Publications

Chuvieco, E 2009, Fundamentals of Satellite Remote Sensing, 1st, CRC Press, Boca Raton, Florida USA.
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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.

Suthers, I & Rissik, D 2009, Plankton A Guide to Their Ecology and Monitoring for Water Quality, CSIRO PUBLISHING.
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This practical book provides a comprehensive introduction to the biology and ecology of plankton and describes its use as a tool for monitoring water quality.

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', Wiley.
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AbstractFingermarks are one of the most valuable types of physical evidence and there is a plethora of techniques that can be used to detect and enhance fingermarks. This entry presents an overview of the most common methods employed, and the sequences that can be applied for maximum exploitation of fingermark evidence.

Ben‐Nissan, B & Choi, AH 2009, 'Nanoceramics for Medical Applications' in Geckeler, KE & Nishide, H (eds), Advanced Nanomaterials, Wiley, Germany, pp. 523-553.
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"Nanostructured materials" refer to certain materials which have delicate structures and sizes that fall within the range of 1 to lOOnm. As a consequence of this size, an extensive development of nanotechnology has taken place in the fields of materials science and engineering during the past decade. Yet, such developments have not come as a surprise, when it is appreciated that these nanostrucrured materials have the ability to be adapted and integrated into biomedical devices. This is possible because most biological systems, including viruses, membranes and protein complexes, exhibit natural nanostructures.

Blaber, M, Ford, M & Cortie, M 2009, 'The Physics and Optical Properties of Gold' in Corti, C & Holliday, R (eds), Gold, CRC Press, Boca Raton, Florida, pp. 13-30.
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The high corrosion resistance of gold is a consequence of its rst ionization potential being 9.2 eV, which is high compared to those of, for example, silver and copper, at 7.6 and 7.7 eV, respectively [6]. This results in such a large barrier to oxidation that elemental gold is ordinarily free of an oxide coating. Gold has the electronic conguration [Xe]4f145d106s1. In this conguration the 4f electrons underscreen the 5d and the 6s, p electrons from the nuclear charge, resulting in an effect analogous to lanthanide contraction. The lanthanide contraction causes the atomic radius of the lanthanides to decrease across the period as the quality of the shielding per electron decreases; in the 5d metal series this effect gives similar lattice constants to the 4d metals. For some years the stability of the Au2 dimer and the reduced lattice constant in bulk gold compared to silver were attributed to a similar contraction [7]. However, gold is in a unique spot on the periodic table where the effects of the lanthanide contraction are also superimposed on the onset of relativistic effects. The latter become increasingly important for the heavier elements because as the atomic number increases, the velocity of the 1s electrons approaches the speed of light. This causes these electrons to increase in mass and so their orbital contracts toward the nucleus. To compensate, the higher s and p orbitals, which also have signicant electron density in the vicinity of the nucleus, also contract, resulting nally in the outermost 6s and 6p orbitals being smaller than they would otherwise have been without relativistic effects (see Figure 2.1; [10-12]). The contraction of the s and p orbitals causes an increased screening of the core for the 5d and 5f electrons, which do not have much electron density in the vicinity of the nucleus and which are therefore, in the rst instance, less susceptible to relativistic effects of their own. Thus, the 5d and 5f orbitals are destabilized ...

Cortie, MB & McDonagh, A 2009, 'Nanoscience of Gold and Gold Surfaces' in Mohr, F (ed), Gold Chemistry, Wiley, Weinheim, pp. 321-356.
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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', Wiley.
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Abstract The society we live in today relies heavily on automobiles for transport. This leads to many wheels on the road and inevitably where a crime is committed an automobile would have some sort of involvement with the crime itself, or the criminal himself. In 2002, the world passenger car fleet hit 531 million cars, with a quarter of these cars being in the United States 1. Of these, 72% of vehicles have four tires with the same tread and design and 14% have two pairs of tires with the same tread and design. Regarding the size, 97% of all cars have four tires with the same tread size, 1.6% has two pairs and 1.4% has three the same and one of different tread size 2. In the majority of cases in which an automobile is involved, the suspect used the automobile to drive to and from the crime scene. Tires are likely to leave some sort of pattern or trace evidence at the scene of crime. Tires are manufactured using natural and synthetic rubber. The rubber is then subject to an entire process in order to manufacture a tire 3. These tires are manufactured with a particular tread pattern to ensure maximum grip and purchase between the tire and the surface of the road. Many different tread patterns exist. Elemental pattern features include waves, lines, diamonds, zigzags, curves, blocks, etc. In addition to these manufacture characteristics, acquired characteristics such as wear and tear, cuts, small holes, etc., can be often present 4. Tire marks can thus be highly informative but unfortunately they are commonly overlooked. As a result, they are often destroyed before any potential exploitation could take place 5. This article presents the examination and value of tire marks in a forensic examination.

Gladstone, W 2009, 'Conservation and Management of Tropical Coastal Ecosystems' in Ecological Connectivity among Tropical Coastal Ecosystems, Springer 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 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.

Gladstone, W 2009, 'Ecological Connectivity among Tropical Coastal Ecosystems' in Nagelkerken, I (ed), Ecological Connectivity among Tropical Coastal Ecosystems, Springer Netherlands, 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

Herbert, B & Harry, E 2009, 'Difficult Proteins' in Sheehan, D & Tyther, R (eds), Methods in Molecular Biology, Humana Press, New York, pp. 47-63.
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The degree of protein diversity and dynamic range within organisms means that even the simplest proteome cannot be captured by any single extraction and separation step. New techniques have focused on major protein classes often under-represented in proteome analysis; low abundance, membrane, and alkaline proteins. The last decade has seen considerable technology development in fractionation tools aimed at complexity reduction in many forms. The key outcome of complexity reduction is that each fraction, or sub-proteome, can be studied in more detail, and proteins which would have remained undetected in a total extract are present in sufficient quantities. However, the tools available are fractionations, not amplifications, and like all mining for rare and difficult items, a large amount of starting material is often required. The key shortcomings of many proteome analysis techniques are now well documented. With this knowledge, the best modern proteomics 'platform' involves combining multiple protein extractions, gel and chromatographic separations, and multiple MS analysis methods.

Luong, S & Roux, C 2009, 'Marks or Impressions of Manufactured Items', Wiley.
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Abstract Marks and impressions can be exploited by the investigator to extract information associated with the crime as part of the forensic investigation. The scope of this article covers fabric impression, which is any mark or imprint left by a material made by a fabric, including glove marks. This article describes the techniques and processes of examination, as well as interpretation and the evidential significance of such types of evidence.

Nedbal, L, Červený, J & Schmidt, H 2009, 'Scaling and Integration of Kinetic Models of Photosynthesis: Towards Comprehensive E-Photosynthesis' in Advances in Photosynthesis and Respiration, Springer Netherlands, pp. 17-29.
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Raymond, JJ, Roux, C & Walsh, SJ 2009, 'Friction Ridge Skin: Interaction between Fingerprint Detection andDNA/Biological Material', Wiley.
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AbstractThe DNA analysis of fingerprints and skin traces has become a routine component of forensic investigations. Research has found that most fingerprint enhancement techniques will not prevent subsequent DNA profiling of treated fingerprints or biological stains; however, the quantity of DNA recovered may be reduced. The exceptions include shortwave ultraviolet (UV) light, diaminobenzidine, and physical developer, which are likely to prevent DNA analysis of fingerprints. Sequencing of more than one fingerprint technique on an item is also likely to reduce the chance of successful DNA recovery. Guidelines are provided to assist the sequencing of fingerprint and DNA evidence.

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', Wiley.
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AbstractOwing to their size and their particular nature, fibers probably constitute the ultimate example of trace evidence. Although fibers are easily transferred during a criminal event and a large pool of techniques can be applied for their characterization, the interpretation of an apparent “fiber match” remains one of the most difficult challenges in the forensic examination of trace evidence. However, our knowledge in this area has significantly improved over the last 25 years. Nowadays, a wealth of empirical data can be used by forensic scientists to determine the value of fiber evidence in the context of a case. In addition, logical and statistical frameworks can also assist them in this endeavor. This article presents a summary of the state of the art in this topic.

SPIE, PO 2009, 'Front Matter: Volume 7404' in Smith, GB, Lakhtakia, A & Lee, C-C (eds), Introduction to Complex Mediums for Optics and Electromagnetics, SPIE, Washington, USA, pp. 740401-740401.
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Stark, D & Ellis, J 2009, 'Entamoeba' in Molecular Detection of Foodborne Pathogens, pp. 677-690.

Suggett, DJ & Moore, CM 2009, 'Fluorometry for Biological Sensing' in Encyclopedia of Ocean Sciences, Elsevier, 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.

Suggett, DJ & Moore, CM 2009, 'Fluorometry for Biological Sensing' in Encyclopedia of Ocean Sciences, Elsevier, 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.

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

Whitney, M & Ryan, L 2009, 'Quantifying Dose–Response Uncertainty Using Bayesian Model Averaging' in Uncertainty Modeling in Dose Response, Wiley, pp. 165-179.
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Whitney, M & Ryan, L 2009, 'Response to Comments' in Uncertainty Modeling in Dose Response, Wiley, pp. 194-196.
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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 colorcenters in chemical vapor deposition diamond is presented. These emitters shownarrow luminescence lines in the near infra-red. Single photon emission wasverified with continuous and pulsed excitation with emission rates atsaturation in the MHz regime, whilst direct lifetime measurements revealexcited state lifetimes ranging from 1-14 ns. In addition, a number of quantumemitters demonstrate two level behavior with no bunching present in the secondorder correlation function. An improved method of evaluating the quantumefficiency through the direct measurement of the collection efficiency from twolevel 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, K-MC, 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-F & 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-H, Kim, Y-J & 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 Sn-Ag 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. © 2008 Elsevier B.V. All rights reserved.

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, DJ 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.

Allen, MA, Lauro, FM, Williams, TJ, Burg, D, Siddiqui, KS, De Francisci, D, Chong, KWY, Pilak, O, Chew, HH, De Maere, MZ, Ting, L, Katrib, M, Ng, C, Sowers, KR, Galperin, MY, Anderson, IJ, Ivanova, N, Dalin, E, Martinez, M, Lapidus, A, Hauser, L, Land, M, Thomas, T & Cavicchioli, R 2009, 'The genome sequence of the psychrophilic archaeon,Methanococcoides burtonii: the role of genome evolution in cold adaptation', The ISME Journal, vol. 3, no. 9, pp. 1012-1035.
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AbstractPsychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five-tiered evidence rating (ER) system that ranked annotations from ER1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea, which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino-acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall, membrane, envelope biogenesis COG genes are overrepresented. Likewise, signal transduction (COG category T) genes are overrepresented and M. burtonii has a high ‘IQ’ (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two overrepresented COG categories appear to have been acquired from ɛ- and δ-Proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they have an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have ...

Al-Qassab, S, 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 AND 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, S, Reichel, MP, Su, C, Jenkins, D, Hall, C, Windsor, PA, Dubey, JP & Ellis, J 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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Amoako Johnson, F, Padmadas, SS & 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

Apanasovich, TV, Carroll, RJ & Maity, A 2009, 'SIMEX and standard error estimation in semiparametric measurement error models', Electronic Journal of Statistics, vol. 3, no. none, 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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Aslan, K, Weisenberg, M, Hortle, E & Geddes, CD 2009, 'Fixed-angle observation of surface plasmon coupled chemiluminescence from palladium thin films', Applied Physics Letters, vol. 95, no. 12, pp. 123117-123117.
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In this letter, the fixed-angle observation of surface plasmon coupled chemiluminescence (SPCC) from palladium thin films is reported. Fresnel calculations predict that light 492–549 nm spectral range can efficiently induce surface plasmon modes in 15 nm palladium thin films. Free-space emission from blue, green, and chartreuse chemiluminescent solutions on palladium thin films was isotropic, while the SPCC emission was highly directional and predominantly p-polarized in accordance with the predictions of the Fresnel calculations. In addition, the decay rates of the SPCC and free-space emission were similar, which suggests that palladium thin films have no catalytic effect on chemiluminescence emission.

Aslan, K, Weisenberg, M, Hortle, E & Geddes, CD 2009, 'Surface plasmon coupled chemiluminescence from iron thin films: Directional and approaching fixed angle observation', Journal of Applied Physics, vol. 106, no. 1, pp. 014313-014313.
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We report the observation of surface plasmon coupled chemiluminescence (SPCC) from iron thin films. Theoretical Fresnel calculations were employed to determine the optimum thickness of iron thin films to be 15 nm, which is assessed by the value of minimum reflectivity curves for incident light upon the thin film. An overlayer 10 nm thick SiO2 was used to protect the iron thin films from oxidation by air or physical changes induced by chemiluminescent solutions. SPCC emission from blue, green, and chartreuse chemiluminescent solutions on iron films can be observed at a fixed angle of 60° for all the chemiluminescent solutions, while free-space emission was isotropic. Iron thin films do not have a catalytic effect on chemiluminescence emission.

Austin, C, Hare, D, Rozelle, AL, Robinson, WH, Grimm, R & Doble, P 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. © 2009 The Royal Society of Chemistry.

Bai, H, Cortie, MB, Maaroof, AI, Dowd, A, Kealley, C & Smith, GB 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. © 2008 Elsevier Ltd. All rights reserved.

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.

Bandyopadhyay, M 2009, 'On quasi Einstein almost pseudo Ricci symmetric manifolds', Tensor, vol. 71, no. 3, pp. 274-284.
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Bandyopadhyay, M 2009, 'On some interesting properties of super quasi Einstein manifold', Tensor, vol. 71, no. 3, pp. 246-257.

Barard, S, Heeney, M, Chen, L, Cölle, 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, pp. 013701-013701.
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Time of flight photocurrent transient studies on thin films of bimodal polytriarylamine (PTAA) show two distinct and separate arrival times for hole transport in the same sample at a single field. The corresponding mobilities differ by two orders of magnitude, typically μfast∼10−3 cm2 V−1 s−1 and μslow∼10−5 cm2 V−1 s−1 at room temperature, and are measured parametric in electric field and temperature. The mobility data are analyzed using the correlated disorder model by Novikov, yielding a fitting parameter set. The two conduction paths are believed to come about as a result of phase segregation between the shorter and longer polymer chains with the shorter chains giving rise to the faster conduction pathways (as confirmed by results obtained for monomodal, shorter, and longer chain PTAA, by sample thickness scaling of the photocurrents and by reversal of the illuminated electrode). Separate arrival times are also obtained in a blend of the two short and long chain monomodal polymers. The phase separation within the film is inferred by the appearance of two glass transition temperatures using dynamic mechanical thermal analysis.

Barraud, N, Schleheck, D, Klebensberger, J, Webb, JS, Hassett, DJ, Rice, SA & Kjelleberg, S 2009, 'Nitric Oxide Signaling inPseudomonas aeruginosaBiofilms 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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ABSTRACTBacteria in biofilms often undergo active dispersal events and revert to a free-swimming, planktonic state to complete the biofilm life cycle. The signaling molecule nitric oxide (NO) was previously found to trigger biofilm dispersal in the opportunistic pathogenPseudomonas aeruginosaat low, nontoxic concentrations (N. Barraud, D. J. Hassett, S. H. Hwang, S. A. Rice, S. Kjelleberg, and J. S. Webb, J. Bacteriol. 188:7344-7353, 2006). NO was further shown to increase cell motility and susceptibility to antimicrobials. Recently, numerous studies revealed that increased degradation of the secondary messenger cyclic di-GMP (c-di-GMP) by specific phosphodiesterases (PDEs) triggers a planktonic mode of growth in eubacteria. In this study, the potential link between NO and c-di-GMP signaling was investigated by performing (i) PDE inhibitor studies, (ii) enzymatic assays to measure PDE activity, and (iii) direct quantification of intracellular c-di-GMP levels. The results suggest a role for c-di-GMP signaling in triggering the biofilm dispersal event induced by NO, as dispersal requires PDE activity and addition of NO stimulates PDE and induces the concomitant decrease in intracellular c-di-GMP levels inP. aeruginosa. Furthermore, gene expression studies indicated global responses to low, nontoxic levels of NO inP. aeruginosabiofilms, including upregulation of genes involved in motility and energy metabolism and downregulation of adhesins and virulence factors. Finally, site-directed mutagenesis of candidate genes and physiological characterization of the corresponding mutant strains uncovered that the chemotaxis transducer BdlA is involved in the biofilm dispersal response induced by NO.

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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SummaryStrategies to induce biofilm dispersal are of interest due to their potential to prevent biofilm formation and biofilm‐related infections. Nitric oxide (NO), an important messenger molecule in biological systems, was previously identified as a signal for dispersal in biofilms of the model organism Pseudomonas aeruginosa. In the present study, the use of NO as an anti‐biofilm agent more broadly was assessed. Various NO donors, at concentrations estimated to generate NO levels in the picomolar and low nanomolar range, were tested on single‐species biofilms of relevant microorganisms and on multi‐species biofilms from water distribution and treatment systems. Nitric oxide‐induced dispersal was observed in all biofilms assessed, and the average reduction of total biofilm surface was 63%. Moreover, biofilms exposed to low doses of NO were more susceptible to antimicrobial treatments than untreated biofilms. For example, the efficacy of conventional chlorine treatments at removing multi‐species biofilms from water systems was increased by 20‐fold in biofilms treated with NO compared with untreated biofilms. These data suggest that combined treatments with NO may allow for novel and improved strategies to control biofilms and have widespread applications in many environmental, industrial and clinical settings.

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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Abstract The leading intraseasonal mode of atmospheric and oceanic variability, the Madden–Julian oscillation (MJO), influences tropical and extratropical sea level pressure, temperature, divergent and rotational wind components, moisture, and deep convection. As a 40- to 50-day oscillation, the MJO is also known to influence tropical phenomena, including tropical cyclone (TC) activity in various TC basins. The links between the MJO and multiple measures of TC activity, including genesis, landfall, and an integrative accumulated cyclone energy (ACE) index, were quantified for multiple TC-formation basins across the Western Hemisphere, including the North Atlantic and northeast Pacific Ocean and subbasins, for the period 1978–2006. Using this relatively long (29 yr) TC dataset and employing an upper-tropospheric MJO diagnostic that is physically meaningful over the entire Western Hemisphere, this study extends existing research on the relationships between the MJO and TCs. The NOAA Climate Prediction Center’s operational MJO index, derived from 200-hPa velocity potential data, was divided into three phases. Relative frequencies of the MJO phases were compared with observed levels of TC activity using a binomial distribution hypothesis test. The MJO was found to statistically significantly modulate the frequency of TC genesis, intensification, and landfall in the nine TC basins studied. For example, when an MJO index was large and positive at 120°W, hurricanes and intense hurricanes were 4 times as likely to make landfall in the North Atlantic. This modulation of TC activity, including landfall patterns in the North Atlantic, was physically linked to the upper-atmospheric response to the eastward-propagating MJO and is evident as a dipole of TC activity between Pacific and Atlantic subbasins.

BARTLETT, CY, MANUA, C, CINNER, J, SUTTON, S, JIMMY, R, SOUTH, R, NILSSON, 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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Abstract:  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, Vázquez Domínguez, 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 l-1 and from 0.2 to 0.6 μg C l-1 h-1, 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 (0.4-1.2 μm); however, after the crash of the diatom bloom, the majority of TEP were in the ≥1.2 μm size fraction. In the GF/Cfiltered 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 m-2 d-1, 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 wate...

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, SM, Mechler, A, Nichols, RJ, Praporski, S, di Maio, IL, Islam, H, Girard‐Egrot, AP, Cornell, BA, Prashar, J, Caruso, F, Martin, LL & Martin, DK 2009, 'Inside Front Cover: Novel Engineered Ion Channel Provides Controllable Ion Permeability for Polyelectrolyte Microcapsules Coated with a Lipid Membrane (Adv. Funct. Mater. 2/2009)', Advanced Functional Materials, vol. 19, no. 2, pp. NA-NA.
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Battle, AR, Valenzuela, SM, Mechler, A, Nichols, RJ, Praporski, S, di Maio, IL, Islam, H, Girard‐Egrot, AP, Cornell, BA, Prashar, J, Caruso, F, Martin, LL & Martin, DK 2009, 'Novel Engineered Ion Channel Provides Controllable Ion Permeability for Polyelectrolyte Microcapsules Coated with a Lipid Membrane', Advanced Functional Materials, vol. 19, no. 2, pp. 201-208.
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AbstractThe development of nanostructured microcapsules based on a biomimetic lipid bilayer membrane (BLM) coating of poly(sodium styrenesulfonate) (PSS)/poly(allylamine hydrochloride) (PAH) polyelectrolyte hollow microcapsules is reported. A novel engineered ion channel, gramicidin (bis‐gA), incorporated into the lipid membrane coating provides a functional capability to control transport across the microcapsule wall. The microcapsules provide transport and permeation for drug‐analog neutral species, as well as positively and negatively charged ionic species. This controlled transport can be tuned for selective release biomimetically by controlling the gating of incorporated bis‐gA ion channels. This system provides a platform for the creation of “smart” biomimetic delivery vessels for the effective and selective therapeutic delivery and targeting of drugs.

Beagley, K, 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, GER 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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Behnia, S, Akhshani, A, Ahadpour, S, Akhavan, A & Mahmodi, H 2009, 'Cryptography based on chaotic random maps with position dependent weighting probabilities', Chaos, Solitons & Fractals, vol. 40, no. 1, pp. 362-369.
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Behnia, S, Akhshani, A, Akhavan, A & Mahmodi, H 2009, 'Applications of tripled chaotic maps in cryptography', Chaos, Solitons & Fractals, vol. 40, no. 1, pp. 505-519.
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Bell, TDM, Bhosale, SV, Ghiggino, KP, Langford, SJ & Woodward, CP 2009, 'Synthesis and Photophysical Properties of a Conformationally Flexible Mixed Porphyrin Star-Pentamer', Australian Journal of Chemistry, vol. 62, no. 7, pp. 692-692.
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The synthesis of a porphyrin star-pentamer bearing a free-base porphyrin core and four zinc(ii) metalloporphyrins, which are tethered by a conformationally flexible linker about the central porphyrin’s antipody, is described. The synthetic strategy is highlighted by the use of olefin cross metathesis to link the five chromophores together in a directed fashion in high yield. Photoexcitation into the Soret absorption band of the zinc porphyrin chromophores at 425 nm leads to a substantial enhancement of central free-base porphyrin fluorescence, indicating energy transfer from the photoexcited zinc porphyrin (outer periphery) to central free-base porphyrin. Time-resolved fluorescence decay profiles required three exponential decay components for satisfactory fitting. These are attributed to emission from the central free-base porphyrin and to two different rates of energy transfer from the zinc porphyrins to the free-base porphyrin. The faster of these decay components equates to an energy-transfer rate constant of 3.7 × 109 s–1 and an efficiency of 83%, whereas the other is essentially unquenched with respect to reported values for zinc porphyrin fluorescence decay times. The relative contribution of these two components to the initial fluorescence decay is ~3:2, similar to the 5:4 ratio of cis and trans geometric isomers present in the pentamer.

Bell, TDM, Yap, S, Jani, CH, Bhosale, SV, Hofkens, J, De Schryver, FC, Langford, SJ & Ghiggino, KP 2009, 'Synthesis and Photophysics of Core‐Substituted Naphthalene Diimides: Fluorophores for Single Molecule Applications', Chemistry – An Asian Journal, vol. 4, no. 10, pp. 1542-1550.
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AbstractThe synthesis and photophysics of two new aminopropenyl naphthalene diimide (SANDI) dyes are reported. A general and convenient method for the synthesis of the precursor mono‐, di‐, and tetrabrominated 1,4,5,8‐naphthalene tetracarboxylic dianhydrides is described. The two core‐substituted SANDIs exhibit many of the photophysical properties required for fluorescence labeling applications including high photostability and high fluorescence quantum yields (>0.5) in the visible region of the spectrum. The emission wavelength is sensitive to the number of substituents on the NDI core, and the fluorescence decay times are in the range of ∼8–12 ns for both compounds in the solvents investigated. Preliminary fluorescence emission data from single molecules of the compounds embedded in poly(methyl methacrylate) films are also reported and show that single molecules have very low yields of photobleaching, particularly the di‐substituted system. Furthermore, only a small proportion (<10 %) of the single molecules studied display fluorescence intermittencies or “blinks” in their photon trajectory. The compounds appear to be excellent candidates for applications at the single molecule level, for example, as FRET labels.

Bellomo, R, Morimatsu, H, Presneill, J, French, C, Cole, L, Story, D, Uchino, S, Naka, T, Finfer, S, Cooper, DJ & Myburgh, J 2009, 'Effects of saline or albumin resuscitation on standard coagulation tests', Critical Care and Resuscitation, vol. 11, no. 4, pp. 250-256.
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Benson, SJ, Lennard, CJ, Maynard, P, Hill, DM, Andrew, AS & Roux, C 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. Crown Copyright © 2009.

Benson, SJ, Lennard, CJ, Maynard, P, Hill, DM, Andrew, AS & Roux, C 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.

Bhatia, VK, Kealley, CS, Wuhrer, R, Wallwork, KS & 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, A & 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.

Bhosale, SV, Bhosale, SV, Kalyankar, MB & Langford, SJ 2009, 'RETRACTED: A Core-Substituted Naphthalene Diimide Fluoride Sensor', Organic Letters, vol. 11, no. 23, pp. 5418-5421.
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Bhosale, SV, Bhosale, SV, Langford, SJ & Krsta, D 2009, 'Construction of trimeric porphyrin-fullerene-porphyrin stacks within surface-derived pores of nano-scale dimensions', Chemical Communications, no. 22, pp. 3166-3166.
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Bhosale, SV, Kalyankar, MB, Bhosale, SV, Langford, SJ, Reid, EF & Hogan, CF 2009, 'The synthesis of novel core-substituted naphthalene diimides via Suzuki cross-coupling and their properties', New Journal of Chemistry, vol. 33, no. 12, pp. 2409-2409.
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Bhosale, SV, Kalyankar, MB, Langford, SJ, Bhosale, SV & Oliver, RF 2009, 'Synthesis and Supramolecular Properties of a Novel Octaphosphonate Porphyrin', European Journal of Organic Chemistry, vol. 2009, no. 24, pp. 4128-4134.
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AbstractTwo complementary routes were developed for preparing novel octaphosphonate porphyrins. The use of protected/deprotected phosphonate‐substituted precursors in the rational synthesis gave an overall yield 16 %. A more streamlined synthetic path gave 21 % overall yield of the target molecule. Octaphosphonate porphyrin possesses promising properties in supramolecular aggregate formation with cyclam. Cofacial reversible self‐assembly of a meso‐substituted octaphosphonate porphyrin with cyclam yields micrometer‐long nanowires with a height of about 1–1.5 nm. The resulting wires were characterized by UV/Vis absorption, emission and atomic force microscopy and transmission electron microscopy.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Bhosale, SV, Langford, SJ & Bhosale, SV 2009, 'Comparative binding study of neurotransmitters in hydrophobic and hydrophilic yoctowells in water', Supramolecular Chemistry, vol. 21, no. 1-2, pp. 18-23.
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Biro, PA & 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. © Springer Science+Business Media B.V. 2009.

