Aharonovich, I & Prawer, S 2010, 'Fabrication strategies for diamond based ultra bright single photon sources', DIAMOND AND RELATED MATERIALS, vol. 19, no. 7-9, pp. 729-733.
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Color centers in diamond attract a major attention due to their potential use in quantum information processing. In this work several methodologies to fabricate diamond based single photon emitters are presented: Ion implantation of an impurity into diam
Aharonovich, I, Castelletto, S, Johnson, BC, McCallum, JC, Simpson, DA, Greentree, AD & Prawer, S 2010, 'Chromium single-photon emitters in diamond fabricated by ion implantation', PHYSICAL REVIEW B, vol. 81, no. 12, pp. 1-4.
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Controlled fabrication and identification of bright single-photon emitters is at the heart of quantum optics. Here we demonstrate controlled engineering of a chromium bright single-photon source in bulk diamond by ion implantation. The Cr center has full
Aharonovich, I, Castelletto, S, Simpson, DA, Greentree, AD & Prawer, S 2010, 'Photophysics of chromium-related diamond single-photon emitters', PHYSICAL REVIEW A, vol. 81, no. 4.
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A detailed study of the photophysical properties of several chromium-related color centers produced within chemical vapor deposition diamond is presented. These emitters show narrow luminescence lines in the range of 740-770nm. Single-photon emission was verified with continuous and pulsed excitation with detected emission rates at saturation in the range of (2-3)×106 counts/s, while direct lifetime measurements reveal excited state lifetimes for the distinct centers ranging 1-14 ns. In addition, a number of quantum emitters demonstrate two-level behavior with no bunching present in the second-order correlation function. The three-level systems revealed typically photoluminescence lines with width half-maximum of ~4nm while the two-level emitters have full width half-maximum of ~10nm at room temperature. In addition, the quantum efficiency of the two-level system was measured to be four times higher than that of the three-level system. © 2010 The American Physical Society.
Al Kadiri, M, Carroll, RJ & Wand, MP 2010, 'Marginal longitudinal semiparametric regression via penalized splines', STATISTICS & PROBABILITY LETTERS, vol. 80, no. 15-16, pp. 1242-1252.
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We study the marginal longitudinal nonparametric regression problem and some of its semiparametric extensions. We point out that, while several elaborate proposals for efficient estimation have been proposed, a relative simple and straightforward one, based on penalized splines, has not. After describing our approach, we then explain how Gibbs sampling and the BUGS software can be used to achieve quick and effective implementation. Illustrations are provided for nonparametric regression and additive models. © 2010 Elsevier B.V.
Al-Qassab, S, Reichel, MP & Ellis, J 2010, 'A second generation multiplex PCR for typing strains of Neospora caninum using six DNA targets', MOLECULAR AND CELLULAR PROBES, vol. 24, no. 1, pp. 20-26.
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Genetic diversity of Neospora caninum was investigated through a study of repetitive sequences found in the genome of this species. Twenty different loci were studied, and three were identified that varied in repeat content amongst isolates. No relationship was found between the copy number of repetitive sequences present and host type or geographical location from which the isolates were derived. A multiplex PCR assay was developed for multilocus-strain typing using three microsatellites and three minisatellites, based on the polymorphisms found in the repetitive sequences. This study therefore extends knowledge on the repetitive sequences found in the N. caninum genome and the diversity found within the species. It also provides a second generation multiplex assay that can be used to study the biology of N. caninum. In addition, this study included Neospora hughesi (along with other closely related apicomplexans) as controls. The present study shows N. hughesi to be quite distinct from N. caninum in these repetitive sequences, thereby potentially providing a new approach for the differentiation of these two taxa.
Al-Qassab, SE, Reichel, MP & Ellis, JT 2010, 'On the Biological and Genetic Diversity in Neospora caninum', Diversity, vol. 2, no. 3, pp. 411-438.
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Neospora caninum is a parasite regarded a major cause of foetal loss in cattle. A key requirement to an understanding of the epidemiology and pathogenicity of N caninum is knowledge of the biological characteristics of the species and the genetic diversity within it. Due to the broad intermediate host range of the species, worldwide geographical distribution and its capacity fQr sexual reproduction, significant biological and genetic differences might be expected to exist. N caninum has now been isolated from a variety of different host species including dogs and cattle. Although isolates of this parasite show only minor differences in ultrastructure, considerable differences have been reported in pathogenicity using mainly mouse models. At the DNA level, marked levels of polymorphism between isolates were detected in mini- and microsatellites found in the genome of N caninum. Knowledge of what drives the biological differences that have been observed between the various isolates at the molecular level is crucial in aiding our understanding of the epidemiology of this parasite and, in tum, the development of efficacious strategies, such as live vaccines, for controlling its impact. The purpose of this review is to document and discuss for the first time, the nature of the diversity found within the species Neospora caninum.
Arnold, MD, Blaber, MG, Ford, MJ & Harris, N 2010, 'Universal scaling of local plasmons in chains of metal spheres', OPTICS EXPRESS, vol. 18, no. 7, pp. 7528-7542.
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The position, width, extinction, and electric field of localized plasmon modes in closely-coupled linear chains of small spheres are investigated. A dipole-like model is presented that separates the universal geometric factors from the specific metal permittivity. An electrostatic surface integral method is used to deduce universal parameters that are confirmed against results for different metals (bulk experimental Ag, Au, Al, K) calculated using retarded vector spherical harmonics and finite elements. The mode permittivity change decays to an asymptote with the number of particles in the chain, and changes dramatically from 1/f3to 1/f 1/2 as the gap fraction (ratio of gap between spheres to their diameter), f, gets smaller. Scattering increases significantly with closer coupling. The mode sharpness, strength and electric field for weakly retarded calculations are consistent with electrostatic predictions once the effect of radiative damping is accounted for. ©2010 Optical Society of America.
Asatryan, AA, Botten, LC, Byrne, MA, Freilikher, VD, Gredeskul, SA, Shadrivov, IV, McPhedran, RC & Kivshar, YS 2010, 'Effects of polarization on the transmission and localization of classical waves in weakly scattering metamaterials', PHYSICAL REVIEW B, vol. 82, no. 20, pp. 1-15.
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We summarize the results of our comprehensive analytical and numerical studies of the effects of polarization on the Anderson localization of classical waves in one-dimensional random stacks. We consider homogeneous stacks composed entirely of normal materials or metamaterials, and also mixed stacks composed of alternating layers of a normal material and a metamaterial. We extend the theoretical study developed earlier for the case of normal incidence to the case of off-axis incidence. For the general case where both the refractive indices and layer thicknesses are random, we obtain the long-wave and short-wave asymptotics of the localization length over a wide range of incidence angles (including the Brewster 'anomaly' angle). At the Brewster angle, we show that the long-wave localization length is proportional to the square of the wavelength, as for the case of normal incidence, but with a proportionality coefficient substantially larger than that for normal incidence. In mixed stacks with only refractive-index disorder, we demonstrate that p -polarized waves are strongly localized, while for s polarization the localization is substantially suppressed, as in the case of normal incidence. In the case of only thickness disorder, we study also the transition from localization to delocalization at the Brewster angle. © 2010 The American Physical Society.
Asatryan, AA, Gredeskul, SA, Botten, LC, Byrne, MA, Freilikher, VD, Shadrivov, IV, McPhedran, RC & Kivshar, YS 2010, 'Anderson localization of classical waves in weakly scattering metamaterials', PHYSICAL REVIEW B, vol. 81, no. 7, pp. 1-17.
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We study the propagation and localization of classical waves in one-dimensional disordered structures composed of alternating layers of left- and right-handed materials (mixed stacks) and compare them with structures composed of different layers of the same material (homogeneous stacks). For weakly scattering layers, we have developed an effective analytical approach and have calculated the transmission length within a wide range of the input parameters. This enables us to describe, in a unified way, the localized and ballistic regimes as well as the crossover between them. When both refractive index and layer thickness of a mixed stack are random, the transmission length in the long-wave range of the localized regime exhibits a quadratic power wavelength dependence with different coefficients of proportionality for mixed and homogeneous stacks. Moreover, the transmission length of a mixed stack differs from the reciprocal of the Lyapunov exponent of the corresponding infinite stack. In both the ballistic regime of a mixed stack and in the near long-wave region of a homogeneous stack, the transmission length of a realization is a strongly fluctuating quantity. In the far long-wave part of the ballistic region, the homogeneous stack becomes effectively uniform and the transmission length fluctuations are weaker. The crossover region from the localization to the ballistic regime is relatively narrow for both mixed and homogeneous stacks. In mixed stacks with only refractive-index disorder, Anderson localization at long wavelengths is substantially suppressed, with the localization length growing with wavelength much faster than for homogeneous stacks. The crossover region becomes essentially wider and transmission resonances appear only in much longer stacks. The effects of absorption on one-dimensional transport and localization have also been studied, both analytically and numerically. Specifically, it is shown that the crossover region is particularly ...
Austin, C, Hare, D, Rawling, T, McDonagh, AM & Doble, P 2010, 'Quantification method for elemental bio-imaging by LA-ICP-MS using metal spiked PMMA films', JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY, vol. 25, no. 5, pp. 722-725.
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A method for quantitative analysis of biological soft tissues by laser ablation-inductively coupled plasma-mass spectrometry has been developed. Polymer film standards were produced by spin coating spiked solutions of polymethylmethacrylate onto quartz substrates. Calibration curves throughout the range of 0-400 μg g-1 yielded correlation coefficients better than 0.999 for 66Zn and 63Cu. Spiked, homogenised soft tissue standards were quantified by LA-ICP-MS against the thin film standards. The results agreed with values calculated from solution nebulisation ICP-MS. A procedure for internal standardisation by employing ruthenium or yttrium in the underlying thin film was also assessed. © The Royal Society of Chemistry 2010.
Baker, AC & Murray, BR 2010, 'Relationships between leaf-litter traits and the emergence and early growth of invasive Pinus radiata seedlings', WEED RESEARCH, vol. 50, no. 6, pp. 586-596.
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Summary: Pinus radiata is an invasive weed in Australia that spreads from plantations and establishes in surrounding native eucalypt woodlands. To determine factors linked to the invasiveness of P. radiata, we compared emergence and growth traits of P. radiata seedlings at five different depths of leaf litter under pine needles, native eucalypt leaves and an equal mix of the two. Seedling emergence, height, survival and establishment were significantly reduced as leaf-litter depth increased. Seedlings had lower root:shoot ratios and higher specific leaf area (SLA) under deeper litter treatments, shifts linked to the provision of more surface area for light capture and greater light access by seedlings. Total seedling dry weight was highest in treatments with 1 cm of litter cover due to greater moisture retention provided by a small amount of leaf litter outweighing the costs of seedling penetration through leaf litter. Importantly, we found that at any given depth of leaf litter, there were no significant differences in emergence and growth traits between pine, eucalypt or mixed leaf-litter treatments. The ability of P. radiata seedlings to succeed equally well under a range of different leaf-litter types is undoubtedly an important trait linked to its invasiveness. Given ethical concerns of introducing highly invasive species, such as P. radiata into remnant native woodland in field-based studies, glasshouse research is highly desirable and invaluable in elucidating important factors underpinning the invasiveness of weed species such as P. radiata. © 2010 The Authors. Weed Research © 2010 European Weed Research Society.
Ballestriero, F, Thomas, T, Burke, C, Egan, S & Kjelleberg, S 2010, 'Identification of Compounds with Bioactivity against the Nematode Caenorhabditis elegans by a Screen Based on the Functional Genomics of the Marine Bacterium Pseudoalteromonas tunicata D2', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 76, no. 17, pp. 5710-5717.
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Marine bacteria are a rich, yet underexplored, resource of compounds with inhibitory bioactivity against a range of eukaryotic target organisms. Identification of those inhibitors, however, requires a culturable or genetically tractable producer strain, a prerequisite that is not often fulfilled. This study describes a novel functional genomic screen that is based on expression of inhibitors in a heterogeneous recombinant host (i.e., Escherichia coli). Functional libraries were screened by selective grazing by the nematode Caenorhabditis elegans, in a simple, rapid, high-throughput manner. We applied our approach to discover inhibitors of C. elegans produced by the marine bacterium Pseudoalteromonas tunicata D2, a model organism for exploring a range of antagonistic activities between bacteria and eukaryotes and a known producer of several toxic compounds. Expression of P. tunicata DNA in E. coli and grazing selection by the nematode Caenorhabditis elegans identified two clones, with slow-and fast-killing modes of action. Genomic analysis of the slow-killing clone revealed that the activity was due to a small molecule, tambjamine, while the fast-killing activity involved a gene encoding for a novel protein. Microscopic analysis showed substantial colonization of the intestinal lumen, or rapid death of the nematode without colonization, for the two activities, respectively. The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions. Copyright © 2010, American Society for Microbiology.
Barratt, JLN, Banik, GR, Harkness, J, Marriott, D, Ellis, JT & Stark, D 2010, 'Newly defined conditions for the in vitro cultivation and cryopreservation of Dientamoeba fragilis: new techniques set to fast track molecular studies on this organism', PARASITOLOGY, vol. 137, no. 13, pp. 1867-1878.
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Dientamoeba fragilis is a pathogen of the human gastrointestinal tract that is a common cause of diarrhoea. A paucity of knowledge on the in vitro cultivation and cryopreservation of Dientamoeba has meant that few studies have been conducted to investigate its biology. The objective of this study was to define, for the first time, in vitro culture conditions able to support the long-term in vitro growth of Dientamoeba. Also, we aimed to define a suitable method for cryopreserving viable Dientamoeba trophozoites. A modified BD medium, TYGM-9, Loeffler's slope medium, Robinson's medium, Medium 199, Trichosel and a Tritrichomonas fetus medium were compared, using cell counts, for their ability to support the growth of D. fragilis at various temperatures and atmospheric conditions. Loeffler's slope medium supported significantly better growth compared to other media. A temperature of 42C and a microaerophilic atmosphere were also optimum for Dientamoeba growth. To our knowledge, this is the first study to describe and compare different culture media and conditions for the growth of clinical isolates of D. fragilis. This new technology will aid the development of diagnostics for dientamoebiasis as well as facilitate large-scale sequencing projects that will fast track molecular studies on D. fragilis. © Cambridge University Press 2010.
Barratt, JLN, Harkness, J, Marriott, D, Ellis, JT & Stark, D 2010, 'Importance of Nonenteric Protozoan Infections in Immunocompromised People', CLINICAL MICROBIOLOGY REVIEWS, vol. 23, no. 4, pp. 795-+.
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There are many neglected nonenteric protozoa able to cause serious morbidity and mortality in humans, particularly in the developing world. Diseases caused by certain protozoa are often more severe in the presence of HIV. While information regarding neglected tropical diseases caused by trypanosomatids and Plasmodium is abundant, these protozoa are often not a first consideration in Western countries where they are not endemic. As such, diagnostics may not be available in these regions. Due to global travel and immigration, this has become an increasing problem. Inversely, in certain parts of the world (particularly sub-Saharan Africa), the HIV problem is so severe that diseases like microsporidiosis and toxoplasmosis are common. In Western countries, due to the availability of highly active antiretroviral therapy (HAART), these diseases are infrequently encountered. While free-living amoebae are rarely encountered in a clinical setting, when infections do occur, they are often fatal. Rapid diagnosis and treatment are essential to the survival of patients infected with these organisms. This paper reviews information on the diagnosis and treatment of nonenteric protozoal diseases in immunocompromised people, with a focus on patients infected with HIV. The nonenteric microsporidia, some trypanosomatids, Toxoplasma spp., Neospora spp., some free-living amoebae, Plasmodium spp., and Babesia spp. are discussed.
Bateman, JE, Dalgliesh, RM, Duxbury, DM, Holt, SA, McPhail, DJ, Marsh, AS, Rhodes, NJ, Schooneveld, EM, Spill, EJ & Stephenson, R 2010, 'The FastGas detector', Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, vol. 616, no. 1, pp. 59-64.
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Bell, TDM, Bhosale, SV, Forsyth, CM, Hayne, D, Ghiggino, KP, Hutchison, JA, Jani, CH, Langford, SJ, Lee, MA-P & Woodward, CP 2010, 'Melt-induced fluorescent signature in a simple naphthalenediimide', Chemical Communications, vol. 46, no. 27, pp. 4881-4881.
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BELLWOOD, DR, KLANTEN, S, COWMAN, PF, PRATCHETT, MS, KONOW, N & Van HERWERDEN, L 2010, 'Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes', Journal of Evolutionary Biology, vol. 23, no. 2, pp. 335-349.
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AbstractOf the 5000 fish species on coral reefs, corals dominate the diet of just 41 species. Most (61%) belong to a single family, the butterflyfishes (Chaetodontidae). We examine the evolutionary origins of chaetodontid corallivory using a new molecular phylogeny incorporating all 11 genera. A 1759‐bp sequence of nuclear (S7I1 and ETS2) and mitochondrial (cytochrome b) data yielded a fully resolved tree with strong support for all major nodes. A chronogram, constructed using Bayesian inference with multiple parametric priors, and recent ecological data reveal that corallivory has arisen at least five times over a period of 12 Ma, from 15.7 to 3 Ma. A move onto coral reefs in the Miocene foreshadowed rapid cladogenesis within Chaetodon and the origins of corallivory, coinciding with a global reorganization of coral reefs and the expansion of fast‐growing corals. This historical association underpins the sensitivity of specific butterflyfish clades to global coral decline.
Bennett, S, Roux, CP & Robertson, J 2010, 'The significance of fibre transfer and persistence – A case study', Australian Journal of Forensic Sciences, vol. 42, no. 3, pp. 221-228.
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In April, 1995 the body of a young woman was found in a suburb of Sydney, Australia. The body was fully clothed and bore a number of injuries to the neck, face and fingers. There were no signs of sexual assault and she appeared to have been strangled. The only physical evidence located at the scene was a number of dark, coarse fibres adhering to the soles of her shoes. These fibres consisted of nine grey polypropylene, 12 blue polypropylene and 50 black polyester fibres. The source of these fibres was found to be the carpet of a 1991 Honda CRX that belonged to the suspect. Almost all other possible sources of these fibres were eliminated. At trial, the source of the fibres was not disputed by the defence. Instead the issue became how long these fibres had persisted on the shoe soles. A number of experiments were conducted to investigate the factors influencing the transfer and persistence of carpet fibres to shoe soles and the results of these experiments became a critically important part of the prosecution.
Benson, SJ, Lennard, CJ, Hill, DM, Maynard, P & Roux, C 2010, 'Forensic Analysis of Explosives Using Isotope Ratio Mass Spectrometry (IRMS)—Part 1: Instrument Validation of the DELTAplusXP IRMS for Bulk Nitrogen Isotope Ratio Measurements', Journal of Forensic Sciences, vol. 55, no. 1, pp. 193-204.
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Abstract: A significant amount of research has been conducted into the use of stable isotopes to assist in determining the origin of various materials. The research conducted in the forensic field shows the potential of isotope ratio mass spectrometry (IRMS) to provide a level of discrimination not achievable utilizing traditional forensic techniques. Despite the research there have been few, if any, publications addressing the validation and measurement uncertainty of the technique for forensic applications. This study, the first in a planned series, presents validation data for the measurement of bulk nitrogen isotope ratios in ammonium nitrate (AN) using the DELTAplusXP (Thermo Finnigan) IRMS instrument equipped with a ConFlo III interface and FlashEA™ 1112 elemental analyzer (EA). Appropriate laboratory standards, analytical methods and correction calculations were developed and evaluated. A validation protocol was developed in line with the guidelines provided by the National Association of Testing Authorities, Australia (NATA). Performance characteristics including: accuracy, precision/repeatability, reproducibility/ruggedness, robustness, linear range, and measurement uncertainty were evaluated for the measurement of nitrogen isotope ratios in AN. AN (99.5%) and ammonium thiocyanate (99.99+%) were determined to be the most suitable laboratory standards and were calibrated against international standards (certified reference materials). All performance characteristics were within an acceptable range when potential uncertainties, including the manufacturer’s uncertainty of the technique and standards, were taken into account. The experiments described in this article could be used as a model for validation of other instruments for similar purposes. Later studies in this series will address the more general issue of demonstrating that the IRMS technique is scientifically sound and fit‐for‐purpose ...
Benson, SJ, Lennard, CJ, Maynard, P, Hill, DM, Andrew, AS, Neal, K, Stuart‐Williams, H, Hope, J, Stewart Walker, G & Roux, C 2010, 'Forensic Analysis of Explosives Using Isotope Ratio Mass Spectrometry (IRMS)—Part 2: Forensic Inter‐Laboratory Trial: Bulk Carbon and Nitrogen Stable Isotopes in a Range of Chemical Compounds (Australia and New Zealand)', Journal of Forensic Sciences, vol. 55, no. 1, pp. 205-212.
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Abstract: Comparability of data over time and between laboratories is a key issue for consideration in the development of global databases, and more broadly for quality assurance in general. One mechanism that can be utilized for evaluating traceability is an inter‐laboratory trial. This paper addresses an inter‐laboratory trial conducted across a number of Australian and New Zealand isotope ratio mass spectrometry (IRMS) laboratories. The main objective of this trial was to determine whether IRMS laboratories in these countries would record comparable values for the distributed samples. Four carbon containing and four nitrogen containing compounds were distributed to seven laboratories in Australia and one in New Zealand. The laboratories were requested to analyze the samples using their standard procedures. The data from each laboratory was evaluated collectively using International Standard ISO 13528 (Statistical methods for use in proficiency testing by inter‐laboratory comparisons). “Warning signals” were raised against one participant in this trial. “Action signals” requiring corrective action were raised against four participants. These participants reviewed the data and possible sources for the discrepancies. This inter‐laboratory trial was successful in providing an initial snapshot of the potential for traceability between the participating laboratories. The statistical methods described in this article could be used as a model for others needing to evaluate stable isotope results derived from multiple laboratories, e.g., inter‐laboratory trials/proficiency testing. Ongoing trials will be conducted to improve traceability across the Australian and New Zealand IRMS community.
Berle, CA, Cobbin, D, Smith, N & Zaslawski, C 2010, 'A Novel Approach to Evaluate Traditional Chinese Medicine Treatment Outcomes Using Pattern Identification', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 16, no. 4, pp. 357-367.
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Introduction: Traditional Chinese Medicine (TCM), a modern interpretation of Chinese medicine, developed in the 1950s. It differentiates biomedical diseases into patterns. Each pattern comprises symptom/signs that have their own unique treatment protocol. Most TCM research has used fixed formula treatments for Western-defined diseases with outcomes often measured using objective biomedical markers. More recently, a number of trials have attempted to accommodate TCM clinical practice within the framework of rigorous evidence-based medical research. The aim of this article is to describe a novel outcome measure based on TCM patterns that was used in a pilot study for people with hepatitis C virus (HCV). Methods: Sixteen (16) participants with HCV were enrolled in a randomized, controlled pilot study and allocated to a treatment or control group. TCM pattern diagnosis was obtained at baseline and used to guide acupuncture treatment for the treatment group. Each individual's primary, secondary, and tertiary TCM patterns were identified, which involved the systematic evaluation of the participant's information against the TCM patterns and conversion of the pattern to a percentage. Baseline and postintervention percentages for the three TCM patterns for the two groups were compared to assess change. Results: There was a significant mean percentage decrease in pattern expression at week 12 compared to baseline for the secondary and tertiary patterns of the treatment group (56.3% versus 47.5%; p = 0.045 and 48.1% versus 33.6%; p = 0.037, respectively). No significant change was found for the primary, secondary, or tertiary patterns for the control group or for the primary pattern associated with the treatment group. Conclusions: The quantification of TCM patterns in this study permitted statistical evaluation of TCM pattern change. Previously, TCM pattern identification had only been used as a basis for developing the treatment protocol in clinical trials. This...
Berle, CA, Cobbin, D, Smith, N & Zaslawski, C 2010, 'Response to Cox-North's Comments on 'A Novel Approach to Evaluate TCM Treatment Outcomes Using Pattern Identification'', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 16, no. 11, pp. 1135-1135.
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Bhosale, SV, Bhosale, SV, Kalyankar, MB, Langford, SJ & Lalander, CH 2010, 'Self-Assembly of Protoporphyrin IX-TEG Derivatives into Tunable Nanoscaled Spherical Structures — RETRACTED', Australian Journal of Chemistry, vol. 63, no. 9, pp. 1326-1329.
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The results of a solvo-controlled self-assembly process involving a novel non-ionic protoporphyrin IX functionalized with triethylene glycol (Proto-NTEG) chains is discussed. In relatively non-polar aprotic solvents (cyclohexane/CHCl3), the protoporphyrin forms stable, uniformly-sized multilamellar micro-vesicles of approximately 65 nm diameter, while in more polar protic solvent mixes (CHCl3/MeOH), the same protoporphyrin forms micellar aggregates with dimensions of approximately 6 nm. The solvo-control operates based on the differing properties of glycol units in cyclohexane and methanol leading to inverse self-assembled structures.
Bishop, S, King, J, Windsor, P, Reichel, MP, Ellis, J & Slapeta, J 2010, 'The first report of ovine cerebral neosporosis and evaluation of Neospora caninum prevalence in sheep in New South Wales', VETERINARY PARASITOLOGY, vol. 170, no. 1-2, pp. 137-142.
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Presence of Neospora caninum DNA was detected in the brain and spinal cord of an adult Merino sheep suspected of dying with acute non-suppurative meningoencephalitis and mild to moderate non-suppurative myelitis. The most severe neurological lesions were found in the midbrain at the rostral coliculi with moderate to severe multifocal vasculitis and gliosis. As this was the first known occurrence of cerebral disease in sheep in Australia caused by N. caninum, we surveyed sera from five sheep properties in New South Wales (NSW) to obtain information on the likely prevalence of N. caninum infection in NSW sheep flocks. Serology using a commercial indirect enzyme-linked immunosorbent assay (ELISA) revealed no N. caninum antibody-positive sheep (n = 184). However an observed prevalence for N. caninum antibodies using a commercially available competitive ELISA was 2.2% (5/232). We conclude that although the diagnosis of fatal ovine cerebral neosporosis is of importance to our surveillance program for transmissible spongiform encephalopathy (TSE) exclusion, sheep in NSW are not commonly infected with N. caninum and this species likely plays only a minor role in the life cycle of this parasite in Australia.
Blaber, MG, Arnold, MD & Ford, MJ 2010, 'Designing materials for plasmonic systems: the alkali-noble intermetallics', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 22, no. 9, pp. 1-8.
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We use electronic structure calculations based upon density functional theory to search for ideal plasmonic materials among the alkali-noble intermetallics. Importantly, we use density functional perturbation theory to calculate the electron-phonon interaction and from there use a first order solution to the Boltzmann equation to estimate the phenomenological damping frequency in the Drude dielectric function. We discuss the necessary electronic features of a plasmonic material and investigate the optical properties of the alkali-noble intermetallics in terms of some generic plasmonic system quality factors. We conclude that at low negative permittivities, KAu, with a damping frequency of 0.0224eV and a high optical gap to bare plasma frequency ratio, outperforms gold and to some extent silver as a plasmonic material. Unfortunately, a low plasma frequency (1.54eV) reduces its utility in modern plasmonics applications. We also discuss, briefly, the effect of local fields on the optical properties of these materials. © 2010 IOP Publishing Ltd.
Bolitho, C, Hahn, MA, Baxter, RC & Marsh, DJ 2010, 'The chemokine CXCL1 induces proliferation in epithelial ovarian cancer cells by transactivation of the epidermal growth factor receptor', Endocrine-Related Cancer, vol. 17, no. 4, pp. 929-940.
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The chemokine CXCL1 is elevated in plasma and ascites from patients with ovarian cancer. We have previously shown that CXCL1 is a marker of phosphatidylinositol 3-kinase signalling in epithelial ovarian cancer (EOC) cell lines, a pathway that is commonly activated in ovarian tumours. To investigate whether CXCL1 also has functional significance in ovarian cancer, this chemokine was either down-regulated using siRNAs or overexpressed by transfection of CXCL1 into the EOC cell lines SKOV3 and OVCAR-3 and proliferation assessed over 7 days. Overexpression of CXCL1 increased proliferation of ovarian cancer cells over 7 days, while down-regulation was inhibitory. Treatment of cells with recombinant CXCL1 induced epidermal growth factor receptor (EGFR) phosphorylation at Y1068, indicating crosstalk between the CXCL1 G-protein-coupled receptor CXCR2 and the EGFR. CXCL1-induced proliferation was also decreased by inhibition of EGFR kinase activity and was dependent on extracellular matrix metalloproteinase-mediated release of heparin-binding EGF (HB-EGF). Involvement of mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase 1/2 (ERK1/2) signalling was also evident since inhibition of both Ras and MEK activity decreased CXCL1-induced proliferation. CXCL1-induced ERK1/2 phosphorylation was inhibited by the MEK1 inhibitor PD98059; however, EGFR phosphorylation was unaffected, indicating that CXCL1 activation of MAPK signalling is downstream of the EGFR. Taken together, these data show that CXCL1 functions through CXCR2 to transactivate the EGFR by proteolytic cleavage of HB-EGF, leading to activation of MAPK signalling and increased proliferation of EOC cells.
Bradfield, LA & McNally, GP 2010, 'The role of nucleus accumbens shell in learning about neutral versus excitatory stimuli during Pavlovian fear conditioning', Learning & Memory, vol. 17, no. 7, pp. 337-343.
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We studied the role of nucleus accumbens shell (AcbSh) in Pavlovian fear conditioning. Rats were trained to fear conditioned stimulus A (CSA) in Stage I, which was then presented in compound with a neutral stimulus and paired with shock in Stage II. AcbSh lesions had no effect on fear-learning to CSA in Stage I, but selectively prevented learning about the neutral conditioned stimulus (CS) in Stage II. These results add to a growing body of evidence indicating an important role for the ventral striatum in fear-learning. They suggest that the ventral striatum and AcbSh, in particular, directs learning toward or away from a CS as a consequence of how well that CS predicts the shock unconditioned stimulus (US). AcbSh is required to reduce the processing of established predictors, thereby permitting neutral or less predictive stimuli to be learned about.
Bridges, DJ, Bunn, J, van Mourik, JA, Grau, G, Preston, RJS, Molyneux, M, Combes, V, O'Donnell, JS, de Laat, B & Craig, A 2010, 'Rapid activation of endothelial cells enables Plasmodium falciparum adhesion to platelet-decorated von Willebrand factor strings', Blood, vol. 115, no. 7, pp. 1472-1474.
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Abstract During Plasmodium falciparum malaria infections, von Willebrand factor (VWF) levels are elevated, postmortem studies show platelets colocalized with sequestered infected erythrocytes (IEs) at brain microvascular sites, whereas in vitro studies have demonstrated platelet-mediated IE adhesion to tumor necrosis factor-activated brain endothelium via a bridging mechanism. This current study demonstrates how all these observations could be linked through a completely novel mechanism whereby IEs adhere via platelet decorated ultra-large VWF strings on activated endothelium. Using an in vitro laminar flow model, we have demonstrated tethering and firm adhesion of IEs to the endothelium specifically at sites of platelet accumulation. We also show that an IE pro-adhesive state, capable of supporting high levels of binding within minutes of induction, can be removed through the action of the VWF protease ADAMTS-13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13). We propose that this new mechanism contributes to sequestration both independently of and in concert with current adhesion mechanisms.
Bridson, M, Burillo, J, Elder, M & Sunic, Z 2010, 'On groups whose geodesic growth is polynomial', International Journal of Algebra and Computation, vol. 22, pp. 1250048-13.
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This note records some observations concerning geodesic growth functions. Ifa nilpotent group is not virtually cyclic then it has exponential geodesicgrowth with respect to all finite generating sets. On the other hand, if afinitely generated group $G$ has an element whose normal closure is abelian andof finite index, then $G$ has a finite generating set with respect to which thegeodesic growth is polynomial (this includes all virtually cyclic groups).
Brown, JJ, Bohua, L & Padmadas, SS 2010, 'A multilevel analysis of the effects of a reproductive health programme that encouraged informed choice of contraceptive method rather than use of officially preferred methods, China 2003–2005', Population Studies, vol. 64, no. 2, pp. 105-115.
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Historically, the Chinese government's family planning (FP) policy has emphasized post-partum IUD use after first birth and sterilization after subsequent births. Was the influence of this policy-driven programme on women's contraceptive choices weakened
Brownless, JS, Mahmoodian, S, Dossou, KB, Lawrence, FJ, Botten, LC & de Sterke, CM 2010, 'Coupled waveguide modes in hexagonal photonic crystals', OPTICS EXPRESS, vol. 18, no. 24, pp. 25346-25360.
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We investigate the modes of coupled waveguides in a hexagonal photonic crystal. We find that for a substantial parameter range the coupled waveguide modes have dispersion relations exhibiting multiple intersections, which we explain both intuitively and using a rigorous tight-binding argument. © 2010 Optical Society of America.
Bruti-Liberati, N, Nikitopoulos-Sklibosios, C & Platen, E 2010, 'Real-world jump-diffusion term structure models', QUANTITATIVE FINANCE, vol. 10, no. 1, pp. 23-37.
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This paper considers interest rate term structure models in a market attracting both continuous and discrete types of uncertainty. The event-driven noise is modelled by a Poisson random measure. Using as numeraire the growth optimal portfolio, interest rate derivatives are priced under the real-world probability measure. In particular, the real-world dynamics of the forward rates are derived and, for specific volatility structures, finite-dimensional Markovian representations are obtained. Furthermore, allowing for a stochastic short rate in a non-Markovian setting, a class of tractable affine term structures is derived where an equivalent risk-neutral probability measure may not exist. © 2010 Taylor & Francis.
Burgess, JK, Boustany, S, Moir, LM, Weckmann, M, Lau, JY, Grafton, K, Baraket, M, Hansbro, PM, Hansbro, NG, Foster, PS, Black, JL & Oliver, BG 2010, 'Reduction of Tumstatin in Asthmatic Airways Contributes to Angiogenesis, Inflammation, and Hyperresponsiveness', AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, vol. 181, no. 2, pp. 106-115.
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Rationale: Angiogenesis is a prominent feature of remodeling in asthma. Many proangiogenic factors are up-regulated in asthma, but little is known about levels of endogenous antiangiogenic agents. Collagen IV is decreased in the airway basement membrane in asthma. It has six α chains, of which the noncollagenous domain-1 domains have endogenous antiangiogenic properties. Objectives: To study the expression of the noncollagenous domain-1 of the α3 chain of collagen IV, tumstatin, in the airways of subjects with and without asthma and to examine the potential for tumstatin to regulate angiogenesis and inflammation. Methods: We used immunohistochemistry and dot blots to examine the expression of tumstatin in bronchial biopsies, bronchoalveolar lavage fluid, and serum. We then used an in vitro angiogenesis assay and a murinemodel of allergic airways disease to explore tumstatin's biological function. Measurements and Main Results: The level of tumstatin is decreased 18-fold in the airways of patients with asthma but not in subjects without asthma, including those with chronic obstructive pulmonary disease, cystic fibrosis, and bronchiectasis. In vitro, recombinant tumstatin inhibited primary pulmonary endothelial cell tube formation. In a mouse model of chronic allergic airways disease, tumstatin suppressed angiogenesis, airway hyperresponsiveness, inflammatory cell infiltration, and mucus secretion and decreased levels of vascular endothelial growth factor and IL-13. Conclusions: The observation that tumstatin is decreased in asthmatic airways and inhibits airway hyperresponsiveness and angiogenesis demonstrates the potential use of antiangiogenic agents such as tumstatin as a therapeutic intervention in diseases that are characterized by aberrant angiogenesis and tissue remodeling, such as asthma.
Busschaert, N, Gale, PA, Haynes, CJE, Light, ME, Moore, SJ, Tong, CC, Davis, JT & Harrell, WA 2010, 'Tripodal transmembrane transporters for bicarbonate', Chemical Communications, vol. 46, no. 34, pp. 6252-6252.
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C. Nevill, J, J. Hancock, P, R. Murray, B, F. Ponder, W, F. Humphreys, W, L. Phillips, M & K. Groom, P 2010, 'Groundwater-dependent ecosystems and the dangers of groundwater overdraft: a review and an Australian perspective', Pacific Conservation Biology, vol. 16, no. 3, pp. 187-187.
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In many parts of the world, access to groundwater is needed for domestic, agricultural and industrial uses, and global groundwater exploitation continues to increase. The significance of groundwater in maintaining the health of rivers, streams, wetlands and associated vegetation is often underestimated or ignored, resulting in a lack of scrutiny of groundwater policy and management. It is essential that management of groundwater resources considers the needs of natural ecosystems, including subterranean. We review the limited Australian literature on the ecological impacts of groundwater overdraft and place Australian information within an international context, focusing on lentic, lotic, stygobitic and hyporheic communities as well as riparian and phreatophytic vegetation, and some coastal marine ecosystems. Groundwater overdraft, defined as abstracting groundwater at a rate which prejudices ecosystem or anthropocentric values, can substantially impact natural communities which depend, exclusively or seasonally, on groundwater. Overdraft damage is often underestimated, is sometimes irreversible, and may occur over time scales at variance to those used by water management agencies in modelling, planning and regulation. Given the dangers of groundwater overdraft, we discuss policy implications in the light of the precautionary principle, and make recommendations aimed at promoting the conservation of groundwater-dependent ecosystems within a sustainable use context.
Cain, AK, Liu, X, Djordjevic, SP & Hall, RM 2010, 'Transposons Related to Tn1696in IncHI2 Plasmids in Multiply Antibiotic ResistantSalmonella entericaSerovar Typhimurium from Australian Animals', Microbial Drug Resistance, vol. 16, no. 3, pp. 197-202.
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Conjugative IncHI2 plasmids carrying tetracycline, trimethoprim, and sulphonamide resistance genes were recovered from two multiply antibiotic resistant Salmonella enterica serovar Typhimurium isolates from Australian food-producing animals. Transposons related to the mercury resistance transposon Tn1696 were identified in both IncHI2 plasmids. These transposons contained an In4-type class 1 integron that carried a dfrA5 trimethoprim resistance gene cassette and the sul1 sulfonamide resistance gene. These integrons were located in the same position as In4 in Tn1696. The integron from one isolate includes a large transposon-like structure containing four IS26 and the strAB, sul2, blaTEM, and aphA1 genes conferring resistance to streptomycin, sulphonamides, ampicillin, kanamycin, and neomycin, respectively. This structure is flanked by an 8-bp duplication, but it includes both the aphA1-containing transposon Tn4352 and a transposon, Tn6029, carrying genes derived from RSF1010 and from Tn2. However, Tn4352 and Tn6029 overlap, sharing one IS26 copy. This suggests that they do not move by a standard transpositional mechanism. A circular intermediate, carrying only the region containing the resistance gene(s) and one of the IS26 bounding it, is proposed as an intermediate. © 2010 Mary Ann Liebert, Inc.
Calderon, CP, Martinez, JG, Carroll, RJ & Sorensen, DC 2010, 'Erratum: P-Splines Using Derivative Information', Multiscale Modeling & Simulation, vol. 8, no. 5, pp. 2097-2097.
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Calderon, CP, Martinez, JG, Carroll, RJ & Sorensen, DC 2010, 'P-Splines Using Derivative Information', Multiscale Modeling & Simulation, vol. 8, no. 4, pp. 1562-1580.
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Carpintero, R, Gruaz, L, Brandt, KJ, Scanu, A, Faille, D, Combes, V, Grau, GE & Burger, D 2010, 'HDL Interfere with the Binding of T Cell Microparticles to Human Monocytes to Inhibit Pro-Inflammatory Cytokine Production', PLoS ONE, vol. 5, no. 7, pp. e11869-e11869.
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Background: Direct cellular contact with stimulated T cells is a potent mechanism that induces cytokine production in human monocytes in the absence of an infectious agent. This mechanism is likely to be relevant to T cell-mediated inflammatory diseases such as rheumatoid arthritis and multiple sclerosis. Microparticles (MP) generated by stimulated T cells (MPT) display similar monocyte activating ability to whole T cells, isolated T cell membranes, or solubilized T cell membranes. We previously demonstrated that high-density lipoproteins (HDL) inhibited T cell contact- and MPT-induced production of IL-1β but not of its natural inhibitor, the secreted form of IL-1 receptor antagonist (sIL-1Ra). Methodology/Principal Findings: Labeled MPT were used to assess their interaction with monocytes and T lymphocytes by flow cytometry. Similarly, interactions of labeled HDL with monocytes and MPT were assessed by flow cytometry. In parallel, the MPT-induction of IL-1β and sIL-1Ra production in human monocytes and the effect of HDL were assessed in cell cultures. The results show that MPT, but not MP generated by activated endothelial cells, bond monocytes to trigger cytokine production. MPT did not bind T cells. The inhibition of IL-1β production by HDL correlated with the inhibition of MPT binding to monocytes. HDL interacted with MPT rather than with monocytes suggesting that they bound the activating factor(s) of T cell surface. Furthermore, prototypical pro-inflammatory cytokines and chemokines such as TNF, IL-6, IL-8, CCL3 and CCL4 displayed a pattern of production induced by MPT and inhibition by HDL similar to IL-1β, whereas the production of CCL2, like that of sIL-1Ra, was not inhibited by HDL. Conclusions/Significance: HDL inhibit both MPT binding to monocytes and the MPT-induced production of some but not all cytokines, shedding new light on the mechanism by which HDL display their anti-inflammatory functions. © 2010 Carpintero et al.
Carroll, RJ, Chen, X & Hu, Y 2010, 'Identification and estimation of nonlinear models using two samples with nonclassical measurement errors', Journal of Nonparametric Statistics, vol. 22, no. 4, pp. 379-399.
