student-t copula with Student-t marginals iss uperior to the alternative copula models investigated, as well the Riskmetics approach.

Norton, N, Spigel, B, Sutherland, D & Howard-Williams, C 2009, 'Waitaki Lakes Water Quality: a method to define sustainable thresholds for nutrient loading for regional planning'.

Norton, N, Spigel, B, Sutherland, D, Trolle, D & Plew, D 2009, 'Lake Benmore water quality: a modelling method to assist with assessments for nutrient loadings'.

Pilz, K & Schlogl, E 2009, 'A hybrid commodity and interest rate', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 261 Abstract: A joint model of commodity price and interest rate risk is constructed analogously to the multi-currency LIBOR Market Model (LMM). Going beyond a simple âre-interpretation❠of the multi-currency LMM, issues arising in the application of the model to actual commodity market data are specifically addressed. Firstly, liquid market prices are only available for options on commodity futures, rather than forwards, thus the difference between forward and futures prices must be explicitly taken into account in the calibration. Secondly, we construct a procedure to achieve a consistent fit of the model to market data for interest options, commodity options and historically estimated correlations between interest rates and commodity prices. We illustrate the model by an application to real market data and derive pricing formulas for commodity spread options.

Platen, E 2009, 'A benchmark approach to investing and pricing', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 253 Abstract: This paper introduces a general market modeling framework, the benchmark approach, which assumes the existence of the numeraire portfolio. This is the strictly positive portfolio that when used as benchmark makes all benchmarked nonnegative portfolios supermartingales, that is intuitively speaking downward trending or trendless. It can be shown to equal the Kelly portfolio which maximizes expected logarithmic utility. In several ways the Kelly or numeraire portfolio is the "best" performing portfolio and can not be out performed systematically by any other nonnegative portfolio. Its use in pricing as numeraire leads directly to the real world pricing formula, which employs the real world probability when calculating conditional expectations. In a large regular financial market, the Kelly portfolio is shown to be approximated by well diversified portfolios.

Platen, E 2009, 'Real world pricing of long term contracts', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 262 Abstract: Long dated contingent claims are relevant in insurance, pension fund management and derivative pricing. This paper proposes a paradigm shift in the valuation of long term contracts, away from classical no-arbitrage pricing towards pricing under the real world probability measure. In contrast to risk neutral pricing, the long term excess return of the equity market, known as the equity premium, is taken into account. Further, instead of the savings account, the numeraire portfolio isused, as the fundamental unit of value in the analysis. The numeraire portfolio is the strictly positive, tradable portfolio that when used as benchmark makes all benchmarked non negative portfolios supermartingales, which means intuitively that these are downward trending or at least trendless. Furthermore, the benchmarked real world price of a benchmarked claimis defined to be its real world conditional expectation. This yields the minimal possible price for its hedgable part and minimizes the variance of the benchmarked hedge error. The pooled total benchmarked replication error of a large insurance company or bank essentially vanishes due to diversification. Interestingly, in long terml iability and asset valuation, real world pricing can lead to significantly lower prices than suggested by classical no-arbitragea rguments. Moreover, since the existence of some equivalent risk neutral probability measure is no longer required, a wider and more realistic modeling framework is available for exploration. Classical actuarial and risk neutral pricing emerge as special cases of real world pricing.

Platen, E & Rendek, RJ 2009, 'Exact scenario simulation for selected multi-dimensional stochastic processes', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 259 Abstract: Accurate scenario simulation methods for solutions of multi-dimensional stochastic differential equations find application in stochastic analysis, the statistics of stochastic processes and many other areas, for instance, in finance. They have been playing a crucial role as standard models in various areas and dominate often the communication and thinking in a particular field of application, even that they may be too simple for more advanced tasks. Various discrete time simulation methods have been developed over the years. However, the simulation of solutions of some stochastic differential equations can be problematic due to systematic errors and numerical instabilities. Therefore, it is valuable to identify multi-dimensional stochastic differential equations with solutions that can be simulated exactly. This avoids several of the theoretical and practical problems encountered by those simulation methods that use discrete time approximations. This paper provides a survey of methods for the exact simulation of paths of some multi-dimensional solutions of stochastic differential equations including Ornstein-Uhlenbeck, square root, squared Bessel, Wishart and Levy type processes.

Platen, E & Rendek, RJ 2009, 'Quasi-exact approximation of hidden Markov chain filters', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 258 Abstract: This paper studies the application of exact simulation methods for multi-dimensional multiplicative noise stochastic differential equations to filtering. Stochastic differential equations with multiplicative noise naturally occur as Zakai equation in hidden Markov chain filtering. The paper proposes a quasi-exact approximation method for hidden Markov chain filters, which can be applied when discrete time approximations, such as the Euler scheme, may fail in practice.

Platen, E & Rendek, RJ 2009, 'Simulation of diversified portfolios in a continuous financial market', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 264 Abstract: In this paper we analyze the simulated behavior of diversified portfolios in a continuous financial market. In particular, we focus on equally weighted portfolios. Wei llustrate that these well diversified portfolios constitute good proxies of the growth optimal portfolio. The multi-asset market models considered include the Black-Scholes model, the Heston model, the ARCH diffusion model, the geometric Ornstein-Uhlenbeck volatility model and the multi-currency minimal market model. The choice of these models was motivated by the fact that they can be simulated almost exactly and, therefore, very accurately also over longer periods of time. Finally, we provide examples, which demonstrate the robustness of the diversification phenomenon when approximating the growth optimal portfolio of a market by an equal value weighted portfolio. Significant outperformance of the market capitalization weighted portfolio by the equal value weightedp ortfolio can be observed for models.

Platen, E & Semmler, W 2009, 'Asset markets and monetary policy', Research Paper Series, Quantitative Finance Research Centre, University of Technology, Sydney.
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Research Paper Number: 247 Abstract: Monetary policy has pursued the concept of inflation targeting. This has been implemented in many countries. Here interest rates are supposed to respond to an inflation gap and output gap. Despite long term continuing growth of the world financial assets, recently, monetary policy, in particular in the U.S. after the subprime credit crisis, was challenged by severe disruptions and a meltdown of the financial market. Subsequently, academics have been in search of a type of monetary policy that does allow to influence in an appropriate manner the investor's behavior and, thus, the dynamics of the economy and its financial market. The paper suggests a dynamic portfolio approach. It allows one to study the interaction between investors` strategic behavior and monetary policy. The article derives rules that explain how monetary authorities should set the short term interest rate in interaction with inflation rate, economic growth, asset prices, risk aversion, asset price volatility, and consumption rates. Interesting is that the inflation rate needs to have a certain minimal level to allow the interest rate to be a viable control instrument. A particular target interest rate has been identified for the desirable optimal regime. If the proposed monetary policy rule is applied properly, then the consumption rate will remain stable and the inflation rate can be kept close to a minimal possible level. Empirical evidence is provided to support this view. Additionally, in the case of an economic crisis the proposed relationships indicate in which direction to act to bring the economy back on track.

Spigel, B, Trolle, D, Sutherland, D, Plew, DR, Norton, N & Howard-Williams, C 2009, 'Waitaki Lakes Water Quality: a method to define sustainable thresholds for nutrient loading for regional planning'.

Sutherland, D 2009, 'Results of the pre-MTAD baseline surveys in Lakes Te Anau, Manaporui, Hauroko and the Waiau Arm'.

Sutherland, D, Spigel, B, Plew, D, Norton, N & Howard-Williams, C 2009, 'Water quality, macrophyte, periphyton and phytoplankton growth in the Upper Waitaki lakes'.