Bishop, MJ, Morgan, T, Coleman, MA, Kelaher, BP, Hardstaff, LK & Evenden, RW 2009, 'Facilitation of molluscan assemblages in mangroves by the fucalean alga Hormosira banksii', MARINE ECOLOGY PROGRESS SERIES, vol. 392, no. 0, pp. 111-122.
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The fucalean macroalga Hormosira banksii facilitates diverse rocky intertidal communities. Along the east coast of Australia, the alga can also persist in mangroves as a free-living form trapped amongst pneumatophores. We investigated (1) whether the alga has an effect on molluscan species richness and abundance in mangroves similar to that on rocky shores, and (2) whether, in mangroves, the source (phenotypically distinct estuarine or rocky shore populations) of H. banksii influences the outcome of its interspecific interactions. Sampling of 3 rocky shore and 3 mangrove sites along the east coast of Australia revealed that patches of H. banksii consistently supported a greater species richness of molluscs than adjacent substratum. Whereas the alga increased the abundance of molluscs in the mangrove forest, it had no effect or decreased molluscan abundance on the rocky shore. Transplant of H. banksii from rocky shores and estuarine tidal flats into the mangrove indicated that the source of the algae influenced the magnitude of effects. Although all algae enhanced molluscan abundance and species richness, estuarine H. banksii, which had larger vesicles and a longer thallus, supported more molluscs of more species than rocky shore H. banksii. These results support the growing consensus that the influence of foundation species at the community level is dependent on environmental conditions. As human activities place increasing pressure on coastal ecosystems, it will be important to understand the mechanisms and conditions that determine community-level effects of foundation species so that biodiversity may be conserved.

Blaber, MG, Arnold, MD & Ford, MJ 2009, 'Designing materials for plasmonic systems', J. Phys.: Condens. Matter, vol. 22, p. 095501.
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We use electronic structure calculations based upon density functional theoryto search for ideal plasmonic materials among the alkali noble intermetallics.Importantly, we use density functional perturbation theory to calculate theelectron-phonon interaction and from there use a first order solution to theBoltzmann equation to estimate the phenomenological damping frequency in theDrude dielectric function. We discuss the necessary electronic features of aplasmonic material and investigate the optical properties of the alkali-nobleintermetallics in terms of some generic plasmonic system quality factors. Weconclude that at low negative permittivities, KAu with a damping frequency of0.0224 eV and a high optical gap to bare plasma frequency ratio, outperformsgold and to some extent silver as a plasmonic material. Unfortunately, a lowplasma frequency (1.54 eV) reduces its utility in modern plasmonicsapplications. We also discuss, briefly, the effect of local fields on theoptical properties of these materials.

Blaber, MG, Arnold, MD & Ford, MJ 2009, 'Optical properties of intermetallic compounds from first principles calculations: a search for the ideal plasmonic material', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 21, no. 14, 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. © 2009 IOP Publishing Ltd.

Black, JL, Oliver, BGG & Roth, M 2009, 'Molecular Mechanisms of Combination Therapy With Inhaled Corticosteroids and Long-Acting β-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: β2-agonists, both short acting and long acting; and corticosteroids (CSs). Although the properties of each drug class are well described, their use in combination delivered either separately or through one device has provided some clear and important clinical advantages. The mechanisms underlying these interactions have emerged as novel and provocative. β2-Agonists can stimulate the glucocorticoid receptor (GR) and promote its translocation to the nucleus, resulting in increased CS-mediated gene transcription. In structural airway cells, such as fibroblasts and smooth muscle, this gene transcription is associated with the formation of a complex between the GR and another transcription factor, CCAAT enhancer-binding protein (C/EBP)-α. Airway smooth muscle cells from persons with asthma are deficient in C/EBP-α, which may explain the finding that CSs do not inhibit the proliferation of these cells in vitro. Whether this deficiency can explain the increased bulk of muscle in the asthmatic airway remains to be established. β2-Agonists can inhibit mast cell mediator release, but this response is susceptible to desensitization, a process that CSs can inhibit. CSs also can increase the transcription of the β2- receptor gene in the lung and the nasal mucosa. These effects of CSs mitigate against the reduced transcription of β2-receptors, which occurs as a consequence of long-term β2-agonist administration. Delineation of the exact mechanisms underlying these effects will ensure rational, direct therapy. © 2009 American College of Chest Physicians.

Blair, SE, Cokcetin, NN, Harry, EJ & Carter, DA 2009, 'The unusual antibacterial activity of medical-grade Leptospermum honey: antibacterial spectrum, resistance and transcriptome analysis', European Journal of Clinical Microbiology & Infectious Diseases, 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. © 2009 Springer-Verlag.

Bond, DM, Dennis, ES & Finnegan, EJ 2009, 'Hypoxia', Plant Signaling & 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.

Bond, DM, Dennis, ES & Finnegan, EJ 2009, 'Hypoxia: a novel function for VIN3.', Plant Signal Behav, 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. Vernalization is the acquisition of the competence to flower after exposure to prolonged low temperatures, which in Arabidopsis is associated with the epigenetic repression of the floral repressor FLOWERING LOCUS C (FLC). During vernalization VIN3 binds to the chromatin of the FLC locus, and interacts with conserved components of Polycomb-group Repressive Complex 2 (PRC2). This complex catalyses the tri-methylation of histone H3 lysine 27 (H3K27me3), a repressive chromatin mark that increases at the FLC locus as a result of vernalization. In our recent paper we found that VIN3 is also induced by hypoxic conditions, 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.

Bond, DM, Dennis, ES, Pogson, BJ & Finnegan, EJ 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, DM, Wilson, IW, Dennis, ES, Pogson, BJ & Finnegan, EJ 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.

Borup, L 2009, 'RCT of acupuncture for relieving labour pain reports promising results', Focus on Alternative and Complementary Therapies, vol. 14, no. 3, pp. 202-203.
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Botman, A, Hagen, CW, Li, J, Thiel, BL, Dunn, KA, Mulders, JJL, 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 & Technology B: Microelectronics and Nanometer Structures Processing, Measurement, and Phenomena, 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±15μΩcm. 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.

Brown, AG, Sommerville, D, Reedy, BJ, Shimmon, RG & 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 & Schlögl, 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. © 2009 Springer Science+Business Media, LLC.

Brzoska, A, Withers, R, Turner, K, Robinson, A, Dixon, N, Harry, L & Lewis, P 2009, 'Identification of novel drug targets using model organisms', MICROBIOLOGY AUSTRALIA, vol. 30, no. 2, pp. 95-97.
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A review that describes the potential for inhibiting essential, fundamental processes in model pathogens to facilitate the development of new antibiotics.

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). © 2009 Springer-Verlag.

Burall, LS, Rodolakis, A, Rekiki, A, Myers, GSA & Bavoil, PM 2009, 'Genomic Analysis of an AttenuatedChlamydia abortusLive Vaccine Strain Reveals Defects in Central Metabolism and Surface Proteins', Infection and Immunity, vol. 77, no. 9, pp. 4161-4167.
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ABSTRACTComparative genomic analysis of a wild-type strain of the ovine pathogenChlamydia abortusand its nitrosoguanidine-induced, temperature-sensitive, virulence-attenuated live vaccine derivative identified 22 single nucleotide polymorphisms unique to the mutant, including nine nonsynonymous mutations, one leading to a truncation ofpmpG, which encodes a polymorphic membrane protein, and two intergenic mutations potentially affecting promoter sequences. Other nonsynonymous mutations mapped to apmpGpseudogene and to predicted coding sequences encoding a putative lipoprotein, a sigma-54-dependent response regulator, a PhoH-like protein, a putative export protein, two tRNA synthetases, and a putative serine hydroxymethyltransferase. One of the intergenic mutations putatively affects transcription of two divergent genes encoding pyruvate kinase and a putative SOS response nuclease, respectively. These observations suggest that the temperature-sensitive phenotype and associated virulence attenuation of the vaccine strain result from disrupted metabolic activity due to altered pyruvate kinase expression and/or alteration in the function of one or more membrane proteins, most notably PmpG and a putative lipoprotein.

Burgess, JK, Ceresa, C, Johnson, SR, Kanabar, V, Moir, LM, Nguyen, TTB, Oliver, BGG, 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. The mechanisms leading to airway remodelling are not well understood. ASM cells have the potential to play a key role in these processes through the production and release of ECM proteins. The ASM cells and ECM proteins are each able to influence the behaviour and characteristics of the other. The modified ECM profile in the asthmatic airway may contribute to the altered behaviour of the ASM cells, such responses to ECM proteins are modulated through the cell surface expression of integrin receptors. ASM cells from asthmatic individuals express different levels of some integrin subunits compared to nonasthmatic ASM cells, which have the potential to further influence their responses to the ECM proteins in the airways. ECM homeostasis requires the presence and activation of matrix metalloproteinases and their tissue inhibitors, which in turn modulate the interaction of the ASM cells and the ECM proteins. Furthermore, the complex interactions of the ASM cells and the ECM in the asthmatic airways and the role played by external stimuli, such as viral infections, to modulate airway remodelling are currently unknown. This review summarises our current understanding of the influence of the ECM on ASM function. © 2008 Elsevier Ltd. All rights reserved.

Buxton, L, Badger, M & Ralph, P 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 (Ci) 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, O2 production at 26°C was significantly limited at Ci concentrations below ambient seawater (∼2.2 mM). Further additions of Ci up to ∼10 mM caused no further stimulation of oxygenic photosynthesis. Following exposure to 30°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°C, 2 d). Whole corals and cultured zooxanthellae differed considerably in their responses to Ci 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 Ci (<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. © 2009 Phycological Society of America.

Caltagirone, C & Gale, PA 2009, 'ChemInform Abstract: Anion Receptor Chemistry: Highlights from 2007', ChemInform, vol. 40, no. 19.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Caltagirone, C, Mulas, A, Isaia, F, Lippolis, V, Gale, PA & Light, ME 2009, 'Metal-induced pre-organisation for anion recognition in a neutral platinum-containing receptor', Chemical Communications, no. 41, pp. 6279-6279.
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Campbell, S, Botten, LC, McPhedran, RC & Martijn de Sterke, C 2009, 'Modal method for conical diffraction by slanted lamellar gratings', Journal of the Optical Society of America A, vol. 26, no. 4, pp. 938-938.
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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.

Carney, FP, Morris, CA, Milthorpe, B, Flanagan, JL & Willcox, MDP 2009, 'In Vitro Adsorption of Tear Proteins to Hydroxyethyl Methacrylate-Based Contact Lens Materials', Eye & Contact Lens: Science & 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.

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, '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.

Červený, J & Nedbal, L 2009, 'Metabolic Rhythms of the Cyanobacterium Cyanothece sp. ATCC 51142 Correlate with Modeled Dynamics of Circadian Clock', Journal of Biological Rhythms, vol. 24, no. 4, pp. 295-303.
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These experiments aim to reveal the dynamic features that occur during the metabolism of the unicellular, nitrogen fixing cyanobacterium Cyanothece sp. when exposed to diverse circadian forcing patterns (LD 16:8, LD 12:12, LD 8:16, LD 6:6). The chlorophyll concentration grew rapidly from subjective morning when first illuminated to around noon, then remained stable from later in the afternoon and throughout the night. The optical density measured at 735 nm was stable during the morning chlorophyll accumulation, then increased in the early afternoon toward a peak, followed at dusk by a rapid decline toward the late night steady state. The authors propose that these dynamics largely reflect accumulation and subsequent consumption of glycogen granules. This hypothesis is consistent with the sharp peak of respiration that coincides with the putative hydrocarbon catabolism. In the long-day regimen (LD 16:8), these events may mark the transition from the aerobic photosynthetic metabolism to microaerobic nitrogen metabolism that occurs at dusk, and thus cannot be triggered by the darkness that comes later. Rather, control is likely to originate in the circadian clock signaling an approaching night. To explore the dynamics of the link between respiration and circadian oscillations, the authors extrapolated an earlier model of the KaiABC oscillator from Synechococcus elongatus to Cyanothece sp. The measured peak of respiratory activity at dusk correlated strongly in its timing and time width with the modeled peak in accumulation of the KaiB4 complex, which marks the late afternoon phase of the circadian clock. The authors propose a hypothesis that high levels of KaiB4 (or of its Cyanothece sp. analog) trigger the glycogen catabolism that is reflected in the experiments in the respiratory peak. The degree of the correlation between the modeled KaiB4 dynamics and the dynamics of experimentally...

Červený, J, Šetlík, I, Trtílek, M & Nedbal, L 2009, 'Photobioreactor for cultivation and real‐time, in‐situ measurement of O₂ and CO₂ exchange rates, growth dynamics, and of chlorophyll fluorescence emission of photoautotrophic microorganisms', Engineering in Life Sciences, vol. 9, no. 3, pp. 247-253.
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AbstractA detailed knowledge about the dynamics of phytoplanktonic photosynthesis and respiration is crucial for the determination of primary productivity in open oceans as well as for biotechnological applications. The dynamics are best studied in photobioreactors that are able to simulate natural conditions in such, that light can be modulated not only diurnally but also mimicking effects of solar elevation angle from sunrise to sunset, variable cloudiness, light modulation in refractory sun flecks due to water waves, or light intermittence due to turbulent flow in dense suspensions. In addition, high performance photobioreactors ought to be able to monitor in real time photosynthetic and respiratory activities as well as culture growth. Here, we demonstrate performance of a newly designed bench‐top laboratory photobioreactor that meets these needs, with a study of green alga Scenedesmus quadricauda. The algal suspension was exposed to simulated daily variations of total photosynthetic active irradiance and spectral profile, with a larger proportion of red photons in the morning and evening hours. The instrument monitored automatically the culture growth by measuring the optical densities at 735 nm and 680 nm and by measuring steady state and maximal chlorophyll fluorescence emission yields. The photochemical yields were estimated from chlorophyll fluorescence data. These widely used but rather indirect yield estimates were confronted with direct measurements of oxygen evolution and consumption quantum yields. The CO2 fluxes in and out of the culture media as well as the dissolved CO2 in algal suspension were also recorded. The experiments demonstrated potential of the new photobioreactor to reveal minute modulations in gas exchange rates as well as to yield data for calculation of photon requirement of oxygen evolution in the suspension volume that i...

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 hav...

Chan, CX, Darling, AE, Beiko, RG & Ragan, MA 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 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 hav...

Chen, H & Morris, MJ 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 (15.33 kJ/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 postweaning 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 (AgRP) 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, although anorexigenic signaling appeared impaired in these animals. This may contribute to their hyperphagia and faster growth.

Chen, H, Simar, D & Morris, MJ 2009, 'Hypothalamic Neuroendocrine Circuitry is Programmed by Maternal Obesity: Interaction with Postnatal Nutritional Environment', PLoS ONE, vol. 4, no. 7, pp. e6259-e6259.
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Objective: 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. Research Design and Methods: Female Sprague Dawley rats were exposed to chow or HFD for 5 weeks before mating, throughout gestation and lactation. On postnatal day 1, litters were adjusted to 3/litter to induce postnatal overnutrition (vs. 12 in control). At postnatal day 20, half of the rats from each maternal group were weaned onto chow or HFD for 15 weeks. Hypothalamic appetite regulators, and fuel (glucose and lipid) metabolic markers were measured. Results: Offspring from obese dams gained more weight than those from lean dams independent of post-weaning diet. Maternal obesity interacted with post-weaning HFD consumption to cause greater levels of hyperphagia, adiposity, hyperlipidemia, and glucose intolerance in offspring. This was linked to increased hypothalamic NPY signaling and leptin resistance in adult offspring. Litter size reduction had a detrimental impact on insulin and adiponectin, while hypothalamic NPY and POMC mRNA expression were suppressed in the face of normal energy intake and weight gain. Conclusions: Maternal obesity, postnatal litter size reduction and post-weaning HFD consumption caused obesity via different neuroendocrine mechanims. There were strong additive effects of maternal obesity and post-weaning HFD consumption to increase the metabolic disorders in offspring. © 2009 Chen et al.

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, BC, Westhorpe, DP, Mitrovic, SM & Hardwick, L 2009, 'Trophic linkages between periphyton and grazing macroinvertebrates in rivers with different levels of catchment development', HYDROBIOLOGIA, vol. 625, pp. 135-150.
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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 ( 1H-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. © 2008 John Wiley & Sons, Ltd.

Chowdhury, PR, Merlino, J, Labbate, M, Cheong, EY-L, Gottlieb, T & Stokes, HW 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. Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Christianson, JA, Wilson, IW, Llewellyn, DJ & 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, no. 3, pp. 724-732.
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SummaryClimate change is emerging as one of the greatest threats to coral reef ecosystems. Climate‐induced warming events trigger coral bleaching and mortality, which can indirectly affect coral reef fishes. Managing fisheries across coral mortality events is expected to influence the persistence of species and reef recovery potential. The most common management recommendation has been to prohibit fishing using fisheries closures, but this response often has limited support from resource users.Here, we explore an alternative of managing fishing gear commonly used in artisanal coral reef fisheries. We examined fisheries landing data from 15 sites in Papua New Guinea and Kenya to explore whether or how specific gears select for: (i) species that depend on coral reefs for feeding or habitat and are likely to be susceptible to the loss of coral, and (ii) different functional groups of fishes.Only 6% of the fishes targeted by fishers were susceptible to the immediate effects of coral mortality; however, loss of habitat structure following coral mortality is expected to affect 56% of targeted species.Importantly, 25% of target species had feeding characteristics (i.e. reef scrapers/excavators and grazers) that contribute to the recovery of coral reef ecosystems, and gears differed considerably in catches of these species.Spear guns and traps target a high proportion of species likely to be affected by bleaching and key for the recovery of corals. These gears are strong candidates for management restrictions in reefs with high coral mortality. In contrast, line fishing catches the lowest proportion of susceptible and recovery‐enabling species and is preferential fo...

Clark, CR, Kawachi, I, Ryan, L, Ertel, K, Fay, ME & Berkman, LF 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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Background. We investigated whether lack of perceived neighborhood safety due to crime, or living in high crime neighborhoods was associated with incident mobility disability in elderly populations. We hypothesized that low-income elders and elders at retirement age (65 74) would be at greatest risk of mobility disability onset in the face of perceived or measured crime-related safety hazards. Methods. We conducted the study in the New Haven Established Populations for Epidemiologic Studies of the Elderly (EPESE), a longitudinal cohort study of community-dwelling elders aged 65 and older who were residents of New Haven, Connecticut in 1982. Elders were interviewed beginning in 1982 to assess mobility (ability to climb stairs and walk a half mile), perceptions of their neighborhood safety due to crime, annual household income, lifestyle characteristics (smoking, alcohol use, physical activity), and the presence of chronic co-morbid conditions. Additionally, we collected baseline data on neighborhood crime events from the New Haven Register newspaper in 1982 to measure local area crime rates at the census tract level. Results. At baseline in 1982, 1,884 elders were without mobility disability. After 8 years of follow-up, perceiving safety hazards was associated with increased risk of mobility disability among elders at retirement age whose incomes were below the federal poverty line (HR 1.56, 95% CI 1.02 2.37). No effect of perceived safety hazards was found among elders at retirement age whose incomes were above the poverty line. No effect of living in neighborhoods with high crime rates (measured by newspaper reports) was found in any sub-group. Conclusion. Perceiving a safety hazard due to neighborhood crime was associated with increased risk of incident mobility disability among impoverished elders near retirement age. Consistent with prior literature, retirement age appears to be a vulnerable period with respect to the effect of neighborhood conditio...

Colella, M, Parkinson, A, Evans, T, Lennard, C & Roux, C 2009, 'The Recovery of Latent Fingermarks from Evidence Exposed to Ionizing Radiation', JOURNAL OF FORENSIC SCIENCES, vol. 54, no. 3, pp. 583-590.
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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, CJ, Lavery, PS, Ralph, PJ & Masini, RJ 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. sinuosa. Physiological, morphological and growth attributes were repeatedly measured during 198 d of shade treatments and a subsequent 384 d recovery period at ambient PPFD. Shoot density declined by 82% within 105 d under HS treatment, though 6% of shoots remained after 198 d. We estimate that complete shoot loss in HS would have taken 2 years. Rhizome sugar concentrations declined to 32 - 52% of the controls at the end of the most severe shading treatments but after shoot loss, sugar concentrations declined more slowly or increased, suggesting a return to positive carbon balance. In the treatments below MLR, shading induced changes in physiological, morphological and growth characteristics, including reduced leaf length and width, reduced δ13C and photosynthetic adaptation to low light (increased α, reduced Ek and ETRmax), though not consistently. After removal of shading, photosynthetic characteristics became more typical of high light adaptation, possibly induced by greater light penetration through the thinned canopy, including reversal of the changes in α, Ek and ETRmax and induction of non-photochemical quenching. Carbohydrate concentrations increased to ambient concentrations within 115 d at ambient PPFD. Recovery of shoot density was slow, remaining significantly reduced in the MS and HS treatments after 384 d recovery. Shoot...

Cortie, MB, Stokes, N & McDonagh, A 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, MJ & 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. © 2009 American Chemical Society.

Craddock, M 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, M & Lennox, KA 2009, 'The calculation of expectations for classes of diffusion processes by Lie symmetry methods', The 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, S & 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, NT, 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, no. 1, 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. Crown Copyright © 2009.

Darling, AE, Mau, B & Perna, NT 2009, 'Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangement'.
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Multiple genome alignment remains a challenging problem. Effects ofrecombination including rearrangement, segmental duplication, gain, and losscan create a mosaic pattern of homology even among closely related organisms.We describe a method to align two or more genomes that have undergonelarge-scale recombination, particularly genomes that have undergone substantialamounts of gene gain and loss (gene flux). The method utilizes a novelalignment objective score, referred to as a sum-of-pairs breakpoint score. Wealso apply a probabilistic alignment filtering method to remove erroneousalignments of unrelated sequences, which are commonly observed in other genomealignment methods. We describe new metrics for quantifying genome alignmentaccuracy which measure the quality of rearrangement breakpoint predictions andindel predictions. The progressive genome alignment algorithm demonstratesmarkedly improved accuracy over previous approaches in situations where genomeshave undergone realistic amounts of genome rearrangement, gene gain, loss, andduplication. We apply the progressive genome alignment algorithm to a set of 23completely sequenced genomes from the genera Escherichia, Shigella, andSalmonella. The 23 enterobacteria have an estimated 2.46Mbp of genomic contentconserved among all taxa and total unique content of 15.2Mbp. We documentsubstantial population-level variability among these organisms driven byhomologous recombination, gene gain, and gene loss. Free, open-source softwareimplementing the described genome alignment approach is available fromhttp://gel.ahabs.wisc.edu/mauve .

Davis, JT, Gale, PA, Okunola, OA, Prados, P, Iglesias-Sánchez, JC, Torroba, T & Quesada, R 2009, 'Using small molecules to facilitate exchange of bicarbonate and chloride anions across liposomal membranes', Nature Chemistry, vol. 1, no. 2, pp. 138-144.
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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. ©2009 Optical Society of America.

Dean, D, Bruno, WJ, Wan, R, Gomes, JP, Devignot, S, Mehari, T, de Vries, HJC, Morré, SA, Myers, G, Read, TD & Spratt, BG 2009, 'Predicting Phenotype and Emerging Strains amongChlamydia trachomatisInfections', Emerging Infectious Diseases, vol. 15, no. 9, pp. 1385-1394.
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Dedousis-Wallace, A & Shute, RH 2009, 'Indirect bullying: Predictors of teacher intervention, and outcome of a pilot educational presentation about impact on adolescent mental health', Australian Journal of Educational and Developmental Psychology, vol. 9, pp. 2-17.
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We examined teacher characteristics predicting likelihood of intervening in indirect bullying (N=55) and piloted a 45-minute educational presentation about its mental health impact. Teachers' global empathy and perceived seriousness of indirect bullying vignettes were predictors of their likelihood of intervening, but knowledge of mental health impact was not. The presentation increased knowledge of impact and perceived seriousness, immediately and seven weeks later, compared with a treated control group. However, empathy for victims and likelihood of intervening did not increase. Recommendations include adding skills-based material, a self-efficacy measure and a focus on increasing global empathy rather than specific empathy for victims.

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, JAM, Huete, AR, Ferreira Jr., LG, Nanni, MR, Alves, MC & 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, pp. 57-57.
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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, A & 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 elucidate this genetic flux, but there are many methodological challenges involved in inferring evolutionary events from collections of genome sequences. Here we describe a model-based method for using whole-genome sequences to infer the patterns of genome content evolution. A fundamental property of our model is that it allows the rates at which genetic elements are gained or lost to vary in time and from one lineage to another. Our approach is purely sequence based, and does not rely on gene identification. We show how inference can be performed under our model and illustrate its use on three datasets fromFrancisella tularensis, Streptococcus pyogenes, andEscherichia coli. In all three examples, we found interesting variations in the rates of genetic material gain and loss, which strongly correlate with their lifestyle. The algorithms we describe are implemented in a computer software named GenoPlast.

Dilda, PJ, Decollogne, S, Weerakoon, L, Norris, MD, Haber, M, Allen, JD & Hogg, PJ 2009, 'Optimization of the Antitumor Efficacy of a Synthetic Mitochondrial Toxin by Increasing the Residence Time in the Cytosol', Journal of Medicinal Chemistry, vol. 52, no. 20, pp. 6209-6216.
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Djordjevic, SP, Cain, AK, Evershed, NJ, Falconer, L, Levings, RS, Lightfoot, D & Hall, RM 2009, 'Emergence and Evolution of Multiply Antibiotic-ResistantSalmonella entericaSerovar Paratyphi Bd-Tartrate-Utilizing Strains Containing SGI1', Antimicrobial Agents and Chemotherapy, vol. 53, no. 6, pp. 2319-2326.
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ABSTRACTThe first Australian isolate ofSalmonella entericaserovar Paratyphi Bd-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-resistantS. entericaserovar 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 completesul1gene but were susceptible to sulfamethoxazole due to a point mutation that creates a premature termination codon. This SGI1 type was designated SGI1-R. The loss of resistance genes also was examined. When strains were grown for many generations in the absence of antibiotic selection, the loss of SGI1 was not detected. However, variants SGI1-C (resistance profile SmSpSu) and SGI1-B (resistant to ApSu), which had lost part of the integron, arose spontaneously, presumably via homologous recombination b...

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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Du, W, K. Webb, J & Shine, R 2009, 'Heat, sight and scent: multiple cues influence foraging site selection by an ambush-foraging snake Hoplocephalus bungaroides (Elapidae)', Current Zoology, vol. 55, no. 4, pp. 266-271.
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Abstract Most mobile organisms respond to multiple cues when selecting habitat types, and laboratory experiments that manipulate only single cues may fail to reveal the true complexity of habitat-selection behaviour. In south- eastern Australia, broad headed snakes Hoplocephalus bungaroides (Elapidae) lie in wait under sun-warmed rocks to ambush velvet geckos Oedura leseuerii (Gekkonidae). Previous laboratory work has shown that both the geckos and the snakes actively select hotter rather than colder rocks, and that the snakes actively select rocks scented by geckos. We manipulated rock temperature and the presence of two types of cues from geckos (chemical and visual information) to clarify the causal basis for foraging site selection by the juveniles of this snake. When given a choice between cold lizard-scented rocks and hot unscented rocks, our captive snakes gave a higher priority to lizard scent than to temperature. The snakes also selected shelter-sites that provided visual as well as scent cues from lizards, rather than shelter-sites with scent cues alone. Thus, although broad-headed snakes show a direct preference for hotter rather than colder rocks in the laboratory, their choice of foraging site in the field may also be influenced by the presence of scent cues from prey. Our laboratory results suggest that habitat selection by broad-headed snakes may be more complex than has been suggested by previous single-factor laboratory trials.

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, UT & Rodgers, KJ 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, MP 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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AbstractMotivated 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, Sadeuh Mba, SA, 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, pp. e5520-e5520.
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Duxbury, Z, Schliep, M, Ritchie, RJ, Larkum, AWD & 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.

Edwards, PR, Hiscock, JR & Gale, PA 2009, 'Stabilisation of alkylcarbamate anions using neutral hydrogen bond donors', Tetrahedron Letters, vol. 50, no. 34, pp. 4922-4924.
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Elder, M 2009, 'A linear-time algorithm to compute geodesics in solvable Baumslag-Solitar groups', Illinois Journal of Mathematics, vol. 54, pp. 109-128.
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We present an algorithm to convert a word of length $n$ in the standardgenerators of the solvable Baumslag-Solitar group $BS(1,p)$ into a geodesicword, which runs in linear time and $O(n\log n)$ space on a random accessmachine.