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Carroll, RJ, Chen, X & Hu, Y 2010, 'Identification and estimation of nonlinear models using two samples with nonclassical measurement errors', Journal of Nonparametric Statistics, vol. 22, no. 4, pp. 419-423.
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Castorina, A, Giunta, S & D'Agata, V 2010, 'Protective effect of the dopamine D(3) receptor agonist (7-OH-PIPAT) against apoptosis in malignant peripheral nerve sheath tumor (MPNST) cells.', Int J Oncol, vol. 37, no. 4, pp. 927-934.
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Emerging evidence indicates that the dopamine D(3) receptor (D(3)R) mediates protective roles both in neuronal and non-neuronal cell lines. In a previous study we proposed that neurofibromin, a large tumor suppressor protein encoded by the neurofibromatosis type 1 gene (NF1), may increase susceptibility to apoptosis after serum deprivation in malignant peripheral nerve sheath tumor (MPNST) cells, thus acting as a proapoptotic gene. In addition, it has been observed that D(3)Rs are functionally correlated to neurofibromin. In this study, we examined whether 7-OH-PIPAT, a potent dopamine D(3)R agonist, exerts an antiapoptotic role under the same culture conditions and then correlated this effect to changes in NF1 expression. Results showed that serum deprivation caused a significant reduction of cell viability (MTT assay) both after 24 and 48 h (p<0.001). Treatment with increasing concentrations of 7-OH-PIPAT (10(-9)-10(-5) M) induced a progressive increase in cell viability both after 24 and 48 h as compared to vehicle-treated cells, with significant changes at the highest concentrations tested (10(-6) and 10(-5) M). Consistently, at the latter two concentrations, a significant reduction in oligonucleosomes formation was observed, thus suggesting an antiapoptotic role of 7-OH-PIPAT. These results were confirmed by Hoechst 33254 nuclear staining. To investigate whether these effects were correlated to changes in NF1 transcript and protein expression, quantitative real-time PCR, Western blot and immunofluorescence analyses were performed. Results demonstrated that the upregulation of NF1 transcripts and protein levels induced by serum withdrawal were remarkably attenuated by 10(-6) and 10(-5) M agonist treatment within 24 h (p<0.01 and p<0.001, respectively), whereas similar effects were observed already at a lower concentration (10(-7) M) after 48 h treatment (p<0.001). In conclusion, these results suggest that D(3)R might mediate the protective response ...
Castorina, A, Giunta, S, Mazzone, V, Cardile, V & D’Agata, V 2010, 'Effects of PACAP and VIP on hyperglycemia-induced proliferation in murine microvascular endothelial cells', Peptides, vol. 31, no. 12, pp. 2276-2283.
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Castorina, A, Tiralongo, A, Giunta, S, Carnazza, ML, Scapagnini, G & D’Agata, V 2010, 'Early effects of aluminum chloride on beta-secretase mRNA expression in a neuronal model of ß-amyloid toxicity', Cell Biology and Toxicology, vol. 26, no. 4, pp. 367-377.
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Chaiyong, S, Jatisatienr, A, Mungkornasawakul, P, Sastraruji, T, Pyne, SG, Ung, AT, Urathamakul, T & Lie, W 2010, 'Phytochemical Investigations of Stemona curtisii and Synthetic Studies on Stemocurtisine Alkaloids', JOURNAL OF NATURAL PRODUCTS, vol. 73, no. 11, pp. 1833-1838.
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The isolation of two new Stemona alkaloids, 1-hydroxyprotostemonine and stemocurtisine N-oxide, and a new benzofuran, stemofuran L, from the root extracts of Stemona curtisii is reported. The major known alkaloids from this plant extract, stemocurtisine, stemocurtisinol, and oxyprotostemonine, were also isolated along with oxystemokerrine N-oxide. The nonalkaloid components of this extract included a new benzofuran derivative, stemofuran L, the known stemofurans F, J, and K, dihydro-γ-tocopherol, and stigmasterol. Stemocurtisine and stemocurtisinol were converted to their respective N-oxides by oxidation. Stemocurtisine was converted to a tetracyclic derivative by oxidative cleavage of the γ-butyrolactone ring, while stemocurtisinol gave a novel lactam derivative by oxidative cleavage of the C-4 side chain under basic conditions. The acetylcholinesterase inhibitory activities of some known and new alkaloids and their derivatives are also reported. All were 10-20 times less active as acetylcholinesterase inhibitors than the pyrrolo[1,2-a]azepine Stemona alkaloids stemofoline and 1â²,2â²-didehydrostemofoline. None of the stemofuran compounds showed significant antibacterial or antifungal activities.
Chaloub, RM, Reinert, F, Nassar, CAG, Fleury, BG, Mantuano, DG & Larkum, AWD 2010, 'Photosynthetic properties of three Brazilian seaweeds', Revista Brasileira de Botânica, vol. 33, no. 2, pp. 371-374.
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Photosynthetic performance of distinct marine macroalgae, Ulva fasciata Delile (green alga), Lobophora variegata (J. V. Lamouroux) Womersley ex E. C. Oliveira (brown alga), and Plocamium brasiliensis (Greville) M. A. Howe & W. R. Taylor (red alga), were compared using a pulse amplitude-modulated fluorometer. The maximum quantum yield (Fv/Fm) ranged from 0.80 to 0.51, and the lowest value was found in P. brasiliensis. Under 400 μmol photons m-2 s-1 irradiance, the highest value of photochemical quenching (qP = 0.92 ± 0.13) was observed for U. fasciata. The red alga P. brasiliensis dissipated high amounts of excitation energy (qN = 0.56 ± 0.09), resulting in relatively low values for the effective quantum yield of PS-II (0.23 ± 0.04), as well as for the relative electron transport rate (3.3 ± 0.7). The high photosynthetic potential found for U. fasciata partially explains the species ability for rapid growth and high productivity.
Chan, J, Shimmon, R, Spindler, X, Maynard, P, Lennard, C, Roux, C & Stuart, BH 2010, 'An investigation of isatin as a potential reagent for latent fingermark detection on porous surfaces', Journal of Forensic Identification, vol. 60, no. 3, pp. 320-336.
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This study investigated isatin as a potential fingermark enhancement reagent for use on porous surfaces. A number of parameters were investigated, including concentration, solvent system, pH of the solution, and optimization of the development conditions. It was determined that isatin at a concentration of 0.05% (w/v) provided the optimum balance between the luminescence of the fingermark ridges and background. A carrier solvent of dioxane mixed with acetone [12.5% (v/v)] produced the most intense luminescence. It was determined that the optimum pH for the development of fingermarks was 5.0 and that this could be reached by the addition of 4% (v/v) sodium carbonate buffer. The use of a dry heat press at 180°C for 10 s provided optimal development conditions. The possible enhancement of isatin-treated fingermark impressions using metal salts was investigated and it was determined that secondary treatment with an ethanolic zinc chloride solution provided enhanced luminescence emission. However, little color change to the developed fingermarks was observed. A comparison of isatin with 1,2-indanedione-zinc (IND-Zn) and DFO demonstrated that the latter two reagents provided greater sensitivity and luminescence than isatin despite the fact that isatin generated strong room-temperature luminescence.
Chan, J, Spindler, X, Brust, A, Shimmon, R, Maynard, P, Lennard, C, Stoilovic, M & Roux, C 2010, 'Evaluation of DFO and 1,2-indanedione formulations under two different Australian conditions', Science & Justice, vol. 50, no. 1, pp. 38-38.
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Chan, L & Platen, E 2010, 'Exact Pricing and Hedging Formulas of Long Dated Variance Swaps under a $3/2$ Volatility Model', Journal of Computational and Applied Mathematics (2015), pp. 181-196, vol. 278, pp. 181-196.
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This paper investigates the pricing and hedging of variance swaps under a$3/2$ volatility model. Explicit pricing and hedging formulas of variance swapsare obtained under the benchmark approach, which only requires the existence ofthe num\'{e}raire portfolio. The growth optimal portfolio is the num\'{e}raireportfolio and used as num\'{e}raire together with the real world probabilitymeasure as pricing measure. This pricing concept provides minimal prices forvariance swaps even when an equivalent risk neutral probability measure doesnot exist.
Chatterjee, N, Chen, Y-H, Luo, S & Carroll, RJ 2010, 'Analysis of Case-Control Association Studies: SNPs, Imputation and Haplotypes', Statistical Science, vol. 24, no. 4, pp. 489-502.
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Although prospective logistic regression is the standard method of analysisfor case-control data, it has been recently noted that in genetic epidemiologicstudies one can use the ``retrospective'' likelihood to gain major power byincorporating various population genetics model assumptions such asHardy-Weinberg-Equilibrium (HWE), gene-gene and gene-environment independence.In this article we review these modern methods and contrast them with the moreclassical approaches through two types of applications (i) association testsfor typed and untyped single nucleotide polymorphisms (SNPs) and (ii)estimation of haplotype effects and haplotype-environment interactions in thepresence of haplotype-phase ambiguity. We provide novel insights to existingmethods by construction of various score-tests and pseudo-likelihoods. Inaddition, we describe a novel two-stage method for analysis of untyped SNPsthat can use any flexible external algorithm for genotype imputation followedby a powerful association test based on the retrospective likelihood. Weillustrate applications of the methods using simulated and real data.
Chen, PY, McPhedran, RC, de Sterke, CM, Poulton, CG, Asatryan, AA, Botten, LC & Steel, MJ 2010, 'Group velocity in lossy periodic structured media', PHYSICAL REVIEW A, vol. 82, no. 5.
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Chen, YA, Almeida, JS, Richards, AJ, Müller, P, Carroll, RJ & Rohrer, B 2010, 'A Nonparametric Approach to Detect Nonlinear Correlation in Gene Expression', Journal of Computational and Graphical Statistics, vol. 19, no. 3, pp. 552-568.
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Chen, Y-C, Christiani, DC, Su, H-JJ, Hsueh, Y-M, Smith, TJ, Ryan, LM, Chao, S-C, Lee, JY-Y & Guo, Y-LL 2010, 'Early-life or lifetime sun exposure, sun reaction, and the risk of squamous cell carcinoma in an Asian population', CANCER CAUSES & CONTROL, vol. 21, no. 5, pp. 771-776.
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Background It has been widely accepted that sun exposure is a risk factor of squamous cell carcinoma (SCC) among fair-skinned populations. However, sun exposure and sun reaction have not been explored in Asians and no gender-specific data were available. Method In a case-control study, 176 incident skin cancer cases were recruited from National Cheng-Kung University Medical Center from 1996 to 1999. Controls included 216 age-, gender-, and residency-matched subjects from the southwestern Taiwan. A questionnaire was administered to collect information on life style and other risk factors. Logistic regression analysis was performed to evaluate the association between sun exposure or sun reaction and the risk of SCC by gender. Results Early-age (age 15 to 24) and lifetime sun exposure were significantly associated with increased risk of SCC in a dose-response pattern [odds ratio (OR) = 1.49-3.08, trend p = 0.009 and 0.0007, respectively]. After stratified by gender, the third tertile of early-age sun exposure was significantly associated with the SCC risk among men (OR = 3.08). The second and third tertiles of lifetime sun exposure was significantly associated with SCC risk among women (OR = 3.78 and 4.53, respectively). Skin reaction after 2-h sun exposure during childhood and adolescence was not significantly associated with the risk of SCC. Conclusions Lifetime sun exposure was more related to SCC risk in women, while early-age sun exposure was more relevant to men's SCC risk. This may be attributable to different lifestyle between men and women. © Springer Science+Business Media B.V. 2010.
Christianson, JA, Dennis, ES, Llewellyn, DJ & Wilson, IW 2010, 'ATAF NAC transcription factors: Regulators of plant stress signaling', Plant Signaling & Behavior, vol. 5, no. 4, pp. 428-432.
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NAC proteins are one of the largest classes of plant-specific transcriptional regulators. Since the first NAC gene NO APICAL MERSITEM (NAM) was identified from petunia in 1996,1 NAC genes have been implicated in important plant developmental processes like boundary cell formation in shoot apical mersitems,1,2 secondary cell wall formation,3 and lateral root development.4 However, recent work indicates that NAC genes are also important regulators in stress responses. Nowhere is this more evident than the ATAF subgroup of NAC domain transcription factors. This mini-review aims at highlighting recent evidence of the importance of the ATAFlike NAC group in a diverse array of stress related signaling processes. © 2010 Landes Bioscience.
Christianson, JA, Llewellyn, DJ, Dennis, ES & Wilson, IW 2010, 'Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species', Plant Signaling & Behavior, vol. 5, no. 8, pp. 1006-1009.
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Waterlogging is a serious impediment to crop productivity worldwide which acts to reduce oxygen levels in the rhizosphere due to the low diffusion rate of molecular oxygen in water. Plants respond to low oxygen through rapid and specific changes at both the transcriptional and translational levels. Transcriptional changes to low-oxygen (hypoxia) stress have been studied in a number of plant species using whole genome microarrays. Using transcriptome data from root tissue from early time points (4-5 h) from cotton (Gossypium hirsutum), Arabidopsis and gray poplar (Populus x canescens), we have identified a core set of orthologous genes that responded to hypoxia in similar ways between species, and others that showed species specific responses. Responses to hypoxia were most similar between Arabidopsis and cotton, while the waterlogging tolerant poplar species exhibited some significant differences. © 2010 Landes Bioscience.
Christianson, JA, Llewellyn, DJ, Dennis, ES & Wilson, IW 2010, 'Global Gene Expression Responses to Waterlogging in Roots and Leaves of Cotton (Gossypium hirsutum L.)', PLANT AND CELL PHYSIOLOGY, vol. 51, no. 1, pp. 21-37.
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Waterlogging stress causes yield reduction in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging caused significant reductions in stem elongation, shoot mass, root mass and leaf number, and altered the expression of 1,012 genes (4 of genes assayed) in root tissue as early as 4 h after flooding. Many of these genes were associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global gene expression in leaf tissues, significantly changing the expression of 1,305 genes (5 of genes assayed) after 24 h of flooding. Genes affected were associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism The implications of these results for the development of waterlogging-tolerant cotton are discussed.
Christianson, JA, Llewellyn, DJ, Dennis, ES & Wilson, IW 2010, 'Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.).', Plant Cell Physiol, vol. 51, no. 1, pp. 21-37.
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Waterlogging stress causes yield reduction in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging caused significant reductions in stem elongation, shoot mass, root mass and leaf number, and altered the expression of 1,012 genes (4% of genes assayed) in root tissue as early as 4 h after flooding. Many of these genes were associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global gene expression in leaf tissues, significantly changing the expression of 1,305 genes (5% of genes assayed) after 24 h of flooding. Genes affected were associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism The implications of these results for the development of waterlogging-tolerant cotton are discussed.
Combes, V, El-Assaad, F, Faille, D, Jambou, R, Hunt, NH & Grau, GER 2010, 'Microvesiculation and cell interactions at the brain–endothelial interface in cerebral malaria pathogenesis', Progress in Neurobiology, vol. 91, no. 2, pp. 140-151.
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Cordingley, R, Kohan, L & Ben-Nissan, B 2010, 'What happens to femoral neck bone mineral density after hip resurfacing surgery?', The Journal of Bone and Joint Surgery. British volume, vol. 92-B, no. 12, pp. 1648-1653.
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The major advantage of hip resurfacing is the decreased amount of bone resection compared with a standard total hip replacement. Fracture of the femoral neck is the most common early complication and poor bone quality is a major risk factor. We undertook a prospective consecutive case control study examining the effect of bone mineral density changes in patients undergoing hip resurfacing surgery. A total of 423 patients were recruited with a mean age of 54 years (24 to 87). Recruitment for this study was dependent on pre-operative bilateral femoral bone mineral density results not being osteoporotic. The operated and non-operated hips were assessed. Bone mineral density studies were repeated over a two-year period. The results showed no significant deterioration in the bone mineral density in the superolateral region in the femoral neck, during that period. These findings were in the presence of a markedly increased level of physical activity, as measured by the short-form 36 health survey physical function score.
Cortie, MB, Giddings, J & Dowd, A 2010, 'Optical properties and plasmon resonances of titanium nitride nanostructures', NANOTECHNOLOGY, vol. 21, no. 11, pp. 1-8.
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We examine the optical properties of nanostructures comprised of titanium nitride, TiN, an electrically conducting intermetallic-like compound. This material can be deposited in the form of durable films by physical vapor deposition. Use of nanosphere templating techniques extends the range of nanostructures that can be produced to include the versatile semi-shell motif. The dielectric properties of TiN1 - x depend upon stoichiometry and are favorable for plasmon resonance phenomena in the mid-visible to near-infrared range of the spectrum and for x≈0. We analyze the optical phenomena operating in such structures using a combination of experiment and simulation and show that semi-shells of TiN exhibit a tunable localized plasmon resonance with light. The material is, however, unsuitable for applications in which a long-distance surface plasmon polariton is desired. © 2010 IOP Publishing Ltd.
Couper, KN, Barnes, T, Hafalla, JCR, Combes, V, Ryffel, B, Secher, T, Grau, GE, Riley, EM & de Souza, JB 2010, 'Parasite-Derived Plasma Microparticles Contribute Significantly to Malaria Infection-Induced Inflammation through Potent Macrophage Stimulation', PLoS Pathogens, vol. 6, no. 1, pp. e1000744-e1000744.
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There is considerable debate as to the nature of the primary parasite-derived moieties that activate innate pro-inflammatory responses during malaria infection. Microparticles (MPs), which are produced by numerous cell types following vesiculation of the cellular membrane as a consequence of cell death or immune-activation, exert strong pro-inflammatory activity in other disease states. Here we demonstrate that MPs, derived from the plasma of malaria infected mice, but not naive mice, induce potent activation of macrophages in vitro as measured by CD40 up-regulation and TNF production. In vitro, these MPs induced significantly higher levels of macrophage activation than intact infected red blood cells. Immunofluorescence staining revealed that MPs contained significant amounts of parasite material indicating that they are derived primarily from infected red blood cells rather than platelets or endothelial cells. MP driven macrophage activation was completely abolished in the absence of MyD88 and TLR-4 signalling. Similar levels of immunogenic MPs were produced in WT and in TNF-/-, IFN-γ-/-, IL-12-/- and RAG-1-/- malaria-infected mice, but were not produced in mice injected with LPS, showing that inflammation is not required for the production of MPs during malaria infection. This study therefore establishes parasitized red blood cell-derived MPs as a major inducer of systemic inflammation during malaria infection, raising important questions about their role in severe disease and in the generation of adaptive immune responses. © 2010 Couper et al.
Coutts, MJ, Zareie, HM, Cortie, MB, Phillips, MR, Wuhrer, R & McDonagh, AM 2010, 'Exploiting Zinc Oxide Re-emission to Fabricate Periodic Arrays', ACS APPLIED MATERIALS & INTERFACES, vol. 2, no. 6, pp. 1774-1779.
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The synthesis of hexagonal ring-shaped structures of zinc oxide using nanosphere lithography and metal/metal oxide sputtering is demonstrated. This synthesis exploits the surface re-emission of zinc oxide to deposit material in regions lying out of the line-of-sight of the sputtering source. These rings can nucleate the hydrothermal growth of zinc oxide crystals. Control over the growth could be exercised by varying growth solution concentration or temperature or by applying an external potential. © 2010 American Chemical Society.
Craddock, MJ & Dooley, AH 2010, 'On the equivalence of Lie symmetries and group representations', JOURNAL OF DIFFERENTIAL EQUATIONS, vol. 249, no. 3, pp. 621-653.
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We consider families of linear, parabolic PDEs in n dimensions which possess Lie symmetry groups of dimension at least four. We identify the Lie symmetry groups of these equations with the (2n+1)-dimensional Heisenberg group and SL(2, R). We then show th
Csaszar, NBM, Ralph, PJ, Frankham, R, Berkelmans, R & van Oppen, MJH 2010, 'Estimating the Potential for Adaptation of Corals to Climate Warming', PLOS ONE, vol. 5, no. 3, pp. 1-8.
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The persistence of tropical coral reefs is threatened by rapidly increasing climate warming, causing a functional breakdown of the obligate symbiosis between corals and their algal photosymbionts (Symbiodinium) through a process known as coral bleaching. Yet the potential of the coral-algal symbiosis to genetically adapt in an evolutionary sense to warming oceans is unknown. Using a quantitative genetics approach, we estimated the proportion of the variance in thermal tolerance traits that has a genetic basis (i.e. heritability) as a proxy for their adaptive potential in the widespread Indo-Pacific reef-building coral Acropora millepora. We chose two physiologically different populations that associate respectively with one thermotolerant (Symbiodinium clade D) and one less tolerant symbiont type (Symbiodinium C2). In both symbiont types, pulse amplitude modulated (PAM) fluorometry and high performance liquid chromatography (HPLC) analysis revealed significant heritabilities for traits related to both photosynthesis and photoprotective pigment profile. However, quantitative real-time polymerase chain reaction (qRT-PCR) assays showed a lack of heritability in both coral host populations for their own expression of fundamental stress genes. Coral colony growth, contributed to by both symbiotic partners, displayed heritability. High heritabilities for functional key traits of algal symbionts, along with their short clonal generation time and high population sizes allow for their rapid thermal adaptation. However, the low overall heritability of coral host traits, along with the corals' long generation time, raise concern about the timely adaptation of the coral-algal symbiosis in the face of continued rapid climate warming. © 2010 Császár et al.
Cumming, JL, Hawker, DW, Matthews, C, Chapman, HF & Nugent, K 2010, 'Analysis of polymeric quaternary ammonium salts as found in cosmetics by metachromatic polyelectrolyte titration', Toxicological & Environmental Chemistry, vol. 92, no. 9, pp. 1595-1608.
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Metachromatic polyelectrolyte titration was investigated as a means of analyzing polymeric quaternary ammonium salts (polyquaterniums) of relatively low charge density used as ingredients in cosmetics. They are of possible toxicological concern, but little is known of their environmental fate and behavior. With o-toluidine blue as the indicator, determination of the concentration of a range of polyquaterniums of commercial importance and cosmetic origin was possible. Using a visual endpoint, normalities as low as 3x10-5 N could be determined, while with a spectrophotometric endpoint, the technique was effective to approximately 3x10-6 N. The concentrations (g L-1) to which these normalities correspond depend on the charge density of the polymer. Polyquaterniums are frequently used in association with anionic surfactants in cosmetic formulations and the presence of an anionic surfactant even in excess did not affect results although the color change was less stable. Titration in the presence of prepared humic acid was also possible. © 2010 Taylor & Francis.
Cummings, DO, Booth, DJ, Lee, RW, Simpson, SJ & Pile, AJ 2010, 'Ontogenetic diet shifts in the reef fish Pseudanthias rubrizonatus from isolated populations on the North-West Shelf of Australia', MARINE ECOLOGY PROGRESS SERIES, vol. 419, pp. 211-222.
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The red-barred anthias Pseudanthias rubrizonatus is a common tropical deep reef fish species found in Australia, but little is known about its dietary preferences and trophic interactions. We examined the gut contents and stable isotope signatures (δ13C and δ15N) of P. rubrizonatus from populations on the North-West Shelf of Australia to determine differences in diet relative to site, depth and fish size. We sampled 5 fish populations from a series of sub-sea structures, from 82 to 152 m depth, which had been submerged for up to 15 yr. Gut content analysis suggested that P. rubrizonatus displays an opportunistic feeding strategy and utilises both pelagic and benthic resources, including larval fishes, heteropods, isopods and mysids. Stable isotope analyses revealed that at all depths P. rubrizonatus underwent an ontogenetic diet shift. Values for δ13C in muscle ranged from -19.7% for small fish to -16.2% for larger individuals, and δ15N ranged from 8.2% for smaller fish to 13.2% for larger fish, indicating that a diet shift occurs at the end of juvenile development between 30 and 50 mm standard length. By simultaneously analysing gut contents and stable isotope signatures of the collected specimens, we have documented opportunistic dietary strategies that may assist P. rubrizonatus to colonise isolated structures. © Inter-Research 2010.
Cywinski, PJ, Idzik, KR, Cranfield, CG, Beckert, R & Mohr, GJ 2010, 'Synthesis and sensing properties of a new carbazole fluorosensor for detection of abacavir', SUPRAMOLECULAR CHEMISTRY, vol. 22, no. 10, pp. 598-602.
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Danilenko, AI & Dooley, AH 2010, 'SIMPLE Z(2)-ACTIONS TWISTED BY APERIODIC AUTOMORPHISMS', ISRAEL JOURNAL OF MATHEMATICS, vol. 175, no. 1, pp. 285-299.
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Darling, AE, Mau, B & Perna, NT 2010, 'progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement', PLOS ONE, vol. 5, no. 6, pp. 1-17.
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Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. Methodology/Principal Findings We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs breakpoint score, which facilitates accurate detection of rearrangement breakpoints when genomes have unequal gene content. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The new genome alignment algorithm demonstrates high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental gain and loss. We apply the new algorithm to a set of 23 genomes from the genera Escherichia, Shigella, and Salmonella. Analysis of whole-genome multiple alignments allows us to extend the previously defined concepts of core- and pan-genomes to include not only annotated genes, but also non-coding regions with potential regulatory roles. The 23 enterobacteria have an estimated core-genome of 2.46Mbp conserved among all taxa and a pan-genome of 15.2Mbp. We document substantial population-level variability among these organisms driven by segmental gain and loss. Interestingly, much variability lies in intergenic regions, suggesting that the Enterobacteriacae may exhibit regulatory diver...
Dawes, FE, Kuzevski, A, Bettelheim, KA, Hornitzky, MA, Djordjevic, SP & Walker, MJ 2010, 'Distribution of Class 1 Integrons with IS26-Mediated Deletions in Their 3′-Conserved Segments in Escherichia coli of Human and Animal Origin', PLoS ONE, vol. 5, no. 9, pp. e12754-e12754.
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Class 1 integrons play a role in the emergence of multi-resistant bacteria by facilitating the recruitment of gene cassettes encoding antibiotic resistance genes. 512 E. coli strains sourced from humans (n = 202), animals (n = 304) and the environment (n = 6) were screened for the presence of the intI1 gene. In 31/79 integron positive E. coli strains, the gene cassette regions could not be PCR amplified using standard primers. DNA sequence analysis of 6 serologically diverse strains revealed atypical integrons harboured the dfrA5 cassette gene and only 24 bp of the integron 3?-conserved segment (CS) remained, due to the insertion of IS26. PCR targeting intI1 and IS26 followed by restriction fragment length polymorphism (RFLP) analysis identified the integron-dfrA5-IS26 element in 27 E. coli strains of bovine origin and 4 strains of human origin. Southern hybridization and transformation studies revealed the integron-dfrA5-IS26 gene arrangement was either chromosomally located or plasmid borne. Plasmid location in 4/9 E. coli strains and PCR linkage of Tn21 transposition genes with the intI1 gene in 20/31 strains, suggests this element is readily disseminated by horizontal transfer.
Deng, W, Jin, D, Drozdowicz-Tomsia, K, Yuan, J & Goldys, EM 2010, 'Europium Chelate (BHHCT-Eu3+) and Its Metal Nanostructure Enhanced Luminescence Applied to Bioassays and Time-Gated Bioimaging', Langmuir, vol. 26, no. 12, pp. 10036-10043.
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Deutscher, AT, Jenkins, C, Minion, FC, Seymour, LM, Padula, MP, Dixon, NE, Walker, MJ & Djordjevic, SP 2010, 'Repeat regions R1 and R2 in the P97 paralogue Mhp271 of Mycoplasma hyopneumoniae bind heparin, fibronectin and porcine cilia', Molecular Microbiology, vol. 78, no. 2, pp. 444-458.
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Summary Mycoplasma hyopneumoniae, the causative agent of porcine enzootic pneumonia, adheres to ciliated respiratory epithelia resulting in ciliostasis and epithelial cell death. The cilium adhesin P97 (Mhp183) contains two repeat regions, designated R1 and R2, that play key roles in adherence. Eight pentapeptide repeats in R1 are sufficient to bind porcine cilia; however, both R1 and R2 are needed to bind heparin. Mhp271, a paralogue of P97, is the only other M. hyopneumoniae protein to contain both R1 and R2 repeats. These repeats are arranged as a set of three pentapeptide repeats (designated R1A271), two decapeptide repeats (designated R2271), and a second set of six pentapeptide repeats (designated R1B271). To determine their function, recombinant proteins containing R1A271 (F1271) and R2271‐R1B271 (F2271) were constructed and used in in vitro binding assays. F2271, but not F1271, bound heparin (KD = 8.1 ± 0.4 nM), fibronectin (KD = 174 ± 13 nM) and porcine cilia. Pre‐incubation of F2271 with 100 µM heparin blocked cilium binding by ∼69%. Cell surface shaving with trypsin combined with two‐dimensional liquid chromatography coupled to tandem mass spectrometry analysis identified Mhp271 as surface‐exposed. Our data suggest that both R1 and R2 in Mhp271 are involved in binding to host molecules.
Dhavala, SS, Datta, S, Mallick, BK, Carroll, RJ, Khare, S, Lawhon, SD & Adams, LG 2010, 'Bayesian Modeling of MPSS Data: Gene Expression Analysis of BovineSalmonellaInfection', Journal of the American Statistical Association, vol. 105, no. 491, pp. 956-967.
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Didelot, X, Lawson, D, Darling, A & Falush, D 2010, 'Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences', Genetics, vol. 186, no. 4, pp. 1435-1449.
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Abstract Bacteria and archaea reproduce clonally, but sporadically import DNA into their chromosomes from other organisms. In many of these events, the imported DNA replaces an homologous segment in the recipient genome. Here we present a new method to reconstruct the history of recombination events that affected a given sample of bacterial genomes. We introduce a mathematical model that represents both the donor and the recipient of each DNA import as an ancestor of the genomes in the sample. The model represents a simplification of the previously described coalescent with gene conversion. We implement a Monte Carlo Markov chain algorithm to perform inference under this model from sequence data alignments and show that inference is feasible for whole-genome alignments through parallelization. Using simulated data, we demonstrate accurate and reliable identification of individual recombination events and global recombination rate parameters. We applied our approach to an alignment of 13 whole genomes from the Bacillus cereus group. We find, as expected from laboratory experiments, that the recombination rate is higher between closely related organisms and also that the genome contains several broad regions of elevated levels of recombination. Application of the method to the genomic data sets that are becoming available should reveal the evolutionary history and private lives of populations of bacteria and archaea. The methods described in this article have been implemented in a computer software package, ClonalOrigin, which is freely available from http://code.google.com/p/clonalorigin/.
Doblin, MA, Murphy, KR & Ruiz, GM 2010, 'Thresholds for tracing ships' ballast water: an Australian case study', MARINE ECOLOGY PROGRESS SERIES, vol. 408, pp. 19-32.
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To limit the spread of non-indigenous marine species, ships can be legally required to conduct ballast water exchange (BWE) prior to discharging ballast water. It has been proposed to verify BWE by measuring concentrations of coastal tracers in ballast tanks, which should track their removal. Using 3 Australian ports as case studies (Port Botany, Port Curtis and Port Phillip Bay), each representing a different BWE verification difficulty level, the spatial and temporal variability of chromophoric dissolved organic matter (CDOM) and 3 trace elements (manganese [Mn], barium [Ba] and phosphorus [P]), were measured to assess their utility as tracers of coastal (unexchanged) ballast water. CDOM fluorescence at λex/λem = 320/414 nm (C2*) and 370/494 nm (C3*) and Mn concentrations were significantly higher in ports than in the adjacent Tasman Sea, except near port entrances and at a few sites in Port Botany. Ba concentrations demonstrated the least power to discriminate coastal sources, but P easily discriminated water from mesotrophic Port Phillip Bay. In general, tracers showed greater variation between and within ports, rather than between seasons. Conservative BWE thresholds were calculated to be 1.6 quinine sulphate equivalents for C2*, 0.9 quinine sulphate equivalents for C3*, 1.4 μg lâ1 for Mn and 6.9 μg lâ1 for Ba. Overall, these thresholds would allow water sourced from eastern Australian ports to be identified as coastal at 92%, 69% and 74% of sites examined using C3*, Mn and Ba, respectively, requiring 71 ± 26%, 54 ± 40% and 59 ± 38% replacement with mid-ocean water to be within ocean baseline concentration ranges.
Donnelly, S, O'Neill, SM, Stack, CM, Robinson, MW, Turnbull, L, Whitchurch, C & Dalton, JP 2010, 'Helminth Cysteine Proteases Inhibit TRIF-dependent Activation of Macrophages via Degradation of TLR3', JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 285, no. 5, pp. 3383-3392.
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Helminth pathogens prepare a Th2 type immunological environment in their hosts to ensure their longevity. They achieve this by secreting molecules that not only actively drive type 2 responses but also suppress type 1 responses. Here, we show that the major cysteine proteases secreted from the helminth pathogens Fasciola hepatica (FheCL1) and Schistosoma mansoni (SmCB1) protect mice from the lethal effects of lipopolysaccharide by preventing the release of inflammatory mediators, nitric oxide, interleukin-6, tumor necrosis factor α, and interleukin-12, from macrophages. The proteases specifically block the MyD88-independent TRIF-dependent signaling pathway of Toll-like receptor (TLR)4 and TLR3. Microscopical and flow cytometric studies, however, show that alteration of macrophage function by cysteine protease is not mediated by cleavage of components of the TLR4 complex on the cell surface but occurs by degradation of TLR3 within the endosome. This is the first study to describe a parasite molecule that degrades this receptor and pinpoints a novel mechanism by which helminth parasites modulate the innate immune responses of their hosts to suppress the development of Th1 responses. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.
Dowling, DJ, Hamilton, CM, Donnelly, S, La Course, J, Brophy, PM, Dalton, J & O'Neill, SM 2010, 'Major Secretory Antigens of the Helminth Fasciola hepatica Activate a Suppressive Dendritic Cell Phenotype That Attenuates Th17 Cells but Fails To Activate Th2 Immune Responses', INFECTION AND IMMUNITY, vol. 78, no. 2, pp. 793-801.
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Fasciola hepatica is a helminth pathogen that drives Th2/Treg immune responses in its mammalian host. The parasite releases a large number of molecules that are critical to inducing this type of immune response. Here we have selected recombinant forms of two major F. hepatica secreted molecules, the protease cathepsin L (rFhCL1) and an antioxidant, sigma class glutathione transferase (rFhGST-si), to examine their interactions with dendritic cells (DCs). Despite enzymatic and functional differences between these molecules, both induced interleukin-6 (IL-6), IL-12p40, and macrophage inflammatory protein 2 (MIP-2) secretion from DCs and enhanced CD40 expression. While this induction was mediated by Toll-like receptor 4 (TLR4), the subsequent intracellular signaling pathways differed; rFhCL1 signaled through p38, and rFhGST-si mediated its effect via c-Jun N-terminal kinase (JNK), p38, p-NF-κBp65, and IRF5. Neither rFhCL1 nor rFhGST-si enhanced DC phagocytosis or induced Th2 immune responses in vivo. However, DCs matured in the presence of either enzyme attenuated IL-17 production from OVA peptide-specific T cells in vivo. In addition, DCs exposed to either antigen secreted reduced levels of IL-23. Therefore, both F. hepatica FhCL1 and FhGST-si modulate host immunity by suppressing responses associated with chronic inflammation-an immune modulatory mechanism that may benefit the parasite's survival within the host. Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Duval, L, Fourment, M, Nerrienet, E, Rousset, D, Sadeuh, SA, Goodman, SM, Andriaholinirina, NV, Randrianarivelojosia, M, Paul, RE, Robert, V, Ayala, FJ & Ariey, F 2010, 'African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus', Proceedings of the National Academy of Sciences, vol. 107, no. 23, pp. 10561-10566.
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We investigated two mitochondrial genes ( cytb and cox1 ), one plastid gene ( tufA ), and one nuclear gene ( ldh ) in blood samples from 12 chimpanzees and two gorillas from Cameroon and one lemur from Madagascar. One gorilla sample is related to Plasmodium falciparum , thus confirming the recently reported presence in gorillas of this parasite. The second gorilla sample is more similar to the recently defined Plasmodium gaboni than to the P. falciparum–Plasmodium reichenowi clade, but distinct from both. Two chimpanzee samples are P. falciparum . A third sample is P. reichenowi and two others are P. gaboni . The other chimpanzee samples are different from those in the ape clade: two are Plasmodium ovale , and one is Plasmodium malariae . That is, we have found three human Plasmodium parasites in chimpanzees. Four chimpanzee samples were mixed: one species was P. reichenowi ; the other species was P. gaboni in three samples and P. ovale in the fourth sample. The lemur sample, provisionally named Plasmodium malagasi , is a sister lineage to the large cluster of primate parasites that...
Earp, AA & Smith, GB 2010, 'Metal nanoparticle plasmonics inside reflecting metal films', APPLIED PHYSICS LETTERS, vol. 96, no. 24, pp. 1-3.
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Oxide coated metal nanoparticles buried within a thin metal layer support a surface plasmon resonance. A local dip occurs in spectral reflectance along with a switching off of the film's plasmonic response. Models are introduced in which these resonances
Earp, AA, Rawling, T, Franklin, JB & Smith, GB 2010, 'Perylene dye photodegradation due to ketones and singlet oxygen', DYES AND PIGMENTS, vol. 84, no. 1, pp. 59-61.
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The photodegradation rate of a perylene dye (Lumogen F Yellow 083) in methyl isobutyrate was found to increase with ketone concentration for two different ketones. Of the ketones employed, methyl pyruvate, an impurity in methyl methacrylate, was found to be particularly deleterious to dye stability. In agreement with other published studies, the addition of the anti-oxidant DABCO (1,4-diazabicyclo-[2.2.2] octane) to the dye matrix was found to increase dye stability; however when ketones were present, DABCO lead to increased photodegradation. These results highlight the importance of removing ketone impurities from dye matrices during production of Luminescent Solar Concentrators (LSCs). © 2009 Elsevier Ltd. All rights reserved.
Ellis, J, Sinclair, D, Morrison, D, Al-Qassab, S, Springett, K & Ivens, A 2010, 'Microarray analyses of mouse responses to infection by Neospora caninum identifies disease associated cellular pathways in the host response', MOLECULAR AND BIOCHEMICAL PARASITOLOGY, vol. 174, no. 2, pp. 117-127.
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Neospora caninum is a coccidian cyst-forming parasite found in a wide range of host species such as mice, dogs and cattle. The development of methods such as vaccines to prevent abortion and fetal loss due to neosporosis would be greatly assisted by further knowledge on immunity and host responses to infection. In this study we used microarray technology to investigate the protective host responses occurring at 6 h post infection in the spleen of mice infected with a prototype live N. caninum vaccine. Naive non-pregnant mice were infected with the NC-Nowra isolate as such infections are known to induce protective host responses that will prevent transplacental transmission of a challenge given using pregnancy. The expression data was analysed by SAM (significance of microarrays), ANOVA and clustering methods. Gene lists were investigated for enrichment of gene ontology terms by functional annotation using hypergeometric tests. The results show that Qs and BALB/c mice infected with NC-Nowra differ in their transcriptional responses to infection and these affect a wide range of biological and molecular processes. Transcriptional changes in the Jak-STAT signaling pathway (as well as Irf and other IFN-? regulated molecules such as GTPases) confirmed the influence of IFN-? in the mouse response to N. caninum. Gene ontology analyses also assigned some of the molecules involved to well known disease pathways associated with cancer, Parkinson's and Alzheimer's diseases, which were linked to the cell cycle, mitochondrial electron transport chain and coupled proton transport pathways amongst others. Although infection of mice with NC-Nowra causes little or no signs of clinical disease, the molecular functions, processes and pathways identified through these studies clearly warrant further investigation for their role in the development of protective immunity as well as pathogenesis. These studies therefore provide new, exciting leads by which to study neosporosis.
Epple, R, Blanes, L, Beavis, A, Roux, C & Doble, P 2010, 'Analysis of amphetamine-type substances by capillary zone electrophoresis using capacitively coupled contactless conductivity detection', ELECTROPHORESIS, vol. 31, no. 15, pp. 2608-2613.
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CE with capacitively coupled contactless conductivity detection (C4D) was employed for the separation and detection of seven amphetamine analogues as well as amphetamine, dextroamphetamine, methamphetamine and 3,4-methylenedioxymethamphetamine. The separation electrolyte was 30 mM hydroxypropyl-~-cyclodextrin (HPPCD) in a 75 mM acetic acid+25 mM sodium acetate buffer adjusted to pH 4.55. Conductivity detection was compared with UV detection using this same electrolyte. Average detection limits for C4D and UV were 1.3 and 1.0 ppm, respectively. The effects of HPPCO -concentration and BGE composition on the selectivity of the separation were also investigated. An illicit, street-grade sample of 3,4-methylenedioxymethamphetamine (Ecstasy) and a prescription dextroamphetamine tablet were also analysed.
Eriksson, AC, Booth, DJ & Biro, PA 2010, ''Personality' in two species of temperate damselfish', MARINE ECOLOGY PROGRESS SERIES, vol. 420, pp. 273-276.
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The extent and importance of consistent individual differences in behaviour, often referred to as 'personality' or 'temperament', is a relatively recent question in ecology. It indicates that animal behaviour is much less flexible than usually assumed, and suggests that individuals consistently differ in the way they perceive and react to changes in the environment. There is evidence of animal personality in a wide variety of animal taxa, including many freshwater fish species, but there seems to be very little evidence for this phenomenon in marine fish. To address this paucity, we repeatedly measured 3 behavioural traits of 2 temperate marine damselfish species, Parma microlepis and P. unifasciata, over a 2 wk period. Consistent individual differences in boldness, aggressiveness and activity were observed in both species, but average levels of these traits did not differ between species. A correlation between personality traits was also observed, with bolder individuals also tending to be more aggressive. The existence of personality in marine fish has implications for practical issues such as sampling bias, vulnerability to harvest and links between personality and lifehistory traits that affect fitness. © Inter-Research 2010.
