Publications

Cole, LJ, Huston, WM & Moir, JWB 2008, Delivery of Nitric Oxide for Analysis of the Function of Cytochrome c′, Elsevier.
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BEN-NISSAN, B, CHOI, AH & CORDINGLEY, R 2008, 'Alumina ceramics' in Kokubo, T (ed), Bioceramics and their Clinical Applications, Elsevier, Cambridge UK, pp. 223-242.
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Black, J, Burgess, J, Oliver, B & Moir, L 2008, 'Altered Properties of Airway Smooth Muscle in Asthma' in Airway Smooth Muscle in Asthma and COPD, Wiley, pp. 181-199.
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Booth, D, Provan, J & Maggs, CA 2008, 'Seaweed Invasions' in Johnson, CR (ed), Seaweed Invasions: A Synthesis of Ecological, Economic and Legal Imperatives, Walter de Gruyter, pp. 65-76.
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A wide range of vectors is currently introducing a plethora of alien marine species into indigenous marine species assemblages. Over the past two decades, molecular studies of non-native seaweeds, including cryptic invaders, have successfully identified the species involved and their sources; we briefly review these studies. As yet, however, little research has been directed towards examining the genetic consequences of seaweed invasions. Here we provide an overview of seaweed invasions from a genetic perspective, focusing on invader species for which the greatest amount of information is available. We review invasion processes, and rationalize evolutionary and genetic consequences for the indigenous and invader species into two main groups: (1) changes in genepool composition, in population structure and allele frequencies; and (2) changes in genome organization at the species level through hybridization, and in individual gene expression profiles at the levels of expressed messenger RNA and the proteome (i.e., all proteins synthesized) and thus the phenotype. We draw on studies of better-known aquatic and terrestrial organisms to point the way forward in revealing the genetic consequences of seaweed invasions. We also highlight potential applications of more recent methodological and statistical approaches, such as microarray technology, assignment tests and mixed stock analysis. © 2007 by Walter de Gruyter GmbH & Co. KG, 10785 Berlin All rights reserved.

Booth, DJ & Biro, P 2008, 'Adaptation' in Jorgensen, SE (ed), Encyclopedia of Ecology, Elsevier, Amsterdam, pp. 43-47.
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© 2008 Elsevier B.V. All rights reserved. While adaptations to local environments are well recognized, their actual influence on the dynamics of organisms (e.g., demography of mortality, growth, and reproduction) at a population level are less studied. Here, we review some of the evidence that morphological, behavioral, life-history, and physiological adaptations can affect populations. We emphasize the fact that adaptations and adaptive changes can be both a cause and consequence of observed population dynamics. Individual responses to the environment integrate to affect dynamics of populations but may also indicate how well the individual is adapted. We also note how adaptations at larger scales (e.g., clinal differences in energy budgets across latitudes) affect population dynamics.

Booth, DJ & Figueira, WF 2008, 'Resistance and Buffer Capacity' in Jorgensen, SE (ed), Encyclopedia of Ecology, Elsevier, Amsterdam, pp. 3004-3009.
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© 2008 Elsevier B.V. All rights reserved. Populations differ considerably in their ability to resist environmental changes, such as physical disturbances (storms, etc.) and biological pressures (e.g., pulses of predators, invasive species). Individual responses such as shelter-seeking behavior, cyst formation, and burrowing may protect them from mortality or enhance reproduction. These responses, coupled with population-level processes such as density-dependent demography and propagule connectivity, help to determine how well a population is buffered from a changing environment. Here, we review the ways in which populations are more or less resistant to the environment, how this affects their persistence, and what are the implications for the management of renewable resources.

Booth, DJ & Murray, BR 2008, 'Coexistence' in Jørgensen, SE & Fath, BD (eds), Encyclopedia of Ecology, Elsevier, Amsterdam, pp. 664-668.
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© 2008 Elsevier B.V. All rights reserved. Despite theoretical arguments regarding the difficulties of similar species coexisting, many habitats support large numbers of species and populations in high densities. In this article, we discuss the mechanisms by which populations and species coexist. Most of the types of interactions between species and individuals, including predation and competition, have the potential to promote or reduce coexistence. For instance, strongly asymmetrical competition may cause one species to go extinct, but competitive networks may promote coexistence of three or more species. Explanations for coexistence of huge numbers of species on coral reefs or rainforests have expanded from niche diversification hypotheses to, more recently, disturbance-mediated regimes and random recruitment from larval assemblages. Life-history tradeoffs and resting stages such as seed banks in plants can also promote coexistence, and neutral models that assume that the above forces are not important can also lead to a level of coexistence.

Chen, M, Donohoe, K, Crossett, B, Schliep, MT & Larkum, A 2008, 'Molecular bases of antenna systems adaptation in a Chl d- containing organism' in Allen, JF, Ganntt, E, Golbeck, J & Osmond, B (eds), Photosynthesis: Energy from the Sun, Springer.

Chiarella, C, El-Hassan, N & Kucera, A 2008, 'The Evaluation of Discrete Barrier Options in a Path Integral Framework' in Kontoghiorghes, E, Rustem, B & Winker, P (eds), Computational Methods in Financial Engineering, Springer Berlin Heidelberg, Germany, pp. 117-144.
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The pricing of discretely monitored barrier options is a difficult problem. In general, there is no known closed form solution for pricing such options. A path integral approach to the evaluation of barrier options is developed. This leads to a backward recursion functional equation linking the pricing functions at successive barrier points. This functional equation is solved by expanding the pricing functions in Fourier-Hermite series. The backward recursion functional equation then becomes the backward recurrence relation for the coefficients in the Fourier-Hermite expansion of the pricing functions. A very efficient and accurate method for generating the pricing function at any barrier point is thus obtained. A number of numerical experiments with the method are performed in order to gain some understanding of the nature of convergence. Results for various volatility values and different numbers of basis functions in the Fourier-Hermite expansion are presented. Comparisons are given between pricing of discrete barrier option in the path integral framework and by use of finite difference methods.

Green, DW & Ben-Nissan, B 2008, 'Biomimetics: Bio-inspired Engineering of Human Tissue Scaffolding for Regenerative Medicine' in Tateishi, T (ed), Biomaterials in Asia, WORLD SCIENTIFIC, Singapore, pp. 364-385.
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Huete, A, Kim, Y, Ratana, P, Didan, K, Shimabukuro, Y & Miura, T 2008, 'Assessment of Phenologic Variability in Amazon Tropical Rainforests Using Hyperspectral Hyperion and MODIS Satellite Data' in Kalacska, M & Sanchez-Azofeifa, A (eds), Hyperspectral Remote Sensing of Tropical and Sub-Tropical Forests, CRC Press, Boca Raton, Florida, USA, pp. 233-259.
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© 2008 by Taylor & Francis Group, LLC. Phenology represents the seasonal timing and annual repetition of biologic life cycle events and is a characteristic property of ecosystem functioning and predictor of ecosystem processes. Shifts in phenology depict a canopy’s integrated response to environmental change and influence local biogeochemical processes, including nutrient dynamics, photosynthesis, water cycling, soil moisture depletion, and canopy physiology [1]. An understanding of vegetation phenology is prerequisite to interannual studies and predictive modeling of land surface responses to climate change [2-4].

Kjelleberg, S, McDougald, D, Rasmussen, TB & Givskov, M 2008, 'Quorum-Sensing Inhibition' in Winans, SC & Bassler, BL (eds), Chemical Communication among Bacteria, ASM Press, pp. 393-416.
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Kordzakhia, N & Novikov, A 2008, 'Pricing of Defaultable Securities under Stochastic Interest' in Sarychev, A, Shiryaev, A, Guerra, M & Grossinho, M (eds), Mathematical Control Theory and Finance, Springer, Berlin, pp. 251-263.

McDougald, D, Klebensberger, J, Tolker‐Nielsen, T, Webb, JS, Conibear, T, Rice, SA, Kirov, SM, Matz, C & Kjelleberg, S 2008, 'Pseudomonas aeruginosa: A Model for Biofilm Formation' in Pseudomonas, Wiley, pp. 215-253.
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Miura, T, Huete, A, Guima√£es Ferreira, L, Sano, E & Yoshioka, H 2008, 'A Technique for Reflectance Calibration of Airborne Hyperspectral Spectrometer Data Using a Broad, Multiband Radiometer' in Kalacska, M & Sanchez-Azofeifa, A (eds), Hyperspectral Remote Sensing of Tropical and Sub-Tropical Forests, CRC Press, Boca Raton, Florida, USA, pp. 213-232.
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© 2008 by Taylor & Francis Group, LLC. Airborne radiometers have been employed for various remote sensing applications, including optical characterizations of forest canopies [1], surface reflectance factor retrievals from satellite imagery [2], spatial extrapolation of evaporation over agricultural fields [3], and scaling up and validation of satellite data products [4,5]. These studies have found the utility of airborne radiometers because (1) they can rapidly obtain data over rather large areas, encompassing fields having considerably different surface properties [3]; and (2) they can measure reflectance factors of tall objects that cannot be reached from ground (e.g., forest canopies) [1]. Airborne or helicopter-based radiometers are typically flown at low altitudes (<150 m above ground level) “below atmosphere.” On the ground, another radiometer (the same model) cross-calibrated with the ones in air is set up, continuously measuring radiances reflected off a white reference panel during the flights, to later convert airborne data to reflectance factors by ratioing (e.g., Holm et al. [5]).

Rice, SA, Kjelleberg, S, Givskov, M, De Boer, W & Chernin, LS 2008, 'Section 8 update: Detection of bacterial homoserine lactone quorum sensing signals' in Molecular Microbial Ecology Manual, Springer Netherlands, pp. 3531-3551.
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Saunders, BM, Orme, IM & Basaraba, RJ 2008, 'Immunopathology of Tuberculosis' in Handbook of Tuberculosis, Wiley, pp. 245-278.
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Schlögl, E & Schlögl, L 2008, 'Factor Distributions Implied by Quoted CDO Spreads' in Cont, R (ed), Frontiers in Quantitative Finance, Wiley, New Jersey, USA, pp. 217-234.
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Upadhyaya, NM, Zhou, X-R, Zhu, Q-H, Eamens, A, Ramm, K, Wu, L, Sivakumar, R, Kumar, S, Narayanan, KK, Thomas, G, Kato, T, Yun, D-W, Peacock, WJ & Dennis, ES 2008, 'A gene machine for rice' in Rice Genetics Collection, World Scientific Publishing Company, pp. 352-355.
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Zhang, Y, Chen, M, Church, B, Larkum, AWD & Jermiin, LS 2008, 'Modelling the Structure of the IsiA-PS I Supercomplex' in Photosynthesis. Energy from the Sun, Springer Netherlands, pp. 347-350.
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Abbott, B, Abbott, R, Adhikari, R, Agresti, J, Ajith, P, Allen, B, Amin, R, Anderson, SB, Anderson, WG, Arain, M, Araya, M, Armandula, H, Ashley, M, Aston, S, Aufmuth, P, Aulbert, C, Babak, S, Ballmer, S, Bantilan, H, Barish, BC, Barker, C, Barker, D, Barr, B, Barriga, P, Barton, MA, Bayer, K, Belczynski, K, Betzwieser, J, Beyersdorf, PT, Bhawal, B, Bilenko, IA, Billingsley, G, Biswas, R, Black, E, Blackburn, K, Blackburn, L, Blair, D, Bland, B, Bogenstahl, J, Bogue, L, Bork, R, Boschi, V, Bose, S, Brady, PR, Braginsky, VB, Brau, JE, Brinkmann, M, Brooks, A, Brown, DA, Bullington, A, Bunkowski, A, Buonanno, A, Burmeister, O, Busby, D, Byer, RL, Cadonati, L, Cagnoli, G, Camp, JB, Cannizzo, J, Cannon, K, Cantley, CA, Cao, J, Cardenas, L, Casey, MM, Castaldi, G, Cepeda, C, Chalkley, E, Charlton, P, Chatterji, S, Chelkowski, S, Chen, Y, Chiadini, F, Chin, D, Chin, E, Chow, J, Christensen, N, Clark, J, Cochrane, P, Cokelaer, T, Colacino, CN, Coldwell, R, Conte, R, Cook, D, Corbitt, T, Coward, D, Coyne, D, Creighton, JDE, Creighton, TD, Croce, RP, Crooks, DRM, Cruise, AM, Cumming, A, Dalrymple, J, D'Ambrosio, E, Danzmann, K, Davies, G, DeBra, D, Degallaix, J, Degree, M, Demma, T, Dergachev, V, Desai, S, DeSalvo, R, Dhurandhar, S, Diaz, M, Dickson, J, Di Credico, A, Diederichs, G, Dietz, A, Doomes, EE, Drever, RWP, Dumas, J-C, Dupuis, RJ, Dwyer, JG, Ehrens, P, Espinoza, E, Etzel, T, Evans, M, Evans, T, Fairhurst, S, Fan, Y, Fazi, D, Fejer, MM, Finn, LS, Fiumara, V, Fotopoulos, N, Franzen, A, Franzen, KY, Freise, A, Frey, R, Fricke, T, Fritschel, P, Frolov, VV, Fyffe, M, Galdi, V, Garofoli, J, Gholami, I, Giaime, JA, Giampanis, S, Giardina, KD, Goda, K, Goetz, E, Goggin, LM, Gonzalez, G, Gossler, S, Grant, A, Gras, S, Gray, C, Gray, M, Greenhalgh, J, Gretarsson, AM, Grosso, R, Grote, H, Grunewald, S, Guenther, M, Gustafson, R, Hage, B, Hammer, D, Hanna, C, Hanson, J, Harms, J, Harry, G, Harstad, E, Hayler, T, Heefner, J, Heng, IS, Heptonstall, A, Heurs, M, Hewitson, M, Hild, S, Hirose, E, Hoak, D, Hosken, D, Hough, J, Howell, E, Hoyland, D, Huttner, SH, Ingram, D, Innerhofer, E, Ito, M, Itoh, Y, Ivanov, A, Jackrel, D, Johnson, B, Johnson, WW, Jones, DI, Jones, G, Jones, R, Ju, L, Kalmus, P, Kalogera, V, Kasprzyk, D, Katsavounidis, E, Kawabe, K, Kawamura, S, Kawazoe, F, Kells, W, Keppel, DG, Khalili, FY, Kim, C, King, P, Kissel, JS, Klimenko, S, Kokeyama, K & et al. 2008, 'All-sky search for periodic gravitational waves in LIGO S4 data', PHYSICAL REVIEW D, vol. 77, no. 2.
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Aharonovich, I, Tamir, S & Lifshitz, Y 2008, 'Growth of SiO(x) nanowires by laser ablation', NANOTECHNOLOGY, vol. 19, no. 6, pp. 1-8.
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Amorphous SiOx nanowires (NWs) were synthesized using laser ablation of silicon-containing targets. The influence of various parameters such as target composition, substrate type, substrate temperature and carrier gas on the growth process was studied. The NWs were characterized using high resolution scanning and transmission electron microscopes (HRSEM and HRTEM) with their attachments: electron dispersive spectroscopy (EDS) and energy electron loss spectroscopy (EELS). A metal catalyst was found essential for the NW growth. A growth temperature higher than 1000 ?C was necessary for the NW formation using an Ar-based carrier gas at 500 Torr. The use of Ar5%H2 instead of pure Ar resulted in a higher yield and longer NWs. Application of a diffusion barrier on top of the Si substrate guaranteed the availability of metal catalyst droplets on the surface, essential for the NW growth. Ni was found to be a better catalyst than Au in terms of the NW yield and length. Two alternative sequences for the evolution of the amorphous SiOx NWs were considered: (a) the formation of Si NWs first and their complete oxidation afterwards, which seems to be doubtful, (b) the direct formation of SiOx NWs, which is more likely to occur. The direct formation mechanism was proposed to advance in three stages: preferential adsorption of SiOx clusters on the catalyst surface first, a successive surface diffusion to the catalyst droplet lower hemisphere, and finally the formation and growth of the NW between the catalyst and the substrate.

Aharonovich, I, Zhou, C, Stacey, A, Treussart, F, Roch, J-F & Prawer, S 2008, 'Formation of color centers in nanodiamonds by plasma assisted diffusion of impurities from the growth substrate', APPLIED PHYSICS LETTERS, vol. 93, no. 24, p. 243112.
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A technique to create nickel-related single color centers in individual nanodiamonds is demonstrated. The method involves implantation of nickel ions into a substrate onto which the diamond nanocrystals are subsequently grown by chemical vapor deposition

Ajami, K, Pitman, MR, Wilson, CH, Park, J, Menz, RI, Starr, AE, Cox, JH, Abbott, CA, Overall, CM & Gorrell, MD 2008, 'Corrigendum to “Stromal cell‐derived factors 1α and 1β, inflammatory protein‐10 and interferon‐inducible T cell chemo‐attractant are novel substrates of dipeptidyl peptidase 8” [FEBS Lett. 582 (2008) 819–825]', FEBS Letters, vol. 582, no. 7, pp. 1168-1168.
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Ajami, K, Pitman, MR, Wilson, CH, Park, J, Menz, RI, Starr, AE, Cox, JH, Abbott, CA, Overall, CM & Gorrell, MD 2008, 'Stromal cell‐derived factors 1α and 1β, inflammatory protein‐10 and interferon‐inducible T cell chemo‐attractant are novel substrates of dipeptidyl peptidase 8', FEBS Letters, vol. 582, no. 5, pp. 819-825.
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N‐terminal truncation of chemokines by proteases including dipeptidyl peptidase (DP) IV significantly alters their biological activity; generally ablating cognate G‐protein coupled receptor engagement and often generating potent receptor antagonists. DP8 is a recently recognised member of the prolyl oligopeptidase gene family that includes DPIV. Since DPIV is known to process chemokines we surveyed 27 chemokines for cleavage by DP8. We report DP8 cleavage of the N‐terminal two residues of IP10 (CXCL10), ITAC (CXCL11) and SDF‐1 (CXCL12). This has implications for DP8 substrate specificity. Chemokine cleavage and inactivation may occur in vivo upon cell lysis and release of DP8 or in the inactivation of internalized chemokine/receptor complexes.

Andersson, CR, Helliwell, CA, Bagnall, DJ, Hughes, TP, Finnegan, EJ, Peacock, WJ & Dennis, ES 2008, 'The FLX Gene of Arabidopsis is required for FRI-dependent activation of FLC expression', PLANT AND CELL PHYSIOLOGY, vol. 49, no. 2, pp. 191-200.
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The Arabidopsis FLOWERING LOCUS C (FLC) gene encodes a MADS box protein that acts as a dose-dependent repressor of flowering. Mutants and ecotypes with elevated expression of FLC are late flowering and vernalization responsive. In this study we describe

Apanasovich, TV, Ruppert, D, Lupton, JR, Popovic, N, Turner, ND, Chapkin, RS & Carroll, RJ 2008, 'Aberrant Crypt Foci and Semiparametric Modeling of Correlated Binary Data', Biometrics, vol. 64, no. 2, pp. 490-500.
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Summary Motivated by the spatial modeling of aberrant crypt foci (ACF) in colon carcinogenesis, we consider binary data with probabilities modeled as the sum of a nonparametric mean plus a latent Gaussian spatial process that accounts for short‐range dependencies. The mean is modeled in a general way using regression splines. The mean function can be viewed as a fixed effect and is estimated with a penalty for regularization. With the latent process viewed as another random effect, the model becomes a generalized linear mixed model. In our motivating data set and other applications, the sample size is too large to easily accommodate maximum likelihood or restricted maximum likelihood estimation (REML), so pairwise likelihood, a special case of composite likelihood, is used instead. We develop an asymptotic theory for models that are sufficiently general to be used in a wide variety of applications, including, but not limited to, the problem that motivated this work. The splines have penalty parameters that must converge to zero asymptotically: we derive theory for this along with a data‐driven method for selecting the penalty parameter, a method that is shown in simulations to improve greatly upon standard devices, such as likelihood crossvalidation. Finally, we apply the methods to the data from our experiment ACF. We discover an unexpected location for peak formation of ACF.

Arroyo, M, Birkin, PR, Gale, PA, García-Garrido, SE & Light, ME 2008, 'Anion-triggered electrodeposition in ferrocene-functionalised ortho-phenylenediamine-based receptors', New Journal of Chemistry, vol. 32, no. 7, pp. 1221-1221.
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Arulsamy, AD & Fronzi, M 2008, 'Length-dependent resistance model for a single-wall carbon nanotube', Physica E: Low-dimensional Systems and Nanostructures, vol. 41, no. 1, pp. 74-79.
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Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2008, '2,3,10,11-Tetramethoxy-6,7,14,15-tetrahydro-6,14-methanocycloocta[1,2-b;5,6-b′]diquinoline', Acta Crystallographica Section E Structure Reports Online, vol. 64, no. 1, pp. o48-o48.
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Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2008, '5bα,6,7,13bα,14,15-Hexahydroacridino[4,3-c]acridine', Acta Crystallographica Section E Structure Reports Online, vol. 64, no. 6, pp. o1136-o1136.
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Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2008, 'Synthesis and inclusion properties of new nitrated C2− symmetric diquinoline hosts', CrystEngComm, vol. 10, no. 7, pp. 839-839.
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Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2008, 'The structural convergence of two aromatic inclusion host families', CrystEngComm, vol. 10, no. 1, pp. 131-137.
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Asquith, KL, Ramshaw, HS, Hansbro, PM, Beagley, KW, Lopez, AF & Foster, PS 2008, 'The IL-3/IL-5/GM-CSF Common β Receptor Plays a Pivotal Role in the Regulation of Th2 Immunity and Allergic Airway Inflammation', The Journal of Immunology, vol. 180, no. 2, pp. 1199-1206.
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Abstract The eosinophil is a central effector cell in allergic asthma. Differentiation and function of eosinophils are regulated by the CD4 Th2 cytokines IL-3, IL-5, and GM-CSF, which all signal through a common β receptor subunit (βc). Recent therapeutic approaches targeting IL-5 alone have not ablated tissue accumulation of eosinophils and have had limited effects on disease progression, suggesting important roles for IL-3 and GM-CSF. By using a mouse model of allergic airways inflammation, we show that allergen-induced expansion and accumulation of eosinophils in the lung are abolished in βc-deficient (βc−/−) mice. Moreover, βc deficiency resulted in inhibition of hallmark features of asthma, including airways hypersensitivity, mucus hypersecretion, and production of Ag-specific IgE. Surprisingly, we also identified a critical role for this receptor in regulating type 2 immunity. Th2 cells in the lung of allergen-challenged βc−/− mice were limited in their ability to proliferate, produce cytokines, and migrate to effector sites, which was attributed to reduced numbers of myeloid dendritic cells in the lung compartment. Thus, the βc plays a critical role in allergen-induced eosinophil expansion and infiltration and is pivotal in regulating molecules that promote both early and late phases of allergic inflammation, representing a novel target for therapy.

Baladandayuthapani, V, Mallick, BK & Carroll, RJ 2008, 'Correction', Journal of Computational and Graphical Statistics, vol. 17, no. 2, pp. 515-515.
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Baladandayuthapani, V, Mallick, BK, Young Hong, M, Lupton, JR, Turner, ND & Carroll, RJ 2008, 'Bayesian Hierarchical Spatially Correlated Functional Data Analysis with Application to Colon Carcinogenesis', Biometrics, vol. 64, no. 1, pp. 64-73.
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Summary In this article, we present new methods to analyze data from an experiment using rodent models to investigate the role of p27, an important cell‐cycle mediator, in early colon carcinogenesis. The responses modeled here are essentially functions nested within a two‐stage hierarchy. Standard functional data analysis literature focuses on a single stage of hierarchy and conditionally independent functions with near white noise. However, in our experiment, there is substantial biological motivation for the existence of spatial correlation among the functions, which arise from the locations of biological structures called colonic crypts: this possible functional correlation is a phenomenon we term crypt signaling. Thus, as a point of general methodology, we require an analysis that allows for functions to be correlated at the deepest level of the hierarchy. Our approach is fully Bayesian and uses Markov chain Monte Carlo methods for inference and estimation. Analysis of this data set gives new insights into the structure of p27 expression in early colon carcinogenesis and suggests the existence of significant crypt signaling. Our methodology uses regression splines, and because of the hierarchical nature of the data, dimension reduction of the covariance matrix of the spline coefficients is important: we suggest simple methods for overcoming this problem.

Barken, KB, Pamp, SJ, Yang, L, Gjermansen, M, Bertrand, JJ, Klausen, M, Givskov, M, Whitchurch, CB, Engel, JN & Tolker-Nielsen, T 2008, 'Roles of type IV pili, flagellum-mediated motility and extracellular DNA in the formation of mature multicellular structures in Pseudomonas aeruginosa biofilms', ENVIRONMENTAL MICROBIOLOGY, vol. 10, no. 9, pp. 2331-2343.
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When grown as a biofilm in laboratory flow chambers Pseudomonas aeruginosa can develop mushroom-shaped multicellular structures consisting of distinct subpopulations in the cap and stalk portions. We have previously presented evidence that formation of the cap portion of the mushroom-shaped structures in P. aeruginosa biofilms occurs via bacterial migration and depends on type IV pili (Mol Microbiol 50: 61-68). In the present study we examine additional factors involved in the formation of this multicellular substructure. While pilA mutants, lacking type IV pili, are deficient in mushroom cap formation, pilH and chpA mutants, which are inactivated in the type IV pili-linked chemosensory system, showed only minor defects in cap formation. On the contrary, fliM mutants, which are non-flagellated, and cheY mutants, which are inactivated in the flagellum-linked chemotaxis system, were largely deficient in cap formation. Experiments involving DNase treatment of developing biofilms provided evidence that extracellular DNA plays a role in cap formation. Moreover, mutants that are deficient in quorum sensing-controlled DNA release formed microcolonies upon which wild-type bacteria could not form caps. These results constitute evidence that type IV pili, flagellum-mediated motility and quorum sensing-controlled DNA release are involved in the formation of mature multicellular structures in P. aeruginosa biofilms. © 2008 The Authors.

Barratt, J, Al Qassab, S, Reichel, MP & Ellis, JT 2008, 'The development and evaluation of a nested PCR assay for detection of Neospora caninum and Hammondia heydorni in feral mouse tissues', MOLECULAR AND CELLULAR PROBES, vol. 22, no. 4, pp. 228-233.
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The development of a novel nested polymerase chain reaction is described and used for detecting the presence of Neospora caninum and Hammondia heydorni DNA in DNA extracted from feral rodent tissues. A unique strategy was used for design of an assay that could be adapted for detecting DNA from more than one member of Toxoplasmatinae simultaneously with a minimal number of additional steps. The level of sensitivity described for this assay is comparable to real time-PCR and other nested PCR assays. Twenty-eight of 104 feral mice tested positive for N. caninum in at least one tissue (the brain, heart or liver) studied. In this study, eight instances are reported where the brain tested negative to N. caninum while at least one other tissue was positive. This suggests that prior studies, which screened only the brain, describe prevalence levels that are under-represented. None of 54 mouse brains tested positive for H. heydorni DNA. This suggests that mice are rarely infected by H. heydorni although this hypothesis needs to be explored further. Data obtained in the current study suggest that N. caninum is a common parasite of feral rodents which may be important in the epidemiology of the disease. © 2008 Elsevier Ltd. All rights reserved.

Bates, GW, Gale, PA, Light, ME, Ogden, MI & Warriner, CN 2008, 'Structural diversity in the first metal complexes of 2,5-dicarboxamidopyrroles and 2,5-dicarbothioamidopyrroles', Dalton Transactions, no. 31, pp. 4106-4106.
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Beard, JR, Earnest, A, Morgan, G, Chan, H, Summerhayes, R, Dunn, TM, Tomaska, NA & Ryan, L 2008, 'Socioeconomic disadvantage and acute coronary events - A spatiotemporal analysis', EPIDEMIOLOGY, vol. 19, no. 3, pp. 485-492.
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BACKGROUND: The associations between socioeconomic disadvantage and ischemic heart disease are not well understood. We explore the relationship between socioeconomic factors and acute coronary events using spatiotemporal analysis. METHODS: We studied all deaths from acute myocardial infarction and hospital admissions for acute coronary syndrome and related revascularization procedures for the state of New South Wales, Australia, from 1996 through 2002. We used conditional autoregressive models to describe how characteristics of subjects' place of residence (socioeconomic disadvantage, proportion of the population of indigenous background, and metropolitan versus nonmetropolitan area) influenced admissions and mortality. RESULTS: There were 32,534 deaths due to acute myocardial infarction and 129,045 admissions for acute coronary syndrome. We found a relationship between increasing socioeconomic disadvantage and mortality (unadjusted relative risk for highest quartile of disadvantage relative to lowest = 1.40; 95% confidence interval = 1.27-1.54) as well as admissions (1.41; 1.28-1.55). After accounting for admission rates, socioeconomic disadvantage was associated with lower rates of angiography (0.75; 0.63-0.88) and interventional angiography (0.70; 0.56-0.85). After adjusting for socioeconomic disadvantage, areas with higher proportions of the population identified as indigenous had higher rates of admission and mortality, while residency in the state capital was associated with higher admission rates and more interventional angiography. After accounting for admission rates, the association of socioeconomic disadvantage with mortality was reduced. CONCLUSIONS: Socioeconomic disadvantage increases both the risk of acute coronary syndrome and related mortality. A contributing factor appears to be a reduced chance of receiving appropriate care. Regions with a higher proportion of indigenous residents show risk beyond the effects of general socioeconomic ...

Beavis, A, Dawson, M, Doble, P, Scolyer, RA, Bourne, R, Li, L-XL, Murali, R, Stretch, JR, Lean, CL, Uren, RF & Thompson, JF 2008, 'Confirmation of sentinel lymph node identity by analysis of fine-needle biopsy samples using inductively coupled plasma-mass spectrometry', ANNALS OF SURGICAL ONCOLOGY, vol. 15, no. 3, pp. 934-940.
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Background: The sentinel lymph node (SLN) biopsy technique is a reliable means of determining the tumor-harboring status of regional lymph nodes in melanoma patients. When technetium 99 m-labeled antimony trisulfide colloid ((99) Tc-m-Sb2S3) particles ar

Behnia, S, Akhshani, A, Mahmodi, H & Akhavan, A 2008, 'A novel algorithm for image encryption based on mixture of chaotic maps', Chaos, Solitons & Fractals, vol. 35, no. 2, pp. 408-419.
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BEHNIA, S, AKHSHANI, A, MAHMODI, H & AKHAVAN, A 2008, 'CHAOTIC CRYPTOGRAPHIC SCHEME BASED ON COMPOSITION MAPS', International Journal of Bifurcation and Chaos, vol. 18, no. 01, pp. 251-261.
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In recent years, a growing number of cryptosystems based on chaos have been proposed. But most of them have encountered many problems such as small key space and weak security. In the present paper, a new kind of chaotic cryptosystem based on Composition of Trigonometric Chaotic Maps is proposed. These maps which are defined as ratios of polynomials of degree N, have interesting properties such as invariant measure, ergodicity, variable chaotic region with respect to the control parameters and ability to construct composition form of maps. We have used a composition of chaotic map to shuffle the position of image pixels. Another composition of chaotic map is used in diffusion process. According to the performed analysis, the introduced algorithm can satisfy the required performances such as high level security, large key space and the acceptable encryption speed.

Behnia, S, Akhshani, A, Mahmodi, H & Hobbenagi, H 2008, 'On the calculation of chaotic features for nonlinear time series', Chinese Journal of Physics, vol. 46, no. 4, pp. 394-404.
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Recent developments in the theory of nonlinear dynamics have paved the way for analyzing signals generated from nonlinear biological systems. This study is aimed at investigating the application of nonlinear analysis in differentiating between patients and healthy persons, as well as in investigating the relation between ergodicity and stationarity in the dynamics of the heart. The nonlinear analysis in this work includes attractor reconstruction, estimation of the correlation dimension, calculation of the largest Lyapunov exponent, the approximate entropy, the sample entropy, and a Poincaré plot. Four groups of electrical cardiograph (ECG) signals have been investigated. Our results, obtained from clinical data, confirm the previous studies; this allows one to distinguish between a healthy group and a group of patients with more confidence than the standard methods for heart rate time series. Furthermore we extended our understanding of heart dynamics using entropies and a Poincaré plot along with the correlation dimension and the largest Lyapunov exponent. We have also obtained the results that stationarity and ergodicity are related to each other in heart dynamics. © 2008 THE PHYSICAL SOCIETY OF THE REPUBLIC OF CHINA.

Bertinshaw, J, Kirkup, L, Phillips, M & Placido, F 2008, 'A system for supplying constant electrical power for postprocessing tin-doped indium oxide films', REVIEW OF SCIENTIFIC INSTRUMENTS, vol. 79, no. 7, pp. 1-3.
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Annealing tin doped indium oxide (ITO) thin films by self-heating shows potential for reducing the crystallization temperature required to optimize the optical and electrical properties of the films. It also shows promise as a cost effective method of studying the heat treatment process in situ. A computer based solution was developed to allow for a precise control over the annealing process. To anneal at a fixed temperature, a feedback loop senses changes in the resistance of the sample and adjusts the current across the load accordingly to ensure constant delivery of power to an ITO film. © 2008 American Institute of Physics.

Bhosale, SV & Langford, SJ 2008, 'ChemInform Abstract: The Development of Yoctowells as a Basis for Modeling Biological Systems.', ChemInform, vol. 39, no. 14.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Bhosale, SV, Bissett, MA, Forsyth, C, Langford, SJ, Neville, SM, Shapter, JG, Weeks, L & Woodward, CP 2008, 'Designing Functionalized Porphyrins Capable of Pseudo-2D Self-Assembly on Surfaces', Organic Letters, vol. 10, no. 14, pp. 2943-2946.
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Bhosale, SV, Chong, C, Forsyth, C, Langford, SJ & Woodward, CP 2008, 'ChemInform Abstract: Investigations of Rotamers in Diaxial Sn(IV)porphyrin Phenolates — Towards a Molecular Timepiece.', ChemInform, vol. 39, no. 45.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Bhosale, SV, Chong, C, Forsyth, C, Langford, SJ & Woodward, CP 2008, 'Investigations of rotamers in diaxial Sn(IV)porphyrin phenolates—towards a molecular timepiece', Tetrahedron, vol. 64, no. 36, pp. 8394-8401.
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Bhosale, SV, Jani, CH & Langford, SJ 2008, 'ChemInform Abstract: Chemistry of Naphthalene Diimides', ChemInform, vol. 39, no. 21.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Bojko, K, Roux, C & Reedy, BJ 2008, 'An Examination of the Sequence of Intersecting Lines Using Attenuated Total Reflectance-Fourier Transform Infrared Spectral Imaging', JOURNAL OF FORENSIC SCIENCES, vol. 53, no. 6, pp. 1458-1467.
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In this study, the potential of attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectral imaging as a technique to determine the sequence of line crossings was examined. The technique was successful in determining the sequence of heterogeneous line intersections produced using ballpoint pens and laser printers. By imaging at characteristic frequencies, it was possible to form spectral images showing the spatial distribution of the materials. By examining the spectral images from the inks, it was possible to determine whether the ink was above or below the toner. In blind testing, ATR-FTIR spectral imaging results were directly compared to those obtained by eight experienced forensic document examiners using methods regularly employed in casework. ATR-FTIR spectral imaging was shown to achieve a 100% success rate in the blind tests, whereas some incorrect sequence determinations were made by the forensic document examiners when using traditional techniques. The technique was unable to image ink-jet printing, gel pens, roller ball pens, and felt-tip pens, and was also unable to determine the sequence of intersecting ballpoint pen lines. © 2008 American Academy of Forensic Sciences.

Bosire, JO, Dahdouh-Guebas, F, Walton, M, Crona, BI, Lewis, RR, Field, C, Kairo, JG & Koedam, N 2008, 'Functionality of restored mangroves: A review', Aquatic Botany, vol. 89, no. 2, pp. 251-259.
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Widespread mangrove degradation coupled with the increasing awareness of the importance of these coastal forests have spurred many attempts to restore mangroves but without concomitant assessment of recovery (or otherwise) at the ecosystem level in many areas. This paper reviews literature on the recovery of restored mangrove ecosystems using relevant functional indicators. While stand structure in mangrove stands is dependent on age, site conditions and silvicultural management, published data indicates that stem densities are higher in restored mangroves than comparable natural stands; the converse is true for basal area. Biomass increment rates have been found to be higher in younger stands than older stands (e.g. 12 t ha-1 year-1 for a 12 years plantation compared to 5.1 t ha-1 year-1 for a 80-year-old plantation). Disparities in patterns of tree species recruitment into the restored stands have been observed with some stands having linear recruitment rates with time (hence enhancing stand complexity), while some older stands completely lacked the understorey. Biodiversity assessments suggest that some fauna species are more responsive to mangrove degradation (e.g. herbivorous crabs and mollusks in general), and thus mangrove restoration encourages the return of such species, in some cases to levels equivalent to those in comparable natural stands. The paper finally recommends various mangrove restoration pathways in a functional framework dependent on site conditions and emphasizes community involvement and ecosystem level monitoring as integral components of restoration projects. © 2008 Elsevier B.V. All rights reserved.