Elder, M & Rechnitzer, A 2009, 'Some geodesic problems in groups', Groups. Complexity. Cryptology, vol. 2, pp. 223-229.
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We consider several algorithmic problems concerning geodesics in finitelygenerated groups. We show that the three geodesic problems considered byMiasnikov et al [arXiv:0807.1032] are polynomial-time reducible to each other.We study two new geodesic problems which arise in a previous paper of theauthors and Fusy [arXiv:0902.0202] .

Elder, M, Fusy, E & Rechnitzer, A 2009, 'Counting elements and geodesics in Thompson's group $F$', Journal of Algebra, vol. 324, pp. 102-121.
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We present two quite different algorithms to compute the number of elementsin the sphere of radius $n$ of Thompson's group $F$ with standard generatingset. The first of these requires exponential time and polynomial space, butadditionally computes the number of geodesics and is generalisable to manyother groups. The second algorithm requires polynomial time and space and allows us tocompute the size of the spheres of radius $n$ with $n \leq 1500$. Using theresulting series data we find that the growth rate of the group is boundedabove by $2.62167...$. This is very close to Guba's lower bound of$\tfrac{3+\sqrt{5}}{2}$ \cite{Guba2004}. Indeed, numerical analysis of theseries data strongly suggests that the growth rate of the group is exactly$\tfrac{3+\sqrt{5}}{2}$.

Esteban-Marcos, A, Darling, AE & Ragan, MA 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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ABSTRACT 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, M, Johengen, T & Reid, D 2009, 'Marine dinoflagellate cysts in the ballast tank sediments of ships entering the Laurentian Great Lakes', INTERNATIONAL ASSOCIATION OF THEORETICAL AND APPLIED LIMNOLOGY, VOL 30, PT. 7, PROCEEDINGS, vol. 30, no. 7, pp. 1035-1038.

Faille, D, Combes, V, Mitchell, AJ, Fontaine, A, Juhan-Vague, I, Alessi, M-C, Chimini, G, Fusaï, T & Grau, GE 2009, 'Platelet microparticles: a new player in malaria parasite cytoadherence to human brain endothelium', The 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, G 2009, 'Platelet-endothelial cell interactions in cerebral malaria: The end of a cordial understanding', Thrombosis and Haemostasis, vol. 102, no. 12, pp. 1093-1102.
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SummaryCerebral malaria is an acute encephalopathy evolving from an infection with Plasmodium falciparum which kills more than one million people each year. Brain tissues from patients who died with cerebral malaria revealed multifocal capillary obstruction by parasitised red blood cells, platelets, and leukocytes. Many studies are unified in their proposal of two major hypotheses consisting of cell adhesion to the brain endothelium and excessive immune stimulation resulting in further vascular inflammation, prothrombotic cell activation, mechanical obstruction of cerebral capillaries and, consequently, blood-brain barrier disruption. Platelets and endothelial cells communicate on multiple levels. Infection-induced changes in platelets and endothelial cells occur in cerebral malaria, resulting in their concomitant activation, increased interactions between these two cell types, and a secondary procoagulant or hypercoagulable state. Here we review evidence for these mechanisms and highlight the possible role of platelets as effectors of endothelial damage in cerebral malaria. A better understanding of the complex regulation of these various interactions between brain endothelial cells and platelets in the context of cerebral malaria may prove useful in the development of new approaches to the treatment of this disease.

Farrell, GC, Larter, CZ, Hou, JY, Zhang, RH, Yeh, MM, Williams, J, Dela Peňa, 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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AbstractBackground 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‐α‐receptor (TNF‐R)1, TNF‐R2, Fas, and TNFα‐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, 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, Malhi, Y, Bonal, D, Da Rocha, HR, De Araujo, AC, Gamo, M, Goulden, ML, Hirano, T, Huete, AR, Kondo, H, Kumagai, T, Loescher, HW, Miller, S, Nobre, AD, Nouvellon, Y, Oberbauer, SF, Panuthai, S, Roupsard, O, Saleska, S, 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 Ω 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 1370mmyr-1, but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096mmyr-1) is considered in discussion on the use of flux data to validate and interpolate models. © 2009 The Authors Journal compilation © 2009 Blackwell Publishing Ltd.

Fisher, MG, Gale, PA, Hiscock, JR, Hursthouse, MB, Light, ME, Schmidtchen, FP & Tong, CC 2009, '1,2,3-Triazole-strapped calix[4]pyrrole: a new membrane transporter for chloride', Chemical Communications, no. 21, pp. 3017-3017.
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Fisher, MG, Gale, PA, Hiscock, JR, Hursthouse, MB, Light, ME, Schmidtchen, FP & Tong, CC 2009, 'ChemInform Abstract: 1,2,3‐Triazole‐Strapped Calix[4]pyrrole: A New Membrane Transporter for Chloride.', ChemInform, vol. 40, no. 42.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Ford, M, Russo, S & Gale, J 2009, 'Proceedings of the International Conference on Nanoscience and Nanotechnology (Melbourne, 25–29 February 2008)', Journal of Physics: Condensed Matter, vol. 21, no. 14, pp. 140301-140301.
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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. 9188-9188.
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Fronzi, M, Soon, A, Delley, B, Traversa, E & Stampfl, C 2009, 'Stability and morphology of cerium oxide surfaces in an oxidizing environment: A first-principles investigation', The Journal of Chemical Physics, vol. 131, no. 10, pp. 104701-104701.
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We present density functional theory investigations of the bulk properties of cerium oxides (CeO2 and Ce2O3) and the three low index surfaces of CeO2, namely, (100), (110), and (111). For the surfaces, we consider various terminations including surface defects. Using the approach of “ab initio atomistic thermodynamics,” we find that the most stable surface structure considered is the stoichiometric (111) surface under “oxygen-rich” conditions, while for a more reducing environment, the same (111) surface, but with subsurface oxygen vacancies, is found to be the most stable one, and for a highly reducing environment, the (111) Ce-terminated surface becomes energetically favored. Interestingly, this latter surface exhibits a significant reconstruction in that it becomes oxygen terminated and the upper layers resemble the Ce2O3(0001) surface. This structure could represent a precursor to the phase transition of CeO2 to Ce2O3.

Fry, DR, McSporran, KD, 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, BGG, Burgess, JK, Moriwaki, A, Tanaka, K, Kubo, M, Hoshino, T, Tanaka, H, McKenzie, ANJ, Matsumoto, K, Aizawa, H, Nakanishi, Y, Yoshimura, A, Black, JL & 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 signaling (SOCS) family protein, a negative regulator of the Janus kinase/STAT signaling pathway, contributes to helper T cell differentiation during immune responses, the role of SOCS proteins within the structural cells of a target organ has not been clarified in allergy. Objectives: To study the local function of SOCS in the development of asthma. Methods: We used mouse models of IL-13- and ovalbumin (OVA)-induced allergic airway disease. Airway smooth muscle cells were cultured from patients with asthma. Measurements and Main Results: The administration of IL-13 induced not only airway responses but also SOCS1 expression at the local inflammatory site. The up-regulated SOCS1 markedly suppressed IL-13-dependent STAT6 activation and eotaxin expression and subsequently down-regulated IL-13-induced airway inflammatory responses. The inactivation of SOCS1 induced airway hyperresponsiveness after IL-13 treatment even in hyporesponsive C57BL/6 background mice. In an OVA-induced model of allergic airway disease, allergen exposure up-regulated local SOCS1 expression, and the induction of SOCS1 in the airways attenuated allergen-induced airway responses. Inactivation of IL-13 inhibited SOCS1 induction in a model of allergic airway disease. Interestingly, airway smooth muscle cells from individuals with asthma had impaired upregulation of SOCS1 after IL-13 stimulation. Conclusions: SOCS1 induction by IL-13 in airway structural cells is critical to negatively control allergic airway disease.

Gale, PA 2009, 'ChemInform Abstract: Synthetic Indole, Carbazole, Biindole and Indolocarbazole‐Based Receptors: Applications in Anion Complexation and Sensing', ChemInform, vol. 40, no. 1.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Gentle, AR, Smith, GB & 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, PG 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.

Godlewski, M, Wojcik-Glodowska, A, Guziewicz, E, Yatsunenko, S, Zakrzewski, A, Dumont, Y, Chikoidze, E & Phillips, MR 2009, 'Optical properties of manganese doped wide band gap ZnS and ZnO', OPTICAL MATERIALS, vol. 31, no. 12, 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. © 2009 Elsevier B.V. All rights reserved.

Goh, F, Irvine, KM, Lovelace, E, Donnelly, S, Jones, MK, Brion, K, Hume, DA, Kotze, AC, Dalton, JP, Ingham, A & Sweet, MJ 2009, 'Selective induction of the Notch ligand Jagged-1 in macrophages by soluble egg antigen from Schistosoma mansoni involves ERK signalling', IMMUNOLOGY, vol. 127, no. 3, pp. 326-337.
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Summary Soluble egg antigen (SEA) from the helminth Schistosoma mansoni promotes T helper type 2 (Th2) responses by modulating antigen-presenting cell function. The Jagged/Notch pathway has recently been implicated in driving Th2 development. We show here that SEA rapidly up-regulated mRNA and protein expression of the Notch ligand Jagged-1 in both murine bone marrow-derived macrophages (BMMs) and human monocyte-derived macrophages (HMDMs). Another potential Th2-promoting factor, interleukin (IL)-33, was not transcriptionally induced by SEA in BMMs. Up-regulation of Jagged-1 mRNA by SEA was also apparent in conventional dendritic cells (DCs), although the effect was less striking than in BMMs. Conversely, SEA-pulsed DCs, but not BMMs, promoted IL-4 production upon T-cell activation, suggesting that Jagged-1 induction alone is insufficient for instructing Th2 development. A comparison of the responses initiated in BMMs by SEA and the bacterial endotoxin lipopolysaccharide (LPS) revealed common activation of extracellular signal-regulated kinase-1/2 (ERK-1/2) and p38 phosphorylation, as well as induction of Jagged-1 mRNA. However, only LPS triggered IκB degradation, phosphorylation of c-Jun N-terminal kinase (Jnk) and signal transducer and activator of transcription 1 (Stat1) Tyr701, and IL-33 and IL-12p40 mRNA up-regulation. Inducible gene expression was modified by the presence of the macrophage growth factor colony-stimulating factor (CSF)-1, which inhibited Jagged-1 induction by SEA and LPS, but enhanced LPS-induced IL-12p40 expression. Unlike LPS, SEA robustly activated signalling in HEK293 cells expressing either Toll-like receptor 2 (TLR2) or TLR4/MD2. Pharmacological inhibition of the ERK-1/2 pathway impaired SEA- and LPS-inducible Jagged-1 expression in BMMs. Taken together, our data suggest that Jagged-1 is an ERK-dependent target of TLR signalling that has a macrophage-specific function in the response to SEA. © 2008 Blackwell Publishing Ltd.

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 & Wand, MP 2009, 'Recent Bioinformatics Advances in the Analysis of High Throughput Flow Cytometry Data', Advances in Bioinformatics, vol. 2009, pp. 1-2.
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Gou, X, Li, R, Wang, G, Chen, Z & Wexler, D 2009, 'Room-temperature solution synthesis of Bi₂O₃nanowires for gas sensing application', Nanotechnology, vol. 20, no. 49, pp. 495501-495501.
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Greenup, A, Peacock, WJ, 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, WA, Doblin, MA, Eyre, B & Steinberg, PD 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, BT, de Sterke, CM & Poulton, CG 2009, 'Modelling of photonic crystal fiber based on layered inclusions', Journal of the Optical Society of America B, vol. 26, no. 10, pp. 1852-1852.
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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. © 2009 Optical Society of America.

Gueidan, C, Savić, S, Thüs, H, Roux, C, Keller, C, Tibell, L, Prieto, M, Heiðmarsson, S, Breuss, O, Orange, A, Fröberg, L, Wynns, AA, Navarro-Rosinés, P, Krzewicka, B, Pykälä, 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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AbstractRecent molecular phylogenetic analyses and morphological studies have shown that it is necessary to revise the present morphology‐based generic delineation of the lichen family Verrucariaceae in order to account for evolutionary relatedness between species. Consequently, several genera were recently described or resurrected, and others were re‐circumscribed. As an additional step toward this generic revision, three new genera (Hydropunctaria, Parabagliettoa, Wahlenbergiella) and eleven new combinations are proposed here. A summary of the current taxonomic and morphological circumscription of all genera investigated so far is also presented. Several monophyletic groups are identified for which further taxonomical changes will be required, but for which taxon and gene sampling is presently viewed as insufficient. Clear morphological synapomorphies were found to be rare for newly delimited genera. In some cases (reduced morphology or plesiomorphism), even the combinations of slightly homoplasious phenotypic characters do not allow a clear morphological generic circumscription. Molecular features are envisioned as characters for delimiting these taxa.

Guha, S, Ryan, L & 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 squares (IWLS). High computational costs and memory space constraints make it difficult to apply these iterative procedures to datasets having a very large number of records. We propose a computationally efficient strategy based on the Gauss-Seidel algorithm that iteratively fits submodels of the GLMM to collapsed versions of the data. The strategy is applied to investigate the relationship between ischemic heart disease, socioeconomic status, and age/gender category in New South Wales, Australia, based on outcome data consisting of approximately 33 million records. For Poisson and binomial regression models, the Gauss-Seidel approach is found to substantially outperform existing methods in terms of maximum analyzable sample size. Remarkably, for both models, the average time per iteration and the total time until convergence of the Gauss-Seidel procedure are less than 0.3% of the corresponding times for the IWLS algorithm. Platform-independent pseudo-code for fitting GLMS, as well as the source code used to generate and analyze the datasets in the simulation studies, are available online as supplemental materials. © 2009 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America.

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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A reversible antimicrobial photoswitching of nanosilver using an optical wavelength-selective technique was reported. Finely dispersed nanosilver on semiconductor support (TiO2) was synthesized rapidly through a one-step flame spray pyrolysis (FSP) of silver benzoate and titanium isopropoxide co-dissolved in acetonitrile/xylene. The results show that only a very minimal extent of nanosilver particle size increase takes place during the UV-A induced reduction due to its mild an dry condition. The nanometallic silver is found to be responsive to the visible light through its surface plasmon resonance, resulting in the excitation and reverse electron flow from the silver deposits to the conduction band (CB) of TiO2. Switching-off of the sample by re-irradiating with UV-A for 40h results in fully reversible and indefinite cyclic characteristics of the Ag/TiO2.

Ha, S, Sukhorukov, AA, Dossou, KB, Botten, LC, de Sterke, CM & Kivshar, YS 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 procedure by extending the concepts of high-resolution spectral methods previously developed for temporal data series to take into account the symmetry properties of Bloch modes simultaneously at all spatial locations. We illustrate the application of our method to a photonic crystal waveguide interface and confirm its robustness in the presence of noise. © 2009 Optical Society of America.

Haapkylä, J, Seymour, AS, Barneah, O, Brickner, I, Hennige, S, Suggett, D & 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, flat and slope at six sites in 2006 and eight sites in 2007. Four of the sites were common in both years. In total 69 transects were surveyed in 2006, and 87 transects in 2007. A total of 4.8% of all observed hard corals were associated with acoel worms in 2006 and 2.6% of hard and soft corals in 2007. Acoels were present on 16 and 21 of the coral taxa studied in 2006 and 2007 respectively. The worms were strongly associated with the azooxanthellate coral Tubastrea spp. and were rare or absent on the most abundant coral genera Montipora and Porites. The mean number of corals having acoels was highest on reef slopes, whereas acoels were virtually absent on reef flats. Corals that had a high and a medium cover of worms were more common in 2007 than in 2006. No significant trend in the adaptation of the zooxanthellae of Waminoa sp. to different depths at different sites was revealed. The impact of the worm on the coral is unknown, but high numbers may have a shading effect and a negative impact on the coral's photophysiology. This acoel merits more study of its life cycle, its photophysiology, and its impact on its host corals. © 2009 Springer-Verlag.

Hagge, DA, Saunders, BM, Ebenezer, GJ, Ray, NA, Marks, VT, Britton, WJ, Krahenbuhl, JL & Adams, LB 2009, 'Lymphotoxin-α and TNF Have Essential but Independent Roles in the Evolution of the Granulomatous Response in Experimental Leprosy', The 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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Mutations in the tumour suppressor HRPT2 occur in patients with parathyroid carcinoma, kidney tumours and Hyperparathyroidism–Jaw Tumour syndrome. Disruption of exonic splicing through mutation of donor/acceptor splice sites or exonic splice enhancer (ESE) sites leads to loss of function of a number of major tumour suppressors including BRCA1, APC and MLH1. Given that the effect of HRPT2 mutations on splicing has not been widely studied, we used an in vitro splicing assay to determine whether 17 HRPT2 mutations located in hot-spot and other exons predicted to disrupt ESE consensus sites led to aberrant splicing. Using two independent web-based prediction programs, the majority of these mutations were predicted to disrupt ESE consensus sites; however, aberrant splicing of HRPT2 transcripts was not observed. Canonical donor or acceptor splice site mutations were also investigated using this splicing assay and transcripts assessed from tumour tissue. Splice site mutations were shown to lead to either exon skipping or retention of intronic sequences through the use of cryptic splice sites comprised of non-classical splicing signals. Aberrant splicing caused by disruption of ESE sites does not appear to have a major role in HRPT2-associated disease; however, premature truncation of parafibromin as the result of canonical donor or acceptor splice site mutations is associated with pathogenicity. Functional splicing assays must be undertaken in order to confirm web-based software predictions of the modification of putative ESE sites by disease-associated mutations.

Hamidian, M, Tajbakhsh, M, Walther-Rasmussen, J & Zali, M-R 2009, 'Emergence of Extended-Spectrum β-Lactamases in Clinical Isolates of <i>Salmonella enterica</i> in Tehran, Iran', Japanese Journal of Infectious Diseases, vol. 62, no. 5, pp. 368-371.
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The purpose of the current study was to investigate the presence and molecular type(s) of extended-spectrum beta-lactamases (ESBLs) in Salmonella spp. isolates obtained from patients with diarrhea in hospitals of Tehran, Iran. Over a period of 17 months, 129 Salmonella spp. were isolated from fecal samples and tested for susceptibility using the Kirby-Bauer disk diffusion method; then, screening for ESBL-producing isolates and determination of their minimum inhibitory concentrations were carried out using the combined disk method and standard agar dilution method, respectively. The presence and type of ESBL-encoding genes were determined by PCR and sequence analysis. The isolates were all identified as Salmonella enterica of different serovars. The highest resistance in the collected Salmonella isolates was to nalidixic acid (45.7%), followed by tetracycline (43.4%), trimethoprim-sulfamethoxazole (36.4%), ampicillin (15.5%), and chloramphenicol (14.7%). All the isolates were susceptible to ciprofloxacin, gentamicin, and cefoxitin. Three S. enterica isolates were resistant to ampicillin, piperacillin, ceftazidime, cefotaxime, ceftriaxone, cefpodoxime, cephalothin, and aztreonam. PCR and DNA sequencing revealed that two of the three isolates harbored both a bla(CTX-M-15) and a bla(TEM) gene while the third one carried only a bla(CTX-M-15) gene. This is the first study providing structural data for a CTX-M-type beta-lactamase produced by Salmonella isolates recovered in Iran.

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.

Hansbro, PM, Starkey, MR, Horvat, JC, Kim, RY, Phipps, S, Gibson, PG & Foster, PS 2009, 'Early life chlamydial infection enhances allergic airways disease through age-dependent differences in immunopathology (79.20)', The Journal of Immunology, vol. 182, no. 1_Supplement, pp. 79.20-79.20.
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Abstract Chlamydial respiratory tract infections are associated with the development and exacerbation of asthma in both children and adults, but the mechanisms underpinning this association remain unknown. We investigated the effect of the age of chlamydial infection on key features of asthma in later life using mouse models of Ovalbumin-induced allergic airways disease (AAD). Neonatal and infant, but not adult infection resulted in differential and permanent alterations in airway eosinophils, T-cell cytokines and dendritic cells (DCs). Infection of neonates suppressed eosinophil influx into the airways and reduced T-cell cytokine release which correlated with a significant reduction in the number and activation of DCs. In stark contrast, infant infection augmented eosinophil influx and increased T-cell cytokine release which correlated with increased DC numbers and activation. Importantly, both neonatal and infant infections enhanced physiological (mucus secreting cell hyperplasia and airways hyper-responsiveness) responses in AAD in later life, which correlated with enhanced IL-13 expression in the lung. Furthermore, neonatal infection induced substantial alterations in lung structure which was linked with increased TGF-β in lung tissue. Thus, early life infection enhances pivotal features of AAD through age dependent, differential affects on immune responses and lung structure.

Hansen, RR, Nielsen, DA, Schramm, A, Nielsen, LP, Revsbech, NP & Hansen, MN 2009, 'Greenhouse Gas Microbiology in Wet and Dry Straw Crust Covering Pig Slurry', Journal of Environmental Quality, vol. 38, no. 3, pp. 1311-1319.
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Liquid manure (slurry) storages are sources of gases such as ammonia (NH3) and methane (CH4). Danish slurry storages are required to be covered to reduce NH3 emissions and often a floating crust of straw is applied. This study investigated whether physical properties of the crust or crust microbiology had an effect on the emission of the potent greenhouse gases CH4 and nitrous oxide (N2O) when crust moisture was manipulated (“dry”, “moderate”, and “wet”). The dry crust had the deepest oxygen penetration (45 mm as compared to 20 mm in the wet treatment) as measured with microsensors, the highest amounts of nitrogen oxides (NO2− and NO3−) (up to 36 μmol g−1 wet weight) and the highest emissions of N2O and CH4 Fluorescent in situ hybridization and gene‐specific polymerase chain reaction (PCR) were used to detect occurrence of bacterial groups. Ammonia‐oxidizing bacteria (AOB) were abundant in all three crust types, whereas nitrite‐oxidizing bacteria (NOB) were undetectable and methane‐oxidizing bacteria (MOB) were only sparsely present in the wet treatment. A change to anoxia did not affect the CH4 emission indicating the virtual absence of aerobic methane oxidation in the investigated 2‐mo old crusts. However, an increase in N2O emission was observed in all crusted treatments exposed to anoxia, and this was probably a result of denitrification based on NOx− that had accumulated in the crust during oxic conditions. To reduce overall greenhouse gas emissions, floating crust should be managed to optimize conditions for methanotrophs.

Hare, D, Bishop, D, Austin, C & Doble, P 2009, 'The answer is elemental', The Biochemist, vol. 31, no. 1, pp. 46-49.
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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.

Hare, D, Burger, F, Austin, C, Fryer, F, Grimm, R, Reedy, B, Scolyer, RA, Thompson, JF & Doble, P 2009, 'Elemental bio-imaging of melanoma in lymph node biopsies', 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, D, Reedy, B, Grimm, R, Wilkins, S, Volitakis, I, George, JL, Cherny, RA, Bush, AI, Finkelstein, DI & Doble, P 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, MJ 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. © 2009 American Chemical Society.

Hart, JE, Yanosky, JD, Puett, RC, Ryan, L, Dockery, DW, Smith, TJ, 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 μm 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, high-intensity 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', The Australian Journal of Indigenous Education, vol. 38, no. S1, pp. 46-58.
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Abstract 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.

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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Objective  To identify and gain an understanding of the influenza viruses circulating in wild birds in Australia.Design  A total of 16,303 swabs and 3782 blood samples were collected and analysed for avian influenza (AI) viruses from 16,420 wild birds in Australia between July 2005 and June 2007. Anseriformes and Charadriiformes were primarily targeted.Procedures  Cloacal, oropharyngeal and faecal (environmental) swabs were tested using polymerase chain reaction (PCR) for the AI type A matrix gene. Positive samples underwent virus culture and subtyping. Serum samples were analysed using a blocking enzyme‐linked immunosorbent assay for influenza A virus nucleoprotein.Results  No highly pathogenic AI viruses were identified. However, 164 PCR tests were positive for the AI type A matrix gene, 46 of which were identified to subtype. A total of five viruses were isolated, three of which had a corresponding positive PCR and subtype identification (H3N8, H4N6, H7N6). Low pathogenic AI H5 and/or H7 was present in wild birds in New South Wales, Tasmania, Victoria and Western Australia. Antibodies to influenza A were also detected in 15.0% of the birds sampled.Conclusions  Although low pathogenic AI virus subtypes are currently circulating in Australia, their prevalence is low (1.0% positive PCR). Surveillance activities for AI in wild birds should be continued to provide further epidemiological information about circulating viruses and to identify any changes in subtype prevalence.

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.

He, L, Malcolm, AS, Dimitrijev, M, Onaizi, SA, Shen, H-H, Holt, SA, Dexter, AF, Thomas, RK & Middelberg, APJ 2009, 'Cooperative Tuneable Interactions between a Designed Peptide Biosurfactant and Positional Isomers of SDOBS at the Air−Water Interface', Langmuir, vol. 25, no. 7, pp. 4021-4026.
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Heather, A, Li, X-H, McGrath, K, Rye, K & Barter, P 2009, 'Abstract: 1066 HIGH DENSITY LIPOPROTEINS (HDLS) INDUCE A MILD OXIDATIVE STRESS RESPONSE IN HUMAN ENDOTHELIAL CELLS THAT INCREASES CELLULAR ANTIOXIDANT PROTEIN EXPRESSION AND PROTECTS AGAINST INFLAMMATORY INSULT', Atherosclerosis Supplements, vol. 10, no. 2, pp. e415-e415.
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Heather, AK, Li, XH, McGrath, KCY, Rye, KA & Barter, PJ 2009, 'HDL induces anergy to proinflammatory cytokines in endothelial cells through a mild oxidative stress response', Heart, Lung and Circulation, vol. 18, pp. S243-S243.
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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, no. 1.
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Abstract 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 ...

Hemming, MN, Fieg, S, Peacock, WJ, 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 photobiology is becoming dominated by routine assessments using state-of-the-art non-invasive bio-optical or chlorophyll a fluorescence (bio-physical) techniques. Multiple genetic types of Symbiodinium are now known to exist; however, little focus has been given as to how these types differ in terms of characteristics that are observable using these techniques. Therefore, this investigation aimed to revisit and expand upon a pivotal study by Iglesias-Prieto and Trench (1994) by comparing the photoacclimation characteristics of different Symbiodinium types based on their bio-physical (chlorophyll a fluorescence, reaction centre counts) and bio-optical (optical absorption, pigment concentrations) 'signatures'. Signatures described here are unique to Symbiodinium type and describe phenotypic responses to set conditions, and hence are not suitable to describe taxonomic structure of in hospite Symbiodinium communities. In this study, eight Symbiodinium types from clades and sub-clades (A-B, F) were grown under two PFDs (Photon Flux Density) and examined. The photoacclimation response by Symbiodinium was highly variable between algal types for all bio-physical and for many bio-optical measurements; however, a general preference to modifying reaction centre content over effective antennae-absorption was observed. Certain bio-optically derived patterns, such as light absorption, were independent of algal type and, when considered per photosystem, were matched by reaction centre stoichiometry. Only by better understanding genotypic and phenotypic variability between Symbiodinium types can future studies account for the relative taxonomic and physiological contribution by Symbiodinium to coral acclimation. © 2008 Springer-Verlag.

Herok, GH, Mudgil, P & Millar, TJ 2009, 'The Effect of Meibomian Lipids and Tear Proteins on Evaporation Rate under Controlled In Vitro Conditions', CURRENT EYE RESEARCH, vol. 34, no. 7, pp. 589-597.
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Hill, R, Ulstrup, KE & 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.