Ewing, B, Cooper, TJ, Baturo, AR, Matthews, C & Sun, H 2010, 'Contextualising the Teaching and Learning of Measurement within Torres Strait Islander Schools', The Australian Journal of Indigenous Education, vol. 39, no. 1, pp. 11-23.
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Abstract A one-year mathematics project that focused on measurement was conducted with six Torres Strait Islander schools and communities. Its key focus was to contextualise the teaching and learning of measurement within the students' culture, communities and home languages. Six teachers and two teacher aides participated in the project. This paper reports on the findings from the teachers' and teacher aides' survey questionnaire used in the first Professional Development session to identify: a) teachers' experience of teaching in the Torres Strait Islands, b) teachers' beliefs about effective ways to teach Torres Strait Islander students, and c) contexualising measurement within Torres Strait Islander culture, communities and home languages. A wide range of differing levels of knowledge and understanding about how to contextualise measurement to support student learning were identified and analysed. For example, an Indigenous teacher claimed that mathematics and the environment are relational, that is, they are not discrete and in isolation from one another, rather they interconnect with mathematical ideas emerging from the environment of the Torres Strait communities.
Exton, DA, Smith, DJ, McGenity, TJ, Steinke, M, Hills, AJ & Suggett, DJ 2010, 'Application of a Fast Isoprene Sensor (FIS) for measuring isoprene production from marine samples', Limnology and Oceanography: Methods, vol. 8, no. 5, pp. 185-195.
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Research into isoprene production from marine sources traditionally relies on gas chromatography techniques which are labor intensive, provide a slow sample turnover, and require significant method training. An alternative method is the use of a Fast Isoprene Sensor (FIS), a chemiluminescence‐based approach that provides real time isoprene analysis, but is relatively simple to run and also portable. Until now, the FIS has been used in terrestrial but not aquatic isoprene studies. Due to the added difficulties with marine compared with terrestrial sampling, particularly potential interference from dimethyl sulfide (DMS), we have developed a new protocol that allows accurate and reliable data to be obtained from FIS analysis. The detection limit of our modified system to standard gas was 0.02 nM (0.5 ppbv), while minimum isoprene production detected by the FIS was 0.59 nmol h−1 (for Thalassiosira weissflogii). We also compared our FIS‐based approach with GC analysis of isoprene emission from marine samples of micro‐ and macro‐algae, and demonstrated a strong similarity (r2 = 0.910, slope = 1.003). The ability to use FIS analysis with marine samples will significantly broaden the scope of isoprene research in marine environments, permitting remote field work, and allow previously unanswered questions to be addressed.
Ferreira, NC, Ferreira, LG & Huete, AR 2010, 'Assessing the response of the MODIS vegetation indices to landscape disturbance in the forested areas of the legal Brazilian Amazon', INTERNATIONAL JOURNAL OF REMOTE SENSING, vol. 31, no. 3, pp. 745-759.
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In this study we assessed the impacts of forest fragmentation on the Amazon landscape using remote sensing techniques. Landscape disturbance, obtained for an area of approximately 3.5 × 106 km2 through simple spatial metrics (i.e. number of fragments, mean fragment area and border size) and principal component transformation were then compared to the MODIS (Moderate Resolution Imaging Spectroradiometer) NDVI (Normalized Difference Vegetation Index) and EVI (Enhanced Vegetation Index) seasonal responses. As expected, higher disturbance values prevail in the southern border of the Amazon, near the intensively converted deforestation arc, and close to the major roads. NDVI seasonal responses more closely follow human-induced patterns, i.e. forest remnants from areas more intensively converted were associated with higher NDVI seasonal values. The significant correlation between NDVI seasonal responses and landscape disturbances were corroborated through analysis of geographically weighted regression (GWR) parameters and predictions. On the other hand, EVI seasonal responses were more complex with significant variations found over intact, less fragmented forest patches, thus restricting its utility to assess landscape disturbance. Although further research is needed, our results suggest that the degree of fragmentation of the forest remnants can be remotely sensed with MODIS vegetation indices. Thus, it may become possible to upscale field-based data on overall canopy condition and fragmentation status for basin-wide extrapolations. © 2010 Taylor & Francis.
Figueira, WF & Booth, DJ 2010, 'Increasing ocean temperatures allow tropical fishes to survive overwinter in temperate waters', GLOBAL CHANGE BIOLOGY, vol. 16, no. 2, pp. 506-516.
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The southeast coast of Australia is a global hotspot for increasing ocean temperatures due to climate change. The temperate incursion of the East Australian Current (EAC) is increasing, affording increased connectivity with the Great Barrier Reef. The survival of tropically sourced juveniles over the winter is a significant stumbling block to poleward range shifts of marine organisms in this region. Here we examine the dependence of overwintering on winter severity and prewinter recruitment for eight species of juvenile coral reef fishes which are carried into temperate SE Australia (30-371S) by the EAC during the austral summer. The probability of persistence was most strongly influenced by average winter temperature and there was no effect of recruitment strength. Long-term (138 years) data indicate that winter water temperatures throughout this region are increasing at a rate above the global average and predictions indicate a further warming of >2 °C by the end of the century. Rising ocean temperatures are resulting in a higher frequency of winter temperatures above survival thresholds. Current warming trajec-tories predict 100% of winters will be survivable by at least five of the study species as far south as Sydney (34°S) by 2080. The implications for range expansions of these and other species of coral reef fish are discussed. © 2009 Blackwell Publishing Ltd.
Fogarty, S, Harris, D, Zaslawski, C, McAinch, AJ & Stojanovska, L 2010, 'Acupuncture as an adjunct therapy in the treatment of eating disorders: A randomised cross-over pilot study', COMPLEMENTARY THERAPIES IN MEDICINE, vol. 18, no. 6, pp. 233-240.
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Objective: This study examines the role of acupuncture as an adjunct therapy in the treatment of eating disorders in female patients. Design: A randomised cross-over study was used in this study. The two treatments phases were the private multi-disciplinary outpatient eating disorder facility in Melbourne, Australia, only (referred to as their treatment as usual) and a continuation of their treatment as usual supplemented by acupuncture. Participants: Patients receiving treatment at a private multi-disciplinary outpatient eating disorder facility in Melbourne, Australia were asked to participate in the study. Nine consenting women (5 with Anorexia Nervosa, 4 with Bulimia Nervosa), aged (mean and SD) 23.7 (9.6) years, participated in the study. Main outcome measures: The main outcome measure was the Eating Disorder Inventory-3. Secondary outcome measures were the Becks Depression Inventory-2, State Trait Anxiety Inventory and the Eating Disorder Quality of Life Scale. Results: There was evidence that acupuncture improved the participants' Quality of Life as measured by the physical/cognitive and psychological components of the Eating Disorder Quality of Life scale. There was also evidence of decreases in anxiety (both State and Trait as measured by the State Trait Anxiety Intervention) and perfectionism (as measured by the Eating Disorder Inventory-3). Conclusion: This pilot study shows potential of the benefit of acupuncture as an adjunct therapy in the treatment of eating disorders particularly in the area of quality of life. © 2010.
Foley, M, Ton-That, C & Phillips, MR 2010, 'Luminescent properties of ZnO structures grown with a vapour transport method', THIN SOLID FILMS, vol. 518, no. 15, pp. 4231-4233.
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ZnO structures were synthesised on the sapphire (112̄0) substrate by a vapour transport method in a gas flowing furnace. The influence of the oxygen content in the gas mixture on the morphology and luminescent properties of ZnO structures grown on a strip-like substrate was investigated, with all other growth parameters being kept nominally identical. Integrated electron microscopy and cathodoluminescence analysis shows gradual variations of structural and optical emission properties for ZnO structures grown on the long substrate. Defect-related green luminescence of ZnO is found to be highly dependent on the oxygen vapour in the growth region of the furnace. Our findings demonstrate that the green luminescence is associated with oxygen deficiency in ZnO. © 2009 Elsevier B.V. All rights reserved.
Ford, JR, Williams, RJ, Fowler, AM, Cox, DR & Suthers, IM 2010, 'Identifying critical estuarine seagrass habitat for settlement of coastally spawned fish', Marine Ecology Progress Series, vol. 408, pp. 181-193.
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Fourment, M, Mardy, S, Channa, M & Buchy, P 2010, 'Evidence for Persistence of and Antiviral Resistance and Reassortment Events in Seasonal Influenza Virus Strains Circulating in Cambodia', Journal of Clinical Microbiology, vol. 48, no. 1, pp. 295-297.
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ABSTRACT The analysis of A/H1N1 and A/H3N2 influenza viruses collected between 2005 and 2008 in Cambodia detected strains resistant to oseltamivir and confirmed widespread resistance to adamantanes. Phylogenetic analyses revealed intrasubtype reassortment, probable reemergence of A/H3N2 viruses in two consecutive seasons, and cocirculation of different lineages in each subtype.
Fourment, M, Wood, JT, Gibbs, AJ & Gibbs, MJ 2010, 'Evolutionary dynamics of the N1 neuraminidases of the main lineages of influenza A viruses', Molecular Phylogenetics and Evolution, vol. 56, no. 2, pp. 526-535.
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Freire, MJ, Jelinek, L, Marques, R & Lapine, M 2010, 'On the applications of metamaterial lenses for magnetic resonance imaging', Journal of Magnetic Resonance, vol. 203, no. 1, pp. 81-90.
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Fu, S, Lewis, J, Wang, H, Keegan, J & Dawson, M 2010, 'A Novel Reductive Transformation of Oxazepam to Nordiazepam Observed During Enzymatic Hydrolysis', JOURNAL OF ANALYTICAL TOXICOLOGY, vol. 34, no. 5, pp. 243-251.
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β-Glucuronidase is an enzyme often employed to de-conjugate β-glucuronides during urinary drug testing for benzodiazepines. It is commonly accepted that use of β-glucuronidase is a preferred method of hydrolysis over acid-catalyzed hydrolysis, which is known to induce benzodiazepine degradation and transformation. Literature to date, however, has not reported any cases of benzodiazepine transformation initiated by commercial β-glucuronidase products. In this study, urine specimens containing either oxazepam or oxazepam glucuronide were incubated with β-glucuronidase enzymes obtained from Escherichia coli, Helix pomatia, and Patella vulgata under various incubation conditions. After liquid-liquid extraction, the extract was analyzed by both liquid chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry for the presence of benzodiazepines. All three enzyme preparations examined were capable of reducing oxazepam or oxazepam glucuronide into nordiazepam (desmethyldiazepam). Nordiazepam formation was positively correlated with incubation temperature, incubation time, oxazepam concentration, and enzyme concentration. Under all enzymatic hydrolysis conditions investigated, the percentage of nordiazepam formation is < 2.5% relative to the amount of oxazepam present in the system. The findings of this study have both clinical and forensic implications, and it is clear that the detection of nordiazepam in biological samples subjected to testing involving enzyme-catalyzed hydrolysis should be interpreted with care.
Fu, WJ, Stromberg, AJ, Viele, K, Carroll, RJ & Wu, G 2010, 'Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology☆', The Journal of Nutritional Biochemistry, vol. 21, no. 7, pp. 561-572.
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Fung, C, Naughton, S, Turnbull, L, Tingpej, P, Rose, B, Arthur, J, Hu, H, Harmer, C, Harbour, C, Hassett, DJ, Whitchurch, CB & Manos, J 2010, 'Gene expression of Pseudomonas aeruginosa in a mucin-containing synthetic growth medium mimicking cystic fibrosis lung sputum', JOURNAL OF MEDICAL MICROBIOLOGY, vol. 59, no. 9, pp. 1089-1100.
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Pseudomonas aeruginosa airway infection is the leading cause of morbidity and mortality in cystic fibrosis (CF) patients. Various in vitro models have been developed to study P. aeruginosa pathobiology in the CF lung. In this study we produced a modified artificial-sputum medium (ASMDM) more closely resembling CF sputum than previous models, and extended previous work by using strain PAO1 arrays to examine the global transcription profiles of P. aeruginosa strain UCBPP-PA14 under early exponential-phase and stationary-phase growth. In early exponential phase, 38/39 nutrition-related genes were upregulated in line with data from previous in vitro models using UCBPP-PA14. Additionally, 23 type III secretion system (T3SS) genes, several anaerobic respiration genes and 24 quorum-sensing (QS)-related genes were upregulated in ASMDM, suggesting enhanced virulence factor expression and priming for anaerobic growth and biofilm formation. Under stationary phase growth in ASMDM, macroscopic clumps resembling microcolonies were evident in UCBPP-PA14 and CF strains, and over 40 potentially important genes were differentially expressed relative to stationary-phase growth in Luria broth. Most notably, QS-related and T3SS genes were downregulated in ASMDM, and iron-acquisition and assimilatory nitrate reductase genes were upregulated, simulating the iron-depleted, microaerophilic/anaerobic environment of CF sputum. ASMDM thus appears to be highly suitable for gene expression studies of P. aeruginosa in CF. © 2010 SGM Printed in Great Britain.
Gale, PA 2010, 'Anion receptor chemistry: highlights from 2008 and 2009', Chemical Society Reviews, vol. 39, no. 10, pp. 3746-3746.
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Gale, PA & Gunnlaugsson, T 2010, 'Preface: supramolecular chemistry of anionic species themed issue', Chemical Society Reviews, vol. 39, no. 10, pp. 3595-3595.
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Gale, PA, Hiscock, JR, Jie, CZ, Hursthouse, MB & Light, ME 2010, 'Acyclic indole and carbazole-based sulfate receptors', Chemical Science, vol. 1, no. 2, pp. 215-215.
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Gale, PA, Hiscock, JR, Moore, SJ, Caltagirone, C, Hursthouse, MB & Light, ME 2010, 'Anion–Anion Proton Transfer in Hydrogen Bonded Complexes', Chemistry – An Asian Journal, vol. 5, no. 3, pp. 555-561.
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AbstractComplexation of dihydrogen phosphate by an anion receptor containing six hydrogen bond donor groups has been shown to reduce the pKa of the bound anionic species to such an extent that addition of further aliquots of dihydrogen phosphate result in deprotonation of the bound species with the resultant formation of a monohydrogen phosphate receptor complex. X‐ray crystallographic studies confirm monohydrogen phosphate complex formation in the solid state. In this way, this study explains the formation of complexes with unusual stoichiometries when investigating the binding of dihydrogenphosphate anion to hydrogen‐bonding receptors.
Gale, PA, Tong, CC, Haynes, CJE, Adeosun, O, Gross, DE, Karnas, E, Sedenberg, EM, Quesada, R & Sessler, JL 2010, 'Octafluorocalix[4]pyrrole: A Chloride/Bicarbonate Antiport Agent', Journal of the American Chemical Society, vol. 132, no. 10, pp. 3240-3241.
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Ge, Q, Moir, LM, Black, JL, Oliver, BG & Burgess, JK 2010, 'TGF beta 1 Induces IL-6 and Inhibits IL-8 Release in Human Bronchial Epithelial Cells: The Role of Smad2/3', JOURNAL OF CELLULAR PHYSIOLOGY, vol. 225, no. 3, pp. 846-854.
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Human bronchial epithelial (HBE) cells contribute to asthmatic airway inflammation by secreting cytokines, chemokines, and growth factors, including interleukin (IL)-6, IL-8 and transforming growth factor (TGF) β1, all of which are elevated in asthmatic airways. This study examines the signaling pathways leading to TGFβ1 induced IL-6 and IL-8 in primary HBE cells from asthmatic and non-asthmatic volunteers. HBE cells were stimulated with TGFβ1 in the presence or absence of signaling inhibitors. IL-6 and IL-8 protein and mRNA were measured by ELISA and real-time PCR respectively, and cell signaling kinases by Western blot. TGFβ1 increased IL-6, but inhibited IL-8 production in both asthmatic and non-asthmatic cells; however, TGF induced significantly more IL-6 in asthmatic cells. Inhibition of JNK MAP kinase partially reduced TGFβ1 induced IL-6 in both cell groups. TGFβ1 induced Smad2 phosphorylation, and blockade of Smad2/3 prevented both the TGFβ1 modulated IL-6 increase and the decrease in IL-8 production in asthmatic and non-asthmatic cells. Inhibition of Smad2/3 also increased basal IL-8 release in asthmatic cells but not in non-asthmatic cells. Using CHIP assays we demonstrated that activated Smad2 bound to the IL-6, but not the IL-8 promoter region. We conclude that the Smad2/3 pathway is the predominant TGFβ1 signaling pathway in HBE cells, and this is altered in asthmatic bronchial epithelial cells. Understanding the mechanism of aberrant pro-inflammatory cytokine production in asthmatic airways will allow the development of alternative ways to control airway inflammation. © 2010 Wiley-Liss, Inc.
Gentle, AR & Smith, GB 2010, 'Radiative Heat Pumping from the Earth Using Surface Phonon Resonant Nanoparticles', NANO LETTERS, vol. 10, no. 2, pp. 373-379.
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Nanoparticles that have narrow absorption bands that lie entirely within the atmosphere's transparent window from 7.9 to 13 m can be used to radiatively cool to temperatures that are well below ambient. Heating from incoming atmospheric radiation in the remainder of the Planck radiation spectrum, where the atmosphere is nearly 'black', is reduced if the particles are dopants in infrared transmitting polymers, or in transmitting coatings on low emittance substrates. Crystalline SiC nanoparticles stand out with a surface phonon resonance from 10.5 to 13 m clear of the atmospheric ozone band. Resonant SiO2 nanoparticles are complementary, absorbing from 8 to 10 m, which includes atmospheric ozone emissions. Their spectral location has made SiC nanoparticles in space dust a feature in ground-based IR astronomy. Optical properties are presented and subambient cooling performance analyzed for doped polyethylene on aluminum. A mixture of SiC and SiO2 nanoparticles yields high performance cooling at low cost within a practical cooling rig. © 2010 American Chemical Society.
Ghazal, P, Fatima Shad, K & Sidduiqui, N 2010, 'Troponin based studies in search of a biomarker for cardiac arrest', Health, vol. 02, no. 01, pp. 70-77.
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Giunta, S, Castorina, A, Adorno, A, Mazzone, V, Carnazza, ML & D’Agata, V 2010, 'PACAP and VIP affect NF1 expression in rat malignant peripheral nerve sheath tumor (MPNST) cells', Neuropeptides, vol. 44, no. 1, pp. 45-51.
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Glenn, EP, Nagler, PL & Huete, AR 2010, 'Vegetation Index Methods for Estimating Evapotranspiration by Remote Sensing', SURVEYS IN GEOPHYSICS, vol. 31, no. 6, pp. 531-555.
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Evapotranspiration (ET) is the largest term after precipitation in terrestrial water budgets. Accurate estimates of ET are needed for numerous agricultural and natural resource management tasks and to project changes in hydrological cycles due to potential climate change. We explore recent methods that combine vegetation indices (VI) from satellites with ground measurements of actual ET (ETa) and meteorological data to project ETa over a wide range of biome types and scales of measurement, from local to global estimates. The majority of these use time-series imagery from the Moderate Resolution Imaging Spectrometer on the Terra satellite to project ET over seasons and years. The review explores the theoretical basis for the methods, the types of ancillary data needed, and their accuracy and limitations. Coefficients of determination between modeled ETa and measured ETa are in the range of 0.45-0.95, and root mean square errors are in the range of 10-30% of mean ETa values across biomes, similar to methods that use thermal infrared bands to estimate ETa and within the range of accuracy of the ground measurements by which they are calibrated or validated. The advent of frequent-return satellites such as Terra and planed replacement platforms, and the increasing number of moisture and carbon flux tower sites over the globe, have made these methods feasible. Examples of operational algorithms for ET in agricultural and natural ecosystems are presented. The goal of the review is to enable potential end-users from different disciplines to adapt these methods to new applications that require spatially-distributed ET estimates. © 2010 Springer Science+Business Media B.V.
Goebbert, KH & Leslie, LM 2010, 'Interannual Variability of Northwest Australian Tropical Cyclones', Journal of Climate, vol. 23, no. 17, pp. 4538-4555.
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Abstract Tropical cyclone (TC) activity over the southeast Indian Ocean has been studied far less than other TC basins, such as the North Atlantic and northwest Pacific. The authors examine the interannual TC variability of the northwest Australian (NWAUS) subbasin (0°–35°S, 105°–135°E), using an Australian TC dataset for the 39-yr period of 1970–2008. Thirteen TC metrics are assessed, with emphasis on annual TC frequencies and total TC days. Major findings are that for the NWAUS subbasin, there are annual means of 5.6 TCs and 42.4 TC days, with corresponding small standard deviations of 2.3 storms and 20.0 days. For intense TCs (WMO category 3 and higher), the annual mean TC frequency is 3.0, with a standard deviation of 1.6, and the annual average intense TC days is 7.6 days, with a standard deviation of 4.5 days. There are no significant linear trends in either mean annual TC frequencies or TC days. Notably, all 13 variability metrics show no trends over the 39-yr period and are less dependent upon standard El Niño–Southern Oscillation (ENSO) variables than many other TC basins, including the rest of the Australian region basin. The largest correlations with TC frequency were geopotential heights for June–August at 925 hPa over the South Atlantic Ocean (r = −0.65) and for April–June at 700 hPa over North America (−0.64). For TC days the largest correlations are geopotential heights for July–September at 1000 hPa over the South Atlantic Ocean (−0.7) and for April–June at 850 hPa over North America (−0.58). Last, wavelet analyses of annual TC frequencies and TC days reveal periodicities at ENSO and decadal time scales. However, the TC dataset is too short for conclusive evidence of multidecadal periodicities. Given the large correlations revealed by this study, developing and testing of a multivariate seasonal TC prediction scheme has commenc...
Golden, O, Flynn, RJ, Read, C, Sekiya, M, Donnelly, SM, Stack, C, Dalton, JP & Mulcahy, G 2010, 'Protection of cattle against a natural infection of Fasciola hepatica by vaccination with recombinant cathepsin L1 (rFhCL1)', VACCINE, vol. 28, no. 34, pp. 5551-5557.
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The liver fluke, Fasciola hepatica causes liver fluke disease, or fasciolosis, in ruminants such as cattle and sheep. An effective vaccine against the helminth parasite is essential to reduce our reliance on anthelmintics, particularly in light of frequent reports of resistance to some frontline drugs. In our study, Friesian cattle (13 per group) were vaccinated with recombinant F. hepatica cathepsin L1 protease (rFhCL1) formulated in mineral-oil based adjuvants, Montanide™ ISA 70VG and ISA 206VG. Following vaccination the animals were exposed to fluke-contaminated pastures for 13 weeks. At slaughter, there was a significant reduction in fluke burden of 48.2% in the cattle in both vaccinated groups, relative to the control non-vaccinated group, at p≤0.05. All vaccinated animals showed a sharp rise in total IgG levels to rFhCL1 post-vaccination which was maintained over the course of the 13-week challenge infection and was significantly higher than levels reached in the control group. Arginase levels in the macrophages of vaccinated cattle were significantly lower than those of the control cattle, indicating that the parasite-induced alternative-activation of the macrophages was altered by vaccination. The data demonstrate the potential for recombinant FhCL1 vaccine in controlling fasciolosis in cattle under field conditions. © 2010 Elsevier Ltd.
Gorrie, CA, Hayward, I, Cameron, N, Kailainathan, G, Nandapalan, N, Sutharsan, R, Wang, J, Mackay-Sim, A & Waite, PME 2010, 'Effects of human OEC-derived cell transplants in rodent spinal cord contusion injury', BRAIN RESEARCH, vol. 1337, no. 1, pp. 8-20.
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Numerous reports indicate that rodent olfactory ensheathing cells (OECs) assist in spinal cord repair and clinical trials have been undertaken using autologous transplantation of human olfactory ensheathing cells (hOECs) as a treatment for spinal cord injury. However, there are few studies investigating the efficacy of hOECs in animal models of spinal cord injury. In this study hOECs were derived from biopsies of human olfactory mucosa, purifed by culture in a serum-free medium containing neurotrophin-3, genetically labelled with EGFP, and stored frozen. These hOEC-derived cells were thawed and transplanted into the spinal cord injury site 7 days after a moderate contusion injury of the spinal cord at thoracic level T10 in the athymic rat. Six weeks later the animals receiving the hOEC-derived transplants had greater functional improvement in their hindlimbs than controls, assessed using open field (BBB scale) and horizontal rung walking tests. Histological analysis demonstrated beneficial effects of hOEC-derived cell transplantation: reductions in the volume of the lesion and the cavities within the lesion. The transplanted cells were located at the periphery of the lesion where they integrated with GFAP-positive astrocytes resulting in a significant reduction of GFAP staining intensity adjacent to the lesion. Although their mechanism of action is unclear we conclude that hOEC-derived cell transplants improved functional recovery after transplantation into the contused spinal cord, probably by modulating inflammatory responses and reducing secondary damage to the cord. © 2010 Elsevier B.V. All rights reserved.
Greentree, AD, Aharonovich, I, Castelletto, S, Doherty, MW, McGuinness, LP & Simpson, DA 2010, '21^st-Century Applications of Nanodiamonds', Optics and Photonics News, vol. 21, no. 9, pp. 20-20.
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Diamond is taking on a new role as a versatile and practical platform for harnessing the new quantum physics. Here, we outline some of the biological and quantum applications of nanodiamonds and the central role of diamond color centers.
Greenup, AG, Sasani, S, Oliver, SN, Talbot, MJ, Dennis, ES, Hemming, MN & Trevaskis, B 2010, 'ODDSOC2 Is a MADS Box Floral Repressor That Is Down-Regulated by Vernalization in Temperate Cereals', PLANT PHYSIOLOGY, vol. 153, no. 3, pp. 1062-1073.
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In temperate cereals, such as wheat (Triticum aestivum) and barley (Hordeum vulgare), the transition to reproductive development can be accelerated by prolonged exposure to cold (vernalization). We examined the role of the grass-specific MADS box gene OD
Greive, KA, Staton, JA, Miller, PF, Peters, BA & Oppenheim, VMJ 2010, 'Development of Melaleuca oils as effective natural‐based personal insect repellents', Australian Journal of Entomology, vol. 49, no. 1, pp. 40-48.
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AbstractFor many decades effective insect repellents have relied on synthetic actives such as N,N‐diethyl‐meta‐toluamide. Increasingly, consumers are seeking natural‐based alternatives to many everyday products including insect repellents. While many studies have been published detailing the potential of essential oils to act as insect repellents, few oils have been identified as viable alternatives to synthetic actives. This study details the process involved in the selection of Australian essential oils effective as repellents and the subsequent testing of natural‐based insect repellents using the selected oils. Using a combination of laboratory‐based and field‐based testing, oil from Melaleuca ericifolia was identified as being an effective insect repellent. When formulated into three different bases: an alcohol‐based spray, an emulsion and a gel, these Melaleuca‐based repellents were shown to be as effective at repelling mosquitoes Aedes vigilax (Skuse) (Diptera: Culicidae) and Verrallina carmenti (Edwards) (Diptera: Culicidae), the bush fly Musca vetustissima (Walker) (Diptera: Muscidae), and biting midges Culicoides ornatus (Taylor) (Diptera: Ceratopogonidae) and Culicoides immaculatus (Lee & Reye) (Diptera: Ceratopogonidae) as a synthetic‐based commercial repellent. This study has shown that effective insect repellents based on natural active ingredients can deliver repellency on par with synthetic actives in the field. Three Melaleuca‐based formulations have been registered as repellents and are now commercially available.
Groen, L, Botten, L & Blazek, K 2010, 'Optimising the location of tsunami detection buoys and sea-level monitors in the Indian Ocean', International Journal of Operational Research, vol. 8, no. 2, pp. 174-174.
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In the wake of the 2004 Boxing Day tsunami disaster, a global response to implement a tsunami warning system in the Indian Ocean became imperative. Steps in this direction were initiated in 2005 with plans for the deployment of up to 24 tsunami detection buoys. The purpose of this paper is to investigate the optimal placement of tsunami detection buoys and sea-level monitors, in order to provide warning to the greatest population potentially affected. We adopt a mathematical programming approach to examine this problem. It is determined that 10 sites are essential in ensuring that the maximum population can be warned. This has implications for construction and maintenance of the tsunami warning system in the Indian Ocean.
Hadwen, WL, Fellows, CS, Westhorpe, DP, Rees, GN, Mitrovic, SM, Taylor, B, Baldwin, DS, Silvester, E & Croome, R 2010, 'LONGITUDINAL TRENDS IN RIVER FUNCTIONING: PATTERNS OF NUTRIENT AND CARBON PROCESSING IN THREE AUSTRALIAN RIVERS', RIVER RESEARCH AND APPLICATIONS, vol. 26, no. 9, pp. 1129-1152.
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Understanding longitudinal trends in the processing of carbon in rivers represents a much conceptualised, but infrequently tested, issue in aquatic ecology. In this study, we conducted concurrent longitudinal examinations of three very different rivers in eastern Australia to determine whether general principles in river functioning exist across broad geographic and hydrologic scales. Specifically, we examined trends in ambient basic water chemistry, nutrient concentrations, dissolved organic carbon (DOC), extracellular enzymes and food web structure and functioning and conducted bioassays to examine the degree to which DOC and nutrients limit heterotrophic bacterial respiration. These parameters revealed striking similarities across all sites. For metazoan communities, stable isotope analysis showed that algal carbon was the dominant basal resource utilised by consumers in all three rivers, suggesting that in-stream primary producers strongly underpin trophic pathways regardless of the position within a catchment or catchment condition. Analyses of extracellular enzymes revealed that microbial communities are actively utilising DOC at all sites. In fact, heterotrophic microbial respiration was strongly limited by DOC at all sites, with nutrient additions resulting in only relatively minor increases in respiration.
Handmer, CJ, de Sterke, CM, McPhedran, RC, Botten, LC, Steel, MJ & Rahmani, A 2010, 'Blazing evanescent grating orders: a spectral approach to beating the Rayleigh limit', OPTICS LETTERS, vol. 35, no. 17, pp. 2846-2848.
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We develop a way to enhance the amplitudes of the nonpropagating evanescent orders of resonant dielectric gratings. We use this blazing to design gratings with spectra tailored to generate steerable sub-Rayleigh field concentrations on a surface. We investigate the enhancement and customization of evanescent fields necessary to create a virtual and passive scanning probe with no moving parts. Spot size can be decreased 1 order of magnitude below the free-space Rayleigh limit. © 2010 Optical Society of America.
Handmer, CJ, de Sterke, CM, McPhedran, RC, Botten, LC, Steel, MJ & Rahmani, A 2010, 'Stacked dielectric gratings for sub-wavelength surface field synthesis', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, vol. 27, no. 12, pp. 2580-2594.
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A method is developed to enhance the amplitudes of the non-propagating evanescent orders of resonant dielectric gratings. The origin of these resonances is analyzed in detail. The method relies on interactions between stacked gratings with different periods, and so a formalism is developed to model such stacks mathematically. In addition, a theoretical approach is developed to design gratings that enhance or blaze desired orders. These orders, controlled independently by incident fields from different angles, interfere and are optimized to produce steerable sub-Rayleigh field concentrations on a surface. These spots may function as a virtual scanning probe for non-invasive sub-Rayleigh microscopy. Optimization is conducted using a Monte Carlo Markov chain, and spots are generated which are both 1 order of magnitude narrower than the free space Rayleigh limit and robust to noise in the incident fields. © 2010 Optical Society of America.
Hansbro, PM, Warner, S, Tracey, JP, Arzey, KE, Selleck, P, O’Riley, K, Beckett, EL, Bunn, C, Kirkland, PD, Vijaykrishna, D, Olsen, B & Hurt, AC 2010, 'Surveillance and Analysis of Avian Influenza Viruses, Australia', Emerging Infectious Diseases, vol. 16, no. 12, pp. 1896-1904.
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We investigated carriage of avian influenza viruses by wild birds in Australia, 2005-2008, to assess the risks to poultry industries and human health. We collected 21,858 (7,357 cloacal, 14,501 fecal) samples and detected 300 viruses, representing a detection rate of ≈1.4%. Rates were highest in autumn (March-May) and differed substantially between bird types, areas, and years. We typed 107 avian influenza viruses and identified 19 H5, 8 H7, and 16 H9 (40% of typed viruses). All were of low pathogenicity. These viruses formed clearly different phylogenetic clades to lineages from Eurasia or North America, suggesting the potential existence of Australian lineages. H7 viruses were similar to highly pathogenic H7 strains that caused outbreaks in poultry in Australia. Several periods of increased detection rates (numbers or subtypes of viruses) were identified. This study demonstrates the need for ongoing surveillance to detect emerging pathogenic strains and facilitate prevention of outbreaks.
Hare, D, Tolmachev, S, James, A, Bishop, D, Austin, C, Fryer, F & Doble, P 2010, 'Elemental Bio-imaging of Thorium, Uranium, and Plutonium in Tissues from Occupationally Exposed Former Nuclear Workers', ANALYTICAL CHEMISTRY, vol. 82, no. 8, pp. 3176-3182.
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Internal exposure from naturally occurring radionuclides (including the inhaled long-lived actinides 232Th and 238U) is a component of the ubiquitous background radiation dose (National Council on Radiation Protection and Measurements. Ionizing radiation exposure of the population of the United States; NCRP Report No. 160; NCRP: Bethesda, MD, 2009). It is of interest to compare the concentration distribution of these natural ?-emitters in the lungs and respiratory lymph nodes with those resulting from occupational exposure, including exposure to anthropogenic plutonium and depleted and enriched uranium. This study examines the application of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS) to quantifying and visualizing the mass distribution of uranium and thorium isotopes from both occupational and natural background exposure in human respiratory tissues and, for the first time, extends this application to the direct imaging of plutonium isotopes. Sections of lymphatic and lung tissues taken from deceased former nuclear workers with a known history of occupational exposure to specific actinide elements (uranium, plutonium, or americium) were analyzed by LA-ICPMS.
Hare, DJ, George, JL, Grimm, R, Wilkins, S, Adlard, PA, Cherny, RA, Bush, AI, Finkelstein, DI & Doble, P 2010, 'Three-dimensional elemental bio-imaging of Fe, Zn, Cu, Mn and P in a 6-hydroxydopamine lesioned mouse brain', METALLOMICS, vol. 2, no. 11, pp. 745-753.
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Three dimensional maps of iron (Fe), zinc (Zn), copper (Cu), manganese (Mn) and phosphorous (P) in a 6-hydroxydopamine (6-OHDA) lesioned mouse brain were constructed employing a novel quantitative laser ablation-inductively coupled plasma-mass spectromet
Hennige, SJ, Smith, DJ, Walsh, S-J, McGinley, MP, Warner, ME & Suggett, DJ 2010, 'Acclimation and adaptation of scleractinian coral communities along environmental gradients within an Indonesian reef system', Journal of Experimental Marine Biology and Ecology, vol. 391, no. 1-2, pp. 143-152.
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In 2007 and 2008, multiple sites were identified in the Wakatobi Marine National Park, South East Sulawesi, Indonesia, which each represented a point along a gradient of light quality, temperature and turbidity. This gradient included 'optimal', intermediate and marginal sites, where conditions were close to the survival threshold limit for corals. Coral communities changed across this gradient from diverse, mixed growth form assemblages to specialised, massive growth form dominated communities. The massive coral Goniastrea aspera was the only species identified at the most marginal and optimal sites. Branching species Acropora formosa and Porites cylindrica were only identified at optimal sites. The in hospite Symbiodinium community also changed across the environmental gradient from members of the Symbiodinium clade C on optimal reefs (in branching and massive species) to clade D on marginal reefs (in massive species). Substantial variability in respiration and photosynthesis was observed in massive coral species under different environmental conditions, which suggests that all corals cannot be considered equal across environments. Studying present-day marginal environments is crucial to further understanding of future reef bio-diversity, functioning and accretion, and from work presented here, it is likely that as future climate change extends marginal reef range, branching coral diversity may decrease relative to massive, more resilient corals. © 2010 Elsevier B.V.
Herbert, JDK, Godfrey, SS, Bull, CM & Menz, RI 2010, 'Developmental stages and molecular phylogeny of Hepatozoon tuatarae, a parasite infecting the New Zealand tuatara, Sphenodon punctatus and the tick, Amblyomma sphenodonti', International Journal for Parasitology, vol. 40, no. 11, pp. 1311-1315.
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Herrera-Silveira, JA, Cebrian, J, Hauxwell, J, Ramirez-Ramirez, J & Ralph, P 2010, 'Evidence of negative impacts of ecological tourism on turtlegrass (Thalassia testudinum) beds in a marine protected area of the Mexican Caribbean', AQUATIC ECOLOGY, vol. 44, no. 1, pp. 23-31.
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Many marine protected areas (MPAs) have been established in recent years. Some MPAs are open to tourists to foster environmental education and generate revenue for the MPA. This has been coined âecological tourismâ. Here, we examine the impact of ecological tourism on turtlegrass (Thalassia testudinum) health in one area of the âCosta Occidental de Isla Mujeres, Punta Cancún y Punta Nizucâ MPA in the Mexican Caribbean. A heavily visited location was compared with an unvisited location. Turtlegrass leaves at the visited location were sparser, shorter, grew more slowly, and had more epiphytes than at the unvisited location. Vertical and horizontal rhizomes of turtlegrass also grew more slowly at the visited than at the unvisited location. There is reasonable evidence to suggest that the observed differences are likely due to the deleterious impacts of novice and careless snorkelers. If continuing, these impacts could cause severe degradation of the visited areas in this MPA and, thus, changes in management policies seem in order.
Hinz, J & Novikov, A 2010, 'On fair pricing of emission-related derivatives', Bernoulli journal, vol. 16, no. 4, pp. 1240-1261.
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Tackling climate change is at the top of many agendas. In this context, emission trading schemes are considered as promising tools. The regulatory framework for an emission trading scheme introduces a market for emission allowances and creates a need for risk management by appropriate financial contracts. In this work, we address logical principles underlying their valuation.
Hinz, M, Wilson, IW, Yang, J, Buerstenbinder, K, Llewellyn, D, Dennis, ES, Sauter, M & Dolferus, R 2010, 'Arabidopsis RAP2.2: An Ethylene Response Transcription Factor That Is Important for Hypoxia Survival', PLANT PHYSIOLOGY, vol. 153, no. 2, pp. 757-772.
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Arabidopsis (Arabidopsis thaliana) RAP2.2 (At3g14230) is an APETALA2/ethylene response factor-type transcription factor that belongs to the same subfamily as the rice (Oryza sativa) submergence tolerance gene SUB1A. RAP2.2 is expressed at constitutively
Hiscock, JR, Gale, PA, Caltagirone, C, Hursthouse, MB & Light, ME 2010, 'Fluorescent carbazolylurea- and carbazolylthiourea-based anion receptors and sensors', Supramolecular Chemistry, vol. 22, no. 11-12, pp. 647-652.
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Hitchcock, JN, Mitrovic, SM, Kobayashi, T & Westhorpe, DP 2010, 'Responses of Estuarine Bacterioplankton, Phytoplankton and Zooplankton to Dissolved Organic Carbon (DOC) and Inorganic Nutrient Additions', ESTUARIES AND COASTS, vol. 33, no. 1, pp. 78-91.
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The response of planktonic bacteria and phytoplankton to various additions of dissolved organic carbon (DOC) as glucose, with and without inorganic nutrients (nitrogen and phosphorus), was tested in the upper to mid Hunter Estuary, Australia. In situ microcosms (1.25 L) were performed at two sites with varying salinities over three seasons. Analysis of variance showed a significant difference among control and treatments for all seasons for the bacterial, dissolved oxygen and chlorophyll a responses (P < 0.05). A significant interaction between treatment and site was found in autumn for dissolved oxygen, autumn and spring for bacterial and spring for chlorophyll a responses. At both sites for each season, and on nearly all occasions, bacterial surface area was enhanced by DOC addition as indicated by both increased bacterial abundance and dissolved oxygen utilisation. DOC in combination with inorganic nutrients sometimes further enhanced the bacterial response compared to DOC alone. Inorganic nutrients alone did not enhance growth of the heterotrophic bacterioplankton. Addition of DOC alone led to decreased chlorophyll a relative to the control, probably due to competition for limited inorganic nutrients with the bacterioplankton DOC non-limiting conditions. Results suggest that the heterotrophic community was limited by DOC at both sites and across seasons. An experiment with a larger volume (70 L), performed over a longer time, compared a control with DOC addition. Increased bacterial biomass as a result of DOC addition occurred at day 2. Chlorophyll a did not significantly differ between treatments. An increase in zooplankton density was recorded in the DOC treatment relative to the control at day 10. This study supports the contention that increased DOC delivery with river inflows through environmental flow allocations will stimulate heterotrophic bacterioplankton production in the upper Hunter Estuary. © Coastal and Estuarine Research Federation 2009.
Ho, KKK, Cole, N, Chen, R, Willcox, MDP, Rice, SA & Kumar, N 2010, 'Characterisation and in vitro activities of surface attached dihydropyrrol-2-ones against Gram-negative and Gram-positive bacteria', Biofouling, vol. 26, no. 8, pp. 913-921.
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Hoile, R, Banos, C, Colella, M, Walsh, SJ & Roux, C 2010, 'Gamma Irradiation as a Biological Decontaminant and Its Effect on Common Fingermark Detection Techniques and DNA Profiling', JOURNAL OF FORENSIC SCIENCES, vol. 55, no. 1, pp. 171-177.