Boynton-Jarrett, R, Ryan, LM, Berkman, LF & Wright, RJ 2008, 'Cumulative Violence Exposure and Self-Rated Health: Longitudinal Study of Adolescents in the United States', PEDIATRICS, vol. 122, no. 5, pp. 961-970.
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Objective. The goal was to determine whether cumulative exposure to violence in childhood and adolescence contributes to disparities in self-rated health among a nationally representative sample of US adolescents. Methods. The National Longitudinal Survey of Youth 1997 is an ongoing, 8-year (1997-2004), longitudinal, cohort study of youths who were 12 to 18 years of age at baseline (N = 8224). Generalized estimating equations were constructed to investigate the relationship between cumulative exposure to violence and risk for poor health. Results. At baseline, 75% of subjects reported excellent or very good health, 21.5% reported good health, and 4.5% reported fair or poor health. Cumulative violence exposures (witnessed gun violence, threat of violence, repeated bullying, perceived safety, and criminal victimization) were associated with a graded increase in risk for poor health and reduced the strength of the relationship between household income and poor health. In comparison with subjects with no violence exposure, risk for poor self-rated health was 4.6 times greater among subjects who reported ≥5 forms of cumulative exposure to violence, controlling for demographic features and household income. Trend analysis revealed that, for each additional violence exposure, the risk of poor health increased by 38%. Adjustment for alcohol use, drug use, smoking, depressive symptoms, and family and neighborhood environment reduced the strength of the relationships between household income and cumulative exposure to violence scores and poor self-rated health, which suggests partial mediation of the effects of socioeconomic status and cumulative exposure to violence by these factors. Conclusions. In this nationally representative sample, social inequality in risk for poor self-rated health during the transition from adolescence to adulthood was partially attributable to disparities in cumulative exposure to violence. A strong graded association was noted between...

Bradfield, L & McNally, GP 2008, 'Unblocking in Pavlovian fear conditioning.', Journal of Experimental Psychology: Animal Behavior Processes, vol. 34, no. 2, pp. 256-265.
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Bruti Liberati, N, Martini, F, Piccardi, M & Platen, E 2008, 'A Hardware Generator of Multi-Point Distributed Random Numbers for Monte Carlo Simulation', Mathematics and Computers in Simulation, vol. 77, no. 1, pp. 45-56.
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Monte Carlo simulation of weak approximation of stochastic differential equations constitutes an intensive computational task. In applications such as finance, for instance, to achieve 'real time' execution, as often required, one needs highly efficient implementations of the multi-point distributed random number generator underlying the simulations. In this paper, a fast and flexible dedicated hardware solution on a field programmable gate array is presented. A comparative performance analysis between a software-only and the poposed hardware solution demonstrated that the hardware solution is bottleneck-free, retains the flexibility of the software solution and significantly increases the computational efficiency. Moreover, simulations in Applications wuch as economics insurance, physics, population dynamics, epidemiology, structural mechanics, checmistry and biotechnology can benefit from the obtained speedups.

Bruti-Liberati, N & Platen, E 2008, 'Strong predictor-corrector Euler methods for stochastic differential equations', STOCHASTICS AND DYNAMICS, vol. 8, no. 3, pp. 561-581.
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This paper introduces a new class of numerical schemes for the pathwise approximation of solutions of stochastic differential equations (SDEs). The proposed family of strong predictor-corrector Euler methods are designed to handle scenario simulation of solutions of SDEs. It has the potential to overcome some of the numerical instabilities that are often experienced when using the explicit Euler method. This is of importance, for instance, in finance where martingale dynamics arise for solutions of SDEs with multiplicative diffusion coefficients. Numerical experiments demonstrate the improved asymptotic stability properties of the new symmetric predictor-corrector Euler methods.

Burgess, JK, Lee, JH, Ge, Q, Ramsay, EE, Poniris, MH, Parmentier, J, Roth, M, Johnson, PRA, Hunt, NH, Black, JL & Ammit, AJ 2008, 'Dual ERK and phosphatidylinositol 3‐kinase pathways control airway smooth muscle proliferation: Differences in asthma', Journal of Cellular Physiology, vol. 216, no. 3, pp. 673-679.
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AbstractHyperplasia of airway smooth muscle (ASM) within the bronchial wall of asthmatic patients has been well documented and is likely due to increased muscle proliferation. We have shown that ASM cells obtained from asthmatic patients proliferate faster than those obtained from non‐asthmatic patients. In ASM from non‐asthmatics, mitogens act via dual signaling pathways (both ERK‐ and PI 3‐kinase‐dependent) to control growth. In this study we are the first to examine whether dual pathways control the enhanced proliferation of ASM from asthmatics. When cells were incubated with 0.1% or 1% FBS, ERK activation was significantly greater in cells from asthmatic subjects (P < 0.05). In contrast, when cells were stimulated with 10% FBS, ERK activity was significantly greater in the non‐asthmatic cells. However, cell proliferation in asthmatic cells was still significantly higher in cells stimulated by both 1% and 10% FBS. Pharmacological inhibition revealed that although dual proliferative pathways control ASM growth in cells from non‐asthmatics stimulated with 10% FBS to an equal extent ([3H]‐thymidine incorporation reduced to 57.2 ± 6.9% by the PI 3‐kinase inhibitor LY294002 and 57.8 ± 1.1% by the ERK‐pathway inhibitor U0126); in asthmatics, the presence of a strong proliferative stimulus (10% FBS) reduces ERK activation resulting in a shift to the PI 3‐kinase pathway. The underlying mechanism appears to be upregulation of an endogenous MAPK inhibitor—MKP‐1—that constrains ERK signaling in asthmatic cells under strong mitogenic stimulation. This study suggests that the PI 3‐kinase pathway may be an attractive target for reversing hyperplasia in asthma. J. Cell. Physiol. 216: 673–679, 2008, © 2008 Wiley‐Liss, Inc.

Caltagirone, C, Gale, PA, Hiscock, JR, Brooks, SJ, Hursthouse, MB & Light, ME 2008, '1,3-Diindolylureas: high affinity dihydrogen phosphate receptors', Chemical Communications, no. 26, pp. 3007-3007.
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Caltagirone, C, Hiscock, JR, Hursthouse, MB, Light, ME & Gale, PA 2008, '1,3‐Diindolylureas and 1,3‐Diindolylthioureas: Anion Complexation Studies in Solution and the Solid State', Chemistry – A European Journal, vol. 14, no. 33, pp. 10236-10243.
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Abstract1,3‐Diindolylureas and thioureas have been synthesised and their anion complexation properties in solution studied. Whilst diindolylthioureas showed only moderate affinities and selectivities, diindolylureas show remarkably high affinity for dihydrogen phosphate in solution for an acyclic, neutral receptor in water/[D6]DMSO mixtures. These easy‐to‐make compounds adopt relatively planar conformations in the solid‐state and are able to donate four hydrogen bonds and yet not fill the coordination sphere of carbonate or phosphate, allowing two or three receptors to bind to each anion in the solid‐state.

Campbell, S, Botten, LC, McPhedran, RC & de Sterke, CM 2008, 'Modal method for classical diffraction by slanted lamellar gratings', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, vol. 25, no. 10, pp. 2415-2426.
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We consider lamellar gratings made of dielectric or lossy materials used in classical diffraction mounts. We show how the modal diffraction formulation may be generalized to deal with slanted lamellar gratings and illustrate the accuracy and versatility of the new method through study of highly slanted gratings in a homog- enization limit. We also comment on the completeness of the eigenmode basis and present tests enabling this completeness to be verified numerically. © 2008 Optical Society of America.

Cankurtaran, BO, Gale, JD & Ford, MJ 2008, 'First principles calculations using density matrix divide-and-conquer within the SIESTA methodology', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 20, no. 29, pp. 1-12.
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The density matrix divide-and-conquer technique for the solution of Kohn-Sham density functional theory has been implemented within the framework of the SIESTA methodology. Implementation details are provided where the focus is on the scaling of the computation time and memory use, in both serial and parallel versions. We demonstrate the linear-scaling capabilities of the technique by providing ground state calculations of moderately large insulating, semiconducting and (near-) metallic systems. This linear-scaling technique has made it feasible to calculate the ground state properties of quantum systems consisting of tens of thousands of atoms with relatively modest computing resources. A comparison with the existing order-N functional minimization (Kim-Mauri-Galli) method is made between the insulating and semiconducting systems. © 2008 IOP Publishing Ltd.

Carroll, RJ & Wang, Y 2008, 'Nonparametric variance estimation in the analysis of microarray data: a measurement error approach', Biometrika, vol. 95, no. 2, pp. 437-449.
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Castorina, A, Tiralongo, A, Cavallo, D, Loreto, C, Carnazza, ML, Iavicoli, S & D’Agata, V 2008, 'Expression profile of ErbB receptor’s family in human alveolar type 2-like cell line A549 exposed to hexavalent chromium', Toxicology in Vitro, vol. 22, no. 2, pp. 541-547.
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Castorina, A, Tiralongo, A, Giunta, S, Carnazza, ML, Rasi, G & D'Agata, V 2008, 'PACAP and VIP prevent apoptosis in schwannoma cells', Brain Research, vol. 1241, pp. 29-35.
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Chefi, S, Madani, A, Boussetta, H, Roux, C & Hammou, A 2008, 'Electrical properties of Al-doped oxyapatites at intermediate temperature', Journal of Power Sources, vol. 177, no. 2, pp. 464-469.
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Chen, H, Hansen, MJ, Jones, JE, Vlahos, R, Anderson, GP & Morris, MJ 2008, 'Long-term cigarette smoke exposure increases uncoupling protein expression but reduces energy intake', Brain Research, vol. 1228, no. 4, pp. 81-88.
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The appetite suppressing effect of tobacco is a major driver of smoking behaviour; however few studies have addressed the effects of chronic cigarette smoke exposure (SE) on appetite, body weight and metabolic markers. We compared the effects of SE to equivalent food restriction (pair-fed, PF), against sham-exposure, on body weight, adiposity, cytokines, and levels of uncoupling proteins (UCP) and brain neuropeptide Y (NPY) in male Balb/C mice. SE rapidly induced anorexia, and after 12 weeks, SE and PF groups were lighter than control animals (23.9 ± 0.2, 25.5 ± 0.5, 26.8 ± 0.4 g respectively, P < 0.05). White fat (WAT) masses were reduced by both SE and PF. Plasma leptin and insulin were reduced in SE mice; insulin was further reduced by PF. Brown fat UCP1 and 3 mRNA were increased in SE animals relative to PF animals, possibly promoting thermogenesis. WAT mRNA expression of the inflammatory cytokine, TNFα was doubled by SE, while IL-6 was reduced by both PF and SE. Hypothalamic NPY content was increased by SE (89.3 ± 2.8 vs. 75.9 ± 2.4 ng control, P < 0.05), and more by PF (100.7 ± 3.4 ng, P < 0.05 compared to both groups), suggesting disinhibition due to reduced adipose derived leptin. In contrast to equivalent food restriction, cigarette smoke exposure reduced body weight and total hypothalamic NPY, and increased thermogenesis and markers of inflammation. The suppressed hypothalamic NPY and increased UCPs may contribute to the spontaneous hypophagia and extra weight loss in SE animals. These findings contribute to our understanding of weight loss in smoking-related lung disease, suggesting a greater impact than that due to anorexia alone. Crown Copyright © 2008.

Chen, H, Simar, D, Lambert, K, Mercier, J & Morris, MJ 2008, 'Maternal and Postnatal Overnutrition Differentially Impact Appetite Regulators and Fuel Metabolism', Endocrinology, vol. 149, no. 11, pp. 5348-5356.
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Maternal obesity is increasing, and it is known that the intrauterine experience programs fetal and newborn metabolism. However, the relative contributions of pre- or postnatal factors are unknown. We hypothesized that maternal overnutrition caused by long-term maternal obesity would exert a stronger detrimental impact than postnatal overnutrition on offspring metabolic homeostasis, with additional postnatal overnutrition exaggerating these alterations. Female Sprague Dawley rats were exposed to chow or high-fat cafeteria diet for 5 wk before mating and throughout gestation and lactation. On postnatal d 1, litters were adjusted to three per litter to induce postnatal overnutrition (vs. 12 in control). Hypothalamic appetite regulators neuropeptide Y and proopiomelanocortin, glucose transporter 4, and lipid metabolic markers were measured. At postnatal d 20, male pups born of obese dams, or those overnourished postnatally, were 42% heavier than controls; combining both interventions led to 80% greater body weight. Maternal obesity increased pup adiposity and led to glucose intolerance in offspring; these were exaggerated by additional postnatal overnutrition during lactation. Maternal obesity was also linked to hyperlipidemia in offspring and reduced hypothalamic neuropeptide Y and increased proopiomelanocortin mRNA expression. Postnatal overnutrition of offspring from obese dams amplified these hypothalamic changes. Both maternal and postnatal overnutrition reduced muscle glucose transporter 4. Adipose carnitine palmitoyl-transferase-1 and adipose triglyceride lipase mRNA was up-regulated only by postnatal overnutrition. Maternal overnutrition appears to alter central appetite circuits and promotes early-onset obesity; postnatal overnutrition interacted to cause peripheral lipid and glucose metabolic disorders, supporting the critical message to reduce early-life adverse nutritional impact.

Chen, Y-H, Chatterjee, N & Carroll, RJ 2008, 'Retrospective analysis of haplotype-based case-control studies under a flexible model for gene-environment association', Biostatistics, vol. 9, no. 1, pp. 81-99.
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Cheng, YY, Jin, H, Liu, X, Siu, JMT, Wong, YP, Ng, EKO, Yu, J, Leung, W-K, Sung, JJY & Chan, FKL 2008, 'Fibulin 1 is downregulated through promoter hypermethylation in gastric cancer', British Journal of Cancer, vol. 99, no. 12, pp. 2083-2087.
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Chivers, WJ, Gladstone, W & Herbert, RD 2008, 'Spatial effects in an individual-based model of producer–herbivore interaction', Natural Resource Modeling, vol. 21, no. 1, pp. 72-92.
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In this paper, we describe an individual-based model of the interaction between a producer and herbivore species. The interaction occurs in a 2-dimensional matrix of individual cells. The producer organism grows in the cells and the herbivores move between the cells, towards areas of high concentration of producer. Herbivores may die of starvation or they may reproduce asexually. The model is not built to represent a specific existing system but is a parsimonious generalized model of producer–herbivore interaction designed to test spatial effects. Although the model algorithm is kept simple—the herbivores have no learning or social behavior and have a minimal foraging strategy—the model displays some characteristics of real systems such as metapopulation behavior. We find significant effects on the herbivore and producer populations of the maximum move distance per step of the herbivores, the shape of the two-dimensional matrix, the quality of a corridor between patches habitable by the herbivores, and edge effects with fuzzy edges. The behavior of the model is comparable with empirical observations found in the literature, and we suggest that this simple model may be used to investigate the mechanism of these real effects. © 2008 Blackwell Publishing, Inc.

Cho, Y, Martinez, JG, Turner, ND, Taddeo, SS, Davidson, LA, Wang, N, Vannucci, M, Carroll, RJ, Chapkin, RS & Lupton, JR 2008, 'Fish oil and pectin may suppress colon carcinogenesis via inhibition of the MAPK and TGFβpathways', The FASEB Journal, vol. 22, no. S1.
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We have shown that fish oil/pectin(FP) diets are protective against colon cancer compared to corn oil/cellulose(CC). In this study we determined if the protection is conferred by influencing the temporal changes in expression of genes relevant to the MAPK and TGF βpathway that are involved in colon carcinogenesis. Diets contained either FP or CC. Half of the rats were exposed to radiation (1 Gy, 1 GeV/nucleon iron) and all rats were injected with azoxymethane (2x, 15 mg/kg BW, sc) 10 and 17 d after irradiation. Exfoliated colonocyte polyA+ RNA was collected at 7, 14, and 28 wk in the same rats and gene expression determined using GE Codelink arrays. There were 301 differentially expressed genes for the diet X time interaction including five genes relevant to the MAPK pathway, e.g. expression of IL‐1βwas maintained over time in FP‐fed rats whereas expression in the 28 wk sample was 4.7 times (P=0.01) that in the 7 wk sample in CC‐fed rats. Also, three genes related to the TGF βpathway were affected by the interaction, e.g. expression of Smad4, a tumor suppressor, was maintained over time in the FP‐fed rats but decreased at the tumor stage in CC‐fed rats (P=0.03). Our data indicate that a diet containing fish oil/pectin could suppress colon carcinogenesis by regulating expression of genes within the MAPK/TGF βsignaling axis. Funded by NSBRI NASA NCC 9‐58, NIEHS (P30‐ES09106), and NIH (CA59034, CA57030).

Choi, MJ, McBean, KE, Ng, PHR, McDonagh, AM, Maynard, PJ, Lennard, C & Roux, C 2008, 'An evaluation of nanostructured zinc oxide as a fluorescent powder for fingerprint detection', JOURNAL OF MATERIALS SCIENCE, vol. 43, no. 2, pp. 732-737.
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Zinc oxide is evaluated as a fluorescent powder for the detection of fingermarks on non-porous surfaces. Pure and lithium-doped nanostructured zinc oxide powders were characterized using scanning electron microscopy, X-ray diffraction, and fluorescence spectroscopy. The zinc oxide powders were applied to fresh and aged fingermarks deposited on non-porous surfaces such as glass, polyethylene and aluminium foil. Zinc oxide was found to produce clear fluorescent impressions of the latent fingermarks when illuminated with long-wave UV light. © 2007 Springer Science+Business Media, LLC.

Choi, MJ, McDonagh, AM, Maynard, P & Roux, C 2008, 'Metal-containing nanoparticles and nano-structured particles in fingermark detection', Forensic Science International, vol. 179, no. 2-3, pp. 87-97.
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This article reviews the application of metal-containing nanoparticles and nano-structured particles to fingermark detection. This area of research is attracting significant interest as advances in nanoscience are being incorporated into the field of forensic fingermark detection. Although more research is needed before some of the techniques presented can be implemented in routine casework, nanotechnology is likely to play a major role in the future to deliver more selective and more sensitive ways to detect and enhance fingermarks. © 2008 Elsevier Ireland Ltd. All rights reserved.

Chotikadachanarong, K, Dheeranupattana, S, Jatisatienr, A, Jatisatienr, C, Pyne, SG, Ung, AT & Sastraruji, T 2008, 'Secondary compound production in root cultures of Stemona curtisii Hook. f', Planta Medica, vol. 74, no. 09.
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Clark, C, Ryan, L, Kawachi, I, Canner, MJ, Berkman, L & Wright, RJ 2008, 'Witnessing community violence in residential neighborhoods: A mental health hazard for urban women', JOURNAL OF URBAN HEALTH-BULLETIN OF THE NEW YORK ACADEMY OF MEDICINE, vol. 85, no. 1, pp. 22-38.
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We examined the prevalence and psychological correlates of witnessing community violence among women of low socioeconomic status living in urban neighborhoods in the northeastern United States. Three hundred eighty-six women receiving their health care at an urban community health center were sampled to assess their violence exposures. Women were asked to report the location and timing of their exposure to witnessing violent neighborhood events in which they were not participants. The Brief Symptoms Inventory was used to assess anxiety and depressive symptoms. Controlling for marital status, educational attainment, age, and intimate partner violence victimization, women who witnessed violent acts in their neighborhoods were twice as likely to experience depressive and anxiety symptoms compared to women who did not witness community violence. Central American-born women had particularly high exposures. We conclude that witnessing neighborhood violence is a pervasive experience in this urban cohort, and is associated with anxiety and depressive symptoms, even among women who are not direct participants in violence to which they are exposed. Community violence interventions must incorporate efforts to protect the mental health of adult women who witness events in their neighborhoods. © 2007 The New York Academy of Medicine.

Cole, JN, Djordjevic, SP & Walker, MJ 2008, 'Isolation and Solubilization of Gram-Positive Bacterial Cell Wall-Associated Proteins', Methods in Molecular Biology, vol. 425, pp. 295-311.
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Cole, LT 2008, 'Justifiable Herbicide?', SCIENTIFIC AMERICAN, vol. 299, no. 5, pp. 12-12.

Collier, CJ, Lavery, PS, Ralph, PJ & Masini, RJ 2008, 'Physiological characteristics of the seagrass Posidonia sinuosa along a depth-related gradient of light availability', MARINE ECOLOGY PROGRESS SERIES, vol. 353, pp. 65-79.
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Physiological plasticity has the capacity to prolong seagrass survival under reduced light conditions. However, when light is attenuated across a depth gradient, the relative importance of this over other mechanisms for tolerating long-term light reduction (such as morphological adjustments and shoot loss) has been guestioned. This study aimed to describe a number of the physiological characteristics of Posidonia sinuosa Cambridge et Kuo along a depth-related gradient of light availability (1.6 to 9.0 m depth) and infer how these characteristics are important for the long-term maintenance of the meadow. Rapid light curve-derived parameters, light harvesting pigments, photoprotective pigments and nutrient and carbohydrate concentrations exhibited few differences among depth strata, but showed some (albeit limited) adjustment between the seasons. It was inferred that some physiological plasticity is possible in P. sinuosa but that differences in the depth-related gradient of long-term light availability were not sufficient to induce physiological differences, even at the depth limit. Shoot density reductions, which reduce the effects of self-shading, possibly offset depth-related light reductions. Because the physiological characteristics we examined did not explain the adaptations by P. sinuosa to the long-term gradient of light availability, they may not be useful indicators of long-term light reduction. © Inter-Research 2008.

Colville, A, Jones, P, Pablo, F, Krassoi, F, Hose, G & Lim, R 2008, 'Effects of chlorpyrifos on macroinvertebrate communities in coastal stream mesocosms', Ecotoxicology, vol. 17, no. 3, pp. 173-180.
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This study measured the effects of a single pulse of chlorpyrifos at nominal concentrations of 1 and 10 mu g/l on the macroinvertebrate community structure of a coastal stream mesocosm system. Analysis of data using Principal Response Curves (PRC) and Monte Carlo tests showed significant changes in the treated stream mesocosms relative to that of the controls. These changes in the macroinvertebrate assemblages occurred within 6 h, and persisted for at least 124 days after dosing. Significant community-level effects were detected at the lowest concentration on days 2 and 16 post-dosing, giving a no-observed effect concentration (NOECcommunity) of 1.2 mu g/l (measured). The mayflies Atalophlebia sp. and Koorrnonga sp., Chironomidae and Acarina were all sensitive to chlorpyrifos and decreased in abundance in treated mesocosms after dosing. The fauna of these coastal stream mesocosms showed similar sensitivity to chlorpyrifos with that of other reported studies, but there was no evidence of recovery after 124 days.

Combes, V, Faille, D, Mitchell, A, Juhan‐Vague, I, Chimini, G, Fusai, T & Grau, GE 2008, 'Platelet microparticles enhance Plasmodium falciparum‐parasitised red blood cell cytoadherence and activate human brain endothelial cells', The FASEB Journal, vol. 22, no. S1.
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One of the mechanisms of cerebral malaria (CM) is the sequestration, within brain microvessels, of P. falciparum‐parasitised red blood cells (RBC), leucocytes and platelets. Besides, CM is characterised by an overproduction of pro‐inflammatory cytokines and endothelial activation with upregulation of adhesion molecules and microparticle (MP) release from vascular cells. MP are submicron membrane elements carrying on their surface proteins from their cell of origin. Platelets have been shown to modulate PRBC cytoadherence, thus we analysed the role of platelet MP in this binding. Confocal microscopy showed that MP adhered to and penetrated in human brain microvascular endothelial cells (HBEC). MP upregulated ICAM‐1 and VCAM‐1 expression on HBEC. Furthermore, MP adhered to parasitised, but also to normal RBC, as revealed by detection of CD41 on RBC. MP binding to RBC was not affected by temperature or phosphatidylserine blockade by annexin V, but was significantly reduced when PRBC were incubated with MP in the presence of blocking antibodies against platelet‐specific antigens. Lastly, MP, while interacting with the two other cell types, dramatically increased the binding of parasitised but also of normal RBC to HBEC and altered endothelial functions. MP thus appear to be an important element in RBC sequestration and in endothelial pathology, suggesting a novel mechanism in CM pathogenesis.

Cordwell, SJ, Len, ACL, Touma, RG, Scott, NE, Falconer, L, Jones, D, Connolly, A, Crossett, B & Djordjevic, SP 2008, 'Identification of membrane‐associated proteins from Campylobacter jejuni strains using complementary proteomics technologies', PROTEOMICS, vol. 8, no. 1, pp. 122-139.
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AbstractCampylobacter jejuni is the leading cause of food‐ and water‐borne illness world‐wide. The membrane‐associated proteome of a recent C. jejuni gastrointestinal isolate (JHH1) was generated by sodium carbonate precipitation and ultracentrifugation followed by 2‐DE and MALDI‐TOF MS as well as 2‐DLC (strong cation exchange followed by RP chromatography) of trypsin digests coupled to MS/MS (2‐DLC/MS/MS). 2‐DE/MS identified 77 proteins, 44 of which were predicted membrane proteins, while 2‐DLC/MS/MS identified 432 proteins, of which 206 were predicted to be membrane associated. A total of 453 unique proteins (27.4% of the C. jejuni theoretical proteome), including 187 bona fide membrane proteins were identified in this study. Membrane proteins were also compared between C. jejuni JHH1 and ATCC 700297 to identify factors potentially associated with increased gastrointestinal virulence. We identified 28 proteins that were significantly (>two‐fold) more abundant in, or unique to, JHH1, including eight proteins involved in chemotaxis signal transduction and flagellar motility, the amino acid‐binding surface antigens CjaA and CjaC, and four outer membrane proteins (OMPs) of unknown function (Cj0129c, Cj1031, Cj1279c, and Cj1721c). Immunoblotting using convalescent patient sera generated postgastrointestinal infection revealed 13 (JHH1) and 12 (ATCC 700297) immunoreactive proteins. These included flagellin (FlaA) and CadF as well as Omp18, Omp50, Cj1721c, PEB1A, PEB2, and PEB4A. This study provides a comprehensive analysis of membrane‐associated proteins from C. jejuni.

Croak, BM, Pike, DA, Webb, JK & Shine, R 2008, 'Three-dimensional crevice structure affects retreat site selection by reptiles', ANIMAL BEHAVIOUR, vol. 76, no. 6, pp. 1875-1884.
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When selecting retreat sites, rock-dwelling animals assess thermal and hydric properties of the rocks under which they shelter. Another obvious, but harder to measure, factor that may affect retreat site selection is the size and structure of the three-dimensional crevice beneath the rock. We developed a novel technique to quantify crevice structure beneath rocks and compared crevices used by snakes and lizards with unused crevices. Multiple attributes of crevice structure such as the height of the crevice above the substrate, the area of the crevice suitable for fitting the entire body of the animal, the degree of closure of the crevice and the amount of fragmentation within the crevice affected the suitability of a crevice as a retreat site. Therefore, crevice structural attributes, not simply size and thickness of the overlying rock, may be important factors driving retreat site selection by ectotherms. We also found that crevice structure directly alters thermal regimes, and may be more important than rock thickness in this respect. Understanding the characteristics of the space actually occupied by animals can yield a greater understanding of habitat selection, and our novel technique for quantifying crevice geometry should be readily transferable to other systems. © 2008 The Association for the Study of Animal Behaviour.

Crossley, MJ, Sheehan, CS, Khoury, T, Reimers, JR & Sintic, PJ 2008, 'Construction of building blocks for extended porphyrin arrays by nitration of porphyrin-2,3-diones and quinoxalino[2,3-b]porphyrins', NEW JOURNAL OF CHEMISTRY, vol. 32, no. 2, pp. 340-352.
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Nitration of metal(II) porphyrin-2,3-diones 3-5 and quinoxalino[2,3-b] porphyrins 13-15 with nitrogen dioxide gave a mixture of β-pyrrolic functionalised nitro-porphyrin isomers in relative abundance of 7-nitro- > 12-nitro- > 8-nitro. The large selectivity for reaction at the 7-position over the adjacent 8-position (>5 to 1 in the diones 3-5 and about 3 to 1 in the quinoxalinoporphyrins 13-15) is especially striking. This selectivity results mainly from electronic effects and is consistent with a mechanism involving a porphyrin π-cation radical intermediate. A key step incorporated into the isomer separation sequence was to make use of the different chromatographic polarity of metalated compounds compared to unmetalated compounds coupled with the observation that introduction of a nitro group to the 7-position of free-base porphyrin-dione greatly increases its rate of metalation while introduction of the nitro group at the 12-position greatly decreases its rate of metalation, relative to the unsubstituted parent. Thus demetalation of zinc(ii) nitro-porphyrin-dione isomers, which are difficult to separate, allows for highly selective remetalation of the 7-isomer and its very easy separation from the unmetalated 12-nitro-porphyrin-dione. These nitrated compounds are useful building blocks for more elaborate systems. © The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

Crossman, LC, Castillo-Ramírez, S, McAnnula, C, Lozano, L, Vernikos, GS, Acosta, JL, Ghazoui, ZF, Hernández-González, I, Meakin, G, Walker, AW, Hynes, MF, Young, JPW, Downie, JA, Romero, D, Johnston, AWB, Dávila, G, Parkhill, J & González, V 2008, 'A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria', PLoS ONE, vol. 3, no. 7, pp. e2567-e2567.
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This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Darling, AE, Miklos, I & Ragan, MA 2008, 'Dynamics of Genome Rearrangement in Bacterial Populations', PLOS GENETICS, vol. 4, no. 7.
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Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of 'symmetric inversions' - inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent...

Davila, YC & Wardle, GM 2008, 'Variation in native pollinators in the absence of honeybees: implications for reproductive success of an Australian generalist-pollinated herb Trachymene incisa (Apiaceae)', BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, vol. 156, no. 3, pp. 479-490.
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Day, DM & Wallman, JF 2008, 'Effect of preservative solutions on preservation of Calliphora augur and Lucilia cuprina larvae (Diptera: Calliphoridae) with implications for post-mortem interval estimates', Forensic Science International, vol. 179, no. 1, pp. 1-10.
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de Burgh, MD, Langford, NK, Doherty, AC & Gilchrist, A 2008, 'Choice of measurement sets in qubit tomography', Physical Review A, vol. 78, no. 5.
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Demir, E, Coyne, KJ, Doblin, MA, Handy, SM & Hutchins, DA 2008, 'Assessment of microzooplankton grazing on Heterosigma akashiwo using a species-specific approach combining quantitative real-time PCR (QPCR) and dilution methods', MICROBIAL ECOLOGY, vol. 55, no. 4, pp. 583-594.
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Delaware's Inland Bays (DIB) are subject to numerous mixed blooms of harmful raphidophytes each year, and Heterosigma akashiwo is one of the consistently occurring species. Often, Chattonella subsalsa, C. cf. verruculosa, and Fibrocapsa japonica co-occur

Demir, E, Coyne, KJ, Doblin, MA, Handy, SM & Hutchins, DA 2008, 'Assessment of microzooplankton grazing on Heterosigma akashiwo using a species-specific approach combining quantitative real-time PCR (QPCR) and dilution methods (vol 55, pg 583, 2008)', MICROBIAL ECOLOGY, vol. 55, no. 4, pp. 581-582.
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Dennis, ES, Ellis, J, Green, A, Llewellyn, D, Morell, M, Tabe, L & Peacock, WJ 2008, 'Genetic contributions to agricultural sustainability', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 363, no. 1491, pp. 591-609.
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The current tools of enquiry into the structure and operation of the plant genome have provided us with an understanding of plant development and function far beyond the state of knowledge that we had previously. We know about key genetic controls repressing or stimulating the cascades of gene expression that move a plant through stages in its life cycle, facilitating the morphogenesis of vegetative and reproductive tissues and organs. The new technologies are enabling the identification of key gene activity responses to the range of biotic and abiotic challenges experienced by plants. In the past, plant breeders produced new varieties with changes in the phases of development, modifications of plant architecture and improved levels of tolerance and resistance to environmental and biotic challenges by identifying the required phenotypes in a few plants among the large numbers of plants in a breeding population. Now our increased knowledge and powerful gene sequence-based diagnostics provide plant breeders with more precise selection objectives and assays to operate in rationally planned crop improvement programmes. We can expect yield potential to increase and harvested product quality portfolios to better fit an increasing diversity of market requirements. The new genetics will connect agriculture to sectors beyond the food, feed and fibre industries; agri-business will contribute to public health and will provide high-value products to the pharmaceutical industry as well as to industries previously based on petroleum feedstocks and chemical modification processes. © 2007 The Royal Society.

Deplazes, E, van Bronswijk, W, Zhu, F, Barron, LD, Ma, S, Nafie, LA & Jalkanen, KJ 2008, 'A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion', Theoretical Chemistry Accounts, vol. 119, no. 1-3, pp. 155-176.
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Dilda, PJ, Perrone, GG, Philp, A, Lock, RB, Dawes, IW & Hogg, PJ 2008, 'Insight into the selectivity of arsenic trioxide for acute promyelocytic leukemia cells by characterizing Saccharomyces cerevisiae deletion strains that are sensitive or resistant to the metalloid', The International Journal of Biochemistry & Cell Biology, vol. 40, no. 5, pp. 1016-1029.
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Dilda, PJ, Ramsay, EE, Corti, A, Pompella, A & Hogg, PJ 2008, 'Metabolism of the Tumor Angiogenesis Inhibitor 4-(N-(S-Glutathionylacetyl)amino)phenylarsonous Acid', Journal of Biological Chemistry, vol. 283, no. 51, pp. 35428-35434.
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Dixon, S, Brown, RCD & Gale, PA 2008, 'ChemInform Abstract: A Biaryl Cross‐Coupling Strategy for Functionalization of Benzocrown Ethers.', ChemInform, vol. 39, no. 2.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Doble, P, Hare, D, Austin, C, Dawson, M, Fryer, F, Svenningsson, P, Andren, P, Grimm, R, Zhang, X & Reedy, B 2008, 'Metal-Imaging Mass spectrometry (MIMS): A New Imaging Mass Spectrometry Technology to Determine the Distribution of Metal Ions in Tissue Samples', Journal of Proteomics & Bioinformatics, vol. S2, no. 01, pp. 053-054.
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Donnelly, S, Stack, CM, O'Neill, SM, Sayed, AA, Williams, DL & Dalton, JP 2008, 'Helminth 2-Cys peroxiredoxin drives Th2 responses through a mechanism involving alternatively activated macrophages', FASEB JOURNAL, vol. 22, no. 11, pp. 4022-4032.
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During helminth infections, alternatively activated macrophages (AAMacs) are key to promoting Th2 responses and suppressing Th1-driven inflammatory pathology. Th2 cytokines IL-4 and/or IL-13 are believed to be important in the induction and activation of AAMacs. Using murine models for the helminth infections caused by Fasciola hepatica (Fh) and Schistosoma mansoni (Sm), we show that a secreted antioxidant, peroxiredoxin (Prx), induces alternative activation of macrophages. These activated, Ym1-expressing macrophages enhanced the secretion of IL-4, IL-5, and IL-13 from naive CD4+ T cells. Administration of recombinant FhPrx and SmPrx to wild-type and IL-4 -/- and IL-13-/- mice induced the production of AAMacs. In addition, Prx stimulated the expression of markers of AAMacs (particularly, Ym1) in vitro, and therefore can act independently of IL-4/IL-13 signaling. The immunomodulatory property of Prx is not due to its antioxidant activity, as an inactive recombinant variant with active site Cys residues replaced by Gly could also induce AAMacs and Th2 responses. Immunization of mice with recombinant Prx or passive transfer of anti-Prx antibodies prior to infection with Fh not only blocked the induction of AAMacs but also the development of parasite-specific Th2 responses. We propose that Prx activates macrophages as an initial step in the induction of Th2 responses by helminth parasites and is thereby a novel pathogen-associated molecular pattern. © FASEB.

Dooley, AH, Golodets, VY, Rudolph, DJ & Sinel'shchikov, SD 2008, 'Non-Bernoulli systems with completely positive entropy', ERGODIC THEORY AND DYNAMICAL SYSTEMS, vol. 28, pp. 87-124.
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Dossou, KB, Botten, LC, McPhedran, RC, Poulton, CG, Asatryan, AA & de Sterke, CM 2008, 'Shallow defect states in two-dimensional photonic crystals', PHYSICAL REVIEW A, vol. 77, no. 6, pp. 1-17.
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We investigate localized defect states near the edge of a band gap in a two-dimensional photonic crystal. An asymptotic approach based on Green's functions leads to analytical results both for the frequency and for the spatial behavior of the defect states. In particular, we find a simple exponential law which relates the change in frequency of the defect states to the relative change in electrical energy of the Bloch modes on the band edge, and to the density of states in the photonic crystal. We find that the symmetries of the Bloch modes at band extrema play an important role in the manifestation and evolution of defect states. We confirm the analysis with numerical simulations based on the fictitious source superposition method. © 2008 The American Physical Society.