Hiscock, JR, Caltagirone, C, Light, ME, Hursthouse, MB & Gale, PA 2009, 'Fluorescent carbazolylurea anion receptors', Organic & Biomolecular Chemistry, vol. 7, no. 9, pp. 1781-1781.
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HOGG, PJ 2009, 'Contribution of allosteric disulfide bonds to regulation of hemostasis', Journal of Thrombosis and Haemostasis, vol. 7, pp. 13-16.
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Holt, SA, Le Brun, AP, Majkrzak, CF, McGillivray, DJ, Heinrich, F, Lösche, M & Lakey, JH 2009, 'An ion-channel-containing model membrane: structural determination by magnetic contrast neutron reflectometry', Soft Matter, vol. 5, no. 13, pp. 2576-2586.
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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', The Journal of Clinical Endocrinology & Metabolism, vol. 94, no. 2, pp. 434-441.
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Abstract Context: Parafibromin, encoded by HRPT2, is the first marker with significant benefit in the diagnosis of parathyroid carcinoma. However, because parafibromin is only involved in up to 70% of parathyroid carcinomas and loss of parafibromin immunoreactivity may not be observed in all cases of HRPT2 mutation, a complementary marker is needed. Objective: We sought to determine the efficacy of increased expression of protein gene product 9.5 (PGP9.5), encoded by ubiquitin carboxyl-terminal esterase L1 (UCHL1) as an additional marker to loss of parafibromin immunoreactivity for the diagnosis of parathyroid carcinoma. Design: In total, 146 parathyroid tumors and nine normal tissues were analyzed for the expression of parafibromin and PGP9.5 by immunohistochemistry and for UCHL1 by quantitative RT-PCR. These samples included six hyperparathyroidism-jaw tumor syndrome-related tumors and 24 sporadic carcinomas. Results: In tumors with evidence of malignancy, strong staining for PGP9.5 had a sensitivity of 78% for the detection of parathyroid carcinoma and/or HRPT2 mutation and a specificity of 100%. Complete lack of nuclear parafibromin staining had a sensitivity of 67% and a specificity of 100%. PGP9.5 was positive in a tumor with the HRPT2 mutation L64P that expressed parafibromin. Furthermore, UCHL1 was highly expressed in the carcinoma/hyperparathyroidism-jaw tumor syndrome group compared to normal (P &lt; 0.05) and benign specimens (P &lt; 0.001). Conclusion: These results suggest that positive staining for PGP9.5 has utility as a marker for parathyroid malignancy, with a slightly superior sensitivity (P = 0.03) and similar high specificity to that of parafibromin.

Huang, KY, Filarsky, M, Padula, MP, 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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AbstractThe 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, J, Dawson, M, Roux, C & 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, Joël Bertrand, PM, Honoré, FK, Odette, Z, Salomé, N, Valéry, C, Georges, GE & Paul Henri, AZ 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 & Reza Zali, M 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, pp. e56-e62.
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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 tetra‐cycline, 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.

Jambou, R, El-Assaad, F, Combes, V & Grau, GE 2009, 'Citicoline (CDP-choline): What role in the treatment of complications of infectious diseases', The International Journal of Biochemistry & Cell Biology, vol. 41, no. 7, pp. 1467-1470.
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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 μ-targets in high-background biosamples', Journal of Biomedical Optics, vol. 14, no. 2, pp. 024023-024023.
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Jin, D, Rong, Y, Lou, W, Qin, X, Wu, W, Nin, X, Nin, X, Wang, D, Kuang, T & Qin, Y 2009, 'Therapeutic vaccination against advanced pancreatic cancer by autologous dendritic cells pulsed with a MUC1 peptide: Preclinical results of a clinical phase I trial', Journal of Clinical Oncology, vol. 27, no. 15_suppl, pp. e15652-e15652.
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e15652 Background: Pancreatic ductal adenocarcinoma has a particularly poor prognosis. Therefore, novel therapeutic strategies such as immunotherapy are required. The aim of the present phase I study was to evaluate the safety, immune responses and clinical activity of a vaccine based on autologous dendritic cells (DC) pulsed with a specific MUC1 peptide in advanced pancreatic cancer patients. Methods: Five patients who had pancreatic cancer ductal adenocarcinoma expressing MUC1 in stage of III/IV were enrolled to the clinical trial. Patients underwent leukapheresis to generate dendritic cells by culture in vitro with granulocyte macrophage colony-stimulating factor and interleukin-4 for 5 days. Dendritic cells were then pulsed overnight with MUC1 peptide (GVTSAPDTRPAPGSTAPPAH) and harvested for vaccination. Dendritic cells (3×106-6×106) were injected intradermally every 2 weeks for 3–4 times. Results: All patients remained with progressive disease. Four patients developed strong T-cell IFN-γ and Granzyme B Elispot responses to the vaccine. Most interestingly, the patient who was treated with the highest number of DC(6×106) had more number of CTL than other patients and showed delayed-type hypersensitivity responses at injection sites and this patient stopped application of the analgetics. Another patient with relapsed pancreatic cancer who had finished the 4 times of vaccination and then followed 6 times of chemotherapy with Gemcitabine had a surprisingly long term of survival of 12 month. No evidence of significant treatment related toxicity or auto-immunity was observed. Conclusions: This study showed the safety and clinical response of MUC1 peptide-pulsed dendritic cell therapy for patients with advanced pancreatic cancer. It confirms the capability of this DC vaccine to stimulate an immune response in patients with pancreatic cancer even in the presence of a l...

Jin, H, Liu, X, Wang, X, Lam, EKY, Shin, VY, Cheng, YY, Lam, YW, Yu, J, Chan, FKL & Sung, JJ 2009, 'M1976 Warburg Effect Revisited: An Epigenetic Link Between Aerobic Glycolysis and Gastric Carcinogenesis', Gastroenterology, vol. 136, no. 5, pp. A-459.
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Jin, XL, Chandrakanthan, V, Morgan, HD & O'Neill, C 2009, 'Preimplantation Embryo Development in the Mouse Requires the Latency of TRP53 Expression, Which Is Induced by a Ligand-Activated PI3 Kinase/AKT/MDM2-Mediated Signaling Pathway', BIOLOGY OF REPRODUCTION, vol. 80, no. 2, pp. 286-294.
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Jin, XL, Chandrakanthan, V, Morgan, HD & O'Neill, C 2009, 'Preimplantation Embryo Development in the Mouse Requires the Latency of TRP53 Expression, Which Is Induced by a Ligand-Activated PI3 Kinase/AKT/MDM2-Mediated Signaling Pathway (vol 80, pg 286, 2009)', BIOLOGY OF REPRODUCTION, vol. 81, no. 1, pp. 233-242.
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Jones, AC, Arns, CH, Hutmacher, DW, Milthorpe, BK, Sheppard, AP & Knackstedt, MA 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 ∼100 μm is observed for ingrowth. The elastic properties of different types of scaffolds are simulated and can be described by standard cellular solids theory: (E/E0) = (ρ/ρs)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. Crown Copyright © 2008.

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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AbstractABC 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 γ‐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. Proteins 2009. © 2008 Wiley‐Liss, Inc.

Jones, PM, O’Mara, ML & 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.

Kabakova, IV, Corcoran, B, Bolger, JA, de Sterke, M & Eggleton, BJ 2009, 'All-optical self-switching in optimized phase-shifted fiber Bragg grating', Optics Express, vol. 17, no. 7, pp. 5083-5083.
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Kamal, MA, 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 Alzheimer's 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-α, 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-α 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-α 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'. © 2009 Springer Science+Business Media, LLC.

Kaneez, FS & Saeed, SA 2009, 'Investigating GABA and its function in platelets as compared to neurons', Platelets, vol. 20, no. 5, pp. 328-333.
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We have recently suggested that platelets could be used as a model for neuronal receptors. In this paper we have investigated γ-aminobutyric acid (GABA) metabolism and GABA receptors in platelets and in cultured neurons to see whether platelets' GABA mimics neuronal GABA receptor activities. We used the ELISA technique for detecting the GABA concentration in platelet rich plasma and cultured neurons. The functional effects of GABA and its receptor ligands on platelets were determined using an aggregometer. We found that the GABA concentration is 30% lower in platelets than in neurons and in both preparations GABA was metabolized by GABA transaminase (GABA-T). GABA potentiated calcium dependent platelet aggregation with a higher value in washed platelets suspension (WPS) then in platelet rich plasma (PRP). This effect was inhibited by benzodiazepines, calcium channel blockers and the selective phosphoinositide 3-kinase antagonist Wortmannin. GABA neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. We concluded that platelets could be further developed to be used as a peripheral model to study neuronal GABAergic function and its abnormality in diseases such as epilepsy and schizophrenia. Furthermore our results indicated that PI3-kinase is involved in calcium dependent GABA induced platelet aggregation as this synergistic effect is inhibited by Wortmannin in dose dependent manner. © 2009 Informa Healthcare Ltd.

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. © Cambridge University Press 2009.

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, ML, Hoffman, E, Hsueh, Y-M, Afroz, S, Quamruzzaman, Q, Rahman, M, Mahiuddin, G, Ryan, L & Christiani, DC 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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Background: Urinary arsenic metabolites (UAs) are used as biomarkers of exposure and metabolism. Ojectives: To characterize inter- and intraindividual variability in UAs 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 UAs 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 LiNi 1/3Mn1/3Co1/3O2 cathode materials', Journal of New Materials for Electrochemical Systems, vol. 12, no. 4, pp. 207-212.
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A Sn phosphate was successfully coated to the surface of LiNi 1/3Co1/3Mn1/3O2 particles using a new method we developed. The elements Sn and P were observed to be uniformly distributed on the surface of the LiNi1/3Co1/3Mn 1/3O2 After the Sn phosphate coating, the onset temperature shifted up to about 250 °C, 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 LiNi1/3Co 1/3Mn1/3O2materials was enhanced at room temperature and 60 °C. 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 °C. It is believed that the oxide coating layer prevented direct contact with the organic electrolyte. © J. New Mat. Electrochem. Systems.

Kim, JJY, Xiao, H, Tan, Y, Wang, Z-Z, Paul Seale, J & 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. 06, 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 μg/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 μg/ml of SPN increased glucose uptake by 64% (p < 0.001). Immunofluorescence imaging and analysis have revealed that 50 and 100 μg/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 μg/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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SummaryDietary assessment of episodically consumed foods gives rise to nonnegative data that have excess zeros and measurement error.Tooze et al.(2006, Journal of the American Dietetic Association 106, 1575–1587) describe a general statistical approach (National Cancer Institute method) for modeling such food intakes reported on two or more 24‐hour recalls (24HRs) and demonstrate its use to estimate the distribution of the food's usual intake in the general population. In this article, we propose an extension of this method to predict individual usual intake of such foods and to evaluate the relationships of usual intakes with health outcomes. Following the regression calibration approach for measurement error correction, individual usual intake is generally predicted as the conditional mean intake given 24HR‐reported intake and other covariates in the health model. One feature of the proposed method is that additional covariates potentially related to usual intake may be used to increase the precision of estimates of usual intake and of diet‐health outcome associations. Applying the method to data from the Eating at America's Table Study, we quantify the increased precision obtained from including reported frequency of intake on a food frequency questionnaire (FFQ) as a covariate in the calibration model. We then demonstrate the method in evaluating the linear relationship between log blood mercury levels and fish intake in women by using data from the National Health and Nutrition Examination Survey, and show increased precision when including the FFQ information. Finally, we present simulation results evaluating the performance of the proposed method in this context.

Klein, J-M, Hénault, 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 & Devers, T 2009, 'Nanostructured Metal Oxides as Electrode Materials for Electrochemical Capacitors', Journal of Nanoscience and Nanotechnology, vol. 9, no. 2, pp. 1263-1267.
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In this study; nanostructured transition metal oxides, such as Co304, NiO and Mn02 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 m2Ig. The high surface area is a compulsory condition for high capacitance. The best Mn02 materials yielded up to 406 F/g. Copyright © 2009 American Scientific Publishers All rights reserved.

Kreiner, M, Chillakuri, CR, Pereira, P, Fairhead, M, Li, Z, Mardon, HJ, Holt, SA & van der Walle, CF 2009, 'Orientation and surface coverage of adsorbed fibronectin cell binding domains and bound integrin α5β1 receptors', Soft Matter, vol. 5, no. 20, pp. 3954-3954.
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Krimmer, DI, Loseli, M, Hughes, JM, Oliver, BGG, 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-α) and interferon-gamma (IFN-γ) on ASM CD40 and OX40L expression. Methods: CD40 and OX40L expression on human ASM cells from asthmatic and nonasthmatic donors following stimulation with TNF-α and/or IFN-γ 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-γ and TNF-α synergistically increased CD40 expression to a greater extent on asthmatic than on nonasthmatic ASM. In contrast, IFN-γ reduced TNF-α-induced OX40L expression to a similar extent in both cell types. TNF-α and IFN-γ induced CD40 via nuclear factor-κB (NF-κB) and signal transducer and activator of transcription-3 in both cell types and modulated OX40L via NF-κB and c-Jun N terminal kinase in nonasthmatic cells. Similar effects on the induction of OX40L in asthmatic cells were seen with NF-κB, but these were not statistically significant. The reduced OX40L expression with TNF-α and IFN-γ 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-γ may regulate ASM pro-inflammatory actions by differentially modulating ASM CD40 and OX40L expression. © 2009 Blackwell Munksgaard.

Kropinski, AM, Borodovsky, M, Carver, TJ, Cerdeño-Tárraga, AM, Darling, A, Lomsadze, A, Mahadevan, P, Stothard, P, Seto, D, Domselaar, G & Wishart, DS 2009, 'In Sffamily 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.

KUANG, TT, JIN, DY, WANG, DS, XU, XF, NI, XL, WU, WC & LOU, WH 2009, 'Clinical epidemiological analysis of the relationship between pancreatic cancer and diabetes mellitus: Data from a single institution in China', Journal of Digestive Diseases, vol. 10, no. 1, pp. 26-29.
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OBJECTIVE:  To investigate the relationship between pancreatic cancer (PC) and diabetes mellitus.METHODS:  All PC patients diagnosed and treated at Zhongshan hospital from January 1991 to December 2007 were retrospectively analyzed. During this period, 770 non‐digestive tract, non‐neoplastic and non‐hormone‐related patients matched for sex and age were collected as controls. The incidence of diabetes mellitus between the two groups was compared.RESULTS:  Between the PC group and the control group, sex and age of the patients were well matched. The incidence of diabetes mellitus was 34.63% in the PC group and 8.83% in the control group (P < 0.001, RR = 5.19). In the PC group there was no correlation between age, sex, site of the cancer, tumor differentiation, lymph node metastasis, TNM staging and the incidence of diabetes mellitus. In this group with diabetes, 74.56% experienced onset within two years of cancer diagnosis. Of the control patients, 57.35% had had diabetes for under 2 years (P = 0.009, RR = 2.18). In the PC group with diabetes, 5.9% had had diabetes for more than 10 years while compared with 8.8% of the controls (P = 0.42).CONCLUSION:  Whether diabetes mellitus is a result of or a risk factor for PC is still unclear. The incidence of diabetes mellitus is much higher in the PC patients. The onset of diabetes mellitus in adults might be an alerting factor that could lead to an early diagnosis of pancreatic cancer.

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, no. D9.
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Central eastern Australia is a major global source region for atmospheric dust. Time series of surface dust observations show that a striking multidecadal oscillation of dust frequency has occurred in this large region since the late 1950s. From 1959 to 1973, there was a pronounced and consistent dust maximum, after which a sharp decline was followed by a much more dust‐free 1977–2006. Time series of surface and 925 hPa (∼725 m) winds reveal that the dust oscillation was associated locally with strengthening and then weakening of the southerly component of the low level wind over the dust‐prone region. Composite maps for 1959–1973 (dusty) and 1977–2006 (more dust‐free) indicate that these local wind changes reflected the relative speed of the southerly‐southeasterly airflow into southeastern Australia. Correlation analyses show that this multidecadal regional wind oscillation was associated with similar timescale changes in the behavior of the Pacific climate system, including the latitudinal displacement of the South Pacific Convergence Zone, and more remotely with the sea surface temperature changes of the Pacific Decadal Oscillation (tropical North Pacific and extratropical North‐Northeast Pacific) and North Pacific Oscillation (central subtropical North Pacific). Further correlation analyses suggest these Pacific climate system oscillations modulated other key environmental conditions (cloud regime, sunshine duration, rainfall rate) across the Southwest Pacific, including northern New Zealand sunshine.

Lanyon, BP & Langford, NK 2009, 'Experimentally generating and tuning robust entanglement between photonic qubits', New Journal of Physics, vol. 11, no. 1, pp. 013008-013008.
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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, Marqués, R & Kivshar, Y 2009, 'Structural tunability in metamaterials', Applied Physics Letters, vol. 95, no. 8, pp. 084105-084105.
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We propose an efficient approach for tuning the transmission characteristics of metamaterials through a continuous adjustment of the lattice structure and confirm it experimentally in the microwave range. The concept is rather general and applicable to various metamaterials as long as the effective medium description is valid. The demonstrated continuous tuning of a metamaterial response is highly desirable for a number of emerging applications of metamaterials, including sensors, filters, and switches, realizable in a wide frequency range.

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, vol. 106, no. 37, pp. 15527-15533.
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Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.

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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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.

Lee, KA, Lozan, V, Langford, SJ & Kersting, B 2009, 'Ternary complexes composed of naphthalene diimides and binucleating metallocavitands: preparation, characterisation and structure of [(Ni2L)2(NDI)][BPh4]2', Dalton Transactions, no. 36, pp. 7481-7481.
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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, pp. 024022-024022.
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Leong, GWS, Gorrie, CA, Ng, K, Rutkowski, S & Waite, PME 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 spinal cord injuries unit. Methods: Cutaneous electrical stimulation of 4 dermatomes at ASIA sensory key points (C3, T1, L3, and S2) was performed on 40 control subjects. The lowest ascending stimulus intensity at which sensation was perceived was recorded as the EPT. Mean EPT values for each dermatome, as determined by 2 testers at 2 time points, were examined and plotted against a normative template. Differences and associations between intra- and inter-rater measurements and left-right measurements were studied. EPT results for 2 people with spinal cord injuries were also examined. Results: EPT measurements from left and right sides, obtained from the 2 time points and 2 testers, were found to be strongly associated, with the exception of left and right side measurements at the S2 dermatome. No significant differences in the mean EPT for tester or time period were found. The intra- and inter-rater reliability was good for all dermatomes tested. Mean EPT measurements fell within the range of a normative template at each of the 4 dermatomes tested. Conclusion: EPT is an objective, reproducible, and quantifiable method of assessing sensation in a control group. However, caution should be applied in certain dermatomes such as S2, where there was large variation between left and right side measurements. © 2009 by the American Paraplegia Society.

Lessard, BD, Wallman, JF & Dowton, M 2009, 'Incorrect report of cryptic species within Chrysomya rufifacies (Diptera:Calliphoridae)', Invertebrate Systematics, vol. 23, no. 6, pp. 507-507.
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Chrysomya rufifacies is an ecologically and forensically important blowfly, widespread in Australasia, the Orient and the Americas. The recent molecular studies of Wallman et al. (2005) showed significant levels of nucleotide divergence between Australian populations of this species based on the cytochrome oxidase subunit two (COII) gene, suggesting that Ch. rufifacies is in fact two species. The present study used COII to verify the existence of these two putative species. A 642-bp fragment of COII was sequenced from 37 specimens sampled from 35 diverse Australian geographical locations and analysed using the Kimura-two-parameter distance model and Bayesian methods. Surprisingly, all Ch. rufifacies sequences demonstrated typical levels of mean intraspecific variation (mean = 0.042%, range = 0.000–0.315%, standard error = 0.003) and were resolved as a monophyletic group on the Bayesian tree. Reassessment of the original COII data of Wallman et al. (2005) showed that the high nucleotide divergence within Ch. rufifacies was attributed to two COII sequences actually derived from specimens of Lucilia porphyrina. Ultimately, this study does not support the hypothesis that Australian Ch. rufifacies comprises two cryptic species but instead confirms its existing status as a single taxon.

Lim, CED, Wilkinson, JM, Wong, WSF & Cheng, NCL 2009, 'Effect of Acupuncture on Induction of Labor', The Journal of Alternative and Complementary Medicine, vol. 15, no. 11, pp. 1209-1214.
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Lim, CED, Yii, MF, Cheng, NCL & Kwan, YKM 2009, 'The role of micronutrients in pregnancy.', Aust Fam 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 & Wong, V 2009, 'Menopausal Syndrome', Journal of Complementary Medicine, vol. 8, no. 2, pp. 55-57.
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• Menopausal women often suffer from different symptoms, including vasomotor flushes • Oestrogen-only HRT currently remains the gold standard for relief of menopausal symptoms • Short-term HRT may be beneficial in the management of moderateto- severe vasomotor flushes but long-term use is no longer recommended • Menstruation is related to the functions of the Penetrating and Conception vessels in traditional Chinese medicine • Menopause occur when the Conception meridian becomes depleted and deficient, the blood in the Penetrating meridian is exhausted, and menstruation ceases • 50-75% of postmenopausal women use alternative therapies for management of menopausal symptoms.

Lim, DCE, Cheng, LNC & Wong, FWS 2009, 'Could it be Henoch-Schonlein purpura?', Aust Fam 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, Liu, JP, Chen, W & Cheng, LNC 2009, 'Acupuncture for polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, no. 2.
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Liong, E, McGrath, K, Tan, J, Li, X-H, Dy, V, Barter, P, Rye, K & Heather, A 2009, 'Abstract: 1510 ROLE OF 3B-HYDROXYSTEROID-[DELTA]24 REDUCTASE IN MEDIATING THE ANTI-INFLAMMATORY EFFECTS OF HIGH-DENSITY LIPOPROTEINS IN ENDOTHELIAL CELLS', Atherosclerosis Supplements, vol. 10, no. 2, pp. e464-e464.
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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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α-Fe2O3 nanorods were synthesized by a facile hydrothermal method. The as-prepared α-Fe2O3 nanorods have a high quality crystalline nanostructure with diameters in the range of 60-80 nm and lengths extending from 300 to 500 nm. The crystal structure of the α-Fe2O3 nanorods was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The α-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 α-Fe2O3 powders. © 2008 Elsevier Ltd. All rights reserved.

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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Liu, X, Jin, H, Lam, EK, Wang, X, Lam, YW, Cheng, YY, Yu, J, Chan, FKL & Sung, JJ 2009, '1089 Promoter Hypermethylation Mediates Downregulation of Thiamin Receptor SLC19A3 But Not SLC19A2 in Gastric Cancer', Gastroenterology, vol. 136, no. 5, pp. A-168.
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Liu, X, Lam, EKY, Wang, X, Zhang, J, Cheng, YY, Lam, YW, Ng, EKO, Yu, J, Chan, FKL, Jin, H & Sung, JJY 2009, 'Promoter Hypermethylation Mediates Downregulation of Thiamine Receptor SLC19A3 in Gastric Cancer', Tumor Biology, vol. 30, no. 5-6, pp. 242-248.
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Lobo, GP, Waite, KA, Planchon, SM, Romigh, T, Nassif, NT & 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. © 2009 The Author(s).

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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AbstractThe 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. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009

Lowther, J, Robinson, MW, Donnelly, SM, Xu, W, Stack, CM, Matthews, JM & 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 ∼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 ∼45% activity when incubated at 37°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. © 2009 Lowther et al.

Luo, M, Platten, D, Chaudhury, A, Peacock, WJ & 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 ESC-like 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, B 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 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.

Machado, A, Wu, Y, Yang, Y, Llewellyn, DJ & 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 non-transgenic 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. © 2009 Blackwell Publishing Ltd.

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. © 2009 Optical Society of America.

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, no. 1, pp. 75-96.
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SummaryMotivated from the problem of testing for genetic effects on complex traits in the presence of gene–environment interaction, we develop score tests in general semiparametric regression problems that involves Tukey style 1 degree-of-freedom form of interaction between parametrically and non-parametrically modelled covariates. We find that the score test in this type of model, as recently developed by Chatterjee and co-workers in the fully parametric setting, is biased and requires undersmoothing to be valid in the presence of non-parametric components. Moreover, in the presence of repeated outcomes, the asymptotic distribution of the score test depends on the estimation of functions which are defined as solutions of integral equations, making implementation difficult and computationally taxing. We develop profiled score statistics which are unbiased and asymptotically efficient and can be performed by using standard bandwidth selection methods. In addition, to overcome the difficulty of solving functional equations, we give easy interpretations of the target functions, which in turn allow us to develop estimation procedures that can be easily implemented by using standard computational methods. We present simulation studies to evaluate type I error and power of the method proposed compared with a naive test that does not consider interaction. Finally, we illustrate our methodology by analysing data from a case–control study of colorectal adenoma that was designed to investigate the association between colorectal adenoma and the candidate gene NAT2 in relation to smoking history.

Makuc, D, Lenarčič, M, Bates, GW, Gale, PA & Plavec, J 2009, 'Anion-induced conformational changes in 2,7-disubstituted indole-based receptors', Organic & Biomolecular Chemistry, vol. 7, no. 17, pp. 3505-3505.
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Manso-Silvan, L, Vilei, EM, Sachse, K, Djordjevic, SP, Thiaucourt, F & Frey, J 2009, 'Mycoplasma leachii sp. nov. 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 subsp. capri', INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol. 59, no. 6, 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.

Maric, S, Donnelly, SM, Robinsin, MW, Skinner-Adams, T, Trenholme, KR, Gardiner, DL, 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 a 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 1 is readily exchangeable with several divalent metal ions and displays a preference in the order of preference Zn 2+ > Mn 2+ > Co 2+ > Mg 2+. While it is likely that native PfLAP contains a Zn 2+ 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. © 2009 American Chemical Society.

Mark Moore, C, Mills, MM, Achterberg, EP, Geider, RJ, LaRoche, J, Lucas, MI, McDonagh, EL, Pan, X, Poulton, AJ, Rijkenberg, MJA, Suggett, DJ, Ussher, SJ & Woodward, EMS 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. A number of factors, including iron limitation, can restrict nitrogen fixation, introducing the potential for decoupling of nitrogen inputs and losses. 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. 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 surface waters 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, and that subsequent interactions with ocean circulation patterns contribute to the decoupling of nitrogen fixation and loss. © 2009 Macmillan Publishers Limited. All rights reserved.

Martelli, C, Canning, J, Reimers, JR, Sintic, M, Stocks, D, Khoury, T & Crossley, MJ 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) [CI-Sn(THP)-CI] 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 CI-Sn(THP)-CI 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. © 2009 American Chemical Society.

Martin, JL, Lin, MZ, McGowan, EM & Baxter, RC 2009, 'Potentiation of Growth Factor Signaling by Insulin-like Growth Factor-binding Protein-3 in Breast Epithelial Cells Requires Sphingosine Kinase Activity', Journal of Biological Chemistry, vol. 284, no. 38, pp. 25542-25552.
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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, SS 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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SummaryFemale 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 number of different mechanisms. Using the 2003 data from the Kenyan Demographic and Health Survey (KDHS), this study investigates the potential association between FGC and HIV. The 2003 KDHS provides a unique opportunity to link the HIV test results with a large number of demographic, social, economic and behavioural characteristics of women, including women's FGC status. It is hypothesized that FGC increases the risk of HIV infection if HIV/AIDS is present in the community. A multilevel binary logistic regression technique is used to model the HIV status of women, controlling for selected individual characteristics of women and interaction effects. The results demonstrate evidence of a statistically significant association between FGC and HIV, after controlling for the hierarchical structure of the data, potential confounding factors and interaction effects. The results show that women who had had FGC and a younger or the same-age first-union partner have higher odds of being HIV positive than women with a younger or same-age first-union partner but without FGC; whereas women who had had FGC and an older first-union partner have lower odds of being HIV positive than women with an older first-union partner but without FGC. The findings suggest the behavioural pathway of association between FGC and HIV as well as an underlying complex interplay of bio-behavioural and social variables being important in disentangling the association between FGC and HIV.