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The use of disease-causing organisms and their toxins against the civilian population has defined bioterrorism and opened forensic science up to the challenges of processing contaminated evidence. This study sought to detennine the use of gamma irradiation as an effective biological decontaminant and its effect on the recovery of latent fingennarks from both porous and nonporous items. Test items were contaminated with viable spores marked with latent pIinrs and then decontaminated using a cobalt 60 gamma irradiator. Fingerrnark detection was the focus with standard methods inclurJing 1,2-inrJanedione, ninhydrin, diazafluoren-9-one, and physical developer used during this study. DNA recovery using 20% Chelex extraction and quantitative real-time polymerdse chain reaction was also explored. Gamma irradiation proved effective as a bacterial decontaminant with D-values ranging from 458 to 500 Gy for nonporous items and 797-808 Gy for porous ones. The results demonstrated the successful recovel)' of latent marks and DNA establishing gamma irradiation as a viable decontamination option.
Hollands, A, Pence, MA, Timmer, AM, Osvath, SR, Turnbull, L, Whitchurch, CB, Walker, MJ & Nizet, V 2010, 'Genetic Switch to Hypervirulence Reduces Colonization Phenotypes of the Globally Disseminated Group A Streptococcus M1T1 Clone', JOURNAL OF INFECTIOUS DISEASES, vol. 202, no. 1, pp. 11-19.
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Background. The recent resurgence of invasive group A streptococcal disease has been paralleled by the emergence of the M1T1 clone. Recently, invasive disease initiation has been linked to mutations in the covR/S 2component regulator. We investigated whether a fitness cost is associated with the covS mutation that counterbalances hypervirulence. Methods. Wild-type M1T1 group A Streptococcus and an isogenic covS-mutant strain derived from animal passage were compared for adherence to human laryngeal epithelial cells, human keratinocytes, or fibronectin; biofilm formation; and binding to intact mouse skin. Targeted mutagenesis of capsule expression of both strains was performed for analysis of its unique contribution to the observed phenotypes. Results. The covS-mutant bacteria showed reduced capacity to bind to epithelial cell layers as a consequence of increased capsule expression. The covS-mutant strain also had reduced capacity to bind fibronectin and to form biofilms on plastic and epithelial cell layers. A defect in skin adherence of the covS-mutant strain was demonstrated in a murine model. Conclusion. Reduced colonization capacity provides a potential explanation for why the covS mutation, which confers hypervirulence, has not become fixed in the globally disseminated M1T1 group A Streptococcus clone, but rather may arise anew under innate immune selection in individual patients. © 2010 by the Infectious Diseases Society of America. All rights reserved.
Horvat, JC, Starkey, MR, Kim, RY, Beagley, KW, Preston, JA, Gibson, PG, Foster, PS & Hansbro, PM 2010, 'Chlamydial Respiratory Infection during Allergen Sensitization Drives Neutrophilic Allergic Airways Disease', The Journal of Immunology, vol. 184, no. 8, pp. 4159-4169.
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Abstract Neutrophilic asthma is a prevalent, yet recently described phenotype of asthma. It is characterized by neutrophilic rather than eosinophilic airway inflammation and airways hyperresponsiveness (AHR) and may have an infectious origin. Chlamydial respiratory infections are associated with asthma, but how these Th1-inducing bacteria influence Th2-mediated asthma remains unknown. The effects of chlamydial infection on the development of asthma were investigated using a BALB/c mouse model of OVA-induced allergic airways disease (AAD). The effects of current and resolved Chlamydia muridarum infection during OVA sensitization on AAD were assessed and compared with uninfected and nonsensitized controls. Current, but not resolved, infection attenuated hallmark features of AAD: pulmonary eosinophil influx, T cell production of IL-5, mucus-secreting cell hyperplasia, and AHR. Current infection also induced robust OVA-driven neutrophilic inflammation and IFN-γ release from T cells. The phenotype of suppressed but persistent Th2 responses in association with enhanced neutrophilia is reminiscent of neutrophilic asthma. This phenotype was also characterized by increased pulmonary IL-12 and IL-17 expression and activation of APCs, as well as by reduced thymus- and activation-regulated chemokine. Inhibition of pulmonary neutrophil influx during infection blocked OVA-induced neutrophilic inflammation and T cell IFN-γ production and reversed the suppressive effects on mucus-secreting cell hyperplasia and AHR during AAD. These changes correlated with decreased IL-12 and IL-17 expression, increased thymus- and activation-regulated chemokine and altered APC activation. Blocking IFN-γ and IL-17 during OVA challenge had no effect. Thus, active chlamydial respiratory infection during sensitization enhances subsequent neutrophilic inflammation and Th1/Th17 responses during allergen exposure and may have a role in the patho...
Horvat, JC, Starkey, MR, Kim, RY, Phipps, S, Gibson, PG, Beagley, KW, Foster, PS & Hansbro, PM 2010, 'Early-life chlamydial lung infection enhances allergic airways disease through age-dependent differences in immunopathology', Journal of Allergy and Clinical Immunology, vol. 125, no. 3, pp. 617-625.e6.
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Huston, WM 2010, 'Bacterial proteases from the intracellular vacuole niche; protease conservation and adaptation for pathogenic advantage', FEMS Immunology & Medical Microbiology, vol. 59, no. 1, pp. 1-10.
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Huston, WM, Armitage, CW, Lawrence, A, Gloeckl, S, Bell, SJ, Debattista, J, Allan, JA, Timms, P & Res, QCC 2010, 'HtrA, RseP, and Tsp proteins do not elicit a pathology-related serum IgG response during sexually transmitted infection with Chlamydia trachomatis', JOURNAL OF REPRODUCTIVE IMMUNOLOGY, vol. 85, no. 2, pp. 168-171.
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Hutchinson, AT, Ramsland, PA, Jones, DR, Agostino, M, Lund, ME, Jennings, CV, Bockhorni, V, Yuriev, E, Edmundson, AB & Raison, RL 2010, 'Free Ig Light Chains Interact with Sphingomyelin and Are Found on the Surface of Myeloma Plasma Cells in an Aggregated Form', JOURNAL OF IMMUNOLOGY, vol. 185, no. 7, pp. 4179-4188.
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Free kappa L chains (FkappaLCs) are expressed on the surface of myeloma cells and are being assessed as a therapeutic target for the treatment of multiple myeloma. Despite its clinical potential, the mechanism by which FkappaLCs interact with membranes remains unresolved. In this study, we show that FkappaLCs associate with sphingomyelin on the plasma membrane of myeloma cells. Moreover, membrane-bound FkappaLCs are aggregated, suggesting that aggregation is required for intercalation with membranes. Finally, we propose a model where the binding of FkappaLCs with sphingomyelin on secretory vesicle membranes is stabilized by self-aggregation, with aggregated FkappaLCs exposed on the plasma membrane after exocytosis. Although it is well known that protein aggregates bind membranes, this is only the second example of an aggregate being found on the surface of cells that also secrete the protein in its native form. We postulate that many other aggregation-prone proteins may associate with cell membranes by similar mechanisms.
Ignatieva, K & Platen, E 2010, 'Modelling co-movements and tail dependency in the international stock market via copulae', Asia-Pacific Financial Markets, vol. 17, no. 3, pp. 261-302.
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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 on marginals 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 outperforms some alternative mixture copula models which allow to reflect 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 tail dependency in the equity index returns.
Ignatieva, K, Platen, E & Rendek, R 2010, 'Using Dynamic Copulae for Modeling Dependency in Currency Denominations of a Diversifed World Stock Index', Journal of Statistical Theory and Practice, vol. 5, no. 3, pp. 425-452.
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The aim of this paper is to model the dependency among log-returns when security account prices are expressed in units of a well diversified world stock index. The dependency in log-returns of currency denominations of the index is modeled using time-varying copulae, aiming to identify the best fitting copula family. The Student-t copula turns generally out to be superior to e.g. the Gaussian copula, where the dependence structure relates to the multivariate normal distribution. It is shown that merely changing the distributional assumption for the log-returns of the marginals from normal to Student-t leads to a significantly better fit. The Student-t copula with Student-t marginals is able to better capture dependent extreme values than the other models considered. Furthermore, the paper applies copulae to the estimation of the Value-at-Risk and the expected shortfall of a portfolio constructed of savings accounts of different currencies. The proposed copula-based approach allows to split market risk into general and specific market risk, as defined in regulatory documents. The paper demonstrates that the approach performs clearly better than the RiskMetrics approach, a widely used methodology for Value-at-Risk estimation.
Jambou, R, Combes, V, Jambou, M-J, Weksler, BB, Couraud, P-O & Grau, GE 2010, 'Plasmodium falciparum Adhesion on Human Brain Microvascular Endothelial Cells Involves Transmigration-Like Cup Formation and Induces Opening of Intercellular Junctions', PLoS Pathogens, vol. 6, no. 7, pp. e1001021-e1001021.
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Jenerette, GD, Scott, RL & Huete, AR 2010, 'Functional differences between summer and winter season rain assessed with MODIS-derived phenology in a semi-arid region', JOURNAL OF VEGETATION SCIENCE, vol. 21, no. 1, pp. 16-30.
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Questions: We asked several linked questions about phenology and precipitation relationships at local, landscape, and regional spatial scales within individual seasons, between seasons, and between year temporal scales. (1) How do winter and summer phenological patterns vary in response to total seasonal rainfall? (2) How are phenological rates affected by the previous season rainfall? (3) How does phenological variability differ at landscape and regional spatial scales and at season and interannual temporal scales? Location: Southern Arizona, USA. Methods: We compared satellite-derived phenological variation between 38 distinct 625-km2 landscapes distributed in the northern Sonoran Desert region from 2000 to 2007. Regression analyses were used to identify relationships between landscape phenology dynamics in response to precipitation variability across multiple spatial and temporal scales. Results:While both summer and winter seasons show increases of peak greenness and peak growth with more precipitation, the timing of peak growth was advanced with more precipitation in winter, while the timing of peak greenness was advanced with more precipitation in summer. Surprisingly, summer maximum growth was negatively affected by winter precipitation. The spatial variations between summer and winter phenology were similar in magnitude and response. Larger-scale spatial and temporal variation showed strong differences in precipitation patterns; however the magnitudes of phenological spatial variability in these two seasons were similar. Conclusions: Vegetation patterns were clearly coupled to precipitation variability, with distinct responses at alternative spatial and temporal scales. Disaggregating vegetation into phenological variation, spanning value, timing, and integrated components revealed substantial complexity in precipitation- phenological relationships. © 2009 International Association for Vegetation Science.
Jiang, H, Wang, G, Zhang, W, Liu, X, Ye, Z, Jin, D, Yuan, J & Liu, Z 2010, 'Preparation and Time-Resolved Luminescence Bioassay Application of Multicolor Luminescent Lanthanide Nanoparticles', Journal of Fluorescence, vol. 20, no. 1, pp. 321-328.
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Jiang, L, Wu, J, Wang, G, Ye, Z, Zhang, W, Jin, D, Yuan, J & Piper, J 2010, 'Development of a Visible-Light-Sensitized Europium Complex for Time-Resolved Fluorometric Application', Analytical Chemistry, vol. 82, no. 6, pp. 2529-2535.
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Jiang, Z & Huete, AR 2010, 'Linearization of NDVI Based on its Relationship with Vegetation Fraction', PHOTOGRAMMETRIC ENGINEERING AND REMOTE SENSING, vol. 76, no. 8, pp. 965-975.
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Jobbins, SE, Hill, CJ, D’Souza-Basseal, JM, Padula, MP, Herbert, BR & Krockenberger, MB 2010, 'Immunoproteomic Approach to Elucidating the Pathogenesis of Cryptococcosis Caused by Cryptococcus gattii', Journal of Proteome Research, vol. 9, no. 8, pp. 3832-3841.
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Cryptococcosis caused by Cryptococcus gattii is a devastating disease of immunocompetent hosts with an incompletely understood pathogenesis. Utilizing an immunoproteomic approach in a naturally occurring koala model of disease, a number of key proteins and pathways are identified in the early and late pathogenesis of cryptococcosis for the first time. In particular, the thioredoxin system appears important in the pathogenesis of cryptococcosis caused by C. gattii VGII. © 2010 American Chemical Society.
Johnson, FA, Chandra, H, Brown, JJ & Padmadas, SS 2010, 'District-level estimates of institutional births in ghana: Application of small area estimation technique using census and DHS data', Journal of Official Statistics, vol. 26, no. 2, pp. 341-359.
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The Ghana Health Service functions under a decentralised approach; however, the lack of district level statistics implies that local authorities are faced with difficulties in making policy decisions without relevant statistics. The Ghanain Demographic and Health Surveys provide a range of invaluable data at the regional/national level; they cannot be used directly to produce reliable district-level estimates due to small sample sizes. This article uses small area estimation techniques to derive model-based district-level estimates of institutional births in Ghana by linking data from the 2003 GDHS and the 2000 Population and Housing Census. The models indicate considerable variability in the estimates, with institutional births ranging between 7% and 27% in the districts of the Northern region, compared to 78% and 85% in the districts of the Greater Accra Region. The diagnostic measures indicate that the model-based estimates are reliable and representative of the district to which they belong.
JONES, LR, BLACK, HL, WHITE, CM, JOHNSTON, NP, MCGEE, ME, DONAHUE, SW & EGGETT, DL 2010, 'Effects of Calcium‐Loading on Egg Production in Ring‐Necked Pheasants', The Journal of Wildlife Management, vol. 74, no. 6, pp. 1295-1300.
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Abstract: Ring‐necked pheasants (Phasianus colchicus) are able to store dietary calcium as medullary bone, which they may mobilize for future eggshell synthesis. We define this mechanism as calcium‐loading. Previous experiments on pheasants conducted to document the importance of calcium in limiting distribution did not account for calcium‐loading. We hypothesized that calcium‐loading could override experimental calcium treatments of the diet. We measured egg production, egg characteristics, and femoral mineral content for pheasants that were not calcium‐loaded on 7 diets differing in calcium from 0.2% to 4.5% and compared these results to a similar study on calcium‐loaded pheasants. We predicted that calcium‐loaded pheasants would produce more eggs than those that were not calcium‐loaded. We also predicted that there would be no significant difference between femur ash fractions in non‐calcium‐loaded pheasants, but that the ash fraction in calcium‐loaded pheasants would differ significantly between the beginning and end of the experiment. Egg production was higher in calcium‐loaded pheasants above 2% dietary calcium. Femur ash fraction was not different in non–calcium‐loaded pheasants but differed significantly before and after the experiment and between high (>2%) and low (<2%) dietary levels in calcium‐loaded pheasants. Calcium‐loading may account for short‐term persistence of captive pheasants introduced on calcium‐poor soils, followed by their eventual population failure. Managers may improve survival of captive pheasants before introduction by surveying habitat for adequate calcium and by calcium‐loading.
Kabakova, IV, de Sterke, CM & Eggleton, BJ 2010, 'Bistable switching and reshaping of optical pulses in a Bragg grating cavity', Journal of the Optical Society of America B, vol. 27, no. 12, pp. 2648-2648.
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Kabakova, IV, Walsh, T, de Sterke, CM & Eggleton, BJ 2010, 'Performance of field-enhanced optical switching in fiber Bragg gratings', Journal of the Optical Society of America B, vol. 27, no. 7, pp. 1343-1343.
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Kalaitzis, JA, Chau, R, Kohli, GS, Murray, SA & Neilan, BA 2010, 'Biosynthesis of toxic naturally-occurring seafood contaminants', TOXICON, vol. 56, no. 2, pp. 244-258.
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Outbreaks of human illness caused by the consumption of contaminated seafood, continues to be a major problem particularly for the shellfish industry. Toxins from marine, brackish and freshwater environments, which are often produced as a result of harmful algal blooms, have been implicated as the causative agents of these poisonings. Commonly, poisoning events have been grouped into one of six classes, Paralytic Shellfish Poisoning (PSP), Diarrhetic Shellfish Poisoning (DSP), Neurotoxic Shellfish Poisoning (NSP), Ciguatera Fish Poisoning (CFP), Azaspiracid Shellfish Poisoning (AZP), and Amnesiac Shellfish Poisoning (ASP). The causative agents of these specific poisonings along with their biosyntheses are discussed in this review. The highly unusual and complex structures of most common seafood toxins have made them interesting targets for biosynthetic studies. Many of the toxins presented are biosynthesized via complex pathways that have been elucidated either through isotope labelled precursor feeding studies and/or characterization of the genes encoding the producing organism's biosynthetic machinery. Feeding studies key to our understanding of a particular toxin's biosynthesis, such as the incorporation of unusual precursors, as well as unique biosynthetic pathways and rare chemical mechanisms involved in the assembly process are highlighted. More recently, however, modern genomics-based techniques have been used for the elucidation of biosynthetic pathways and these are presented in the context of polyketide, non-ribosomal peptide, and hybrid pathway derived, toxin assembly. © 2009 Elsevier Ltd.
Kan, DJ, Asatryan, AA, Poulton, CG & Botten, LC 2010, 'Multipole method for modeling linear defects in photonic woodpiles', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, vol. 27, no. 2, pp. 246-258.
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We extend the multipole method to allow for rod-type defects in woodpiles composed of infinitely long cylinders. A coupled-resonator optical waveguide and a linear waveguide are considered, where each waveguide is embedded in a woodpile cladding. For both structures, low-loss waveguiding is observed (Q̃1×104-3×104). Decreasing the radius of the defect rod shifts the transmission resonances to shorter wavelengths. The reflection and transmission coefficients of the woodpile are derived for the case of normal incidence in the longwavelength limit, and it is shown that both the individual layers and the entire assemblage of layers homogenize to one-dimensional dielectric slabs. Expressions for the effective permittivities are given. © 2010 Optical Society of America.
Kaparakis, M, Turnbull, L, Carneiro, L, Firth, S, Coleman, HA, Parkington, HC, Le Bourhis, L, Karrar, A, Viala, J, Mak, J, Hutton, ML, Davies, JK, Crack, PJ, Hertzog, PJ, Philpott, DJ, Girardin, SE, Whitchurch, CB & Ferrero, RL 2010, 'Bacterial membrane vesicles deliver peptidoglycan to NOD1 in epithelial cells', CELLULAR MICROBIOLOGY, vol. 12, no. 3, pp. 372-385.
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Gram-negative bacterial peptidoglycan is specifically recognized by the host intracellular sensor NOD1, resulting in the generation of innate immune responses. Although epithelial cells are normally refractory to external stimulation with peptidoglycan, these cells have been shown to respond in a NOD1-dependent manner to Gram-negative pathogens that can either invade or secrete factors into host cells. In the present work, we report that Gram-negative bacteria can deliver peptidoglycan to cytosolic NOD1 in host cells via a novel mechanism involving outer membrane vesicles (OMVs). We purified OMVs from the Gram-negative mucosal pathogens: Helicobacter pylori, Pseudomonas aeruginosa and Neisseria gonorrhoea and demonstrated that these peptidoglycan containing OMVs upregulated NF-κB and NOD1-dependent responses in vitro. These OMVs entered epithelial cells through lipid rafts thereby inducing NOD1-dependent responses in vitro. Moreover, OMVs delivered intragastrically to mice-induced innate and adaptive immune responses via a NOD1-dependent but TLR-independent mechanism. Collectively, our findings identify OMVs as a generalized mechanism whereby Gram-negative bacteria deliver peptidoglycan to cytosolic NOD1. We propose that OMVs released by bacteria in vivo may promote inflammation and pathology in infected hosts. © 2009 Blackwell Publishing Ltd.
Kardaras, C & Platen, E 2010, 'Minimizing the expected market time to reach a certain wealth level', SIAM Journal on Financial Mathematics, vol. 1, no. 1, pp. 16-29.
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In a financial market model, we consider variations of the problem of minimizing the expected time to upcross a certain wealth level. For exponential L´evy markets, we show the asymptotic optimality of the growth-optimal portfolio for the above problem and obtain tight bounds for the value function for any wealth level. In an Ito market, we employ the concept of market time, which is a clock that runs according to the underlying market growth. We show the optimality of the growth-optimal portfolio for minimizing the expected market time to reach any wealth level. This reveals a general definition of market time which can be useful from an investors point of view. We utilize this last definition to extend the previous results in a general semimartingale setting.
Kauermann, G, Ormerod, JT & Wand, MP 2010, 'Parsimonious Classification Via Generalized Linear Mixed Models', Journal of Classification, vol. 27, no. 1, pp. 89-110.
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We devise a classification algorithm based on generalized linear mixed model (GLMM) technology. The algorithm incorporates spline smoothing, additive model-type structures and model selection. For reasons of speed we employ the Laplace approximation, rather than Monte Carlo methods. Tests on real and simulated data show the algorithm to have good classification performance. Moreover, the resulting classifiers are generally interpretable and parsimonious. © 2010 Springer Science+Business Media, LLC.
Kealley, CS & Cortie, MB 2010, 'A Computational Exploration of the Color Gamut of Nanoscale Hollow Scalene Ellipsoids of Ag and Au', PLASMONICS, vol. 5, no. 1, pp. 37-43.
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Hollow, nanoscale, scalene ellipsoids of Ag or Au provide an exceedingly tunable localized surface plasmon resonance. Here, we use numerical simulations to determine the limits of the color space that would be possible from colloidal suspensions of these
Kealley, CS, Arnold, MD, Porkovich, A & Cortie, MB 2010, 'Sensors based on monochromatic interrogation of a localised surface plasmon resonance', SENSORS AND ACTUATORS B-CHEMICAL, vol. 148, no. 1, pp. 34-40.
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The localised surface plasmon resonance in gold nanoparticles can be used as the basis of a refractometric sensor. Usually, this is accomplished by monitoring a shift in wavelength of the resonance peak, a task which requires measurements over a range of wavelengths. Here we investigate a different scheme, in which interrogation of the sensor is carried out at a single wavelength. We have used numerical simulations to estimate the effect that the shape of gold nanoparticles would have on the performance on such sensors. A variety of geometries of gold nanoparticles were investigated, including nano-spheres, nano-rods, nano-triangles, and nano-bowties. The performance of a sensor that operates at a single wavelength is controlled by dT/dn, the change in transmittance T with refractive index n, determined at the interrogation wavelength. In turn, dT/dn depends upon the extinction cross-section of the nanoparticles at the chosen wavelength, and on the density of the nanoparticles in the light path. Contributions to the sensor efficiency also include the shift in wavelength of the plasmon resonance and, importantly, the peak sharpness. Of the particles examined, gold nano-rods will provide the most sensitive sensors by a large margin. © 2010 Elsevier B.V. All rights reserved.
Kealley, CS, Cortie, MB, Maaroof, AI & Xu, X 2010, 'Erratum: The versatile colour gamut of coatings of plasmonic metal nanoparticles (Physical Chemistry Chemical Physics (2009) 11 (5897-5902) DOI: 10.1039/b903318a)', Physical Chemistry Chemical Physics, vol. 12, no. 45, pp. 15141-15143.
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Kealley, CS, Cortie, MB, Maaroof, AI & Xu, X 2010, 'The versatile colour gamut of coatings of plasmonic metal nanoparticles (vol 11, pg 5897, 2009)', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 12, no. 45, pp. 15141-15143.
Kerr, ID, Jones, PM & George, AM 2010, 'Multidrug efflux pumps: The structures of prokaryotic ATP‐binding cassette transporter efflux pumps and implications for our understanding of eukaryotic P‐glycoproteins and homologues', The FEBS Journal, vol. 277, no. 3, pp. 550-563.
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One of the Holy Grails of ATP‐binding cassette transporter research is a structural understanding of drug binding and transport in a eukaryotic multidrug resistance pump. These transporters are front‐line mediators of drug resistance in cancers and represent an important therapeutic target in future chemotherapy. Although there has been intensive biochemical research into the human multidrug pumps, their 3D structure at atomic resolution remains unknown. The recent determination of the structure of a mouse P‐glycoprotein at subatomic resolution is complemented by structures for a number of prokaryotic homologues. These structures have provided advances into our knowledge of the ATP‐binding cassette exporter structure and mechanism, and have provided the template data for a number of homology modelling studies designed to reconcile biochemical data on these clinically important proteins.
Khan, N-UH, Pandya, N, Kumar, M, Bera, PK, Kureshy, RI, Abdi, SHR & Bajaj, HC 2010, 'Influence of chirality using Mn(iii) salen complexes on DNA binding and antioxidant activity', Organic & Biomolecular Chemistry, vol. 8, no. 19, pp. 4297-4297.
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Kim, Y, Huete, AR, Miura, T & Jiang, Z 2010, 'Spectral compatibility of vegetation indices across sensors: band decomposition analysis with Hyperion data', JOURNAL OF APPLIED REMOTE SENSING, vol. 4.
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King, JS, Slapeta, J, Jenkins, DJ, Al-Qassab, SE, Ellis, JT & Windsor, PA 2010, 'Australian dingoes are definitive hosts of Neospora caninum', INTERNATIONAL JOURNAL FOR PARASITOLOGY, vol. 40, no. 8, pp. 945-950.
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To provide objective data on the potential role of dingoes (Canis lupus dingo) in the life cycle of Neospora caninum in Australia, the production of N. caninum oocysts by experimentally infected canids was investigated. Three dingo pups raised in captivity and three domestic dogs were fed tissue from calves infected with an Australian isolate of N. caninum, Nc-Nowra. Oocysts of N. caninum, confirmed by species-specific PCR, were shed in low numbers by one dingo pup at 12-14. days p.i. The remaining animals did not shed oocysts. Furthermore, the blood from two out of three dingoes tested positive for DNA of N. caninum using PCR tests at 14 and 28. days p.i. Oocyst shedding from the intestinal tract of a dingo demonstrates that dingoes are definitive hosts of N. caninum and horizontal transmission of N. caninum from dingoes to farm animals and wildlife may occur in Australia. © 2010 Australian Society for Parasitology Inc.
Koelsch, M, Mallak, R, Graham, GG, Kajer, T, Milligan, MK, Nguyen, LQ, Newsham, DW, Keh, JS, Kettle, AJ, Scott, KF, Ziegler, JB, Pattison, DI, Fu, S, Hawkins, CL, Rees, MD & Davies, MJ 2010, 'Acetaminophen (paracetamol) inhibits myeloperoxidase-catalyzed oxidant production and biological damage at therapeutically achievable concentrations', BIOCHEMICAL PHARMACOLOGY, vol. 79, no. 8, pp. 1156-1164.
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The heme peroxidase enzyme myeloperoxidase (MPO) is released by activated neutrophils and monocytes, where it uses hydrogen peroxide (H2O2) to catalyze the production of the potent oxidants hypochlorous acid (HOCl), hypobromous acid (HOBr) and hypothiocyanous acid (HOSCN) from halide and pseudohalide (SCN-) ions. These oxidants have been implicated as key mediators of tissue damage in many human inflammatory diseases including atherosclerosis, asthma, rheumatoid arthritis, cystic fibrosis and some cancers. It is shown here that acetaminophen (paracetamol), a phenol-based drug with analgesic and antipyretic actions, is an efficient inhibitor of HOCl and HOBr generation by isolated MPOH2O2halide systems. With physiological halide concentrations, acetaminophen concentrations required for 50% inhibition of oxidant formation (IC50) were 77 ± 6 µM (100 mM Cl-) and 92 ± 2 µM (100 mM Cl- plus 100 µM Br-), as measured by trapping of oxidants with taurine. The IC50 for inhibition of HOCl generation by human neutrophils was ca. 100 µM. These values are lower than the maximal therapeutic plasma concentrations of acetaminophen (=150 µM) resulting from typical dosing regimes. Acetaminophen did not diminish superoxide generation by neutrophils, as measured by lucigenin-dependent chemiluminescence. Inhibition of HOCl production was associated with the generation of fluorescent acetaminophen oxidation products, consistent with acetaminophen acting as a competitive substrate of MPO. Inhibition by acetaminophen was maintained in the presence of heparan sulfate and extracellular matrix, materials implicated in the sequestration of MPO at sites of inflammation in vivo. Overall, these data indicate that acetaminophen may be an important modulator of MPO activity in vivo.
Korecko, J, Jirka, V, Sourek, B & Cerveny, J 2010, 'Module greenhouse with high efficiency of transformation of solar energy, utilizing active and passive glass optical rasters', Solar Energy, vol. 84, no. 10, pp. 1794-1808.
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Kuang, Z, Lewis, RS, Curtis, JM, Zhan, Y, Saunders, BM, Babon, JJ, Kolesnik, TB, Low, A, Masters, SL, Willson, TA, Kedzierski, L, Yao, S, Handman, E, Norton, RS & Nicholson, SE 2010, 'The SPRY domain–containing SOCS box protein SPSB2 targets iNOS for proteasomal degradation', Journal of Cell Biology, vol. 190, no. 1, pp. 129-141.
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Inducible nitric oxide (NO) synthase (iNOS; NOS2) produces NO and related reactive nitrogen species, which are critical effectors of the innate host response and are required for the intracellular killing of pathogens such as Mycobacterium tuberculosis and Leishmania major. We have identified SPRY domain–containing SOCS (suppressor of cytokine signaling) box protein 2 (SPSB2) as a novel negative regulator that recruits an E3 ubiquitin ligase complex to polyubiquitinate iNOS, resulting in its proteasomal degradation. SPSB2 interacts with the N-terminal region of iNOS via a binding interface on SPSB2 that has been mapped by nuclear magnetic resonance spectroscopy and mutational analyses. SPSB2-deficient macrophages showed prolonged iNOS expression, resulting in a corresponding increase in NO production and enhanced killing of L. major parasites. These results lay the foundation for the development of small molecule inhibitors that could disrupt the SPSB–iNOS interaction and thus prolong the intracellular lifetime of iNOS, which may be beneficial in chronic and persistent infections.
Kulygin, O, Price, AD, Chong, S, Städler, B, Zelikin, AN & Caruso, F 2010, 'Subcompartmentalized Polymer Hydrogel Capsules with Selectively Degradable Carriers and Subunits', Small, vol. 6, no. 14, pp. 1558-1564.
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AbstractSubcompartmentalized hydrogel capsules (SHCs) with selectively degradable carriers and subunits are designed for potential applications in drug delivery and microencapsulated biocatalysis. Thiolated poly(methacrylic acid) and poly(N‐vinyl pyrrolidone) are used to assemble 3‐µm‐diameter carrier capsules and 300‐nm‐diameter subunits, independently stabilized by a diverse range of covalent linkages. This paper presents examples of SHCs with tens of subcompartments and their successful drug loading, as well as selective degradation of the SHC carrier and/or subunits in response to multiple chemical stimuli.
Kumar, D & Shad, KF 2010, 'PW01-185 - Genetic Profile Of Schizophrenic Patients In Pakistan', European Psychiatry, vol. 25, no. S1, pp. 1613-1613.
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BackgroundSchizophrenia is a brain disease that has distressed human kind since the beginning of the written history. Firm knowledge about this illness is limited to certain areas including cognitive, risk genes etc. Basic question remains unanswered about the diagnostic heterogeneity and tissue neurochemistry. Several lines of evidence focus on direct involvement of glutamergic system in the pathophysiology of psyhosis.MethodsThe pilot study measured the difference between the plasma serine recemase level of normal and schizophrenic patients and estimated the D-isomers excreted in the urine using gas chromatography and Gas chromatography and mass selectivity (GCMS) respectively.ResultsPlasma and urine samples of normal and schizophrenic patients from UAE shows that the level of serine recemase and D-serine respectively is lower in schizophrenic pateints than that of the normal subjects.DiscussionThe hypofunction of the glutamate N-methyl-D-Aspartate receptor (NMDAR) has been proposed as a model of schizophrenia in humans using molecular marker and also due to evidence suggesting modulation of glutamate cicuitries after antipyschotic administration. In this regard there is increasing evidence from pharmacological and genetic studies that suggest that D-serine an endogenous co agonist to the NMDA subtype glutamate receptor, may be implicated in schizophrenia (SCZ). Although an association of genes for D-serine degradation such as D-amino acid oxidase and G72 has been reported, a role of recemase in SCZ is unclear.
Kumar, M, Kumari, P, Gupta, V, Anisha, PA, Reddy, CRK & Jha, B 2010, 'Differential responses to cadmium induced oxidative stress in marine macroalga Ulva lactuca (Ulvales, Chlorophyta)', BioMetals, vol. 23, no. 2, pp. 315-325.
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Kumar, M, Kumari, P, Gupta, V, Reddy, CRK & Jha, B 2010, 'Biochemical responses of red alga Gracilaria corticata (Gracilariales, Rhodophyta) to salinity induced oxidative stress', Journal of Experimental Marine Biology and Ecology, vol. 391, no. 1-2, pp. 27-34.
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Kumari, P, Kumar, M, Gupta, V, Reddy, CRK & Jha, B 2010, 'Tropical marine macroalgae as potential sources of nutritionally important PUFAs', Food Chemistry, vol. 120, no. 3, pp. 749-757.
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Lapine, M, Jelinek, L, Freire, MJ & Marqués, R 2010, 'Realistic metamaterial lenses: Limitations imposed by discrete structure', Physical Review B, vol. 82, no. 16.
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Lapine, M, Jelinek, L, Marqués, R & Freire, MJ 2010, 'Exact modelling method for discrete finite metamaterial lens', IET Microwaves, Antennas & Propagation, vol. 4, no. 8, pp. 1132-1132.
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Larkum, AWD 2010, 'Limitations and prospects of natural photosynthesis for bioenergy production', CURRENT OPINION IN BIOTECHNOLOGY, vol. 21, no. 3, pp. 271-276.
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Solar energy is clearly a major future source of energy for humans. While solar photovoltaic and thermal harvesting are attractive there will be a need for biofuels to replace fossil fuels. Natural photosynthesis offers a means to do this, but photosynthesis is inherently inefficient. Terrestrial plants have already been used as a source of biofuels and this use will increase in the future, despite a number of attendant problems. Microalgae as a source of biofuels have to be technically proven and artificial photosynthesis/biohydrogen production lies further into the future. Consideration of these approaches must be weighed against (i) crop production in a hungry, as well as a fuel-hungry, world and (ii) the need to sustain biodiversity. © 2010 Elsevier Ltd.
Lau, JY, Oliver, BG, Baraket, M, Beckett, EL, Hansbro, NG, Moir, LM, Wilton, SD, Williams, C, Foster, PS, Hansbro, PM, Black, JL & Burgess, JK 2010, 'Fibulin-1 Is Increased in Asthma - A Novel Mediator of Airway Remodeling?', PLOS ONE, vol. 5, no. 10.
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Background: The extracellular matrix is a dynamic and complex network of macromolecules responsible for maintaining and influencing cellular functions of the airway. The role of fibronectin, an extracellular matrix protein, is well documented in asthma. However, the expression and function of fibulin-1, a secreted glycoprotein which interacts with fibronectin, has not been reported. Fibulin-1 is widely expressed in basement membranes in many organs including the lung. There are four isoforms in humans (A-D) of which fibulin-1C and 1D predominate. The objective of this study was to study the expression of fibulin-1 in volunteers with and without asthma, and to examine its function in vitro. Methodology/Principal Findings: We used immunohistochemistry and dot-blots to examine fibulin-1 levels in bronchial biopsies, bronchoalveolar lavage fluid and serum. Real-time PCR for fibulin-1C and 1D, and ELISA and western blotting for fibulin-1 were used to study the levels in airway smooth muscle cells. The function of fibulin-1C was determined by assessing its role, using an antisense oligonucleotide, in cell proliferation, migration and wound healing. A murine model of airway hyperresponsiveness (AHR) was used to explore the biological significance of fibulin-1. Levels of fibulin-1 were significantly increased in the serum and bronchoalveolar lavage fluid of 21 asthmatics compared with 11 healthy volunteers. In addition fibulin-1 was increased in asthma derived airway smooth muscle cells and fibulin-1C contributed to the enhanced proliferation and wound repair in these cells. These features were reversed when fibulin-1C was suppressed using an antisense oligomer. In a mouse model of AHR, treatment with an AO inhibited the development of AHR to methacholine. Conclusions: Our data collectively suggest fibulin-1C may be worthy of further investigation as a target for airway remodeling in asthma. © 2010 Lau et al.
Lau, JY, Oliver, BG, Moir, LM, Black, JL & Burgess, JK 2010, 'Differential expression of peroxisome proliferator activated receptor gamma and cyclin D1 does not affect proliferation of asthma- and non-asthma-derived airway smooth muscle cells', RESPIROLOGY, vol. 15, no. 2, pp. 303-312.
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Background and objective: Airway remodelling involves thickening of the airway smooth muscle (ASM) bulk. Proliferation of asthma-derived ASM cells is increased in vitro, but underlying mechanisms remain unknown. Peroxisome proliferators activated receptor-γ (PPARγ) regulates the cell cycle. It is suggested that PPARγ agonists have anti-inflammatory effects, which may be valuable in the treatment of asthma, but information regarding their antiproliferative properties in ASM is lacking. Although corticosteroids reduce airway inflammation, in vitro they inhibit proliferation in only non-asthma ASM cells by reducing cyclin D1. We therefore investigated the effects of mitogenic stimulation (foetal bovine serum (FBS)), and a PPARγ ligand (ciglitazone), on PPARγ and cyclin D1 expression and proliferation of ASM cells. In addition, we examined the effects of ciglitazone on ASM cell proliferation. Methods: We assessed PPARγ and cyclin D1 mRNA and protein levels using quantitative PCR and immunoblotting. Cell proliferation was assessed using bromodeoxyuridine uptake. Results: In the presence of 5% FBS, PPARγ and cyclin D1 expression decreased over time in non-asthmatic cells but increased in asthmatic cells (compared with sub-confluent cells). FBS-induced proliferation of asthmatic cells increased at all time points, but occurred only at day 7 with non-asthmatic cells (compared with unstimulated time-matched control). Ciglitazone increased PPARγ expression in both groups, but did not alter cell proliferation, while fluticasone increased PPARγ protein only in asthmatic cells. Conclusions: Although in the presence of a mitogenic stimulus, PPARγ was differentially expressed in asthma-and non-asthma-derived ASM; its expression was not related to the increased proliferation observed in asthmatic ASM. © 2009 Asian Pacific Society of Respirology.
Lavery, TJ, Roudnew, B, Gill, P, Seymour, J, Seuront, L, Johnson, G, Mitchell, JG & Smetacek, V 2010, 'Iron defecation by sperm whales stimulates carbon export in the Southern Ocean', Proceedings of the Royal Society B: Biological Sciences, vol. 277, no. 1699, pp. 3527-3531.
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The iron-limited Southern Ocean plays an important role in regulating atmospheric CO 2 levels. Marine mammal respiration has been proposed to decrease the efficiency of the Southern Ocean biological pump by returning photosynthetically fixed carbon to the atmosphere. Here, we show that by consuming prey at depth and defecating iron-rich liquid faeces into the photic zone, sperm whales ( Physeter macrocephalus ) instead stimulate new primary production and carbon export to the deep ocean. We estimate that Southern Ocean sperm whales defecate 50 tonnes of iron into the photic zone each year. Molar ratios of C export ∶Fe added determined during natural ocean fertilization events are used to estimate the amount of carbon exported to the deep ocean in response to the iron defecated by sperm whales. We find that Southern Ocean sperm whales stimulate the export of 4 × 10 5 tonnes of carbon per year to the deep ocean and respire only 2 × 10 5 tonnes of carbon per year. By enhancing new primary production, the populations of 12 000 sperm whales in the Southern Ocean act as a carbon sink, removing 2 × 10 5 tonnes more carbon from the atmosphere than they add during respiration. The ability of the Southern Ocean to act as a carbon sink may have been diminished by large-scale removal of sperm whales during industrial whaling.
Lawrence, FJ, Botten, LC, Dossou, KB, McPhedran, RC & de Sterke, CM 2010, 'Photonic-crystal surface modes found from impedances', PHYSICAL REVIEW A, vol. 82, no. 5, pp. 1-8.
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We present a method for finding surface modes at interfaces between two-dimensional photonic crystals (PCs), in which the surface modes are represented as superpositions of the PCs' propagating and evanescent Bloch modes. We derive an existence condition for surface modes at an air-PC interface in terms of numerically calculated PC impedance matrices, and use the condition to find surface modes in the partial band gap of a PC. We also derive a condition for modes of a three-layer structure with two interfaces, and find both coupled surface modes and waveguide modes. We show that some waveguide modes cross the band edge and become coupled surface modes. © 2010 The American Physical Society.
Le Marshall, J & Leslie, L 2010, 'Tropical cyclone Tracy - numerical guidance then and now', Australian Meteorological and Oceanographic Journal, vol. 60, no. 3, pp. 179-185.
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Leonardi, T, Vanamala, J, Taddeo, SS, Davidson, LA, Murphy, ME, Patil, BS, Wang, N, Carroll, RJ, Chapkin, RS, Lupton, JR & Turner, ND 2010, 'Apigenin and naringenin suppress colon carcinogenesis through the aberrant crypt stage in azoxymethane-treated rats', Experimental Biology and Medicine, vol. 235, no. 6, pp. 710-717.