Duggin, IG, McCallum, SA & Bell, SD 2008, 'Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 43, pp. 16737-16742.
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The 'baby machine' provides a means of generating synchronized cultures of minimally perturbed cells. We describe the use of this technique to establish the key cell-cycle parameters of hyperthermophilic archaea of the genus Sulfolobus. The 3 DNA replication origins of Sulfolobus acidocaldarius were mapped by 2D gel analysis to near 0 (oriC2), 579 (oriC1), and 1,197 kb (oriC3) on the 2,226-kb circular genome, and we present a direct demonstration of their activity within the first few minutes of a synchronous cell cycle. We also detected X-shaped DNA molecules at the origins in log-phase cells, but these were not directly associated with replication initiation or ongoing chromosome replication in synchronized cells. Whole-genome marker frequency analyses of both synchronous and log-phase cultures showed that origin utilization was close to 100% for all 3 origins per round of replication. However, oriC2 was activated slightly later on average compared with oriC1 and oriC3. The DNA replication forks moved bidirectionally away from each origin at 88 bp per second in synchronous culture. Analysis of the 3 Orc1/Cdc6 initiator proteins showed a uniformity of cellular abundance and origin binding throughout the cell cycle. In contrast, although levels of the MCM helicase were constant across the cell cycle, its origin localization was regulated, because it was strongly enriched at all 3 origins in early S phase. © 2008 by The National Academy of Sciences of the USA.

Duggin, IG, Wake, RG, Bell, SD & Hill, TM 2008, 'The replication fork trap and termination of chromosome replication', MOLECULAR MICROBIOLOGY, vol. 70, no. 6, pp. 1323-1333.
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Bacteria that have a circular chromosome with a bidirectional DNA replication origin are thought to utilize a `replication fork trap to control termination of replication. The fork trap is an arrangement of replication pause sites that ensures that the two replication forks fuse within the terminus region of the chromosome, approximately opposite the origin on the circular map. However, the biological significance of the replication fork trap has been mysterious, as its inactivation has no obvious consequence. Here we review the research that led to the replication fork trap theory, and we aim to integrate several recent findings that contribute towards an understanding of the physiological roles of the replication fork trap. Likely roles include the prevention of over-replication, and the optimization of post-replicative mechanisms of chromosome segregation, such as that involving FtsK in Escherichia coli.

Dunlop, RA, Dean, RT & Rodgers, KJ 2008, 'The impact of specific oxidized amino acids on protein turnover in J774 cells', BIOCHEMICAL JOURNAL, vol. 410, no. 1, pp. 131-140.
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Oxidized protein deposition and accumulation have been implicated in the aetiology of a wide variety of age-related pathologies. Protein oxidation in vivo commonly results in the in situ modification of amino acid side chains, generating new oxidized ami

Duong, T, Cowling, A, Koch, I & Wand, MP 2008, 'Feature significance for multivariate kernel density estimation', Computational Statistics & Data Analysis, vol. 52, no. 9, pp. 4225-4242.
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Multivariate kernel density estimation provides information about structure in data. Feature significance is a technique for deciding whether features-such as local extrema-are statistically significant. This paper proposes a framework for feature significance in d-dimensional data which combines kernel density derivative estimators and hypothesis tests for modal regions. For the gradient and curvature estimators distributional properties are given, and pointwise test statistics are derived. The hypothesis tests extend the two-dimensional feature significance ideas of Godtliebsen et al. [Godtliebsen, F., Marron, J.S., Chaudhuri, P., 2002. Significance in scale space for bivariate density estimation. Journal of Computational and Graphical Statistics 11, 1-21]. The theoretical framework is complemented by novel visualization for three-dimensional data. Applications to real data sets show that tests based on the kernel curvature estimators perform well in identifying modal regions. These results can be enhanced by corresponding tests with kernel gradient estimators. © 2008 Elsevier Ltd. All rights reserved.

Eamus, D, Taylor, DT, Macinnis-Ng, CMO, Shanahan, S & De Silva, L 2008, 'Comparing model predictions and experimental data for the response of stomatal conductance and guard cell turgor to manipulations of cuticular conductance, leaf-to-air vapour pressure difference and temperature: feedback mechanisms are able to account for all observations', PLANT CELL AND ENVIRONMENT, vol. 31, no. 3, pp. 269-277.
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Stomata respond to increasing leaf-to-air vapour pressure difference (LAVPD) (D) by closing. The mechanism by which this occurs is debated. A role for feedback and peristomatal transpiration has been proposed. In this paper, we apply a recent mechanistic model of stomatal behaviour, and compare model and experimental data for the influence of increasing D on stomatal conductance. We manipulated cuticular conductance (gc) by three independent methods. First, we increased gc by using a solvent mixture applied to both leaf surfaces prior to determining stomatal responses to D; second, we increased gc by increasing leaf temperature at constant D; and third, we coated a small area of leaf with a light oil to decrease gc. In all three experiments, experimental data and model outputs showed very close agreement. We conclude, from the close agreement between model and experimental data and the fact that manipulations of gc, and hence cuticular transpiration, influenced gs in ways consistent with a feedback mechanism, that feedback is central in determining stomatal responses to D. © 2008 The Authors.

Ellis, J, Miller, C, Quinn, H, Ryce, C & Reichel, MP 2008, 'Evaluation of recombinant proteins of Neospora caninum as vaccine candidates (in a mouse model)', VACCINE, vol. 26, no. 47, pp. 5989-5996.
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Abortion resulting from infections by the parasite Neospora caninum is a mojor cause of economic loss to both the dairy and beef industries of cattle-producing countries of the world. Vaccination as a means of preventing abortion and/or infection represents a viable control strategy; indeed a commercial vaccine is available in some countries, albeit of unlnown efficacy.

Faille, D, Combes, V, Mitchell, A, Juhan-Vague, I, Chimini, G, Fusaï, T & Graug, GE 2008, 'Platelet microparticles: a new player in cerebral malaria pathogenesis', BMC Proceedings, vol. 2, no. S1.
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Fan, Y, Leslie, DS & Wand, MP 2008, 'Generalised linear mixed model analysis via sequential Monte Carlo sampling', Electronic Journal of Statistics, vol. 2, no. 9, pp. 6-938.
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We present a sequential Monte Carlo sampler algorithm for the Bayesiananalysis of generalised linear mixed models (GLMMs). These models support avariety of interesting regression-type analyses, but performing inference isoften extremely difficult, even when using the Bayesian approach combined withMarkov chain Monte Carlo (MCMC). The Sequential Monte Carlo sampler (SMC) is anew and general method for producing samples from posterior distributions. Inthis article we demonstrate use of the SMC method for performing inference forGLMMs. We demonstrate the effectiveness of the method on both simulated andreal data, and find that sequential Monte Carlo is a competitive alternative tothe available MCMC techniques.

Feller, JM, Simpson, AM, Nelson, M, Swan, MA, O'Connell, PJ, Hawthorne, WJ, Tao, C & O'Brien, BA 2008, 'Growth-Promoting Effect of Rh(D) Antibody on Human Pancreatic Islet Cells', The Journal of Clinical Endocrinology & Metabolism, vol. 93, no. 9, pp. 3560-3567.
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Context/Objective: Hyperinsulinism with islet cell hyperplasia is a frequent complication, of unknown cause, in hemolytic disease of the newborn, occurring in Rh(D)-positive infants of Rh-isoimmunized Rh(D)-negative mothers, but not in infants with other hemolytic disorders. We investigated the possibility that trans-placentally acquired anti-D Ig is the cause of both conditions.Design: Monolayer cultures of human islet cells were exposed to sera from Rh-isoimmunized mothers and newborns, where jaundice, hyperinsulinism, and hypoglycemia in the infant had ensued. Parallel cultures with anti-D, specific anti-D monoclonal antibodies, normal human Ig (15 μg/ml), and serum controls were also undertaken. Islet cell proliferation was determined by [3H]thymidine incorporation. Insulin storage and chronic and acute insulin secretion to glucose were analyzed by RIA. Rh(D) surface antigen expression was determined on islet cells by flow cytometric analysis.Results: Islet cell proliferation and insulin secretion were significantly greater in coculture with test sera (P &lt; 0.01; n = 8) and with anti-D (P &lt; 0.001; n = 8), compared with either controls or Ig. After 8 d of growth, the static incubation experiment showed a 3.5-fold response to glucose stimulus in all sera. Rh(D) antigen expression was detected on the islet cell surface by flow cytometry, and islet cell morphology was normal. Colocalization of the proliferation marker Ki67 with insulin by immunofluorescent staining further indicated that Rh(D) antibody promoted islet growth.Conclusions: The anti-Rh(D) islet cell proliferative effect generates neonatal hyperinsulinism in Rh isoimmunization. Anti-Rh(D) may have application for islet cell proliferation in diabetes mellitus treatment for Rh(D)-positive subjects. Further analysis is required.

Ferrari, P, Carroll, RJ, Gustafson, P & Riboli, E 2008, 'A Bayesian multilevel model for estimating the diet/disease relationship in a multicenter study with exposures measured with error: The EPIC study', Statistics in Medicine, vol. 27, no. 29, pp. 6037-6054.
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AbstractIn a multicenter study, the overall relationship between diet and cancer risk can be broken down into: (a) within‐center relationships, which reflect the relationships at the individual level in each of the centers, and (b) a between‐center relationship, which captures the association between exposure and disease risk at the aggregate level. In this work, we propose the use of a Bayesian multilevel model that takes into account the within‐ and between‐center levels of evidence, using information at the individual and aggregate level. Correction for measurement error is performed in order to correct for systematic between‐center measurement error in dietary exposure, and for attenuation biases in relative risk estimates within centers. The estimation of the parameters is carried out in a Bayesian framework using Gibbs sampling. The model entails a measurement, an exposure, and a disease component. Within the European Prospective Investigation into Cancer and Nutrition (EPIC) the association between lipid intake, assessed through dietary questionnaire and 24‐hour dietary recall, and breast cancer incidence was evaluated. This analysis involved 21 534 women and 334 incident breast cancer cases from the EPIC calibration study. In this study, total energy intake was positively associated with breast cancer incidence at the aggregate level, whereas no effect was observed for fat. At the individual level, height was positively related to breast cancer incidence, whereas a weaker association was observed for fat. The use of multilevel models, which constitute a very powerful approach to estimating individual vs aggregate levels of evidence should be considered in multicenter studies. Copyright © 2008 John Wiley & Sons, Ltd.

Fierro, AO, Leslie, LM, Mansell, ER & Straka, JM 2008, 'Numerical Simulations of the Microphysics and Electrification of the Weakly Electrified 9 February 1993 TOGA COARE Squall Line: Comparisons with Observations', Monthly Weather Review, vol. 136, no. 1, pp. 364-379.
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Abstract A cloud scale model with a 12-class bulk microphysics scheme, including 10 ice phases and a 3D lightning parameterization, was used to investigate the electrical properties of a well-documented tropical squall line from the Tropical Ocean Global Atmosphere Coupled Ocean–Atmosphere Response Experiment (TOGA COARE). Consistent with observations, the simulated maximum updraft speeds across the squall line seldom exceeded 10 m s−1, which was expected given the relatively shallow 30-dBZ echo tops that rarely extended above the top of the mixed-phase layer (−20°C isotherm). Enhanced warm rain processes caused most of the liquid water to precipitate near the gust front at lower levels (below 4 km AGL), which accounted for the small amounts of graupel and cloud water content present in the mixed-phase region and, consequently, for generally weak charging and electrification. Most of the charge present in the squall line was generated within a few storm cells just behind the leading edge of the gust front that had sufficiently strong updraft speeds near the melting level to produce moderate values of graupel mixing ratio (&gt;0.5 g kg−1). In contrast, the trailing stratiform region at the back of the line, which was mainly composed of ice crystals and snow particles, contained only weak net charge densities (&lt;0.03 nC m−3). The spatial collocation of regions characterized by charge densities exceeding 0.01 nC m−3 and noninductive (NI) charging rates greater than 0.1 pC m−3 s−1 in this stratiform region suggests that NI charging is a plausible source for the majority of this charge, which was confined to discrete regions having small amounts of graupel (approximately 0.1–0.3 g kg−1) and cloud water content (CWC; ∼0.1 g m−3). The simulated weak updraft speeds and shallow echo tops resulted in a system exhibiting little overall total li...

Figueira, WF, Booth, DJ & Gregson, MA 2008, 'Selective mortality of a coral reef damselfish: role of predator-competitor synergisms', OECOLOGIA, vol. 156, no. 1, pp. 215-226.
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Phenotypic variability within cohorts of juvenile organisms can serve as the basis for selective mortality. Previous studies have demonstrated the important role that predators play in this process but not the impact of competitors on selective predation. We use a combination of lab and field studies to evaluate the effect of the presence of adult competitor damselfish (Dascyllus aruanus and Pomacentrus moluccensis; family Pomacentridae) on the selective mortality of newly-arrived (settled) lemon damselfish (P. moluccensis) by resident predator fishes (Pseudochromis fuscus Pseudochromidae and Cheilodipterus quinquelineatus Apogonidae). Lab trials consisted of mesocosm experiments in which the behaviour, mortality, and physiological condition (measured as lipid content) of surviving P. moluccensis settlers from each of three treatments: (1) predators absent, (2) predators present, and (3) predators and competitors present, were compared. The field study involved stocking newly settled P. moluccensis on natural bommies (patch reefs) which had either been subject to a partial removal of resident fish (predators and competitors) or left alone. Results indicated there was very strong condition-based selective mortality in both the lab and field trials. In both cases there was a strong positive relationship between mortality and the lipid content of surviving fish; implying low-condition fish were selectively removed. The mesocosm trials indicated that the strength of mortality as well as condition selectivity was higher when competitors were present than when they were absent. Behavioural observations in the mesocosm study suggest that attention by juvenile P. moluccensis to the movements and occasional chases of the competitors (especially D. aruanus) reduced their vigilance to the predators. These results suggest the important and interactive roles which condition of newly settled reef fish and interspecific competition can play in the outcomes of post-set...

Finnegan, EJ & Dennis, ES 2008, 'Polycomb repression', Plant Signaling & Behavior, vol. 3, no. 6, pp. 412-414.
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In our recent paper1 we suggested a molecular explanation for the long standing observation that plants need to be mitotically active to respond to a prolonged period of low temperatures by flowering early (vernalization).2 In Arabidopsis, vernalization is associated with the epigenetic repression of the floral repressor, FLC.3-5 FLC repression is established during the low temperature treatment and is marked by the loss of chromatin marks associated with active genes and the gain of histone H3 trimethyl-lysine 27 (K27me3) at the start of transcription/translation. 1 After the end of the cold treatment, this repressive modification spreads across FLC chromatin to mark the entire locus.1 In cells not undergoing mitosis, we found that FLC is repressed by low temperatures, but that this repression is only partially maintained. We concluded that DNA replication is not required for the initial response to low temperatures, but rather for the maintenance of this response. Here we discuss the implications of our observations in terms of the plasticity of chromatin modifications in plants. ©2008 Landes Bioscience.

Fisher, MG, Gale, PA, Light, ME & Loeb, SJ 2008, 'Metal–organic anion receptors: trans-functionalised platinum complexes', Chemical Communications, no. 44, pp. 5695-5695.
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Fisher, MG, Gale, PA, Light, ME & Quesada, R 2008, 'Hydrogen bonded networks in N–alkyl substituted thiourea platinum (II) oxocarbodianion and carboxylate salts', CrystEngComm, vol. 10, no. 9, pp. 1180-1180.
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Foley, M, Ton-That, C & Phillips, MR 2008, 'Cathodoluminescence inhomogeneity in ZnO nanorods', APPLIED PHYSICS LETTERS, vol. 93, no. 24, pp. 1-3.
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Luminescence properties of vertically aligned, crystalline ZnO nanorods are studied by cathodoluminescence (CL) spectroscopy and microscopy. Results show that luminescence characteristics vary dramatically with location on the nanorod as well as CL excitation depth. CL inhomogeneity is observed between the nanorod tip and sidewalls, accompanied by a variation in the chemical environment of surface oxygen ions as probed by photoemission spectroscopy. Our findings demonstrate that CL can provide useful information on the local optical properties of nanostructured materials, which is simply beyond the capability of other methods. © 2008 American Institute of Physics.

Ford, MJ, Hoft, RC, McDonagh, AM & Cortie, MB 2008, 'Rectification in donor-acceptor molecular junctions', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 20, no. 37.
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Forno, E, Onderdonk, AB, McCracken, J, Litonjua, AA, Laskey, D, Delaney, ML, DuBois, AM, Gold, DR, Ryan, LM, Weiss, ST & Celedón, JC 2008, 'Diversity of the gut microbiota and eczema in early life', Clinical and Molecular Allergy, vol. 6, no. 1.
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AbstractBackgroundA modest number of prospective studies of the composition of the intestinal microbiota and eczema in early life have yielded conflicting results.ObjectiveTo examine the relationship between the bacterial diversity of the gut and the development of eczema in early life by methods other than stool culture.MethodsFecal samples were collected from 21 infants at 1 and 4 months of life. Nine infants were diagnosed with eczema by the age of 6 months (cases) and 12 infants were not (controls). After conducting denaturating gradient gel electrophoresis (DGGE) of stool samples, we compared the microbial diversity of cases and controls using the number of electrophoretic bands and the Shannon index of diversity (H') as indicators.ResultsControl subjects had significantly greater fecal microbial diversity than children with eczema at ages 1 (meanH'for controls = 0.75 vs. 0.53 for cases, P = 0.01) and 4 months (meanH'for controls = 0.92 vs. 0.59 for cases, P = 0.02). The increase in diversity from 1 to 4 months of age was significant in controls (P = 0.04) but not in children who developed eczema by 6 months of age (P = 0.32).ConclusionOur findings suggest that reduced microbial diversity is associated with the development of eczema in early life.

Fotedar, R, Stark, D, Marriott, D, Ellis, J & Harkness, J 2008, 'Entamoeba moshkovskii infections in Sydney, Australia', EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES, vol. 27, no. 2, pp. 133-137.
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Entamoeba moshkovskii is considered to be a free-living ameba which is morphologically similar, but biochemically and genetically different to Entamoeba histolyticca and Entamoeba dispar. However recent studies have suggested that E. moshkovskii may be a "potential" pathogen with infections giving rise to diarrhea and toehr intetinal disorders.

Fourment, M & Gibbs, MJ 2008, 'The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences', BMC Bioinformatics, vol. 9, no. 1.
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Fourment, M & Gillings, MR 2008, 'A comparison of common programming languages used in bioinformatics', BMC Bioinformatics, vol. 9, no. 1.
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Fourment, M, Gibbs, AJ & Gibbs, MJ 2008, 'SWeBLAST: A Sliding Window Web-based BLAST tool for recombinant analysis', Journal of Virological Methods, vol. 152, no. 1-2, pp. 98-101.
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Fowler, AM, Leis, JM & Suthers, IM 2008, 'Onshore-offshore distribution and abundance of tuna larvae (Pisces: Scombridae: Thunnini) in near-reef waters of the Coral Sea', Fishery Bulletin, vol. 106, no. 4, pp. 405-416.
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The on-offshore distributions of tuna larvae in near-reef waters of the Coral Sea, near Lizard Island (14°30'S, 145°27'E), Australia, were investigated during four cruises from November 1984 to February 1985 to test the hypothesis that larvae of these oceanic fishes are found in highest abundance near coral reefs. Oblique bongo net tows were made in five on-offshore blocks in the Coral Sea, ranging from 0-18.5 km offshore of the outer reefs of the Great Barrier Reef, as well as inside the Great Barrier Reef Lagoon. The smallest individuals (<3.2 mm SL) of the genus Thunnus could not be identified to species, and are referred to as Thunnus spp. We found species-specific distributional patterns. Thunnus spp. and T. alalunga (albacore) larvae were most abundant (up to 68 larvae/100 m2) in near-reef (0-5.5 km offshore) waters, whereas Katsuwonus pelamis (skipjack tuna) larvae increased in abundance in the offshore direction (up to 228 larvae/100 m2, 11.1-18.5 km offshore). Larvae of T. albacares (yellowfin tuna) and Euthynnus affinis (kawakawa) were relatively rare throughout the study region, and the patterns of their distributions were inconclusive. Few larvae of any tuna species were found in the lagoon. Size-frequency distributions revealed a greater proportion of small larvae inshore compared to offshore for K. pelamis and T. albacares. The absence of significant differences in size-frequency distributions for other species and during the other cruises was most likely due to the low numbers of larvae. Larval distributions probably resulted from a combination of patterns of spawning and vertical distribution, combined with wind-driven onshore advection and downwelling on the seaward side of the outer reefs.

Freedman, LS, Midthune, D, Carroll, RJ & Kipnis, V 2008, 'A comparison of regression calibration, moment reconstruction and imputation for adjusting for covariate measurement error in regression', Statistics in Medicine, vol. 27, no. 25, pp. 5195-5216.
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AbstractRegression calibration (RC) is a popular method for estimating regression coefficients when one or more continuous explanatory variables, X, are measured with an error. In this method, the mismeasured covariate, W, is substituted by the expectation E(X|W), based on the assumption that the error in the measurement of X is non‐differential. Using simulations, we compare three versions of RC with two other ‘substitution’ methods, moment reconstruction (MR) and imputation (IM), neither of which rely on the non‐differential error assumption. We investigate studies that have an internal calibration sub‐study. For RC, we consider (i) the usual version of RC, (ii) RC applied only to the ‘marker’ information in the calibration study, and (iii) an ‘efficient’ version (ERC) in which the estimators (i) and (ii) are combined. Our results show that ERC is preferable when there is non‐differential measurement error. Under this condition, there are cases where ERC is less efficient than MR or IM, but they rarely occur in epidemiology. We show that the efficiency gain of usual RC and ERC over the other methods can sometimes be dramatic. The usual version of RC carries similar efficiency gains to ERC over MR and IM, but becomes unstable as measurement error becomes large, leading to bias and poor precision. When differential measurement error does pertain, then MR and IM have considerably less bias than RC, but can have much larger variance. We demonstrate our findings with an analysis of dietary fat intake and mortality in a large cohort study. Copyright © 2008 John Wiley & Sons, Ltd.

Friedberg, R, Darling, AE & Yancopoulos, S 2008, 'Genome Rearrangement by the Double Cut and Join Operation', Methods in Molecular Biology, vol. 452, pp. 385-416.
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The Double Cut and Join is an operation acting locally at four chromosomal positions without regard to chromosomal context. This chapter discusses its application and the resulting menu of operations for genomes consisting of arbitrary numbers of circular chromosomes, as well as for a general mix of linear and circular chromosomes. In the general case the menu includes: inversion, translocation, transposition, formation and absorption of circular intermediates, conversion between linear and circular chromosomes, block interchange, fission, and fusion. This chapter discusses the well-known edge graph and its dual, the adjacency graph, recently introduced by Bergeron et al. Step-by-step procedures are given for constructing and manipulating these graphs. Simple algorithms are given in the adjacency graph for computing the minimal DCJ distance between two genomes and finding a minimal sorting; and use of an online tool (Mauve) to generate synteny blocks and apply DCJ is described. © 2008 Humana Press, a part of Springer Science+Business Media, LLC.

Friedberg, R, Darling, AE & Yancopoulos, S 2008, 'Genome rearrangement by the double cut and join operation.', Methods in molecular biology (Clifton, N.J.), vol. 452, pp. 385-416.
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The Double Cut and Join is an operation acting locally at four chromosomal positions without regard to chromosomal context. This chapter discusses its application and the resulting menu of operations for genomes consisting of arbitrary numbers of circular chromosomes, as well as for a general mix of linear and circular chromosomes. In the general case the menu includes: inversion, translocation, transposition, formation and absorption of circular intermediates, conversion between linear and circular chromosomes, block interchange, fission, and fusion. This chapter discusses the well-known edge graph and its dual, the adjacency graph, recently introduced by Bergeron et al. Step-by-step procedures are given for constructing and manipulating these graphs. Simple algorithms are given in the adjacency graph for computing the minimal DCJ distance between two genomes and finding a minimal sorting; and use of an online tool (Mauve) to generate synteny blocks and apply DCJ is described.

Fu, K-MC, Santori, C, Barclay, PE, Aharonovich, I, Prawer, S, Meyer, N, Holm, AM & Beausoleil, RG 2008, 'Coupling of nitrogen-vacancy centers in diamond to a GaP waveguide', APPLIED PHYSICS LETTERS, vol. 93, no. 23.
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Fu, S & Lewis, J 2008, 'Novel automated extraction method for quantitative analysis of urinary 11-nor-Delta(9)-tetrahydrocannabinol-9-carboxylic acid (THC-COOH)', JOURNAL OF ANALYTICAL TOXICOLOGY, vol. 32, no. 4, pp. 292-297.
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An automated extraction method for extracting the major urinary metabolite of cannabis, 11-nor-?9-tetrahydrocannabinol-9-carboxylic acid (THC-COOH) was developed on the four-probe Gilson ASPEC XL4? solid-phase extraction (SPE) system. The method works on liquid-liquid extraction principles but does not require the use of SPE cartridges. The limits of detection and quantitation and the upper limit of linearity (ULOL) of the developed method were found to be 1, 2, and 1500 ng/mL, respectively. There was no detectable carry over after 10,000 ng/mL analyte. For a batch of 76 samples, the process uses less than 100 mL methanol, 450 mL extracting solvent hexane/ethyl acetate (5:1, v/v) and 1 L rinsing solvent, 30% methanol in water. The automated extraction process takes 5 h to complete. Precision and accuracy of the method are comparable to both manual liquid-liquid extraction and automated SPE methods. The method has proven to be a simple, speedy, and economical alternative to the currently popular automated SPE method for the quantitative analysis of urinary THC-COOH.

Fuentes, S, Palmer, AR, Taylor, D, Zeppel, M, Whitley, R & Eamus, D 2008, 'An automated procedure for estimating the leaf area index (LAI) of woodland ecosystems using digital imagery, MATLAB programming and its application to an examination of the relationship between remotely sensed and field measurements of LAI', FUNCTIONAL PLANT BIOLOGY, vol. 35, no. 9-10, pp. 1070-1079.
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Leaf area index (LAI) is one of the most important variables required for modelling growth and water use of forests. Functional-structural plant models use these models to represent physiological processes in 3-D tree representations. Accuracy of these models depends on accurate estimation of LAI at tree and stand scales for validation purposes. A recent method to estimate LAI from digital images (LAID) uses digital image capture and gap fraction analysis (Macfarlane et al. 2007b) of upward-looking digital photographs to capture canopy LAID (cover photography). After implementing this technique in Australian evergreen Eucalyptus woodland, we have improved the method of image analysis and replaced the time consuming manual technique with an automated procedure using a script written in MATLAB 7.4 (LAIM). Furthermore, we used this method to compare MODIS LAI values with LAID values for a range of woodlands in Australia to obtain LAI at the forest scale. Results showed that the MATLAB script developed was able to successfully automate gap analysis to obtain LAIM. Good relationships were achieved when comparing averaged LAID and LAI M (LAIM=1.009 - 0.0066 LAID; R 2=0.90) and at the forest scale, MODIS LAI compared well with LAID (MODIS LAI=0.9591 LAID - 0.2371; R2=0.89). This comparison improved when correcting LAID with the clumping index to obtain effective LAI (MODIS LAI=1.0296 LAIe+0.3468; R 2=0.91). Furthermore, the script developed incorporates a function to connect directly a digital camera, or high resolution webcam, from a laptop to obtain cover photographs and LAI analysis in real time. The later is a novel feature which is not available on commercial LAI analysis softwares for cover photography. This script is available for interested researchers. © CSIRO 2008.

Fullagar, WK, Holt, SA & Gentle, IR 2008, 'Structure of SP-B/DPPC Mixed Films Studied by Neutron Reflectometry', Biophysical Journal, vol. 95, no. 10, pp. 4829-4836.
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Gale, PA 2008, 'Synthetic indole, carbazole, biindole and indolocarbazole-based receptors: applications in anion complexation and sensing', Chemical Communications, no. 38, pp. 4525-4525.
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Gale, PA, Garcia‐Garrido, SE & Garric, J 2008, 'ChemInform Abstract: Anion Receptors Based on Organic Frameworks: Highlights from 2005 and 2006', ChemInform, vol. 39, no. 18.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Gao, F, Wang, G & Zhang, C 2008, 'Strong photon-mixing of terahertz waves in semiconductor quantum wells induced by Rashba spin–orbit coupling', Nanotechnology, vol. 19, no. 46, pp. 465401-465401.
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Gentle, A & Smith, GB 2008, 'Dual metal-insulator and insulator-insulator switching in nanoscale and Al doped VO(2)', JOURNAL OF PHYSICS D-APPLIED PHYSICS, vol. 41, no. 1, pp. 1-5.
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Thin films of VO2 doped with aluminium, or with nanoscale grain sizes, have been produced. They display semiconductor resistive behaviour above the transition temperature T-c, but a metallic and plasmonic optical response. All samples optically switch ov

Gentle, A, Maaroof, A & Smith, G 2008, 'Temperature dependence of optical and transport properties in VO2 with high temperature anomalies', CURRENT APPLIED PHYSICS, vol. 8, no. 3-4, pp. 229-232.
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Thermochromic VO2 is of interest for energy efficient glazing, and for fast telecommunications because it optically switches in the near IR. Despite extensive study several aspects of its apparently diverse behaviour have not been explained satisfactorily. The visible-NIR permittivity and dc electrical conductivity of high quality thin films of VO2, across the metal-insulator phase transition and well into the metallic phase to temperatures up to 100 °C above Tc are studied as a function of temperature and grain size. Experimental behaviour is partly explained with effective medium models, existing band structures and classical transport theory. Anomalies however include: unphysically fast relaxation rate, counter-intuitive and significant differences between optical and dc, and bulk and thin film parameters; and residual "non-metallic" features above the transition in highly oriented films. Residual, but transient high temperature d-electron singlet pairing on V dimers, which is sensitive to nanostructure, is examined as a source of some anomalies. © 2007 Elsevier B.V. All rights reserved.

Gentle, AR & Smith, GB 2008, 'Five layer narrow band position variable filters for sharp colours and ultra low emittance', APPLIED PHYSICS B-LASERS AND OPTICS, vol. 92, no. 1, pp. 67-72.
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A simplified approach to creating narrow visible and near IR transmission bands with thin films is outlined utilising just five layers on glass, three of which are thin silver. These films have very high reflection at most wavelengths except for a narrow

George, S, Tushar, KV, Unnikrishn, KP, Hashim, KM & Balachandr, I 2008, 'Hemidesmus indicus (L.) R. Br. A Review', Journal of Plant Sciences, vol. 3, no. 2, pp. 146-156.
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Hemidesmus indicus (L.) R. Br. (Periplocaceae) is being used widely in Ayurvedic medicine. The history of its medicinal importance dates back to ancient times. The present review deals with studies undertaken in various aspects of this plant in the areas of morphology, anatomy, pharmacology, chemistry and ethnobotany along with medicinal uses. © 2008 Academic Journals Inc.

Gilman, EL, Ellison, J, Duke, NC & Field, C 2008, 'Threats to mangroves from climate change and adaptation options: A review', Aquatic Botany, vol. 89, no. 2, pp. 237-250.
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Mangrove ecosystems are threatened by climate change. We review the state of knowledge of mangrove vulnerability and responses to predicted climate change and consider adaptation options. Based on available evidence, of all the climate change outcomes, relative sea-level rise may be the greatest threat to mangroves. Most mangrove sediment surface elevations are not keeping pace with sea-level rise, although longer term studies from a larger number of regions are needed. Rising sea-level will have the greatest impact on mangroves experiencing net lowering in sediment elevation, where there is limited area for landward migration. The Pacific Islands mangroves have been demonstrated to be at high risk of substantial reductions. There is less certainty over other climate change outcomes and mangrove responses. More research is needed on assessment methods and standard indicators of change in response to effects from climate change, while regional monitoring networks are needed to observe these responses to enable educated adaptation. Adaptation measures can offset anticipated mangrove losses and improve resistance and resilience to climate change. Coastal planning can adapt to facilitate mangrove migration with sea-level rise. Management of activities within the catchment that affect long-term trends in the mangrove sediment elevation, better management of other stressors on mangroves, rehabilitation of degraded mangrove areas, and increases in systems of strategically designed protected area networks that include mangroves and functionally linked ecosystems through representation, replication and refugia, are additional adaptation options. © 2008 Elsevier B.V. All rights reserved.

Gladstone, W 2008, 'Towards conservation of a globally significant ecosystem: the Red Sea and Gulf of Aden', AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS, vol. 18, no. 1, pp. 1-5.
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The Red Sea and Gulf of Aden (RSGA) are renowned for their unique marine and coastal environments and species. An extreme pace of unmanaged development and a severe shortage of technical and conservation expertise threatened these globally important conservation values. Spurred to action, a period of intense activity in marine conservation, training and science by individual nations, the region, and the international donor community began in 1995. Many gains were made in marine environmental and resource management, however, this overview is con?ned to marine conservation. Marine conservation in the RSGA highlights the need for the most basic foundations to be laid by building political support and understanding, growing technical and management expertise, gathering relevant scienti?c information, and addressing the socioeconomic issues that threaten conservation values. The primary sources for much of the information presented here can be found in PERSGA (2006)

Glasner, JD, III, PG, Anderson, BD, Baumler, DJ, Biehl, BS, Burland, V, Cabot, EL, Darling, AE, Mau, B, Neeno-Eckwall, EC, Pot, D, Qiu, Y, Rissman, AI, Worzella, S, Zaremba, S, Fedorko, J, Hampton, T, Liss, P, Rusch, M, Shaker, M, Shaull, L, Shetty, P, Thotakura, S, Whitmore, J, Blattner, FR, Greene, JM & Perna, NT 2008, 'Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria', NUCLEIC ACIDS RESEARCH, vol. 36, no. SUPPL. 1, pp. D519-D523.
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ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense - diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats. © 2007 The Author(s).

Glenn, EP, Huete, AR, Nagler, PL & Nelson, SG 2008, 'Relationship between remotely-sensed vegetation indices, canopy attributes and plant physiological processes: What vegetation indices can and cannot tell us about the landscape', SENSORS, vol. 8, no. 4, pp. 2136-2160.
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Vegetation indices (VIs) are among the oldest tools in remote sensing studies. Although many variations exist, most of them ratio the reflection of light in the red and NIR sections of the spectrum to separate the landscape into water, soil, and vegetation. Theoretical analyses and field studies have shown that VIs are near-linearly related to photosynthetically active radiation absorbed by a plant canopy, and therefore to lightdependent physiological processes, such as photosynthesis, occurring in the upper canopy. Practical studies have used time-series VIs to measure primary production and évapotranspiration, but these are limited in accuracy to that of the data used in ground truthing or calibrating the models used. VIs are also used to estimate a wide variety of other canopy attributes that are used in Soil-Vegetation-Atmosphere Transfer (SVAT), Surface Energy Balance (SEB), and Global Climate Models (GCM). These attributes include fractional vegetation cover, leaf area index, roughness lengths for turbulent transfer, emissivity and albedo. However, VIs often exhibit only moderate, non-linear relationships to these canopy attributes, compromising the accuracy of the models. We use case studies to illustrate the use and misuse of VIs, and argue for using VIs most simply as a measurement of canopy light absorption rather than as a surrogate for detailed features of canopy architecture. Used this way, VIs are compatible with 'Big Leaf SVAT and GCMs that assume that canopy carbon and moisture fluxes have the same relative response to the environment as any single leaf, simplifying the task of modeling complex landscapes. © 2008 by MDPI.

Glibert, PM, Azanza, R, Burford, M, Furuya, K, Abal, E, Al-Azri, A, Al-Yamani, F, Andersen, P, Anderson, DM, Beardall, J, Berg, GM, Brand, L, Bronk, D, Brookes, J, Burkholder, JM, Cembella, A, Cochlan, WP, Collier, JL, Collos, Y, Diaz, R, Doblin, M, Drennen, T, Dyhrman, S, Fukuyo, Y, Furnas, M, Galloway, J, Graneli, E, Ha, DV, Hallegraeff, G, Harrison, J, Harrison, PJ, Heil, CA, Heimann, K, Howarth, R, Jauzein, C, Kana, AA, Kana, TM, Kim, H, Kudela, R, Legrand, C, Mallin, M, Mulholland, M, Murray, S, O'Neil, J, Pitcher, G, Qi, Y, Rabalais, N, Raine, R, Seitzinger, S, Salomon, PS, Solomon, C, Stoecker, DK, Usup, G, Wilson, J, Yin, K, Zhou, M & Zhu, M 2008, 'Ocean urea fertilization for carbon credits poses high ecological risks', MARINE POLLUTION BULLETIN, vol. 56, no. 6, pp. 1049-1056.
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The proposed plan for enrichment of the Sulu Sea, Philippines, a region of rich marine biodiversity, with thousands of tonnes of urea in order to stimulate algal blooms and sequester carbon is flawed for multiple reasons. Urea is preferentially used as a nitrogen source by some cyanobacteria and dinoflagellates, many of which are neutrally or positively buoyant. Biological pumps to the deep sea are classically leaky, and the inefficient burial of new biomass makes the estimation of a net loss of carbon from the atmosphere questionable at best. The potential for growth of toxic dinoflagellates is also high, as many grow well on urea and some even increase their toxicity when grown on urea. Many toxic dinoflagellates form cysts which can settle to the sediment and germinate in subsequent years, forming new blooms even without further fertilization. If large-scale blooms do occur, it is likely that they will contribute to hypoxia in the bottom waters upon decomposition. Lastly, urea production requires fossil fuel usage, further limiting the potential for net carbon sequestration. The environmental and economic impacts are potentially great and need to be rigorously assessed. © 2008 Elsevier Ltd. All rights reserved.