Matic, JN, Terry, TD, Van Bockel, D, Maddocks, T, Tinworth, D, Jennings, MP, Djordjevic, SP & Walker, MJ 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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ABSTRACT Live-vaccine delivery systems expressing two model antigens from Mycoplasma hyopneumoniae , F2 P97 (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 witho...

Matthews, Z, Padmadas, SS, Hutter, I, McEachran, J & Brown, J 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, P, Jenkins, J, Edey, C, Payne, G, Lennard, C, McDonagh, A & Roux, C 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 650-1100nm. 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.

Mbere‐Nguyen, U, Ung, AT & Pyne, SG 2009, 'ChemInform Abstract: The Synthesis of Carbon‐Linked Bisbenzylisoquinolines via Ruthenium‐Mediated Olefin‐Metathesis.', ChemInform, vol. 40, no. 46.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

McCracken, JP, Schwartz, J, Bruce, N, Mittleman, M, Ryan, LM & Smith, KR 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 are often imprecise due to within-subject variability, group-level measures tend to be inaccurate due to residual between-subject variability within groups. Rather than choose between these error-prone estimates, we borrow strength from each by use of mixed-model prediction and we compare the predictive validity. METHODS: We compared alternative measures of long-term exposure to carbon monoxide (CO) among children in the RESPIRE woodstove randomized control trial during years 2003 and 2004. The main study included 1932 repeated 48-hour-average personal CO measures among 509 children from 0-18 months of age. We used a validation study with additional CO measures among a random subsample of 70 of the children to compare the predictive validity of individual-level estimates (based on observed short-term exposures), group-level estimates (based on stove type and other residential characteristics), and mixed-model predictions that combine these 2 sources of information. RESULTS: The estimated error variance for mixed-model prediction was 63% lower than the individual-level measure based on the exposure data and 58% lower than the corresponding group-level measure. CONCLUSIONS: When both individual- and group-level estimates are available but imperfect, mixed-model prediction may provide substantially better measures of long-term exposure, potentially increasing the sensitivity of epidemiologic studies to underlying causal relations. © 2009 Lippincott Williams & Wilkins, Inc.

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, KR, Teuscher, F, Donnelly, SM, Grembecka, J, Mucha, A, Kafarski, P, DeGori, R, Buckle, AM, Gardiner, DL, Whisstock, JC & 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[CH 2]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. © 2009 by The National Academy of Sciences of the USA.

McGrath, KCY, Li, XH, Puranik, R, Liong, EC, Tan, JTM, Dy, VM, DiBartolo, BA, Barter, PJ, Rye, KA & Heather, AK 2009, 'Role of 3β-Hydroxysteroid-Δ24 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 cells (HCAECs) were exposed to reconstituted HDLs (rHDLs) for 16 hours before being activated with tumor necrosis factor-α (TNF-α) for 5 hours. rHDLs decreased vascular cell adhesion molecule-1 (VCAM-1) promoter activity by 75% ( P <0.05), via the nuclear factor-kappa B (NF-κB) binding site. rHDLs suppressed the canonical NF-κB pathway and decreased many NF-κB target genes. Suppression of NF-κB and VCAM-1 expression by rHDLs or native HDLs was dependent on an increase in 3β-hydroxysteroid-Δ24 reductase (DHCR24) levels ( P <0.05). The effect of HDLs on DHCR24 is dependent on SR-BI but not ABCAI or ABCGI. Silencing DHCR24 expression increased NF-κB (1.2-fold, P <0.05), VCAM-1 (30-fold, P <0.05), and NF-κB p50 (4-fold, P <0.05) and p65 subunits (150-fold, P <0.05). TNF-α activation of siDHCR24-treated cells increased expression of VCAM-1 (550-fold, P <0.001) and NF-κB (9-fold, P <0.001) that could no longer be suppressed by rHDLs. Conclusions—

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, vol. 80, no. 2.
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© 2009 The American Physical Society. 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, 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.', Phys Rev E Stat Nonlin Soft Matter Phys, 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, N-AP, 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, JD, Missmer, SA, Altshul, L, Vitonis, AF, Ryan, L, Cramer, DW & Hauser, R 2009, 'Serum and follicular fluid organochlorine concentrations among women undergoing assisted reproduction technologies', ENVIRONMENTAL HEALTH, vol. 8, no. 32, pp. 32-10.
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BACKGROUND: Exposure to persistent organic pollutants, including polychlorinated biphenyls (PCBs) and organochlorine pesticides, is widespread among the general population. There is evidence of adverse effects on reproduction and early pregnancy in relation to organochlorine exposure but human studies remain limited. The increased use of assisted reproductive technologies (ART) presents unique opportunities for the assessment of environmental influences on early pregnancy outcomes not otherwise observable in humans, but studies need to be designed to maximize the efficiency of the exposure data collected while minimizing exposure measurement error. METHODS: The present study was conducted to assess the correlation between concentrations of organochlorines in serum and follicular fluid samples collected from a subset of women undergoing ART in a large study that took place between 1994 and 2003, as well as the temporal reliability of serum organochlorine concentrations among women undergoing multiple ART cycles in the study. PCB congeners (118, 138, 153, and 180), 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (p,p'-DDT), the DDT metabolite p,p'-DDE, hexachlorobenzene (HCB), oxychlordane, trans-nonachlor and mirex were measured in 72 follicular fluid samples and 265 serum samples collected from 110 women. RESULTS: Organochlorine concentrations in paired serum and follicular fluid samples were correlated, with Pearson and Spearman coefficients ranging from 0.60 to 0.92. Serum organochlorine concentrations were two- to three-fold greater than in follicular fluid, and a significant inverse trend was observed in the distribution of follicular fluid:serum ratios with increasing molecular weight of the compound (p-value for trend < 0.0001). Serum organochlorine concentrations were highly reliable over the course of several months, with intraclass correlation coefficients ranging from 0.86 to 0.98. Finally, there was evidence for a declining trend in organochlor...

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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Abstract Tornadoes often strike as isolated events, but many occur as part of a major outbreak of tornadoes. Nontornadic outbreaks of severe convective storms are more common across the United States but pose different threats than do those associated with a tornado outbreak. The main goal of this work is to distinguish between significant instances of these outbreak types objectively by using statistical modeling techniques on numerical weather prediction output initialized with synoptic-scale data. The synoptic-scale structure contains information that can be utilized to discriminate between the two types of severe weather outbreaks through statistical methods. The Weather Research and Forecast model (WRF) is initialized with synoptic-scale input data (the NCEP–NCAR reanalysis dataset) on a set of 50 significant tornado outbreaks and 50 nontornadic severe weather outbreaks. Output from the WRF at 18-km grid spacing is used in the objective classification. Individual severe weather parameters forecast by the model near the time of the outbreak are analyzed from simulations initialized at 24, 48, and 72 h prior to the outbreak. An initial candidate set of 15 variables expected to be related to severe storms is reduced to a set of 6 or 7, depending on lead time, that possess the greatest classification capability through permutation testing. These variables serve as inputs into two statistical methods, support vector machines and logistic regression, to classify outbreak type. Each technique is assessed based on bootstrap confidence limits of contingency statistics. An additional backward selection of the reduced variable set is conducted to determine which variable combination provides the optimal contingency statistics. Results for the contingency statistics regarding the verification of discrimination capability are best at 24 h; at 48 h, modest degradation is present. By 72 h, the contingency statistics...

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, 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, pp. 1-10.
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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-γ, 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-γ 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. © 2009 Miller et al.

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, pp. e5692-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.

Miura, T & Huete, AR 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 post- flight 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. The performances of the CP method in retrieving accuratez reflectance factors were consistent throughout time of day and for various flight durations. Based on the dataset analyzed in this study, the uncertainty of the CP method has been estimated to be 0.0025 ± 0.0005 reflectance units for the wavelength regions not affected by atmospheric absorptions. The RM method can produce reasonable results only for a very short-term flight (e.g., < 15 minutes) conducted around a local solar noon. The flight duration should be kept shorter than 30 minutes for the LI method to produce results with reasonable accuracies. ...

Monahan, LG, Robinson, A & Harry, EJ 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. © 2009 Blackwell Publishing Ltd.

Moody, SJ, Phillips, MR & Toth, M 2009, 'Assessment of SEM Image Quality using 1D Power Spectral Density Estimation', Microscopy and Microanalysis, vol. 15, no. S2, pp. 48-49.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009

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. © 2009 Optical Society of America.

Moriya, S, Kawai, Y, Kaji, S, Smith, A, Harry, EJ & Errington, J 2009, 'Effects of oriC relocation on control of replication initiation in Bacillus subtilis', Microbiology, vol. 155, no. 9, pp. 3070-3082.
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In bacteria, DNA replication initiation is tightly regulated in order to coordinate chromosome replication with cell growth. InEscherichia 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 bacteriumBacillus 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. WhenoriCwas 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 twooriC-relocated strains (oriCatargGorpnbA, 25 ° or 30 ° on the 36 ° 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 nativeoriClocus.

Morris, MJ & 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, Physical and Engineering Sciences, 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.

Moxon, JV, Padula, MP, Herbert, BR & Golledge, J 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, no. 3, pp. 346-355.
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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, pp. O1878-U3157.
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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, S, Ip, CL-C, 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, MK & Gonsalvez, CJ 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 HumanChlamydia pneumoniaeWas Zoonotically Acquired', Journal of Bacteriology, vol. 191, no. 23, pp. 7225-7233.
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ABSTRACTZoonotic infections are a growing threat to global health.Chlamydia pneumoniaeis a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease.C. pneumoniaewas first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species ofChlamydia,C. pecorumandC. pneumoniae. Transmission ofC. pneumoniaebetween animals and humans has not been reported; however, two other chlamydial species,C. psittaciandC. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain ofC. pneumoniae(LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates ofC. pneumoniaeshow that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) ofC. pneumoniaewhich adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.

Naumann, U & Wand, MP 2009, 'Automation in high‐content flow cytometry screening', Cytometry Part A, vol. 75A, no. 9, pp. 789-797.
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AbstractHigh‐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. © 2009 International Society for Advancement of Cytometry

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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AbstractThe correct identification of forensically important arthropods for post‐mortem interval estimation is crucial, as the rate of larval development can vary substantially between species. The identification of forensically important blowflies of the genus Chrysomya (Diptera: Calliphoridae) may be hampered by their close morphological similarities, especially as immatures. The aim of this study was to establish whether genetically closely related blowfly species would share similar developmental profiles. This could permit the application of developmental data to a number of closely related species, including those for which thermodevelopmental studies are lacking. If Australian Chrysomya were found to share developmental profiles, identification of the blowfly specimen to a level beyond genus may not be necessary, or at least it may not be necessary to distinguish morphologically similar sister species. The three Chrysomya species studied were collected from the same geographical location (Cairns, Australia), reducing the effects of acclimation and population‐level genetic variation. The experimental conditions in this study were virtually identical, which enabled direct comparisons to be made among the species. Blowfly larval lengths were obtained for 24‐hourly intervals at constant temperatures of 25, 30, and 35 °C. The thermal preferences of newly‐hatched feeding larvae were determined by their positions on a temperature gradient apparatus. This study established that all three species investigated differed significantly in their developmental profiles, despite the genetic closeness of the sister species Chrysomya megacephala (Fabricius) and Chrysomya saffranea (Bigot). Because of this, genetic distance was not considered to be a useful factor for predicting thermodevelopment pro...

Ng, E 2009, 'Two further studies investigating the impact of acupuncture on pregnancy outcome of in vitro fertilisation treatment', Focus on Alternative and Complementary Therapies, vol. 14, no. 1, pp. 37-39.
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Ng, PHR, Walker, S, Tahtouh, M & Reedy, B 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.

Ngo, HH, Chuang, H, Guo, WS, Ho, DP, Pham, TTN, Johnston, A, Lim, R & Listowski, A 2009, 'Resident's strategy survey on a new end use of recycled water in Australia', DESALINATION AND WATER TREATMENT, vol. 11, no. 1-3, pp. 93-97.
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The concept of using recycled water for washing machine was introduced as a new end use. As there is a noticeable lack social research in understanding the general public perceptions of this application, the resident's strategy survey was carried out at some selective suburbs in Sydney with demographically based significant differences of general, gender, age, education, and property style and ownership. The survey indicates that the majority in the community considers the use of recycled water for washing machine is indispensable in view of continuing drought and the associated water shortages. Given safety assurance and demonstration, recycled water for washing machine has a considerable proportion within the responses. The general level of knowledge in community clearly understand that recycled water is more environmentally friendly option, whereas from cleanness and public health point of view, higher quality water is required to be reused in washing machine. Moreover, the residents reckon to have a small unit for pre-treatment (point of use) before recycled water entering washing machines might assure the quality and safety. The survey also shows the major concerns for a resident to use recycled water for washing machine are public health, water cleanness and washing machine durability. © 2009 Desalination Publications.

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.

Novikov, AA 2009, 'On Distributions of First Passage Times and Optimal Stopping of AR(1) Sequences', Theory of Probability & 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. © 2009 Society for Industrial and Applied Mathematics.

Nowak, D, Florek, M, Nowak, J, 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

O'Grady, AP, Cook, PG, Eamus, D, Duguid, A, Wischusen, JDH, Fass, T & Worldege, D 2009, 'Convergence of tree water use within an arid-zone woodland', OECOLOGIA, vol. 160, no. 4, pp. 643-655.
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We examined spatial and temporal patterns of tree water use and aspects of hydraulic architecture in four common tree species of central Australia-Corymbia opaca, Eucalyptus victrix, E. camaldulensis and Acacia aneura-to better understand processes that constrain water use in these environments. These four widely distributed species occupy contrasting niches within arid environments including woodlands, floodplains and riparian environments. Measurements of tree water use and leaf water potential were made at two sites with contrasting water table depths during a period of high soil water availability following summer rainfall and during a period of low soil water availability following 7 months of very little rainfall during 2007. There were significant differences in specific leaf area (SLA), sapwood area to leaf area ratios and sapwood density between species. Sapwood to leaf area ratio increased in all species from April to November indicating a decline in leaf area per unit sapwood area. Despite very little rainfall in the intervening period three species, C. opaca, E. victrix and E. camaldulensis maintained high leaf water potentials and tree water use during both periods. In contrast, leaf water potential and water use in the A. aneura were significantly reduced in November compared to April. Despite contrasting morphology and water use strategies, we observed considerable convergence in water use among the four species. Wood density in particular was strongly related to SLA, sapwood area to leaf area ratios and soil to leaf conductance, with all four species converging on a common relationship. Identifying convergence in hydraulic traits can potentially provide powerful tools for scaling physiological processes in natural ecosystems.

Oliver, SN, Finnegan, EJ, Dennis, ES, Peacock, WJ & 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. Vernalizationinduced flowering is an epigenetic phenomenon. In Arabidopsis, stable down-regulation of FLOWERING LOCUS C (FLC) by vernalization is associated with changes in histone modifications at FLC chromatin. In cereals, the vernalization response is mediated by stable induction of the floral promoter VERNALIZATION1 (VRN1), which initiates reproductive development at the shoot apex. We show that in barley (Hordeum vulgare), repression of HvVRN1 before vernalization is associated with high levels of histone 3 lysine 27 trimethylation (H3K27me3) at HvVRN1 chromatin. Vernalization caused increased levels of histone 3 lysine 4 trimethylation (H3K4me3) and a loss of H3K27me3 at HvVRN1, suggesting that vernalization promotes an active chromatin state at VRN1. Levels of these histone modifications at 2 other floweringtime genes, VERNALIZATION2 and FLOWERING LOCUS T, were not altered by vernalization. Our study suggests that maintenance of an active chromatin state at VRN1 is likely to be the basis for epigenetic memory of vernalization in cereals. Thus, regulation of chromatin state is a feature of epigenetic memory of vernalization in Arabidopsis and the cereals; however, whereas vernalizationinduced flowering in Arabidopsis is mediated by epigenetic regulation of the floral repressor FLC, this phenomenon in cereals is mediated by epigenetic regulation of the floral activator, VRN1.

Ottosen, LDM, Poulsen, HV, Nielsen, DA, Finster, K, Nielsen, LP & Revsbech, NP 2009, 'Observations on microbial activity in acidified pig slurry', Biosystems Engineering, vol. 102, no. 3, pp. 291-297.
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Acidification of pig slurry to pH 5.5 is used as a measure to reduce ammonia emission from pits and storages. The slurry is acidified with sulphuric acid in a process tank and pumped back to the slurry pits or to a storage tank. We investigated the effect of acidification on microbial activity. Oxygen consumption rate, methanogenesis and sulphate reduction were all reduced by more than 98% in the stored acidified slurry compared to untreated slurry. Despite higher sulphate concentration, the microbial metabolism was greatly compromised or absent in the acidified slurry. This could be explained by the high concentration of protonized short-chained volatile fatty acids in the acidified slurry (approximately 25 mM, compared to untreated slurry <0.1 mM), which act as an uncoupling agent of the cell membrane potential and thereby arrest microbial metabolism. In total the consequences of slurry acidification are greatly reduced production rates and loss of sulphide and methane, and eliminated loss of ammonia. On the other hand, increased volatilization and loss of smelly fatty acids is to be expected.

Owen, MH, Ryan, LM & Holmes, LB 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. © 2008 Wiley-Liss, Inc.

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 200-300 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 thewalls of Co3O4 hollownanospheres have a uniform thickness of ∼40nm and are constructed by an oriented aggregation of Co3O 4 nanocrystals. The optical absorption properties of the Co 3O4 hollow nanospheres were investigated by UV-vis 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 Co3O 4 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. © 2008 Elsevier B.V. All rights reserved.

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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Patra, RW, Chapman, JC, Lim, RP, Gehrke, PC & Sunderam, RM 2009, 'EFFECTS OF TEMPERATURE ON VENTILATORY BEHAVIOR OF FISH EXPOSED TO SUBLETHAL CONCENTRATIONS OF ENDOSULFAN AND CHLORPYRIFOS', ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, vol. 28, no. 10, pp. 2182-2190.
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The ventilation amplitude and frequency of silver perch Bidyanus bidyanus, and the ventilation frequency of rainbow fish Melanotaenia duboulayi and rainbow trout Oncorhynchus mykiss, were determined at different temperatures upon exposure to endosulfan and chlorpyrifos, respectively. Silver perch and rainbow fish were tested at 15, 20, 25, 30, and 35 degrees C, while rainbow trout was tested at 10, 15, 20, and 25 degrees C. Although some trend of increasing amplitudes with increasing temperature was evident; there was no significant temperature response of ventilation frequency rates over time in silver perch pre-exposed to 10 mu g L-1 endosulfan for 18 h. The rate of ventilation frequency of rainbow fish pre-exposed to 200 mu g L-1 of chlorpyrifos for 96 h was lower in treatments than in the control at 15 degrees C. However, between 20 and 35 degrees C, rates were significantly higher in the treatments than those of the control. In rainbow trout pre-exposed to 100 mu g L-1 of chlorpyrifos, the rates of frequency were significantly lower than those of controls in temperatures between 10 and 20 degrees C but higher at 25 degrees C. The amplitude of silver perch seemed to increase with the increase in temperature; however, the corresponding temperature quotient values at various temperature regimes and over exposure time showed no significant differences. The ventilation frequency of rainbow fish and rainbow trout significantly increased at the higher test temperatures, and their corresponding temperature quotient values for both fish also increased at the elevated temperatures.

Pearce, ND & Wand, MP 2009, 'Explicit connections between longitudinal data analysis and kernel machines', Electronic Journal of Statistics, vol. 3, no. none, 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. © 2009, Institute of Mathematical Statistics. All rights reserved.

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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The concentrations of 16 trace elements were investigated and compared for the first time in the digestive and excreting tissues of two Nautilus species (Cephalopoda: Nautiloidea) from two geologically contrasted areas: (1) N. macromphalus from New Caledonia, a region characterized by its richness in nickel ores and its lack of tectonic activities and (2) N. pompilius from the Vanuatu archipelago showing high volcanic and tectonic activities. In both Nautilus species, results clearly highlighted that the digestive gland played a key role in the bioaccumulation and storage of Ag, Cd, Ce, Co, Cu, Fe, La, Nd, V, and Zn whereas As, Cr, Mn, Ni, Pb, and Se were accumulated in a greater extent in the excreting tissues (i.e. pericardial and renal appendages). Despite contrasting environments, no significant difference (p<0.05) was found between the two Nautilus species in the concentrations of most of the essential and non-essential elements, including Ni and associated metals in Ni ores (i.e. Co and Mn). As nautilus lives on the outer shelf of barrier reefs, these results strongly support the hypothesis that the New Caledonian lagoon traps the major amount of the trace elements derived from natural erosion and the intense mining activities conducted on land. In contrast, the concentrations of the rare earth elements (Ce, La, and Nd) were significantly higher in N. pompilius than in N. macromphalus, probably as a result of the local enrichment of Vanuatu waters by specific environmental processes, such as volcanism or upwelling. © 2008 Elsevier Inc. All rights reserved.

Petőcz, G, Rangits, G, Shaw, M, Bod, HD, Williams, DBG & Kollár, 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, MR, Drouin, D, Moody, SJ & Ton-That, C 2009, 'Imaging Fundamental Electronic Excitations at High Spatial Resolution Using Scanning Cathodoluminescence Microscopy', MICROSCOPY AND MICROANALYSIS, vol. 15, no. SUPPL. 2, 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 & Experimental Allergy, vol. 39, no. 12, pp. 1920-1928.
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SummaryBackground 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 microbi...

Pickett, J, Och, D & Leitch, E 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.
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Two assemblages of rugose and tabulate corals, with accessory stromatoporoids and chaetetids, are described from the Touchwood and Mile Road Formations of the Wauchope - Port Macquarie district of northeastern New South Wales. Both assemblages are derived from allochthonous limestone clasts, except that the Mile Road fauna is accompanied at the same level by branching tabulate corals occurring in the matrix, indicating probable contemporaneity. The fauna from the Touchwood Formation indicates an Early Devonian (Emsian) age. Macrofossils from the Mile Road Formation indicate a broad Middle Devonian, probably Givetian age; conodonts accompanying the coral assemblage yield a precise age in the upper part of the early Givetian varcus Zone. Geographic affinities of the assemblages are typically eastern Australian, so that if terranes are represented in the block, these were not remote. Stratigraphie and structural relationships of the units are discussed. The name Mile Road Formation is formally defined.

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, pp. e398-e398.
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Pissuwan, D, Valenzuela, SM, 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.

Potter, C, Klooster, S, Huete, A, Genovese, V, Bustamante, M, Ferreira, LG, Jr, DORC & Zepp, R 2009, 'Terrestrial carbon sinks in the Brazilian Amazon and Cerrado region predicted from MODIS satellite data and ecosystem modeling', BIOGEOSCIENCES, vol. 6, no. 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 andCerradoregions over the period 2000-2004. 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 Rondônia and the northern portions of the state of Pará. These areas were not significantly impacted by the 2002-2003 El Niño 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 Maranhão 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 measured 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.

Potter, C, Klooster, S, Huete, A, Genovese, V, Bustamante, M, Guimaraes Ferreira, L, Cosme de Oliveira Junior, R & Zepp, R 2009, 'Terrestrial carbon sinks in the Brazilian Amazon and Cerrado region predicted from MODIS satellite data and ecosystem modeling', Biogeosciences Discussions, vol. 6, no. 1, pp. 947-969.
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Abstract. 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 regions over the period 2000–2004. 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 Rondônia and the northern portions of the state of Pará. These areas were not significantly impacted by the 2002–2003 El Niño 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 Maranhão 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 measured 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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1. 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. 2. 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. 3. Both classification methods revealed substantial, monotonic decreases (by 24-77%) in the percentage cover of bare rock from 1941 to 2006 at all sites, with concomitant (although non-monotonic) net increases in percentage tree-canopy cover of 3-70%. The cover of herbaceous and low-shrub vegetation appeared variable and was poorly resolved in the classifications. 4. Both classification methods yielded adequate (> 70%) accuracy for most images, but the object-based classifications were consistently more accurate than the pixel-based classifications and performed better when analysing images (from 1971) with comparatively low resolution. 5. Synthesis and applications. Our study indicates that habitat availability for broad-headed snakes has decreased considerably over 65 years due to increased shading from vegetation, and that object-based image analysis is a promising tool for assessing habitat trends using historical photographs. Multiple studies have reported woody-vegetation increases over multi-decadal time-scales in Australi...

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-B, Tapiolas, D, 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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ABSTRACTMarine 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 coral-associated bacteria. Two coral species,Montipora aequituberculataandAcropora millepora, were sampled and their bacterial communities were characterized by both culture-dependent and molecular techniques. Four genera,Roseobacter, Spongiobacter, Vibrio, andAlteromonas, 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 withRoseobactersp. constituted 28% of theM. aequituberculatatissue libraries, while 59% of the clones from theA. milleporalibraries were affiliated with sequences related to theSpongiobactergenus.Vibriospp. 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 todddD, anddddL, 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...

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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Abstract Advances in observations, theory, and modeling have revealed that inner-core asymmetries are a common feature of tropical cyclones (TCs). In this study, the inner-core asymmetries of a severe Southern Hemisphere tropical cyclone, TC Larry (2006), are investigated using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5) and the Kepert–Wang boundary layer model. The MM5-simulated TC exhibited significant asymmetries in the inner-core region, including rainfall distribution, surface convergence, and low-level vertical motion. The near-core environment was characterized by very low environmental vertical shear and consequently the TC vortex had almost no vertical tilt. It was found that, prior to landfall, the rainfall asymmetry was very pronounced with precipitation maxima consistently to the right of the westward direction of motion. Persistent maxima in low-level convergence and vertical motion formed ahead of the translating TC, resulting in deep convection and associated hydrometeor maxima at about 500 hPa. The asymmetry in frictional convergence was mainly due to the storm motion at the eyewall, but was dominated by the proximity to land at larger radii. The displacement of about 30°–120° of azimuth between the surface and midlevel hydrometeor maxima is explained by the rapid cyclonic advection of hydrometeors by the tangential winds in the TC core. These results for TC Larry support earlier studies that show that frictional convergence in the boundary layer can play a significant role in determining the asymmetrical structures, particularly when the environmental vertical shear is weak or absent.

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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ABSTRACT The mouse chlamydial pathogen Chlamydia muridarum has been used as a model organism for the study of human Chlamydia trachomatis urogenital and respiratory tract infections. To date, two commonly used C. muridarum isolates have been used interchangeably and are essentially taken to be identical. Herein, we present data that indicate that this is not the case. The C. muridarum Weiss isolate and C. muridarum Nigg isolate varied significantly in their virulences in vivo and possessed different growth characteristics in vitro. Distinct differences were observed in intravaginal 50% infectious doses and in challenge infections, with the Weiss isolate displaying greater virulence. Respiratory infection by the intranasal route also indicated a greater virulence of the Weiss isolate. In vitro, morphometric analysis revealed that the Weiss isolate produced consistently smaller inclusions in human cervical adenocarcinoma cells (HeLa 229) and smaller plaques in monolayers of mouse fibroblasts (L929) than did the Nigg isolate. In addition, the Weiss isolate possessed significantly higher replicative yields in vitro than did the Nigg isolate. In plaque-purified isolates derived from our stocks of these two strains, total genomic sequencing identified several unique nonsynonymous single nucleotide polymorphisms and insertion/deletion mutations when our Weiss ( n = 4) and Nigg ( n = 5) isolates were compared with the published Nigg sequence. In addition, the two isolates shared 11 mutations compared to the published Nigg sequence. These results prove that...