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Epidemiological evidence suggests that a diet abundant in fruits and vegetables may protect against colon cancer. Bioactive compounds, including flavonoids and limonoids, have been shown to possess antiproliferative and antitumorigenic effects in various cancer models. This experiment investigated the effects of four citrus flavonoids and one limonoid mixture at the promotion stage of chemically induced colon cancer in rats. Male Sprague–Dawley rats ( n = 10 rats/group) were randomly allocated to one of six diets formulated to contain 0.1% apigenin, 0.02% naringenin, 0.1% hesperidin, 0.01% nobiletin, 0.035% limonin glucoside/obacunone glucoside mixture or a control diet (0% flavonoid/limonoid). Rats received experimental diets for 10 weeks and were injected with azoxymethane (15 mg/kg) at weeks 3 and 4. Excised colons were evaluated for aberrant crypt foci (ACF) formation, colonocyte proliferation (proliferating cell nuclear antigen assay), apoptosis (terminal deoxynucleotidyl transferase dUTP nick end labeling assay) and expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) (immunoblotting). When compared with the control diet, apigenin lowered the number of high multiplicity ACF (HMACF >4 aberrant crypts/focus) by 57% ( P < 0.05), while naringenin lowered both the number of HMACF by 51% ( P < 0.05) and the proliferative index by 32% ( P < 0.05). Both apigenin and naringenin increased apoptosis of luminal surface colonocytes (78% and 97%, respectively; P < 0.05) when compared with the control diet. Hesperidin, nobiletin and the limonin glucoside/obacunone glucoside mixture did not affect these variables. The colonic mucosal protein levels of iNOS or COX-2 were not different among the six diet groups. The ability of dietary apigenin and naringenin to reduce HMACF, lower proliferation (naringenin only) and increase apoptosis may contribute toward colon cancer prevention. However, these effects were not ...
Leusch, FDL, de Jager, C, Levi, Y, Lim, R, Puijker, L, Sacher, F, Tremblay, LA, Wilson, VS & Chapman, HF 2010, 'Comparison of Five in Vitro Bioassays to Measure Estrogenic Activity in Environmental Waters', Environmental Science & Technology, vol. 44, no. 10, pp. 3853-3860.
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Bioassays are well established in the pharmaceutical industry and single compound analysis, but there is still uncertainty about their usefulness in environmental monitoring. We compared the responses of five bioassays designed to measure estrogenic acti
Lewis, K, Wuhrer, R, Ben-Nissan, B, Valenzuela, SM & Moran, K 2010, 'X-Ray Mapping of Mineral Phases Incorporated into Liposomes', Microscopy Today, vol. 18, no. 2, pp. 30-32.
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A liposome is a spherical particle formed by a lipid bilayer enclosing an aqueous compartment at its center. These particles can be comprised of a variety of lipids, particularly phospholipids. They have been long considered as potential delivery devices in the medical and pharmaceutical industries because of their ability to encapsulate different compounds as the lipids form into liposomes. The biocompatibility of many liposomes has been widely studied, and this has led to the development of a number of drug formulations. The ability of liposomes to be stored in the body and to be taken up by cells makes them ideal for drug delivery.
Li, JJ, Wang, W, Baines, KJ, Bowden, NA, Hansbro, PM, Gibson, PG, Kumar, RK, Foster, PS & Yang, M 2010, 'IL-27/IFN-γ Induce MyD88-Dependent Steroid-Resistant Airway Hyperresponsiveness by Inhibiting Glucocorticoid Signaling in Macrophages', The Journal of Immunology, vol. 185, no. 7, pp. 4401-4409.
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Abstract Inflammation and airway hyperresponsiveness (AHR) are hallmark features of asthma and often correlate with the severity of clinical disease. Although these features of asthma can be effectively managed with glucocorticoid therapy, a subgroup of patients, typically with severe asthma, remains refractory to therapy. The mechanisms leading to steroid resistance in severe asthmatics are poorly understood but may be related to the activation of innate host defense pathways. Previously, we have shown that IFN-γ–producing cells and LPS, two factors that are associated with severe asthma, induce steroid-resistant AHR in a mouse model. We now demonstrate that cooperative signaling induced by IFN-γ and LPS results in the production of IL-27 by mouse pulmonary macrophages. IL-27 and IFN-γ uniquely cooperate to induce glucocorticoid-resistant AHR through a previously unknown MyD88-dependent mechanism in pulmonary macrophages. Importantly, integrated signaling by IL-27/IFN-γ inhibits glucocorticoid-induced translocation of the glucocorticoid receptor to the nucleus of macrophages. Furthermore, expression of both IL-27 and IFN-γ was increased in the induced sputum of steroid-refractory asthmatics. These results suggest that a potential mechanism for steroid resistance in asthma is the activation of MyD88-dependent pathways in macrophages that are triggered by IL-27 and IFN-γ, and that manipulation of these pathways may be a therapeutic target.
Li, Y, Wang, N & Carroll, RJ 2010, 'Generalized Functional Linear Models With Semiparametric Single-Index Interactions', Journal of the American Statistical Association, vol. 105, no. 490, pp. 621-633.
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Lilley, RM, Ralph, PJ & Larkum, AWD 2010, 'The determination of activity of the enzyme Rubisco in cell extracts of the dinoflagellate alga Symbiodinium sp by manganese chemiluminescence and its response to short-term thermal stress of the alga', PLANT CELL AND ENVIRONMENT, vol. 33, no. 6, pp. 995-1004.
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The dinoflagellate alga Symbiodinium sp., living in symbiosis with corals, clams and other invertebrates, is a primary producer in coral reefs and other marine ecosystems. The function of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) in dinoflagellates is difficult to study because its activity is rapidly lost after extraction from the cell. We report procedures for the extraction of Rubisco from Symbiodinium cells and for stable storage. We describe a continuous assay for Rubisco activity in these crude cell extracts using the Mn2+ chemiluminescence of Rubisco oxygenase. Chemiluminescence time courses exhibited initial transients resembling bacterial Form II Rubisco, followed by several minutes of linearly decreasing activity. The initial activity was determined from extrapolation of this linear section of the time course. The activity of fast-frozen cell extracts was stable at -80 °C and, after thawing and storage on ice, remained stable for up to 1 h before declining non-linearly. Crude cell extracts bound [14C] 2-carboxy-D-arabitinol 1,5-bisphosphate to a high molecular mass fraction separable by gel filtration chromatography. After pre-treatment of Symbiodinium cell cultures in darkness at temperatures above 30 °C, the extracted Rubisco activities decreased, with almost complete loss of activity above 36 °C. The implications for the sensitivity to elevated temperature of Symbiodinium photosynthesis are assessed. © 2010 Blackwell Publishing Ltd.
Lim, CED & Wong, WSF 2010, 'Current evidence of acupuncture on polycystic ovarian syndrome', Gynecological Endocrinology, vol. 26, no. 6, pp. 473-478.
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Objective. This paper aims to provide a literature review on evaluating the efficacy of acupuncture therapy in the treatment of polycystic ovarian syndrome (PCOS) by reviewing clinical trials; randomised and non-randomised and observational studies on PCOS. The paper will also determine the possible mechanism of acupuncture treatment in PCOS, limitations of recruited studies and suggest further improvements in future studies. Design. A comprehensive literature search was conducted through the databases Medline, PubMed, EMBASE, Cochrane, AMED (Allied and Complementary Medicine), NCCAM (The National Centre for Complementary and Alternative Medicine) to identify relevant monographs. Results. Four studies were recruited. Several studies showed that acupuncture significantly increases β-endorphin levels for periods up to 24h and may have regulatory effect on FSH, LH and androgen. β-endorphin increased levels secondary to acupuncture affects the hyperthalamic-pituitary-adrenal (HPA) axis through promoting the release of ACTH through stimulation of its precursor pro-opiomelanocortin synthesis. Inclusion criteria. All available acupuncture studies on human subjects with PCOS from June 1970 to June 2009. Exclusion criteria. Studies not meeting the inclusion criteria, published in languages other than English or animal studies. Conclusion. Acupuncture is a safe and effective treatment to PCOS as the adverse effects of pharmacologic interventions are not expected by women with PCOS. Acupuncture therapy may have a role in PCOS by: increasing of blood flow to the ovaries, reducing of ovarian volume and the number of ovarian cysts, controlling hyperglycaemia through increasing insulin sensitivity and decreasing blood glucose and insulin levels, reducing cortisol levels and assisting in weight loss and anorexia. However, well-designed, randomised controlled trials are needed to elucidate the true effect of acupuncture on PCOS. © 2010 Informa UK Ltd.
Lim, D, Chen, WM & Lian, XF 2010, 'Clinical trials of TCM and Parkinson's disease in China', Focus on Alternative and Complementary Therapies, vol. 15, no. 4, pp. 312-313.
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Chen WM, Lian XF. Systematic evaluation of traditional Chinese medicine for treating Parkinson's disease. Neural Regen Res 2010; 5: 602–10.
Liptser, R, Novikov, A & Tartakovsky, AG 2010, 'Preface: Celebrating Albert Shiryaev's 75th Anniversary', Sequential Analysis, vol. 29, no. 2, pp. 107-111.
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Liu, H, Park, J & Wang, G 2010, 'Nanosize SnO2 for Highly Responsive Gas Sensor Application', SENSOR LETTERS, vol. 8, no. 2, pp. 243-246.
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Novel nanosize SnO2 particles were synthesized by a hard template method. The crystal structure and morphologies were characterized by X-ray diffraction and transmission electron microscopy. The particle size is around 4 nm, which is less than two times the depth (L) of the of the surface depletion layer. The sensing properties towards a series of gases, including ethanol, isopropanol, 1-butanol, formaldehyde, acetic acid, acetone, and 92# gasoline, were tested at different gas concentrations. The results reveal that the SnO2 nanoparticles have high responsivity towards forementioned toxic and flammable gases.
Liu, W, Sukhorukov, A, Miroshnichenko, A, Poulton, C, Xu, Z, Neshev, D & Kivshar, Y 2010, 'Complete spectral gap in coupled dielectric waveguides embedded into metal', Appl. Phys. Lett., vol. 97, no. 2, pp. 021106-3.
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We study a plasmonic coupler involving backward (TM_01) and forward (HE_11)modes of dielectric waveguides embedded into infinite metal. The simultaneouslyachievable contradirectional energy flows and codirectional wavevectors indifferent channels lead to a spectral gap, despite the absence of periodicstructures along the waveguide. We demonstrate that a complete spectral gap canbe achieved in a symmetric structure composed of four coupled waveguides.
Lobach, I, Fan, R & Carroll, RJ 2010, 'Genotype‐based association mapping of complex diseases: gene‐environment interactions with multiple genetic markers and measurement error in environmental exposures', Genetic Epidemiology, vol. 34, no. 8, pp. 792-802.
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AbstractWith the advent of dense single nucleotide polymorphism genotyping, population‐based association studies have become the major tools for identifying human disease genes and for fine gene mapping of complex traits. We develop a genotype‐based approach for association analysis of case‐control studies of gene‐environment interactions in the case when environmental factors are measured with error and genotype data are available on multiple genetic markers. To directly use the observed genotype data, we propose two genotype‐based models: genotype effect and additive effect models. Our approach offers several advantages. First, the proposed risk functions can directly incorporate the observed genotype data while modeling the linkage disequilibrium information in the regression coefficients, thus eliminating the need to infer haplotype phase. Compared with the haplotype‐based approach, an estimating procedure based on the proposed methods can be much simpler and significantly faster. In addition, there is no potential risk due to haplotype phase estimation. Further, by fitting the proposed models, it is possible to analyze the risk alleles/variants of complex diseases, including their dominant or additive effects. To model measurement error, we adopt the pseudo‐likelihood method by Lobach et al. [2008]. Performance of the proposed method is examined using simulation experiments. An application of our method is illustrated using a population‐based case‐control study of association between calcium intake with the risk of colorectal adenoma development. Genet. Epidemiol. 34:792‐802, 2010. © 2010 Wiley‐Liss, Inc.
Luo, X, Lim, CED, Li, L & Wong, WSF 2010, 'Hysteroscopic Appearance of Endometrial Cavity after Microwave Endometrial Ablation', Journal of Minimally Invasive Gynecology, vol. 17, no. 1, pp. 30-36.
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Study Objective: To assess the appearance of the endometrial cavity after microwave endometrial ablation. Design: Prospective observational study. Setting: GuangDong Women's and Children's Hospital, GuangDong, China. Patients: A total of 349 patients who underwent microwave endometrial ablation from January 2000 through August 2008 were followed up for 1 month to 8 years. At follow-up in 2007 and 2008, patients were advised of this clinical study and were randomly selected for participation if they agreed to undergo outpatient hysteroscopy to assess the uterine cavity during follow-up visits. Fifty three patients (median [range] age, 43.1 [33-53] years) were recruited into the study at the time of endometrial ablation. Intervention: Outpatient hysteroscopy. Main Results: Within the first 3 months after ablation, outpatient hysteroscopy revealed varying amounts of necrotic tissue from the endometrium and superficial myometrium of the uterus. Six months postablation, a granulomatous reaction and fibrosis were present. A fibrotic cavity was also evident, and menstrual flow was reduced or had ceased. One year after ablation, hysteroscopy demonstrated a fibrotic cavity with myofibrous scars. Most patients developed amenorrhea at this time. Two years or more postablation, a second hysteroscopy demonstrated various types of intrauterine adhesions in 28 of the 53 women (52.8%). A cervical adhesion was observed in 1 patient (1.9%), focal adhesions in the fundal area in 12 (22.6%), a narrowed and scarred uterine cavity with bilateral stenotic tubal ostia in 11 (20.7%), and complete obliteration of the cavity in 4 (7.5%). Of these 28 women, 22 had amenorrhea, 3 had vaginal spotting during menstruation, and 2 had hypomenorrhea. Of those without intrauterine adhesions, only 5 had amenorrhea, 10 had vaginal spotting, and 8 had hypomenorrhea. Conclusion: The hysteroscopic appearance of the uterine cavity after microwave endometrial ablation varies considerably. In this study, t...
Ma, R, Shimmon, R, Maynard, P, Lennard, C & Roux, C 2010, 'Further research into novel fingermark detection techniques using anti-Stokes luminescence', Science & Justice, vol. 50, no. 1, pp. 43-43.
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Macinnis-Ng, CMO, Fuentes, S, O'Grady, AP, Palmer, AR, Taylor, D, Whitley, RJ, Yunusa, I, Zeppel, MJB & Eamus, D 2010, 'Root biomass distribution and soil properties of an open woodland on a duplex soil', PLANT AND SOIL, vol. 327, no. 1-2, pp. 377-388.
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Data on the distribution of root biomass are critical to understanding the ecophysiology of vegetation communities. This is particularly true when models are applied to describe ecohydrology and vegetation function. However, there is a paucity of such in
Mahmoodian, S, Sukhorukov, AA, Ha, S, Lavrinenko, AV, Poulton, CG, Dossou, KB, Botten, LC, McPhedran, RC & de Sterke, CM 2010, 'Paired modes of heterostructure cavities in photonic crystal waveguides with split band edges', OPTICS EXPRESS, vol. 18, no. 25, pp. 25693-25701.
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We investigate the modes of double heterostructure cavities where the underlying photonic crystal waveguide has been dispersion engineered to have two band-edges inside the Brillouin zone. By deriving and using a perturbative method, we show that these structures possess two modes. For unapodized cavities, the relative detuning of the two modes can be controlled by changing the cavity length, and for particular lengths, a resonant-like effect makes the modes degenerate. For apodized cavities no such resonances exist and the modes are always non-degenerate. © 2010 Optical Society of America.
Manoharan, V, Yunusa, IAM, Loganathan, P, Lawrie, R, Murray, BR, Skilbeck, CG & Eamus, D 2010, 'Boron contents and solubility in Australian fly ashes and its uptake by canola (Brassica napus L.) from the ash-amended soils', AUSTRALIAN JOURNAL OF SOIL RESEARCH, vol. 48, no. 5, pp. 480-487.
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Phytotoxicity due to excessive boron (B) uptake by plants impedes routine agronomic utilisation of coal fly ash. We assessed 11 fly ashes (pH 3.1410.77) having total B content (Bt) of 12136mg/kg, of which 2030% was hot water soluble (Bs) in the acidic ashes (pH 5) and 510% in the alkaline ashes, for their potential to supply B to plants and their risk associated with phytotoxicity. We found the Bs/Bt to be negatively correlated (R2≤0.63, N≤11) with ash pH. We conducted two pot trials in which canola was grown in soils amended with fly ash. In the first trial, an alkaline fly ash (Bt 66mg/kg) was incorporated at 5 rates of up to 625Mg/ha into the top 50mm of 2 acidic soils in 0.30-m-long intact cores, and sown with canola. Boron concentration in leaves at flowering reached the phytotoxic threshold, and both plant growth and seed yield were reduced, only at 625Mg/ha. In the second trial, 4 fly ashes (pH 3.2910.77, Bt 12127mg/kg) were incorporated at 4 rates of up to 108Mg/ha into the top 0.10m of 2 acidic soils in 1.0-m-long intact cores and then sown with canola. Ashes with highest Bt, when applied at 108Mg/ha, increased B concentration in the topsoil only. Of the 2 ashes with the highest B t, only that which produced low soil pH and applied at 108Mg/ha increased B concentration in the shoot, but was still below phytotoxic threshold. The results suggest that B derived from these ashes may not cause phytotoxicity and excessive soil B accumulation if the ashes are applied at modest rates (36Mg/ha) to the topsoil layers. © 2010 CSIRO.
Manoharan, V, Yunusa, IAM, Loganathan, P, Lawrie, R, Skilbeck, G, Burchett, MD, Murray, BR & Eamus, D 2010, 'Assessments of Class F fly ashes for amelioration of soil acidity and their influence on growth and uptake of Mo and Se by canola', FUEL, vol. 89, no. 11, pp. 3498-3504.
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Coal fly ash can be used to ameliorate productivity constraints in agricultural soils, but their efficacy still remains highly variable. To ascertain the capacity of Class F fly ashes to modify pH of acidic soils, and their effects on the yield and uptake of molybdenum (Mo) and selenium (Se) by canola (Brassica napus L.), we applied two acidic and two alkaline Class F ashes at rates equivalent to 0, 12, 36, and 108 Mg/ha to the top layer (0-10 cm) of 100 cm long intact cores of acidic sandy clay and clay loam soils. Only the alkaline ash which had the highest calcium carbonate equivalent (2.43%) increased the pH of the top 10 cm of the sandy clay soil. However, this ash was also highly saline and when applied at ≥36 Mg/ha it increased the electrical conductivity in the top soil layer. Increases in soil pH as a result of alkaline ash addition also elevated concentrations of Se in the plant shoot. The ashes with high concentrations of Mo and Se generally increased uptake of these elements in the plant shoot and/or seed. When these ashes were applied at 108 Mg/ha they increased the concentrations of these elements in the treated topsoil. © 2010 Elsevier Ltd. All rights reserved.
Marley, JK & Wand, MP 2010, 'Non-Standard Semiparametric Regression viaBRugs', Journal of Statistical Software, vol. 37, no. 5, pp. 1-30.
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We provide several illustrations of Bayesian semiparametric regression analyses in the BRugs package. BRugs facilitates use of the BUGS inference engine from the R computing environment and allows analyses to be managed using scripts. The examples are chosen to represent an array of non-standard situations, for which mixed model software is not viable. The situations include: the response variable being outside of the one-parameter exponential family, data subject to missingness, data subject to measurement error and parameters entering the model via an index.
Martinez, JG, Carroll, RJ, Muller, S, Sampson, JN & Chatterjee, N 2010, 'A Note on the Effect on Power of Score Tests via Dimension Reduction by Penalized Regression under the Null', The International Journal of Biostatistics, vol. 6, no. 1.
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Martinez, JG, Huang, JZ, Burghardt, RC, Barhoumi, R & Carroll, RJ 2010, '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 ($\mathrm {Ca}^{2+}$) 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) andweighted versions of them (WSVD) to extract the signals from such movies, in away that is semi-automatic and tuned closely to the actual data and their manycomplexities. These complexities include the following. First, the imagesthemselves are of no interest: all interest focuses on the behavior ofindividual cells across time, and thus, the cells need to be segmented in anautomated manner. Second, the cells themselves have 100$+$ pixels, so that theyform 100$+$ curves measured over time, so that data compression is required toextract the features of these curves. Third, some of the pixels in some of thecells are subject to image saturation due to bit depth limits, and thissaturation needs to be accounted for if one is to normalize the images in areasonably unbiased manner. Finally, the $\mathrm {Ca}^{2+}$ signals haveoscillations or waves that vary with time and these signals need to beextracted. Thus, our aim is to show how to use multiple weighted and standardsingular value decompositions to detect, extract and clarify the $\mathrm{Ca}^{2+}$ signals. Our signal extraction methods then lead to simple althoughfinely focused statistical methods to compare $\mathrm {Ca}^{2+}$ signalsacross experimental conditions.
Martinez, JG, Liang, F, Zhou, L & Carroll, RJ 2010, 'Longitudinal functional principal component modelling via Stochastic Approximation Monte Carlo', Canadian Journal of Statistics, vol. 38, no. 2, pp. 256-270.
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AbstractThe authors consider the analysis of hierarchical longitudinal functional data based upon a functional principal components approach. In contrast to standard frequentist approaches to selecting the number of principal components, the authors do model averaging using a Bayesian formulation. A relatively straightforward reversible jump Markov Chain Monte Carlo formulation has poor mixing properties and in simulated data often becomes trapped at the wrong number of principal components. In order to overcome this, the authors show how to apply Stochastic Approximation Monte Carlo (SAMC) to this problem, a method that has the potential to explore the entire space and does not become trapped in local extrema. The combination of reversible jump methods and SAMC in hierarchical longitudinal functional data is simplified by a polar coordinate representation of the principal components. The approach is easy to implement and does well in simulated data in determining the distribution of the number of principal components, and in terms of its frequentist estimation properties. Empirical applications are also presented. The Canadian Journal of Statistics 38: 256–270; 2010 © 2010 Statistical Society of Canada
Masaki, L, Brooks, EM, Robertson, J, Maynard, P & Roux, C 2010, 'The forensic examination of black, brown, blond, and red hairs using digital imaging and colour analysis', Science & Justice, vol. 50, no. 1, pp. 39-39.
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Mbere-Nguyen, U, Ung, AT & Pyne, SG 2010, 'Synthesis of 2 '-aminoalkyl-1-benzylisoquinoline derivatives and medium sized ring analogues with mu opiod receptor binding activities', TETRAHEDRON, vol. 66, no. 23, pp. 4133-4143.
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Novel 20-aminoalkyl-1-benzylisoquinoline compounds and medium size ring analogues have been prepared using reductive alkylation methods. Four of these analogues were tested for biological activity across 48 different CNS receptors and were showed to have binding activities at the mu opiod receptor.
McGrath, KC-Y, Hill, MD, McRobb, LS & Heather, AK 2010, 'The androgen receptor drives the sex-specific expression of vascular cell adhesion molecule-1 in endothelial cells but not lipid metabolism genes in monocyte-derived macrophages', hmbci, vol. 2, no. 1, pp. 203-209.
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Abstract Background: Anecdotal evidence suggests that male sex hormones are proatherogenic. We hypothesized that the male sex hormone receptor, the androgen receptor (AR), acts as a molecular switch in sex-specific inflammatory signaling in vascular cells. Materials and methods: AR expression in human umbilical vein endothelial cells (HUVECs), human monocyte-derived macrophages (MDMs) or HeLa cells was modulated by transfection with AR siRNA or human AR cDNA expression vector. Activity and expression levels were measured by luciferase reporter assays, Western blotting or real-time PCR analysis. Results: AR knockdown reduced expression of vascular cell adhesion molecule-1 (VCAM-1) in genetically male HUVECs. Conversely, AR upregulation in genetically female HUVECs induced VCAM-1 expression and increased dihydrotestosterone-stimulated monocyte adhesion. Co-transfection of an AR expression vector with VCAM-1 or NF-κB-reporter vectors into phenotypically female, AR-negative HeLa cells confirmed AR regulation of VCAM-1 expression as well as AR activation of NF-κB. AR upregulation was not sufficient to increase ICAM-1 levels in female HUVECs or lipoprotein metabolism gene expression in female MDMs, despite AR knockdown limiting expression in their male counterparts. Conclusions: AR acts as a molecular switch to induce VCAM-1 expression. Low AR levels in female HUVECs limit NF-κB/VCAM-1 induction and monocyte adhesion and could contribute to the gender bias in cardiovascular disease. Unidentified factors in female cells limit induction of other proatherogenic genes not primarily regulated by NF-κB.
McMinn, A, Pankowskii, A, Ashworth, C, Bhagooli, R, Ralph, P & Ryan, K 2010, 'In situ net primary productivity and photosynthesis of Antarctic sea ice algal, phytoplankton and benthic algal communities', MARINE BIOLOGY, vol. 157, no. 6, pp. 1345-1356.
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Primary production at Antarctic coastal sites is contributed from sea ice algae, phytoplankton and benthic algae. Oxygen microelectrodes were used to estimate sea ice and benthic primary production at several sites around Casey, a coastal area in eastern Antarctica. Maximum oxygen export from sea ice was 0. 95 mmol O2 m-2 h-1 (~11. 7 mg C m-2 h-1) while from the sediment it was 6. 08 mmol O2 m-2 h-1 (~70. 8 mg C m-2 h-1). When the ice was present O2 export from the benthos was either low or negative. Sea ice algae assimilation rates were up to 3. 77 mg C (mg Chl-a)-1 h-1 while those from the benthos were up to 1. 53 mg C (mg Chl-a)-1 h-1. The contribution of the major components of primary productivity was assessed using fluorometric techniques. When the ice was present approximately 55-65% of total daily primary production occurred in the sea ice with the remainder unequally partitioned between the sediment and the water column. When the ice was absent, the benthos contributed nearly 90% of the primary production. © 2010 Springer-Verlag.
McPhedran, RC, Nicorovici, NA & Botten, LC 2010, 'Resonant cloaking and local density of states', Metamaterials, vol. 4, no. 2-3, pp. 149-152.
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We discuss methods for hiding of objects from detection by electromagnetic waves (cloaking), and also ways by which cloaked objects may be detected. The possibility of detection by means of thermal radiation emitted when electromagnetic energy is resonantly absorbed motivates the calculation of local density of states (LDOS), which controls the ability of a source inside a structured system to radiate. We give the first results of an investigation of the LDOS for systems which cloak by resonant interaction with electromagnetic fields.
Minovich, A, Neshev, DN, Powell, DA, Shadrivov, IV, Lapine, M, McKerracher, I, Hattori, HT, Tan, HH, Jagadish, C & Kivshar, YS 2010, 'Tilted response of fishnet metamaterials at near-infrared optical wavelengths', Physical Review B, vol. 81, no. 11.
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Mitchell, CM, Hovis, KM, Bavoil, PM, Myers, GSA, Carrasco, JA & Timms, P 2010, 'Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species', BMC Genomics, vol. 11, no. 1.
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Abstract Background Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species. Results We performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes). Conclusions We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.
Mitchell, CM, Hutton, S, Myers, GSA, Brunham, R & Timms, P 2010, 'Chlamydia pneumoniae Is Genetically Diverse in Animals and Appears to Have Crossed the Host Barrier to Humans on (At Least) Two Occasions', PLoS Pathogens, vol. 6, no. 5, pp. e1000903-e1000903.
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Mititelu, G, Areepong, Y, Sukparungsee, S & Novikov, A 2010, 'Explicit analytical solutions for the average run length of CUSUM and EWMA charts', East-West Journal of Mathematics, vol. special, no. 1, pp. 253-265.
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NA
Mitrovic, SM, Hitchcock, JN, Davie, AW & Ryan, DA 2010, 'Growth responses of Cyclotella meneghiniana (Bacillariophyceae) to various temperatures', JOURNAL OF PLANKTON RESEARCH, vol. 32, no. 8, pp. 1217-1221.
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The growth of Cyclotella meneghiniana was examined at temperatures between 13 and 28°C at 3°C intervals. Growth increased linearly with temperature to a growth maximum at 25°C, with growth decreasing at 28°C. © The Author 2010.
Moheimani, F, Morgan, PE, van Reyk, DM & Davies, MJ 2010, 'Deleterious effects of reactive aldehydes and glycated proteins on macrophage proteasomal function: Possible links between diabetes and atherosclerosis', BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, vol. 1802, no. 6, pp. 561-571.
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People with diabetes experience chronic hyperglycemia and are at a high risk of developing atherosclerosis and microvascular disease. Reactions of glucose, or aldehydes derived from glucose (e.g. methylglyoxal, glyoxal, or glycolaldehyde), with proteins result in glycation that ultimately yield advanced glycation end products (AGE). AGE are present at elevated levels in plasma and atherosclerotic lesions from people with diabetes, and previous in vitro studies have postulated that the presence of these materials is deleterious to cell function. This accumulation of AGE and glycated proteins within cells may arise from either increased formation and/or ineffective removal by cellular proteolytic systems, such as the proteasomes, the major multi-enzyme complex that removes proteins within cells. In this study it is shown that whilst high glucose concentrations fail to modify proteasome enzyme activities in J774A.1 macrophage-like cell extracts, reactive aldehydes enhanced proteasomal enzyme activities. In contrast BSA, pre-treated with high glucose for 8 weeks, inhibited both the chymotrypsin-like and caspase-like activities. BSA glycated using methylglyoxal or glycolaldehyde, also inhibited proteasomal activity though to differing extents. This suppression of proteasome activity by glycated proteins may result in further intracellular accumulation of glycated proteins with subsequent deleterious effects on cellular function.
Mohr, R, Voß, B, Schliep, M, Kurz, T, Maldener, I, Adams, DG, Larkum, ADW, Chen, M & Hess, WR 2010, 'A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris', The ISME Journal, vol. 4, no. 11, pp. 1456-1469.
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Abstract Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (23° 26′ 31.2″ S, 151° 54′ 50.4″ E). The 16S ribosomal RNA is 2% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371 965 nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms.
Moldovan, D, Spriggs, A, Dennis, ES & Wilson, IW 2010, 'The hunt for hypoxia responsive natural antisense short interfering RNAs', Plant Signaling & Behavior, vol. 5, no. 3, pp. 247-251.
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Small ribonucleic acids (smRNA) have been identified as important post-transcriptional regulators of gene expression. One important class of smRNA implicated in stress responses are natural antisense short interfering RNA (natsiRNA). These natsiRNAs are generated from two overlapping mRNA that are processed into short-interfering RNAs and target complementary mRNA sequences for degradation. A feature of natsiRNA is the inverse regulation of gene expression that is observed after environmental or developmental stimuli. Genome-wide expression analysis of hypoxia treated Arabidopsis roots in combination with the examination of gene expression in plants defective in natsiRNA processing, was used to find putative natsiRNA regulated genes. The results indicate the potential involvement of natsiRNA in regulating lipid signaling in hypoxia. © 2010 Landes Bioscience.
Moldovan, D, Spriggs, A, Yang, J, Pogson, BJ, Dennis, ES & Wilson, IW 2010, 'Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis', JOURNAL OF EXPERIMENTAL BOTANY, vol. 61, no. 1, pp. 165-177.
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Low-oxygen (hypoxia) stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries o
Monahan, LG & Harry, L 2010, 'The bacterial cytoskeleton', Australian Biochemist, vol. 40, no. 2, pp. 4-8.
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Review in token-refereed journal on the bacterial cytoskeketon
Morgan, KA, Harris, AW, Luscombe, G, Tran, Y, Herkes, G & Bartrop, RW 2010, 'The effect of music on brain wave functioning during an acute psychotic episode: A pilot study', Psychiatry Research, vol. 178, no. 2, pp. 446-448.
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This pilot study compared the differences in the quantified electroencephalogram (qEEG) between two conditions; eyes closed resting and eyes closed listening to music of 15 subjects currently experiencing an acute psychotic episode. The results showed a
Moriya, S, Rashid, RA, Rodrigues, CDA & Harry, EJ 2010, 'Influence of the nucleoid and the early stages of DNA replication on positioning the division site in Bacillus subtilis', Molecular Microbiology, vol. 76, no. 3, pp. 634-647.
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Although division site positioning in rod-shaped bacteria is generally believed to occur through the combined effect of nucleoid occlusion and the Min system, several lines of evidence suggest the existence of additional mechanisms. Studies using outgrown spores of Bacillus subtilis have shown that inhibiting the early stages of DNA replication, leading up to assembly of the replisome at oriC, influences Z ring positioning. Here we examine whether Z ring formation at midcell under various conditions of DNA replication inhibition is solely the result of relief of nucleoid occlusion. We show that midcell Z rings form preferentially over unreplicated nucleoids that have a bilobed morphology (lowering DNA concentration at midcell), whereas acentral Z rings form beside a single-lobed nucleoid. Remarkably however, when the DnaB replication initiation protein is inactivated midcell Z rings never form over bilobed nucleoids. Relieving nucleoid occlusion by deleting noc increased midcell Z ring frequency for all situations of DNA replication inhibition, however not to the same extent, with the DnaB-inactivated strain having the lowest frequency of midcell Z rings. We propose an additional mechanism for Z ring positioning in which the division site becomes increasingly potentiated for Z ring formation as initiation of replication is progressively completed. © 2010 Blackwell Publishing Ltd.
Moutzouris, JP, Che, W, Ramsay, EE, Manetsch, M, Alkhouri, H, Bjorkman, AM, Schuster, F, Ge, Q & Ammit, AJ 2010, 'Proteasomal inhibition upregulates the endogenous MAPK deactivator MKP-1 in human airway smooth muscle: Mechanism of action and effect on cytokine secretion', Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol. 1803, no. 3, pp. 416-423.
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Munoz, L & Ammit, AJ 2010, 'Targeting p38 MAPK pathway for the treatment of Alzheimer's disease', Neuropharmacology, vol. 58, no. 3, pp. 561-568.
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Munoz, L, Ramsay, EE, Manetsch, M, Ge, Q, Peifer, C, Laufer, S & Ammit, AJ 2010, 'Novel p38 MAPK inhibitor ML3403 has potent anti-inflammatory activity in airway smooth muscle', European Journal of Pharmacology, vol. 635, no. 1-3, pp. 212-218.
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Murray, BR & Phillips, ML 2010, 'Investment in seed dispersal structures is linked to invasiveness in exotic plant species of south-eastern Australia', BIOLOGICAL INVASIONS, vol. 12, no. 7, pp. 2265-2275.
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Naturalized plant species disperse their populations over considerable distances to become invasive. We tested the hypothesis that this shift from naturalization to invasion is facilitated by increased investment of resources in seed dispersal appendages, using an assemblage of naturalized plants of south-eastern Australia. Compared with non-invasive species, we found in both cross-species and independent-contrasts analyses that invasive species invested more heavily in seed dispersal appendages, regardless of the structure present on the seed associated with the mode of dispersal (e. g., wings versus fleshy fruits). Invasive species such as Lonicera japonica, Hedera Helix and Acetosa sagittata were found to invest as much as 60-70% of total diaspore mass in dispersal appendages. The positive relationship between dispersal investment and invasion success was still prevalent after controlling for the effects of plant growth form, seed mass and capacity for vegetative growth. Our findings demonstrate that a plant's investment in dispersal appendages helps to overcome the dispersal barrier in the shift from naturalization to invasion. © 2009 Springer Science+Business Media B.V.
Musicki, K, Briscoe, H, Britton, WJ & Saunders, BM 2010, 'LIGHT contributes to early but not late control of Mycobacterium tuberculosis infection', International Immunology, vol. 22, no. 5, pp. 353-358.
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Naumann, U, Luta, G & Wand, MP 2010, 'The curvHDR method for gating flow cytometry samples', BMC Bioinformatics, vol. 11, no. 1, pp. 44-56.
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Abstract Background High-throughput flow cytometry experiments produce hundreds of large multivariate samples of cellular characteristics. These samples require specialized processing to obtain clinically meaningful measurements. A major component of this processing is a form of cell subsetting known as gating. Manual gating is time-consuming and subjective. Good automatic and semi-automatic gating algorithms are very beneficial to high-throughput flow cytometry. Results We develop a statistical procedure, named , for automatic and semi-automatic gating. The method combines the notions of significant high negative curvature regions and highest density regions and has the ability to adapt well to human-perceived gates. The underlying principles apply to dimension of arbitrary size, although we focus on dimensions up to three. Accompanying software, compatible with contemporary flow cytometry infor-matics, is developed. Conclusion The method is seen to adapt well to nuances in the data and, to a reasonable extent, match human perception of useful gates. It offers big savings in human labour when processing high-throughput flow cytometry data whilst retaining a good degree of efficacy.
Nedbal, L, Červený, J, Keren, N & Kaplan, A 2010, 'Experimental validation of a nonequilibrium model of CO2 fluxes between gas, liquid medium, and algae in a flat-panel photobioreactor', Journal of Industrial Microbiology & Biotechnology, vol. 37, no. 12, pp. 1319-1326.
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Nicorovici, N-AP, McPhedran, RC & Botten, LC 2010, 'Relative local density of states for homogeneous lossy materials', PHYSICA B-CONDENSED MATTER, vol. 405, no. 14, pp. 2915-2919.
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We derive the appropriate form of the relative local density of states (RLDOS) for the two-dimensional Helmholtz equation in a homogeneous lossy medium, and give the corresponding result for the three-dimensional equation. The RLDOS enables the calculati
Nicorovici, N-AP, McPhedran, RC, Botten, LC, Poulton, CG & Asatryan, AA 2010, 'Green's functions and relative local density of states in two-dimensional lossy structured systems', WAVES IN RANDOM AND COMPLEX MEDIA, vol. 20, no. 4, pp. 656-677.
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The local density of states (LDOS) is a function of spatial position and frequency which governs the radiation properties of sources placed within structured optical systems. We show how the enhancement or suppression of the relative LDOS, comparing two-dimensional systems, may be computed from Green's tensors obeying the two-dimensional Helmholtz equation and electromagnetic boundary conditions, both around and within a coated, lossy, non-magnetic cylinder. We illustrate the spatial and spectral variation of this relative LDOS with numerical results for both principal cases of polarization, with either the magnetic or the electric field of the Green's function source along the cylinder axis.
Nielsen, DA, Nielsen, LP, Schramm, A & Revsbech, NP 2010, 'Oxygen Distribution and Potential Ammonia Oxidation in Floating, Liquid Manure Crusts', Journal of Environmental Quality, vol. 39, no. 5, pp. 1813-1820.
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Floating, organic crusts on liquid manure, stored as a result of animal production, reduce emission of ammonia (NH3) and other volatile compounds during storage. The occurrence of NO2− and NO3− in the crusts indicate the presence of actively metabolizing NH3‐oxidizing bacteria (AOB) which may be partly responsible for this mitigation effect. Six manure tanks with organic covers (straw and natural) were surveyed to investigate the prevalence and potential activity of AOB and its dependence on the O2 availability in the crust matrix as studied by electrochemical profiling. Oxygen penetration varied from <1 mm in young, poorly developed natural crusts and old straw crusts, to several centimeters in the old natural crusts. The AOB were ubiquitously present in all crusts investigated, but nitrifying activity could only be detected in old natural crusts and young straw crust with high O2 availability. In old natural crusts, total potential NH3 oxidation rates were similar to reported fluxes of NH3 from slurry without surface crust. These results indicate that old, natural surface crusts may develop into a porous matrix with high O2 availability that harbors an active population of aerobic microorganisms, including AOB. The microbial activity may thus contribute to a considerable reduction of ammonia emissions from slurry tanks with well‐developed crusts.
NIU, GM, JIN, DY, JI, Y, HOU, J, WANG, DS & LOU, WH 2010, 'Survival analysis of pancreatic and periampullary collision cancers', Journal of Digestive Diseases, vol. 11, no. 4, pp. 231-236.
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OBJECTIVE: Collision cancers are malignancies in the same organ or anatomical site that comprises at least two different tumor components, with no mixed or transitional area between two components. Collision cancers are very rare in the pancreas and periampullary region. The aim of this study was to analyze the clinical and pathological features and prognosis of collision cancer in the pancreas and periampullary region.METHODS: Patients with collision cancers of the pancreas and periampullary region (n= 10) who had undergone radical surgery were retrospectively studied. Their clinical and pathological features were summarized and the prognostic data were compared with patients with pancreatic adenocarcinomas who underwent radical surgery (n= 87) and with patients with pancreatic or periampullary malignancies who underwent palliative surgery (n= 89).RESULTS: Compared with other cancers at these sites, collision cancer presents no specific clinical features. However, the median survival period of patients with such malignancies was only 10.0 months, which was much less than those with pancreatic adenocarcinomas who underwent radical surgery (27.0 months) and those who received a palliative operation (20.9 months) only.CONCLUSION: Collision cancers of the pancreas and periampullary region are difficult to diagnose preoperatively. Their prognosis is poor even after radical resection and adjuvant chemotherapy were given.
Nunn, J, Dorner, U, Michelberger, P, Reim, KF, Lee, KC, Langford, NK, Walmsley, IA & Jaksch, D 2010, 'Quantum memory in an optical lattice', Physical Review A, vol. 82, no. 2.
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Oliver, RL, Mitrovic, SM & Rees, C 2010, 'INFLUENCE OF SALINITY ON LIGHT CONDITIONS AND PHYTOPLANKTON GROWTH IN A TURBID RIVER', RIVER RESEARCH AND APPLICATIONS, vol. 26, no. 7, pp. 894-903.
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A turbid lowland river in Australia was studied to describe factors influencing the light conditions for phytoplankton growth. Vertical attenuation coefficients correlated with nepholometric turbidity enabling estimation of euphotic depths (zeu) from long term turbidity monitoring. Light conditions were assessed from the ratio of zeu to the maximum water depth (zm). Predominantly zeu/zm ratios were below 0.2, a value indicating the minimum light conditions required to support phytoplankton growth. A transitional state with zeu/zm between 0.2 and 0.35 occurred 15% of the time, while light sufficiency occurred for 30% of the time. Peaks in eukaryotic phytoplankton biomass developed when zeu/zm was at or above transitional values. Large increases in cyanobacterial numbers (Anabaena sp.) only occurred when zeu/zm exceeded 0.35. Turbidity increased quickly with elevated flows but did not decline substantially as flows reduced and light limiting conditions extended into low flow periods otherwise conducive to phytoplankton growth.
Ormerod, JT & Wand, MP 2010, 'Explaining Variational Approximations', The American Statistician, vol. 64, no. 2, pp. 140-153.