Gorrie, CA, Brown, J & Waite, PME 2008, 'Crash characteristics of older pedestrian fatalities: Dementia pathology may be related to 'at risk' traffic situations', ACCIDENT ANALYSIS AND PREVENTION, vol. 40, no. 3, pp. 912-919.
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Older people are over represented among pedestrian casualties, and cognitive decline is an often cited possible contributory factor. Cognitive decline and dementia are intimately associated, however the role dementia might play in older pedestrian crashe

Gorrie, CA, Waite, PME & Rogers, LJ 2008, 'Correlations Between Hand Preference and Cortical Thickness in the Secondary Somatosensory (SII) Cortex of the Common Marmoset, Callithrix jacchus', BEHAVIORAL NEUROSCIENCE, vol. 122, no. 6, pp. 1343-1351.
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Cortical asymmetries are well established in humans for language and motor regions and correlate with handedness. Here the authors investigate structural differences in the hemispheres of left- and right-handed common marmosets using surface photography

Gou, X, Wang, G, Kong, X, Wexler, D, Horvat, J, Yang, J & Park, J 2008, 'Flutelike Porous Hematite Nanorods and Branched Nanostructures: Synthesis, Characterisation and Application for Gas‐Sensing', Chemistry – A European Journal, vol. 14, no. 19, pp. 5996-6002.
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AbstractFlute‐like porous α‐Fe2O3 nanorods and branched nanostructures such as pentapods and hexapods were prepared through dehydration and recrystallisation of hydrothermally synthesised β‐FeOOH precursor. Transmission electron microscopy (TEM), high‐resolution TEM and selected area electron diffraction analyses reveal that the nanorods, which grow along the [110] direction, have nearly hollow cavities and porous walls with a pore size of 20–50 nm. The hexapods have six symmetric arms with a diameter of 60–80 nm and length of 400–900 nm. The growth direction of the arms in the hexapod‐like nanostructure is also along the [110] direction, and there is a dihedral angle of 69.5o between adjacent arms. These unique iron oxide nanostructures offer the first opportunity to investigate their magnetic and gas sensing properties. The nanostructures exhibited unusual magnetic behaviour, with two different Morin temperatures under field‐cooled and zero‐field‐cooled conditions, owing to their shape anisotropy and magnetocrystalline anisotropy. Furthermore, the α‐Fe2O3 nanostructures show much better sensing performance towards ethanol than that of the previously reported polycrystalline nanotubes. In addition, the α‐Fe2O3 nanostructure based sensor can selectively detect formaldehyde and acetic acid among other toxic, corrosive and irritant vapours at a low working temperature with rapid response, high sensitivity and good stability.

Gou, X, Wang, G, Park, J, Liu, H & Yang, J 2008, 'Monodisperse hematite porous nanospheres: synthesis, characterization, and applications for gas sensors', NANOTECHNOLOGY, vol. 19, no. 12.
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Gou, X, Wang, G, Yang, J, Park, J & Wexler, D 2008, 'Chemical synthesis, characterisation and gas sensing performance of copper oxide nanoribbons', Journal of Materials Chemistry, vol. 18, no. 9, pp. 965-965.
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Single crystalline copper oxide nanoribbons were synthesized via a surfactant-assisted hydrothermal route. The resulting CuO nanoribbons contain substantial amounts of nanorings and nanoloops. High resolution TEM analysis identified CuO nanoribbons growing along the [010] direction. CuO nanoribbons exhibited excellent sensing performance towards formaldehyde and ethanol vapours with rapid response and high sensitivity at low operating temperatures. We found that the loading of a small amount of Au or Pt nanoparticles on the surface of CuO nanoribbons can effectively enhance and functionalize the gas sensing performance of CuO nanoribbons. © The Royal Society of Chemistry.

Grigg, AH, Macfarlane, C, Evangelista, C, Eamus, D & Adams, MA 2008, 'Does initial spacing influence crown and hydraulic architecture of Eucalyptus marginata?', TREE PHYSIOLOGY, vol. 28, no. 5, pp. 753-760.
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Long-term declines in rainfall in south-western Australia have resulted in increased interest in the hydraulic characteristics of jarrah (Eucalyptus marginata Donn ex Smith) forest established in the region's drinking water catchments on rehabilitated bauxite mining sites. We hypothesized that in jarrah forest established on rehabilitated mine sites: (1) leaf area index (L) is independent of initial tree spacing; and (2) more densely planted trees have less leaf area for the same leaf mass, or the same sapwood area, and have denser sapwood. Initial stand densities ranged from about 600 to 9000 stems ha -1, and trees were 18 years old at the time of sampling. Leaf area index was unaffected by initial stand density, except in the most sparsely stocked stands where L was 1.2 compared with 2.0-2.5 in stands at other spacings. The ratio of leaf area to sapwood area (Al:As) was unaffected by tree spacing or tree size and was 0.2 at 1.3 m height and 0.25 at the crown base. There were small increases in sapwood density and decreases in leaf specific area with increased spacing. Tree diameter or basal area was a better predictor of leaf area than sapwood area. At the stand scale, basal area was a good predictor of L (r2 = 0.98, n = 15) except in the densest stands. We conclude that the hydraulic attributes of this forest type are largely independent of initial tree spacing, thus simplifying parameterization of stand and catchment water balance models. © 2008 Heron Publishing.

Gross, DE, Schmidtchen, FP, Antonius, W, Gale, PA, Lynch, VM & Sessler, JL 2008, 'Cooperative Binding of Calix[4]pyrrole–Anion Complexes and Alkylammonium Cations in Halogenated Solvents', Chemistry – A European Journal, vol. 14, no. 26, pp. 7822-7827.
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AbstractCalix[4]pyrrole–chloride interactions are affected not only by the choice of countercation in halogenated solvents, but show a specific dependence on the way in which these cations are bound within the electron rich, bowl‐like calix[4]pyrrole cavity formed upon chloride anion complexation. In dichloromethane, the affinities of simple meso‐octamethylcalix[4]pyrrole (1) for methyl‐, ethyl‐, and n‐butylammonium chlorides are on the order of 105, 104, and 102 M−1, respectively, as determined from isothermal titration calorimetry (ITC) analyses. These cation‐dependent anion affinity effects, while clearly evident, are less pronounced in other halogenated solvents, such as 1,2‐dichloroethane. Support for the proposed cation complexation selectivity is provided by solid state X‐ray crystallographic analyses.

Gu, HY 2008, 'Computation of approximate alpha-points for large scale single machine scheduling problem', COMPUTERS & OPERATIONS RESEARCH, vol. 35, no. 10, pp. 3262-3275.
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This paper studies the linear programming (LP) relaxation of xjt-formulation of the single machine scheduling problem 1|rj|?wjCj. The Lagrangian relaxation approach is proposed to cope with the computational difficulties for large problems. Since it can still be time consuming if highly accurate LP relaxation is required, the effect of approximate solution is studied with respect to the a-point heuristic. A two-stage proximal bundle algorithm is designed for the computation of the approximate solution. Results of numerical experiments show the efficiency of the proposed algorithm for large problems

Gunawan, C, Breuer, M, Hauer, B, Rogers, PL & Rosche, B 2008, 'Improved (R)-phenylacetylcarbinol production with Candida utilis pyruvate decarboxylase at decreased organic to aqueous phase volume ratios', Biotechnology Letters, vol. 30, no. 2, pp. 281-286.
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The effect of decreasing the organic (octanol) to aqueous phase volume ratio was evaluated in a two-phase enzymatic process for (R)- phenylacetylcarbinol (PAC) production. Decreasing the ratio from 1:1 to 0.43:1 at 4°C increased PAC in the organic phase from 112 g/l to 183 g/l with a 10% improvement in overall productivity. Interestingly, the rate of enzyme (pyruvate decarboxylase) activity loss was unaffected by the reduced phase ratio over the reaction period (48 h). At 20°C and 0.43:1 phase ratio the organic phase PAC concentration increased to 212 g/l and the overall productivity increased by 30% although the PAC yield (based on pyruvate) declined by about 10% due to greater byproduct acetoin formation at the higher temperature. Product recovery in such a system is facilitated both by the higher PAC concentration and the reduced organic phase volume. © 2007 Springer Science+Business Media B.V.

Gunning, SJ, Maggio, F, Windley, MJ, Valenzuela, SM, King, GF & Nicholson, GM 2008, 'The Janus-faced atracotoxins are specific blockers of invertebrate K(Ca) channels', FEBS JOURNAL, vol. 275, no. 16, pp. 4045-4059.
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The Janus-faced atracotoxins are a unique family of excitatory peptide toxins that contain a rare vicinal disulfide bridge. Although lethal to a wide range of invertebrates, their molecular target has remained enigmatic for almost a decade. We demonstrate here that these toxins are selective, high-affinity blockers of invertebrate Ca2+-activated K+ (K Ca) channels. Janus-faced atracotoxin (J-ACTX)-Hv1c, the prototypic member of this toxin family, selectively blocked KCa channels in cockroach unpaired dorsal median neurons with an IC50 of 2 nm, but it did not significantly affect a wide range of other voltage-activated K +, Ca2+ or Na+ channel subtypes. J-ACTX-Hv1c blocked heterologously expressed cockroach large-conductance Ca 2+-activated K+ (pSlo) channels without a significant shift in the voltage dependence of activation. However, the block was voltage-dependent, indicating that the toxin probably acts as a pore blocker rather than a gating modifier. The molecular basis of the insect selectivity of J-ACTX-Hv1c was established by its failure to significantly inhibit mouse mSlo currents (IC50 ∼ 10 μm) and its lack of activity on rat dorsal root ganglion neuron KCa channel currents. This study establishes the Janus-faced atracotoxins as valuable tools for the study of invertebrate KCa channels and suggests that KCa channels might be potential insecticide targets. © 2008 The Authors.

Ha, S, Sukhorukov, AA, Dossou, KB, Botten, LC, Lavrinenko, AV, Chigrin, DN & Kivshar, YS 2008, 'Dispersionless tunneling of slow light in antisymmetric photonic crystal couplers', OPTICS EXPRESS, vol. 16, no. 2, pp. 1104-1114.
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We suggest a novel and general approach to the design of photonic-crystal directional couplers operating in the slow-light regime. We predict, based on a general symmetry analysis, that robust tunneling of slow-light pulses is possible between antisymmetrically coupled photonic crystal waveguides. We demonstrate, through Bloch mode frequency-domain and finite-difference time-domain (FDTD) simulations that, for all pulses with strongly reduced group velocities at the photonic band-gap edge, complete switching occurs at a fixed coupling length of just a few unit cells of the photonic crystal. © 2008 Optical Society of America.

Han, X, Kennan, RM, Davies, JK, Reddacliff, LA, Dhungyel, OP, Whittington, RJ, Turnbull, L, Whitchurch, CB & Rood, JI 2008, 'Twitching motility is essential for virulence in Dichelobacter nodosus', JOURNAL OF BACTERIOLOGY, vol. 190, no. 9, pp. 3323-3335.
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Type IV fimbriae are essential virulence factors of Dichelobacter nodosus, the principal causative agent of ovine foot rot. The fimA fimbrial subunit gene is required for virulence, but fimA mutants exhibit several phenotypic changes and it is not certain if the effects on virulence result from the loss of type IV fimbria-mediated twitching motility, cell adherence, or reduced protease secretion. We showed that mutation of either the pilT or pilU gene eliminated the ability to carry out twitching motility. However, the pilT mutants displayed decreased adhesion to epithelial cells and reduced protease secretion, whereas the pilU mutants had wild-type levels of extracellular protease secretion and adherence. These data provided evidence that PilT is required for the type IV fimbria-dependent protease secretion pathway in D. nodosus. It was postulated that sufficient fimbrial retraction must occur in the pilU mutants to allow protease secretion, but not twitching motility, to take place. Although no cell movement was detected in a pilU mutant of D. nodosus, aberrant motion was detected in an equivalent mutant of Pseudomonas aeruginosa. These observations explain how in D. nodosus protease secretion can occur in a pilU mutant but not in a pilT mutant. In addition, virulence studies with sheep showed that both the pilT and pilU mutants were avirulent, providing evidence that mutation of the type IV fimbrial system affects virulence by eliminating twitching motility, not by altering cell adherence or protease secretion. Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Hansbro, NG, Horvat, JC, Wark, PA & Hansbro, PM 2008, 'Understanding the mechanisms of viral induced asthma: New therapeutic directions', Pharmacology & Therapeutics, vol. 117, no. 3, pp. 313-353.
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Asthma is a common and debilitating disease that has substantially increased in prevalence in Western Societies in the last 2 decades. Respiratory tract infections by respiratory syncytial virus (RSV) and rhinovirus (RV) are widely implicated as common causes of the induction and exacerbation of asthma. These infections in early life are associated with the induction of wheeze that may progress to the development of asthma. Infections may also promote airway inflammation and enhance T helper type 2 lymphocyte (Th2 cell) responses that result in exacerbations of established asthma. The mechanisms of how RSV and RV induce and exacerbate asthma are currently being elucidated by clinical studies, in vitro work with human cells and animal models of disease. This research has led to many potential therapeutic strategies and, although none are yet part of clinical practise, they show much promise for the prevention and treatment of viral disease and subsequent asthma.

Harel, M, Ben-Dov, E, Rasoulouniriana, D, Siboni, N, Kramarsky-Winter, E, Loya, Y, Barak, Z, Wiesman, Z & Kushmaro, A 2008, 'A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa', FEMS MICROBIOLOGY ECOLOGY, vol. 64, no. 3, pp. 378-387.
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Harris, N, Ford, MJ, Mulvaney, P & Cortie, MB 2008, 'Tunable infrared absorption by meta nanoparticles: The case for gold rods and shells', GOLD BULLETIN, vol. 41, no. 1, pp. 5-14.
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Nanoparticles of elements such as Au, Al or Ag have optical extinction cross-section that considerably surpass their geometric cross-sections at certain wavelengths of light. While the absorption and scattering maxima for nanospheres of these elements are relatively insensitive to particle diameter, the surface plasmon resonance of Au nanoshells and nanorods can be readily tuned from the visible into the infrared by changing the shape of the particle. Here we compare nanoshells and nanorods in terms of their ease of synthesis, their optical properties, and their longer term technological prospects as tunable 'plasmonic absorbers'. While both particle types are now routinely prepared by wet chemistry, we submit that it is more convenient to prepare rods. Furthermore, the plasmon resonance and peak absorption efficiency in nanorods may be readily tuned into the infrared by an increase of their aspect ratio, whereas in nanoshells such tuning may require a decrease in shell thickness to problematic dimensions.

He, B, Luo, L, Hu, J & Gu, HY 2008, 'Smoothing algorithm for high speed machining at corner', Shanghai Jiaotong Daxue Xuebao Journal of Shanghai Jiaotong University, vol. 42, no. 1, pp. 83-86.
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Making feed speed smooth along the corner of two adjoining moves is the key measure to protect the machine tools and assure the machining quality and the efficiency of high speed machinery process. This paper presented an algorithm to make smooth the track and the velocity by adding adjoining moves vectors based on trapezoidal velocity profile. The algorithm is proposed for interpolating adjoining moves simultaneously according to the maximum distance decelerating to zero. This algorithm is verified to get good machining quality and velocity at the corner when high speed machining.

Hemming, MN, Peacock, WJ, Dennis, ES & Trevaskis, B 2008, 'Integration of seasonal flowering time responses in temperate cereals', Plant Signaling & Behavior, vol. 3, no. 8, pp. 601-602.
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Hemming, MN, Peacock, WJ, Dennis, ES & Trevaskis, B 2008, 'Low-temperature and daylength cues are integrated to regulate FLOWERING LOCUS T in barley', PLANT PHYSIOLOGY, vol. 147, no. 1, pp. 355-366.
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Interactions between flowering time genes were examined in a doubled haploid barley (Hordeum vulgare) population segregating for H. vulgare VERNALIZATION1 (HvVRN1), HvVRN2, and PHOTOPERIOD1 (PPD-H1). A deletion allele of HvVRN2 was associated with rapid inflorescence initiation and early flowering, but only in lines with an active allele of PPD-H1. In these lines, the floral promoter FLOWERING LOCUS T (HvFT1) was expressed at high levels without vernalization, and this preceded induction of HvVRN1. Lines with the deletion allele of HvVRN2 and the inactive ppd-H1 allele did not undergo rapid inflorescence initiation and were late flowering. These data suggest that HvVRN2 counteracts PPD-H1 to prevent flowering prior to vernalization. An allele of HvVRN1 that is expressed at high basal levels (HvVRN1-1) was associated with rapid inflorescence initiation regardless of HvVRN2 or PPD-H1 genotype. HvFT1 was expressed without vernalization in lines with the HvVRN1-1 allele and HvFT1 transcript levels were highest in lines with the active PPD-H1 allele; this correlated with rapid apex development postinflorescence initiation. Thus, expression of HvVRN1 promotes inflorescence initiation and up-regulates HvFT1. Analysis of HvVRN1 expression in different genetic backgrounds postvernalization showed that HvVRN2, HvFT1, and PPD-H1 are unlikely to play a role in low-temperature induction of HvVRN1. In a vernalization responsive barley, HvFT1 is not induced by low temperatures alone, but can be induced by long days following prolonged low-temperature treatment. We conclude that low-temperature and daylength flowering-response pathways are integrated to control expression of HvFT1 in barley, and that this might occur through regulation of HvVRN2 activity.

Henderson, DJ, Carroll, RJ & Li, Q 2008, 'Nonparametric estimation and testing of fixed effects panel data models', Journal of Econometrics, vol. 144, no. 1, pp. 257-275.
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Heness, G, Booth, N & Ben-Nissan, B 2008, 'Does Size Matter? - The Effect of Volume on the Compressive Strength of Open Cell Brittle Ceramics', Advanced Materials Research, vol. 41-42, pp. 221-226.
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This study investigates the effect of specimen volume on the compressive strength ofopen cell brittle ceramics. A series of unconfined compression tests were carried out on specimensranging in volume. The crushing strength and apparent stiffness were measured and these results arecorrelated with the volume of material stressed. It was found that as the volume of material testeddecreased the strength decreased.

Hennige, SJ, Smith, DJ, Perkins, R, Consalvey, M, Paterson, DM & Suggett, DJ 2008, 'Photoacclimation, growth and distribution of massive coral species in clear and turbid waters', Marine Ecology Progress Series, vol. 369, pp. 77-88.
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Massive coral species play a key role in coral reef ecosystems, adding significantly to physical integrity, long term stability and reef biodiversity. This study coupled the assessment of the distribution and abundance of 4 dominant massive coral species, Diploastrea heliopora, Favia speciosa, F. matthaii and Porites lutea, with investigations into species-specific photoacclimatory responses within the Wakatobi Marine National Park of southeast Sulawesi, Indonesia, to determine the potential of photoacclimation to be a driver of biological success. For this, rapid light curves using pulse amplitude modulated (PAM) chlorophyll a fluorescence techniques were employed with additional manipulations to circumvent differences of light quality and absorption between species and across environmental gradients. P. lutea was examined over a range of depths and sites to determine patterns of photoacclimation, and all 4 species were assessed at a single depth between sites for which long-term data for coral community structure and growth existed. Light availability was more highly constrained with depth than between sites; consequently, photoacclimation patterns for P. lutea appeared greater with depth than across environmental gradients. All 4 species were found to differentially modify the extent of non-photochemical quenching to maintain a constant photochemical operating efficiency (qP). Therefore, our results suggest that these massive corals photoacclimate to ensure a constant light-dependent rate of reduction of the plastoquinone pool across growth environments. © Inter-Research 2008.

Herbert, BR, Hill, C, Padula, MP, DSouza-Bassea, JM, Krockenberger, MB, Malik, R, Ngamskulrungroj, P, Chong, HS, Meyer, W, Harry, EJ & Carter, DA 2008, 'Fungal Lung Infection : Understanding Cryptococcus Gattii Infection and the Challenges of Mixed Proteomes', Journal of Proteomics & Bioinformatics, vol. S2, no. 01, pp. 097-098.
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Herok, GH, Millar, TJ, Anderton, PJ & Martin, DK 2008, 'Role of Chloride Channels in Regulating the Volume of Acinar Cells of the Rabbit Superior Lacrimal Gland', INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, vol. 49, no. 12, pp. 5517-5525.
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PURPOSE. To characterize the outward chloride currents (Cl-OR) in single acinar cells isolated from the rabbit superior lacrimal gland (RSLG) to investigate the hypothesis that Cl-OR may have a role in regulating the volume of RSLG acini. METHODS. Cl-OR

Hill, R & Ralph, PJ 2008, 'Dark-induced reduction of the plastoquinone pool in zooxanthellae of scleractinian corals and implications for measurements of chlorophyll a fluorescence', SYMBIOSIS, vol. 46, no. 1, pp. 45-56.
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Fluorometric measurements of maximum quantum yield (Fv/F m) and fast induction curves (FICs) require coral samples to be dark-adapted (DA). Pathways causing dark-reduction of the plastoquinone (PQ) pool are shown here to be active in corals. Early morning sunlight and far-red light successfully increased Fv/Fm and lowered the O and J steps of FICs in corals that were darkened overnight. The thick-tissued massive coral, Cyphastrea serailia, was shown to be more prone to reduction of the PQ pool, with significant reductions in Fv/Fm occurring after 10 min of DA, and elevated J steps occurring within 200 s following a far-red flash. In thinner-tissued branching species, Pocillopora damicornis and Acropora nobilis, elevation of the J step also occurred within 200 s of DA, but a drop in Fv/Fm was only manifested after 30 min. Pre-exposure to far-red light is an effective and simple procedure to ensure determination of the true maximum quantum yield of Photosystem II (PSII) and accurate FICs which require a fully oxidised inter-system electron transport chain and open PSII reaction centres. ©2008 Balaban.

Hill, R & Ralph, PJ 2008, 'Impact of bleaching stress on the function of the oxygen evolving complex of zooxanthellae from scleractinian corals', JOURNAL OF PHYCOLOGY, vol. 44, no. 2, pp. 299-310.
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Global climate change is leading to the rise of ocean temperatures and is triggering mass coral bleaching events on reefs around the world. The expulsion of the symbiotic dinoflagellate algae is believed to occur as a result of damage to the photosynthetic apparatus of these symbionts, although the specific site of initial impact is yet to be conclusively resolved. Here, the sensitivity of the oxygen evolving complex (OEC) to bleaching stress was studied as well as its natural variation between seasons. The artificial electron donor, diphenyl carbazide (DPC), was added to cultured, freshly isolated and expelled (bleaching treatments only) zooxanthellae suspensions. Chl a fluorescence and oxygen production measurements showed that upon addition of DPC, no restoration of diminished photochemical efficiency occurred under control or bleaching conditions. This result was consistent between 12 h and 5 d bleaching treatments on Pocilloporadamicornis, indicating that the OEC is not the primary site of damage, and that zooxanthellae expulsion from the host is a nonselective process with respect to the functioning of the OEC. Further experiments measuring fast induction curves (FICs) revealed that in both summer and winter, the temperature when OEC function was lost occurred between 7°C and 14°C above the sea surface temperature. FIC and oxygen production measurements of P. damicornis during exposure to bleaching stress demonstrated that the thermotolerance of the OEC increased above the temperature of the bleaching treatment over a 4 h period. This finding indicates that the OEC has the capacity to acclimate between seasons and remains functional at temperatures well above bleaching thresholds. © 2008 Phycological Society of America.

Hills, N, Hose, GC, Cantlay, AJ & Murray, BR 2008, 'Cave invertebrate assemblages differ between native and exotic leaf litter', AUSTRAL ECOLOGY, vol. 33, no. 3, pp. 271-277.
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Allochtonous leaf litter is an important source of energy and nutrients for invertebrates in cave ecosystems. A change to the quality or quantity of litter entering caves has the potential to disrupt the structure and function of cave communities. In this study, we adopted an experimental approach to examine rates of leaf litter decomposition and the invertebrate assemblages colonizing native and exotic leaf litter in limestone caves in the Jenolan Caves Karst Conservation Reserve, New South Wales, Australia. We deployed traps containing leaf litter from exotic sycamore (Acer pseudoplatanus) and radiata pine (Pinus radiata) trees and native eucalypts (Eucalyptus spp.) in twilight zones (near the cave entrance) and areas deep within the caves for 3 months. Thirty-two invertebrate morphospecies were recorded from the litter traps, with greater richness and abundance evident in the samples from the twilight zone compared with areas deep within the cave. Sycamore litter had significantly greater richness and abundance of invertebrates compared with eucalypt and pine litter in samples from the twilight zone, but there was no difference in richness or abundance among litter samples placed deep within the cave. Relative rates of decay of the three litters were sycamore > eucalypt > pine. We discuss the potential for the higher decomposition rates and specific leaf area in sycamores to explain their higher invertebrate diversity and abundance. Our findings have important implications for the management of exotic plants and the contribution of their leaf litter to subterranean ecosystems. © 2008 The Authors.

Hoft, RC, Ford, MJ, Garcia-Suarez, VM & Lambert, CJ 2008, 'The effect of stretching thiyl- and ethynyl-Au molecular junctions', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 20, no. 2, pp. 1-9.
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We perform density functional theory (DFT) calculations of the stretching of Au(111)-X-Au(111) molecular junctions where X is either a thiyl or ethynyl biradical. The equilibrium geometries for the radicals adsorbing on the surface are first calculated and the radicals then placed in the junction geometry. The unit cell is stepwise increased in length and the geometry relaxed at each step. When stretching the ethynyl junction, a single gold atom is detached from the rest of the surface and the gold-carbon bond does not break. In contrast, the gold-sulfur bond in the thiyl junction breaks without detaching any gold atoms. This behaviour can be attributed to the enhanced strength of the Au-C interaction over the Au-S interaction. In both junctions the conductance calculated using the non-equilibrium Green's function formalism (NEGF) decreases as the junction is stretched. After breakage of the Au-S bond, the thiyl radical contains an unpaired electron on the sulfur atom and the system is in a spin doublet state. Transmission spectra were calculated for the spin-unpolarized case only; evaluation of the spin-polarized density of states suggests that an enhanced conductance for electrons of one spin type may be observed after the Au-S bond is broken. © 2008 IOP Publishing Ltd.

Hoile, R, Walsh, SJ & Bioterrorism, RC 2008, 'Erratum', Journal of Forensic Sciences, vol. 53, no. 6, pp. 1499-1499.
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Hong, MY, Baladandayuthapani, V, Li, Y, Carroll, RJ, Turner, ND & Lupton, JR 2008, 'Coordinated p27 Kip1 expression as a function of distance between crypts ‐ Potential inter‐crypt signaling', The FASEB Journal, vol. 22, no. S1.
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Colonic epithelial cells are arranged in patterns called crypts. There has been a conjecture that a coordinated response exists at the crypt level, i.e. that biological responses in one crypt affects the biological responses in neighboring crypts. P27Kip1 (p27) is a cyclin dependent kinase inhibitor, which arrests cell cycle progression and induces apoptosis. We hypothesized if a crypt has high p27 expression, the neighboring crypts are likely to have high p27 expression. To test the hypothesis, 20 colonic crypts in each of 12 rats were analyzed for p27 levels and the distance between the crypts were measured. The correlation between the p27 expression between the crypts were analyzed using Bayesian statistical methods. The correlation at 25 μm was 0.57 and the correlation was positive for distances up to 400 μm (p<0.05). The closer crypts were to one another the better the correlation. This observation supports the existence of inter‐crypt signaling; p27 expression in crypts which are in close proximity tend to have similar expression levels. This type of inter‐crypt signaling may be responsible for the formation of aberrant crypt foci, polyps and eventually colon adenomas. This spatial analysis is a novel mathematical approach to study of colon carcinogenesis. Funded by NIH (CA61750, CA82907, CA59034), NSBRI NASA NCC 9–58 and NIEHS P30‐ES09106.

Horton, NJ, Roberts, K, Ryan, L, Suglia, SF & Wright, RJ 2008, 'A maximum likelihood latent variable regression model for multiple informants', STATISTICS IN MEDICINE, vol. 27, no. 24, pp. 4992-5004.
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Studies pertaining to childhood psychopathology often incorporate information from multiple sources (or informants). For example, measurement of some factor of particular interest might be collected from parents, teachers as well as the children being studied. We propose a latent variable modeling framework to incorporate multiple informant predictor data. Several related models are presented, and likelihood ratio tests are introduced to formally compare fit. The incorporation of partially observed subjects is addressed under a variety of missing data mechanisms. The methods are motivated by and applied to a study of the association of chronic exposure to violence on asthma in children. Copyright © 2008 John Wiley & Sons, Ltd.

Howe, CJ, Barbrook, AC, Nisbet, RER, Lockhart, PJ & Larkum, AWD 2008, 'The origin of plastids', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 363, no. 1504, pp. 2675-2685.
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It is generally accepted that plastids first arose by acquisition of photosynthetic prokaryotic endosymbionts by non-photosynthetic eukaryotic hosts. It is also accepted that photosynthetic eukaryotes were acquired on several occasions as endosymbionts by non-photosynthetic eukaryote hosts to form secondary plastids. In some lineages, secondary plastids were lost and new symbionts were acquired, to form tertiary plastids. Most recent work has been interpreted to indicate that primary plastids arose only once, referred to as a 'monophyletic' origin. We critically assess the evidence for this. We argue that the combination of Ockham's razor and poor taxon sampling will bias studies in favour of monophyly. We discuss possible concerns in phylogenetic reconstruction from sequence data. We argue that improved understanding of lineage-specific substitution processes is needed to assess the reliability of sequence-based trees. Improved understanding of the timing of the radiation of present-day cyanobacteria is also needed. We suggest that acquisition of plastids is better described as the result of a process rather than something occurring at a discrete time, and describe the 'shopping bag' model of plastid origin. We argue that dinoflagellates and other lineages provide evidence in support of this. © 2008 The Royal Society.

Howlett, C, Seini, M, Matthews, C, Dillon, B & Hauser, V 2008, 'Retaining Indigenous Students in Tertiary Education: Lessons from the Griffith School of Environment', The Australian Journal of Indigenous Education, vol. 37, no. 1, pp. 18-27.
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Abstract Low retention of Indigenous peoples in all Australian universities has been identified as a problematic issue by the Australian Federal government. Griffith University (GU), Queensland, Australia, provided funding to examine the factors affecting Indigenous retention in higher education, with the aim of developing innovative participation and retention strategies specifically for Indigenous students. This paper focuses on research conducted within the Griffith School of Environment that questioned the possible links between the provision of information to commencing Indigenous students and their retention. It essentially examines to what extent current university structures support Indigenous enrolments and retention, via the information they receive upon enrolling. From interviews conducted in an informal discussion format with currently enrolled Indigenous students in the Griffith School of Environment, critical deficiencies were identified in the information Indigenous students receive during the early transition phase of university entrance. A key finding of this study, and which is the subject of current research, was the support amongst the students for the development of an Indigenised curriculum in science as a strategy for improving the attraction and retention of Indigenous students. This paper details the research project and its findings.

Huete, AR, Restrepo-Coupe, N, Ratana, P, Didan, K, Saleska, SR, Ichii, K, Panuthai, S & Gamo, M 2008, 'Multiple site tower flux and remote sensing comparisons of tropical forest dynamics in Monsoon Asia', AGRICULTURAL AND FOREST METEOROLOGY, vol. 148, no. 5, pp. 748-760.
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The spatial and temporal dynamics of tropical forest functioning are poorly understood, partly attributed to a weak seasonality and high tree species diversity at the landscape scale. Recent neotropical rainforest studies with local tower flux measurements have revealed strong seasonal carbon fluxes that follow the availability of sunlight in intact forests, while in areas of forest disturbance, carbon fluxes more closely tracked seasonal water availability. These studies also showed a strong seasonal correspondence of satellite measures of greenness, using the Enhanced Vegetation Index (EVI) with ecosystem carbon fluxes in both intact and disturbed forests, which may enable larger scale extension of tower flux measurements. In this study, we investigated the seasonal patterns and relationships of local site tower flux measures of gross primary productivity (Pg) with independent Moderate Resolution Imaging Spectroradiometer (MODIS) satellite greenness measures across three Monsoon Asia tropical forest types, encompassing drought-deciduous, dry evergreen, and humid evergreen secondary tropical forests. In contrast to neotropical forests, the tropical forests of Monsoon Asia are more extensively degraded and heterogeneous due to intense land use pressures, and therefore, may exhibit unique seasonal patterns of ecosystem fluxes that are more likely water-limited and drought-susceptible. Our results show significant phenologic variability and response to moisture and light controls across the three tropical forest sites and at the regional scale. The drier tropical forests were primarily water-limited, while the wet evergreen secondary forest showed a slight positive trend with light availability. Satellite EVI greenness observations were generally synchronized and linearly related with seasonal and inter-annual tower flux Pg measurements at the multiple sites and provided better opportunities for tower extension of carbon fluxes than other satellite produc...

Huston, WM, Naylor, J, Cianciotto, NP, Jennings, MP & McEwan, AG 2008, 'Functional analysis of the multi-copper oxidase from Legionella pneumophila', Microbes and Infection, vol. 10, no. 5, pp. 497-503.
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Huston, WM, Theodoropoulos, C, Mathews, SA & Timms, P 2008, 'Chlamydia trachomatis responds to heat shock, penicillin induced persistence, and IFN-gamma persistence by altering levels of the extracytoplasmic stress response protease HtrA', BMC Microbiology, vol. 8, no. 1, pp. 190-190.
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Background. Chlamydia trachomatis, an obligate intracellular human pathogen, is the most prevalent bacterial sexually transmitted infection worldwide and a leading cause of preventable blindness. HtrA is a virulence and stress response periplasmic serine protease and molecular chaperone found in many bacteria. Recombinant purified C. trachomatis HtrA has been previously shown to have both activities. This investigation examined the physiological role of Chlamydia trachomatis HtrA. Results. The Chlamydia trachomatis htrA gene complemented the lethal high temperature phenotype of Escherichia coli htrA- (>42°C). HtrA levels were detected to increase by western blot and immunofluorescence during Chlamydia heat shock experiments. Confocal laser scanning microscopy revealed a likely periplasmic localisation of HtrA. During penicillin induced persistence of Chlamydia trachomatis, HtrA levels (as a ratio of LPS) were initially less than control acute cultures (20 h post infection) but increased to more than acute cultures at 44 h post infection. This was unlike IFN-γ persistence where lower levels of HtrA were observed, suggesting Chlamydia trachomatis IFN-γ persistence does not involve a broad stress response. Conclusion. The heterologous heat shock protection for Escherichia coli, and increased HtrA during cell wall disruption via penicillin and heat shock, indicates an important role for HtrA during high protein stress conditions for Chlamydia trachomatis. © 2008 Huston et al; licensee BioMed Central Ltd.

Hutchison, JA, Bell, TDM, Ganguly, T, Ghiggino, KP, Langford, SJ, Lokan, NR & Paddon-Row, MN 2008, 'Photoinduced electron transfer dynamics in porphyrin donor dyads', Journal of Photochemistry and Photobiology A: Chemistry, vol. 197, no. 2-3, pp. 220-225.
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Huttunen, J, Doble, P, Dawson, M, Roux, C & Robertson, J 2008, 'Physical evidence in drug intelligence, Part 2: discrimination of packaging tapes by colour', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 40, no. 1, pp. 73-83.
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The authors have considered routine exploitation of physical evidence from seized shipments of illicit drugs for intelligence purposes. Part 1 of this series addressed the identification of polymer type within the adhesive pf packaging tapes and raised important issues with regard to how data should be collated in a databse as a basis for reliable drug intelligence. this article expands onthis topic by addressingt eh sue of colour for achieving the same aim. By using a relatively simple instrumental technique to analyse opaque 'brown' packaging tapes, it was found that colour was an effective way to discriminate between different adhesive tape samples. However, unitial results showed that the analysis of colour in packaging tapes was more complex than assigning seminsubjective names to particular hues (e.g. light brown, greenm brown etc). Instead, samples in the population often differed only slightly from one another and hence proved difficult to categorise. Thus, a database or analyst must avoid using such 'discrete' labels and instead make use of 'continuous' numerical data. Here, CIELab chromaticity coordinates were used to define representative colour spaces for each tape sample and these were then compared to determine whether two such volumes intersected. This process would decide whether or not the sampes could be discriminated. While several sets of data were compared, further work needs to be carried out into the consistency of colour within single rolls of tape or batches of tape.