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.

Ranjbartoreh, AR & 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. © 2009 World Scientific Publishing Company.

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, C, Buchholz, F, Colbran, SB & McDonagh, AM 2009, 'Ruthenium Phthalocyanine-Bipyridyl Dyads as Sensitizers for Dye-Sensitized 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 TiO 2 electrode surfaces, several of the new complexes were more efficient at photocurrent 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. © 2009 American Chemical Society.

Rawling, T, Austin, CE, Hare, D, Doble, PA, Zareie, HM & McDonagh, AM 2009, 'Thin Films of Ruthenium Phthalocyanine Complexes', NANO RESEARCH, vol. 2, no. 9, 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 complex-containing solution. © Tsinghua University Press and Springer-Verlag 2009.

Rawson, CA, Tremblay, LA, Warne, MSJ, Ying, G-G, Kookana, R, Laginestra, E, Chapman, JC & Lim, RP 2009, 'Bioactivity of POPs and their effects in mosquitofish in Sydney Olympic Park, Australia', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 407, no. 12, pp. 3721-3730.
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The site of the 2000 Olympic Games (Sydney Olympic Park (SOP), Sydney, Australia) was contaminated by persistent organic pollutants (POPs) prior to remediation in the 1990s. This study investigates the bioactivity of POPs in the sediment and water of wetlands across SOP by in vitro 2,3,7,8-TCDD equivalence (TCDDeq) measurement (H4IIE cell line bioassay). Further, it examines whether disturbance of these sediments is likely to mobilise ligands for this receptor into the water column.

Raymond, JJ, van Oorschot, RAH, Gunn, PR, Walsh, SJ & Roux, C 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, RAH, Gunn, PR, Walsh, SJ & Roux, C 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, RAH, Walsh, SJ, Roux, C & 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.

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, no. 5.
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We have applied a scalable and extensible geo‐fluid model (SEGMENT) that considers soil mechanics, vegetation transpiration and root mechanical reinforcement, and hydrological processes to simulate two dimensional maps of the landslides occurrence following the 2008 Wenchuan earthquake. Modeled locations and areas generally agree with observations. The model suggests that the potential energy of earth was lowered by 1.52 × 1015 J by these landslides. With this, the vegetation destroyed transfer ∼235 Tg C to the dead respiring pool and transforms 5.54 × 10−2 Tg N into unavailable sediments pools and the atmosphere. The cumulative CO2 release to the atmosphere over the coming decades is comparable to that caused by hurricane Katrina 2005 (∼105 Tg) and equivalent to ∼2% of current annual carbon emissions from global fossil fuel combustion. The nitrogen loss is twice as much as that released by the 2007 California Fire (∼2.5 × 10−2 Tg). A significant proportion of the nitrogen loss (14%) is in the form of nitrous oxide, which can affect the atmospheric ozone layer.

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', The ISME Journal, vol. 3, no. 3, pp. 271-282.
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Abstract Mature Pseudomonas aeruginosa biofilms undergo specific developmental events. Using a bacteriophage mutant, generated by deletion of the entire filamentous Pf4 prophage, we show that the phage is essential for several stages of the biofilm life cycle and that it significantly contributes to the virulence of P. aeruginosa in vivo. Here, we show for the first time that biofilms of the Pf4 phage-deficient mutant did not develop hollow centres or undergo cell death, typical of the differentiation process of wild-type (WT) P. aeruginosa PAO1 biofilms. Furthermore, microcolonies of the Pf4 mutant were significantly smaller in size and less stable compared with the WT biofilm. Small colony variants (SCVs) were detectable in the dispersal population of the WT biofilm at the time of dispersal and cell death, whereas no SCVs were detected in the effluent of the Pf4 mutant biofilm. This study shows that at the time when cell death occurs in biofilms of the WT, the Pf4 phage converts into a superinfective form, which correlates with the appearance of variants in the dispersal population. Unexpectedly, mice infected with the Pf4 mutant survived significantly longer than those infected with its isogenic WT strain, showing that Pf4 contributes to the virulence of P. aeruginosa. Hence, a filamentous prophage is a major contributor to the life cycle and adaptive behaviour of P. aeruginosa and offers an explanation for the prevalence of phage in this organism.

Rissman, AI, Mau, B, Biehl, BS, Darling, AE, Glasner, JD & Perna, NT 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 reordering algorithm coupled with a powerful drill-down display allowing detailed exploration of results. © 2009 The Author(s).

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. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.

Robson, TC, Baker, AC & Murray, BR 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. We suggest that implementation of The Plantation Biodiversity Benefits Score will be a fruitful way forward to assess the environmental benefits that can...

Rodgers, KJ, Ford, JL & Brunk, UT 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

Rong, Y, Jin, D, Wu, W, Lou, W, Wang, D, Kuang, T, Ni, X & Qin, X 2009, 'Induction of protective and therapeutic anti-pancreatic cancer immunity using a reconstructed MUC1 DNA vaccine', BMC Cancer, vol. 9, no. 1.
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Abstract Background Pancreatic cancer is a common, highly lethal disease with a rising incidence. MUC1 is a tumor-associated antigen that is over-expressed in pancreatic adenocarcinoma. Active immunotherapy that targets MUC1 could have great treatment value. Here we investigated the preventive and therapeutic effect of a MUC1 DNA vaccine on the pancreatic cancer. Methods MUC1-various tandem repeat units(VNTR) DNA vaccine was produced by cloning one repeat of VNTR and inserting the cloned gene into the pcDNA3.1. In the preventive group, female C57BL/6 mice were immunized with the vaccine, pcDNA3.1 or PBS; and challenged with panc02-MUC1 or panc02 cell. In the therapeutic group the mice were challenged with panc02-MUC1 or panc02 cell, and then immunized with the vaccine, pcDNA3.1 or PBS. The tumor size and the survival time of the animals were compared between these groups. Results The DNA vaccine pcDNA3.1-VNTR could raise cytotoxic T lymphocyte (CTL) activity specific for MUC1. In the preventive experiment, the mice survival time was significantly longer in the vaccine group than in the control groups (P < 0.05). In the therapeutic experiment, the DNA vaccine prolonged the survival time of the panc02-MUC1-bearing mice (P < 0.05). In both the preventive and therapeutic experiments, the tumor size was significantly less in the vaccine group than in the control groups (P < 0.05). This pcDNA3.1-VNTR vaccine, however, could not prevent the mice attacked by panc02 cells and had no therapeutic effect on the mice attacked by panc02 cells. <...

Ruppert, D, Wand, MP & Carroll, RJ 2009, 'Semiparametric regression during 2003–2007', Electronic Journal of Statistics, vol. 3, no. none, 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. © 2009, Institute of Mathematical Statistics. All rights reserved.

Rutlidge, HT & Reedy, BJ 2009, 'Classification of Heterogeneous Solids Using Infrared Hyperspectral Imaging', APPLIED SPECTROSCOPY, 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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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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Saltré, F, Chuine, I, Brewer, S & Gaucherel, C 2009, 'A phenomenological model without dispersal kernel to model species migration', Ecological Modelling, vol. 220, no. 24, pp. 3546-3554.
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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.', Can J Clin Pharmacol, vol. 16, no. 1, pp. e156-e162.
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BACKGROUND: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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, BN, 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. © Institute of Mathematical Statistics, 2009.

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, SA, Smith, PV, King, BV, Reimers, JR, Wallace, BJ & Crossley, MJ 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 CH2 group is substituted by the trifluoroacetoxy OC(O)CF3 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. © 2009 American Chemical Society.

Sasani, S, Hemming, MN, Oliver, SN, Greenup, A, Tavakkol-Afshari, R, Mahfoozi, S, Poustini, K, Sharifi, H-R, Dennis, ES, Peacock, WJ & 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

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, pp. e5513-e5513.
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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. 13178-13178.
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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. © 2009 Optical Society of America.

Scott, NE, Bogema, DR, Connolly, AM, Falconer, L, Djordjevic, SP & Cordwell, SJ 2009, 'Mass Spectrometric Characterization of the Surface-Associated 42 kDa Lipoprotein JlpA 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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AbstractThis 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 var...

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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Abstract Horn of Africa rainfall varies on multiple time scales, but the underlying climate system controls on this variability have not been examined comprehensively. This study therefore investigates the linkages between June–September Horn of Africa (especially Ethiopian) rainfall and regional atmospheric circulation and global sea surface temperature (SST) variations on several key time scales. Wavelet analysis of 5-day average or monthly total rainfall for 1970–99 identifies the dominant coherent modes of rainfall variability. Several regional atmospheric variables and global SST are then identically wavelet filtered, based on the rainfall frequency bands. Regression, correlation, and composite analyses are subsequently used to identify the most important rainfall–climate system time-scale relationships. The results show that Ethiopian monsoon rainfall variation is largely linked with annual time-scale atmospheric circulation patterns involving variability in the major components of the monsoon system. Although variability on the seasonal (75–210 days), quasi-biennial (QB; 1.42–3.04 yr), and El Niño–Southern Oscillation (ENSO; 3.04–4.60 yr) time scales accounts for much less variance than the annual mode (210 days–1.42 yr), they significantly affect Ethiopian rainfall by preferentially modulating the major regional monsoon components and remote teleconnection linkages. The seasonal time scale largely acts in phase with the annual mode, by enhancing or reducing the lower-tropospheric southwesterlies from the equatorial Atlantic during wet or dry periods. The wet QB phase strengthens the Azores and Saharan high and the tropical easterly jet (TEJ) over the Arabian Sea, while the wet ENSO phase enhances the Mascarene high, the TEJ, and the monsoon trough more locally. The effects of tropical SST on Ethiopian rainfall also are prominent on the QB and ENSO time scales. While ...

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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AbstractThis study evaluates the ability of the Abdus Salam International Center for Theoretical Physics (ICTP) version 3 Regional Climate Model (RegCM3) to reproduce the observed rainfall amounts and distribution over the topographically varied region of the Horn of Africa. Simulations are performed for the widespread very dry 1984 and locally very wet 1996 years using all of the alternative convective schemes available in the ICTP RegCM3. Extensive comparisons of simulations for 1984 and 1996 reveal that the Emanuel scheme best captures the rainfall patterns and interannual variations for the two extreme years over the Horn of Africa. This scheme therefore is selected for specific adaptation for the region, despite its excessive rainfall estimation there and its demonstrated deficiencies over other regions of Africa not of interest in this study.To reduce rainfall overestimation by the Emanuel scheme, several sensitivity experiments are performed by varying the key parameters that control the rate of convective mass flux, the fraction of condensed water converted to precipitation, and the heating and moistening characteristics of the environment. Results show that the amount of condensed water that ultimately falls out as rain crucially affects simulated rainfall amounts. With an appropriate adjustment to this key parameter, the excessive rainfall amount produced by the Emanuel scheme is reduced substantially. Furthermore, evaluation of RegCM3 simulations for 1982–1999 shows that the modified Emanuel convective scheme not only reproduces the 18‐year average rainfall realistically but also captures the interannual variability adequately over the Horn of Africa. The correlation between the modified Emanuel‐simulated and Ethiopian station rainfall is quite strong (+0.66). This customized ICTP RegCM3 model now can be used with confidence for the Horn of Africa to study regional rainfall processes and varia...

Seidel, P, Merfort, I, Hughes, JM, Oliver, BGG, Tamm, M & Roth, M 2009, 'Dimethylfumarate inhibits NF-kappa B 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. L326-L339.
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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-κB 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 TNFα-induced asthma-relevant cytokines and NF-κB activation by primary human asthmatic and nonasthmatic airway smooth muscle cells (ASMC). Confluent nonasthmatic and asthmatic ASMC were incubated with DMF (0.1-100 μM) and/or dexamethasone (0.0001-0.1 μM), NF-κB p65 siRNA (100 nM), the NF-κB inhibitor helenalin (1 μM) before stimulation with PDGF-BB or TNFα (10 ng/ml). Cytokine release was measured by ELISA. NF-κB, mitogen and stress-activated kinase (MSK-1), and CREB activation was determined by immunoblotting and EMSA. TNFα-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-κB p65 siRNA and/or the NF-κB inhibitor helenalin reduced PDGF-BB- and TNFα-induced cytokine expression, suggesting the involvement of NF-κB signaling. DMF inhibited TNFα-induced NF-κB p65 phosphorylation, NF-κB nuclear entry, and NF-κB-DNA complex formation, whereas PDGF-BB appeared not to activate NF-κB within 60 min. Both stimuli induced the phosphorylation of MSK-1, NF-κB p65 at Ser276, and CREB, and all were inhibited by DMF. These data suggest that DMF downregulates cytokine secretion not only by inhibiting NF-κB but a wider range of NF-κB-linked signaling proteins, which may explain its potential beneficial effect in asthma. Copyright © 2009 the American Physiological Society.

Şentürk, 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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Summary Motivated by molecular data on female premutation carriers of the fragile X mental retardation 1 (FMR1) gene, we present a new method of covariate adjusted correlation analysis to examine the association of messenger RNA (mRNA) and number of CGG repeat expansion in the FMR1 gene. The association between the molecular variables in female carriers needs to adjust for activation ratio (ActRatio), a measure which accounts for the protective effects of one normal X chromosome in females carriers. However, there are inherent uncertainties in the exact effects of ActRatio on the molecular measures of interest. To account for these uncertainties, we develop a flexible adjustment that accommodates both additive and multiplicative effects of ActRatio nonparametrically. The proposed adjusted correlation uses local conditional correlations, which are local method of moments estimators, to estimate the Pearson correlation between two variables adjusted for a third observable covariate. The local method of moments estimators are averaged to arrive at the final covariate adjusted correlation estimator, which is shown to be consistent. We also develop a test to check the nonparametric joint additive and multiplicative adjustment form. Simulation studies illustrate the efficacy of the proposed method. (Application to FMR1 premutation data on 165 female carriers indicates that the association between mRNA and CGG repeat after adjusting for ActRatio is stronger.) Finally, the results provide independent support for a specific jointly additive and multiplicative adjustment form for ActRatio previously proposed in the literature.

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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Abstract Uncertainty exists concerning the links between synoptic-scale processes and tornado outbreaks. With continuously improving computer technology, a large number of high-resolution model simulations can be conducted to study these outbreaks to the storm scale, to determine the degree to which synoptic-scale processes appear to influence the occurrence of tornado outbreaks, and to determine how far in advance these processes are important. To this end, 50 tornado outbreak simulations are compared with 50 primarily nontornadic outbreak simulations initialized with synoptic-scale input using the Weather Research and Forecasting (WRF) mesoscale model to determine if the model is able to distinguish the outbreak type 1, 2, and 3 days in advance of the event. The model simulations cannot resolve tornadoes explicitly; thus, the use of meteorological covariates (in the form of numerous severe-weather parameters) is necessary to determine whether or not the model is predicting a tornado outbreak. Results indicate that, using the covariates, the WRF model can discriminate outbreak type consistently at least up to 3 days in advance. The severe-weather parameters that are most helpful in discriminating between outbreak types include low-level and deep-layer shear variables and the lifting condensation level. An analysis of the spatial structures and temporal evolution, as well as the magnitudes, of the severe-weather parameters is critical to diagnose the outbreak type correctly. Thermodynamic instability parameters are not helpful in distinguishing the outbreak type, primarily because of a strong seasonal dependence and convective modification in the simulations.

Sheldon, CC, Finnegan, EJ, Peacock, WJ & 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 ultraviolet-visible 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. © 2009 Elsevier B.V. All rights reserved.

Shi, C, Jin, D, Xu, B & Lou, W 2009, 'Value of monitoring postoperative intra‐abdominal drainage fluid for the diagnosis of postoperative pancreatic fistula: Results of a prospective study in 134 patients', Surgical Practice, vol. 13, no. 4, pp. 102-107.
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Objective:  To evaluate the value of monitoring postoperative intra‐abdominal drainage in the diagnosis and treatment of postoperative pancreatic fistula (POPF).Methods:  Intra‐abdominal drainage adjacent to the pacreaticoenteric anastomosis was prospectively collected from 134 patients accepted for pancreatic surgery in our department between November 2005 and August 2007 to determine the concentration of amylase and bacteriology. Also, the clinical outcome of each patient was recorded. The international study group definition was used to diagnose POPF.Results:  The overall incidence of POPF was 39.6% in 53 patients diagnosed as POPF, among which 50 patients (37.3%, 50/134) were graded as I/II of POPF. The rising trend of the amylase level in the drainage fluid (P = 0.001), the texture of the pancreatic remnant (P = 0.042), and the amylase level on the 3rd and 7th postoperative days demonstrated good diagnostic values in univariate analysis (P < 0.001). The amylase value in drains on the 3rd postoperative day (POD3) and the 7th postoperative day (POD7) were the predicting factors (P < 0.001) of POPF by multivariate analysis.Conclusions:  The amylase values in drains on the 3rd postoperative day and on the 7th postoperative day (POD7) were both valuable factors in the diagnoses of POPF. It is very important to monitor the dynamic change of amylase concentration in the drainage, not the result of a single test. These clinical factors could help us to detect the incidence of POPF earlier.

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, A & Novikov, AA 2009, 'On a stochastic version of the trading rule “Buy and Hold”', Statistics & Decisions, vol. 26, no. 4, pp. 289-302.
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Abstract The paper deals with the problem of finding an optimal one-time rebalancing strategy assuming that in the Black–Scholes 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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AbstractThe 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.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.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.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.

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 suitable 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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Sieveking, DP, Lim, P, Chow, RW, Dunn, LL, Bao, S, McGrath, KC, Heather, AK, Handelsman, DJ, Celermajer, DS & Ng, MK 2009, 'Abstract 5684: A Sex-Specific Role for Androgens in Angiogenesis', Circulation, vol. 120, no. suppl_18.
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The role of androgens in cardiovascular disease remains controversial. Although men tend to develop CVD earlier than women, consistent with increased atherosclerosis, repair/adaptation mechanisms may be enhanced in males. For example, male gender is associated with increased collateralization in patients with severe coronary artery lesions. As angiogenesis, is critical to cardiovascular repair/regeneration, we hypothesized that androgens may modulate this process. We studied the effects of androgens on angiogenesis using human endothelial cells (ECs) and two distinct in vivo models. Dihydrotestosterone (DHT), a potent natural androgen specific for the androgen receptor (AR) augmented key angiogenic events in vitro , including EC migration, proliferation and tubulogenesis. Strikingly, this occurred in male but not female ECs. AR antagonism and siRNA-mediated knockdown abrogated all DHT effects in male ECs, while AR overexpression conferred androgen sensitivity in female ECs. In vivo , castration dramatically reduced vascularization of matrigel plugs in male and female mice. This reduction was fully reversed with DHT treatment in male but not female mice (Fig. 1 ). Additionally, male castration impaired neovascularization and blood flow recovery in hindlimb ischemia, a finding that was rescued with DHT treatment. These findings were also mirrored in hypoxia inducible factor-1 α and stromal cell-derived factor-1 α expression, and the mobilzation of various angiogenic/progenitor cells. Our findings suggest endogenous androgens play an important role in angiogenesis in males but not females, with implications for the role of androgen r...

Singh, MD, Kreiner, M, McKimmie, CS, Holt, S, van der Walle, CF & Graham, GJ 2009, 'Dimeric integrin α5β1 ligands confer morphological and differentiation responses to murine embryonic stem cells', Biochemical and Biophysical Research Communications, vol. 390, no. 3, pp. 716-721.
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Singh, SK, Verma, PRP & Razdan, B 2009, 'Development and characterization of a carvedilol-loaded self-microemulsifying delivery system', Clinical Research and Regulatory Affairs, vol. 26, no. 3, pp. 50-64.
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Siyushev, P, Jacques, V, Aharonovich, I, Kaiser, F, Mueller, T, Lombez, L, Atatuere, 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, BJ, Hoy, JA, Percifield, R, Kundu, S, Hargrove, MS, Sarath, G, Hilbert, J-L, Watts, RA, Dennis, ES, Peacock, WJ, Dewilde, S, Moens, L, Blouin, GC, Olson, JS & Appleby, CA 2009, 'Correlations Between Oxygen Affinity and Sequence Classifications of Plant Hemoglobins', BIOPOLYMERS, vol. 91, no. 12, pp. 1083-1096.
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Plants express three phylogenetic classes of hemoglobins (Hb) based on sequence analyses. Class 1 and 2 Hbs are full-length globins with the classical eight helix Mb-like fold, whereas Class 3 plant Hbs resemble the truncated globins found in bacteria. With the exception of the specialized leghemoglobins, the physiological functions of these plant hemoglobins remain unknown. We have reviewed and, in some cases, measured new oxygen binding properties of a large number of Class 1 and 2 plant nonsymbiotic Hbs and leghemoglobins. We found that sequence classification correlates with distinct extents of hexacoordination with the distal histidine and markedly different overall oxygen affinities and association and dissociation rate constants. These results suggest strong selective pressure for the evolution of distinct physiological functions. The leghemoglobins evolved from the Class 2 globins and show no hexacoordination, very high rates of O2 binding (∼250 μM-1 s -1), moderately high rates of O2 dissociation (∼5-15 s-1), and high oxygen affinity (Kd or P50 ≈ 50 nM). These properties both facilitate O2 diffusion to respiring N2 fixing bacteria and reduce O2 tension in the root nodules of legumes. The Class 1 plant Hbs show weak hexacoordination (K HisE7 ≈ 2), moderate rates of O2 binding (∼25 μM-1 s-1), very small rates of O2 dissociation (∼0.16 s-1), and remarkably high O2 affinities (P50 ≈ 2 nM), suggesting a function involving O 2 and nitric oxide (NO) scavenging. The Class 2 Hbs exhibit strong hexacoordination (KHisE7 ≈ 100), low rates of O2 binding (∼1 μM-1 s-1), moderately low O2 dissociation rate constants (∼1 s-1), and moderate, Mb-like O2 affinities (P50 ≈ 340 nM), perhaps suggesting a sensing role for sustained low, micromolar levels of oxygen. © 2009 Wiley Periodicals, Inc.

Smith, GB 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 μm and 13 μm 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° C below ambient, under a 45° aperture lined with shiny aluminium, can achieve a net output power near 135 W m-2 under a clear sky. © 2009 Elsevier B.V. All rights reserved.

Smith, GB 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, J & 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, M, 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. 01, 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 synthesis of spatially isolated high quality micro- and nano-diamonds using a microwave plasma chemical vapor deposition technique (MPCVD). The growth from nano-seeds rather than other nucleation techniques allows improved control over the final size of the crystals and the density of the crystals on the substrate. The growth rate of the diamond crystals was found to be 22 nm/min. Various parameters of the growth sequence were studied and the microwave power density was found to have the major influence on the crystal morphology, with the best quality diamond formed under conditions of relatively high pressure and plasma density. Our ability to control size, dispersion and levels of perfection constitutes an enabler for future quantum information applications utilizing diamond color centers. © 2008 Elsevier B.V. All rights reserved.

Stark, D, Barratt, J, Ellis, J, Harkness, J & Marriott, D 2009, 'Repeated Dientamoeba fragilis infections: a case report of two families from Sydney, Australia', Infectious Disease Reports, vol. 1, no. 1, pp. e4-9.
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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, D, Barratt, JLN, van Hal, S, Marriott, D, Harkness, J & Ellis, JT 2009, 'Clinical Significance of Enteric Protozoa in the Immunosuppressed Human Population', CLINICAL MICROBIOLOGY REVIEWS, vol. 22, no. 4, pp. 634-+.
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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, D, van Hal, S, Barratt, J, Ellis, J, Marriott, D & Harkness, J 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, MP 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, AJ, Argent, E, Newsome, TP, Rawlinson, WD & Tovey, ER 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 respiratory viruses. The exhaled samples from a subset of 10 subjects who were PCR positive for rhinovirus were also examined by cell culture for this virus. Of the 50 subjects, among the 33 with symptoms of upper respiratory tract infections, 21 had at least one virus detected by PCR, while amongst the 17 asymptomatic subjects, 4 had a virus detected by PCR. Overall, rhinovirus was detected in 19 subjects, influenza in 4 subjects, parainfluenza in 2 subjects, and human metapneumovirus in 1 subject. Two subjects were co-infected. Of the 25 subjects who had virus-positive nasal mucus, the same virus type was detected in 12 breathing samples, 8 talking samples, and in 2 coughing samples. In the subset of exhaled samples from 10 subjects examined by culture, infective rhinovirus was detected in 2. These data provide further evidence that breathing may be a source of respirable particles carrying infectious virus. © 2009 Wiley-Liss, Inc.

Stephens, RS, Myers, G, Eppinger, M & Bavoil, PM 2009, 'Divergence without difference: phylogenetics and taxonomy ofChlamydiaresolved', FEMS Immunology & Medical Microbiology, vol. 55, no. 2, pp. 115-119.
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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 TOXICOLOGY, 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. © 2008 Springer Science+Business Media, LLC.

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 fluorescencebased 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. © Inter-Research 2009.

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 σPSII) and photochemical efficiency (termed Fv/Fm). Both Fv/F m and σPSII 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 σPSII also contain taxonomic information. Here, we present a synthesis of previously unpublished and published data, which show that F v/Fm and σPSII 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 σPSII 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 σPSII have been repeatedly demonstrated on relief of iron limitation. Overall, FRR fluorescence measurements of both Fv/Fm and σPSII in natural populations represent a combination of the taxonomic 'signature' (values of Fv/Fm and σPSII 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. © Inter-Research 2009.

Summerhayes, SA, Bishop, MJ, 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. © 2009 Elsevier B.V. All rights reserved.

Sun, H-S, Huang, J-F, Huete, AR, Peng, D-L & Zhang, F 2009, 'Mapping paddy rice with multi-date moderate-resolution imaging spectroradiometer (MODIS) data in China', JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE A, 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 moderateresolution 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. © 2009 Zhejiang University and Springer Berlin Heidelberg.

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, 'Corrigendum', Molecular Plant, vol. 2, no. 5, pp. 1123-1123.
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Sung, ZR, Furner, I, Yadgari, R, Pikaard, C, Wagner, D, Michaels, S & Dennis, L 2009, 'Editorial', Molecular Plant, vol. 2, no. 4, pp. 553-553.
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Tan, J, Li, X-H, Bartusch, M, DY, V, Liong, E, McGrath, K, Barter, P & Heather, A 2009, 'Abstract: P655 LOW DHCR24 LEVELS ARE ASSOCIATED WITH CHRONIC INFLAMMATION AND APOPTOSIS IN HUMAN ENDOTHELIAL CELLS', Atherosclerosis Supplements, vol. 10, no. 2, pp. e841-e841.
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Thompson, AM, Dunlop, RA, Dean, RT & Rodgers, KJ 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 yr-1. All stations showed positive trends in temperature, with the fastest surface warming (0.0202°C yr-1 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 yr-1. A pronounced decline in silicate was evident at the 3 east coast stations, with concentrations falling by as much as 58 nM yr-1 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. © Inter-Research 2009.