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Variational approximations facilitate approximate inference for the parameters in complex statistical models and provide fast, deterministic alternatives to Monte Carlo methods. However, much of the contemporary literature on variational approximations is in Computer Science rather than Statistics, and uses terminology, notation, and examples from the former field. In this article we explain variational approximation in statistical terms. In particular, we illustrate the ideas of variational approximation using examples that are familiar to statisticians. © 2010 American Statistical Association.
Orwa, JO, Aharonovich, I, Jelezko, F, Balasubramanian, G, Balog, P, Markham, M, Twitchen, DJ, Greentree, AD & Prawer, S 2010, 'Nickel related optical centres in diamond created by ion implantation', JOURNAL OF APPLIED PHYSICS, vol. 107, no. 9, p. 093512.
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Ni-related optical centres in diamond are promising as alternatives to the nitrogen vacancy (NV) centre for quantum applications and biomarking. In order to achieve the reliability and reproducibility required, a method for producing the Ni-related centres in a controllable manner needs to be established. In this study, we have attempted this control by implanting high purity CVD diamond samples with Ni and N followed by thermal annealing. Samples implanted with Ni show a new Ni-related PL peak centered at 711 nm and a well known doublet at 883/885 nm along with weak NV luminescence. The optical properties of the two Ni-related defects are investigated. In particular, an excited state lifetime of the 883/885 nm peak is measured to be 11.6 ns
Palmer, AR, Fuentes, S, Taylor, D, Macinnis-Ng, C, Zeppel, M, Yunusa, I & Eamus, D 2010, 'Towards a spatial understanding of water use of several land-cover classes: an examination of relationships amongst pre-dawn leaf water potential, vegetation water use, aridity and MODIS LAI', ECOHYDROLOGY, vol. 3, no. 1, pp. 1-10.
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Leaf area index (LAI) is a key physical variable which controls the exchange of water and CO, between the earth and the atmosphere. Recent improvements in the quality of satellite-derived estimates of LAI, specifically the MODIS LAI product, have led to
Pankoui Mfonkeu, JB, Gouado, I, Fotso Kuaté, H, Zambou, O, Amvam Zollo, PH, Grau, GER & Combes, V 2010, 'Elevated Cell-Specific Microparticles Are a Biological Marker for Cerebral Dysfunctions in Human Severe Malaria', PLoS ONE, vol. 5, no. 10, pp. e13415-e13415.
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Cerebral malaria (CM) and severe anemia (SA) are the most severe complications of Plasmodium falciparum infections. Although increased release of endothelial microparticles (MP) correlates with malaria severity, the full extent of vascular cell vesiculation remains unknown. Here, we characterize the pattern of cell-specific MP in patients with severe malaria. We tested the hypothesis that systemic vascular activation contributes to CM by examining origins and levels of plasma MP in relation to clinical syndromes, disease severity and outcome. Patients recruited in Douala, Cameroon, were assigned to clinical groups following WHO criteria. MP quantitation and phenotyping were carried out using cell-specific markers by flow cytometry using antibodies recognizing cell-specific surface markers. Platelet, erythrocytic, endothelial and leukocytic MP levels were elevated in patients with cerebral dysfunctions and returned to normal by discharge. In CM patients, platelet MP were the most abundant and their levels significantly correlated with coma depth and thrombocytopenia. This study shows for the first time a widespread enhancement of vesiculation in the vascular compartment appears to be a feature of CM but not of SA. Our data underpin the role of MP as a biomarker of neurological involvement in severe malaria. Therefore, intervention to block MP production in severe malaria may provide a new therapeutic pathway. © 2010 Pankoui Mfonkeu et al.
Pankoui Mfonkeu, JB, Gouado, I, Fotso Kuaté, H, Zambou, O, Combes, V, Raymond Grau, GE & Amvam Zollo, PH 2010, 'Biochemical markers of nutritional status and childhood malaria severity in Cameroon', British Journal of Nutrition, vol. 104, no. 6, pp. 886-892.
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To investigate the part played by undernutrition in malaria severity, some biomarkers of nutritional status were assessed in children with severe malarial anaemia (MA) and cerebral malaria (CM) in comparison with healthy children or those with uncomplicated malaria. Undernutrition was assessed using the weight-for-ageZscore (WAZ). Retinol was determined by HPLC; lipid profile, Ca, Mg and albumin were determined by spectrophotometry. Severe and moderate undernutritions were more prevalent in children with MA and those with the combined symptoms of CM and MA, but not in those with CM alone. Some perturbations were noticed in the lipid profile, but most of the values remained within the normal ranges. The risk of vitamin A deficiency, as assessed by plasma retinol concentration, was noteworthy in children with severe malaria: 0·48 × 10− 6and 0·50 × 10− 6 mol/l, respectively, in children with MA and CM (reference value: >0·7 × 10− 6 mol/l). A significant difference was obtained for retinol values after an ANOVA of all the groups (P = 0·0029), with the value in the MA group being significantly low than that in the control group (P < 0·05); likewise, a significant difference was obtained after comparison of all the groups for Mg and albumin (P = 0·0064 and 0·0082, respectively). Despite their low number (n6), fatal cases of CM had a normal mean WAZ on admission, but low values of retinol, albumin and HDL:LDL ratio. Despite these associations, undernutrition itself did not appear to be a primary factor associated with fatal outcome.
Papasani, MR, Thornton, K, Yinggian, Z, Brezas, A, Welch, C, Wang, G, Villasante, A, Pokharel, D, Cheguru, P, Kotla, S & Julien, DC 2010, 'Does obesity reduce load-induced muscle hypertrophy?', The Journal of Physiology, vol. 588, no. 11, pp. 1819-1820.
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Paris, PL, Weinberg, V, Albo, G, Roy, R, Burke, C, Simko, J, Carroll, P & Collins, C 2010, 'A Group of Genome-Based Biomarkers That Add to a Kattan Nomogram for Predicting Progression in Men with High-Risk Prostate Cancer', Clinical Cancer Research, vol. 16, no. 1, pp. 195-202.
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Abstract Purpose: The three main treatment options for primary prostate cancer are surgery, radiation, and active surveillance. Surgical and radiation intervention for prostate cancer can be associated with significant morbidity. Therefore, accurate stratification predictive of outcome for prostate cancer patients is essential for appropriate treatment decisions. Nomograms that use clinical and pathologic variables are often used for risk prediction. Favorable outcomes exist even among men classified by nomograms as being at high risk of recurrence. Experimental Design: Previously, we identified a set of DNA-based biomarkers termed Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) and have shown that they can predict risk of recurrence with 80% accuracy. Here, we examined the risk prediction ability of GEMCaP in a high-risk cohort and compared it to a Kattan nomogram. Results: We determined that the GEMCaP genotype alone is comparable with the nomogram, and that for a subset of cases with negative lymph nodes improves upon it. Conclusion: Thus, GEMCaP shows promise for predicting unfavorable outcomes for negative lymph node high-risk cases, where the nomogram falls short, and suggests that addition of GEMCaP to nomograms may be warranted. Clin Cancer Res; 16(1); 195–202
Paterson, AH, Rong, J-K, Gingle, AR, Chee, PW, Dennis, ES, Llewellyn, D, Dure, LS, Haigler, C, Myers, GO, Peterson, DG, ur Rahman, M, Zafar, Y, Reddy, U, Saranga, Y, Stewart, JM, Udall, JA, Waghmare, VN, Wendel, JF, Wilkins, TA, Wright, RJ, Zaki, E, Hafez, EE & Zhu, J 2010, 'Sequencing and Utilization of the Gossypium Genomes', Tropical Plant Biology, vol. 3, no. 2, pp. 71-74.
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Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge. © 2010 Springer Science+Business Media, LLC.
Patwardhan, SV, Holt, SA, Kelly, SM, Kreiner, M, Perry, CC & van der Walle, CF 2010, 'Silica Condensation by a Silicatein α Homologue Involves Surface-Induced Transition to a Stable Structural Intermediate Forming a Saturated Monolayer', Biomacromolecules, vol. 11, no. 11, pp. 3126-3135.
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Pauc, N, Phillips, MR, Aimez, V & Drouin, D 2010, 'Response to “Comment on ‘Carrier recombination near threading dislocations in GaN epilayers by low voltage cathodoluminescence’” [Appl. Phys. Lett. 97, 166101 (2010)]', Applied Physics Letters, vol. 97, no. 16, pp. 166102-166102.
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Peng, D-L, Huang, J-F, Huete, AR, Yang, T-M, Gao, P, Chen, Y-C, Chen, H, Li, J & Liu, Z-Y 2010, 'Spatial and seasonal characterization of net primary productivity and climate variables in southeastern China using MODIS data', JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B, vol. 11, no. 4, pp. 275-285.
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We developed a sophisticated method to depict the spatial and seasonal characterization of net primary productivity (NPP) and climate variables. The role of climate variability in the seasonal variation of NPP exerts delayed and continuous effects. This study expands on this by mapping the seasonal characterization of NPP and climate variables from space using geographic information system (GIS) technology at the pixel level. Our approach was developed in southeastern China using moderate-resolution imaging spectroradiometer (MODIS) data. The results showed that air temperature, precipitation and sunshine percentage contributed significantly to seasonal variation of NPP. In the northern portion of the study area, a significant positive 32-d lagged correlation was observed between seasonal variation of NPP and climate (P<0.01), and the influences of changing climate on NPP lasted for 48 d or 64 d. In central southeastern China, NPP showed 16-d, 48-d, and 96-d lagged correlation with air temperature, precipitation, and sunshine percentage, respectively (P<0.01); the influences of air temperature and precipitation on NPP lasted for 48 d or 64 d, while sunshine influence on NPP only persisted for 16 d. Due to complex topography and vegetation distribution in the southern part of the study region, the spatial patterns of vegetation-climate relationship became complicated and diversiform, especially for precipitation influences on NPP. In the northern part of the study area, all vegetation NPP had an almost similar response to seasonal variation of air temperature except for broad crops. The impacts of seasonal variation of precipitation and sunshine on broad and cereal crop NPP were slightly different from other vegetation NPP. © 2010 Zhejiang University and Springer-Verlag Berlin Heidelberg.
Perinchery, SM, Kuzhiumparambil, U, Vemulpad, S & Goldys, EM 2010, 'The influence of indoxyl sulfate and ammonium on the autofluorescence of human urine', TALANTA, vol. 80, no. 3, pp. 1269-1276.
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Perinchery, SM, Kuzhiumparambil, U, Vemulpad, S & Goldys, EM 2010, 'The potential of autofluorescence spectroscopy to detect human urinary tract infection', TALANTA, vol. 82, no. 3, pp. 912-917.
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Petrou, K, Hill, R, Brown, CM, Campbell, DA, Doblin, MA & Ralph, PJ 2010, 'Rapid photoprotection in sea-ice diatoms from the East Antarctic pack ice', LIMNOLOGY AND OCEANOGRAPHY, vol. 55, no. 3, pp. 1400-1407.
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Photoinhibition and D1 protein re-synthesis were investigated in bottom-dwelling sea-ice microalgal communities from the East Antarctic pack ice during early spring. Bottom-dwelling sea-ice microalgal communities were dominated by diatoms that exhibited rapid photoprotection when exposed to a range of different light levels (10 μmol photons m-2 s -1, 50 μmol photons m-2 s-1, 100 μmol photons m-2 s-1, and 200 μmol photons m-2 s-1). Photosynthetic capacity of photosystem II (PSII) dropped significantly over 3 h under 200 μmol photons m-2 s-1, but largely recovered when placed in a low-light environment (10 μmol photons m-2 s-1) for an additional 3 h. PSII repair rates increased with increasing irradiance, and the D1-protein pool remained steady even under high light (200 μmol photons m-2 s-1). Sea-ice diatoms showed a low intrinsic susceptibility to photoinactivation of PSII across all the light treatments, and a strong and irradiance-dependent induction of nonphotochemical quenching, which did not depend upon chloroplast protein synthesis, was also seen. These highly plastic organisms, once thought to be adapted to shade, are in fact well equipped to withstand rapid and relatively large changes in light at low temperatures with minimal long-term effect on their photosynthetic machinery. © 2010, by the American Society of Limnology and Oceanography, Inc.
Phillips, M, Merklein, M, Hardy, T, Manning, T & Wintrebert-Fouquet, M 2010, 'A Mechanism for Mg Acceptor Activation in GaN by Low Energy Electron Beam Irradiation', Microscopy and Microanalysis, vol. 16, no. S2, pp. 816-817.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Phillips, ML, Murray, BR, Leishman, MR & Ingram, R 2010, 'The naturalization to invasion transition: Are there introduction-history correlates of invasiveness in exotic plants of Australia?', AUSTRAL ECOLOGY, vol. 35, no. 6, pp. 695-703.
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Of the large number of exotic plant species that become naturalized in new geographic regions, only a subset make the transition to become invasive. Identifying the factors that underpin the transition from naturalization to invasion is important for our understanding of biological invasions. To determine introduction-history correlates of invasiveness among naturalized plant species of Australia, we compared geographic origin, reason for introduction, minimum residence time and growth form between naturalized non-invasive species and naturalized invasive plant species. We found that more invasive species than expected originated from South America and North America, while fewer invasive species than expected originated from Europe and Australasia. There was no significant difference between invasive and non-invasive species with respect to reason for introduction to Australia. However, invasive species were significantly more likely to have been resident in Australia for a longer period of time than non-invasive species. Residence times of invasive species were consistently and significantly higher than residence times of non-invasive species even when each continent of origin was considered separately. Furthermore, residence times for both invasive and non-invasive species varied significantly as a function of continent of origin, with species from South America having been introduced to Australia more recently on average than species from Europe, Australasia and North America. We also found that fewer invasive species than expected were herbs and more invasive species than expected were primarily climbers. Considered together, our results indicate a high propensity for invasiveness in Australia among exotic plant species from South America, given that they appear in general capable of more rapid shifts to invasiveness than aliens from other regions. Furthermore, our findings support an emerging global generality that introduction-history traits must ...
Phillips, ML, Murray, BR, Pysek, P, Pergl, J, Jarosik, V, Chytry, M & Kuehn, I 2010, 'Plant species of the Central European flora as aliens in Australia', PRESLIA, vol. 82, no. 4, pp. 465-482.
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The Central European flora is an important source pool of plant species introduced to many regions throughout the world.In this study, we identifieda total of 759 plant species of the Central European flora that are currently recognized as alien species in Australia. We explored temporal patterns of introduction of these species to Australia in relation to method of introduction, growth form, naturalization status and taxonomy. Across all species, substantially larger numbers of species were introduced between 1840 and 1880 as well as between 1980 and the present, with a small peak of introductions within the 1930s. These patterns reflect early immigration patterns to Australia, recent improvements in fast and efficient transportation around the globe, and emigration away from difficult conditions brought about by the lead up to the Second World War respectively. We found that the majority of species had deliberate (69%) rather than accidental (31%) introductions and most species have not naturalized (66% casual species, 34% naturalized species). A total of 86 plant families comprising 31 tree species, 91 shrub species, 533 herbaceous species and 61 grass species present in Central Europe have been introduced to Australia. Differential patterns of temporal introduction of species were found as a function of both plant family and growth form and these patterns appear linked to variation in human migration numbers to Australia.
Pissuwan, D, Cortie, CH, Valenzuela, SM & Cortie, MB 2010, 'Functionalised gold nanoparticles for controlling pathogenic bacteria', TRENDS IN BIOTECHNOLOGY, vol. 28, no. 4, pp. 207-213.
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The incereasing number of bacterial strains that are resistant to available pharmaceutical compounds is a vital issue for public health. Innovative approaches will be required to improve the methids for both diagnosis and destruction of these organisms. Here we consider the possible role that can be plaued by technologies based on gold nanoparticles. Gold nanoparticles generally are considered to be biologically inert but can be engineered to possess chemical or photothermal functionality. A growing body of research is devoted to the potential use of these nanoparticles in the diagnosis and treatment of bacterial infections. The results are both promising and intriguing and suggest a range of new strategies io identiofy target or destrpy pathogenic organisms.
Platen, E & Rendek, R 2010, 'Approximating the Numeraire Portfolio by Naive Diversification', Journal of Asset Management, vol. 13, no. 1, pp. 34-50.
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Estimation theory has shown, due to the limited estimation window available for real asset data, the sample based Markowitz mean-variance approach produces unreliable weights which fluctuate substantially over time. This paper proposes an alternate approach to portfolio optimization, being the use of naive diversification to approximate the numeraire portfolio. The numeraire portfolio is the strictly positive portfolio that, when used as benchmark, makes all benchmarked nonnegative portfolios either mean decreasing or trendless. Furthermore, it maximizes expected logarithmic utility and outperforms any other strictly positive portfolio in the long run. The paper proves for a well-securitized market that the naive equal value weighted portfolio converges to the numeraire portfolio when the number of constituents tends to infinity. This result is model independent and, therefore, very robust.The systematic construction of diversified stock indices by naive diversification from real data is demonstrated. Even when taking transaction costs into account, these indices significantly outperform the corresponding market capitalization weighted indices in the long run, indicating empirically their asymptotic proximity to the numeraire portfolio. Empirical evidence is presented that the Sharpe ratios of equi-weighted indices surpass significantly those of corresponding market capitalization weighted indices. This empirical stylized fact applies also to the market portfolio of equity markets of countries, which questions the applicability of the intertemporal capital asset pricing model. Finally, in time of financial crisis, a large equi-weighted fund carrying the investments of the major pension funds and insurance companies would provide important liquidity. It would not only dampen the extremes of a crisis but would also moderate the excesses of any asset price bubble.
Politzer, P, Reimers, JR, Murray, JS & Toro-Labbe, A 2010, 'Reaction Force and Its Link to Diabatic Analysis: A Unifying Approach to Analyzing Chemical Reactions', JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 1, no. 19, pp. 2858-2862.
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The reaction force F(R) and the reaction force constant κ(R) provide a rigorously based approach to characterizing a chemical process. The energies associated with its different stages are presented and discussed for a number of examples. Analysis of these suggests an alternative, modified expression for the Hammond-Leffler postulate. We show that diabatic analysis leads to a description of the process that is qualitatively very similar to that coming from F(R) and κ(R), quantitatively so for proton-transfer reactions. Reaction force analysis provides a unifying framework that can encompass a variety of independent concepts relating to chemical processes. © 2010 American Chemical Society.
Pollett, PK, Dooley, AH & Ross, JV 2010, 'Modelling population processes with random initial conditions', MATHEMATICAL BIOSCIENCES, vol. 223, no. 2, pp. 142-150.
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Pongrácz, P, Petőcz, G, Shaw, M, Williams, DBG & Kollár, L 2010, 'Platinum complexes of 2-diphenylphosphinobenzaldehyde-derived P-alkene ligands and their application in the hydroformylation of styrene', Journal of Organometallic Chemistry, vol. 695, no. 22, pp. 2381-2384.
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Poulton, CG, McPhedran, RC, Movchan, NV & Movchan, AB 2010, 'Convergence properties and flat bands in platonic crystal band structures using the multipole formulation', Waves in Random and Complex Media, vol. 20, no. 4, pp. 702-716.
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We present converged band diagrams for Bloch-Floquet bending waves in a thin elastic plate containing a square array of circular perforations, using the multipole formulation developed by Movchan et al. (2007) and applied in the situation where the perforations are no longer considered to be small in comparison with the lattice pitch. We give tables of converged frequencies and the number of multipoles necessary to achieve them, for a range of radii of the perforations for both clamped-edge and free-edge boundary conditions. We find that the larger filling fraction leads to extremely flat bands within the band structure; this can be explained by considering the energy of the vibrational modes. We derive the energy balance relation as well as convenient expressions for the group velocity of eigenmodes, which reveal the interplay between the Helmholtz and the modified Helmholtz components of the eigenfield. © 2010 Taylor & Francis.
Powell, DA, Lapine, M, Gorkunov, MV, Shadrivov, IV & Kivshar, YS 2010, 'Metamaterial tuning by manipulation of near-field interaction', Physical Review B, vol. 82, no. 15.
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Powter, DM, Gladstone, W & Platell, M 2010, 'The influence of sex and maturity on the diet, mouth morphology and dentition of the Port Jackson shark, Heterodontus portusjacksoni', MARINE AND FRESHWATER RESEARCH, vol. 61, no. 1, pp. 74-85.
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Dietary studies are essential for an understanding of elasmobranch ecology and their role in marine ecosystems. The diet, head morphology and dentition of Heterodontus portusjacksoni, an abundant, epibenthic shark in the coastal waters of temperate eastern Australia, were examined in 20042005. The stomach contents of the juvenile, subadult and adult stages of 136 males and 100 females were examined. Diets were broad (32 prey taxa), but dominated by molluscs, teleosts and cephalopods. Analyses of stomach contents data demonstrated that diet differed significantly by ontogenetic stage, but not by sex. Juveniles and subadults consumed mainly benthic infauna and epifauna, with subadults ingesting greater amounts of diogenid crustaceans, and adult diets dominated by demersal/pelagic prey. Trophic level differed ontogenetically, from secondary consumers as juveniles and subadults to tertiary consumers as adults. The mainly tricuspidate juvenile dentition changed with maturity to a greater proportion of large molariform distal teeth, whereas the snout and jaw lengthened and broadened. Adult males retained a greater proportion of anterior S-family teeth than females, which was most likely related to copulation. The ontogenetic variation in dietary composition, facilitated by differences in dentition and mouth morphology, demonstrated that dietary resources were partitioned ontogenetically.
Puntharod, R, Webster, GT, Asghari-Khiavi, M, Bambery, KR, Safinejad, F, Rivadehi, S, Langford, SJ, Haller, KJ & Wood, BR 2010, 'Supramolecular Interactions Playing an Integral Role in the Near-Infrared Raman “Excitonic” Enhancement Observed in β-Hematin (Malaria Pigment) and Other Related Heme Derivatives', The Journal of Physical Chemistry B, vol. 114, no. 37, pp. 12104-12115.
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R. Trenholme, K, L. Brown, C, S. Skinner-Adams, T, Stack, C, Lowther, J, To, J, W. Robinson, M, M. Donnelly, S, P. Dalton, J & L. Gardiner, D 2010, 'Aminopeptidases of Malaria Parasites: New Targets for Chemotherapy', Infectious Disorders - Drug Targets, vol. 10, no. 3, pp. 217-225.
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Novel targets for new drug development are urgently required to combat malaria, a disease that puts half of the world's population at risk. One group of enzymes identified within the genome of the most lethal of the causative agents of malaria, Plasmodium falciparum, that may have the potential to become new targets for antimalarial drug development are the aminopeptidases. These enzymes catalyse the cleavage of the N-terminal amino acids from proteins and peptides. P. falciparum appears to encode for at least nine aminopeptidases, two neutral aminopeptidases, one aspartyl aminopeptidase, one aminopeptidase P, one prolyl aminopeptidase and four methionine aminopeptidases. Recent advances in our understanding of these genes and their protein products are outlined in this review, including their potential for antimalarial drug development. © 2010 Bentham Science Publishers Ltd.
Ragni, M, Airs, RL, Hennige, SJ, Suggett, DJ, Warner, ME & Geider, RJ 2010, 'PSII photoinhibition and photorepair in Symbiodinium (Pyrrhophyta) differs between thermally tolerant and sensitive phylotypes', Marine Ecology Progress Series, vol. 406, pp. 57-70.
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Cnidarians containing symbiotic microalgae often inhabit highly variable light environments where successful growth requires that, during transient (potentially stressful) periods of high light (HL), the microalgal cells invest energy in photoprotection to minimise photodamage, or allow for photodamage to occur and invest in photorepair; however, the relative contribution of photoprotection and photorepair remains uncharacterised. Here we determined the light dependence of Photosystem II (PSII) photoinhibition and photorepair in 2 phylotypes of Symbiodinium displaying different susceptibilities to thermal stress. Upon exposure to photon flux densities (PFDs) >500 μmol photons m-2 s-1 the thermally 'sensitive' Strain A1.1 displayed higher net photoinhibition, measured as a decrease in maximum PSII efficiency (Fv/Fm), than the thermally 'tolerant' Strain A1. In contrast, gross photoinhibition, assessed as the decline of Fv/F m in the presence of an inhibitor of D1 protein synthesis, was similar in the 2 strains. Therefore, photorepair was considered to be the key mechanism minimising net photoinhibition in Strain A1. Consistent with this conclusion, the 2 strains displayed similar capacities for other mechanisms of avoiding photodamage, specifically, photochemical (qP) and non-photochemical (NPQ) excitation energy quenching. Measurements on Strain A1 grown under 2 PFDs (100 and 650 μmol photons m-2 s-1) revealed that photoacclimation to HL involved the upregulation of qP, which minimised gross photoinhibition by maintaining PSII in a more oxidised state. We conclude that both interspecific (e.g. phylotype diversity) and intraspecific (e.g. photoacclimation state) factors affect the susceptibility of Symbiodinium to light stress. © Inter-Research 2010.
Raina, J-B, Dinsdale, EA, Willis, BL & Bourne, DG 2010, 'Do the organic sulfur compounds DMSP and DMS drive coral microbial associations?', Trends in Microbiology, vol. 18, no. 3, pp. 101-108.
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Dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) are key compounds in the global sulfur cycle. Moreover, DMS is particularly important in climate regulation owing to its role in cloud formation. Reef building corals are major contributors to the production of these two compounds and also form diverse and complex associations with bacteria, which are known to play a crucial role in the degradation of DMSP and DMS. Here, we highlight an extensive overlap between bacterial species implicated in DMSP/DMS degradation and those associated with corals, leading to the hypothesis that these two compounds play a major role in structuring coral-associated bacterial communities, with important consequences for coral health and the resilience of coral reefs. We also explore the publically available metagenome databases and show that genes implicated in DMSP metabolism are abundant in the viral component of coral-reef-derived metagenomes, indicating that viruses can act as a reservoir for such genes.
Rajia, S, Chen, H & Morris, MJ 2010, 'Maternal Overnutrition Impacts Offspring Adiposity and Brain Appetite Markers‐Modulation by Postweaning Diet', Journal of Neuroendocrinology, vol. 22, no. 8, pp. 905-914.
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Maternal obesity has long‐term consequences for the development of hypothalamic neurones involved in energy homeostasis and the metabolic profile in offspring. In the present study, we compared the effects of maternal obesity induced by longstanding high‐fat diet (HFD) with milder postnatal overfeeding during suckling induced by litter size reduction. Female Sprague–Dawley rats consumed chow (C) or HFD. On postnatal day 1, litters from chow dams were adjusted to three per dam (small litter, CS) versus 12 control (normal litter, CN). Litters from HFD dams were adjusted to 12 per dam and fed HFD after weaning to induce obesity (HN). Thus, two degrees of maternal overnutrition were produced (CS and HN). To test whether postweaning diet can amplify the effects of maternal obesity, male offspring weaned onto chow or HFD were followed to 21 weeks. Maternal postnatal overnutrition (CS) and HFD‐induced maternal obesity (HN) increased body weight and fat mass in offspring compared to those from control dams (CN). Significant glucose intolerance was induced by both degrees of maternal overnutrition, but only in offspring consuming HFD. HFD‐induced maternal obesity (HN) was linked to increased offspring leptin, insulin, lipids, insulin resistance and hyperphagia, and was exaggerated by postweaning HFD. No effect of maternal postnatal overnutrition (CS) was seen on these parameters. Hypothalamic signal transducer and activator of transcription‐3 and suppressor of cytokine signalling‐3 mRNA were significantly elevated by maternal HFD (HN) in the HFD‐fed offspring. The data obtained suggest that even mild maternal overnutrition (CS) led to increased adiposity, glucose intolerance and altered brain appetite regulators in offspring. A greater impact of HFD‐induced maternal obesity was evident. Marked additive effects were observed when animals consumed a HFD postweaning.
Ranjbartoreh, AR & Wang, G 2010, 'Consideration of mechanical properties of single-walled carbon nanotubes under various loading conditions', Journal of Nanoparticle Research, vol. 12, no. 2, pp. 537-543.
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In this article, mechanical properties of single-walled carbon nanotubes (SWCNTs) with various radiuses under tensile, compressive and lateral loads are considered. Stress-strain curve, elastic modulus, tensile, compressive and rotational stiffness, buckling behaviour, and critical axial compressive load and pressure of eight different zigzag and armchair SWCNTs are investigated to figure out the effect of radius and chirality on mechanical properties of nanotubes. Using molecular dynamic simulation (MDS) method, it can be explained that SWCNTs have higher Young's modulus and tensile stiffness than compressive elastic modulus and compressive stiffness. Critical axial force of zigzag SWCNT is independent from the radius, but that of armchair type rises by increasing of radius, also these two types show different buckling modes. © Springer Science+Business Media B.V. 2009.
Rawling, T, Austin, CE, Zareie, HM & McDonagh, AM 2010, 'Thin films of a dimeric ruthenium phthalocyanine complex on gold', INORGANIC CHEMISTRY COMMUNICATIONS, vol. 13, no. 1, pp. 208-210.
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Thin films of a new dimeric ruthenium phthalocyanine complex bearing a thioester-functionalized axial ligand were formed on gold surfaces. Characterization of the thin films by laser ablation-inductively coupled-mass spectrometry and scanning tunneling microscopy revealed that the films do not have any long-range order. © 2009 Elsevier B.V. All rights reserved.
Rawson, CA, Lim, RP, Tremblay, LA, Warne, MSJ, Ying, G-G, Laginestra, E & Chapman, JC 2010, 'Benthic macroinvertebrate assemblages in remediated wetlands around Sydney, Australia', ECOTOXICOLOGY, vol. 19, no. 8, pp. 1589-1600.
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To investigate potential high organisational level impacts of persistent organic pollution in the wetlands in the Sydney Olympic Park (SOP) remediated site, the benthic macroinvertebrate assemblages of seven wetlands within SOP and two off-site reference wetlands were examined. Sediment cores were collected, stained and preserved from each study site and the macroinvertebrates identified to the appropriate taxonomic level (Class, Order, Family, Subfamily). Data were analysed for taxon richness and macroinvertebrate abundance and multivariate techniques were used to identify chemical/physical characteristics of the sediment, which were important influences on the differences in the assemblage between study sites. Macroinvertebrate abundance was highly variable between study sites and taxon richness was low across all sites. Oligochaetes, nematodes, ostracods and chironomids were the most common taxa found and were the most important in influencing differences between the macroinvertebrate assemblages among the study sites. Sediment grain size and chemical characteristics of the sediments (RPAH, RPCB, TCDDeq and heavy metal concentrations) were important in separating the study sites based on taxon richness and abundance. Canonical correspondence analysis separated the macroinvertebrate assemblages at newly two created wetlands from those at other study sites including the urban reference sites. Increased sediment POP contamination (particularly as measured TCDDeq and RDDT concentrations) is a likely contributor in excluding pollution sensitive taxa and, therefore, alterations to benthic macroinvertebrate assemblages. Further, the influence of TOC suggests the significance of catchment inputs in contributing to changes in macroinvertebrate assemblage. The SOP remediation led to the establishment of wetlands with benthic communities representative of those expected in urban wetlands. © Springer Science+Business Media, LLC 2010.
Raymond, JJ, van Oorschot, RA, Walsh, SJ, Gunn, PR & Roux, C 2010, 'A criminalistic approach to biological evidence: Trace DNA and volume crime', Science & Justice, vol. 50, no. 1, pp. 46-46.
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Reim, KF, Nunn, J, Lorenz, VO, Sussman, BJ, Lee, KC, Langford, NK, Jaksch, D & Walmsley, IA 2010, 'Towards high-speed optical quantum memories', Nature Photonics, vol. 4, no. 4, pp. 218-221.
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Reimers, JR, Wang, Y, Cankurtaran, BO & Ford, MJ 2010, 'Chemical Analysis of the Superatom Model for Sulfur-Stabilized Gold Nanoparticles', JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 132, no. 24, pp. 8378-8384.
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The superatom model for nanoparticle structure is shown to be inadequate for the prediction of the thermodynamic stability of gold nanoparticles. The observed large HOMO-LUMO gaps for stable nanoparticles predicted by this model are, for sulfur-stabilized gold nanoparticles, attributed to covalent interactions of the metal with thiyl adsorbate radicals rather than ionic interactions with thiolate adsorbate ions, as is commonly presumed. In particular, gold adatoms in the stabilizing layer are shown to be of Au(0) nature, subtle but significantly different from the atoms of the gold core owing to the variations in the proportion of gold-gold and gold-sulfur links that form. These interactions explain the success of the superatom model in describing the electronic structure of both known and informatory nanoparticle compositions. Nanoparticle reaction energies are, however, found not to correlate with the completion of superatom shells. Instead, local structural effects are found to dominate the chemistry and in particular the significanctly different chemical properties of gold nanoparticle and bulk surfaces. These conclusions are drawn from density-functional-theory calculations for the Au102(p-mercaptobenzoic acid)44 nanoparticle based on the X-ray structure (Jadzinsky, P. D.; et al. Science 2007, 318, 430), as well calculations for the related Au102(S*-CH 3)44 nanoparticle, for the inner gold-cluster cores, for partially and overly reacted cores, and for Au(111) surface adsorbates. © 2010 American Chemical Society.
Ren, D, Fu, R, Karoly, D, Leslie, L, Chen, J & Wilson, C 2010, 'A new ice sheet model validated by remote sensing of the Greenland ice sheet', Open Geosciences, vol. 2, no. 4, pp. 501-513.
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AbstractAccurate prediction of future sea level rise requires models that accurately reproduce and explain the recent observed dramatic ice sheet behaviours. This study presents a new multi-phase, multiple-rheology, scalable and extensible geofluid model of the Greenland ice sheet that shows the credential of successfully reproducing the mass loss rate derived from the Gravity Recovery and Climate Experiment (GRACE), and the microwave remote sensed surface melt area over the past decade. Model simulated early 21st century surface ice flow compares satisfactorily with InSAR measurements. Accurate simulation of the three metrics simultaneously cannot be explained by fortunate model tuning and give us confidence in using this modelling system for projection of the future fate of Greenland Ice Sheet (GrIS). Based on this fully adaptable three dimensional, thermo-mechanically coupled prognostic ice model, we examined the flow sensitivity to granular basal sliding, and further identified that this leads to a positive feedback contributing to enhanced mass loss in a future warming climate. The rheological properties of ice depend sensitively on its temperature, thus we further verified modelâŹs temperature solver against in situ observations. Driven by the NCEP/NCAR reanalysis atmospheric parameters, the ice model simulated GrIS mass loss rate compares favourably with that derived from the GRACE measurements, or about −147 km3/yr over the 2002–2008 period. Increase of the summer maximum melt area extent (SME) is indicative of expansion of the ablation zone. The modeled SME from year 1979 to 2006 compares well with the cross-polarized gradient ratio method (XPGR) observed melt area in terms of annual variabilities. A high correlation of 0.88 is found between the two time series. In the 30-year model simulation series, the surface melt exhibited large inter-annual and decadal variability, years 2002, 2005 and 2007 being three sig...
Ren, D, Leslie, LM, Fu, R, Dickinson, RE & Xin, X 2010, 'A Storm-Triggered Landslide Monitoring and Prediction System: Formulation and Case Study', Earth Interactions, vol. 14, no. 12, pp. 1-24.
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Abstract Predicting the location and timing of mudslides with adequate lead time is a scientifically challenging problem that is critical for mitigating landslide impacts. Here, a new dynamic modeling system is described for monitoring and predicting storm-triggered landslides and their ecosystem implications. The model ingests both conventional and remotely sensed topographic and geologic data, whereas outputs include diagnostics required for the assessment of the physical and societal impacts of landslides. The system first was evaluated successfully in a series of experiments under idealized conditions. In the main study, under real conditions, the system was assessed over a mountainous region of China, the Yangjiashan Creeping (YC) slope. For this data-rich section of the Changjiang River, the model estimated creeping rates that had RMS errors of ∼0.5 mm yr−1 when compared with a dataset generated from borehole measurements. A prediction of the creeping curve for 2010 was made that suggested significant slope movement will occur in the next 5 years, without any change in the current precipitation morphology. However, sliding will become imminent if a storm occurs in that 5-yr period that produces over 150 mm of precipitation. A sensitivity experiment shows that the identified location fails first, triggering domino-effect slides that progress upslope. This system for predicting storm-triggered landslides is intended to improve upon present warning lead times to minimize the impacts of shallow, fast moving, and therefore hazardous landslides.
Ribaux, O, Baylon, A, Lock, E, Delemont, O, Roux, C, Zingg, C & Margot, P 2010, 'Intelligence-led crime scene processing. Part II: Intelligence and crime scene examination', FORENSIC SCIENCE INTERNATIONAL, vol. 199, no. 1-3, pp. 63-71.
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A better integration of the information conveyed by traces within intelligence-led framework would allow forensic science to participate more intensively to security assessments through forensic intelligence (part I). In this view, the collection of data by examining crime scenes is an entire part of intelligence processes. This conception frames our proposal for a model that promotes to better use knowledge available in the organisation for driving and supporting crime scene examination. The suggested model also clarifies the uncomfortable situation of crime scene examiners who must simultaneously comply with justice needs and expectations, and serve organisations that are mostly driven by broader security objectives. It also opens new perspective for forensic science and crime scene investigation, by the proposal to follow other directions than the traditional path suggested by dominant movements in these fields. © 2010 Elsevier Ireland Ltd.
Ribaux, O, Baylon, A, Roux, C, Delemont, O, Lock, E, Zingg, C & Margot, P 2010, 'Intelligence-led crime scene processing. Part I: Forensic intelligence', FORENSIC SCIENCE INTERNATIONAL, vol. 195, no. 1-3, pp. 10-16.
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Forensic science is generally defined as the application of science to address questions related to the law. Too often, this view restricts the contribution of science to one single process which eventually aims at bringing individuals to court while minimising risk of miscarriage of justice. In order to go beyond this paradigm, we propose to refocus the attention towards traces themselves, as remnants of a criminal activity, and their information content. We postulate that traces contribute effectively to a wide variety of other informational processes that support decision making in many situations. In particular, they inform actors of new policing strategies who place the treatment of information and intelligence at the centre of their systems. This contribution of forensic science to these security oriented models is still not well identified and captured. In order to create the best condition for the development of forensic intelligence, we suggest a framework that connects forensic science to intelligence-led policing (part I). Crime scene attendance and processing can be envisaged within this view. This approach gives indications about how to structure knowledge used by crime scene examiners in their effective practice (part II).
Riglar, D, Richard, D, Boyle, M, Wilson, D, Angrisano, F, Turnbull, L, Whitchurch, C, Cowman, A, Beeson, J, Ralph, S & Baum, J 2010, 'Stepwise dissection of Plasmodium falciparum merozoite invasion of the human erythrocyte', Malaria Journal, vol. 9, no. S2.
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Robertson, J & Roux, C 2010, 'Trace evidence: Here today, gone tomorrow?', Science & Justice, vol. 50, no. 1, pp. 18-22.
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The recent report of the National Research Council of the US National Academies Strengthening Forensic Science in the United States: a Path Forward found evidence that the level of scientific development and evaluation varies substantially among the forensic science disciplines. In this paper the status of trace evidence will be reviewed from an international perspective with particular reference to case studies. The paper will argue that the trace evidence discipline needs to learn from past experience and that serious coordinated action is required at an international level if trace evidence is to continue to meet the standards expected of forensic science in the future. The paper concludes that it is vital that trace evidence remains a key component of forensic investigation due to its important role in addressing the `what happened question.
Robertson, J, Metz, H, Scudder, N & Hodgson, V 2010, 'A Quality System Review: Australian Federal Police Forensic and Data Centres', Forensic Science Policy & Management: An International Journal, vol. 1, no. 4, pp. 209-213.
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Robinson, A, Brzoska, AJ, Turner, KM, Withers, R, Harry, EJ, Lewis, PJ & Dixon, NE 2010, 'Essential Biological Processes of an Emerging Pathogen: DNA Replication, Transcription, and Cell Division in Acinetobacter spp', Microbiology and Molecular Biology Reviews, vol. 74, no. 2, pp. 273-297.
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SUMMARY Within the last 15 years, members of the bacterial genus Acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. The driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. There is an urgent need for new antibacterial compounds to combat the threat imposed by Acinetobacter spp. and other intractable bacterial pathogens. The essential processes of chromosomal DNA replication, transcription, and cell division are attractive targets for the rational design of antimicrobial drugs. The goal of this review is to examine the wealth of genome sequence and gene knockout data now available for Acinetobacter spp., highlighting those aspects of essential systems that are most suitable as drug targets. Acinetobacter spp. show several key differences from other pathogenic gammaproteobacteria, particularly in global stress response pathways. The involvement of these pathways in short- and long-term antibiotic survival suggests that Acinetobacter spp. cope with antibiotic-induced stress differently from other microorganisms.
Robinson, MW, Hutchinson, AT, Dalton, JP & Donnelly, S 2010, 'Peroxiredoxin: a central player in immune modulation', PARASITE IMMUNOLOGY, vol. 32, no. 5, pp. 305-313.
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Peroxiredoxins (Prx) are a family of anti-oxidants that protect cells from metabolically produced reactive oxygen species (ROS). The presence of these enzymes in the secretomes of many parasitic helminths suggests they provide protection against ROS released by host immune effector cells. However, we recently reported that helminth-secreted Prx also contribute to the development of Th2-responses via a mechanism involving the induction of alternatively activated macrophages. In this review, we discuss the role helminth Prx may play in modulating the immune responses of their hosts. © 2010 Blackwell Publishing Ltd.
Robinson, MW, Hutchinson, AT, Donnelly, S & Dalton, JP 2010, 'Worm secretory molecules are causing alarm', TRENDS IN PARASITOLOGY, vol. 26, no. 8, pp. 371-372.