Huynh, KN, Oliver, BG, Stelzer, S, Rawlinson, WD & Tovey, ER 2008, 'A new method for sampling and detection of exhaled respiratory virus aerosols', CLINICAL INFECTIOUS DISEASES, vol. 46, no. 1, pp. 93-95.
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We have developed a mask sampler for exhaled respiratory viruses. Among a group of 9 patients with cold symptoms who had virus-positive nasal mucus specimens, as analyzed by multiplexed polymerase chain reaction, virus-positive mask samples were obtained after coughing (20 times), talking (20 min), or breathing (20 min) from 6, 5, and 3 patients, respectively. © 2007 by the Infectious Diseases Society of America. All rights reserved.

Ismar, Matthews & Hauber 2008, 'Seaweed provisioning behaviour confers thermal benefit for nesting Australasian gannets (Morus serrator)', Behaviour, vol. 145, no. 12, pp. 1823-1837.
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Ito, K, Herbert, C, Siegle, JS, Vuppusetty, C, Hansbro, N, Thomas, PS, Foster, PS, Barnes, PJ & Kumar, RK 2008, 'Steroid-Resistant Neutrophilic Inflammation in a Mouse Model of an Acute Exacerbation of Asthma', American Journal of Respiratory Cell and Molecular Biology, vol. 39, no. 5, pp. 543-550.
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Neutrophilic inflammation in acute exacerbations of asthma tends to be resistant to treatment with glucocorticoids. This may be related to decreased activity and expression of histone deacetylase-2 (HDAC2), which down-regulates expression of proinflammatory genes via recruitment to the glucocorticoid receptor complex. We assessed airway inflammation and response to steroid treatment in a novel mouse model of an acute exacerbation of chronic asthma. Systemically sensitized mice received low-level challenge with aerosolized ovalbumin for 4 weeks, followed by a single moderate-level challenge to induce enhanced inflammation in distal airways. We assessed the effects of pre-treatment with dexamethasone on the accumulation of inflammatory cells in the airways, airway responsiveness to methacholine, expression and enzymatic activity of nuclear proteins including histone acetyl transferase (HAT) and HDAC2, and levels of transcripts for neutrophil chemoattractant and survival cytokines. Dexamethasone suppressed inflammation associated with eosinophil and T-lymphocyte recruitment, but did not prevent neutrophil accumulation or development of airway hyperresponsiveness. Increased activity of HAT was suppressed by steroid treatment, but the marked diminution of HDAC2 activity and increased activity of nuclear factor-κB were not reversed. Correspondingly, elevated expression of mRNA for TNF-α, granulocyte macrophage colony-stimulating factor, IL-8, and p21waf were also not suppressed by dexamethasone. Levels of lipid peroxidation and protein nitration products were elevated in the acute exacerbation model. We conclude that impaired nuclear recruitment of HDAC2 could be an important mechanism of steroid resistance of the neutrophilic inflammation in exacerbations of asthma. Oxidative stress may contribute to decreased HDAC2 activity.

Jafari, F, Shokrzadeh, L, Hamidian, M, Salmanzadeh-Ahrabi, S & Zali, MR 2008, 'Acute Diarrhea Due to Enteropathogenic Bacteria in Patients at Hospitals in Tehran', Japanese Journal of Infectious Diseases, vol. 61, no. 4, pp. 269-273.
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During a study examining causes of diarrhea from May 2004 to May 2005, 808 stool specimens were collected from patients with acute diarrhea in Tehran. Fecal samples were cultured and identified according to the standard biochemical methods. Molecular identification of enteropathogens was carried out by amplification of their virulence genes by polymerase chain reaction. A total of 369 (45.6%) bacterial pathogens were recovered from 808 patients as follows: Shigella spp., 155 (45.6%); diarrheagenic Escherichia coli 143 (38.8%); Salmonella spp., 51 (13.8%); and Campylobacter spp., 20 (5.4%). Most of the diarrheagenic E. coli were Shiga toxin-producing E. coli, with 64 (44.7%) isolates, followed by 47 (32.9%) enterotoxigenic E. coli isolates; among Shigella spp. isolates, 69 (44.5%) Shigella flexneri were predominant. The molecular diagnosis of enteropathogens yielded a more accurate characterization of the prevalence of diarrhea-causing bacterial strains in Iran. The present study revealed a high prevalence of Shigella and diarrheagenic E. coli as the predominant causes of bacterial diarrhea in this region of the world. These two types of bacteria should therefore be considered when designing preventive strategies for people living in Iran.

Janečka, JE, Tewes, ME, Laack, LL, Grassman, LI, Haines, AM & Honeycutt, RL 2008, 'Small effective population sizes of two remnant ocelot populations (Leopardus pardalis albescens) in the United States', Conservation Genetics, vol. 9, no. 4.
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Jenkins, C, Samudrala, R, Geary, SJ & Djordjevic, SP 2008, 'Structural and Functional Characterization of an Organic Hydroperoxide Resistance Protein from Mycoplasma gallisepticum', Journal of Bacteriology, vol. 190, no. 6, pp. 2206-2216.
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ABSTRACT As obligate parasites, Mycoplasma species are continuously exposed to oxidative damage due to host-generated peroxides and reactive oxygen species (ROS). In addition, the production of endogenous oxidants is believed to be a primary virulence mechanism of several Mollicute species, indicating that oxidative stress resistance is crucial to survival of these bacteria in the host milieu. Despite the abundance of oxidants at the site of infection, enzymes responsible for the detoxification of ROS have never been characterized in mycoplasmas. Here we characterize a homolog of the ohr (organic hydroperoxide resistance) family from Mycoplasma gallisepticum (encoding MGA1142). Unlike previously characterized ohr genes, the mga1142 gene is not upregulated in response to oxidative stress but displays a novel pattern of expression. Both organic and inorganic peroxides can act as substrates for MGA1142, but they are degraded with various efficiencies. Furthermore, cumene hydroperoxide, an aromatic peroxide metabolized with high efficiency by other Ohr proteins, was shown to rapidly inactivate MGA1142, accounting for the sensitivity of M. gallisepticum cells to this compound. Comparative modeling of the MGA1142 quaternary structure revealed that the active site of this molecule has a relatively wide conformation. These data indicate that the natural substrate for MGA1142 differs from that for previously characterized Ohr proteins. Triton X-114 partitioning demonstrated that MGA1142 is located in both cytosol and membrane fractions, suggesting that in vivo this molecule plays a role in the detoxificatio...

Jia, B, Norton, AH, Li, J, Rahmani, A, Asatryan, AA, Botten, LC & Gu, M 2008, 'Local observation of modes from three-dimensional woodpile photonic crystals with near-field microspectroscopy under supercontinuum illumination', OPTICS LETTERS, vol. 33, no. 10, pp. 1093-1095.
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A near-field microscope coupled with a near-infrared (NIR) supercontinuum source is developed and applied to characterize optical modes in a three-dimensional (3D) woodpile photonic crystal (PC) possessing a NIR partial bandgap. Spatially resolved near-field intensity distributions under different illumination wavelengths demonstrate that the electric fields preferentially dwell in the polymer rods or in the gaps between rods, respectively, for frequencies below or above the stop gap, as predicted by the 3D finite-difference time-domain modeling. Near-field microspectroscopy further reveals that the position-dependent band-edge effect plays an important role in PC-based all-optical integrated devices.

Jiang, Z, Huete, AR, Didan, K & Miura, T 2008, 'Development of a two-band enhanced vegetation index without a blue band', REMOTE SENSING OF ENVIRONMENT, vol. 112, no. 10, pp. 3833-3845.
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The enhanced vegetation index (EVI) was developed as a standard satellite vegetation product for the Terra and Aqua Moderate Resolution Imaging Spectroradiometers (MODIS). EVI provides improved sensitivity in high biomass regions while minimizing soil and atmosphere influences, however, is limited to sensor systems designed with a blue band, in addition to the red and near-infrared bands, making it difficult to generate long-term EVI time series as the normalized difference vegetation index (NDVI) counterpart. The purpose of this study is to develop and evaluate a 2-band EVI (EVI2), without a blue band, which has the best similarity with the 3-band EVI, particularly when atmospheric effects are insignificant and data quality is good. A linearity-adjustment factor β is proposed and coupled with the soil-adjustment factor L used in the soil-adjusted vegetation index (SAVI) to develop EVI2. A global land cover dataset of Terra MODIS data extracted over land community validation and FLUXNET test sites is used to develop the optimal parameter (L, β and G) values in EVI2 equation and achieve the best similarity between EVI and EVI2. The similarity between the two indices is evaluated and demonstrated with temporal profiles of vegetation dynamics at local and global scales. Our results demonstrate that the differences between EVI and EVI2 are insignificant (within ± 0.02) over a very large sample of snow/ice-free land cover types, phenologies, and scales when atmospheric influences are insignificant, enabling EVI2 as an acceptable and accurate substitute of EVI. EVI2 can be used for sensors without a blue band, such as the Advanced Very High Resolution Radiometer (AVHRR), and may reveal different vegetation dynamics in comparison with the current AVHRR NDVI dataset. However, cross-sensor continuity relationships for EVI2 remain to be studied. © 2008 Elsevier Inc.

Jimenez, IM, Kuehl, M, Larkum, AWD & Ralph, PJ 2008, 'Heat budget and thermal microenvironment of shallow-water corals: Do massive corals get warmer than branching corals?', LIMNOLOGY AND OCEANOGRAPHY, vol. 53, no. 4, pp. 1548-1561.
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Coral surface temperature was investigated with multiple temperature sensors mounted on hemispherical and branching corals under (a) artificial lighting and controlled flow; (b) natural sunlight and controlled flow; and (c) in situ conditions in a shallo

Kabakova, IV & Sukhorukov, AP 2008, 'Spatial switching of an optical signal in a defocusing photorefractive crystal', Bulletin of the Russian Academy of Sciences: Physics, vol. 72, no. 1, pp. 3-5.
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The method of spatial switching of the propagation direction of an optical signal, based on the effect of signal wave reflection upon interaction with a high-power pump beam in bulk photorefractive media with defocusing nonlinearity has been considered for the first time. Criteria of signal reflection from a pump-induced optical inhomogeneity in a material are determined. Trajectories of the signal wave center are obtained for characteristic reflection parameters. © Allerton Press, Inc. 2008.

Kaiko, GE, Horvat, JC, Beagley, KW & Hansbro, PM 2008, 'Immunological decision‐making: how does the immune system decide to mount a helper T‐cell response?', Immunology, vol. 123, no. 3, pp. 326-338.
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SummaryAberrant T‐cell responses underpin a range of diseases, including asthma and allergy and autoimmune diseases. Pivotal immune elements of these diseases are the development of antigen‐specific effector T‐helper type 2 (Th2) cells, Th1 cells, or the recently defined Th17 cells that are associated with the clinical features and disease progression. In order to identify crucial processes in the pathogenesis of these diseases it is critical to understand how the development of these T cells occurs. The phenotype of a polarized T‐cell that differentiates from a naïve precursor is determined by the complex interaction of antigen‐presenting cells with naïve T cells and involves a multitude of factors, including the dominant cytokine environment, costimulatory molecules, type and load of antigen presented and a plethora of signaling cascades. The decision to take the immune response in a certain direction is not made by one signal alone, instead many different elements act synergistically, antagonistically and through positive feedback loops to activate a Th1, Th2, or Th17 immune response. The elucidation of the mechanisms of selection of T‐cell phenotype will facilitate the development of therapeutic strategies to intervene in the development of deleterious T‐cell responses. This review will focus on the pathways and key factors responsible for the differentiation of the various subsets of effector CD4 T cells. We will primarily discuss what is known of the Th1 and Th2 differentiation pathways, while also reviewing the emerging research on Th17 differentiation.

Kaiko, GE, Phipps, S, Hickey, DK, Lam, CE, Hansbro, PM, Foster, PS & Beagley, KW 2008, 'Chlamydia muridarum Infection Subverts Dendritic Cell Function to Promote Th2 Immunity and Airways Hyperreactivity', The Journal of Immunology, vol. 180, no. 4, pp. 2225-2232.
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Abstract There is strong epidemiological evidence that Chlamydia infection can lead to exacerbation of asthma. However, the mechanism(s) whereby chlamydial infection, which normally elicits a strong Th type 1 (Th1) immune response, can exacerbate asthma, a disease characterized by dominant Th type 2 (Th2) immune responses, remains unclear. In the present study, we show that Chlamydia muridarum infection of murine bone marrow-derived dendritic cells (BMDC) modulates the phenotype, cytokine secretion profile, and Ag-presenting capability of these BMDC. Chlamydia-infected BMDC express lower levels of CD80 and increased CD86 compared with noninfected BMDC. When infected with Chlamydia, BMDC secrete increased TNF-α, IL-6, IL-10, IL-12, and IL-13. OVA peptide-pulsed infected BMDC induced significant proliferation of transgenic CD4+ DO11.10 (D10) T cells, strongly inhibited IFN-γ secretion by D10 cells, and promoted a Th2 phenotype. Intratracheal transfer of infected, but not control noninfected, OVA peptide-pulsed BMDC to naive BALB/c mice, which had been i.v. infused with naive D10 T cells, resulted in increased levels of IL-10 and IL-13 in bronchoalveolar lavage fluid. Recipients of these infected BMDC showed significant increases in airways resistance and decreased airways compliance compared with mice that had received noninfected BMDC, indicative of the development of airways hyperreactivity. Collectively, these data suggest that Chlamydia infection of DCs allows the pathogen to deviate the induced immune response from a protective Th1 to a nonprotective Th2 response that could permit ongoing chronic infection. In the setting of allergic airways inflammation, this infection may then contribute to exacerbation of the asthmatic phenotype.

Kamal, MA, Qu, X, Yu, Q-S, Tweedie, D, Holloway, HW, Li, Y, Tan, Y & Greig, NH 2008, 'Tetrahydrofurobenzofuran cymserine, a potent butyrylcholinesterase inhibitor and experimental Alzheimer drug candidate, enzyme kinetic analysis', Journal of Neural Transmission, vol. 115, no. 6, pp. 889-898.
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Synaptic loss, particularly related to the forebrain cholinergic system, is considered to be an early event that leads to Alzheimer's disease (AD) and has led to the development of acetylcholinesterase inhibitors (AChE-Is) as the mainstay of treatment for several degenerative disorders that culminate in dementia. The primary dose-limiting toxicities of all clinically available AChE-Is are, similar to useful actions on cognition, cholinergically mediated and they ultimately limit the value of this drug class in achieving anything but symptomatic improvements. In addition, AChE levels in brain areas associated with AD decline with disease progression, which likely ultimately limits the therapeutic utility of this drug class. New research indicates that selective inhibition of butyrylcholinesterase (BuChE), a closely related enzyme that is markedly elevated in AD brain, increases acetylcholine (ACh) and augments cognition in rodents free of the characteristic undesirable actions of AChE-Is. BuChE inhibition hence represents an innovative treatment approach for AD, and agents are currently being synthesized to optimally achieve this. The novel compound, tetrahydrofurobenzofuran cymserine (THFBFC), is derived from our effort to produce a potent and BuChE-selective inhibitor as a candidate to test the hypothesis that BuChE-Is would be efficacious and better tolerated than AChE-Is in AD. Herein, we applied innovative enzyme kinetic analyses to characterize the quantitative interaction of THFBFC with human BuChE. These provided values for the agent's IC50, together with specific new kinetic constants, such as KT50, KT1/2, RI, oKRT, oPmax, KPT and PT1/2, to aid define target concentrations for clinical translation. Additional classical kinetic parameters, including Ki, Km or Ks, kcat or Vmax and Vmi were also determined. THFBFC proved to be a potent competitive inhibitor of human BuChE and, like its isomer dihydrobenzodioxepine cymserine, is a potentially intere...

Karim, RZ, Scolyer, RA, Li, W, Yee, VSK, McKinnon, JG, Li, L-XL, Uren, RF, Lam, S, Beavis, A, Dawson, M, Doble, P, Hoon, DSB & Thompson, JF 2008, 'False negative sentinel lymph node biopsies in melanoma may result from deficiencies in nuclear medicine, surgery, or pathology', ANNALS OF SURGERY, vol. 247, no. 6, pp. 1003-1010.
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OBJECTIVE: To investigate a cohort of melanoma patients with false negative (FN) sentinel node (SN) biopsies (SNBs) to identify the reasons for the FN result. SUMMARY OF BACKGROUND DATA: SNB is a highly efficient staging method in melanoma patients. However, with long-term follow-up FN SNB results of up to 25% have been reported. METHODS: Seventy-four SNs from 33 patients found to have had an FN SNB were analyzed by reviewing the lymphoscintigraphy, surgical data, and histopathology, and by assessing nodal tissue using multimarker real-time quantitative reverse transcription (qRT) polymerase chain reaction, and antimony concentration measurements (as a marker of "true" SN status) using inductively coupled plasma mass spectroscopy. RESULTS: Nine SNs (12%) from 9 patients (27%) had evidence of melanoma on histopathologic review. Twelve SNs (16%) from 10 patients (30%) were qRT(+). Four of these 12 SNs were positive on histopathology review and 8 were negative. Four patients (12%) were upstaged by qRT. Sixteen patients had their SNB histology, lymphoscintigraphy, and surgical data reviewed. Identifiable causes of the FN SNBs were not found after review of all modalities in 4 patients. SNs from all 4 patients had antimony levels indicative of an SN. Of the SNs evaluable by qRT, 1 was qRT(+) and 7 SNs from 2 patients were qRT(-). CONCLUSIONS: An FN SN can occur because of deficiencies in nuclear medicine, surgery, or pathology. qRT can detect "occult" metastatic melanoma in SNs that have been identified as negative by histopathology. © 2008 Lippincott Williams & Wilkins, Inc.

Kazandjian, A, Shepherd, VA, Rodriguez-Lanetty, M, Nordemeier, W, Larkum, AWD & Quinnell, RG 2008, 'Isolation of Symbiosomes and The Symbiosome Membrane Complex from The Zoanthid Zoanthus Robustus', Phycologia, vol. 47, no. 3, pp. 294-306.
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The zoanthid Zoanthus robustus was used as a model organism to develop procedures for isolating pure symbiosomes and symbiosome membranes. The symbiosome is comprised of a zooxanthella (Symbiodinium sp.) cell that divides rarely and is separated from the host gastrodermal cytoplasm by a symbiosome multimembrane complex. Devising a method to isolate membranes at the interface between the symbiotic partners is a critical first step in characterising the molecular components involved in the metabolic trafficking necessary to sustain an effective symbiosis. After zoanthid gastrodermal cells were extracted, symbiosomes were released by mechanical disruption, recovered by centrifugation, and then purified using discontinuous sucrose gradient centrifugation. The material forming the membrane complex around symbiosomes proved highly resistant to disruption. Methods used to dissociate this interface from symbionts included (1) Triton X-100 detergent solubilisation, (2) osmotic shock with mechanical disruption, and (3) vigorous mechanical disruptions, where powerful shearing forces were used, combined with a series of sucrose density gradient centrifugation steps. The lipophilic styryl fluorochrome FM 1-43, at a concentration of 30 μM, selectively labelled the symbiosome membrane complex, both for isolated symbiosomes and those in hospite. Other cell membranes, including plasma membranes, endoplasmic reticulum, tonoplast, and organelle membranes, were not visibly labelled at this concentration. The selective labelling of the symbiosome membrane complex remained stable even after long exposure times (3 h). At 30 μM concentration, FM 1-43 also labelled symbiosome membrane fragments isolated using methods (1), (2) and (3). Method (3) proved to be the most effective in producing a fraction enriched in FM-143-labelled membrane material, which we call a symbiosome membrane complex. Transmission electron microscopy, together with confocal and conventional epifluorescence microsco...

K-CY, M 2008, 'Androgen therapy and atherosclerotic cardiovascular disease', Vascular Health and Risk Management, vol. 4, no. 1, pp. 11-21.
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Cardiovascular disease (CVD) remains the leading cause of death in Western society today. There is a striking gender difference in CVD with men predisposed to earlier onset and more severe disease. Following the recent reevaluation and ongoing debate regarding the estrogen protection hypothesis, and given that androgen use and abuse is increasing in our society, the alternate view that androgens may promote CVD in men is assuming increasing importance. Whether androgens adversely affect CVD in either men or women remains a contentious issue within both the cardiovascular and endocrinological fraternities. This review draws from basic science, animal and clinical studies to outline our current understanding regarding androgen effects on atherosclerosis, the major CVD, and asks where future directions of atherosclerosis-related androgen research may lie. © 2008 Dove Medical Press Limited. All rights reserved.

Kealley, CS, Latella, BA, van Riessen, A, Elcombe, MM & Ben-Nissan, B 2008, 'Micro- and Nano-Indentation of a Hydroxyapatite-Carbon Nanotube Composite', JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, vol. 8, no. 8, pp. 3936-3941.
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The mechanical properties of pure synthetic hydroxyapatite and hydroxyapatite-carbon nanotube composites were examined. Vickers microhardness and nanoindentation using a Berkovich tipped indenter were used to determine the hardness, fracture toughness an

Kim, H, Turner, ND, Taddeo, SS, Davidson, LA, Wang, N, Vannucci, M, Chapkin, RS, Carroll, RJ & Lupton, JR 2008, 'A fish oil/pectin diet beneficially altered gene profiles during radiation‐enhanced colon carcinogenesis', The FASEB Journal, vol. 22, no. S1.
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The goal of this project was to determine the effect of diet on the patterns of gene expression in exfoliated colonocytes from rats exposed to radiation (+/− 1 Gy, 1 GeV/nucleon Fe ions) and a chemical carcinogen (AOM, 2x, 15 mg/kg BW). Rats received corn oil/cellulose (CC) or fish oil/pectin (FP) diets for 3 wk prior to radiation exposure, which was followed by AOM injections 10 and 17 d later. Isolated poly A+ RNA from exfoliated colonocytes was analyzed using GE Codelink arrays. The radiation and diet interaction resulted in differences in expression of 95 genes, including five genes involved in the MAPK signaling pathway and regulation of autophagy. For example, irradiated rats consuming FP had ∼1.7 times the level of Ppm1b, a MAPK signaling suppressor, found in CC rats (P=0.036), suggesting the FP diet would suppress cell proliferation in rats exposed to radiation. With respect to autophagy, the expression of Atg7 in non‐irradiated rats consuming FP was higher than the level in CC rats (P=0.003), suggesting the FP rats would likely have elevated apoptosis via autophagy. FP may suppress cell proliferation and enhance autophagy in the colon and thereby suppress colon carcinogenesis caused by radiation and AOM. Supported by NSBRI (NASA NCC 9‐58), NIH (CA57030 and CA59034) and NIEHS (P30‐ES09106).

Kim, M, Cobbin, D & Zaslawski, C 2008, 'Traditional Chinese Medicine tongue inspection: An examination of the inter- and intrapractitioner reliability for specific tongue characteristics', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 14, no. 5, pp. 527-536.
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Aim: To examine the reliability of Traditional Chinese Medicine (TCM) tongue inspection by evaluation of inter-and intrapractitioner agreement levels for specific tongue characteristics, achieved by a group of TCM practitioners. Method: Ten (10) realisti

Kim, RY, Lijten, ECE & Strauch, RJ 2008, 'Pronated Oblique View in Assessing Proximal Scaphoid Articular Cannulated Screw Penetration', The Journal of Hand Surgery, vol. 33, no. 8, pp. 1274-1277.
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Kreuzpaintner, W, Störmer, M, Lott, D, Solina, D & Schreyer, A 2008, 'Epitaxial growth of nickel on Si(100) by dc magnetron sputtering', Journal of Applied Physics, vol. 104, no. 11, pp. 114302-114302.
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The influence of the substrate temperature on the growth of highly textured Ni(111) and epitaxial Ni(200) with the relationships Ni[100]∥Si[110] and Ni(001)∥Si(001) on hydrogen terminated Si(100) wafer substrates by means of direct current magnetron sputtering is reported. In order to minimize crystal defect formation and to achieve a high quality epitaxial growth of Ni on Si, a two step deposition process was developed whereby different deposition conditions were used for an initial nickel seed layer and the remaining nickel film. The in-plane and out-of-plane structural properties of the films were investigated using x-ray scattering techniques, whereas magneto-optical Kerr effect and neutron reflectometry were used to confirm the magnetic nature of the epitaxially deposited nickel films.

Kuehl, M, Holst, G, Larkum, AWD & Ralph, PJ 2008, 'Imaging of oxygen dynamics within the endolithic algal community of the massive coral Porites lobata', JOURNAL OF PHYCOLOGY, vol. 44, no. 3, pp. 541-550.
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We used transparent planar oxygen optodes and a luminescence lifetime imaging system to map (at a pixel resolution of <200 ?m) the two-dimensional distribution of O₂ within the skeleton of a Porites lobata colony. The O₂ distribution was closely correlated to the distribution of the predominant endolithic microalga, Ostreobium quekettii Bornet et Flahault that formed a distinct green band inside the skeleton. Oxygen production followed the outline of the Ostreobium band, and photosynthetic O₂ production was detected at only 0.2 ?mol photons m^-2 · s^-1, while saturation occurred at ?37 ?mol photons m^-2 · s^-1. Oxygen levels varied from ?60% to 0% air saturation in the illuminated section of the coral skeleton in comparison to the darkened section. The O₂ production within the Ostreobium band was lower in the region below the upward facing surface of the coral and elevated on the sides. Oxygen consumption in darkness was also greatest within the Ostreobium zone, as well as in the white skeleton zone immediately below the corallites. The rate of O₂ depletion was not constant within zones and between zones, showing pronounced heterogeneity in endolithic respiration. When the coral was placed in darkness after a period of illumination, O₂ levels declined by 50% within 20 min and approached steady-state after 4050 min in darkness. Our study demonstrates the use of an important new tool in endolith photobiology and presents the first data of spatially resolved O₂ concentration and its correlation to the physical structures and specific zones responsible for O₂ production and consumption within the coral skeleton.

Kuo, FY, Dunsmuir, WTM, Sloan, IH, Wand, MP & Womersley, RS 2008, 'Quasi-Monte Carlo for Highly Structured Generalised Response Models', Methodology and Computing in Applied Probability, vol. 10, no. 2, pp. 239-275.
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Highly structured generalised response models, such as generalised linear mixed models and generalised linear models for time series regression, have become an indispensable vehicle for data analysis and inference in many areas of application. However, their use in practice is hindered by high-dimensional intractable integrals. Quasi-Monte Carlo (QMC) is a dynamic research area in the general problem of high-dimensional numerical integration, although its potential for statistical applications is yet to be fully explored. We survey recent research in QMC, particularly lattice rules, and report on its application to highly structured generalised response models. New challenges for QMC are identified and new methodologies are developed. QMC methods are seen to provide significant improvements compared with ordinary Monte Carlo methods. © Springer Science+Business Media, LLC 2007.

Labbate, M, Chowdhury, PR & Stokes, HW 2008, 'A class 1 integron present in a human commensal has a hybrid transposition module compared to Tn402: Evidence of interaction with mobile DNA from natural environments', JOURNAL OF BACTERIOLOGY, vol. 190, no. 15, pp. 5318-5327.
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In a survey of class 1 integrons from human stools, an unusual class 1 integron from a strain of Enterobacter cloacae was isolated and characterized in detail. Sequence analysis of a fosmid containing the class 1 integron revealed a complex set of transposons which included two Tn402-like transposons. One of these transposons, Tn6007, included a class 1 integron with two non-antibiotic-resistance-type gene cassettes and a complete transposition module. This tni module is a hybrid with a boundary within the res site compared to Tn402, implying that a site-specific recombination event generated either Tn6007 or Tn402. The second Tn402-like transposon, Tn6008, possesses neither a mer operon nor an integron, and most of its tni module has been deleted. Tn6007, Tn6008, and the 2,478 bases between them, collectively designated Tn6006, have transposed into a Tn5036/Tn3926-like transposon as a single unit. Tn6006, Tn6007, and Tn6008 could all transpose as discrete entities. Database analysis also revealed that a version of Tn6008 was present in the genome of Xanthomonas campestris pv. vesicatoria. Overall, the E. cloacae isolate further demonstrated that functional class 1 integrons/transposons are probably common in bacterial communities and have the potential to add substantially to the problem of multidrug-resistant nosocomial infections. Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Lanyon, BP, Weinhold, TJ, Langford, NK, O’Brien, JL, Resch, KJ, Gilchrist, A & White, AG 2008, 'Manipulating Biphotonic Qutrits', Physical Review Letters, vol. 100, no. 6.
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Laroucau, K, Thierry, S, Vorimore, F, Blanco, K, Kaleta, E, Hoop, R, Magnino, S, Vanrompay, D, Sachse, K, Myers, GSA, Bavoil, PM, Vergnaud, G & Pourcel, C 2008, 'High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA)', Infection, Genetics and Evolution, vol. 8, no. 2, pp. 171-181.
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Lawrence, FJ, Botten, LC, Dossou, KB & de Sterke, CM 2008, 'Antireflection coatings for two-dimensional photonic crystals using a rigorous impedance definition', APPLIED PHYSICS LETTERS, vol. 93, no. 12, pp. 1-3.
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We show that no consistent scalar definition of impedance is generally possible for photonic crystals. Instead, we present a rigorous semianalytic matrix definition of impedance for square lattice photonic crystals, defined in terms of Bloch modes. We then apply our definition to design a range of multilayer photonic crystal antireflection coatings efficiently. © 2008 American Institute of Physics.

Leal, S, Eamus, D, Grabner, M, Wimmer, R & Cherubini, P 2008, 'Tree rings of Pinus nigra from the Vienna basin region (Austria) show evidence of change in climatic sensitivity in the late 20th century', CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE, vol. 38, no. 4, pp. 744-759.
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The width of tree rings of Pinus nigra Arn. trees growing near the ecological limits for the species, in the Vienna basin, Austria, showed a strong and positive correlation with spring-summer precipitation, indicating a dependence of growth on water avai

Lee, MW, Grillet, C, Poulton, CG, Monat, C, Smith, CL, Mägi, E, Freeman, D, Madden, S, Luther-Davies, B & Eggleton, BJ 2008, 'Characterizing photonic crystal waveguides with an expanded k-space evanescent coupling technique', Optics Express, vol. 16, no. 18, pp. 13800-13800.
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We demonstrate a direct, single measurement technique for characterizing the dispersion of a photonic crystal waveguide (PCWG) using a tapered fiber evanescent coupling method. A highly curved fiber taper is used to probe the Fabry-Pérot spectrum of a closed PCWG over a broad k-space range, and from this measurement the dispersive properties of the waveguide can be found. Waveguide propagation losses can also be estimated from measurements of closed waveguides with different lengths. The validity of this method is demonstrated by comparing the results obtained on a 'W1' PCWG in chalcogenide glass with numerical simulation. © 2008 Optical Society of America.

Leslie, LM, Buckley, BW & Leplastrier, M 2008, 'The Operational Impact of QuikSCAT Winds in Perth, Australia: Examples and Limitations', Weather and Forecasting, vol. 23, no. 1, pp. 183-193.
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Abstract The preparation of accurate operational weather forecasts and the timely issuance of severe marine weather and ocean warnings and advisories for major oceanic weather systems impacting both coastal areas and the open ocean are major forecasting problems facing the Australian Bureau of Meteorology’s Regional Forecast Centre (RFC) and its collocated Tropical Cyclone Warning Centre (TCWC) in Perth, Western Australia. The region of responsibility for the Perth RFC is vast, covering a large portion of the southeast Indian and Southern Oceans, both of which are extremely data sparse, especially for near-surface marine wind data. Given that these coastline and open-ocean areas are subject to some of the world’s most intense tropical cyclones, rapidly intensifying midlatitude cyclones, and powerful cold fronts, there is now a heavy reliance upon NASA Quick Scatterometer (QuikSCAT) data for both routine and severe weather warning forecasts. The focus of this note is on the role of QuikSCAT data in the Perth RFC for the accurate and early detection of maritime severe weather systems, both tropical and extratropical. First, the role of QuikSCAT data is described, and then three cases are presented in which the QuikSCAT data were pivotal in providing forecast guidance. The cases are a severe tropical cyclone in its development phase off the northwest coast of Australia, a strong southeast Indian Ocean cold front, and an explosively developing midlatitude Southern Ocean cyclone. In each case, the Perth RFC would have been unable to provide early and high-quality operational forecast and warning guidance without the timely availability of the QuikSCAT surface wind data.

Leslie, LM, Leplastrier, M & Buckley, BW 2008, 'Estimating future trends in severe hailstorms over the Sydney Basin: A climate modelling study', Atmospheric Research, vol. 87, no. 1, pp. 37-51.
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Leslie, LM, Wang, Y, Lee, D-K & Lamb, PJ 2008, 'Editorial: Special Issue on Regional Climate Studies', Meteorology and Atmospheric Physics, vol. 100, no. 1-4, pp. 1-1.
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Letnic, M, Webb, JK & Shine, R 2008, 'Invasive cane toads (Bufo marinus) cause mass mortality of freshwater crocodiles (Crocodylus johnstoni) in tropical Australia', BIOLOGICAL CONSERVATION, vol. 141, no. 7, pp. 1773-1782.
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Invasive species are frequently blamed for faunal declines, but there is little direct evidence about the pathways, magnitude and size-selectivity of mortality induced by invaders. Top predators are of particular interest in this context, because their removal can generate substantial cascades of secondary effects on community composition. Cane toads (Bufo marinus) are large South American anurans currently spreading rapidly through tropical Australia. Native predators that attempt to consume these highly toxic toads may die as a result. During surveys of the Victoria River in the semi-arid tropical region of the Northern Territory, we documented massive mortality of freshwater crocodiles (Crocodylus johnstoni) at the toad invasion front. Dead crocodiles spanned a wide size range (0.6-2.1 m long) but with significant biases; intermediate-sized animals (0.6-1.5 m long) were more likely to be found dead. Population densities of crocodiles plummeted by as much as 77% following toad invasion, and population size-structures changed. The negative impacts of toads on crocodiles appear to be greater in these hot semi-arid landscapes than in cooler, higher rainfall areas where crocodiles have access to a wider prey base, and the toads are less prone to desiccation and can rehydrate in small, scattered water bodies rather than in the main river. Hence, the impact of cane toad invasion on this top predator may increase with increasing aridity. © 2008 Elsevier Ltd. All rights reserved.

Levings, RS, Djordjevic, SP & Hall, RM 2008, 'SGI2, a Relative ofSalmonellaGenomic Island SGI1 with an Independent Origin', Antimicrobial Agents and Chemotherapy, vol. 52, no. 7, pp. 2529-2537.
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ABSTRACTMultiply antibiotic-resistantSalmonella entericaserovar Emek strains isolated in Australia and the United Kingdom had similar features, suggesting that they all belong to a single clone. These strains all contain SGI2 (formerly SGI1-J), an independently formed relative ofSalmonellagenomic island SGI1. In SGI2, the complex class 1 integron which includes all of the resistance genes is not located betweentnpR(S027) and S044 as in SGI1 and SGI1 variants. Instead,tnpRwas found to be adjacent to S044, and the integron is located 6.9 kb away, within S023. In both SGI1 and SGI2, the 25-bp inverted repeats that mark the outer ends of class 1 integrons are flanked by a 5-bp duplication of the target, indicating that incorporation of the integron was by transposition. A small number of differences between the sequences of the backbones of SGI1 and SGI2 were also found. Hence, a class 1 integron has entered two different variants of the SGI backbone to generate two distinct lineages. Despite this, the integron in SGI2 has a complex structure that is very similar to that of In104 in SGI1. Differences are in the cassette arrays and in the gene which encodes the chloramphenicol and florfenicol efflux protein. The CmlA9 protein, encoded by InEmek, is only 92.8% identical to FloRc (also a CmlA family protein) from SGI1. A variant form of SGI2, SGI2-A, which has lost thetet(G) andcmlA9resistance determinants, was found in one strain.