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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Thornton-Benko, E, Nguyen, HT, Hung, WT & Thornton, BS 2009, 'Improved observer dependent perception of weak edges when scanning an image in real time indicated by introducing 1/f noise into the primary visual cortex V1. Theory and experimental support', AUSTRALASIAN PHYSICAL & ENGINEERING SCIENCES IN MEDICINE, vol. 32, no. 3, pp. 136-149.
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We present results of a new process for generating 1/f type noise sequences and introducing the noise in the primary visual cortex which then enables improved perception of weak edges when an observer is scanning a complex image in real time to detect detail such as in mammogram reading sessions. It can be explained by an adaptation of information theory for functional rather than previous task-based methods for formulating processes for edge formation in early vision. This is enabled from a two "species" classification of the interaction of opposing on-centre and off-centre neuron processes. We show that non-stationary stochastic resonances predicted by theory can occur with 1/f noise in the primary visual cortex VI and suggest that signalling exchanges between VI and the lateral geniculate nucleus (LGN) of the thalamus can initiate neural activity for saccadic action (and observer attention) for weak edge perception. Improvements predicted by our theory were shown from 600 observations by two groups of observers of limited experience and an experienced radiologist for reference (but not for diagnosis). They scanned and rated the definition of microcalcification in clusters separately rated by the experienced radiologist. The results and supporting theory showed dependence on the observer's attention and orderly scanning. Using a compact simplified equipment configuration the methodology has important clinical applications for conjunction searches of features and for detection of objects in poor light conditions for vehicles.

Tileli, V, Knowles, WR, 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. 014904-014904.
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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.

Toth, M, Lobo, CJ, Lysaght, MJ, Vladár, AE & Postek, MT 2009, 'Contamination-free imaging by electron induced carbon volatilization in environmental scanning electron microscopy', Journal of Applied Physics, vol. 106, no. 3, 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, TJ, Darling, AE, Achaz, G, Ragan, MA, Messeguer, X & Rocha, EPC 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, Lobo, JMG, 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, pp. e5519-e5519.
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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', Acta Horticulturae, vol. 841, no. 841, pp. 237-242.
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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 Part A: Molecular & Integrative Physiology, vol. 154, no. 3, pp. 383-388.
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Van Sluyter, SC, Marangon, M, Stranks, SD, Neilson, KA, Hayasaka, Y, Haynes, PA, Menz, RI & Waters, EJ 2009, 'Two-Step Purification of Pathogenesis-Related Proteins from Grape Juice and Crystallization of Thaumatin-like Proteins', Journal of Agricultural and Food Chemistry, vol. 57, no. 23, pp. 11376-11382.
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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.

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, MP 2009, 'SEMIPARAMETRIC REGRESSION AND GRAPHICAL MODELS', Australian & New Zealand Journal of Statistics, vol. 51, no. 1, pp. 9-41.
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SummarySemiparametric 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 asbugsandvibes, 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 50-150 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 40-50 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. © 2008 Elsevier Ltd. All rights reserved.

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 Co3O4-carbon 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 Co3O4-carbon 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 Co3O4-carbon 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. © 2008 Elsevier B.V. All rights reserved.

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 Co 3O4 nanorods have a nanoporous structure, consisting of the textured aggregations of nanocrystals. Optical properties of Co 3O4 nanorods were characterized by Raman and UV-vis spectroscopy. Magnetic property measurement shows that Co3O 4 nanorods have a low Néel transition temperature of 35 K. We observed quite significant exchange bias for nanoporous Co3O 4 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. © 2009 American Chemical Society.

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. Ultraviolet-visible 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. © 2009 Elsevier Ltd. All rights reserved.

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 ultraviolet-visible 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. © 2009 Elsevier Ltd. All rights reserved.

Wang, G, Shen, X, Yao, J, Wexler, D & Ahn, J-H 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. © 2008 Elsevier B.V. All rights reserved.

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 (π-π 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. © 2009 Elsevier Ltd. All rights reserved.

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. © 2008 Elsevier Ltd. All rights reserved.

Wang, G, Wang, B, Wang, X, Park, J, Dou, S, 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. 8378-8378.
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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 (2-5 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. © 2009 The Royal Society of Chemistry.

Wang, GX, Park, JS & Park, MS 2009, 'Growth, Characterization and Technological Applications of Semiconductor SnO<SUB>2</SUB> Nanotubes and In<SUB>2</SUB>O<SUB>3</SUB> Nanowires', Journal of Nanoscience and 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 SnO 2 nanotubes has been investigated. Due to the small grain size and large amount of grain boundary, SnO 2 nanotubes demonstrated good sensitivity in sensing ethanol gas and had an ability to detect ammonia gas without any doping or surface modification. In 2O 3 semiconductor nanowires were synthesized efficiently by the chemical vapor deposition method through carbon thermal reduction. The diameter, length and morphologies of In 2O 3 nanowires can be varied by controlling the synthetic conditions. The In 2O 3 nanowires were characterized by field emission scanning electron microscopy (FE-SEM) and high resolution transmission electron microscopy (HRTEM). The application of In203 nanowires for gas sensors was tested. Copyright © 2009 American Scientific Publishers All rights reserved.

Wang, J-Z, Chou, S-L, Liu, H, Wang, GX, Zhong, C, Chew, SY & Liu, HK 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. © 2009 Elsevier B.V. All rights reserved.

Wang, M-B & 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, pp. 183103-183103.
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The adsorption of Li ions on boron doped graphene was investigated using a first-principles method. Our results show that, as boron doping turns graphene into an electron-deficient system, more Li ions can be captured around boron doped centers than in pristine graphene. One boron atom doped into graphene (6C ring unit) can adsorb six Li ions, which indicates that boron doped graphene is an efficient Li-ion storage material for lithium batteries. Further investigations show that, under limited conditions, boron doped graphene (BC5) can form Li6BC5 compound after Li-ion adsorption, corresponding to a lithium storage capacity of 2271 mAh/g which is six times that of graphite.

Wang, Y, Chi, Q, Hush, NS, 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 (DFT) calculations. The SAM forms in the unusual (8 × √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. © 2009 American Chemical Society.

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, no. 2, pp. 425-445.
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SummaryMicroarrays are one of the most widely used high throughput technologies. One of the main problems in the area is that conventional estimates of the variances that are required in the t-statistic and other statistics are unreliable owing to the small number of replications. Various methods have been proposed in the literature to overcome this lack of degrees of freedom problem. In this context, it is commonly observed that the variance increases proportionally with the intensity level, which has led many researchers to assume that the variance is a function of the mean. Here we concentrate on estimation of the variance as a function of an unknown mean in two models: the constant coefficient of variation model and the quadratic variance–mean model. Because the means are unknown and estimated with few degrees of freedom, naive methods that use the sample mean in place of the true mean are generally biased because of the errors-in-variables phenomenon. We propose three methods for overcoming this bias. The first two are variations on the theme of the so-called heteroscedastic simulation–extrapolation estimator, modified to estimate the variance function consistently. The third class of estimators is entirely different, being based on semiparametric information calculations. Simulations show the power of our methods and their lack of bias compared with the naive method that ignores the measurement error. The methodology is illustrated by using microarray data from leukaemia patients.

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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Abstract:  Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA‐based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single‐nucleotide polymorphisms were utilized as molecular markers for subfamily to species‐level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated “proof of concept” of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

Warren, CA, Paulhill, KJ, Davidson, LA, Lupton, JR, Taddeo, SS, Hong, MY, Carroll, RJ, Chapkin, RS & Turner, ND 2009, 'ERRATUM', The Journal of Nutrition, vol. 139, no. 4, pp. 792-792.
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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', The Journal of Nutrition, vol. 139, no. 1, pp. 101-105.
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Abstract The flavonoid quercetin suppresses cell proliferation and enhances apoptosis in vitro. In this study, we determined whether quercetin protects against colon cancer by regulating the protein level of phosphatidylinositol 3-kinase (PI 3-kinase) and Akt or by suppressing the expression of proinflammatory mediators [cyclooxygenase (COX)-1, COX-2, inducible nitric oxide synthase (iNOS)] during the aberrant crypt (AC) stage. Forty male rats were randomly assigned to receive diets containing quercetin (0 or 4.5 g/kg) and injected subcutaneously with saline or azoxymethane (AOM; 2 times during wk 3 and 4). The colon was resected 4 wk after the last AOM injection and samples were used to determine high multiplicity AC foci (HMACF; foci with >4 AC) number, colonocyte proliferation and apoptosis by immunohistochemistry, expression of PI 3-kinase (p85 and p85α subunits) and Akt by immunoblotting, and COX-1, COX-2, and iNOS expression by real time RT-PCR. Quercetin-fed rats had fewer (P = 0.033) HMACF. Relative to the control diet, quercetin lowered the proliferative index (P = 0.035) regardless of treatment and diminished the AOM-induced elevation in crypt column cell number (P = 0.044) and expansion of the proliferative zone (P = 0.021). The proportion of apoptotic colonocytes in AOM-injected rats increased with quercetin treatment (P = 0.014). Levels of p85 and p85α subunits of PI 3-kinase and total Akt were unaffected by dietary quercetin. However, quercetin tended to suppress (P < 0.06) the expression of COX-1 and COX-2. Expression of iNOS was elevated by AOM injection (P = 0.0001). In conclusion, quercetin suppresses the formation of early preneoplastic lesions in colon carcinogenesis, which occurred in concert with reductions in proliferation and increases in apoptosis. It is possible the effects on proliferation and apoptosis resulted from the tendency for quercetin to suppress the expression of proinflamm...

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. © 2009 The Association for the Study of Animal Behaviour.

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, R, Doble, P & 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 TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES, 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, Oliver & Trian 2009, 'Reconstruction is not renovation &ndash; the role of remodeling in asthma', Journal of Asthma and Allergy, no. 2, pp. 33-33.
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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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Weisenberg, M, Aslan, K, Hortle, E & Geddes, CD 2009, 'Directional surface plasmon coupled chemiluminescence from nickel thin films: Fixed angle observation', Chemical Physics Letters, vol. 473, no. 1-3, pp. 120-125.
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Weuve, J, Korrick, SA, Weisskopf, MA, 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 μg/g bone, 12.6 ± 11.6 μg/g bone, and 2.9 ± 1.9 μg/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.

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. © 2009 The Royal Society.

Whitley, R, Medlyn, B, Zeppel, M, Macinnis-Ng, C & Eamus, D 2009, 'Comparing the Penman-Monteith equation and a modified Jarvis-Stewart model with an artificial neural network to estimate stand-scale transpiration and canopy conductance', JOURNAL OF HYDROLOGY, vol. 373, no. 1-2, pp. 256-266.
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The responses of canopy conductance to variation in solar radiation, vapour pressure deficit and soil moisture have been extensively modelled using a Jarvis-Stewart (JS) model. Modelled canopy conductance has then often been used to predict transpiration using the Penman-Monteith (PM) model. We previously suggested an alternative approach in which the JS model is modified to directly estimate transpiration rather than canopy conductance. In the present study we used this alternative approach to model tree water fluxes from an Australian native forest over an annual cycle. For comparative purposes we also modelled canopy conductance and estimated transpiration via the PM model. Finally we applied an artificial neural network as a statistical benchmark to compare the performance of both models. Both the PM and modified JS models were parameterised using solar radiation, vapour pressure deficit and soil moisture as inputs with results that compare well with previous studies. Both models performed comparably well during the summer period. However, during winter the PM model was found to fail during periods of high rates of transpiration. In contrast, the modified JS model was able to replicate observed sapflow measurements throughout the year although it too tended to underestimate rates of transpiration in winter under conditions of high rates of transpiration. Both approaches to modelling transpiration gave good agreement with hourly, daily and total sums of sapflow measurements with the modified JS and PM models explaining 87% and 86% of the variance, respectively. We conclude that these three approaches have merit at different time-scales.

Williams, D, Caddy, J, Blann, K, Grové, J & Holzapfel, C 2009, 'Chiral Cyclobutanols and Cyclopentane Dimers via Samarium(II) Iodide Induced Keto-Olefin Cyclisations of Carbohydrate-Derived Unsaturated Ketones', Synthesis, vol. 2009, no. 12, pp. 2009-2014.
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Williams, D, Evans, S, de Bod, H, Mokhadinyana, M & Hughes, T 2009, 'Directed ortho Metallation Chemistry and Phosphine Synthesis: New Ligands for the Suzuki-Miyaura Reaction', Synthesis, vol. 2009, no. 18, pp. 3106-3112.
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Williams, DBG & Cullen, A 2009, 'Al(OTf)₃-Mediated Epoxide Ring-Opening Reactions: Toward Piperazine-Derived Physiologically Active Products', The 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, 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, FC, Oneal, DC, Djordjevic, MA, Connolly, A, Barchia, I, Walker, MJ & Djordjevic, SP 2009, 'Mhp493 (P216) is a proteolytically processed, cilium and heparin binding protein ofMycoplasma hyopneumoniae', Molecular Microbiology, vol. 71, no. 3, pp. 566-582.
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SummaryMycoplasma hyopneumoniaeinduces respiratory disease in swine by colonizing cilia causing ciliostasis, cilial loss and epithelial cell death. Heparin binds toM. hyopneumoniaecells 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 TiO2chromatography of trypsin digests of P85 isolated a single peptide with an m/z of 917.3. A phosphoserine residue in the tryptic peptide90VSELpSFR96(position 94 in P85) was identified by MALDI‐MS/MS. Polyhistidine fusion proteins (F1P216, F2P216, F3P216) spanning Mhp493 bound heparin with biologically significant Kd values, and heparin, fucoidan and mucin inhibited this interaction. Latex beads coated with F1P216, F2P216and F3P216adhered 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 byM. hyopneumoniae. Mhp493 contributes significantly to the surface architecture ofM. hyopneumoniaeand 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 sp3 to sp2 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. © 2009 American Chemical Society.

Wong, FWS, Lin, L & Lim, DCE 2009, 'Drug and herb interactions: searching the web.', Aust Fam 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 websites 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, GX, 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 spin-orbit interaction in the optical absorption of π-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 spin-orbit interaction in graphene. It was found that the spin-orbit interaction lifts the nodes in the absorption matrix. Furthermore, in the terahertz frequency regime, the spin-orbit interaction can significantly enhance the optical absorption in graphene, by up to 100%. Crown Copyright © 2008.

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 = 1-3) 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. © 2009 Elsevier B.V. All rights reserved.

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. 1258-1258.
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Wu, W, Jin, D, Lou, W, Fan, J, Wang, D & Qin, X 2009, 'A novel recombinant tandem repeat DNA vaccine targeting at MUC1', Journal of Clinical Oncology, vol. 27, no. 15_suppl, pp. 3066-3066.
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3066 Background: Tandem repeat (TR) is the key epitope of mucin 1 (MUC1) for inducing cytotoxic T lymphocytes (CTL) to kill the tumor cells specifically. A novel recombinant TR DNA vaccine was constructed to study its induced immune responses. Methods: A recombinant human TR (rhTR) gene encoding a single TR polypeptide of MUC1 was synthesized and cloned into the multiple cloning sites of plasmid pcDNA3.1/Myc-his (+) A to construct the recombinant plasmid pcDNA3.1-TR/Myc-his (+) A (pTR plasmid). Expression of pTR plasmid was confirmed by transfection assay and Western blot analysis. C57BL/6 (H-2b) mice were immunized with pTR plasmid (n=15) by tibial muscle injection. Mice inoculated with the empty vector (EV group, n=15) and 0.9% NaCl solution (NS group, n=15) were used as vector and blank control respectively. Four weeks later, all mice were immunized again. Specific antibody detection and cytotoxic assay were used to evaluate the vaccine-induced TR specific immune responses. Results: DNA sequencing confirmed that the pTR plasmid was exactly constructed. Transfection assay and Western blot analysis found that the transfected COS7 cells expressed TR polypeptide of MUC1 48 hours after transfection. Cytotoxic assay showed that immunization with pTR plasmid into C57BL/6 mice resulted in more efficient induction of CTL specific cytolysis against TR polypeptide than that of EV group and NS group (p<0.01). Vaccine immunized mice had a higher equivalent concentration of anti-TR specific antibodies (2324μg/ml±238μg/ml) than that of EV group (1896μg/ml±533μg/ml, p<0.01) and NS group (1736μg/ml±142μg/ml, p<0.01). Conclusions: The novel recombinant TR DNA vaccine targeting at MUC1 was exactly constructed, immunization with which could induce TR specific CTL response and antibodies response in mice. No significant financial relationships to disclose.

Xu, F, Zha, Y, Wang, G, Wang, Y & Li, J 2009, 'Damaging Effect of Visible Light-assisted Illuminated TiO2-Cu2O Nano-composite on Hela Cell', ACTA CHIMICA SINICA, vol. 67, no. 9, pp. 957-963.

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 ultraviolet-visible (UV-vis) spectroscopy methods. © 2008 Elsevier B.V. All rights reserved.

Yao, J, Park, JS, Konstantinov, K, Wang, GX, Ahn, J-H, Wang, J & Liu, HK 2009, 'Electrochemical Performance of Nanocrystalline SnO<SUB>2</SUB>-Carbon Nanotube Composites as Anode in Lithium-Ion Cells', Journal of Nanoscience and Nanotechnology, vol. 9, no. 2, pp. 1474-1478.
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SnO 2-carbon nanotube composites were prepared by chemical treatment of tin chloride salt mixed with carbon nanotubes, followed by heat-treatment at high temperature. Nanosize SnO 2 particles were formed and embedded in a carbon nanotube matrix. TEM and HRTEM observation confirmed the homogeneous distribution of SnO2 nanoparticles. SnO 2-carbon nanotube anodes demonstrated high lithium storage capacity and stable cyclability, which could be attributed to the nanosize SnO 2 crystals and the formation of carbon nanotube networks in the electrode. Copyright © 2009 American Scientific Publishers All rights reserved.

Yao, J, Shen, X, Wang, B, Liu, H & Wang, G 2009, 'In situ chemical synthesis of SnO2–graphene nanocomposite as anode materials for lithium-ion batteries', Electrochemistry Communications, vol. 11, no. 10, pp. 1849-1852.
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An in situ chemical synthesis approach has been developed to prepare SnO2-graphene nanocomposite. Field emission scanning electron microscopy and transmission electron microscopy observation revealed the homogeneous distribution of SnO2 nanoparticles (4-6 nm in size) on graphene matrix. The electrochemical reactivities of the SnO2-graphene nanocomposite as anode material were measured by cyclic voltammetry and galvanostatic charge/discharge cycling. The as-synthesized SnO2-graphene 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 SnO2-graphene nanocomposite. © 2009 Elsevier B.V. All rights reserved.

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.

Ying, G-G, Rawson, CA, Kookana, RS, Peng, P-A, Warne, MSJ, Tremblay, LA, Laginestra, E, Chapman, JC & Lim, RP 2009, 'CONTAMINATION AND SCREENING LEVEL TOXICITY OF SEDIMENTS FROM REMEDIATED AND UNREMEDIATED WETLANDS NEAR SYDNEY, AUSTRALIA', ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, vol. 28, no. 10, pp. 2052-2060.
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The present study assessed contamination and toxicity of sediments from seven remediated and remnant wetland sites within Sydney Olympic Park, Australia, and four unremediated sites adjacent to its boundary using chemical analysis and a luminescent bacterial biosensor assay (Escherichia coli). Concentrations of metals (Pb, Cr, Cu, Ni, Zn, Cd, and As) and persistent organic chemicals (DDT and its metabolites, dichlorodiphenyldichloroethane and dichlorodiphenyldichloroethylene; polycyclic aromatic hydrocarbons; polychlorinated biphenyls; and polychlorinated dibenzo-p-dioxins and dibenzofurans) in sediments and their pore-water samples were determined. Zinc concentrations were the highest of the metals in the sediments (84-618 mg/kg), and at eight sites, metal concentrations in sediments exceeded the Australian ecological trigger values for Pb, Zn, and Ni. Concentrations of organic contaminants in the sediments exceeded the trigger values at all 11 sites for DDTs, at 6 sites for polycyclic aromatic hydrocarbons, and 5 sites for polychlorinated biphenyls. Sediment samples from the four unremediated sites outside the Sydney Olympic Park had dioxin concentrations greater than 200 pg (toxic equivalency per gram). The same four sites were identified as contaminated in pore-water toxicity tests with the luminescent biosensor, generally consistent with the bioavailable fractions of the contaminants (pore-water and Tenax (R) extraction data), as well as dioxin levels, in the sediments. Preliminary toxicity identification and evaluation tests of the pore water from the four sites outside the park demonstrated that organic contaminants were the main cause of toxicity to E. coli, with no evidence that metals contributed to the toxicity of the pore water.

Ying, G-G, Rawson, CA, Kookana, RS, Warne, MSJ, Peng, P-A, Li, X-M, Laginestra, E, Tremblay, LA, Chapman, JC & Lim, RP 2009, 'Distribution of inorganic and organic contaminants in sediments from Sydney Olympic Park and the surrounding Sydney metropolitan area', JOURNAL OF ENVIRONMENTAL MONITORING, vol. 11, no. 9, pp. 1687-1696.
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Yoshioka, H, Miura, T, Dematte, JAM, Batchily, K & Huete, AR 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 infrared 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. © 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.

Yu, J, Cheng, YY, Tao, Q, Cheung, KF, Lam, CNY, Geng, H, Tian, L, Wong, YP, Tong, JHM, Ying, J, Jin, H, To, KF, Chan, FKL & Sung, JJY 2009, 'Methylation of Protocadherin 10, a Novel Tumor Suppressor, Is Associated With Poor Prognosis in Patients With Gastric Cancer', Gastroenterology, vol. 136, no. 2, pp. 640-651.e1.
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Yu, J, Tao, Q, Cheng, YY, Lee, KY, Ng, SSM, Cheung, KF, Tian, L, Rha, SY, Neumann, U, Röcken, C, Ebert, MPA, Chan, FKL & Sung, JJY 2009, 'Promoter methylation of the Wnt/β‐catenin signaling antagonist Dkk‐3 is associated with poor survival in gastric cancer', Cancer, vol. 115, no. 1, pp. 49-60.
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AbstractBACKGROUND:Abnormal activation of the Wnt/β‐catenin signaling pathway is common and critical in the pathogenesis of digestive cancers. In this study, the authors investigated the promoter methylation of the dickkopf homolog 3 gene Dkk‐3 in these cancers and its prognostic significance in gastric cancer.METHODS:Dkk‐3 methylation was assessed in 173 patients with gastric cancers (including 104 patients who were followed for up to 4090 days) and in 128 patients with colorectal cancer. Cell growth was evaluated by using a colony‐formation assay. For survival analyses, the authors used Kaplan‐Meier plots, the log‐rank test, and Cox proportional regression.RESULTS:Dkk‐3 was silenced or down‐regulated in 12 of 17 gastric cancer cell lines (70.6%) and in 3 of 9 colon cancer cell lines (33.3%). The loss of gene expression was associated with promoter methylation, which could be restored by demethylating agents. Ectopic expression of Dkk‐3 suppressed colony formation. Moreover, methylation of Dkk‐3 was detected in 117 of 173 primary gastric tumors (67.6%) and in 67 of 128 colorectal tumors (52.3%). The clinical significance and the prognostic value of Dkk‐3 methylation also were examined in 104 gastric cancers and in 84 colorectal cancers. Multivariate analysis indicated that Dkk‐3 methylation was associated significantly and independently with poor disease survival (relative risk, 2.534; 95% confidence interval, 1.54–4.17; P = .002) in gastric cancer, but not in colorectal cancer. Kaplan‐Meier survival curves revealed that patients who had

Yunusa, IAM, Burchett, MD, Manoharan, V, DeSilva, DL, Eamus, D & Skilbeck, CG 2009, 'Photosynthetic Pigment Concentrations, Gas Exchange and Vegetative Growth for Selected Monocots and Dicots Treated with Two Contrasting Coal Fly Ashes', JOURNAL OF ENVIRONMENTAL QUALITY, vol. 38, no. 4, pp. 1466-1472.
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There is uncertainty as to the races of coal fly ash needed for optimum physiological processes and growth. In the current study we tested the hyothesis that photosynthetic pigments concentrations and CO2 assimilation (A) are more sensitive than dry weights in plants grown on media amended with coal fly ash. We applied the Terrestrial Plant Growth Test (Guideline 208) protocols of the Organization for Economic Cooperation and Development (OECD) to monocots [barley (Hordeum vulgare) and ryegrass (Secale cereale)] and dicots [canola (Brasica napus), radish (Raphanus sativus), field peas (Pisum sativum), and lucerne (Medicago sativa)] on media amended with fly ashes derived from semi-bituminous (gray ash) or lignite (red ash) coals at rates of 0, 2.5, 5.0, 10, or 20 Mg ha(-1). The red ash had higher elemental concentrations and salinity than the gray ash. Fly ash addition had no significant effect on germination by any of the six species. At moderate rates (<= 10 Mg ha(-1)) both ashes increased (P < 0.05) growth rates and concentrations of chlorophylls a and b, but reduced carotenoid concentrations. Addition of either ash increased A in radish and transpiration in barley Growth rates and final dry weights were reduced for all of the six test species when addition rates exceeded 10 Mg ha(-1) for gray ash and 5 Mg ha(-1) for red ash. We concluded that plant dry weights, rather than pigment concentrations and/or instantaneous rates of photosynthesis, are more consistent for assessing subsequent growth in plants Supplied with fly ash. Copyright (C) 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher.

Zeppel, M, Macinnis-Ng, C, Palmer, A, Taylor, D, Whitley, R, Fuentes, S, Yunusa, I, Williams, M & Eamus, D 2009, 'An analysis of the sensitivity of sap flux to soil and plant variables assessed for an Australian woodland using a soil-plant-atmosphere model (vol 35, pg 509, 2008)', FUNCTIONAL PLANT BIOLOGY, vol. 36, no. 12, pp. 1120-U108.
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Zhang, J, Zhou, L, Tang, 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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Zhang, N, Wu, Z, McGowan, E, Shi, J, Hong, Z, Ding, C, Xia, P & Di, W 2009, 'Arsenic trioxide and cisplatin synergism increase cytotoxicity in human ovarian cancer cells: Therapeutic potential for ovarian cancer', Cancer Science, vol. 100, no. 12, pp. 2459-2464.
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Drug resistance is a major concern in the successful treatment of ovarian cancer. In the present study we report a combinational drug regime using arsenic trioxide (ATO) and cisplatin (CDDP) to increase therapeutic potentiality in ovarian cancer cells. ATO‐mediated growth inhibition and apoptosis in human suspension ovarian cancer COC1 cells were evaluated by MTT assay and annexin V assay using flow cytometry, respectively. cDNA arrays were performed to screen ATO‐mediated gene expression. Treatment of COC1 cells with ATO alone resulted in growth inhibition and apoptosis with a dose‐and time‐dependent fashion; further cDNA arrays showed that 34 genes (23 up‐regulated genes and 11 down‐regulated genes) may strongly associate with the antiproliferative and pro‐apoptotic effects induced by ATO. Furthermore, Chou–Talalay analysis was used to evaluate the combinational effect of ATO and CDDP as well as dose‐reduction index (DRI) in a panel of ovarian cancer cells including CDDP‐sensitive and ‐resistant cell lines. The combination index (CI) analysis indicated that the interaction effect of ATO/CDDP exhibited a wide range of synergism in all the adherent ovarian cancer cells (A2780, IGROV‐1, SKOV‐3, and R182) as well as 0.93 to 0.69 for IC50 to IC90 in suspension COC1 cells where CI < 1, =1, and >1, define synergism, additive effect, and antagonism, respectively. More intriguingly, the combination of ATO and CDDP yielded favorable DRIs ranging from 1.23‐fold to 13.51‐fold dose reduction. These results suggest that ATO and its combination with CDDP present therapeutic potential for ovarian cancer, and deserve further preclinical and clinical studies. (Cancer Sci 2009; 100: 2459–2464)

Zhao, H-T, Endo, S, Ishikura, S, Chung, R, Hogg, PJ, Hara, A & El-Kabbani, O 2009, 'Structure/function analysis of a critical disulfide bond in the active site of l-xylulose reductase', Cellular and Molecular Life Sciences, vol. 66, no. 9, pp. 1570-1579.
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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, pp. 141101-141101.
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Near-infrared quantum cutting involving the emission of near-infrared photons by downconversion cooperative energy transfer from Eu2+ to Yb3+ in borate glasses was reported. Electron spin resonance spectra and absorption spectra were measured to prove the existence of Eu2+ in borate glasses. Excitation, emission, and fluorescence decay measurements were performed to examine the occurrence of cooperative energy transfer from Eu2+ to Yb3+ ions. Yb3+ concentration dependent quantum efficiency was calculated and the maximum efficiency approaches 164.19%.