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Damage-associated molecular pattern molecules (DAMPs) are endogenous leaderless molecules that are released into the extracellular environment in response to tissue damage. Most DAMPs have recognised intracellular housekeeping functions and are traditionally regarded as cytosolic or nuclear proteins (Table 1). They activate inflammatory responses by interacting with pattern recognition receptors (PRRs) expressed by immune cells and thus set off an `alarm system, the outcome of which depends on the collection of DAMPs released by the damaged or infected tissue. Although the collection of DAMPs vary considerably depending on the type of tissue involved, these often lead to a wound-healing scenario in response to tissue damage [1]. Besides being released passively by necrotic or damaged cells, it is also known that many DAMPS exit the cell via non-classical secretory pathways
Rong, Y, Jin, D, Hou, C, Hu, J, Wu, W, Ni, X, Wang, D & Lou, W 2010, 'Proteomics analysis of serum protein profiling in pancreatic cancer patients by DIGE: up-regulation of mannose-binding lectin 2 and myosin light chain kinase 2', BMC Gastroenterology, vol. 10, no. 1.
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Abstract Background Pancreatic cancer has significant morbidity and mortality worldwide. Good prognosis relies on an early diagnosis. The purpose of this study was to develop techniques for identifying cancer biomarkers in the serum of patients with pancreatic cancer. Methods Serum samples from five individuals with pancreatic cancer and five individuals without cancer were compared. Highly abundant serum proteins were depleted by immuno-affinity column. Differential protein analysis was performed using 2-dimensional differential in-gel electrophoresis (2D-DIGE). Results Among these protein spots, we found that 16 protein spots were differently expressed between the two mixtures; 8 of these were up-regulated and 8 were down-regulated in cancer. Mass spectrometry and database searching allowed the identification of the proteins corresponding to the gel spots. Up-regulation of mannose-binding lectin 2 and myosin light chain kinase 2, which have not previously been implicated in pancreatic cancer, were observed. In an independent series of serum samples from 16 patients with pancreatic cancer and 16 non-cancer-bearing controls, increased levels of mannose-binding lectin 2 and myosin light chain kinase 2 were confirmed by western blot. Conclusions These results suggest that affinity column enrichment and DIGE can be used to identify proteins differentially expressed in serum from pancreatic cancer patients. These two proteins 'mannose-binding lectin 2 and myosin light chain kinase 2' might be potential biomarkers for the diagnosis of t...
Rong, Y, Wang, D, Lou, W, Kuang, T & Jin, D 2010, 'Granulocytic sarcoma of the pancreas: A case report and review of the literatures', BMC Gastroenterology, vol. 10, no. 1.
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Abstract Background Granulocytic sarcoma (GS) is a form of acute myeloid leukemia (AML), also known as extramedullary myeloid tumor or chloroma. It forms a solid malignant tumor consisting of myelocytes or granulocytes and is typically located in bone while occurrence in other parts of the body is rare. Case presentation We reported a 40-year-old male patient who had jaundice, highly elevated bilirubin, and a mass highly suspicious of pancreatic head carcinoma. We performed surgery and the pathology and immunohistochemistry suggested GS; however the blood test and the bone marrow infiltration showed no evidence of AML. In our review of the published reports of GS, we only found six reports of the GS in the pancreas, and we suggested that immunohistochemical staining should be used to accurately differentiate GS from other pancreatic cancer and other types of leukemia. Conclusions The accurate diagnosis of GS is necessary for determining prognosis and deciding appropriate therapy.
Rosic, NN, Pernice, M, Dunn, S, Dove, S & Hoegh-Guldberg, O 2010, 'Differential Regulation by Heat Stress of Novel Cytochrome P450 Genes from the Dinoflagellate Symbionts of Reef-Building Corals', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 76, no. 9, pp. 2823-2829.
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Exposure to heat stress has been recognized as one of the major factors leading to the breakdown of the coral-alga symbiosis and coral bleaching. Here, we describe the presence of three new cytochrome P450 (CYP) genes from the reef-building coral endosymbiont Symbiodinium (type C3) and changes in their expression during exposure to severe and moderate heat stress conditions. Sequence analysis of the CYP C-terminal region and two conserved domains, the 'PERF' and 'heme-binding' domains, confirmed the separate identities of the CYP genes analyzed. In order to explore the effects of different heat stress scenarios, samples of the scleractinian coral Acropora millepora were exposed to elevated temperatures incrementally over an 18-h period (rapid thermal stress) and over a 120-h period (gradual thermal stress). After 18 h of gradual heating and incubation at 26°C, the Symbiodinium CYP mRNA pool was approximately 30% larger, while a further 6°C increase to a temperature above the average sea temperature (29°C after 72 h) resulted in a 2- to 4-fold increase in CYP expression. Both rapid heat stress and gradual heat stress at 32°C resulted in 50% to 90% decreases in CYP gene transcript abundance. Consequently, the initial upregulation of expression of CYP genes at moderately elevated temperatures (26°C and 29°C) was followed by a decrease in expression under the greater thermal stress conditions at 32°C. These findings indicate that in the coral-alga symbiosis under heat stress conditions there is production of chemical stressors and/or transcriptional factors that regulate the expression of genes, such as the genes encoding cytochrome P450 monooxygenases, that are involved in the first line of an organism's chemical defense. Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Samworth, RJ & Wand, MP 2010, 'Asymptotics and optimal bandwidth selection for highest density region estimation', Annals of Statistics, vol. 38, no. 3, pp. 1767-1792.
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We study kernel estimation of highest-density regions (HDR). Our maincontributions are two-fold. First, we derive a uniform-in-bandwidth asymptoticapproximation to a risk that is appropriate for HDR estimation. Thisapproximation is then used to derive a bandwidth selection rule for HDRestimation possessing attractive asymptotic properties. We also present theresults of numerical studies that illustrate the benefits of our theory andmethodology.
Sánchez, C, Gates, AJ, Meakin, GE, Uchiumi, T, Girard, L, Richardson, DJ, Bedmar, EJ & Delgado, MJ 2010, 'Production of Nitric Oxide and Nitrosylleghemoglobin Complexes in Soybean Nodules in Response to Flooding', Molecular Plant-Microbe Interactions®, vol. 23, no. 5, pp. 702-711.
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Nitric oxide (NO) has gained interest as a major signaling molecule during plant development and in response to environmental cues. Formation of NO during symbiotic interactions has been reported, but the role and sources of NO in nodules remain unclear. In this work, the involvement of denitrification, performed by the symbiont Bradyrhizobium japonicum, in NO formation in soybean nodules in response to flooding conditions has been investigated by inoculating plants with napA-, nirK-, or norC-deficient mutants. Levels of nitrosylleghemoglobin (LbNO) in flooded nirK and norC nodules were significantly higher than those observed in wild-type nodules. In addition, nirK and norC nodules accumulated more nitrite and NO, respectively, than wild-type nodules. By contrast, levels of LbNO, nitrite, and NO in flooded napA nodules were lower than in wild-type nodules. These results suggest that LbNO formation in soybean nodules in response to flooding conditions is caused by nitrite and NO generated from periplasmic nitrate reductase (Nap) and also containing nitrite reductase (NirK) denitrification enzymes. Flooding caused a decrease of nifH expression and nitrogenase activity in wild-type and norC nodules but not in napA or nirK nodules. Incubation of wild-type and norC nodules with a NO scavenger counteracted the effect of flooding. Under free-living conditions, β-galactosidase activity from a nifD′-′lacZ fusion decreased in a norC mutant, which also accumulated NO in the medium. These results suggest that NO formed by Cu-containing nitrite reductase in soybean nodules in response to flooding has a negative effect on expression of nitrogenase. We propose that Lb has a major role in detoxifying NO and nitrite produced by bacteroidal denitrification in response to flooding conditions.
Sastraruji, K, Sastraruji, T, Pyne, SG, Ung, AT, Jatisatienr, A & Lie, W 2010, 'Semisynthesis and Acetylcholinesterase Inhibitory Activity of Stemofoline Alkaloids and Analogues', JOURNAL OF NATURAL PRODUCTS, vol. 73, no. 5, pp. 935-941.
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Semisynthesis of the known Stemona alkaloids oxystemofoline (7) and methoxystemofoline (8) has been achieved starting from (11Z)-1â²,2â²-didehydrostemofoline (6), which confirmed their structures and absolute configurations. The synthesis of (1â²R)-...
Scott, NE, Marzook, NB, Deutscher, A, Falconer, L, Crossett, B, Djordjevic, SP & Cordwell, SJ 2010, 'Mass spectrometric characterization of theCampylobacter jejuniadherence factor CadF reveals post-translational processing that removes immunogenicity while retaining fibronectin binding', PROTEOMICS, vol. 10, no. 2, pp. 277-288.
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Campylobacter jejuni is a major gastrointestinal pathogen that colonizes host mucosa via interactions with extracellular matrix proteins, such as fibronectin (Fn). Fn-binding is mediated by a 37kDa outer membrane protein termed Campylobacter adherence Factor (CadF). The outer membrane protein profile of a recent gastrointestinal C. jejuni clinical isolate (JHH1) was analysed using 2-DE and MS. Several spots were identified as products of the cadF gene. These included mass and pI variants of 34 and 30 kDa, as well as 24 kDa (CadF24) and 22kDa (CadF22) mass variants. CadF variants were fully characterized by MALDI-TOF MS and MALDI-MS/MS. These data confirmed that CadF forms re-folding variants resulting in spots with lower mass and varying pI that are identical at the amino acid sequence level and are not modified posttranslationally. CadF22 and CadF24, however, were characterized as N-terminal, membrane-associated polypeptides resulting from cleavage between serine195 and leucine196, and glycine201 and phenylalanine202, respectively. These variants were more abundant in the virulent (O) isolate of C. jejuni NCTC11168 when compared with the avirulent (genome sequenced) isolate. Hexahistidine fusion constructs of full-length CadF (34 kDa), CadF24, and the deleted C-terminal OmpA domain (14 kDa; CadF14) were created in Escherichia coli. Recombinant CadF variants were probed against patient sera and revealed that only full-length CadF retained reactivity. Binding assays showed that CadF24 retained Fn-binding capability, while CadF14 did not bind Fn. These data suggest that the immunogenic epitope of CadF is cleaved to generate smaller Fnbinding polypeptides, which are not recognized by the host humoral response. CadF cleavage therefore may be associated with virulence in C. jejuni. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.
Sedger, LM, Katewa, A, Pettersen, AK, Osvath, SR, Farrell, GC, Stewart, GJ, Bendall, LJ & Alexander, SI 2010, 'Extreme lymphoproliferative disease and fatal autoimmune thrombocytopenia in FasL and TRAIL double-deficient mice', Blood, vol. 115, no. 16, pp. 3258-3268.
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AbstractTo delineate the relative roles of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and Fas ligand in lymphocyte biology and lymphoproliferative disease, we generated mice defective in both molecules. B6.GT mice develop severe polyclonal lymphoproliferative disease because of accumulating CD3+CD4−CD8−B220+ T cells, CD4+ and CD8+ T cells, and follicular B cells, and mice die prematurely from extreme lymphocytosis, thrombocytopenia, and hemorrhage. Accumulating lymphocytes resembled antigen-experienced lymphocytes, consistent with the maximal resistance of B6.GT CD4+ and CD8+ T cell to activation-induced cell death. More specifically, we show that TRAIL contributes to Fas ligand-mediated activation-induced cell death and controls lymphocyte apoptosis in the presence of interferon-γ once antigen stimulation is removed. Furthermore, dysregulated lymphocyte homeostasis results in the production of anti-DNA and rheumatoid factor autoantibodies, as well as antiplatelet IgM and IgG causing thrombocytopenia. Thus, B6.GT mice reveal new roles for TRAIL in lymphocyte homeostasis and autoimmune lymphoproliferative syndromes and are a model of spontaneous idiopathic thrombocytopenia purpura secondary to lymphoproliferative disease.
Seery, CR & Ralph, PJ 2010, 'Ecological relevance of a chlorophyllafluorescence ecotoxicological endpoint', Toxicological & Environmental Chemistry, vol. 92, no. 8, pp. 1529-1540.
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With the increasing use of new techniques to assess toxic stress and the effects of pollution, it is important to ensure that any 'new' endpoint employed is able to demonstrate a level of eco-relevance. Though recent application of chlorophyll a fluorescence parameters to macroalgal bioassays has been successful, a level of eco-relevance for such use has not been experimentally shown. As such, this article presents a series of experiments designed to establish a link between fluorescence parameters and higher-level effects (supra-individual level). The results show that fluorescence parameters are capable of predicting germination success of macroalgal gametes and can do so much sooner than the actual event of germination. Furthermore, a decline in ΔF/F′m is shown to be strongly associated with a reduced germination success. Thus, a level of eco-relevance has been established for the fluorescence endpoint that is at least equal to that of the widely accepted germination-based macroalgal bioassays. © Taylor & Francis.
Seuront, L, Leterme, SC, Seymour, JR, Mitchell, JG, Ashcroft, D, Noble, W, Thomson, PG, Davidson, AT, van den Enden, R, Scott, FJ, Wright, SW, Schapira, M, Chapperon, C & Cribb, N 2010, 'Role of microbial and phytoplanktonic communities in the control of seawater viscosity off East Antarctica (30-80 degrees E)', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 57, no. 9-10, pp. 877-886.
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Despite the long-standing belief that seawater viscosity is driven by temperature and salinity, biologically increased seawater viscosity has repeatedly been reported in relation to phytoplankton exudates in shallow, productive coastal waters. Here, seawater viscosity was investigated in relation to microbial and phytoplanktonic communities off the coast of East Antarctica along latitudinal transects located between 30°E and 80°E in sub-surface waters and at the deep chlorophyll maximum (DCM). The physical component of seawater viscosity observed along each transects ranged from 1.80 to 1.95 cP, while the actual seawater viscosity ranged from 1.85 to 3.69 cP. This resulted in biologically increased seawater viscosity reaching up to 84.9% in sub-surface waters and 77.6% at the DCM. Significant positive correlations were found between elevated seawater viscosity and (i) bacterial abundance in sub-surface waters and (ii) chlorophyll a concentration and the abundance of flow cytometrically-defined auto- and heterotrophic protists at the DCM. Among the 12 groups and 108 species of protists identified under light microscopy, dinoflagellates and more specifically Alexandrium tamarense and Prorocentrum sp. were the main contributors to the patterns observed for elevated seawater viscosity. Our observations, which generalised the link previously identified between seawater viscosity and phytoplankton composition and standing stock to the Southern Ocean, are the first demonstration of increases in seawater viscosity linked to marine bacterial communities, and suggest that the microbially-increased viscosity might quantitatively be at least as important as the one related to phytoplankton secretion. © 2009 Elsevier Ltd.
Seymour, JR, Ahmed, T, Durham, WM & Stocker, R 2010, 'Chemotactic response of marine bacteria to the extracellular products of Synechococcus and Prochlorococcus', AQUATIC MICROBIAL ECOLOGY, vol. 59, no. 2, pp. 161-168.
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The cyanobacterial genera Prochlorococcus and Synechococcus are key phototrophic organisms in the open ocean, and ecological interactions between these groups and heterotrophic bacteria have fundamental importance for marine carbon and nutrient cycling.
Seymour, JR, Simo, R, Ahmed, T & Stocker, R 2010, 'Chemoattraction to Dimethylsulfoniopropionate Throughout the Marine Microbial Food Web', SCIENCE, vol. 329, no. 5989, pp. 342-345.
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Phytoplankton-produced dimethylsulfoniopropionate (DMSP) provides underwater and atmospheric foraging cues for several species of marine invertebrates, fish, birds, and mammals. However, its role in the chemical ecology of marine planktonic microbes is Largely unknown, and there is evidence for contradictory functions. By using microfluidics and image analysis of swimming behavior, we observed attraction toward microscale pulses of DMSP and related compounds among several motile strains of phytoplankton, heterotrophic bacteria, and bacterivore and herbivore microzooplankton. Because microbial DMSP cycling is the main natural source of cloud-forming sulfur aerosols, our results highlight how adaptations to microscale chemical seascapes shape planktonic food webs, while potentially influencing climate at the global scale.
Seymour, LM, Deutscher, AT, Jenkins, C, Kuit, TA, Falconer, L, Minion, FC, Crossett, B, Padula, M, Dixon, NE, Djordjevic, SP & Walker, MJ 2010, 'A Processed Multidomain Mycoplasma hyopneumoniae Adhesin Binds Fibronectin, Plasminogen, and Swine Respiratory Cilia', Journal of Biological Chemistry, vol. 285, no. 44, pp. 33971-33978.
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Porcine enzootic pneumonia is a chronic respiratory disease that affects swine. The etiological agent of the disease, Mycoplasma hyopneumoniae, is a bacterium that adheres to cilia of the swine respiratory tract, resulting in loss of cilia and epithelial cell damage. A M. hyopneumoniae protein P116, encoded by mhp108, was investigated as a potential adhesin. Examination of P116 expression using proteomic analyses observed P116 as a full-length protein and also as fragments, ranging from 17 to 70 kDa in size. A variety of pathogenic bacterial species have been shown to bind the extracellular matrix component fibronectin as an adherence mechanism. M. hyopneumoniae cells were found to bind fibronectin in a dose-dependent and saturable manner. Surface plasmon resonance was used to show that a recombinant C-terminal domain of P116 bound fibronectin at physiologically relevant concentrations (KD 24 ± 6 nM). Plasmin(ogen)-binding proteins are also expressed by many bacterial pathogens, facilitating extracellular matrix degradation. M. hyopneumoniae cells were found to also bind plasminogen in a dose-dependent and saturable manner; the C-terminal domain of P116 binds to plasminogen (KD 44 ± 5 nM). Plasminogen binding was abolished when the C-terminal lysine of P116 was deleted, implicating this residue as part of the plasminogen binding site. P116 fragments adhere to the PK15 porcine kidney epithelial-like cell line and swine respiratory cilia. Collectively these data suggest that P116 is an important adhesin and virulence factor of M. hyopneumoniae. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.
Shafer, CM, Mercer, AE, Leslie, LM, Richman, MB & Doswell, CA 2010, 'Evaluation of WRF Model Simulations of Tornadic and Nontornadic Outbreaks Occurring in the Spring and Fall', Monthly Weather Review, vol. 138, no. 11, pp. 4098-4119.
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Abstract Recent studies, investigating the ability to use the Weather Research and Forecasting (WRF) model to distinguish tornado outbreaks from primarily nontornadic outbreaks when initialized with synoptic-scale data, have suggested that accurate discrimination of outbreak type is possible up to three days in advance of the outbreaks. However, these studies have focused on the most meteorologically significant events without regard to the season in which the outbreaks occurred. Because tornado outbreaks usually occur during the spring and fall seasons, whereas the primarily nontornadic outbreaks develop predominantly during the summer, the results of these studies may have been influenced by climatological conditions (e.g., reduced shear, in the mean, in the summer months), in addition to synoptic-scale processes. This study focuses on the impacts of choosing outbreaks of severe weather during the same time of year. Specifically, primarily nontornadic outbreaks that occurred during the summer have been replaced with outbreaks that do not occur in the summer. Subjective and objective analyses of the outbreak simulations indicate that the WRF’s capability of distinguishing outbreak type correctly is reduced when the seasonal constraints are included. However, accuracy scores exceeding 0.7 and skill scores exceeding 0.5 using 1-day simulation fields of individual meteorological parameters, show that precursor synoptic-scale processes play an important role in the occurrence or absence of tornadoes in severe weather outbreaks. Low-level storm-relative helicity parameters and synoptic parameters, such as geopotential heights and mean sea level pressure, appear to be most helpful in distinguishing outbreak type, whereas thermodynamic instability parameters are noticeably both less accurate and less skillful.
Siboni, N, Rasoulouniriana, D, Ben-Dov, E, Kramarsky-Winter, E, Sivan, A, Loya, Y, Hoegh-Guldberg, O & Kushmaro, A 2010, 'Stramenopile Microorganisms Associated with the Massive Coral Favia sp.', JOURNAL OF EUKARYOTIC MICROBIOLOGY, vol. 57, no. 3, pp. 236-244.
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Siegle, JS, Hansbro, N, Herbert, C, Rosenberg, HF, Domachowske, JB, Asquith, KL, Foster, PS & Kumar, RK 2010, 'Early-life viral infection and allergen exposure interact to induce an asthmatic phenotype in mice', Respiratory Research, vol. 11, no. 1.
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Background: Early-life respiratory viral infections, notably with respiratory syncytial virus (RSV), increase the risk of subsequent development of childhood asthma. The purpose of this study was to assess whether early-life infection with a species-specific model of RSV and subsequent allergen exposure predisposed to the development of features of asthma.Methods: We employed a unique combination of animal models in which BALB/c mice were neonatally infected with pneumonia virus of mice (PVM, which replicates severe RSV disease in human infants) and following recovery, were intranasally sensitised with ovalbumin. Animals received low-level challenge with aerosolised antigen for 4 weeks to elicit changes of chronic asthma, followed by a single moderate-level challenge to induce an exacerbation of inflammation. We then assessed airway inflammation, epithelial changes characteristic of remodelling, airway hyperresponsiveness (AHR) and host immunological responses.Results: Allergic airway inflammation, including recruitment of eosinophils, was prominent only in animals that had recovered from neonatal infection with PVM and then been sensitised and chronically challenged with antigen. Furthermore, only these mice exhibited an augmented Th2-biased immune response, including elevated serum levels of anti-ovalbumin IgE and IgG1 as well as increased relative expression of Th2-associated cytokines IL-4, IL-5 and IL-13. By comparison, development of AHR and mucous cell change were associated with recovery from PVM infection, regardless of subsequent allergen challenge. Increased expression of IL-25, which could contribute to induction of a Th2 response, was demonstrable in the lung following PVM infection. Signalling via the IL-4 receptor α chain was crucial to the development of allergic inflammation, mucous cell change and AHR, because all of these were absent in receptor-deficient mice. In contrast, changes of remodelling were evident in mice that received chronic aller...
Sieveking, DP, Lim, P, Chow, RWY, Dunn, LL, Bao, S, McGrath, KCY, Heather, AK, Handelsman, DJ, Celermajer, DS & Ng, MKC 2010, 'A sex-specific role for androgens in angiogenesis', Journal of Experimental Medicine, vol. 207, no. 2, pp. 345-352.
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Mounting evidence suggests that in men, serum levels of testosterone are negatively correlated to cardiovascular and all-cause mortality. We studied the role of androgens in angiogenesis, a process critical in cardiovascular repair/regeneration, in males and females. Androgen exposure augmented key angiogenic events in vitro. Strikingly, this occurred in male but not female endothelial cells (ECs). Androgen receptor (AR) antagonism or gene knockdown abrogated these effects in male ECs. Overexpression of AR in female ECs conferred androgen sensitivity with respect to angiogenesis. In vivo, castration dramatically reduced neovascularization of Matrigel plugs. Androgen treatment fully reversed this effect in male mice but had no effect in female mice. Furthermore, orchidectomy impaired blood-flow recovery from hindlimb ischemia, a finding rescued by androgen treatment. Our findings suggest that endogenous androgens modulate angiogenesis in a sex-dependent manner, with implications for the role of androgen replacement in men.
Sinha, S, Mallick, BK, Kipnis, V & Carroll, RJ 2010, 'Semiparametric Bayesian Analysis of Nutritional Epidemiology Data in the Presence of Measurement Error', Biometrics, vol. 66, no. 2, pp. 444-454.
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Summary: We propose a semiparametric Bayesian method for handling measurement error in nutritional epidemiological data. Our goal is to estimate nonparametrically the form of association between a disease and exposure variable while the true values of the exposure are never observed. Motivated by nutritional epidemiological data, we consider the setting where a surrogate covariate is recorded in the primary data, and a calibration data set contains information on the surrogate variable and repeated measurements of an unbiased instrumental variable of the true exposure. We develop a flexible Bayesian method where not only is the relationship between the disease and exposure variable treated semiparametrically, but also the relationship between the surrogate and the true exposure is modeled semiparametrically. The two nonparametric functions are modeled simultaneously via B‐splines. In addition, we model the distribution of the exposure variable as a Dirichlet process mixture of normal distributions, thus making its modeling essentially nonparametric and placing this work into the context of functional measurement error modeling. We apply our method to the NIH‐AARP Diet and Health Study and examine its performance in a simulation study.
Smith, GB & Earp, AA 2010, 'Metal-in-metal localized surface plasmon resonance', NANOTECHNOLOGY, vol. 21, no. 1, pp. 1-8.
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Anomalous strong resonances in silver and gold nanoporous thin films which conduct are found to arise from isolated metal nano-islands separated from the surrounding percolating metal network by a thin loop of insulator. This observed resonant optical response is modelled. The observed peak position is in agreement with the observed average dimensions of the silver core and insulator shell. As the insulating ring thickness shrinks, the resonance moves to longer wavelengths and strengthens. This structure is the Babinet's principle counterpart of dielectric coremetal shell nanoparticles embedded in dielectric. Like for the latter, tuning of resonant absorption is possible, but here the matrix reflects rather than transmits, and tuning to longer wavelengths is more practical. A new class of metal mirror occurring as a single thin layer is identified using the same resonances in dense metal mirrors. Narrow band deep localized dips in reflectance result.
Solntsev, AS, Kitaeva, GK, Naumova, II & Penin, AN 2010, 'Measurement of the extraordinary refractive index dispersion in the MIR for Mg:Nd:LiNbO3 crystals by the use of quasi-phase-matching in a random 1D domain structure', Applied Physics B, vol. 99, no. 1-2, pp. 197-201.
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Spindler, X, Hofstetter, O, Wuhrer, R, McDonagh, A, Roux, C & Lennard, C 2010, 'Targeting amino acids in latent fingermarks using bioconjugated gold-citrate self-assembled monolayer nanoparticles', Science & Justice, vol. 50, no. 1, pp. 42-43.
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Sripa, J, Laha, T, To, J, Brindley, PJ, Sripa, B, Kaewkes, S, Dalton, JP & Robinson, MW 2010, 'Secreted cysteine proteases of the carcinogenic liver fluke, Opisthorchis viverrini: Regulation of cathepsin F activation by autocatalysis and trans-processing by cathepsin B', Cellular Microbiology, vol. 12, no. 6, pp. 781-795.
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Opisthorchis viverrini is an important helminth pathogen of humans that is endemic in Thailand and Laos. Adult flukes reside within host bile ducts and feed on epithelial tissue and blood cells. Chronic opisthorchiasis is associated with severe hepatobiliary diseases such as cholangiocarcinoma. Here we report that adult O. viverrini secrete two major cysteine proteases: cathepsin F (Ov-CF-1) and cathepsin B1 (Ov-CB-1). Ov-CF-1 is secreted as an inactive zymogen that autocatalytically processes and activates to a mature enzyme at pH 4.5 via an intermolecular cleavage at the prosegment-mature domain junction. Ov-CB-1 is also secreted as a zymogen but, in contrast to Ov-CF-1, is fully active against peptide and macromolecular substrates despite retaining the N-terminal prosegment. The active Ov-CB-1 zymogen was capable of trans-activating Ov-CF-1 by proteolytic removal of its prosegment at pH 5.5, a pH at which the Ov-CF-1 zymogen cannot autocatalytically activate. Both cathepsins hydrolyse human haemoglobin but their combined action more efficiently degrades haemoglobin to smaller peptides than each enzyme alone. Ov-CF-1 degraded extracellular matrix proteins more effectively than Ov-CB-1 at physiological pH. We propose that Ov-CB-1 regulates Ov-CF-1 activity and that both enzymes work together to degrade host tissue contributing to the development of liver fluke-associated cholangiocarcinoma. © 2010 Blackwell Publishing Ltd.
Sripa, J, Laha, T, To, J, Brindley, PJ, Sripa, B, Kaewkes, S, Dalton, JP & Robinson, MW 2010, 'Secreted cysteine proteases of the carcinogenic liver fluke, Opisthorchis viverrini: regulation of cathepsin F activation by autocatalysis and trans-processing by cathepsin B', Cellular Microbiology, vol. 12, no. 6, pp. 781-795.
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Opisthorchis viverrini is an important helminth pathogen of humans that is endemic in Thailand and Laos. Adult flukes reside within host bile ducts and feed on epithelial tissue and blood cells. Chronic opisthorchiasis is associated with severe hepatobiliary diseases such as cholangiocarcinoma. Here we report that adult O. viverrini secrete two major cysteine proteases: cathepsin F (Ov-CF-1) and cathepsin B1 (Ov-CB-1). Ov-CF-1 is secreted as an inactive zymogen that autocatalytically processes and activates to a mature enzyme at pH 4.5 via an intermolecular cleavage at the prosegment-mature domain junction. Ov-CB-1 is also secreted as a zymogen but, in contrast to Ov-CF-1, is fully active against peptide and macromolecular substrates despite retaining the N-terminal prosegment. The active Ov-CB-1 zymogen was capable of trans-activating Ov-CF-1 by proteolytic removal of its prosegment at pH 5.5, a pH at which the Ov-CF-1 zymogen cannot autocatalytically activate. Both cathepsins hydrolyse human haemoglobin but their combined action more efficiently degrades haemoglobin to smaller peptides than each enzyme alone. Ov-CF-1 degraded extracellular matrix proteins more effectively than Ov-CB-1 at physiological pH. We propose that Ov-CB-1 regulates Ov-CF-1 activity and that both enzymes work together to degrade host tissue contributing to the development of liver fluke-associated cholangiocarcinoma.
Srivastava, M, Simakov, O, Chapman, J, Fahey, B, Gauthier, MEA, Mitros, T, Richards, GS, Conaco, C, Dacre, M, Hellsten, U, Larroux, C, Putnam, NH, Stanke, M, Adamska, M, Darling, A, Degnan, SM, Oakley, TH, Plachetzki, DC, Zhai, Y, Adamski, M, Calcino, A, Cummins, SF, Goodstein, DM, Harris, C, Jackson, DJ, Leys, SP, Shu, S, Woodcroft, BJ, Vervoort, M, Kosik, KS, Manning, G, Degnan, BM & Rokhsar, DS 2010, 'The Amphimedon queenslandica genome and the evolution of animal complexity', Nature, vol. 466, no. 7307, pp. 720-726.
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Staicu, A-M, Crainiceanu, CM & Carroll, RJ 2010, 'Fast methods for spatially correlated multilevel functional data', Biostatistics, vol. 11, no. 2, pp. 177-194.
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Stanca, SE, Nietzsche, S, Fritzsche, W, Cranfield, CG & Biskup, C 2010, 'Intracellular ion monitoring using a gold-core polymer-shell nanosensor architecture', NANOTECHNOLOGY, vol. 21, no. 5.
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In this study, we describe the design of new ratiometric fluorescent nanosensors, whose architecture is based on a gold core surrounded by a poly(vinyl alcohol)polyacetal shell. To the gold core, indicator dyes and reference dyes are attached via a cysteine linker. This nanosensor architecture is flexible with regards to the number and types of fluorophore linkages possible. The robust poly(vinyl alcohol)polyacetal shell protects the fluorophores linked to the core from non-specific interactions with intracellular proteins. The nanosensors developed in this way are biocompatible and can be easily incorporated into mammalian cells without the use of transfection agents. Here, we show the application of these nanosensors for intracellular pH and sodium ion measurements.
Stark, D, Barratt, J, Roberts, T, Marriott, D, Harkness, J & Ellis, J 2010, 'A Review of the Clinical Presentation of Dientamoebiasis', AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, vol. 82, no. 4, pp. 614-619.
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Among 750 symptomatic and asymptomatic patients, Dientamoeba fragilis was detected at a prevalence of 5.2% and more common than Giardia intestinalis. Most infected patients presented with diarrhea and abdominal pain with symptoms greater than 2 weeks duration being common. Bacterial and viral causes of infection were excluded by routine microbiological techniques. Treatment of D. fragilis infection with either iodoquinol, paromomycin, or combination therapy resulted in the eradication of the parasite and complete resolution of symptoms. Treatment failure/relapses were associated only with the use of metronidazole. Nineteen patients were examined for pin worm, no Enterobius vermicularis, a proposed vector of transmission, were detected. Intermittent shedding of D. fragilis was found to be highly variable. These studies confirm the pathogenic nature of D. fragilis and we recommend laboratories routinely test for the organism. Copyright © 2010 by The American Society of Tropical Medicine and Hygiene.
Stark, D, Barratt, J, Roberts, T, Marriott, D, Harkness, J & Ellis, J 2010, 'Comparison of microscopy, two xenic culture techniques, conventional and real-time PCR for the detection of Dientamoeba fragilis in clinical stool samples', EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES, vol. 29, no. 4, pp. 411-416.
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Dientamoeba fragilis is a pathogenic protozoan parasite that is notoriously difficult to diagnose. The aim of this study was to determine the gold standard for laboratory detection of D. fragilis. A total of 650 human faecal samples were included in the study. All specimens underwent the following: microscopy using a permanent stain (modified iron-haematoxylin), culture using a modified Boeck and Drbohlav's medium (MBD) and TYGM-9, a conventional polymerase chain reaction (PCR) and a real-time PCR (RT-PCR). The overall prevalence of D. fragilis in the study population was 5.4% (35/650). RT-PCR detected 35 isolates, conventional PCR detected 15 isolates, MBD culture detected 14 isolates, TYGM-9 detected ten isolates, while microscopy detected 12 isolates. RT-PCR detected an additional 15 positive samples compared to the other diagnostic methods, all of which were confirmed by sequencing. When all methods were compared to each other, RT-PCR showed a sensitivity and specificity of 100 and 100%, conventional PCR 42.9 and 100%, MBD culture 40 and 100%, TYGM-9 culture 28.6 and 100%, and microscopy 34.3 and 99%, respectively. These results show that RT-PCR is the diagnostic method of choice for the detection of D. fragilis in clinical samples and, as such, should be considered as the gold standard for diagnosis. © 2010 Springer-Verlag.
Starkey, MR, Horvat, JC, Kim, RY & Hansbro, PM 2010, 'Reply', Journal of Allergy and Clinical Immunology, vol. 125, no. 6, pp. 1415-1415.
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Stokes, NL, Edgar, JA, McDonagh, AM & Cortie, MB 2010, 'Spectrally selective coatings of gold nanorods on architectural glass', JOURNAL OF NANOPARTICLE RESEARCH, vol. 12, no. 8, pp. 2821-2830.
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Infrared-blocking coatins n window glass can be produced by dispersing gold nanorods into a polymer coating. The spectral selectivity of the coating is controlled by the shape and aspect ration of the nanoparticles, which are in turn determined by the conditions applied during their synthesis. Coatings of nanorods in polyvinyl alcohol were deposited onto glass and characterised in both laboratory and sun-lit conditions. Selective attenuation of the near-infrared was demonstrated with the test panels transmitting approximately one-third of the incident solar radiatyion and absorbing nearly two-thirds. The high absoprtive cross sections of the gold nanorods suggest that they can be applied in efficacious coatings at relatively low volume fractions.
Sturino, J, Zorych, I, Mallick, B, Pokusaeva, K, Chang, Y-Y, Carroll, RJ & Bliznuyk, N 2010, 'Statistical Methods for Comparative Phenomics Using High-Throughput Phenotype Microarrays', The International Journal of Biostatistics, vol. 6, no. 1.
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Sun, B, Horvat, J, Kim, HS, Kim, W-S, Ahn, J & Wang, G 2010, 'Synthesis of Mesoporous alpha-Fe2O3 Nanostructures for Highly Sensitive Gas Sensors and High Capacity Anode Materials in Lithium Ion Batteries', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 114, no. 44, pp. 18753-18761.
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Mesoporous α-Fe2O3 materials were prepared in large quantity by the soft template synthesis method using the triblock copolymer surfactant F127 as the template. Nitrogen adsorption-desorption isothermal measurements and transmission electron microscope observation revealed that the as-prepared mesoporous α-Fe2O3 nanostructures have large mesopores in a wide size range of 5-30 nm. It has been found that the Morin transition depends on thermal history of mesoporous α-Fe2O3, which is driven by surface anisotropy. Superparamagnetic behavior of mesoporous α-Fe2O3 is also associated with surface spins with blocking temperature around 50 K. When applied as gas sensors, mesoporous α-Fe2O3 nanostructures exhibited high gas sensitivity toward acetic acid and ethanol gas. As anodes in lithium ion cells, mesoporous α-Fe2O 3 materials show a high specific capacity of 1360 mAh/g with excellent cycling stability and high rate capacity. © 2010 American Chemical Society.
Sun, J, Shen, X, Guo, L, Wang, G, Park, J & Wang, K 2010, 'Solvothermal Synthesis of Ternary Sulfides of Sb2 − xBi x S3(x = 0.4, 1) with 3D Flower-Like Architectures', Nanoscale Research Letters, vol. 5, no. 2, pp. 364-369.
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Abstract Flower-like nanostructures of Sb2 − x Bi x S3(x = 0.4, 1.0) were successfully prepared using both antimony diethyldithiocarbamate [Sb(DDTC)3] and bismuth diethyldithiocarbamate [Bi(DDTC)3] as precursors under solvothermal conditions at 180 °C. The prepared Sb2 − x Bi x S3 with flower-like 3D architectures were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectrometry (EDS), high-resolution transmission electron microscopy (HRTEM), and selected area electron diffraction (SAED). The flower-like architectures, with an average diameter of ~4 μm, were composed of single-crystalline nanorods with orthorhombic structures. The optical absorption properties of the Sb2 − x Bi x S3 nanostructures were investigated by UV–Visible spectroscopy, and the results indicate that the Sb2 − x Bi x S3 compounds are semiconducting with direct band gaps of 1.32 and 1.30 eV for x = 0.4 and 1.0, respectively. On the basis of the experimental results, a possible growth mechanism for the flower-like Sb2 − x Bi x S3 nano...
Sun, Y, Wang, C, Wen, Q, Wang, G, Wang, H, Qu, Q & Hu, X 2010, 'Determination of Glyphosate and Aminomethylphosphonic Acid in Water by LC Using a New Labeling Reagent, 4-Methoxybenzenesulfonyl Fluoride', Chromatographia, vol. 72, no. 7-8, pp. 679-686.
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A rapid, low-cost, and highly sensitive analytical method to detect glyphosate and its major metabolite, aminomethylphosphonic acid (AMPA), in water samples has been developed, involving a derivatization with a new labeling reagent, 4-methoxybenzenesulfonyl fluoride, followed by reverse phase liquid chromatography with ultraviolet detection. The limits of detection of both of glyphosate and AMPA in real water samples are 0.1 μg L-1 with simple pre-concentration. This method has proven to be sensitive and reliable for determination of glyphosate and AMPA in water samples. © 2010 Vieweg+Teubner Verlag | Springer Fachmedien Wiesbaden GmbH.
Sutton, DL, Loo, GH, Menz, RI & Schuller, KA 2010, 'Cloning and functional characterization of a typical 2-Cys peroxiredoxin from southern bluefin tuna (Thunnus maccoyii)', Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, vol. 156, no. 2, pp. 97-106.
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Szczepanek, SM, Frasca, S, Schumacher, VL, Liao, X, Padula, M, Djordjevic, SP & Geary, SJ 2010, 'Identification of Lipoprotein MslA as a Neoteric Virulence Factor of Mycoplasma gallisepticum', Infection and Immunity, vol. 78, no. 8, pp. 3475-3483.
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ABSTRACT Many lipoproteins are expressed on the surfaces of mycoplasmas, and some have been implicated as playing roles in pathogenesis. Family 2 lipoproteins of Mycoplasma pneumoniae have a conserved “mycoplasma lipoprotein X” central domain and a “mycoplasma lipoprotein 10” C-terminal domain and are differentially expressed in response to environmental conditions. Homologues of family 2 lipoproteins are Mycoplasma specific and include the lipoprotein of Mycoplasma gallisepticum , encoded by the MGA0674 gene. Comparative transcriptomic analysis of the M. gallisepticum live attenuated vaccine strain F and the virulent strain R low , reported in this study, indicated that MGA0674 is one of several differentially expressed genes. The MGA0674-encoded lipoprotein is a proteolytically processed, immunogenic, TX-114 detergent-phase protein which appears to have antigenic divergence between field strains R low and S6. We examined the virulence of an R low ΔMGA0674 mutant (P1H9) in vivo and observed reduced recovery and attenuated virulence in the tracheas of experimentally infected chickens. The virulence of two additional R low ΔMGA0674 mutants, 2162 and 2204, was assessed in a second in vivo virulence experiment. These mutants exhibited partial to complete attenuation in vivo , but recovery was observed more frequently. Since only Mycoplasma
Teng, Y, Qian, B, Jiang, N, Liu, Y, Luo, F, Ye, S, Zhou, J, Zhu, B, Zeng, H & Qiu, J 2010, 'Light and heat driven precipitation of copper nanoparticles inside Cu2+-doped borate glasses', Chemical Physics Letters, vol. 485, no. 1-3, pp. 91-94.
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Thai, A, Xiao, J, Ammit, AJ & Rohanizadeh, R 2010, 'Development of inhalable formulations of anti-inflammatory drugs to potentially treat smoke inhalation injury in burn victims', International Journal of Pharmaceutics, vol. 389, no. 1-2, pp. 41-52.
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Thomas, CR, Warne, MSJ, Hose, GC & Lim, RP 2010, 'River water and sediment reduce the toxicity of deltamethrin to paratya Australiensis', Australasian Journal of Ecotoxicology, vol. 16, no. 1, pp. 9-16.