Lewis, JB, Taddeo, SS, McDonough, CM, Rooney, LW, Carroll, RJ & Turner, ND 2008, 'Sorghum bran varieties differentially influence endogenous antioxidant enzymes to protect against oxidative stress during colon carcinogenesis', The FASEB Journal, vol. 22, no. S1.
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We have shown that the number of aberrant crypts (AC) decreased in rats consuming black (29%, P < 0.04) and brown (47%, P < 0.006) sorghum diets when compared to a cellulose diet; this decrease was an inverse function of diet antioxidant activity (ABTS). Because of this, we evaluated the effect of these diets on endogenous enzymatic activities (SOD, CAT, and GPx) in the rat colon. Rats consumed diets containing 6% fiber from either cellulose or isolated bran from white, brown (contains tannins), or black (contains anthocyanins) sorghum (n=10/diet). Diets were fed for 10 wk, with two AOM injections (15 mg/kg BW) administered in wk 3 and 4. Total SOD activity increased (16%, P < 0.04) in rats fed black sorghum (79.0 U/mg protein) compared to all other diets. A similar, non‐significant, trend occurred in mitochondrial SOD. White sorghum increased (P < 0.02) CAT activity (122.2 U/mg protein) compared to the cellulose diet, and the black and brown sorghum diets were intermediate. All sorghum diets suppressed GPx activity relative to cellulose. As observed in colon tumors, elevated GPx activity may reflect greater oxidative stress, contributing to greater AC formation in cellulose rats. These data suggest that the suppression in AC formation resulted through the differential actions of the sorghum brans on endogenous and exogenous antioxidant activity. Funded by USDA 58‐5430‐5‐339 and NIEHS P30‐ES09106.

Lewis, K, Valenzuela, SM & Ben-Nissan, B 2008, 'Changes in the Activity of Osteoblast Like Cells with Sol-Gel Derived Hydroxyapatite and Zirconia Nanocoatings', Key Engineering Materials, vol. 361-363, no. 1, pp. 633-636.
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When producing implant materials, achievement of optimal bioactivity and biocompatibility are essential. Nanocoatings can provide an efficient cost effective way to alter the interactions of the implant material with its destined “host” environment. Nanocoatings of sol-gel derived carbonated hydroxyapatite (HAp) and zirconia were produced in this study. The surfaces were characterised by Fourier transform infrared spectroscopy (FTIR) and light microscopy. Cell adhesion, proliferation and viability, as well as expression of alkaline phosphatase (ALP is an indicator of bone formation) were assessed as indicators of biocompatibility. Our results have shown that sol-gel derived nano crystalline HAp acts as an ideal surface for implant coatings.

Li, J, Toth, M, Tileli, V, Dunn, KA, Lobo, CJ & Thiel, BL 2008, 'Evolution of the nanostructure of deposits grown by electron beam induced deposition', Applied Physics Letters, vol. 93, no. 2, pp. 023130-023130.
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Environmental scanning electron microscopy (ESEM) was used to perform electron beam induced deposition (EBID) using a WF6 precursor. The deposits consist of WO3 nanocrystals embedded in an amorphous matrix. Oxide formation is attributed to residual oxidizers present in the ESEM chamber during EBID. Under conditions of fixed low electron flux, the WO3 grain size and the degree of deposit crystallinity increase with time. These changes correlate with the degree of electron energy deposition into the material during growth, indicating that electron beam induced modification of as-grown material is significant in controlling the nanostructure and functionality of materials fabricated by EBID.

Li, W, Cobbin, D & Zaslawski, C 2008, 'A comparison of effects on regional pressure pain threshold produced by deep needling of LI4 and LI11, individually and in combination', COMPLEMENTARY THERAPIES IN MEDICINE, vol. 16, no. 5, pp. 278-287.
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sites (acupoints and nonacupoints) across the body with an algometer. Interventions: The same manual acupuncture techniques were applied to four interventions of large intestine 4 (LI4) unilaterally; LI4 bilaterally; large intestine 11 (LI 11) unilaterally; and LI4 in conjunction with LI11, both unilaterally. Main outcome measures: (1) Percentage change in PPT from preintervention baseline measured at the 10 regional sites following every intervention; (2) participants' perceptions of pain; needling sensations; tension during, and anxiety prior to, each intervention; and changes in practitioner behaviour. Results: Following all four interventions, statistically significant increases in mean PPT were observed. These occurred at nine sites following the LI4 intervention either unilaterally or bilaterally; at six sites for LI11 intervention; and at five sites following the combined LI11 and LI4 intervention. These increases were significantly greater for the bilateral LI4 intervention than the unilateral LI4 intervention at only two sites (p < 0.02 and p < 0.0001). There were no statistically significant differences in the subjective perceptions among the four interventions. Conclusion: The enhanced effects on PPT by the bilateral compared with the unilateral intervention at LI4 although limited, do provide some support for the traditional Chinese medicine (TCM) assumption that bilateral needling of the same point enhances the treatment effect. There was no support for the assumption that combined needling of points from the same channel should enhance the treatment effect and failure to obtain better effects by combined needling of points from the same channel could result from the interaction occurring during the combined needling. Crown Copyright © 2008.

Liang, HPH & Hogg, PJ 2008, 'Critical importance of the cell system when studying tissue factor de-encryption', Blood, vol. 112, no. 3, pp. 912-913.
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Lima, LL, Alencar, MARC, Caetano, DP, Solli, DR & Hickmann, JM 2008, 'The effect of disorder on two-dimensional photonic crystal waveguides', Journal of Applied Physics, vol. 103, no. 12, pp. 123102-123102.
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We investigate the effect of positional disorder on two-dimensional photonic crystal waveguides created by removing a line of cells from a finite 11×11 square lattice. By using transverse magnetic and transverse electric waves, we have studied three different configurations: disorder throughout the whole crystal, disorder only in the waveguide border, and disorder in the whole crystal except the waveguide border. We found that the waveguide performance is quite robust against disorder in the case where the waveguide border is not affected by disorder. In the other cases, disorder changes the size of the waveguide channel, which has a detrimental effect on the performance of the waveguide.

Liu, H, Li, C, Cao, Q, Wu, YP & Holze, R 2008, 'Effects of heteroatoms on doped LiFePO(4)/C composites', JOURNAL OF SOLID STATE ELECTROCHEMISTRY, vol. 12, no. 7-8, pp. 1017-1020.
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A series of supervalent cation doped Li(1-x) M(0.01)Fe(0.99)PO(4)/C composites (M=Ti, Zr, V, Nb, and W) were synthesized by solid-state reaction. The effects of the heteroatoms were studied by X-ray diffraction, cyclic voltammetry, and electrochemical impedance measurement. After doping, the lattice structure of LiFePO(4) is not destroyed and the reversibility of lithium ion intercalation and deintercalation is improved. The diffusion coefficient of lithium ions depends on the radius of the heteroatoms. As the radius of the heteroatom is larger, the diffusion coefficient increases.

Liu, H, Wang, G, Wang, J & Wexler, D 2008, 'Magnetite/carbon core-shell nanorods as anode materials for lithium-ion batteries', ELECTROCHEMISTRY COMMUNICATIONS, vol. 10, no. 12, pp. 1879-1882.
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Carbon coated magnetite (Fe3O4) core-shell nanorods were synthesized by a hydrothermal method using Fe2O3 nanorods as the precursor. Transmission electron spectroscopy (TEM) and high resolution TEM (HRTEM) analysis indicated that a carbon layer was coated on the surfaces of the individual Fe3O4 nanorods. The electrochemical properties of Fe3O4/carbon nanorods as anodes in lithium-ion cells were evaluated by cyclic voltammetry, ac impedance spectroscopy, and galvanostatic charge/discharge techniques. The as-prepared Fe3O4/C core-shell nanorods show an initial lithium storage capacity of 1120 mAh/g and a reversible capacity of 394 mAh/g after 100 cycles, demonstrating better performance than that of the commercial graphite anode material. © 2008 Elsevier B.V. All rights reserved.

Liu, H, Wang, GX, Wexler, D, Wang, JZ & Liu, HK 2008, 'Electrochemical performance of LiFePO4 cathode material coated with ZrO2 nanolayer', ELECTROCHEMISTRY COMMUNICATIONS, vol. 10, no. 1, pp. 165-169.
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ZrO2 nanolayer coated LiFePO4 particles were successfully prepared by a chemical precipitation method. Nanolayer structured ZrO2 was found on the surface of LiFePO4 particles by high resolution transmission electron microscopy (HRTEM). The coating does not affect the crystal structure of the LiFePO4 core, as determined by X-ray diffraction (XRD) and selected area electron diffraction (SAED) on individual particles. The ZrO2 coating can remarkably improve the electrochemical performance at high charge/discharge rate. This improvement may be due to the amelioration of the electrochemical dynamics on the LiFePO4 electrode/electrolyte interface resulting from the effects of the ZrO2 nanolayer coating. © 2007 Elsevier B.V. All rights reserved.

Liu, H, Zhang, P, Li, GC, Wu, Q & Wu, YP 2008, 'LiFePO(4)/C composites from carbothermal reduction method', JOURNAL OF SOLID STATE ELECTROCHEMISTRY, vol. 12, no. 7-8, pp. 1011-1015.
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Using the cheap raw materials lithium carbonate, iron phosphate, and carbon, LiFePO4/C composite can be obtained from the carbothermal reduction method. X-ray diffraction (XRD) and scanning electronic microscope (SEM) observations were used to investigate the structure and morphology of LiFePO4/C.

LIU, L 2008, 'Rescheduling Algorithm Based on Rolling Horizon Decomposition for a Dynamic Job Shop with Uncertain Arriving Time', Chinese Journal of Mechanical Engineering, vol. 44, no. 05, pp. 68-68.
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The dynamic job shop scheduling with uncertain arriving time is studied,and the objective is to minimize total tardiness of all jobs.When rescheduling is frequent,the computational efficiency of the scheduling algorithm is necessarily high.Based on the rolling horizon decomposition,the critical operation set is denoted.A hybrid genetic algorithm is proposed to determine the critical operation set as well as optimizing total tardiness.The hybrid scheduler is used to convert the chromosome into partially feasible schedule,and the improved modified operation rule is used to determine the sequence of the remaining operations out of the chromosome.Then the fitness is evaluated by the objective value of the complete scheduling for the total operations to process.The simulation results of many instances show that the proposed algorithm significantly improves the computational efficiency compared with the genetic algorithm based on the complete operation set,and the performance of scheduling is satisfying

Liu, X, Tripathy, U, Bhosale, SV, Langford, SJ & Steer, RP 2008, 'Photophysics of Soret-Excited Tetrapyrroles in Solution. II. Effects of Perdeuteration, Substituent Nature and Position, and Macrocycle Structure and Conformation in Zinc(II) Porphyrins', The Journal of Physical Chemistry A, vol. 112, no. 38, pp. 8986-8998.
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Lloyd, MM, van Reyk, DM, Davies, MJ & Hawkins, CL 2008, 'Hypothiocyanous acid is a more potent inducer of apoptosis and protein thiol depletion in murine macrophage cells than hypochlorous acid or hypobromous acid', Biochemical Journal, vol. 414, no. 2, pp. 271-280.
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Hypohalous acids are generated by activated leucocytes, via the formation of H2O2 and the release of peroxidase enzymes (myeloperoxidase and eosinophil peroxidase). These species are important bactericidal agents, but HOCl (hypochlorous acid) and HOBr (hypobromous acid) have also been implicated in tissue damage in a number of inflammatory diseases. HOSCN (hypothiocyanous acid; cyanosulfenic acid) is a milder, more thiol-specific, oxidant than HOCl or HOBr and as such may be a more potent inducer of cellular dysfunction due to selective targeting of critical thiol residues on proteins. In the present study, HOCl and HOBr are shown to react rapidly with macrophage (J774A.1) cells, resulting in a greater extent of cell lysis compared with HOSCN. However, HOSCN induces apoptosis and necrosis with greater efficacy, and at lower concentrations, than HOCl or HOBr. Apoptosis occurs in conjunction with an increased release of cytochrome c into the cytosol, but no associated increase in caspase activity. Similarly, apoptosis is observed on treating the cells in the presence of a caspase inhibitor, suggesting that it is mediated by a caspase-independent pathway. HOSCN oxidized protein thiols more efficiently than either HOCl or HOBr. The greater efficacy of HOSCN in inducing apoptosis is attributed to selective damage to critical mitochondrial membrane protein thiol groups, resulting in increased permeability and subsequent leakage of cytochrome c into the cytosol. This induction of damage by HOSCN may be of critical importance in people with elevated levels of SCN− (thiocyanate ions) arising from cigarette smoking, and plays a role in the pathologies associated with this biological insult.

Lobach, I, Carroll, RJ, Spinka, C, Gail, MH & Chatterjee, N 2008, 'Haplotype‐Based Regression Analysis and Inference of Case–Control Studies with Unphased Genotypes and Measurement Errors in Environmental Exposures', Biometrics, vol. 64, no. 3, pp. 673-684.
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SummaryIt is widely believed that risks of many complex diseases are determined by genetic susceptibilities, environmental exposures, and their interaction.Chatterjee and Carroll(2005,Biometrika92,399–418) developed an efficient retrospective maximum‐likelihood method for analysis of case–control studies that exploits an assumption of gene–environment independence and leaves the distribution of the environmental covariates to be completely nonparametric.Spinka, Carroll, and Chatterjee(2005,Genetic Epidemiology29,108–127) extended this approach to studies where certain types of genetic information, such as haplotype phases, may be missing on some subjects. We further extend this approach to situations when some of the environmental exposures are measured with error. Using a polychotomous logistic regression model, we allow disease status to haveK+ 1 levels. We propose use of a pseudolikelihood and a related EM algorithm for parameter estimation. We prove consistency and derive the resulting asymptotic covariance matrix of parameter estimates when the variance of the measurement error is known and when it is estimated using replications. Inferences with measurement error corrections are complicated by the fact that the Wald test often behaves poorly in the presence of large amounts of measurement error. The likelihood‐ratio (LR) techniques are known to be a good alternative. However, the LR tests are not technically correct in this setting because the likelihood function is based on an incorrect model, i.e., a prospective model in a retrospective sampling scheme. We corrected standard asymptotic result...

Lobo, CJ, Toth, M, Wagner, R, Thiel, BL & Lysaght, M 2008, 'High resolution radially symmetric nanostructures from simultaneous electron beam induced etching and deposition', Nanotechnology, vol. 19, pp. 025303-025303.
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Electron beam induced etching (EBIE) and deposition (EBID) are promising fabrication techniques in which an electron beam is used to dissociate surface-adsorbed precursor molecules to achieve etching or deposition. Spatial resolution is normally limited by the electron flux distribution at the substrate surface. Here we present simultaneous EBIE and EBID (EBIED) as a method for surpassing this resolution limit by using adsorbate depletion to induce etching and deposition in adjacent regions within the electron flux profile. Our simulation results indicate the possibility of growth control of radially symmetric nanostructures at the sub-1 nm length scale on bulk substrates. The technique is well suited to the fabrication of ring-shaped nanostructures such as those employed in plasmonics, sensing devices, magneto-optics and magnetoelectronics.

Lobo, CJ, Toth, M, Wagner, R, Thiel, BL & Lysaght, M 2008, 'High resolution radially symmetric nanostructures from simultaneous electron beam induced etching and deposition', Nanotechnology, vol. 19, no. 2, pp. 025303-025303.
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Electron beam induced etching (EBIE) and deposition (EBID) are promising fabrication techniques in which an electron beam is used to dissociate surface-adsorbed precursor molecules to achieve etching or deposition. Spatial resolution is normally limited by the electron flux distribution at the substrate surface. Here we present simultaneous EBIE and EBID (EBIED) as a method for surpassing this resolution limit by using adsorbate depletion to induce etching and deposition in adjacent regions within the electron flux profile. Our simulation results indicate the possibility of growth control of radially symmetric nanostructures at the sub-1 nm length scale on bulk substrates. The technique is well suited to the fabrication of ring-shaped nanostructures such as those employed in plasmonics, sensing devices, magneto-optics and magnetoelectronics. © IOP Publishing Ltd.

Lock, RL & Harry, EJ 2008, 'Cell-division inhibitors: new insights for future antibiotics', Nature Reviews Drug Discovery, vol. 7, no. 4, pp. 324-338.
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The growing problem of antibiotic resistance has been exacerbated by the use of new drugs that are merely variants of older overused antibiotics. While it is naive to expect to restrain the spread of resistance without controlling antibacterial usage, the desperate need for drugs with novel targets has been recognized by health organizations, industry and academia alike. The wealth of knowledge available about the bacterial cell-division pathway has aided target-driven approaches to identify novel inhibitors. Here, we discuss the therapeutic potential of inhibiting bacterial cell division, and review the progress made in this exciting new area of antibacterial discovery.

Lock, RL & Harry, EJ 2008, 'Cell-division inhibitors: new insights for future antibiotics.', Nat Rev Drug Discov, vol. 7, no. 4, pp. 324-338.
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The growing problem of antibiotic resistance has been exacerbated by the use of new drugs that are merely variants of older overused antibiotics. While it is naive to expect to restrain the spread of resistance without controlling antibacterial usage, the desperate need for drugs with novel targets has been recognized by health organizations, industry and academia alike. The wealth of knowledge available about the bacterial cell-division pathway has aided target-driven approaches to identify novel inhibitors. Here, we discuss the therapeutic potential of inhibiting bacterial cell division, and review the progress made in this exciting new area of antibacterial discovery.

Lord, MS, Modin, C, Foss, M, Duch, M, Simmons, A, Pedersen, FS, Besenbacher, F & Milthorpe, BK 2008, 'Extracellular matrix remodelling during cell adhesion monitored by the quartz crystal microbalance', BIOMATERIALS, vol. 29, no. 17, pp. 2581-2587.
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A cell's ability to remodel adsorbed protein layers on surfaces is influenced by the nature of the protein layer itself. Remodelling is often required to accomplish cellular adhesion and extracellular matrix formation which forms the basis for cell spreading, increased adhesion and expression of different phenotypes. The adhesion of NIH3T3 (EGFP) fibroblasts to serum protein (albumin or fibronectin) precoated tantalum (Ta) and oxidised polystyrene (PSox) surfaces was examined using the quartz crystal microbalance with dissipation (QCM-D) monitoring and fluorescence microscopy. The cells were either untreated or treated with cycloheximide to examine the contribution of endogenous protein production during cell adhesion to the QCM-D response over a period of 2 h. Following adsorption of albumin onto Ta and PSox there was no difference detected between the response to seeding untreated and cycloheximide treated cells. The QCM-D was able to detect differences in the untreated cellular responses to fibronectin versus serum precoated Ta and PSox substrates, while cycloheximide treatment of the cells produced the same QCM-D response for fibronectin and serum precoatings on each of the materials. This confirmed that the process of matrix remodelling by the cells is dependent on the underlying substrate and the preadsorbed proteins and that the QCM-D response is dominated by changes in the underlying protein layer. Changes in dissipation correspond to the development of the actin cytoskeleton as visualised by actin staining.

Lord, MS, Pasqui, D, Barbucci, R & Milthorpe, BK 2008, 'Protein adsorption on derivatives of hyaluronan', MACROMOLECULAR SYMPOSIA, vol. 266, no. 1, pp. 17-22.
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Serum protein adsorption and fibroblast cell adhesion on photo reactive hyaluronic acid (Hyal-N3) and its sulfated derivative (HyalS-N3) was analysed using a combination of quartz crystal microbalance (QCM) and cell adhesion assays. There was no significant differences in the amount of protein adsorbed onto the two polymers, however proteins were found to be more loosely bound to HyalS-N3 compared with Hyal-N3. Approximately 17% and 31% of the fibronectin interacting with Hyal-N3 and HyalS-N3 respectively was found to be irreversibly bound after rinsing with MilliQ water, SDS and urea. Proteins were exposed to the polymers before cell adhesion was monitored for a period of 2 hours in serum free conditions. Minimal cell adhesion was observed on albumin-coated materials as well as serum precoated Hyal-N3. Precoating the materials with fibronectin enhanced cell adhesion, although HyalS-N3 experienced higher levels of cell adhesion than Hyal-N3 and similar results were found for the serum precoated materials.

Luo, M, Luo, M-Z, Buzas, D, Finnegan, J, Helliwell, C, Dennis, ES, Peacock, WJ & Chaudhury, A 2008, 'UBIQUITIN-SPECIFIC PROTEASE 26 is required for seed development and the repression of PHERES1 in arabidopsis', GENETICS, vol. 180, no. 1, pp. 229-236.
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The Arabidopsis mutant Atubp26 initiates autonomous endosperm at a frequency of ∼1%in the absence of fertilization and develops arrested seeds at a frequency of ∼65% when self-pollinated. These phenotypes are similar to those of the FERTILIZATION INDEPENDENT SEED (FIS) classmutants, mea, fis2, fie, and Atmsi1, which also show development of the central cell into endosperm in the absence of fertilization and arrest of the embryo following fertilization. Atubp26 results from a T-DNA insertion in the UBIQUITIN-SPECIFIC PROTEASE gene AtUBP26, which catalyzes deubiquitination of histone H2B and is required for heterochromatin silencing. The paternal copy of AtUBP26 is able to complement the loss of function of the maternal copy in postfertilization seed development. This contrasts to the fis classmutants where the paternal FIS copy does not rescue aborted seeds. As in the fis class mutants, the Polycomb group (PcG) complex target gene PHERES1 (PHE1) is expressed at higher levels in Atubp26 ovules than in wild type; there is a lower level of H3K27me3 at the PHE1 locus. The phenotypes suggest that AtUBP26 is required for normal seed development and the repression of PHE1. Copyright © 2008 by the Genetics Society of America.

Maaroof, AL, Cortie, MB, Harris, N & Wieczorek, L 2008, 'Mie and Bragg Plasmons in Subwavelength Silver Semi-Shells', SMALL, vol. 4, no. 12, pp. 2292-2299.
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Mahayni, A & Schlögl, E 2008, 'The Risk Management of Minimum Return Guarantees', BuR - Business Research, vol. 1, no. 1, pp. 55-76.
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Contracts paying a guaranteed minimum rate of return and a fraction of a positive excess rate, which is specified relative to a benchmark portfolio, are closely related to unit-linked life-insurance products and can be considered as alternatives to direct investment in the underlying benchmark. They contain an embedded power option, and the key issue is the tractable and realistic hedging of this option, in order to rigorously justify valuation by arbitrage arguments and prevent the guarantees from becoming uncontrollable liabilities to the issuer. We show how to determine the contract parameters conservatively and implement robust risk-management strategies.

Maity, A, Apanasovich, TV & Carroll, RJ 2008, 'Estimation of population-level summaries in general semiparametric repeated measures regression models', IMS Collections, vol. 1, no. 1, pp. 3-137.
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This paper considers a wide family of semiparametric repeated measuresregression models, in which the main interest is on estimating population-levelquantities such as mean, variance, probabilities etc. Examples of our frameworkinclude generalized linear models for clustered/longitudinal data, among manyothers. We derive plug-in kernel-based estimators of the population levelquantities and derive their asymptotic distribution. An example involvingestimation of the survival function of hemoglobin measures in the Kenyahemoglobin study data is presented to demonstrate our methodology.

Malguth, E, Hoffmann, A & Phillips, MR 2008, 'Fe in III-V and II-VI semiconductors', PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, vol. 245, no. 3, pp. 455-480.
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Many theoretical and experimental studies deal with the realization of room-temperature ferromagnetism in dilute magnetic semiconductors (DMS). However, a detailed quantitative understanding of the electronic properties of transition metal doped semiconductors has often been neglected. This article points out which issues concerning electronic states and charge transfers need to be considered using Fe as an example. Methods to address these issues are outlined, and a wealth of data on the electronic properties of Fe doped III-V and II-VI compound semiconductors that have been obtained over a few decades is reviewed thoroughly. The review is complemented by new results on the effective-mass-like state consisting of a hole bound to Fe2+ forming a shallow acceptor state. The positions of established Fe3+/2+ and Fe2+/1+ charge transfer levels are summarized and predictions on the positions of further charge transfer levels are made based on the internal reference rule. The Fe3+/4+ level has not been identified unambiguously in any of the studied materials. Detailed term schemes of the observed charge states in tetrahedral and trigonal crystal field symmetry are presented including hyperfine structure, isotope effects and Jahn-Teller effect. Particularly, the radiative transitions Fe3+(4T 1 → 1A1) and Fe2+(5E → 5T2) are analyzed in great detail. An effective-mass-like state [Fe2+, h] consisting of a hole bound to Fe2+ is of great significance for a potential realization of spin-coupling in a DMS. New insights on this shallow acceptor state could be obtained by means of stress dependent and temperature dependent absorption experiments in the mK range. The binding energy and effective Bohr radius were determined for GaN, GaP, InP and GaAs and a weak exchange interaction between the hole and the Fe2+ center was detected. With regard to the Fe 3+ ground state, 6A1, in GaP and InP, the hyperfine structure level Γ8 was found to be above the Γ7 level. All results a...

Malguth, E, Hoffmann, A & Phillips, MR 2008, 'Structural and optical inhomogeneities of Fe doped GaN grown by hydride vapor phase epitaxy', JOURNAL OF APPLIED PHYSICS, vol. 104, no. 12.
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Marchenko, YV, Carroll, RJ, Lin, DY, Amos, CI & Gutierrez, RG 2008, 'Semiparametric Analysis of Case–control Genetic Data in the Presence of Environmental Factors', The Stata Journal: Promoting communications on statistics and Stata, vol. 8, no. 3, pp. 305-333.
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In the past decade, many statistical methods have been proposed for the analysis of case–control genetic data with an emphasis on haplotype-based disease association studies. Most of the methodology has concentrated on the estimation of genetic (haplotype) main effects. Most methods accounted for environmental and gene–environment interaction effects by using prospective-type analyses that may lead to biased estimates when used with case–control data. Several recent publications addressed the issue of retrospective sampling in the analysis of case–control genetic data in the presence of environmental factors by developing efficient semiparametric statistical methods. This article describes the new Stata command haplologit, which implements efficient profile-likelihood semiparametric methods for fitting gene–environment models in the very important special cases of a rare disease, a single candidate gene in Hardy–Weinberg equilibrium, and independence of genetic and environmental factors.

Marquez, C, Labbate, M, Ingold, AJ, Chowdhury, PR, Ramirez, MS, Centron, D, Borthagaray, G & Stokes, HW 2008, 'Recovery of a Functional Class 2 Integron from an Escherichia coli Strain Mediating a Urinary Tract Infection', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 52, no. 11, pp. 4153-4154.
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A class 2 integron was found in an Escherichia coli isolate mediating a urinary tract infection. Unlike other class 2 integrons from pathogens, the encoded IntI2 protein was functional. The integron possessed a dfrA14 cassette, and a second novel cassette in which a lipoprotein signal peptidase gene is predicted. Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Marsh, DJ, Trahair, TN, Martin, JL, Chee, WY, Walker, J, Kirk, EP, Baxter, RC & Marshall, GM 2008, 'Rapamycin treatment for a child with germline PTEN mutation', Nature Clinical Practice Oncology, vol. 5, no. 6, pp. 357-361.
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Martyn, AJ, Larkum, AWD, McConchie, R & Offord, CA 2008, 'Photoinhibition and changes in pigments associated with bract browning in waratahs (Telopea spp., Proteaceae)', JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY, vol. 83, no. 3, pp. 367-373.
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The relationship between chronic or long-term photoinhibition, pigment changes, and bract browning in 'Fire and Brimstone', 'Olympic Flame' and 'Wirrimbirra White' waratahs [Telopea speciosissima (Smith) R.Br.] was investigated. Plants were grown under full sun, or under 50% shade-cloth over 2 years, with photoinhibition and pigment changes measured in the bracts and leaves at three stages of floral development (tight bud, juvenile open bud, and mature flower). Photoinhibition of waratah bracts was reduced by shading when applied either from flower initiation in late Summer, or from bud expansion in late Winter, until flower maturity in Spring. Outer bracts showed photoinhibition from the tight bud stage of flower development, and inner bracts from the juvenile open stage, while leaves were not affected. Photoinhibition, measured as pre-dawn photochemical efficiency (PE; Fv/Fm), declined in proportion to bract browning. Bracts on waratah plants kept under shade maintained higher chlorophyll, carotenoid, and anthocyanin levels than bracts exposed to full sun, and thus had a more intense flower colour. A significant decrease in bract pigmentation, combined with photoinhibition, indicates that photodamage occurs in bracts exposed to full sun. Leaf browning did not occur, and waratah leaves maintained a higher chlorophyll concentration than bracts in both full sun and shade conditions. Protection from photoinhibition was correlated with the level of UV-absorbing pigments.

McPhedran, RC, Zucker, IJ, Botten, LC & Nicorovici, N-AP 2008, 'On the Riemann property of angular lattice sums and the one-dimensional limit of two-dimensional lattice sums', PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, vol. 464, no. 2100, pp. 3327-3352.
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We consider a general class of two-dimensional lattice sums consisting of complex powers s of inverse quadratic functions. We consider two cases, one where the quadratic function is negative definite and another more restricted case where it is positive

Middelberg, APJ, He, L, Dexter, AF, Shen, H-H, Holt, SA & Thomas, RK 2008, 'The interfacial structure and Young's modulus of peptide films having switchable mechanical properties', Journal of The Royal Society Interface, vol. 5, no. 18, pp. 47-54.
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We report the structure and Young's modulus of switchable films formed by peptide self-assembly at the air–water interface. Peptide surfactant AM1 forms an interfacial film that can be switched, reversibly, from a high- to low-elasticity state, with rapid loss of emulsion and foam stability. Using neutron reflectometry, we find that the AM1 film comprises a thin (approx. 15 Å) layer of ordered peptide in both states, confirming that it is possible to drastically alter the mechanical properties of an interfacial ensemble without significantly altering its concentration or macromolecular organization. We also report the first experimentally determined Young's modulus of a peptide film self-assembled at the air–water interface ( E =80 MPa for AM1, switching to E <20 MPa). These findings suggest a fundamental link between E and the macroscopic stability of peptide-containing foam. Finally, we report studies of a designed peptide surfactant, Lac21E, which we find forms a stronger switchable film than AM1 ( E =335 MPa switching to E <4 MPa). In contrast to AM1, Lac21E switching is caused by peptide dissociation from the interface (i.e. by self-disassembly). This research confirms that small changes in molecular design can lead to similar macroscopic behaviour via surprisingly different mechanisms.

Midthune, D, Kipnis, V, Freedman, LS & Carroll, RJ 2008, 'Binary Regression in Truncated Samples, with Application to Comparing Dietary Instruments in a Large Prospective Study', Biometrics, vol. 64, no. 1, pp. 289-298.
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Summary We examine two issues of importance in nutritional epidemiology: the relationship between dietary fat intake and breast cancer, and the comparison of different dietary assessment instruments, in our case the food frequency questionnaire (FFQ) and the multiple‐day food record (FR). The data we use come from women participants in the control group of the Dietary Modification component of the Women's Health Initiative (WHI) Clinical Trial. The difficulty with the analysis of this important data set is that it comes from a truncated sample, namely those women for whom fat intake as measured by the FFQ amounted to 32% or more of total calories. We describe methods that allow estimation of logistic regression parameters in such samples, and also allow comparison of different dietary instruments. Because likelihood approaches that specify the full multivariate distribution can be difficult to implement, we develop approximate methods for both our main problems that are simple to compute and have high efficiency. Application of these approximate methods to the WHI study reveals statistically significant fat and breast cancer relationships when a FR is the instrument used, and demonstrate a marginally significant advantage of the FR over the FFQ in the local power to detect such relationships.

MILLER, SHANEM & PLATEN, ECKHARD 2008, 'ANALYTIC PRICING OF CONTINGENT CLAIMS UNDER THE REAL-WORLD MEASURE', International Journal of Theoretical and Applied Finance, vol. 11, no. 08, pp. 841-867.
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This article derives a series of analytic formulae for various contingent claims under the real-world probability measure using the stylised minimal market model (SMMM). This model provides realistic dynamics for the growth optimal portfolio (GOP) as a well-diversified equity index. It captures both leptokurtic returns with correct tail properties and the leverage effect. Under the SMMM, the discounted GOP takes the form of a time-transformed squared Bessel process of dimension four. From this property, one finds that the SMMM possesses a special and interesting relationship to non-central chi-square random variables with zero degrees of freedom. The analytic formulae derived under the SMMM include options on the GOP, options on exchange prices and options on zero-coupon bonds. For options on zero-coupon bonds, analytic prices facilitate efficient calculation of interest rate caps and floors.

Milthorpe, BK 2008, 'Application of biomechanics to tissue engineering: A personal view', JOURNAL OF MECHANICS IN MEDICINE AND BIOLOGY, vol. 8, no. 2, pp. 153-160.
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Cellular biomechanics is an area of study that is receiving more attention as time progresses. The response of cells to their mechanical environment, including biomechanical stimuli, has far-reaching ramifications for the area of tissue engineering, especially for tissues designed to withstand mechanical loading (e.g. bone, cartilage, tendons and ligaments, and arteries). The effects of mechanical stimuli on cells are only recently being examined, and the potential role of mechanical stimuli in tissue engineering is still one that is largely ignored in the design of tissue engineering scaffolds. The relationship of mechanical properties of scaffolds or of mechanical stimuli to cell behavior is complex, but vital to the development of the field. Also, understanding the complex interplay of form and environment on cells involves an increase in our knowledge of how cells react to their total environment including mechanical stimuli and material properties. In order to improve tissue engineering outcomes, a nexus must be developed between the mechanical, biochemical, and biological studies of cellular behavior, in the context of extremely complex systems

Mirsalehian, A, Nakhjavani, F, Peymani, A, Jabalameli, F, Mirafshar, SM & Hamidian, M 2008, 'Frequency of extended spectrum β-Lactamase producing Enterobacteriaceae in intensive care units', Tehran University Medical Journal, vol. 65, no. 1, pp. 33-38.
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Background: The incidence of ESBL producing species have been steadily increased in recent years, resulting in limitation of infection control issues and therapeutic options.The purpose of this study was to evaluate prevalence of Enterobacteriaceae and also assess epidemiology ESBL producing strains isolated from patients admitted in ICUs. Methods: A total of one hundred fifty isolates were collected from urine, sputum, blood, wound and other clinical samples from patient admitted in ICU and then were identified by biochemical tests.All of the samples were screened by DAD method according to The NCCLS Guideline. The species that met NCCLS screening criteria was further tested for Clavulanic Acid effect by confirmatory method. Results: A total of one hundred fifty isolates,133(89.3%) were found to be resistant at least on of the indicators cephalosporin tested according to NCCLS Guideline. 121(80.6%) of the isolates were resistant to all the indicators tested.89(59.3) isolateds were confirmed as ESBL producers. The number of isolates ESBL producing was as follow: Klebsiella pneumoniae 33 (76.74%), E.coli 20 (60.60%), Enterobacter cloacae 8 (47.05%), Citrobacter diversus 6 (54.54%), Enterobacter aerogenes 7 (53.84%), Citrobacter freundii 4 (40%), Klebsiella oxytoca 6 (62.5%), Proteus mirabilis 4 (50%), Serratia marcescens 2 (40%), Proteus Volgaris 0%.All of the isolates sensitive to imipenem. Conclusion: The present study shows high prevalence of ESBL producing Enterobacteriaceae from patients admitted in ICU.The increased rate of these species in most cases due to the administration of inadequate and irrational antimicrobial therapy.To overcome this problem, it needs to develop new antimicrobial agents, limiting the Unnecessary Use of antimicrobial and increasing compliance with infection control issues.

Mitrovic, SM, Chessman, BC, Davie, A, Avery, EL & Ryan, N 2008, 'Development of blooms of Cyclotella meneghiniana and Nitzschia spp. (Bacillariophyceae) in a shallow river and estimation of effective suppression flows', HYDROBIOLOGIA, vol. 596, no. 1, pp. 173-185.
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Diatom blooms in the middle reaches of the shallow, freshwater, Hunter River, Australia, are a frequent nuisance to river users. During a 4-year study, blooms of Cyclotella meneghiniana and Nitzschia spp. coincided with water temperatures above 23°C and flows below 400 Ml d-1 that lasted for more than 12 days. Redundancy analysis showed that water temperature was positively related, and antecedent flow was negatively related, to the abundance of both taxa. Addition experiments indicated that nutrients are seldom limiting to growth. It is suggested that a combination of faster growth rates at higher temperatures and longer retention times at low flows allows bloom populations to develop. Simulation modelling showed that flow regulation and water extraction have decreased flows in the river during summer, and consequently have probably increased the number of diatom blooms. Environmental flows have been provided to the river, but are not sufficient to prevent blooms. Discharges required for bloom suppression are described. © 2007 Springer Science+Business Media B.V.