Zhuang, Y, Teng, Y, Zhou, J, Ye, S, Liu, X, Lin, G, Ruan, J & Qiu, J 2009, 'Broadband downconversion from oxygen-deficient centers to Yb^3+ in germanate glasses', Journal of the Optical Society of America B, vol. 26, no. 11, pp. 2185-2185.
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Alkhouri, H, Roth, M, Oliver, B, Armour, CL & Hughes, JM 1970, 'Role of C/EBP-Isoforms in IP-10 and IL-6 Production by Human Airway Smooth Muscle Cells.', D108. INFLAMMATORY MEDIATORS: OLD AND NEW PLAYERS, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society, pp. A6317-A6317.
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Amaudruz, P-A, Retiere, F, Bishop, D, Oser, S, Olchanski, K, Pearson, C, Ohlmann, C, Poutissou, R, Lindner, T, Braam, N, Hasanen, R, Poffenberger, P, Kirby, B, Tanaka, H, Henderson, R, Karlen, D, Zalipska, J, Miller, A, Mizouchi, K, Gutjahr, C, Honkanen, N & Wilking, M 1970, 'Overview of the T2K Fine Grained Detector data acquisition at J-Parc', 2009 16th IEEE-NPSS Real Time Conference, 2009 16th IEEE-NPSS Real Time Conference (RT), IEEE, pp. 38-42.
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Ammit, AJ, Manetsch, M, Ramsay, EE & Ge, Q 1970, 'Uncovering the Molecular Mechanisms Underlying Mitogen-Activated Protein Kinase Phosphatase 1 Upregulation by Corticosteroids/β₂-Agonists.', B109. AIRWAY SMOOTH MUSCLE PHENOTYPE AND FUNCTION, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society.
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Arnold, MD & Smith, GB 1970, 'Comparisons of enhanced absorption in closely-coupled granting-mirror and random particle-mirror systems', NANOSTRUCTURED THIN FILMS II, 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. © 2009 SPIE.

Asatryan, AA, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC & De Sterke, CM 1970, 'The local density of states of metamaterial photonic crystals', Optics InfoBase Conference Papers, Australian Insitute of Physics, Adelaide, pp. 171-174.
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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, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC & De Sterke, CM 1970, 'The local density of states of metamaterial photonic crystals', Optics InfoBase Conference Papers, 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. © 2009 Optical Society of America.

Asatryan, AA, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC & de Sterke, CM 1970, 'The local density of states of metamaterial photonic crystals', Conference on Lasers and Electro-Optics/International Quantum Electronics Conference, Conference on Lasers and Electro-Optics, OSA, pp. JThE107-JThE107.
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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, Botten, LC, Dossou, KB, Poulton, CG, Chen, P, McPhedran, RC, de Sterke, CM & IEEE 1970, '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. 2531-2532.

Boyce, A, Wilson, F, Chen, H, Gibson, K, Lumbers, E & Morris, M 1970, '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, Sklibosios Nikitopoulos, C, Platen, E & Schlogl, E 1970, 'Alternative Defaultable Term Structure Models', Quantitative Finance Research Centre Research Paper, X Workshop on Quantitative Finance to the Memory of Nicola Bruti-Liberati, Milan, Italy.

Cass, A, Bellomo, R, Cole, L, Finfer, S, Gallagher, M, Lo, S, McArthur, C, McGuinness, S, Myburgh, J, Norton, R, Scheinkestel, C & Su, S 1970, 'INTENSITY OF CONTINUOUS RENAL REPLACEMENT THERAPY IN CRITICALLY ILL PATIENTS WITH SEVERE ACUTE KIDNEY INJURY', NEPHROLOGY, WILEY-BLACKWELL PUBLISHING, INC, pp. A21-A21.

Chan, JH, Shimmon, R, Spindler, X, Maynard, PJ, Lennard, CJ, Roux, CP & Stuart, BH 1970, '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 1970, 'Chemoprotective fish oil/pectin diets temporally alter gene expression profiles in exfoliated colonocytes', The FASEB Journal, Wiley.
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We have demonstrated that fish oil/pectin (FP) diets are protective against colon cancer compared to corn oil/cellulose (CC) in part by upregulating apoptosis at the promotion stage of carcinogenesis and suppressing peroxisome proliferator‐activated receptor δ(PPARδ) expression at the tumor stage. To elucidate the underlying mechanisms whereby FP diets induce apoptosis and suppress PPAR signals, we analyzed the temporal gene expression profiles from exfoliated rat colonocytes. Rats consumed diets containing either FP or CC and were injected with azoxymethane (2x, 15 mg/kg BW, sc). Fecal material was collected at 7, 14, and 28 wk in the same rats and was used for poly A+ RNA extraction. Gene expression signatures were determined using GE Codelink arrays. GO analysis identified 10 genes upregulated by FP at the promotion stage of carcinogenesis involved in apoptosis (p=0.006). KEGG pathway analysis indicated that FP suppressed seven genes in the PPAR signaling pathway at the tumor stage (p=0.056). We conclude that the effects of chemotherapeutic diets on epithelial cell gene expression can be monitored noninvasively throughout the tumorigenic process.Grant Funding SourceFunded by NSBRI NASA NCC 9‐58 and NIH (CA59034, CA57030).

de Sterke, CM, Dossou, KB, White, TP, Botten, LC & McPhedran, RC 1970, '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 1970, 'Direct, efficient coupling into slow light photonic crystal waveguide: role of evanescent modes', Frontiers in Optics 2009/Laser Science XXV/Fall 2009 OSA Optics & Photonics Technical Digest, Frontiers in Optics, OSA, pp. FWF5-FWF5.
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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 1970, 'Role of evanescent modes in direct, efficient coupling into slow light photonic crystal waveguides', Asia Communications and Photonics Conference and Exhibition, Asia Communications and Photonics Conference and Exhibition, OSA, pp. TuV1-TuV1.
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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 1970, '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 1970, '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.

Doblin, MA, Ralph, PJ, Oubelkheir, K, Hassler, CS, Suthers, I & Thompson, P 1970, '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 1970, 'Athletes healthcarebehaviour: an ethnographers conumdrum', Proceedings of 4th Annual International Ethnography Symposium, University of Liverpool, Liverpool England.

Freeman, LM, White, D & Zaslawski, CJ 1970, '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 & IEEE 1970, '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. 3395-3398.
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Fu, K-MC, Santori, C, Barclay, PE, Meyer, N, Holm, AM, Aharonovich, I, Prawer, S & Beausoleil, RG 1970, 'Optical Coupling of Nitrogen-Vacancy Centers in Diamond to GaP Waveguides', Conference on Lasers and Electro-Optics/International Quantum Electronics Conference, International Quantum Electronics Conference, OSA, pp. IThB5-IThB5.
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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 1970, 'Photonic structures for QIP in diamond', ADVANCED OPTICAL CONCEPTS IN QUANTUM COMPUTING, MEMORY, AND COMMUNICATION II.
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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 1970, '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, Elsevier BV, Lisbon, PORTUGAL, pp. 89-89.
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Ge, Q, Oliver, BGG, Moir, LM, Lau, EMT, Black, JL & Burgess, JK 1970, '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.

Gentle, AR & Smith, GB 1970, 'Angular selectivity: impact on optimised coatings for night sky radiative cooling', NANOSTRUCTURED THIN FILMS II, 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 electivity, 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. © 2009 SPIE.

Gracanin, M, Rodgers, KJ, Hawkins, CL & Davies, MJ 1970, '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.

Hansbro, PM, Essilfie, AT, Simpson, JL, Dunkley, ML & Gibson, PG 1970, 'Haemophilus influenzaeInduces Features of Neutrophilic Asthma.', C30. INFLAMMATORY AND IMMUNOLOGICAL MODELS OF ASTHMA, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society, pp. A4251-A4251.
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Hansbro, PM, Starkey, MR, Horvat, JC, Kim, RY, Phipps, S, Gibson, PG, Beagley, KW & Foster, PS 1970, 'Early Life Chlamydial Lung Infection Enhances Allergic Airways Disease through Age-Dependent Differences in Immunopathology.', B102. IMMUNE MECHANISMS IN THE AIRWAY AND RESPONSE TO INJURY AND INFECTION, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society, pp. A3729-A3729.
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Hansbro, PM, Thorburn, AN, Foster, PS & Gibson, PG 1970, '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 1970, 'Prevenar Suppresses Allergic Airways Disease through the Induction of Regulatory T Cells.', A101. MOUSE MODELS OF ALLERGIC INFLAMMATION: MECHANISMS, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society, pp. A2228-A2228.
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Heather, AK, Li, X-H, Bartusch, M, Dy, V, Liong, EC, McGrath, KC & Tan, JT 1970, 'DHCR24 Is a Negative Regulator of Nuclear Factor-kappa B and Chronic Inflammation in Human Endothelial Cells', ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 10th Annual Conference on Arteriosclerosis, Thrombosis and Vascular Biology, LIPPINCOTT WILLIAMS & WILKINS, Washington, DC, pp. E27-E28.

Heather, AK, Li, XH, Bartusch, M, Dy, V, Liong, EC, McGrath, KC & Tan, JTM 1970, 'Arteriosclerosis, Thrombosis, and Vascular Biology Annual Conference 2009', Arteriosclerosis, Thrombosis, and Vascular Biology, You have accessArteriosclerosis, Thrombosis, and Vascular Biology Annual Conference, Ovid Technologies (Wolters Kluwer Health), pp. E27-E28.
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Herbert, C, Scruton, K, Hsu, K, Siegle, JS, Hansbro, N, Foster, PS, Tedla, N & Kumar, RK 1970, 'Enhanced Expression of Cytokines by Pulmonary T-Cells and Macrophages in a Model of Exacerbations of Chronic Asthma.', C30. INFLAMMATORY AND IMMUNOLOGICAL MODELS OF ASTHMA, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society, pp. A4239-A4239.
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Hess, L, Ratana, P, Huete, A, Potter, C, Melack, J & IEEE 1970, '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. 3387-3390.
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Horvat, JC, Starkey, MR, Beagley, KW, Gibson, PG, Foster, PS & Hansbro, PM 1970, 'Chlamydial respiratory infection predisposes to neutrophil dominated allergic airways disease (AAD) (79.5)', The Journal of Immunology, Oxford University Press (OUP), pp. 79.5-79.5.
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Abstract Chlamydial lung infections are associated with asthma but it is unknown how these Th1-inducing infections influence Th2-mediated asthma. We investigated the effect of current and resolved chlamydial infection on the development of hallmark features of asthma using a murine model of ovalbumin (Ova)-induced AAD. BALB/c mice were infected with Chlamydia and had either resolved or current respiratory infection at the time of sensitization to Ova. The effect of infection on AAD was compared with un-infected or non-allergic controls. Current, but not resolved, infection attenuated hallmark features of eosinophilic AAD; pulmonary eosinophil influx, T cell production of IL-5, mucus secreting cell (MSC) hyperplasia and airways hyper-responsiveness (AHR). Importantly, while current infection suppressed Th2-mediated AAD, robust Ova-specific IFN-γ release from T cells and allergen-driven neutrophilic inflammation were induced. This neutrophilic phenotype correlated with increased pulmonary expression of IL-12 and IL-17 and suppression of thymus and activation-related chemokine (TARC). Inhibition of neutrophil and macrophage chemotaxis into the lungs during current infection reversed neutrophilic inflammation and IFN-γ production in AAD and removed the attenuating effect of infection on MSC hyperplasia and AHR. These changes correlated with decreased IL-12 and IL-17 expression, increased TARC and altered antigen presenting cell function. Ongoing chlamydial respiratory infections modify key allergen-specific immune responses in AAD with the composition of cellular inflammatory responses to infection crucial in determining the outcome of allergic phenotype. Supported by the NHMRC

Horvat, JC, Starkey, MR, Beagley, KW, Preston, JA, Gibson, PG, Foster, PS & Hansbro, PM 1970, 'Neutrophil Influx during Chlamydial Lung Infection Determines the Phenotype of Allergic Airways Disease (AAD).', A101. MOUSE MODELS OF ALLERGIC INFLAMMATION: MECHANISMS, American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California, American Thoracic Society, pp. A2230-A2230.
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Jeffries, TC, Newton, K, Leterme, S, Seymour, JR, Dinsdale, E, Gilbert, J, Roudnew, B, Smith, R, Seuront, L & Mitchell, J 1970, '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 1970, 'Functional metagenomics of sediment microbial communities from a hypersaline coastal lagoon', Adelaide, Australia.

Jin, D, Rong, Y, Lou, W, Qin, X, Wu, W, Nin, X, Nin, X, Wang, D, Kuang, T & Qin, Y 1970, 'Therapeutic vaccination against advanced pancreatic cancer by autologous dendritic cells pulsed with a MUC1 peptide: Preclinical results of a clinical phase I trial', JOURNAL OF CLINICAL ONCOLOGY, 45th Annual Meeting of the American-Society-of-Clinical-Oncology, AMER SOC CLINICAL ONCOLOGY, FL, Orlando.

Jin, H, Liu, X, Wang, X, Lam, EKY, Shin, VY, Cheng, YY, Lam, YW, Yu, J, Chan, FKL & Sung, JJ 1970, 'Warburg Effect Revisited: An Epigenetic Link Between Aerobic Glycolysis and Gastric Carcinogenesis', GASTROENTEROLOGY, Digestive Disease Week/110th Annual Meeting of the American-Gastroenterological-Association, W B SAUNDERS CO-ELSEVIER INC, IL, Chicago, pp. A459-A459.

Kabakova, IV, Corcoran, B, Bolger, JA, de Sterke, CM & Eggleton, BJ 1970, 'All-Optical Self-Switching in an Optimized Fiber Bragg Grating with a Phase Shift', Conference on Lasers and Electro-Optics/International Quantum Electronics Conference, Conference on Lasers and Electro-Optics, OSA, pp. CThF1-CThF1.
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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.

Kabakova, IV, Corcoran, B, Bolger, JA, De Sterke, CM & Eggleton, BJ 1970, 'All-optical self-switching in an optimized fiber bragg grating with a π phase shift', Optics InfoBase Conference Papers, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 956-957.
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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.

Kim, H, Turner, ND, Taddeo, SS, Davidson, LA, Wang, N, Vannucci, M, Chapkin, RS, Carroll, RJ & Lupton, JR 1970, 'A fish oil/pectin diet suppresses radiation‐enhanced colon carcinogenesis via down‐regulation of the β‐catenin signaling pathway', The FASEB Journal, Wiley.
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In our previous study, a fish oil/pectin (FP) diet protected against radiation‐enhanced colon carcinogenesis by maintaining an elevated level of apoptosis relative to a corn oil/cellulose (CC) diet. The goal of this study was to determine the differences between the protective and promotive diets in the patterns of gene expression measured in exfoliated colonocytes from rats exposed to radiation (+/‐ 1 Gy, 1 GeV/nucleon Fe ions) and a chemical carcinogen (AOM, 2x, 15 mg/kg BW). Microarray data were analyzed using a mixed model ANOVA procedure, and genes exhibiting differential expression underwent Gene Ontology (GO) enrichment analyses. Radiation treatment affected expression of genes within the Wnt/β‐catenin pathways, which are involved in cell proliferation and apoptosis. FP feeding reduced expression of tyrosine kinase related genes, which are regulators of the Ras‐PI3K/Akt signaling pathway. Therefore, a FP containing diet may suppress β‐catenin signaling induced by the radiation treatment, thereby contributing to the maintenance of apoptosis.Grant Funding SourceSupported by NSBRI (NASA NCC 9‐58) and NIH (CA57030 and CA59034).

Krimmer, DI, Burgess, JK, Black, JL & Oliver, BGG 1970, '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 1970, '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 1970, '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 1970, '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 1970, 'Whales: A net sink or source of carbon to the atmosphere?', Adelaide, Australia.

Lawrence, FJ, Botten, LC, Dossou, KB & de Sterke, CM 1970, 'Impedance of Square and Hexagonal Photonic Crystals', Conference on Lasers and Electro-Optics/International Quantum Electronics Conference, Conference on Lasers and Electro-Optics, OSA, pp. JThE110-JThE110.
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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 1970, '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 & Martijn De Sterke, C 1970, 'Impedance of square and hexagonal photonic crystals', Optics InfoBase Conference Papers, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 2539-+.
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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 1970, '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, Mägi, E, Freeman, D, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'An Expanded k-Space Evanescent Coupling Technique for Characterizing Photonic Crystal Waveguides', Conference on Lasers and Electro-Optics/International Quantum Electronics Conference, Conference on Lasers and Electro-Optics, OSA, pp. CTuDD5-CTuDD5.
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Lee, MW, Grillet, C, Poulton, CG, Monat, C, Smith, CLC, Mägi, E, Freeman, D, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, 'An expanded k-space evanescent coupling technique for characterizing photonic crystal waveguides', Optics InfoBase Conference Papers, Conference on Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), IEEE, Baltimore, MD, pp. 1325-+.
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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.

Lee, MW, Grillet, C, Poulton, CG, Monat, C, Smith, CLC, Mägi, E, Freeman, D, Madden, S, Luther-Davies, B & Eggleton, BJ 1970, '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, K, Wuhrer, R, Ben-Nissan, B, Valenzuela, SM & Moran, K 1970, 'X-Ray Mapping of Minerals Incorporated into Liposomes', MICROSCOPY AND MICROANALYSIS, 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.

Moir, LM, Poniris, MH, Santa, T, Burgess, JK, Oliver, BGG & Black, JL 1970, 'Doxycycline May Modulate Lymphangioleiomyomatosis (LAM) Cell Function In Vitro.', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, AMER THORACIC SOC.

Moore, C, Blaikie, RJ & Arnold, MD 1970, 'Improved Analytical Models for Single- and Multi-Layer Silver Superlenses', MATERIALS FOR NANOPHOTONICS - PLASMONICS, METAMATERIALS AND LIGHT LOCALIZATION, Materials Research Society Symposium Proceedings 1182, Materials Research Society, San Francisco, USA, pp. 29-39.
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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.

Newton, K, Jeffries, TC, Seymour, JR, Leterme, S, Mitchell, J & Seuront, L 1970, 'Impact of salinity on viral morphological diversity', Adelaide, Australia.

Nielsen, JA, Sandmann, K & Schlogl, E 1970, 'Equity-Linked Pension Schemes with Guarantees', 14th International Congress on Insurance: Mathematics and Economics, Toronto, Canada.

Oliver, B, Orpez, T, Lopez-Madrona, JC, Suardiaz, M, Lopez-Gomez, C, Nevado-Alcaide, IA, Maldonado-Sanchez, R, Marin, C & Fernandez, O 1970, '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 1970, 'Dietary lipid source alters quercetin effects on antioxidant enzyme/phase I and II gene expression in rat colon', The FASEB Journal, Wiley.
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We have demonstrated changes in antioxidant enzyme activities and glutathione metabolism in colonocytes from rats consuming diets containing 0.45% quercetin combined with corn oil or fish oil. The goal of this study was to query whether these changes were regulated at the transcriptional level. Therefore, real‐time PCR was used to assess the relative expression of 15 genes involved in maintaining cellular antioxidant levels and xenobiotic metabolism. Fish oil alone enhanced the level of catalase, and did not affect the expression of any other genes tested. Quercetin decreased the expression of six genes (SOD2, GPx2, GPx4, GLR2, Ephx2, Cyp1a1) and elevated the expression of Ephx1. When the interaction between quercetin and dietary lipid was analyzed, it was noted that quercetin and fish oil tended to lower the expression levels of seven genes, when compared with the fish oil rats not consuming quercetin. However, when quercetin was combined with corn oil, there was a tendency for mixed responses with four genes enhanced and two suppressed. These data suggest that the ability of quercetin to suppress expression of genes involved in regulating cellular antioxidant status and xenobiotic activation/ detoxification is amplified by its combination with fish oil. Funding USDA/CSREES 2005‐34402‐16401, 2007‐118409, and NIEHS P30‐ES09106.

Petrou, K, Doblin, MA, Hassler, CS & Ralph, PJ 1970, 'Multiple stressors on the sea ice diatom Fragilariopsis cylindrus - photophysiological impacts of seasonal freezing and melting of sea ice', Japan.

Pilz, KF & Schlogl, E 1970, 'A Hybrid Commodity and Interest Rate Market Model', 6th World Congress of the Bachelier Finance Society, Toronto, Canada.

Platen, E 1970, 'A benchmark approach beyond semi-martingales', Workshop on Non-Semi-Martingale Modelling in Finance, Helsinki, Finland.

Platen, E 1970, 'A Variance Reduction Technique Based on Integral Representations', Seminar Presentation, Fraunhofer Institute and the University of Kaiserslauten, Kaiserslauten, Germany.

Platen, E 1970, 'Asset markets and monetary policy', Seminar Presentation, Technical University Munich, Munich, Germany.

Platen, E 1970, 'Numerical solution of stochastic differential equations with jumps in finance', Seminar Presentation, University of Oxford, Oxford, UK.

Platen, E 1970, 'On interest rate term structure modeling under the benchmark approach', Seminar Presentation, Humboldt University, Berlin, Germany.

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 & Chigrin, DN 1970, 'Semi-analytical models for resonant states near photonic crystal band edges', AIP Conference Proceedings, THEORETICAL AND COMPUTATIONAL NANOPHOTONICS (TACONA-PHOTONICS 2009): Proceedings of the 2nd International Workshop, AIP, Bad Honnef, GERMANY, pp. 78-80.
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Ramelow, S, Ratschbache, L, Fedrizzi, A, Langford, NK & Zeilinger, A 1970, 'Discrete, tunable color-entanglement', Optics InfoBase Conference Papers.

Ramelow, S, Ratschbache, L, Fedrizzi, A, Langford, NK & Zeilinger, A 1970, 'Discrete, tunable color-entanglement', CLEO/Europe - EQEC 2009 - European Conference on Lasers and Electro-Optics and the European Quantum Electronics Conference, 2009 Conference on Lasers & Electro-Optics Europe & 11th European Quantum Electronics Conference (CLEO/EQEC), IEEE, pp. 1-1.
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Seidel, P, Merfort, I, Hughes, JM, Oliver, BGG, Tamm, M & Roth, M 1970, '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.

Seymour, JR 1970, '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 1970, '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.

Sinutok, S, Hill, R & Ralph, PJ 1970, '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.

Tovey, ER, Ng, DSY, Stelzer-Braid, S, Rawlinson, WD & Oliver, BG 1970, 'RETRACTED: Children With Asthma And No URTI, More Commonly Have Rhinovirus In Their Exhaled Breath, Than In Mucous', Journal of Allergy and Clinical Immunology, 65th Annual Meeting of the American-Academy-of-Allergy-Asthma-and-Immunology, Elsevier BV, Washington, DC, pp. S171-S171.
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Trian, T, Moir, LM, Burgess, JK, Black, JL, Reddel, H, Oliver, BG & McParland, B 1970, '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, Turnbull, L, Whitchurch, C & Ranganathan, P 1970, 'Segmentation and tracking individual Pseudomonas aeruginosa bacteria in dense populations of motile cells', 2009 24TH INTERNATIONAL CONFERENCE IMAGE AND VISION COMPUTING NEW ZEALAND (IVCNZ 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.

Wark, PAB, Hsu, A & Hansbro, P 1970, 'Innate immune response of bronchial epithelial cells to infection with influenza (130.7)', The Journal of Immunology, Oxford University Press (OUP), pp. 130.7-130.7.
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Abstract Bronchial epithelial cells are the natural human host for influenza infection but knowledge about the innate immune response is limited. Study objectives; characterise the innate immune response of bronchial epithelial cells to infection with human influenza A virus and relate this to virus replication. Methods; Influenza H3N2, A/Wellington/2004 (H3N2) was cultured and titred using plaque assays on Manine Darby Kidney Cells. Primary bronchial epithelial cells (PBECs) were obtained by bronchoscopy and cultured. Their response was compared to an epithelial cell line, Calu 3. Innate immune response was measured by the induction of mRNA by real time PCR for RIG-I, MDA-5, TLR-3, PKR, interferon (IFN)-β. Protein expression was then measured by western blot in cell lysate or supernatant. Results; H3N2 replicated to significantly higher titres in Calu 3 cells 2.8x106 PFU/ml compared to PBECs 789 PFU/ml (p&lt;0.001). Following infection there was greater than 20 fold induction of RIG-I mRNA in both cells, strong protein expression in PBECs by 24hr, only faint expression in Calu3. A thousand fold induction in MDA-5 mRNA was seen in PBECs at 48hr less than 20 fold in Calu3. Induction of IFN-β mRNA by 24hr and protein release in the supernatant was seen in both cells by 6hr. Conclusions; H3N2 replicates less well in PBECs and this is associated with more vigorous induction of RIG-I during early infection and later induction of MDA-5 mRNA.

Wark, PAB, See, HV, Simpson, JL, Forbes, RL & Hansbro, P 1970, 'Peripheral blood monocytes (PBMCs) display innate antiviral response to rhinovirus (RV) infected bronchial epithelial cells (133.44)', The Journal of Immunology, Oxford University Press (OUP), pp. 133.44-133.44.
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Abstract Rhinovirus (RV) infection is an important trigger of acute asthma and COPD. Study objectives; were to characterise the response of PBMCs and CD8 lymphocytes when exposed to RV infected bronchial epithelial cells. Methods; Human Calu3 cells were used as a model for bronchial epithelial cells and infected with RV-43 and RV-1B. PBMCs were obtained from healthy individuals and separated by Ficoll-Paque centrifugation. CD8 lymphocytes were identified as CD3+, CD8+ by flow cytometry. PBMCs were exposed to infected Calu3 cells, cells exposed to UV inactive RV, PHA and TLR3 agonist PolyI:C. Response was measured by ELISA for release of interferon(IFN)-γ and TNF-α. CD8 activation with expression of perforin or proliferation measured by carboxyfluorescein succinimidyl ester assay. Results: Exposure of PBMCs to Calu3 cells infected with both RV led to significant release of IFN-γ and TNF-α, smaller release was seen in response to UV inactive RV. Exposure to PolyI:C also led to a similar release. CD8+ cells were found to be the primary source of IFN-γ release. CD8+ cells did not show an increase in perforin expression or evidence of proliferation. Conclusions; exposure of PBMCs and CD8+ cells to an RV infected bronchial epithelium alone results in an innate immune response mediated by TLR3 without evidence of a CD8 adaptive immune response.

Wu, W, Jin, D, Lou, W, Fan, J, Wang, D & Qin, X 1970, 'A novel recombinant tandem repeat DNA vaccine targeting at MUC1', JOURNAL OF CLINICAL ONCOLOGY, 45th Annual Meeting of the American-Society-of-Clinical-Oncology, AMER SOC CLINICAL ONCOLOGY, FL, Orlando.

Yunusa, I, Whitley, R, Zeppel, M, Eamus, D & IEEE 1970, 'Simulation of Evapotranspiration and Vadose Zone Hydrology Using Limited Soil Data A comparison of Four Computer Models', PROCEEDINGS OF THE SECOND INTERNATIONAL CONFERENCE ON ENVIRONMENTAL AND COMPUTER SCIENCE, 2nd International Conference on Environmental and Computer Science, IEEE COMPUTER SOC, Dubai, U ARAB EMIRATES, pp. 152-155.
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Zinder, Y & Walker, SJ 1970, '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

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.

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.

Ajani, P 2009, 'Travelling through time: Phytoplankton biodiversity at Port Hacking, New South Wales'.

Breymann, W, Luethi, DR & 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, M & 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.

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.

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.