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Deltamethrin is a pyrethroid insecticide used extensively to control cotton pests in Australia and worldwide. Deltamethrin readily binds to organic and particulate matter in the environment, thereby reducing its bioavailability and toxicity, yet most toxicity data come from studies using clean, organic matter-free water that were conducted under conditions that differ greatly from those in the turbid rivers of the cotton-growing regions of Australia. The aim of this study was to assess the toxicity of deltamethrin to the native glass shrimp, Paratya australiensis, and to consider the role of suspended and bottom sediment in the amelioration of deltamethrin toxicity. We conducted a series of acute single-species toxicity tests in the laboratory and in the field in the Namoi-Gwydir cotton region of northwest New South Wales, Australia. The toxicity of deltamethrin was significantly (p≤0.05) reduced in river water compared with that in laboratory water in laboratory but not field-based tests. The toxicity of deltamethrin in river water was further reduced with the addition of bottom sediment. Despite reductions in toxicity in natural waters, deltamethrin remained highly toxic (i.e. 60-h EC50 values <200 ng/L) to P. australiensis, and thus further investigation of the hazard of deltamethrin is warranted.
Thompson, FL, Thompson, CC, Vicente, ACP & Klose, KE 2010, 'Vibrio2009: the third international conference on the biology of Vibrios', Molecular Microbiology, vol. 77, no. 5, pp. 1065-1071.
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Thorburn, AN & Hansbro, PM 2010, 'Harnessing Regulatory T cells to Suppress Asthma', American Journal of Respiratory Cell and Molecular Biology, vol. 43, no. 5, pp. 511-519.
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Thorburn, AN, O'Sullivan, BJ, Thomas, R, Kumar, RK, Foster, PS, Gibson, PG & Hansbro, PM 2010, 'Pneumococcal conjugate vaccine-induced regulatory T cells suppress the development of allergic airways disease', Thorax, vol. 65, no. 12, pp. 1053-1060.
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Ton-That, C, Foley, M, Lem, LLC, McCredie, G, Phillips, MR & Cowie, BCC 2010, 'Diffusion synthesis and electronic properties of Fe-doped ZnO', MATERIALS LETTERS, vol. 64, no. 3, pp. 386-388.
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Fe-doped ZnO was successfully fabricated by thermal in-diffusion of Fe into ZnO crystals. X-ray absorption near edge structure (XANES), photoemission and cathodoluminescence (CL) spectroscopy have been combined to examine the Fe diffusion and its effects on the electronic and optical properties of the crystal. Depth-resolved CL demonstrates that Fe in-diffusion occurs to at least 4 μm depth and results in intense green luminescence, whereas the undoped crystal exhibits only the ZnO near-band-edge emission. XANES and valence-band photoemission show that Fe is incorporated as Fe2+/3+ ions on substitutional Zn sites. The results suggest that the variation in the CL properties is due to a change in the oxygen vacancy charge state as a result of electron transfer from Fe. Crown Copyright © 2009.
Tooze, JA, Kipnis, V, Buckman, DW, Carroll, RJ, Freedman, LS, Guenther, PM, Krebs‐Smith, SM, Subar, AF & Dodd, KW 2010, 'A mixed‐effects model approach for estimating the distribution of usual intake of nutrients: The NCI method', Statistics in Medicine, vol. 29, no. 27, pp. 2857-2868.
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AbstractIt is of interest to estimate the distribution of usual nutrient intake for a population from repeat 24‐h dietary recall assessments. A mixed effects model and quantile estimation procedure, developed at the National Cancer Institute (NCI), may be used for this purpose. The model incorporates a Box–Cox parameter and covariates to estimate usual daily intake of nutrients; model parameters are estimated via quasi‐Newton optimization of a likelihood approximated by the adaptive Gaussian quadrature. The parameter estimates are used in a Monte Carlo approach to generate empirical quantiles; standard errors are estimated by bootstrap. The NCI method is illustrated and compared with current estimation methods, including the individual mean and the semi‐parametric method developed at the Iowa State University (ISU), using data from a random sample and computer simulations. Both the NCI and ISU methods for nutrients are superior to the distribution of individual means. For simple (no covariate) models, quantile estimates are similar between the NCI and ISU methods. The bootstrap approach used by the NCI method to estimate standard errors of quantiles appears preferable to Taylor linearization. One major advantage of the NCI method is its ability to provide estimates for subpopulations through the incorporation of covariates into the model. The NCI method may be used for estimating the distribution of usual nutrient intake for populations and subpopulations as part of a unified framework of estimation of usual intake of dietary constituents. Copyright © 2010 John Wiley & Sons, Ltd.
Toth, M, Thiel, BL & Knowles, WR 2010, 'Gas Cascade Amplification in Ultra-High-Resolution Environmental Scanning Electron Microcopy', Microscopy and Microanalysis, vol. 16, no. 6, pp. 805-809.
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AbstractWe describe a feedback mechanism in the gas cascade amplification process used in magnetic immersion lens environmental scanning electron microcopy (ESEM). Feedback dominates gas gain under the conditions typically used for ultra-high-resolution ESEM and gives rise to novel dependencies of the imaging signal and noise on microscope operating parameters. It is ascribed tentatively to the generation of free electrons upon de-excitation of metastable species in the gas cascade. The results have implications for optimization of ESEM systems for applications such as critical dimension metrology and real-time imaging of nanostructure growth by gas mediated electron beam induced deposition.
Touzet, N, Farrell, H, Rathaille, AN, Rodriguez, P, Alfonso, A, Botana, LM & Raine, R 2010, 'Dynamics of co-occurring Alexandrium minutum (Global Clade) and A. tamarense (West European) (Dinophyceae) during a summer bloom in Cork Harbour, Ireland (2006)', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 57, no. 3-4, pp. 268-278.
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The dinoflagellate genus Alexandrium contains neurotoxin-producing species, which have adversely affected the aquaculture industry and fisheries worldwide. Seasonal toxic blooms of Alexandrium spp. occur on an annual basis in the North Channel area of Co
Trian, T, Moir, LM, Ge, Q, Burgess, JK, Kuo, C, King, NJC, Reddel, HK, Black, JL, Oliver, BG & McParland, BE 2010, 'Rhinovirus-Induced Exacerbations of Asthma How Is the beta(2)-Adrenoceptor Implicated?', AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, vol. 43, no. 2, pp. 227-233.
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Rhinovirus (RV) infections are the major cause of asthma exacerbations in children and adults. Under normal circumstances, asthmatic airway obstruction improves spontaneously or characteristically briskly in response to inhaled β2-adrenergic receptor (β2AR) agonists. During virus-associated exacerbations, an impaired response to β2AR agonists is observed; the reason for this is not known. The objective of this study was to determine the effect of RV infection on airway smooth muscle β2AR function. The human cell line Beas-2B and primary human bronchial epithelial cells (HBECs) were infected with RV (multiplicity of infection = 1). After 1 or 5 days for primary and Beas-2B cells, respectively, cell culture supernatants were harvested, UV-irradiated to inactivate RV, and applied to human airway smooth muscle cells for 3 days to assess modifications of β2AR function. RV conditioned medium from Beas-2B and HBECs decreased β2AR agonist-induced cAMP by 50 and 65%, respectively (n = 5; P < 0.05). When cAMP was induced independently of the β2AR using forskolin, no impairment was found. Using flow cytometry, we demonstrated that this decrease was likely the result of β2AR desensitization because membrane but not total cell receptor β2AR was decreased. Pretreatment of HBECs and Beas-2B cells but not human airway smooth muscle cells with the corticosteroids dexamethasone or fluticasone abolished virus-mediated β2AR loss of function. This study shows that epithelial infection with RV induces a decrease of β2AR function on airway smooth muscle cells, potentially explaining the clinical observation of loss of β2AR agonist function during RV-induced asthma exacerbations.
Tujula, NA, Crocetti, GR, Burke, C, Thomas, T, Holmstrom, C & Kjelleberg, S 2010, 'Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga', ISME JOURNAL, vol. 4, no. 2, pp. 301-311.
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Venturini, C, Beatson, SA, Djordjevic, SP & Walker, MJ 2010, 'Multiple antibiotic resistance gene recruitment onto the enterohemorrhagic Escherichia coli virulence plasmid', The FASEB Journal, vol. 24, no. 4, pp. 1160-1166.
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Enterohemorrhagic Escherichia coli (EHEC) strains are zoonotic pathogens responsible for a range of severe human disease. The repertoire of virulence determinants promoting EHEC disease is encoded on both the main chromosome and virulence plasmid. We examined a multiply antibiotic-resistant O26 EHEC strain for carriage of resistance genes on the virulence plasmid. The EHEC virulence plasmid containing a complex antibiotic-resistance gene locus, designated as pO26-CRL, was purified from EHEC O26:H- (patient with hemorrhagic colitis) and subjected to shotgun-sequencing and bioinformatic analysis. Determination of the 111,481-bp sequence of pO26-CRL revealed genes encoding a functional enterohemolysin operon (ehxCABD), STEC-specific extracellular serine protease (espP), putative EHEC adhesin (toxB), catalase/peroxidase (katP), and myristoyl transferase (msbB) involved in lipid A synthesis. A 22,609-bp Tn21 derivative is inserted within the conjugal transfer gene traC and encodes resistance to trimethoprim, streptomycin, sulfathiozole, kanamycin, neomycin, β-lactams, and mercuric chloride. Plasmid pO26-CRL is nonconjugative but is mobilizable. This is the first report of an EHEC virulence plasmid containing a complex antibiotic resistance locus, and raises the concern that antibiotic use will coselect for virulence determinants, leading to increased disease potential in both commensal and pathogenic E. coli populations. © FASEB.
Villavedra, M, To, J, Lemke, S, Birch, D, Crosbie, P, Adams, M, Broady, K, Nowak, B, Raison, RL & Wallach, M 2010, 'Characterisation of an immunodominant, high molecular weight glycoprotein on the surface of infectious Neoparamoeba spp., causative agent of amoebic gill disease (AGD) in Atlantic salmon', FISH & SHELLFISH IMMUNOLOGY, vol. 29, no. 6, pp. 946-955.
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Amoebic gill disease can be experimentally induced by the exposure of salmonids to Neoparamoeba spp. freshly isolated from infected fish, while cultured amoebae are non-infective.
Wand, MP & Ormerod, JT 2010, 'Corrigendum: ON SEMIPARAMETRIC REGRESSION WITH O'SULLIVAN PENALISED SPLINES', Australian & New Zealand Journal of Statistics, vol. 52, no. 2, pp. 239-239.
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Wang, A, Garcia, D, Zhang, H, Feng, K, Chaudhury, A, Berger, F, Peacock, WJ, Dennis, ES & Luo, M 2010, 'The VQ motif protein IKU1 regulates endosperm growth and seed size in Arabidopsis', PLANT JOURNAL, vol. 63, no. 4, pp. 670-679.
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P>Arabidopsis seed size is regulated by the IKU pathway that includes IKU2 (a leucine-rich repeat kinase) and MINI3 (a WRKY transcription factor). We report the cloning of the IKU1 (At2g35230) gene. iku1 mutants cause reduced endosperm growth and the pro
Wang, C, Sun, Y, Wen, Q, Wang, G, Wang, Y, Qu, Q, Yang, G & Hu, X 2010, 'Novel reagents for quantitative analysis of valiolamine in biological samples by high-performance liquid chromatography with pre-column UV derivatization', Talanta, vol. 81, no. 4-5, pp. 1613-1618.
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A rapid, low-cost, high sensitive and quantitative method to detect valiolamine in a medium for microbial culture, involving derivatization with a new labeling reagent, 4-methoxybenzenesulfonyl fluoride (MOBS-F), followed by reverse-phase high-performance liquid chromatography with ultraviolet (UV) detection with simple operation procedure. 4-Methoxybenzenesulfonyl chloride (MOBS-Cl) and 2-nitrobenzenesulfonyl chloride (NBS-Cl) were compared with MOBS-F as novel reagents in this paper, and the MOBS-F was chosen as the most suitable derivatization reagent. The column was thermostatic at 35 °C, the mobile phase flow-rate was 1.0 mL/min and the detection wavelength was 240 nm. For a biological sample, the separation of the derivatives was achieved using a gradient mobile system. The elution program is 88% phosphate buffer (50 mM; pH = 3.0) and 12% methanol for 23 min, then 70% of phosphate buffer and 30% methanol for another 15 min and finally 88% of phosphate buffer and 12% of methanol for 5 min to re-equilibrate the column. The optimized conditions of the derivatization were as follows: derivatization reaction temperature 30 °C; derivatization reaction pH value 11.0, reaction time 10 min and MOBS-F concentration higher than 1.5 mg/mL for standard solutions and higher than 5.0 mg/mL for the biological sample. Calibration curves were linear in the range of 0.050-25 μg/mL for the standard solutions and 1.0-75 μg/mL for the biological sample. The sensitive analytical method is helpful to control the biotechnological process of voglibose production and product quality control. © 2010 Elsevier B.V. All rights reserved.
WANG, C-Y, WANG, D-Y, WANG, G-X & HU, X-Y 2010, 'Determination of Lysozyme Using Microcantilever Sensor Based on Atomic Force Microscopy', Chinese Journal of Analytical Chemistry, vol. 38, no. 12, pp. 1771-1775.
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A microcantilever sensor was developed to detect lysozyme in a pharmaceutical formulation based on the principle of atomic force microscopy. By measuring the cantilever bending and deflection using the optical reflection technique, the lysozyme adsorption on a dodecanethiol-modified cantilever surface was detected. Under optimal conditions, a good linear relationship between the deflection of the microcantilever and the logarithm of the lysozyme concentration in the range from 10 ng L-1 to 0.1 mg L-1, with a correlation coefficient of 0.998, was established. The limit of detection was 5.0 ng L-1. The lysozyme in the pharmaceutical formulation sample was determined with the desirable results by using the present method. Copyright © 2010, Changchun Institute of Applied Chemistry.
Wang, G, Liu, H, Horvat, J, Wang, B, Qiao, S, Park, J & Ahn, H 2010, 'Highly Ordered Mesoporous Cobalt Oxide Nanostructures: Synthesis, Characterisation, Magnetic Properties, and Applications for Electrochemical Energy Devices', CHEMISTRY-A EUROPEAN JOURNAL, vol. 16, no. 36, pp. 11020-11027.
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Highly ordered mesoporous Co3O4 nanostructures were prepared using KIT-6 and SBA-15 silica as hard templates. The structures were confirmed by small angle X-ray diffraction, high resolution transmission electron microscopy, and N2 adsorption-desorption isotherm analysis. Both KIT-6 cubic and SBA-15 hexagonal mesoporous Co3O4 samples exhibited a low Néel temperature and bulk antiferromagnetic coupling due to geometric confinement of antiferromagnetic order within the nanoparticles. Mesoporous Co3O4 electrode materials have demonstrated the high lithium storage capacity of more than 1200 mAhg -1 with an excellent cycle life. They also exhibited a high specific capacitance of 370 Fg-1 as electrodes in supercapacitors. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Wang, G, Liu, H, Liu, J, Qiao, S, Lu, GM, Munroe, P & Ahn, H 2010, 'Mesoporous LiFePO4/C Nanocomposite Cathode Materials for High Power Lithium Ion Batteries with Superior Performance', ADVANCED MATERIALS, vol. 22, no. 44, pp. 4944-+.
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Hexagonally ordered mesoporous LiFePO4/C nanocomposites can be synthesised with LiFePO4 nanoparticles embedded in an interconnected carbon framework. Mesoporous LiFePO4/C nanocomposites exhibit superior electrochemical performance and ultra-high specific power density, which makes this architecture suitable for high power applications such as HEVs and stationary energy storage for smart grids. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Wang, H, Ma, Y, Tian, H, Tang, N, Liu, W, Wang, Q & Tang, Y 2010, 'Novel europium complexes covalently bonded to MCM-41 and SBA-15: spatial confinement effects on photoluminescence behavior', Dalton Transactions, vol. 39, no. 32, pp. 7485-7485.
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Wang, S, Qian, L & Carroll, RJ 2010, 'Generalized empirical likelihood methods for analyzing longitudinal data', Biometrika, vol. 97, no. 1, pp. 79-93.
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Abstract Efficient estimation of parameters is a major objective in analyzing longitudinal data. We propose two generalized empirical likelihood-based methods that take into consideration within-subject correlations. A nonparametric version of the Wilks theorem for the limiting distributions of the empirical likelihood ratios is derived. It is shown that one of the proposed methods is locally efficient among a class of within-subject variance-covariance matrices. A simulation study is conducted to investigate the finite sample properties of the proposed methods and compares them with the block empirical likelihood method by You et al. (2006) and the normal approximation with a correctly estimated variance-covariance. The results suggest that the proposed methods are generally more efficient than existing methods that ignore the correlation structure, and are better in coverage compared to the normal approximation with correctly specified within-subject correlation. An application illustrating our methods and supporting the simulation study results is presented.
Wang, W, Jing Li, J, S. Foster, P, M. Hansbro, P & Yang, M 2010, 'Potential Therapeutic Targets for Steroid-Resistant Asthma', Current Drug Targets, vol. 11, no. 8, pp. 957-970.
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Wang, W, Li, JJ, Foster, PS, Hansbro, PM & Yang, M 2010, 'Potential Therapeutic Targets for Steroid-Resistant Asthma', Current Drug Targets, vol. 999, no. 999, pp. 1-14.
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Webb, JK, Du, W, Pike, D & Shine, R 2010, 'Generalization of predator recognition: Velvet geckos display anti-predator behaviours in response to chemicals from non-dangerous elapid snakes', Current Zoology, vol. 56, no. 3 Special Issue, pp. 337-342.
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Many prey species detect chemical cues from predators and modify their behaviours in ways that reduce their risk of predation. Theory predicts that prey should modify their anti-predator responses according to the degree of threat posed by the predator.
West, M, Cooper, T & Kachoyan, B 2010, 'AIS Analysis in Support of Counter-Piracy Operations', Australian Journal of Maritime & Ocean Affairs, vol. 2, no. 4, pp. 110-117.
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© 2010, Copyright 2010 Taylor and Francis Group LLC. Piracy in the Gulf of Aden and the waters around Somalia has increased dramatically in recent years. This paper describes a number of analysis techniques that could be used with Automatic Identification System (AIS) data to help characterise merchant shipping traffic and traffic flows. Through this analysis, the increase in piracy incidents in the Indian Ocean may be explained as a result of naval patrols and ships adhering to advice whilst in the Gulf of Aden, which has forced an evolution in piracy tactics where ships are attacked at a considerable distance offshore. This style of data analysis is useful when planning future counter-piracy operations.
Westhorpe, DP, Mitrovic, SM, Ryan, D & Kobayashi, T 2010, 'Limitation of lowland riverine bacterioplankton by dissolved organic carbon and inorganic nutrients', HYDROBIOLOGIA, vol. 652, no. 1, pp. 101-117.
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Flow regulation in lowland rivers has reduced the amount of allochthonous dissolved organic carbon (DOC) entering main channels through less frequent wetting of benches, flood runners and floodplains. The hypothesis tested was that lowland riverine bacte
White, R, Thomas, P, Phillips, MR, Moran, K & Wuhrer, R 2010, 'X-Ray Mapping and Scatter Diagram Analysis of the Discoloring Products Resulting from the Interaction of Artist's Pigments', MICROSCOPY AND MICROANALYSIS, vol. 16, no. 5, pp. 594-598.
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The discoloring interaction between the artist's pigments cadmium yellow and the copper-containing malachite, an interaction that is conjectured to cause black spotting in oil paintings of the 19th and early 20th centuries, was examined using X-ray mapping and scatter diagram analysis. The application of these coupled techniques confirmed that copper sulfide phases were produced during discoloration reaction. Scatter diagram analysis indicated that two copper sulfide stoichiometries (CuS and Cu3S2) were present as reaction products where previously only crystalline CuS (covellite) had been identified by X-ray diffraction. The results demonstrate the potential of X-ray mapping coupled with scatter diagram analysis for the identification of both crystalline and X-ray amorphous phases produced by such complex heterogeneous interactions and their applicability to the investigation of interactions of artists' pigments. © Microscopy Society of America 2010.
Williams, DBG & Lawton, M 2010, 'Drying of Organic Solvents: Quantitative Evaluation of the Efficiency of Several Desiccants', The Journal of Organic Chemistry, vol. 75, no. 24, pp. 8351-8354.
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Williams, DBG & Lawton, M 2010, 'Metal triflates: On the question of Lewis versus Brønsted acidity in retinyl carbocation formation', Journal of Molecular Catalysis A: Chemical, vol. 317, no. 1-2, pp. 68-71.
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Williams, DBG, Cullen, A, Fourie, A, Henning, H, Lawton, M, Mommsen, W, Nangu, P, Parker, J & Renison, A 2010, 'Mild water-promoted selective deacetalisatison of acyclic acetals', Green Chemistry, vol. 12, no. 11, pp. 1919-1919.
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Williams, DBG, Simelane, SB, Lawton, M & Kinfe, HH 2010, 'Efficient tetrahydropyranyl and tetrahydrofuranyl protection/deprotection of alcohols and phenols with Al(OTf)3 as catalyst', Tetrahedron, vol. 66, no. 25, pp. 4573-4576.
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Williams, HL, Turnbull, L, Thomas, SJ, Murphy, A, Stinear, T, Armstrong, DS & Whitchurch, CB 2010, 'A diagnostic PCR assay for the detection of an Australian epidemic strain of Pseudomonas aeruginosa', ANNALS OF CLINICAL MICROBIOLOGY AND ANTIMICROBIALS, vol. 9.
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Wilson, SK, Adjeroud, M, Bellwood, DR, Berumen, ML, Booth, D, Bozec, Y-M, Chabanet, P, Cheal, A, Cinner, J, Depczynski, M, Feary, DA, Gagliano, M, Graham, NAJ, Halford, AR, Halpern, BS, Harborne, AR, Hoey, AS, Holbrook, SJ, Jones, GP, Kulbiki, M, Letourneur, Y, De Loma, TL, McClanahan, T, McCormick, MI, Meekan, MG, Mumby, PJ, Munday, PL, Ohman, MC, Pratchett, MS, Riegl, B, Sano, M, Schmitt, RJ & Syms, C 2010, 'Crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes', JOURNAL OF EXPERIMENTAL BIOLOGY, vol. 213, no. 6, pp. 894-900.
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Expert opinion was canvassed to identify crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes. Scientists that had published three or more papers on the effects of climate and environmental factors on reef fishes were invited to submit five questions that, if addressed, would improve our understanding of climate change effects on coral reef fishes. Thirty-three scientists provided 155 questions, and 32 scientists scored these questions in terms of: (i) identifying a knowledge gap, (ii) achievability, (iii) applicability to a broad spectrum of species and reef habitats, and (iv) priority. Forty-two per cent of the questions related to habitat associations and community dynamics of fish, reflecting the established effects and immediate concern relating to climate-induced coral loss and habitat degradation. However, there were also questions on fish demographics, physiology, behaviour and management, all of which could be potentially affected by climate change. Irrespective of their individual expertise and background, scientists scored questions from different topics similarly, suggesting limited bias and recognition of a need for greater interdisciplinary and collaborative research. Presented here are the 53 highest-scoring unique questions. These questions should act as a guide for future research, providing a basis for better assessment and management of climate change impacts on coral reefs and associated fish communities. © 2010, Published by The Company of Biologists Ltd.
Wohlthat, S, Reimers, JR & Hush, NS 2010, 'Accurate and computationally efficient third-nearest-neighbor tight-binding model for large graphene fragments', PHYSICAL REVIEW B, vol. 81, no. 19, p. 195125.
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Owing to the large sizes involved, most calculations of the electronic properties of graphene and its fragments involve empirical tight-binding models restricted to nearest-neighbor interactions only. Such approaches fail to predict key electronic and magnetic properties, however, and rely on assumed geometries. While alternative approaches based on density-functional theory are much more successful in predicting properties, they are often computationally prohibitive to apply. We introduce a simple third-nearest-neighbor π -only tight-binding approach that maintains the computational efficiency of the empirical method while achieving the accuracy of the density-functional methods to which it is parametrized. It yields both nuclear geometries and electronic structures of graphene fragments, providing an efficient and accurate replacement for traditional tight-binding models of graphene. © 2010 The American Physical Society.
Wong, FWS, Lim, CED & Smith, W 2010, 'A New Bioimpedance Research Device (BIRD) for Measuring the Electrical Impedance of Acupuncture Meridians', The Journal of Alternative and Complementary Medicine, vol. 16, no. 3, pp. 257-264.
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Objectives: The aim of this article is to introduce an electrical bioimpedance device that uses an old and little-known impedance measuring technique to study the impedance of the meridian and nonmeridian tissue segments. Design: Three (3) pilot experimental studies involving both a tissue phantom (a cucumber) and 3 human subjects were performed using this BIRD-I (Bioimpedance Research Device) device. This device consists of a Fluke RCL meter, a multiplexer box, a laptop computer, and a medical-grade isolation transformer. Segment and surface sheath (or local) impedances were estimated using formulae first published in the 1930s, in an approach that differs from that of the standard four-electrode technique used in most meridian studies to date. Results: Our study found that, when using a quasilinear four-electrode arrangement, the reference electrodes should be positioned at least 10 cm from the test electrodes to ensure that the segment (or core) impedance estimation is not affected by the proximity of the reference electrodes. A tissue phantom was used to determine the repeatability of segment (core) impedance measurement by the device. An applied frequency of 100kHz was found to produce the best repeatability among the various frequencies tested. In another preliminary study, with a segment of the triple energizer meridian on the lower arm selected as reference segment, core resistance-based profiles around the lower arm showed three of the other five meridians to exist as local resistance minima relative to neighboring nonmeridian segments. The profiles of the 2 subjects tested were very similar, suggesting that the results are unlikely to be spurious. Conclusions: In electrical bioimpedance studies, it is recommended that the measuring technique and device be clearly defined and standardized to provide optimal working conditions. In our study using the BIRD I device, we defined our standard experimental conditions as a test frequency of 100kHz and the posit...
Wong, FWS, Lim, CED, Karia, S & Santos, L 2010, 'Cervical endometriosis: Case series and review of literature', Journal of Obstetrics and Gynaecology Research, vol. 36, no. 4, pp. 916-919.
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AbstractCervical endometriosis is uncommon and usually an incidental or retrospective finding on histopathology reports. It can be asymptomatic or present with a diverse range of persistent symptoms and even life‐threatening hemorrhage. The condition can be managed expectantly in asymptomatic patients, however persistent symptoms may warrant surgery. We encountered four cases of histologically proven cervical endometriosis at our tertiary hospital in New South Wales, Australia. All our patients had different symptoms, presentations and indications for their surgery leading to their diagnosis. This review is to report these cases followed by discussion with a review of the literature.
Wong, WSF, Lee, TCE & Lim, CED 2010, 'Novel Vaginal “Paper Roll” Uterine Morcellation Technique for Removal of Large (>500 g) Uterus', Journal of Minimally Invasive Gynecology, vol. 17, no. 3, pp. 374-378.
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At laparoscopic-assisted vaginal hysterectomy with a novel "paper roll" vaginal morcellation technique, large uteri (≥500 g) can be removed via the vagina with safety, speed, and ease. The technique provides protection for the bladder and rectum, and large uteri can be removed in 1 piece, allowing the pathologist to reconstruct the entire uterus. © 2010 AAGL.
Wood, LG, Hazlewood, LC, Foster, PS & Hansbro, PM 2010, 'Lyprinol reduces inflammation and improves lung function in a mouse model of allergic airways disease', Clinical & Experimental Allergy, vol. 40, no. 12, pp. 1785-1793.
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SummaryBackground Asthma is an inflammatory airway disease that is characterized by an influx of eosinophils to the lungs, mucus hypersecretion and T helper type 2 cytokine production. Recent dietary changes, including a decreased ω‐3 polyunsaturated fatty acid (PUFA) intake, may have contributed to increased asthma rates and dietary supplementation with marine oil could have clinical benefits.Objective To assess the effects of dietary supplementation with ω‐3 PUFAs on allergic inflammation and lung function using a mouse model of ovalbumin (OVA)‐induced allergic airway disease (AAD).Methods BALB/c mice received a daily supplement of either fish oil (rich in ω‐3 PUFA) or lyprinol (a complex mixture of various marine lipids plus vitamin E and olive oil) before and during AAD. The effects of supplementation on AAD were assessed.Results Lyprinol but not fish oil treatment reduced eosinophil influx into the bronchoalveolar lavage fluid, the lung tissue surrounding the airways and the blood, decreased mucus hypersecretion in the lung and reduced airway hyperresponsiveness (AHR). The effects of lyprinol were not associated with changes in serum IgG1 or IgG2a, or the release of IL‐4, IL‐5, IL‐13 and IFN‐γ.Conclusions Lyprinol suppresses the development of allergic inflammation and AHR in AAD. The therapeutic potential of dietary supplementation with lyprinol for asthma warrants further investigation. Cite this as: L. G. Wood, L. C. Hazlewood, P. S. Foster and P. M. Hansbro, Clinical & Experimental Allergy, 2010 (40) 1785–1793.
Wood, LG, Simpson, JL, Hansbro, PM & Gibson, PG 2010, 'Potentially pathogenic bacteria cultured from the sputum of stable asthmatics are associated with increased 8-isoprostane and airway neutrophilia', Free Radical Research, vol. 44, no. 2, pp. 146-154.
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Wozniak, TM, Saunders, BM, Ryan, AA & Britton, WJ 2010, 'Mycobacterium bovisBCG-Specific Th17 Cells Confer Partial Protection againstMycobacterium tuberculosisInfection in the Absence of Gamma Interferon', Infection and Immunity, vol. 78, no. 10, pp. 4187-4194.
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ABSTRACTProtective immunity against tuberculosis (TB) requires the integrated response of a network of lymphocytes. Both gamma interferon (IFN-γ)- and interleukin 17 (IL-17)-secreting CD4+T cells have been identified in subjects with latent TB infection and during experimentalMycobacterium tuberculosisinfection, but the contribution of Th17 cells to protective immunity is unclear. To examine their protective effectsin vivo, we transferred mycobacterium-specific IL-17- and IFN-γ-secreting CD4+T cells isolated fromM. tuberculosisBCG-immunized IL-12p40−/−and IFN-γ−/−or wild-type mice, respectively, intoM. tuberculosis-infected IL-12p40−/−or RAG−/−mice. In the absence of IL-12 and IL-23, neither IL-17-secreting (Th17) nor IFN-γ-secreting (Th1) BCG-specific T cells expanded or provided protection againstM. tuberculosis. In RAG−/−recipients with an intact IL-12/IL-23 axis, both Th17 and Th1 cells were activated and induced significant protection againstM. tuberculosis. The reduction in the bacterial load following transfer of IFN-γ−/−Th17 cells was associated with significant prolongation of survival compared to recipients of naïve IFN-γ−/−T cells. This effect was at the cost of an increased inflammatory infiltrate characterized by an excess of neutrophils. Therefore, Th17 cells can provide IFN-γ-independent protection againstM. tuberculosis, and this effect may contribute to the early control ofM. tuberculosisinfection.
Wright, JT, Byers, JE, Koukoumaftsis, LP, Ralph, PJ & Gribben, PE 2010, 'Native species behaviour mitigates the impact of habitat-forming invasive seaweed', OECOLOGIA, vol. 163, no. 2, pp. 527-534.
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Habitat-forming invasive species cause large, novel changes to the abiotic environment. These changes may elicit important behavioural responses in native fauna, yet little is known about mechanisms driving this behaviour and how such trait-mediated responses influence the fitness of native species. Low dissolved oxygen is a key abiotic change created by the habitat-forming invasive seaweed, Caulerpa taxifolia, which influences an important behavioural response (burrowing depth) in the native infaunal bivalve Anadara trapezia. In Caulerpa-colonised areas, Anadara often emerged completely from the sediment, and we experimentally demonstrate that water column hypoxia beneath the Caulerpa canopy is the mechanism instigating this 'pop-up' behaviour. Importantly, pop-up in Caulerpa allowed similar survivorship to that in unvegetated sediment; however, when we prevented Anadara from popping-up, they suffered >50% mortality in just 1 month. Our findings not only highlight the substantial environmental alteration by Caulerpa, but also an important role for the behaviour of native species in mitigating the effects of habitat-forming invasive species. © 2010 Springer-Verlag.
Yano, M, Tong, CC, Light, ME, Schmidtchen, FP & Gale, PA 2010, 'Calix[4]pyrrole-based anion transporters with tuneable transport properties', Organic & Biomolecular Chemistry, vol. 8, no. 19, pp. 4356-4356.
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Yau, S, Liu, X, Djordjevic, SP & Hall, RM 2010, 'RSF1010-Like Plasmids in AustralianSalmonella entericaSerovar Typhimurium and Origin of Theirsul2-strA-strBAntibiotic Resistance Gene Cluster', Microbial Drug Resistance, vol. 16, no. 4, pp. 249-252.
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Salmonella enterica serovar Typhimurium phage type 9 isolates resis1ant tQ streptomycin and sulfonamide have been recovered from both bovine and human sources in Australia. This study aimed to identify the resistance genes and their location. Polymerase chain reaction was used to screen for resistance genes and sul2 (sulphonamide resistance) and strA and strB (streptomycin resistance) were detected. A small streptomycin and sulfonamide resistance plasmid carrying the three resistance genes was recovered from these isolates by transformation and was shown to be essentially identical to the small IncQ plasmid RSFIOIO. The sequences of one plasmid, pSRC15, and RSFIOIO differed at only a few positions that may be errors in the older sequence, RSFIOIO has been recovered from many species and in many countries since its first isolation in the early 1970s. We conclude that this plasmid has persisted unchanged in the environrn"ent for over 30 years. The antibiotic resistance gene cluster containing strA, strB, and sul2 genes has clearly arisen from other known entities by a combination of transposition and homologous recombination using a short segment of homology. This resistance gene cluster is now widely distributed in plasmids and genomic islands in a number of contexts.
Yoshioka, H, Miura, T, Dematte, JAM, Batchily, K & Huete, AR 2010, 'Soil Line Influences on Two-Band Vegetation Indices and Vegetation Isolines: A Numerical Study', REMOTE SENSING, vol. 2, no. 2, pp. 545-561.
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Influences of soil line variations on two-band vegetation indices (VIs) and their vegetation isolines in red and near-infrared (NIR) reflectance space are investigated based on recently derived relationships between the relative variations of VIs with variations of the soil line parameters in the accompanying paper by Yoshioka et al. [1]. The soil line influences are first demonstrated numerically in terms of variations of vegetation isolines and VI values along with the isolines. A hypothetical case is then analyzed by assuming the discrepancies between the general and regional soil lines for a Southern Brazil area reported elsewhere. The results indicate the validity of our analytical approach for the evaluation of soil line influences and the applicability for adjustment of VI errors using external data sources of soil reflectance spectra. © 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.
Yunusa, IAM, Aumann, CD, Rab, MA, Merrick, N, Fisher, PD, Eberbach, PL & Eamus, D 2010, 'Topographical and seasonal trends in transpiration by two co-occurring Eucalyptus species during two contrasting years in a low rainfall environment', AGRICULTURAL AND FOREST METEOROLOGY, vol. 150, no. 9, pp. 1234-1244.
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Understanding the strategies that confer resilience on natural woodlands in drought prone environments is important for the conservation of these and similar ecosystems. Our main aim in this 2-year study was to assess traits (sapwood area, sapwood densit
Yunusa, IAM, Zeppel, MJB, Fuentes, S, Macinnis-Ng, CMO, Palmer, AR & Eamus, D 2010, 'An assessment of the water budget for contrasting vegetation covers associated with waste management', HYDROLOGICAL PROCESSES, vol. 24, no. 9, pp. 1149-1158.
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Revegetation is critical to restoring hydrological function on waste disposal sites in order to minimize runoff and drainage and safeguard the water quality of the catchment. In this study, we determined the components of soil-water balance between late
Zaslawski, C 2010, 'An Interview With Professor Chris Zaslawski: Standardization and its Role in Acupuncture Research', Journal of Acupuncture and Meridian Studies, vol. 3, no. 1, pp. 65-66.
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Zaslawski, C 2010, 'Ethical Considerations for Acupuncture and Chinese Herbal Medicine Clinical Trials: A Cross-cultural Perspective', EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE, vol. 7, no. 3, pp. 295-301.
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Many ethical concerns revolve around the four basic principles of research: merit and integrity, respect for human beings, weighting of riskbenefit and justice. These principles form the basis for any discussion concerning human research ethics and are applicable to all areas of research including acupuncture and Chinese herbal medicine. World Health Organisation document, Guidelines for Clinical Research on Acupuncture, states that `consideration should be given to the different value systems that are involved in human rights such as social, cultural and historical issues and that `further studies should be conducted in relation to ethical issues involved in clinical research on acupuncture. In addition to outlining the four basic principles, this paper will also examine the effect of Asian culture on Western human research ethics and how this may impact upon issues such as informed consent and weighting of riskbenefit.
Zeppel, M, Tissue, D, Taylor, D, Macinnis-Ng, C & Eamus, D 2010, 'Rates of nocturnal transpiration in two evergreen temperate woodland species with differing water-use strategies', TREE PHYSIOLOGY, vol. 30, no. 8, pp. 988-1000.
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Nocturnal fluxes may be a significant factor in the annual water budget of forested ecosystems. Here, we assessed sap flow in two co-occurring evergreen species (Eucalyptus parramattensis and Angophora bakeri) in a temperate woodland for 2 years in order to quantify the magnitude of seasonal nocturnal sap flow (En) under different environmental conditions. The two species showed different diurnal water relations, demonstrated by different diurnal curves of stomatal conductance, sap flow and leaf water potential. The relative influence of several microclimatic variables, including wind speed (U), vapour pressure deficit (D), the product of U and D (UD) and soil moisture content, were quantified. D exerted the strongest influence on En (r2 = 0.59-0.86), soil moisture content influenced En when D was constant, but U and UD did not generally influence En. In both species, cuticular conductance (Gc) was a small proportion of total leaf conductance (Gs) and was not a major pathway for En. We found that En was primarily a function of transpiration from the canopy rather than refilling of stem storage, with canopy transpiration accounting for 50-70% of nocturnal flows. Mean En was 6-8% of the 24-h flux across seasons (spring, summer and winter), but was up to 19% of the 24-h flux on some days in both species. Despite different daytime strategies in water use of the two species, both species demonstrated low night-time water loss, suggesting similar controls on water loss at night. In order to account for the impact of En on pre-dawn leaf water potential arising from the influence of disequilibria between root zone and leaf water potential, we also developed a simple model to more accurately predict soil water potential (ψs). © The Author 2010. Published by Oxford University Press. All rights reserved.
Zhang, J, Li, T, Zhou, L, Tang, L, Xu, L, Wu, T & Lim, DCE 2010, 'Chinese herbal medicine for subfertile women with polycystic ovarian syndrome', Cochrane database of systematic reviews (Online), vol. 9.
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BACKGROUND: Polycystic ovarian syndrome (PCOS) is one of the most common reproductive endocrinology abnormalities, affecting 5% to 10% of women of reproductive age. Western medicines, such as oral contraceptives and insulin sensitizers, have been widely used to improve the symptoms and signs for PCOS. Recently, many studies have been published considering Chinese herbal medicine (CHM) as an alternative treatment for women with PCOS. OBJECTIVES: To evaluate the efficacy and safety of Chinese medicinal herbs for subfertile women with PCOS. SEARCH STRATEGY: We searched the following databases (from inception to March 2010): Menstrual Disorders and Subfertility Group Specialised Register (MDSG), Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, Allied and Complementary Medicine (AMED), PsycINFO, Chinese National Knowledge Infrastructure (CNKI), VIP, Wanfang. In addition, all reference lists of included trials were searched and experts in the field were contacted to locate trials. SELECTION CRITERIA: Randomized controlled trials (RCT) considering the use of CHM for the treatment of subfertile women with PCOS. DATA COLLECTION AND ANALYSIS: Two review authors independently screened appropriate trials for inclusion, assessed methodological quality, and extracted data. We contacted primary authors for additional information. Meta-analysis was conducted. Odds ratio (OR) was used for reporting dichotomous data with 95% confidence intervals (CI). MAIN RESULTS: Four RCTs involving 344 participants were included. The methodological risk of bias of included studies was poor. Different interventions were used in these four RCTs.There was evidence of statistically significant difference seen improving pregnancy rate (per woman) between CHM plus clomiphene and clomiphene (OR 2.97, 95%CI 1.71 to 5.17). However, there was no statistically significant difference seen in the other comparison groups for improving pregnancy rate (per woman).There was no evidence...
Zhou, J, Teng, Y, Liu, X, Ye, S, Xu, X, Ma, Z & Qiu, J 2010, 'Intense infrared emission of Er^3+ in Ca_8Mg(SiO_4)_4Cl_2 phosphor from energy transfer of Eu^2+ by broadband down-conversion', Optics Express, vol. 18, no. 21, pp. 21663-21663.
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Zhou, L, Huang, JZ, Martinez, JG, Maity, A, Baladandayuthapani, V & Carroll, RJ 2010, 'Reduced Rank Mixed Effects Models for Spatially Correlated Hierarchical Functional Data', Journal of the American Statistical Association, vol. 105, no. 489, pp. 390-400.
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Zinder, Y, Su, B, Singh, G & Sorli, R 2010, 'Scheduling UET-UCT tasks: branch-and-bound search in the priority space', OPTIMIZATION AND ENGINEERING, vol. 11, no. 4, pp. 627-646.
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The paper is concerned with the problem of scheduling partially ordered unit execution time tasks on parallel processors with unit communication delays and release times. Two criteria are considered, the maximum lateness and its particular case, the makespan. This problem plays an important role in scheduling theory and was originally inspired by the applications to multi-processor computer systems. It is well known that for both criteria the problem is NP-hard in the strong sense. The paper presents an implementation of the branch-and-bound method which does not partition the feasible region explicitly. The theoretical results are complemented by computational experiments.