Miu, J, Mitchell, AJ, Müller, M, Carter, SL, Manders, PM, McQuillan, JA, Saunders, BM, Ball, HJ, Lu, B, Campbell, IL & Hunt, NH 2008, 'Chemokine Gene Expression during Fatal Murine Cerebral Malaria and Protection Due to CXCR3 Deficiency', The Journal of Immunology, vol. 180, no. 2, pp. 1217-1230.
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Abstract Cerebral malaria (CM) can be a fatal manifestation of Plasmodium falciparum infection. Using murine models of malaria, we found much greater up-regulation of a number of chemokine mRNAs, including those for CXCR3 and its ligands, in the brain during fatal murine CM (FMCM) than in a model of non-CM. Expression of CXCL9 and CXCL10 RNA was localized predominantly to the cerebral microvessels and in adjacent glial cells, while expression of CCL5 was restricted mainly to infiltrating lymphocytes. The majority of mice deficient in CXCR3 were found to be protected from FMCM, and this protection was associated with a reduction in the number of CD8+ T cells in brain vessels as well as reduced expression of perforin and FasL mRNA. Adoptive transfer of CD8+ cells from C57BL/6 mice with FMCM abrogated this protection in CXCR3−/− mice. Moreover, there were decreased mRNA levels for the proinflammatory cytokines IFN-γ and lymphotoxin-α in the brains of mice protected from FMCM. These data suggest a role for CXCR3 in the pathogenesis of FMCM through the recruitment and activation of pathogenic CD8+ T cells.

Mohamad, KY, Rekiki, A, Myers, G, Bavoil, PM & Rodolakis, A 2008, 'Identification and characterisation of coding tandem repeat variants inincAgene ofChlamydophila pecorum', Veterinary Research, vol. 39, no. 6, pp. 56-56.
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Bacteria of the family Chlamydiaceae are obligate intracellular pathogens of human and animals. Chlamydophila pecorum is associated with different pathological conditions in ruminants, swine and koala. To characterize a coding tandem repeat (CTR) identified at the 3' end of incA gene of C. pecorum, 51 strains of different chlamydial species were examined. The CTR were observed in 18 of 18 tested C. pecorum isolates including symptomatic and asymptomatic animals from diverse geographical origins. The CTR were also found in two strains of C. abortus respectively isolated from faeces from a healthy ewe and from a goat belonging to asymptomatic herds, but were absent in C. abortus strains isolated from clinical disease specimens, and in tested strains of C. psittaci, C. caviae, C. felis and C. trachomatis. The number of CTR repeats is variable and encode several motifs that are rich in alanine and proline. The CTR-derived variable structure of incA, which encode the Chlamydiaceae-specific type III secreted inclusion membrane protein, IncA, may be involved in the adaptation of C. pecorum to its environment by allowing it to persist in the host cell. © 2008 INRA EDP Sciences.

Mokkapati, S, Wong-Leung, J, Tan, HH, Jagadish, C, McBean, KE & Phillips, MR 2008, 'Tuning the bandgap of InAs quantum dots by selective-area MOCVD', JOURNAL OF PHYSICS D-APPLIED PHYSICS, vol. 41, no. 8, pp. 0-0.
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In-plane bandgap energy control of InAs quantum dots (QDs) grown on GaAs substrates is demonstrated using selective-area epitaxy. Transmission electron microscopy and cathodoluminescence are used for characterization of the selectively grown dots. A single-step growth of a thin InAs quantum well and InAs QDs emitting at 1010 and 1100 nm (at 77 K) on the same wafer is demonstrated. Non-uniform growth profile is reported for the selectively grown QDs in the mask openings. Surface migration of adatoms from higher order facets to (1 0 0) facets results in enhanced deposition rates closer to the edge of the openings and vapour phase diffusion of adatoms results in density variations across the openings over length scales greater than the surface migration length of the adatoms. © 2008 IOP Publishing Ltd.

Momtaz, S & Gladstone, W 2008, 'Ban on commercial fishing in the estuarine waters of New South Wales, Australia: Community consultation and social impacts', ENVIRONMENTAL IMPACT ASSESSMENT REVIEW, vol. 28, no. 2-3, pp. 214-225.
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In its effort to resolve the conflict between commercial and recreational fishers the New South Wales (NSW) government (NSW Fisheries) banned commercial fishing in the estuarine waters. The NSW Fisheries conducted a number of studies and held meetings with the affected communities including commercial fishers prior to the implementation of the ban. To investigate how community consultation played a role in the decision-making process especially as perceived by the commercial fishers and to determine actual social impacts of the ban on commercial fishers, in-depth interviews were conducted with the commercial fishers. This research reveals that despite the NSW Fisheries' consultations with commercial fishers prior to the closure, the latter were confused about various vital aspects of the decision. It further reveals that, the commercial fishers faced a number of significant changes as a result of this decision. We argue that a better decision-making process and outcome would have been possible through a meaningful consultation with the commercial fishers and a social impact assessment.

Moore, CP, Arnold, MD, Bones, PJ & Blaikie, RJ 2008, 'Image fidelity for single-layer and multi-layer silver superlenses', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, vol. 25, no. 4, pp. 911-918.
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In response to increasing interest in the area of subdiffraction-limited near-field imaging, the performance of several different realizable and theoretical superresolving silver-based lenses is simulated for a variety of different input object profiles. A computationally-efficient T-matrix technique is used to model the lenses, which consist of layers of silver with total width of 40 nm sandwiched between layers of polymethyl methacrylate and silicon dioxide. The lenses are exposed to nonperiodic bright- and dark-slit input patterns, with feature size varied between 1 nm and 2.5 µm. The performance of the lenses is characterized in terms of transfer function, contrast profile, error profile, and input-to-output correlation. It is shown that increasing the number of layers in a lens increases the lens' transmission coefficients at high spatial frequencies; however, this does not always lead to better imaging performance. The main reasons for this are lens-specific resonances that distort features at certain spatial frequencies, and the increased attenuation of the DC component of transmitted images, which reduces image fidelity, particularly for dark-line features. This suggests that, to achieve optimum results, the design of the superresolving lens system should take into account the characteristics of the images that it is expected to transmit

Morgan, SW & Phillips, MR 2008, 'High bandwidth secondary electron detection in variable pressure scanning electron microscopy using a Frisch grid', JOURNAL OF PHYSICS D-APPLIED PHYSICS, vol. 41, no. 5, pp. 1-6.
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The bandwidth and contrast of secondary electron (SE) images obtained using variable pressure scanning electron microscopy are enhanced when a grounded Frisch grid is placed between the SE detecting anode and the negatively biased stage. The improvement in SE image quality occurs as a consequence of the grounded Frisch grid electrostatically screening the 'slow' induced ion current signal, generated below the grid, from the induced current detected above the grid by the anode. Ion induced artefacts, such as image smearing at fast scan rates, are virtually eliminated using a Frisch grid. Gas amplification data are presented to illustrate that gas gain can be optimized by varying the Frisch grid-stage (amplification region) separation Frisch grid-anode (drift region) separation and stage bias. © 2008 IOP Publishing Ltd.

Morris, MJ, Chen, H, Watts, R, Shulkes, A & Cameron-Smith, D 2008, 'Brain neuropeptide Y and CCK and peripheral adipokine receptors: temporal response in obesity induced by palatable diet', International Journal of Obesity, vol. 32, no. 2, pp. 249-258.
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Objective: Palatable food disrupts normal appetite regulation, which may contribute to the etiology of obesity. Neuropeptide Y (NPY) and cholecystokinin play critical roles in the regulation of food intake and energy homeostasis, while adiponectin and carnitine palmitoyltransferase (CPT) are important for insulin sensitivity and fatty acid oxidation. This study examined the impact of short- and long-term consumption of palatable high-fat diet (HFD) on these critical metabolic regulators. Methods: Male C57BL/6 mice were exposed to laboratory chow (12% fat), or cafeteria-style palatable HFD (32% fat) for 2 or 10 weeks. Body weight and food intake were monitored throughout. Plasma leptin, hypothalamic NPY and cholecystokinin, and mRNA expression of leptin, adiponectin, their receptors and CPT-1, in fat and muscles were measured. Results: Caloric intake of the palatable HFD group was 2-3 times greater than control, resulting in a 37% higher body weight. Fat mass was already increased at 2 weeks; plasma leptin concentrations were 2.4 and 9 times higher than control at 2 and 10 weeks, respectively. Plasma adiponectin was increased at 10 weeks. Muscle adiponectin receptor 1 was increased at 2 weeks, while CPT-1 mRNA was markedly upregulated by HFD at both time points. Hypothalamic NPY and cholecystokinin content were significantly decreased at 10 weeks. Conclusion: Palatable HFD induced hyperphagia, fat accumulation, increased adiponectin, leptin and muscle fatty acid oxidation, and reduced hypothalamic NPY and cholecystokinin. Our data suggest that the adaptive changes in hypothalamic NPY and muscle fatty acid oxidation are insufficient to reverse the progress of obesity and metabolic consequences induced by a palatable HFD. © 2008 Nature Publishing Group All rights reserved.

Morton, JK, Gladstone, W, Hughes, JM & Stewart, J 2008, 'Comparison of the life histories of three co-occurring wrasses (Teleostei : Labridae) in coastal waters of south-eastern Australia', MARINE AND FRESHWATER RESEARCH, vol. 59, no. 7, pp. 560-574.
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Labrids are abundant on temperate rocky reefs yet their life histories are poorly known. Three co-occurring Australian labrids (Ophthalmolepis lineolatus, Notolabrus gymnogenis and Pictilabrus laticlavius) exhibited protogynous hermaphroditism typical of labrids. Juveniles reached sexual maturity at 184 mm total length (TL) (2.1 years) in O. lineolatus, 177 mm TL (1.8 years) in N. gymnogenis and <95 mm TL (<0.9 years) in P. laticlavius. Individuals were sexually active initial phase females until changing to a terminal phase male at 295 mm TL (5.2 years) in O. lineolatus, 273 mm TL (4.5 years) in N. gymnogenis and 138 mm TL (2.0 years) in P. laticlavius. The occurrence of males only at greater lengths and older ages suggests that O. lineolatus and N. gymnogenis are monandrous, whereas P. laticlavius appears to be diandrous. Reproduction was asynchronous among species with reproductive activity peaking in JanuaryMarch for O. lineolatus, AprilOctober for N. gymnogenis and OctoberDecember for P. laticlavius. Sectioned otoliths revealed that O. lineolatus and N. gymnogenis grew rapidly to 300 mm TL (6 years) and P. laticlavius to 180 mm TL (3 years). Longevity was at least 13.8, 9.6 and 4.8 years respectively. These life history data will aid management of these frequently harvested species.

Morton, JK, Platell, ME & Gladstone, W 2008, 'Differences in feeding ecology among three co-occurring species of wrasse (Teleostei : Labridae) on rocky reefs of temperate Australia', MARINE BIOLOGY, vol. 154, no. 3, pp. 577-592.
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The foraging behaviours and dietary compositions of three co-occurring labrids (Ophthalmolepis lineolatus, Notolabrus gymnogenis and Pictilabrus laticlavius), which are conspicuous on rocky reefs in temperate south-eastern Australia, were investigated between 2003 and 2005. SCUBA observations at two locations showed that the feeding intensity, and hence the associated effects of these fishes on rocky reef invertebrate prey, was temporally consistent. Relative differences in the contributions of ingested prey and use of different feeding microhabitats demonstrated that the feeding ecology differed significantly among the three species. Thus, O. lineolatus fed on proportionately higher volumes of polychaetes, polyplacophorans, marginellid gastropods (especially Austroginella sp.), bivalves and echinoids, which were sighted opportunistically in a wide selection of microhabitats, but particularly in sand/rubble. Ambush hunting was used regularly by smaller N. gymnogenis and all sizes of P. laticlavius to forage on amphipods, small decapods and small gastropods at algal bases or fronds and Diopatra dentata tubes. Amphipods were similarly important in the diet of smaller O. lineolatus.

Nantakomol, D, Chimma, P, Day, NP, Dondorp, AM, Combes, V, Krudsood, S, Looareesuwan, S, White, NJ, Pattanapanyasat, K & Chotivanich, K 2008, 'Quantitation of cell-derived microparticles in plasma using flow rate based calibration.', Southeast Asian J Trop Med Public Health, vol. 39, no. 1, pp. 146-153.
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Activation of vascular endothelium and blood cells can result in the formation of microparticles (MPs), which are membrane vesicles with a diameter < 1 microm which can play a pathogenetic role in a variety of infectious and other diseases. In this study, we validated a modified quantitative method called 'flow rate based calibration', to measure circulating MPs in plasma of healthy subjects and malaria patients using FACSCalibur flow cytometry. MPs counts obtained from 'flow rate based calibration' correlated closely with the standard method (R2 = 0.9, p = 0.001). The median (range) number of MPs in healthy subjects was 163/microl (81-375/microl). We demonstrated a flow rate based calibration for the quantitation of MPs in P. falciparum malaria-infected patients. The median (range) number of MPs was 2,051/microl (222-6,432/microl), n = 28 in patients with falciparum malaria. The number of MPs in plasma from patients with severe falciparum malaria was significantly higher than in uncomplicated falciparum malaria (2,567/microl (366-6,432/microl), n = 18 versus [1,947/microl (222-4,107/microl), n = 10, p < 0.01]. Cellular origin of MPs in malaria patients were mainly derived from red blood cells (35%), platelets (10%), and endothelial cells (5%). There was no significant correlation between the total number of MPs and parasitemia. Flow rate based calibration is a simple, reliable, reproducible method and more affordable to quantitate MPs.

Nedbal, L, Trtílek, M, Červený, J, Komárek, O & Pakrasi, HB 2008, 'A photobioreactor system for precision cultivation of photoautotrophic microorganisms and for high‐content analysis of suspension dynamics', Biotechnology and Bioengineering, vol. 100, no. 5, pp. 902-910.
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AbstractSmall‐scale photobioreactors for cultivation of photoautotrophic microbes are required for precise characterization of the growth parameters of wild‐type and engineered strains of these organisms, for their screening, and for optimization of culture conditions. Here, we describe the design and use of a flat‐cuvette photobioreactor that allows accurate control of culture irradiance, temperature, pH, and gas composition combined with real‐time monitoring by a built‐in fluorometer and densitometer. The high‐power LED light source generates precise irradiance levels that are programmed by user‐designed protocols. The irradiance, temperature, and gas composition may be static or dynamically modulated, while optical density and pH may be stabilized in turbidostat and pH‐stat modes, respectively. We demonstrate that the instrument is able to detect minute variations of growth caused, for example, by sudden dilution or by circadian rhythms. The sensitivity of the instrument is sufficient to monitor suspension optical density as low as 10−2. This newly designed photobioreactor can significantly contribute to the study and use of photoautotrophic microbes in systems biology and biotechnology. Biotechnol. Bioeng. 2008;100: 902–910. © 2008 Wiley Periodicals, Inc.

Nelson, LA, Wallman, JF & Dowton, M 2008, 'Identification of forensically important Chrysomya (Diptera: Calliphoridae) species using the second ribosomal internal transcribed spacer (ITS2)', Forensic Science International, vol. 177, no. 2-3, pp. 238-247.
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Nguyen, DV, şentürk, D & Carroll, RJ 2008, 'Covariate-adjusted linear mixed effects model with an application to longitudinal data', Journal of Nonparametric Statistics, vol. 20, no. 6, pp. 459-481.
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O'Brien, BA, Archer, NS, Simpson, AM, Torpy, FR & NasSif, NT 2008, 'Association of SLC11A1 promoter polymorphisms with the incidence of autoimmune and inflammatory diseases: A meta-analysis', JOURNAL OF AUTOIMMUNITY, vol. 31, no. 1, pp. 42-51.
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Solute carrier family 11 member a1 (SLC11A1) exerts pleiotropic effects on macrophage function. Expression of SLC11A1 is regulated by a (GT)n microsatellite promoter repeat polymorphism of which nine alleles have been described. Enhanced activation of macrophages, associated with increased expression from allele 3, may be functionally linked to the development of autoimmune and inflammatory diseases. Conversely, low expression, driven by allele 2, may afford resistance. We have performed a meta-analysis to determine the association of SLC11A1 promoter alleles 2 and 3 with autoimmunity and inflammation. A random effects pooled odds ratio (OR) of 1.04 (95% confidence interval [CI] = 0.20) for allele 3 suggested a weak association of this allele with an increased risk of disease. Calculation of the OR in the absence of asymmetry yielded a random effects pooled OR of 0.88 (95% CI = 0.66), effectively reversing the above association. A fixed effects pooled OR of 0.90 (95% CI = 0.24) was obtained for allele 2, suggesting a weak predominance of disease in the absence of this allele. Application of the trim-and-fill method resulted in a fixed effects OR of 0.80 (95% CI = 0.22), thus strengthening this association. Associations of allele 3 with autoimmune and inflammatory diseases reported in several association studies may be attributable to some form of bias amongst published results. © 2008 Elsevier Ltd. All rights reserved.

Oliver, BGG, Lim, S, Wark, P, Laza-Stanca, V, King, N, Black, JL, Burgess, JK, Roth, M & Johnston, SL 2008, 'Rhinovirus exposure impairs immune responses to bacterial products in human alveolar macrophages', Thorax, vol. 63, no. 6, pp. 519-525.
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Background:Rhinovirus infection is responsible for considerable morbidity and mortality as the major cause of exacerbations of asthma, and is also known to induce exacerbations of cystic fibrosis and chronic obstructive pulmonary disease. Exacerbations of these diseases are also frequently associated with bacterial and atypical bacterial infection. Alveolar macrophages are the major immune cells in the airways and are important in defence against bacterial infections.Methods:The authors investigated whether rhinovirus modifies cytokine release, the pattern recognition receptor expression and phagocytosis by human alveolar macrophages in response to bacterial products.Results:Viable rhinovirus was detected in macrophages up to 3 days after exposure and viral RNA expression persisted for 10 days. Infectious but not UV inactivated rhinovirus increased tumour necrosis factor α (TNFα) and interleukin (IL)8 release by macrophages. In contrast, infectious rhinovirus impaired lipopolysaccharide and lipoteichoic acid induced TNFα and IL8 secretion by macrophages. Rhinovirus induced impairment of macrophage antibacterial immune responses did not involve IL10, prostaglandin E2 or downregulation of Toll-like receptor 2. Furthermore, the macrophage phagocytic response to labelled bacterial particles, but not to latex beads, was impaired.Conclusion:The authors have identified impairment of cytokine responses to bacterial lipopolysaccharide and lipoteichoic acid by alveolar macrophages in response to infectious rhinovirus. Virus induced impairment of antibacterial host defence has important implications in the pathogenesis of exacerbations of respiratory diseases.

Ormerod, JT, Wand, MP & Koch, I 2008, 'Penalised spline support vector classifiers: computational issues', Computational Statistics, vol. 23, no. 4, pp. 623-641.
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We study computational issues for support vector classification with penalised spline kernels. We show that, compared with traditional kernels, computational times can be drastically reduced in large problems making such problems feasible for sample sizes as large as ~106. The optimisation technology known as interior point methods plays a central role. Penalised spline kernels are also shown to allow simple incorporation of low-dimensional structure such as additivity. This can aid both interpretability and performance. © 2008 Springer-Verlag.

Pablo, F, Krassoi, FR, Jones, PRF, Colville, AE, Hose, GC & Lim, RP 2008, 'Comparison of the fate and toxicity of chlorpyrifos - Laboratory versus a coastal mesocosm system', ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, vol. 71, no. 1, pp. 219-229.
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The widespread use of chlorpyrifos for pest control in urban and rural environments poses a risk of contamination to aquatic environments via runoff, spray drift or spillage. The aim of this study was to assess the fate of chlorpyrifos and its toxicity t

Padoan, SA & Wand, MP 2008, 'Mixed model-based additive models for sample extremes', Statistics & Probability Letters, vol. 78, no. 17, pp. 2850-2858.
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We consider additive models fitting and inference when the response variable is a sample extreme. Non-linear covariate effects are handled using the mixed model representation of penalised splines. A fitting algorithm based on likelihood approximations is derived. The efficacy of the resulting methodology is demonstrated via application to simulated and real data. © 2008 Elsevier B.V. All rights reserved.

Padula, M, Herbert, BR & Broady, KW 2008, 'Identification of Proteins, Enzymes and Potential Vaccine Candidates from the Aust Paralysis Tick, Ixodes Holocyclus Using 2D-PAGE and Equalizer Technology', Journal of Proteomics & Bioinformatics, vol. S2, no. 01, pp. 208-209.
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Palmer, AR, Fuentes, S, Taylor, D, Macinnis-Ng, C, Zeppel, M, Yunusa, I, February, E & Eamus, D 2008, 'The use of pre-dawn leaf water potential and MODIS LAI to explore seasonal trends in the phenology of Australian and southern African woodlands and savannas', AUSTRALIAN JOURNAL OF BOTANY, vol. 56, no. 7, pp. 557-563.
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Trends in global soil moisture are needed to inform models of soilplantatmosphere interactions. Predawn leaf water potential (?pd), a surrogate for soil moisture and an index of plant water stress, has been routinely collected in Australian forests, woodlands and savannas, but the associated leaf area index (LAI) has seldom been available to enable the preparation of a ?pd on LAI relationship. Following an analysis of ?pd and MODIS LAI data from Australian forests, woodlands and savannas, we identified patterns in ?pd which provide an understanding of the role of soil-moisture status in controlling LAI. In the savanna of northern Australia, the MODIS LAI product had a basal value of 0.96 during the dry season as compared with a mean value of 2.5 for the wet season. The dry season value is equivalent to the LAI of the tree component and corresponds with ground-truthed LAI. ?pd is lowest (more negative) during the height of the dry season (late October) at -2.5 MPa, and highest (-0.1 MPa) during the wet season (early March). We present two models which predict ?pd from the MODIS LAI product. These may be useful surrogates for studying trends in soil moisture in highly seasonal climates and may contribute to climate change research.

Pankoui Mf, JB, Gouado, I, Fotso Kuat, H, Zambou, O, Grau, G, Combes, V & Amvam Zoll, PH 2008, 'Clinical Presentation, Haematological Indices and Management of Children with Severe and Uncomplicated Malaria in Douala, Cameroon', Pakistan Journal of Biological Sciences, vol. 11, no. 20, pp. 2401-2406.
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This study carried out from January to June 2007, was undertaken to describe the clinical presentation of childhood malaria in Douala, a meso-endemic area as far as malaria transmission is concerned. One hundred and seventy eight children were enrolled after informed consent of their parents. The sample characteristics were recorded and clinical as well as preliminary laboratory investigations were performed. Thirty eight children coming for vaccination and counselling was targeted to serve as control. According to the results obtained, cerebral malaria (CM) seems to be associated with young age, whilst Malaria anaemia (MA) was predominant among older children. Hyperpyrexia and hyperparasitaemia were high among CM patients and 11.1% of them died, however, no neurological squeal was noticed immediately after discharge on those who survived. Haemoglobin and glycaemia were low on MA and CM patients; these groups had low percentage in bed nets utilization as well. These results suggest that the clinical presentation of the disease differ with the geographic location and malaria disease features varies according to the severity. Such studies could contribute to the management of the disease. © 2008 Asian Network for Scientific Information.

Park, M, Kang, Y, Wang, G, Dou, S & Liu, H 2008, 'The Effect of Morphological Modification on the Electrochemical Properties of SnO₂ Nanomaterials', Advanced Functional Materials, vol. 18, no. 3, pp. 455-461.
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AbstractThe electrochemical performances of 1D SnO2 nanomaterials, nanotubes, nanowires, and nanopowders, are compared to define the most favorable morphology when SnO2 nanomaterials are adopted as the electrode material for lithium‐ion batteries. Changes in the morphology of SnO2 are closely related with its electrochemical performance. Some SnO2 nanomaterials feature not only an increased energy density but also enhanced Li+ transfer. The correlation between the morphological characteristics and the electrochemical properties of SnO2 nanomaterials is discussed. The interesting electrochemical results obtained here on SnO2 nanomaterials indicate the possibility of designing and fabricating attractive nanostructured materials for lithium‐ion batteries.

Park, M-S, Kang, Y-M, Kim, J-H, Wang, G-X, Dou, S-X & Liu, H-K 2008, 'Effects of low-temperature carbon encapsulation on the electrochemical performance of SnO2 nanopowders', Carbon, vol. 46, no. 1, pp. 35-40.
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Carbon encapsulated SnO2 composites were prepared by a thermal evaporation and decomposition of malic acid (C4H6O5) at low temperature to demonstrate their potential use for application in lithium ion batteries. The solution-based chemical approach was effective for coating amorphous C layers on the surface of SnO2 nanopowders without significant oxygen reduction. The desirable crystalline structure and oxygen stoichiometry of SnO2 were maintained, while amorphous C homogeneously encapsulated SnO2 nanopowders. The strong enhancement on the anodic reversible capacity and cyclic performance was discussed for the C-encapsulated SnO2 composites. It is expected that the low-temperature processing can be a new general route for preparing composites with C from economic point of view. © 2007 Elsevier Ltd. All rights reserved.

Paz-Pellat, F, Bolanos-Gonzalez, M, Palacios-Velez, E, Palacios-Sanchez, LA, Martinez-Menes, M & Huete, A 2008, 'OPTIMIZATION OF THE SPECTRAL VEGETATION INDEX NDVIcp', AGROCIENCIA, vol. 42, no. 8, pp. 925-937.

Pepper, DA, McMurtrie, RE, Medlyn, BE, Keith, H & Eamus, D 2008, 'Mechanisms linking plant productivity and water status for a temperate Eucalyptus forest flux site: analysis over wet and dry years with a simple model', FUNCTIONAL PLANT BIOLOGY, vol. 35, no. 6, pp. 493-508.
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A simple process-based model was applied to a tall Eucalyptus forest site over consecutive wet and dry years to examine the importance of different mechanisms linking productivity and water availability. Measured soil moisture, gas flux (CO2, H2O) and me

Perchyonok, V, Tuck, K, Ryan, S, Langford, S & Hearn, M 2008, 'Facile and Selective Deallylations of Esters under ‘Aqueous’ Free-Radical Conditions', Synlett, vol. 2008, no. 8, pp. 1233-1235.
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Perchyonok, VT, Ryan, SJ, Langford, SJ, Hearn, MT & Tuck, KL 2008, 'ChemInform Abstract: Facile and Selective Deallylations of Esters under “Aqueous” Free‐Radical Conditions.', ChemInform, vol. 39, no. 39.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Perchyonok, VT, Tuck, KL, Langford, SJ & Hearn, MW 2008, 'ChemInform Abstract: On the Scope of Radical Reactions in Aqueous Media Utilizing Quaternary Ammonium Salts of Phosphinic Acids as Chiral and Achiral Hydrogen Donors.', ChemInform, vol. 39, no. 46.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Perchyonok, VT, Tuck, KL, Langford, SJ & Hearn, MW 2008, 'On the scope of radical reactions in aqueous media utilizing quaternary ammonium salts of phosphinic acids as chiral and achiral hydrogen donors', Tetrahedron Letters, vol. 49, no. 32, pp. 4777-4779.
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Petrou, K, Doblin, MA, Smith, RA, Ralph, PJ, Shelly, K & Beardall, J 2008, 'State transitions and nonphotochemical quenching during a nutrient-induced fluorescence transient in phosphorus-starved Dunaliella tertiolecta', JOURNAL OF PHYCOLOGY, vol. 44, no. 5, pp. 1204-1211.
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Assessments of nutrient-limitation in microalgae using chl a fluorescence have revealed that nitrogen and phosphorus depletion can be detected as a change in chl a fluorescence signal when nutrient-starved algae are resupplied with the limiting nutrient. This photokinetic phenomenon is known as a nutrient-induced fluorescence transient, or NIFT. Cultures of the unicellular marine chlorophyte Dunaliella tertiolecta Butcher were grown under phosphate starvation to investigate the photophysiological mechanism behind the NIFT response. A combination of low temperature (77 K) fluorescence, photosynthetic inhibitors, and nonphotochemical quenching analyses were used to determine that the NIFT response is associated with changes in energy distribution between PSI and PSII and light-stress-induced nonphotochemical quenching (NPQ). Previous studies point to state transitions as the likely mechanism behind the NIFT response; however, our results show that state transitions are not solely responsible for this phenomenon. This study shows that an interaction of at least two physiological processes is involved in the rapid quenching of chl a fluorescence observed in P-starved D. tertiolecta: (1) state transitions to provide the nutrient-deficient cell with metabolic energy for inorganic phosphate (Pi)-uptake and (2) energy-dependent quenching to allow the nutrient-stressed cell to avoid photodamage from excess light energy during nutrient uptake. © 2008 Phycological Society of America.

Pfeiffer, RM, Carroll, RJ, Wheeler, W, Whitby, D & Mbulaiteye, S 2008, 'Combining assays for estimating prevalence of human herpesvirus 8 infection using multivariate mixture models', Biostatistics, vol. 9, no. 1, pp. 137-151.
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Phipatanakul, W, Celedon, JC, Hoffman, EB, Abdulkerim, H, Ryan, LM & Gold, DR 2008, 'Mouse allergen exposure, wheeze and atopy in the first seven years of life', ALLERGY, vol. 63, no. 11, pp. 1512-1518.
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Background: Little is known about mouse allergen exposure in home environments and the development of wheezing, asthma and atopy in childhood. Objective: To examine the relation between mouse allergen exposure and wheezing, atopy, and asthma in the first 7 years of life. Methods: Prospective study of 498 children with parental history of allergy or asthma followed from birth to age 7 years, with longitudinal questionnaire ascertainment of reported mouse exposure and dust sample mouse urinary protein allergen levels measured at age 2-3 months. Results: Parental report of mouse exposure in the first year of life was associated with increased risk of transient wheeze and wheezing in early life. Current report of mouse exposure was also significantly associated with current wheeze throughout the first 7 years of life in the longitudinal analysis (P = 0.03 for overall relation of current mouse to current wheeze). However, early life mouse exposure did not predict asthma, eczema or allergic rhinitis at age 7 years. Exposure to detectable levels of mouse urinary protein in house dust samples collected at age 2-3 months was associated with a twofold increase in the odds of atopy (sensitization to >=1 allergen) at school age (95% confidence interval for odds ratio = 1.1-3.7; P = 0.03 in a multivariate analysis. Conclusions: Among children with parental history of asthma or allergies, current mouse exposure is associated with increased risk of wheeze during the first 7 years of life. Early mouse exposure was associated with early wheeze and atopy later in life. © 2008 The Authors.

Phyu, YL, Warne, MSJ & Lim, RP 2008, 'Assessing the biological relevance of exposing freshwater organisms to atrazine and molinate in environmentally realistic exposure test systems', ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, vol. 27, no. 2, pp. 420-424.
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Assessing the toxicity of chemicals in treated laboratory water may not accurately represent the toxicity of chemicals in natural aquatic systems. In natural water, dissolved organic matter, suspended particulate matter, and sediment play key roles in the sorption of contaminants from the water. Our previously published series of papers illustrated that the presence of sediment in aquatic toxicity testing systems significantly (p < 0.05) reduced the bioavailability of the herbicides atrazine and molinate to five Australian freshwater organisms. It is not clear whether the reduced bioavailability means that the trigger values (TVs) in the current Australian and New Zealand water quality guidelines, which are calculated using toxicity data from water-only toxicity tests, provide appropriate environmental protection. Several new sets of TVs were derived in the present study and were compared to each other and to the current Australian and New Zealand TVs for atrazine and molinate. The current Australian and New Zealand TVs for atrazine and molinate provided appropriate protection to Australian freshwater species. Australian freshwater species have a sensitivity distribution similar to those of overseas species to atrazine and molinate

Pissuwan, D, Valenzuela, SM & Cortie, MB 2008, 'Prospects for Gold Nanorod Particles in Diagnostic and Therapeutic Applications', BIOTECHNOLOGY AND GENETIC ENGINEERING REVIEWS, VOL 25, vol. 25, pp. 93-112.
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Rod-shaped gold nanoparticles ('nanorods') have recently attracted widespread attention due to their unique optical properties and facile synthesis. In particular, they can support a longtudinal surface plasmon, which results in suspensions of themhaving a strong extinction peak in the upper visible or near-infrared parts of the spectrum. The position of this peak can be readily tuned by controlling the shape of the rods. In addition, the surface of the nanorods can be functionalised by a very wide variety of molecules. This has led to interest in their use as selctive biomarkers in biodiagnostics or for selective targeting in photothermal therapeutics. Here we review the recent advances in the use of gold nanoparticles in these applications. additionally the information available regarding their biocompatibility in discussed.

Powter, DM & Gladstone, W 2008, 'Demographic analysis of the Port Jackson shark Heterodontus portusjacksoni in the coastal waters of eastern Australia', MARINE AND FRESHWATER RESEARCH, vol. 59, no. 5, pp. 444-455.
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Demographic analyses are used to assess the status and vulnerability of elasmobranchs but their accuracy is often affected by limited basic biological information. Although the Port Jackson shark Heterodontus portusjacksoni (Meyer) is currently not considered at threat, there is insufficient data for eastern Australia to assess this rigorously. The present study determined vital demographic rates of adult and juvenile H. portusjacksoni at four locations on the central and southern coast of New South Wales, Australia from January 2002 to December 2005 using underwater visual census, tagrecapture and samples obtained from a commercial fishery. Natural mortality was low in adults (0.0630.074 year1) and juveniles (0.225 year1), but substantial at the embryonic stage (0.7830.896 year1). Adult growth rates (31.432.7 mm year1) were slightly less than that of juveniles (36.837.5 mm year1). Males at both stages grew slightly faster than females. However, H. portusjacksoni had slower growth rates than many other elasmobranch species. Having a low intrinsic rate of increase (r = 0.069 year1), long generation times (µ1 = 22.5 year) and a low rebound potential, adults are the stage with the greatest impact on population growth. Hence, their life history strategy makes them susceptible to serious decline under exploitation, and management should strive to maintain the adult reproductive stock as a priority.

Powter, DM & Gladstone, W 2008, 'Embryonic mortality and predation on egg capsules of the Port Jackson shark Heterodontus portusjacksoni (Meyer)', JOURNAL OF FISH BIOLOGY, vol. 72, no. 3, pp. 573-584.
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Egg capsules of the Port Jackson shark Heterodontus portusjacksoni were examined during underwater visual census surveys at two sites in New South Wales, Australia, during the 20022005 reproductive seasons (austral winter). Embryonic mortality was high (0·7830·896 per annum) with the majority (99·2%) resulting from predation. The crested horn shark Heterodontus galeatus and common tent shell Astralium tentoriformis (Gastropoda, Turbinidae) were positively identified as egg predators. Gastropod predation was insignificant, accounting for only 2·0 and 2·1% of total mortality at Terrigal Haven and Dent Rock, respectively. Most capsules appeared to have been depredated by large predatory fishes with the eastern blue groper Achoerodus viridis (Labridae) and the black stingray Dasyatis thetidis (Dasyatidae) as possible candidate predators. The rate of embryonic mortality in H. portusjacksoni is higher than that reported for other oviparous elasmobranchs. This high level of mortality has significant consequences for the conservation and management of this species, especially when combined with an understanding of their low fecundity, late maturity and protracted reproductive life.

Powter, DM & Gladstone, W 2008, 'Habitat preferences of Port Jackson sharks, Heterodontus portusjacksoni, in the coastal waters of Eastern Australia', Proceedings of the Linnean Society of New South Wales, vol. 129, pp. 151-165.
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The habitat preferences of juvenile and adult Heterodontus portusjacksoni and ovipositing females were determined from three locations on the central and southern coast of New South Wales. Adults use shallow coastal rocky reefs in July-November for mating and oviposition, whilst juveniles occupy a seagrass nursery in a large coastal embayment. The sand/reef interface on the lee side of reefs was preferred by both sexes, probably as a refuge against strong water movements. Adult females also preferred rocky gutters when available, possibly as a male avoidance strategy. Preferred oviposition sites were narrow, shallow crevices (single capsules) or deep, narrow crevices (multiple capsules) which afforded protection against mechanical dislocation and/or predation. Juveniles exhibited a strong preference for the seagrass bed edge within a shallow nursery area. The visual complexity of this habitat combined with the juvenile's disruptive colouration may provide a refuge from predation, whilst proximity to the seagrass may provide ease of access for foraging. At a large scale, juveniles preferred areas of moderate slope within the nursery that provided protection from strong water movement. This study highlights the need for quantitative studies addressing habitat preferences and a consideration of use-specific factors to fully understand the selection of habitat by elasmobranchs.

Powter, DM & Gladstone, W 2008, 'The reproductive biology and ecology of the Port Jackson shark Heterodontus portusjacksoni in the coastal waters of eastern Australia', JOURNAL OF FISH BIOLOGY, vol. 72, no. 10, pp. 2615-2633.
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The reproductive biology and ecology of the Port Jackson shark Heterodontus portusjacksoni was investigated at three locations on the central and southern coast of New South Wales (NSW), Australia from January 2002 to December 2005 using underwater visual census surveys and samples obtained from a commercial fishery. Adults displayed sexual dimorphism in total length (LT) at sexual maturity, with males maturing between 762 and 772 mm LT and females between 902 and 905 mm LT. The mean ovarian fecundity was estimated at 16 offspring per female but was unrelated to female LT. Male gonado-somatic (IG) and hepato-somatic (IH) indices and female IG declined from July to November as did maximum ovarian follicle diameter and the diameter of the three largest follicles. Adults were absent from inshore reefs between December and July. Hence, H. portusjacksoni has a synchronous annual breeding season in NSW, which occurs between July and November (the austral winter to spring), with a peak in oviposition from August to October. Heterodontus portusjacksoni copulatory and ovipository behaviour are reported for the first time. Copulation was observed and involved oral grasping of the females pectoral fin by a single male, which wrapped his body around hers to insert one clasper. Ovipositing females appeared to search crevices in the reef prior to delivering a single capsule, which was washed into the crevice by water movement, with the female departing very soon after oviposition. This study represents the first rigorously quantitative analysis of H. portusjacksoni reproductive biology and ecology in NSW waters

Quante, T, Ng, YC, Ramsay, EE, Henness, S, Allen, JC, Parmentier, J, Ge, Q & Ammit, AJ 2008, 'Corticosteroids Reduce IL-6 in ASM Cells via Up-Regulation of MKP-1', American Journal of Respiratory Cell and Molecular Biology, vol. 39, no. 2, pp. 208-217.
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Ramaswamy, Y, Wu, C, Van Hummel, A, Combes, V, Grau, G & Zreiqat, H 2008, 'The responses of osteoblasts, osteoclasts and endothelial cells to zirconium modified calcium-silicate-based ceramic', Biomaterials, vol. 29, no. 33, pp. 4392-4402.
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Ramsay, HA & Leslie, LM 2008, 'The Effects of Complex Terrain on Severe Landfalling Tropical Cyclone Larry (2006) over Northeast Australia', Monthly Weather Review, vol. 136, no. 11, pp. 4334-4354.
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Abstract The interaction between complex terrain and a landfalling tropical cyclone (TC) over northeastern Australia is investigated using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5). Severe TC Larry (in March 2006) made landfall over an area of steep coastal orography and caused extensive damage. The damage pattern suggested that the mountainous terrain had a large influence on the TC wind field, with highly variable damage across relatively small distances. The major aims in this study were to reproduce the observed features of TC Larry, including track, intensity, speed of movement, size, decay rate, and the three-dimensional wind field using realistic high-resolution terrain data and a nested grid with a horizontal spacing of 1 km for the finest domain (referred to as CTRL), and to assess how the above parameters change when the terrain height is set to zero (NOTOPOG). The TC track for CTRL, including the timing and location of landfall, was in close agreement with observation, with the model eye overlapping the location of the observed eye at landfall. Setting the terrain height to zero resulted in a more southerly track and a more intense storm at landfall. The orography in CTRL had a large impact on the TC’s 3D wind field, particularly in the boundary layer where locally very high wind speeds, up to 68 m s−1, coincided with topographic slopes and ridges. The orography also affected precipitation, with localized maxima in elevated regions matching observed rainfall rates. In contrast, the precipitation pattern for the NOTOPOG TC was more symmetric and rainfall totals decreased rapidly with distance from the storm’s center. Parameterized maximum surface wind gusts were located beneath strong boundary layer jets. Finally, small-scale banding features were evident in the surface wind field over land for the NOTOPOG TC, owin...

Ramsay, HA, Leslie, LM, Lamb, PJ, Richman, MB & Leplastrier, M 2008, 'Interannual Variability of Tropical Cyclones in the Australian Region: Role of Large-Scale Environment', Journal of Climate, vol. 21, no. 5, pp. 1083-1103.
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AbstractThis study investigates the role of large-scale environmental factors, notably sea surface temperature (SST), low-level relative vorticity, and deep-tropospheric vertical wind shear, in the interannual variability of November–April tropical cyclone (TC) activity in the Australian region. Extensive correlation analyses were carried out between TC frequency and intensity and the aforementioned large-scale parameters, using TC data for 1970–2006 from the official Australian TC dataset. Large correlations were found between the seasonal number of TCs and SST in the Niño-3.4 and Niño-4 regions. These correlations were greatest (−0.73) during August–October, immediately preceding the Australian TC season. The correlations remain almost unchanged for the July–September period and therefore can be viewed as potential seasonal predictors of the forthcoming TC season. In contrast, only weak correlations (&lt;+0.37) were found with the local SST in the region north of Australia where many TCs originate; these were reduced almost to zero when the ENSO component of the SST was removed by partial correlation analysis. The annual frequency of TCs was found to be strongly correlated with 850-hPa relative vorticity and vertical shear of the zonal wind over the main genesis areas of the Australian region. Furthermore, correlations between the Niño SST and these two atmospheric parameters exhibited a strong link between the Australian region and the Niño-3.4 SST. A principal component analysis of the SST dataset revealed two main modes of Pacific Ocean SST variability that match very closely with the basinwide patterns of correlations between SST and TC frequencies. Finally, it is shown that the correlations can be increased markedly (e.g., from −0.73 to −0.80 for the August–October period) by a weighted combination of SST time series from weakly correlated regions.

Ranjbartoreh, AR, Wang, GX, Ghorbanpour Arani, A & Loghman, A 2008, 'Comparative consideration of axial stability of single- and double-walled carbon nanotube and its inner and outer tubes', Physica E: Low-dimensional Systems and Nanostructures, vol. 41, no. 2, pp. 202-208.
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The variations of critical axial forces for the inner and outer tubes of the double-walled carbon nanotube (DWCNT) in different buckling modes are studied in this paper. The effects of growth in the radius, length, and aspect ratio (length/radius) on the stability of a DWCNT and its inner and outer tubes are also considered, while the effects of the surrounding elastic medium on the outer tube and the van der Waals forces between two adjacent tubes are taken into account. Comparison between the DWCNT as a whole, its outer tube, inner tube, and single-walled carbon nanotube (SWCNT) indicates that the critical axial force of the inner tube of a DWCNT is almost two times more than the critical axial force of a SWCNT, showing the positive effect of the van der Waals interaction on the inner tube, DWCNT surrounded by an elastic medium has greater axial stability than DWCNT, without the surrounding elastic medium. This study demonstrates that the critical axial force of DWCNT is larger than for SWCNT, and it rises as the radius and aspect ratio increase. © 2008 Elsevier B.V. All rights reserved.

Rasko, DA, Rosovitz, MJ, Myers, GSA, Mongodin, EF, Fricke, WF, Gajer, P, Crabtree, J, Sebaihia, M, Thomson, NR, Chaudhuri, R, Henderson, IR, Sperandio, V & Ravel, J 2008, 'The Pangenome Structure ofEscherichia coli: Comparative Genomic Analysis ofE. coliCommensal and Pathogenic Isolates', Journal of Bacteriology, vol. 190, no. 20, pp. 6881-6893.
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ABSTRACTWhole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content ofEscherichia coli. Six distinctE. colipathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenicE. coli, enteropathogenicE. coli, and enteroaggregativeE. coli. We also determined the first genome sequence of a human commensalE. coliisolate,E. coliHS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenicE. coli. Comparison of 17E. coligenomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate thatE. coligenomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the speciesE. coli, while descriptive, should provide the basis for future ...

Rawling, T, Buchholz, F & McDonagh, AM 2008, 'Convenient Synthesis and Purification of [Bu4N]2[Ru(4-carboxy-4-carboxylate-2,2′-bipyridine)2(NCS)2]: a Landmark DSC Dye', Australian Journal of Chemistry, vol. 61, no. 6, pp. 405-405.
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We present here a convenient synthesis of the landmark dye-sensitized solar cell dye [Bu4N]2[Ru(4-carboxy-4-carboxylate-2,2′-bipyridine)2(NCS)2] (N719). Key to this synthetic procedure is the protection of the carboxyl functionalities with iso-butyl ester groups. This strategy allows the use of silica chromatography to remove the less efficient S-bound isomers and significantly reduces the time and difficulty of the synthesis.

Rawling, T, McDonagh, AM & Colbran, SB 2008, 'Synthesis, electrochemistry and spectroscopic properties of ruthenium phthalocyanine and naphthalocyanine complexes with triphenylarsine ligands', Inorganica Chimica Acta, vol. 361, no. 1, pp. 49-55.
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The synthesis, electrochemistry and spectroscopic properties of [PcRu(AsPh3)2] (1) and [{(tBu)4Nc}Ru(AsPh3)2] (2), where Pc = phthalocyanine and Nc = naphthalocyanine are reported. These complexes are the first examples of metal phthalocyanine and naphthalocyanine complexes with axially-coordinated arsine ligands. The AsPh3 ligands readily dissociate in non-coordinating solvents with 2 showing more rapid dissociation. In cyclic voltammetry experiments, 1 displayed three macrocycle-centred redox processes; one reduction and two oxidation processes. One reduction and three oxidation processes were observed for 2. The reduction and first oxidation are assigned to macrocycle-centred processes. The UV-Vis spectra of both complexes recorded over time showed macrocycle-centred oxidation. The oxidation was hindered by removing dioxygen from the solvent or adding excess AsPh3. © 2007 Elsevier B.V. All rights reserved.

Rawson, CA, Lim, RP & Warne, MSJ 2008, 'Skeletal morphology and maturation of male Gambusia holbrooki exposed to sewage treatment plant effluent', ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, vol. 70, no. 3, pp. 453-461.
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Sewage effluent has been identified as a major source of endocrine disrupting chemicals (EDCs) in the aquatic environment. The modified hemal spines (modified skeletal structures important in reproduction) of mosquitofish, Gambusia spp. have been shown to be under androgenic control and to be affected by exposure to estrogen. The current study aimed to investigate the effects of two sewage treatment plants (STPs) in Sydney, Australia on the morphology of hemal spines in populations of Gambusia holbrooki and on the ability of the fish to reach sexual maturity. The effluent from the two STPs had different effects on the hemal spines of males. At St. Marys differences in hemal spine morphology between fish upstream and downstream of the STP were not attributable to effluent from the STP. At Quakers Hill, results suggest that the effluent is generally estrogenic to G. holbrooki. There was a decrease in the proportion of males that were morphologically mature downstream of both STPs indicating potential population level effects that were associated with the presence of the STPs. © 2008 Elsevier Inc. All rights reserved.

Raymond, JJ, van Oorschot, RAH, Walsh, SJ & Roux, C 2008, 'Trace DNA analysis: Do you know what your neighbour is doing?', Forensic Science International: Genetics, vol. 2, no. 1, pp. 19-28.
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Since 1997 the analysis of DNA recovered from handled objects or 'trace' DNA has become routine and is frequently demanded from crime scene examinations. However, this anlaysis often produces unpredictable results. The factors affecting the recovery of full profiles are numerous and include varying methods of collectiona nd analysis. Communication between forensic laboratories in Australia and New Zealand has been limited in the past due in some part to sheet distance. Because of its relatively small population and low number of forensic jurisdictions this region is in an excelllent position to provide a collective approach. However, the protocols training methods and research of each jurisdiction had not been widely exchanged. A survey was developed to benchmark the current practices involved in trace DNA analysis, aiming to provide information for training programs and research directions, and to identy factors contributing to the success or failure of the analysis.

Raymond, JJ, Walsh, SJ, van Oorschot, RAH, Gunn, PR, Evans, L & Roux, C 2008, 'Assessing trace DNA evidence from a residential burglary: Abundance, transfer and persistence', Forensic Science International: Genetics Supplement Series, vol. 1, no. 1, pp. 442-443.
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Reichel, MP & Ellis, JT 2008, 'Re-evaluating the economics of neosporosis control', VETERINARY PARASITOLOGY, vol. 156, no. 3-4, pp. 361-362.
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Reimers, JR, Wallace, BB & Hush, NS 2008, 'Towards a comprehensive model for the electronic and vibrational structure of the Creutz-Taube ion', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, vol. 366, no. 1862, pp. 15-31.
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Since the synthesis of the Creutz-Taube ion, the nature of its charge localization has been of immense scientific interest, this molecule providing a model system for the understanding of the operation of biological photosynthetic and electron-transfer processes. However, recent work has shown that its nature remains an open question. Many systems of this type, including photosynthetic reaction centres, are of current research interest, and thereby the Creutz-Taube ion provides an important chemical paradigm: the key point of interest is the details of how such molecules behave. We lay the groundwork for the construction of a comprehensive model for its chemical and spectroscopic properties. Advances are described in some of the required areas including: simulation of electronic absorption spectra; quantitative depiction of the large interaction of the ion's electronic description with solvent motions; and the physics of Ru-NH3 spectator-mode vibrations. We show that details of the solvent electron-phonon coupling are critical in the interpretation of the spectator-mode vibrations, as these strongly mix with solvent motions when 0.75<2J/λ<1. In this regime, a double-well potential exists which does not support localized zero-point vibration, and many observed properties of the Creutz-Taube ion are shown to be consistent with the hypothesis that the ion has this character. © 2007 The Royal Society.

Ren, D, Leslie, LM & Karoly, D 2008, 'Landslide Risk Analysis using a New Constitutive Relationship for Granular Flow', Earth Interactions, vol. 12, no. 4, pp. 1-16.
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AbstractIn this study, landslide potential is investigated, using a new constitutive relationship for granular flow in a numerical model. Unique to this study is an original relationship between soil moisture and the inertial number for soil particles. This numerical model can be applied to arbitrary soil slab profile configurations and to the analysis of natural disasters, such as mudslides, glacier creeping, avalanches, landslips, and other pyroclastic flows. Here the focus is on mudslides.The authors examine the effects of bed slope and soil slab thickness, soil layered profile configuration, soil moisture content, basal sliding, and the growth of vegetation, and show that increased soil moisture enhances instability primarily by decreasing soil strength, together with increasing loading. Moreover, clay soils generally require a smaller relative saturation than sandy soils for sliding to commence. For a stable configuration, such as a small slope and/or dry soil, the basal sliding is absorbed if the perturbation magnitude is small. However, large perturbations can trigger significant-scale mudslides by liquefying the soil slab.The role of vegetation depends on the wet soil thickness and the spacing between vegetation roots. The thinner the saturated soil layer, the slower the flow, giving the vegetation additional time to extract soil moisture and slow down the flow. By analyzing the effect of the root system on the stress distribution, it is shown that closer tree spacing increases the drag effects on the velocity field, provided that the root system is deeper than the shearing zone.Finally, the authors investigated a two-layer soil profile, namely, sand above clay. A significant stress jump occurs at the interface of the two media.

Ren, D, Leslie, LM & Karoly, DJ 2008, 'Sensitivity of an ecological model to soil moisture simulations from two different hydrological models', Meteorology and Atmospheric Physics, vol. 100, no. 1-4, pp. 87-99.
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Rice, SA, McDougald, D, Givskov, M & Kjelleberg, S 2008, 'Detection and Inhibition of Bacterial Cell–Cell Communication', Methods in Molecular Biology, vol. 431, pp. 55-68.
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Bacteria communicate with other members of their community through the secretion and perception of small chemical cues or signals. The recognition of a signal normally leads to the expression of a large suite of genes, which in some bacteria are involved in the regulation of virulence factors, and as a result, these signaling compounds are key regulatory factors in many disease processes. Thus, it is of interest when studying pathogens to understand the mechanisms used to control the expression of virulence genes so that strategies might be devised for the control of those pathogens. Clearly, the ability to interfere with this process of signaling represents a novel approach for the treatment of bacterial infections. There is a broad range of compounds that bacteria can use for signaling purposes, including fatty acids, peptides, N-acylated homoserine lactones, and the signals collectively called autoinducer 2 (AI-2). This chapter will focus on the latter two signaling systems as they are present in a range of medically relevant bacteria, and here we describe assays for determining whether an organism produces a particular signal and assays that can be used to identify inhibitors of the signaling cascade. Lastly, the signal detection and inhibition assays will be directly linked to the expression of virulence factors of specific pathogens. © Humana Press.

Robertson, M, Helliwell, CA & Dennis, ES 2008, 'Post-Translational Modifications of the Endogenous and Transgenic FLC Protein in Arabidopsis thaliana', PLANT AND CELL PHYSIOLOGY, vol. 49, no. 12, pp. 1859-1866.
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FLC is a MADS box transcription factor that acts as a dosage-dependent repressor of flowering. We carried out a 2D gel analysis and showed that the majority of endogenous FLC and overexpressed FLC-FLAG proteins are post-translationally modified. The endogenous and transgenic proteins have different floral repressor activities; however, they have similar, if not the same, profiles of post-translational modifications. The protein modification profile was also not changed by vernalization treatment. The activities of other MADS box proteins have been shown to be affected by phosphorylation and we found that both the endogenous FLC and the transgenic FLC-FLAG protein are phosphorylated. When eight potential serine kinase target sites in FLC were changed to mimic phosphorylated residues, expression of the mutant FLC-FLAG protein led to early flowering, suggesting that the repressive function was abolished. When the same eight serine residues were changed to non-phosphorylatable residues, expression of the resulting protein gave the same weak flowering repression as overexpressed unmodified FLC-FLAG. The non-phosphorylatable variant of FLC-FLAG showed a similar spectrum of post-translational modifications to unmodified FLC-FLAG, indicating that modifications other than the predicted phosphorylations occur. Our data provide evidence for a post-translational regulation of FLC function.

Robinson, MW, Dalton, JP & Donnelly, S 2008, 'Helminth pathogen cathepsin proteases: it's a family affair', TRENDS IN BIOCHEMICAL SCIENCES, vol. 33, no. 12, pp. 601-608.
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Helminth pathogens express papain-like cysteine peptidases, termed cathepsins, which have important roles in virulence, including host entry, tissue migration and the suppression of host immune responses. The liver fluke Fasciola hepatica, an emerging human pathogen, expresses the largest cathepsin L cysteine protease family yet described. Recent phylogenetic, biochemical and structural studies indicate that this family contains five separate clades, which exhibit overlapping but distinct substrate specificities created by a process of gene duplication followed by subtle residue divergence within the protease active site. The developmentally regulated expression of these proteases correlates with the passage of the parasite through host tissues and its encounters with different host macromolecules. © 2008 Elsevier Ltd. All rights reserved.

Robinson, MW, Tort, JF, Lowther, J, Donnelly, SM, Wong, E, Xu, W, Stack, CM, Padula, M, Herbert, B & Dalton, JP 2008, 'Proteomics and phylogenetic analysis of the cathepsin L protease family of the helminth pathogen Fasciola hepatica', MOLECULAR & CELLULAR PROTEOMICS, vol. 7, no. 6, pp. 1111-1123.
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Cathepsin L proteases secreted by the helminth pathogen Fasciola hepatica have functions in parasite virulence including tissue invasion and suppression of host immune responses. Using proteomics methods alongside phylogenetic studies we characterized the profile of cathepsin L proteases secreted by adult F. hepatica and hence identified those involved in host-pathogen interaction. Phylogenetic analyses showed that the Fasciola cathepsin L gene family expanded by a series of gene duplications followed by divergence that gave rise to three clades associated with mature adult worms (Clades 1, 2, and 5) and two clades specific to infective juvenile stages (Clades 3 and 4). Consistent with these observations our proteomics studies identified representatives from Clades 1, 2, and 5 but not from Clades 3 and 4 in adult F. hepatica secretory products. Clades 1 and 2 account for 67.39 and 27.63% of total secreted cathepsin Ls, respectively, suggesting that their expansion was positively driven and that these proteases are most critical for parasite survival and adaptation. Sequence comparison studies revealed that the expansion of cathepsin Ls by gene duplication was followed by residue changes in the S2 pocket of the active site. Our biochemical studies showed that these changes result in alterations in substrate binding and suggested that the divergence of the cathepsin L family produced a repertoire of enzymes with overlapping and complementary substrate specificities that could cleave host macromolecules more efficiently. Although the cathepsin Ls are produced as zymogens containing a prosegment and mature domain, all secreted enzymes identified by MS were processed to mature active enzymes. The prosegment region was highly conserved between the clades except at the boundary of prosegment and mature enzyme. Despite the lack of conservation at this section, sites for exogenous cleavage by asparaginyl endopeptidases and a Leu-Ser ↓ His motif for autocatalytic...

Rodgers, KJ & Shiozawa, N 2008, 'Misincorporation of amino acid analogues into proteins by biosynthesis', INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, vol. 40, no. 8, pp. 1452-1466.
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Despite astounding diversity in their structure and function, proteins are constructed from 22 protein or 'canonical' amino acids. Hundreds of amino acid analogues exist; many occur naturally in plants, some are synthetically produced or can be produced

Rodgers, KJ, Watkins, DJ, Miller, AL, Chan, PY, Karanam, S, Brissette, WH, Long, CJ & Jackson, CL 2008, 'Destabilizing role of cathepsin S in murine atherosclerotic plaques (vol 26, pg 851, 2006)', ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, vol. 28, no. 5.
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Roff, G, Ulstrup, KE, Fine, M, Ralph, PJ & Hoegh-Guldberg, O 2008, 'Spatial heterogeneity of photosynthetic activity within diseased corals from the great barrier reef', JOURNAL OF PHYCOLOGY, vol. 44, no. 2, pp. 526-538.
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Morphological diagnosis and descriptions of seven disease-like syndromes affecting scleractinian corals were characterized from the southern Great Barrier Reef (GBR). Chl a fluorescence of PSII was measured using an Imaging-PAM (pulse amplitude modulated) fluorometer, enabling visualization of the two-dimensional variability in the photophysiology of endosymbiotic dinoflagellates (zooxanthellae) by measuring rapid light curves. Three of four syndromes associated with active tissue loss (type a) were spatially homogenous (white syndrome, brown band, and skeletal eroding band), with no impact on the photochemical function of zooxanthellae populations at or behind the lesion borders. However, a decline in maximum quantum yield (Fv/F m) and elevated levels of maximum nonphotochemical quenching (NPQmax) occurred in visually healthy tissue of black band disease adjacent to the lesion borders, possibly due to hypoxic conditions caused by the black band cyanobacterial mat. Two out of three syndromes associated with pathological change of intact tissue with no active tissue loss (type b) showed variable photophysiological responses (neoplasia and pigmentation response). Only the bleached foci associated with white patch syndrome appeared to impact primarily on the symbiotic dinoflagellates, as evidenced by declines in minimum fluorescence (F0) and maximum quantum yield (Fv/F m), with no indication of degeneration in the host tissues. Our results suggest that for the majority of coral syndromes from the GBR, pathogenesis occurs in the host tissue, while the impact on the zooxanthellae populations residing in affected corals is minimal. © 2008 Phycological Society of America.

Rong, YF, Lou, WH & Jin, DY 2008, 'Pancreatic tuberculosis with splenic tuberculosis mimicking advanced pancreatic cancer with splenic metastasizes: a case report', Cases Journal, vol. 1, no. 1.
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Abstract A 60-year-old woman presented with vague abdominal pain for one week was referred to pancreatic tail carcinoma accompanied with splenic metastasizes. She came to our hospital for further treatment. Ultrasonography and abdominal computed tomography (CT) revealed a pancreatic tail tumor with splenic metastasizes. There was no history of tuberculosis. Laparotomy was performed because pancreatic tail carcinoma with splenic metastasizes was highly suspected. Indurated mass in the pancreatic tail and sporadic metastasizes in the spleen had been found during the surgery. The pancreatic tail and the spleen were removed and proved to be tuberculosis on histological examination of a frozen section. The patient was given antituberculosis therapy and is now getting well. Tuberculosis should be considered in the differential diagnosis of pancreatic masses. The response to antituberculosis treatment is very favorable.

Ross, ON, Moore, CM, Suggett, DJ, MacIntyre, HL & Geider, RJ 2008, 'A model of photosynthesis and photo‐protection based on reaction center damage and repair', Limnology and Oceanography, vol. 53, no. 5, pp. 1835-1852.
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Phytoplankton photosynthesis under the rapidly fluctuating irradiance which results from turbulent mixing through the vertical light gradient is poorly understood. Ship‐based measurements often apply the fast repetition rate fluorescence (FRRF) technique in situ or in vivo to gauge the physiological state of the phytoplankton community and infer some of the physical properties of the water column (such as mixing time scales). We describe the development and validation of a model of photosynthetic electron turnover at photosystemII with consideration of downstream limitation, based on the redox state of photosystem II. We also include empirical formulations for slower processes such as photo‐protection (from nonphotochemical quenching) and photo‐inhibition. By confronting the simple model with laboratory data for Dunaliella tertiolecta, we were able to refine the model so that it faithfully produced rates of photosynthetic electron transfer determined by FRR fluorescence. Further, we were able to validate the model estimates of linear photosynthetic electron transfer rates against completely independent measurements obtained using 14C‐bicarbonate assimilation in photosynthesis‐light curves.

ROUX, C 2008, 'La communauté juive de Tarascon au XVe siècle', Revue des Études Juives, vol. 167, no. 3, pp. 511-569.
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Ryan, L 2008, 'Combining data from multiple sources, with applications to environmental risk assessment', STATISTICS IN MEDICINE, vol. 27, no. 5, pp. 698-710.
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The classical statistical paradigm emphasizes the development and application of methods to account for sampling variability. Many modern day applications, however, require consideration of other sources of uncertainty that are not so easy to quantify. This paper presents a case study involving an assessment of the impact of in-utero methylmercury exposure on the Intelligence Quotient (IQ) of young children. We illustrate how familiar techniques such as hierarchical modeling, Bayesian methods and sensitivity analysis can be used to aid decision making in settings that involve substantial uncertainty. Copyright © 2007 John Wiley & Sons, Ltd.

Ryan, NJ, Mitrovic, SM & Bowling, LC 2008, 'Temporal and spatial variability in the phytoplankton community of Myall Lakes, Australia, and influences of salinity', HYDROBIOLOGIA, vol. 608, no. 1, pp. 69-86.
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The variability in the phytoplankton communities of the Myall Lakes, a series of four interconnected coastal lakes on the lower north coast of New South Wales, was studied between 1999 and 2002. There was considerable spatial variability across the lake system. Bombah Broadwater experienced blooms of Anabaena in 1999 and early 2000, but these were replaced from late 2000 onwards by Chroococcus and a variety of eukaryotic taxa, particularly flagellates and diatoms. In comparison, the phytoplankton community of Myall Lake was dominated for much of the study period by Chroococcus, Merismopedia and chlorophyte taxa. The sites located midway between these two main lakes represent an ecotone, with elements of the phytoplanktonic flora of both main lakes being present. Changes in phytoplankton community composition in Bombah Broadwater occurred fairly frequently. In contrast, the phytoplankton community in Myall Lake changed little during the course of the study and can be considered as being at long-term equilibrium. The reasons for this lie in the morphology and hydrology of the lake system, which in turn create gradients in a number of physico-chemical water quality attributes. Bombah Broadwater is influenced by episodic and stochastic freshwater inflows from the upper Myall River catchment, and in times of drought by saline marine incursions via the lower Myall River. Myall Lake however represents a cul-de-sac, with only a small hydraulic connection to the remainder of the lake system. As it has little input from its small catchment, the limnological conditions within this lake remain relatively constant for long periods of time.

Sastraruji, T, Kotabin, N, Jatisatienr, C, Dheeranupattana, S, Pyne, SG & Ung, AT 2008, 'Phytochemical studies on Stemona plants: biological activities of some stemofoline alkaloids', Planta Medica, vol. 74, no. 09.
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Scheidl, T, Ursin, R, Kofler, J, Ramelow, S, Ma, X-S, Herbst, T, Ratschbacher, L, Fedrizzi, A, Langford, NK, Jennewein, T & Zeilinger, A 2008, 'Violation of local realism with freedom of choice', Proc. Natl. Acad. Sci. USA, vol. 107, no. 46, pp. 19708-19713.
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Bell's theorem shows that local realistic theories place strong restrictionson observable correlations between different systems, giving rise to Bell'sinequality which can be violated in experiments using entangled quantum states.Bell's theorem is based on the assumptions of realism, locality, and thefreedom to choose between measurement settings. In experimental tests,'loopholes' arise which allow observed violations to still be explained bylocal realistic theories. Violating Bell's inequality while simultaneouslyclosing all such loopholes is one of the most significant still open challengesin fundamental physics today. In this paper, we present an experiment thatviolates Bell's inequality while simultaneously closing the locality loopholeand addressing the freedom-of-choice loophole, also closing the latter within areasonable set of assumptions. We also explain that the locality andfreedom-of-choice loopholes can be closed only within non-determinism, i.e. inthe context of stochastic local realism.

Schmidt, T & Novikov, A 2008, 'A Structural Model with Unobserved Default Boundary', Applied Mathematical Finance, vol. 15, no. 2, pp. 183-203.
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A firm-value model similar to the one proposed by Black and Cox (1976) is considered. Instead of assuming a constant and known default boundary, the default boundary is an unobserved stochastic process. This process has a Brownian component, reflecting the influence of uncertain effects on the precise timing of the default, and a jump component, which relates to abrupt changes in the policy of the company, exogenous events or changes in the debt structure. Interestingly, this setup admits a default intensity, so the reduced form methodology can be applied.

Schultz, TJ, Webb, JK & Christian, KA 2008, 'The physiological cost of pregnancy in a tropical viviparous snake', COPEIA, vol. 2008, no. 3, pp. 637-642.
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During pregnancy, the metabolic rate of females may increase above basal levels to support metabolically active tissues and developing embryos. In mammals, this energetic cost of supporting the pregnancy (MCP) is an important component of reproductive effort, but less is known about the magnitude of this cost in ectothermic vertebrates. We estimated the metabolic cost of supporting pregnancy In a tropical viviparous snake, the Northern Death Adder, Acanthophis praelongus. We measured the metabolic rates of non-gravid and gravid females throughout gestation and following parturition. We also measured the oxygen consumption of a sample of neonates from each clutch within 24 h of birth. The metabolic rate of gravid females rose slowly during pregnancy, but was significantly elevated during the last three weeks of gestation. Considering the late term metabolism of gravid females as 100%, then the baseline metabolism of female Death Adders represented 36.6%, embryo metabolism accounted for 37.0%, and the cost of supporting the pregnancy was 26.4% of the total metabolic rate. Neonate metabolism during the first 24 h of birth was 2.9 times higher than the estimate for embryo metabolism. Thus, our results do not support the assumption that the metabolism of embryos (prior to birth) and neonates is similar in this species. Although gravid female Death Adders maintain high and constant body temperatures during late gestation, the energetic cost of supporting the pregnancy is only a minor component of the total reproductive effort for females of this species. © 2008 by the American Society of Ichthyologists and Herpetologists.

Schwartz, J, Coull, B, Laden, F & Ryan, L 2008, 'The effect of dose and timing of dose on the association between airborne particles and survival', ENVIRONMENTAL HEALTH PERSPECTIVES, vol. 116, no. 1, pp. 64-69.
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Background: Understanding the shape of the concentration-response curve for particles is important for public health, and lack of such understanding was recently cited by U.S. Environmental Protection Agency (EPA) as a reason for not tightening the standards. Similarly, the delay between changes in exposure and changes in health is also important in public health decision making. We addressed these issues using an extended follow-up of the Harvard Six Cities Study. Methods: Cox proportional hazards models were fit controlling for smoking, body mass index, and other covariates. Two approaches were used. First, we used penalized splines, which fit a flexible functional form to the concentration response to examine its shape, and chose the degrees of freedom for the curve based on Akaike's information criterion. Because the uncertainties around the resultant curve do not reflect the uncertainty in model choice, we also used model averaging as an alternative approach, where multiple models are fit explicitly and averaged, weighted by their probability of being correct given the data. We examined the lag relationship by model averaging across a range of unconstrained distributed lag models. Results: We found that the concentration-response curve is linear, clearly continuing below the current U.S. standard of 15 μg/m3, and that the effects of changes in exposure on mortality are seen within two years. Conclusions: Reduction in particle concentrations below U.S. EPA standards would increase life expectancy.

Schwartz, TS, Murray, S & Seebacher, F 2008, 'Novel reptilian uncoupling proteins: molecular evolution and gene expression during cold acclimation', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 275, no. 1637, pp. 979-985.
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Many animals upregulate metabolism in response to cold. Uncoupling proteins (UCPs) increase proton conductance across the mitochondrial membrane and can thereby alleviate damage from reactive oxygen species that may form as a result of metabolic upregulation. Our aim in this study was to determine whether reptiles (Crocodylus porosus) possess UCP genes. If so, we aimed to place reptilian UCP genes within a phylogenetic context and to determine whether the expression of UCP genes is increased during cold acclimation. We provide the first evidence that UCP2 and UCP3 genes are present in reptiles. Unlike in other vertebrates, UCP2 and UPC3 are expressed in liver and skeletal muscle of the crocodile, and both are upregulated in liver during cold acclimation but not in muscle. We identified two transcripts of UCP3, one of which produces a truncated protein similar to the UCP3S transcript in humans, and the resulting protein lacks the predicted nucleotide-binding regulatory domain. Our molecular phylogeny suggests that uncoupling protein 1 (UCP1) is ancestral and has been lost in archosaurs. In birds, UCP3 may have assumed a similar function as UCP1 in mammals, which has important ramifications for understanding endothermic heat production. © 2008 The Royal Society.

Seebacher, F & Murray, S 2008, 'Detecting environmental change: Transient receptor potential ion channels control thermoregulatory behaviour in reptiles', Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, vol. 150, no. 3, pp. S170-S170.
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Seth, D, Hogg, PJ, Gorrell, MD, McCaughan, GW & Haber, PS 2008, 'Direct effects of alcohol on hepatic fibrinolytic balance: Implications for alcoholic liver disease', Journal of Hepatology, vol. 48, no. 4, pp. 614-627.
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Seymour, JR, Ahmed, T, Marcos & Stocker, R 2008, 'A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches', LIMNOLOGY AND OCEANOGRAPHY-METHODS, vol. 6, pp. 477-488.
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The nutrient environment experienced by planktonic microorganisms is patchy at spatiotemporal scales commensurate with their motility and the efficiency with which chemotactic microbes can exploit this heterogeneous seascape influences trophodynamics and nutrient cycling rates in aquatic environments.

Seymour, JR, Seuront, L, Doubell, MJ & Mitchell, JG 2008, 'Mesoscale and microscale spatial variability of bacteria and viruses during a Phaeocystis globosa bloom in the Eastern English Channel', ESTUARINE COASTAL AND SHELF SCIENCE, vol. 80, no. 4, pp. 589-597.
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Sampling was conducted within inshore and offshore sites, characterized by highly dissimilar hydrodynamic and hydrobiological conditions, in the Eastern English Channel. The eutrophic inshore site was dominated by the influence of a dense bloom of the Prymnesiophyceae phytoplankton species Phaeocystis globosa, while the offshore site was characterized by more oceanic conditions. Within each site the microscale distributions of chlorophyll a and several flow cytometrically-defined subpopulations of heterotrophic bacteria and viruses were measured at a spatial resolution of 5 cm. The inshore site was characterized by comparatively high levels of microscale spatial variability, with concentrations of chlorophyll a, heterotrophic bacteria, and viruses varying by 8, 11 and 3.5-fold respectively across distances of several centimeters. Within the offshore site, microscale distributions of chlorophyll a and bacteria were markedly less variable than within the inshore site, although viruses exhibited slightly higher levels of heterogeneity. Significant mesoscale variability was also observed when mean microbial parameters were compared between the inshore and offshore sites. However, when the extent of change (max/min and coefficient of variation) was compared between meso- and microscales, the variability observed at the microscale, particularly in the inshore site, was substantially greater. This pattern suggests that microscale processes associated with Phaeocystis globosa bloom dynamics can generate heterogeneity amongst microbial communities to a greater degree than large scale oceanographic discontinuities.

Shanmukaraj, D, Wang, GX, Liu, HK & Murugan, R 2008, 'Synthesis and characterization of SrBi4Ti4O15ferroelectric filler based composite polymer electrolytes for lithium ion batteries', Polymer Bulletin, vol. 60, no. 2-3, pp. 351-361.
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Composite polymer electrolytes (CPEs) based on poly (ethylene oxide) (PEO) (Mol.Wt ∼ 6×105) complexed with LiN(CF3SO 2)2 lithium salt and SrBi4Ti4O 15 ferroelectric ceramic filler have been prepared as films. Citrate gel technique and conventional solid state technique were employed for the synthesis of the ferroelectric fillers in order to study the effect of particle size of the filler on ionic conductivity of the polymer electrolyte. Characterization techniques such as X-ray diffraction (XRD), differential thermal analysis (DTA), scanning electron microscopy (SEM) and temperature dependant DC conductivity studies were taken for the prepared polymer composite electrolytes. The broadening of DTA endotherms on addition of ceramic fillers to the polymer salt complex indicated the reduction in crystallinity. An enhancement in conductivity was observed with the addition of SrBi 4Ti4O15 as filler to the (PEO) 8-LiN(CF3SO2)2 polymer salt complexes. Among the investigated samples (PEO)8-LiN(CF 3SO2)2 +10 wt% SrBi4Ti 4O15 (citrate gel) polymer composite exhibits a maximum conductivity. © 2007 Springer-Verlag.

Shanmukaraj, D, Wang, GX, Murugan, R & Liu, HK 2008, 'Electrochemical studies on LiFe1-xCoxPO4/carbon composite cathode materials synthesized by citrate gel technique for lithium-ion batteries', MATERIALS SCIENCE AND ENGINEERING B-ADVANCED FUNCTIONAL SOLID-STATE MATERIALS, vol. 149, no. 1, pp. 93-98.
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LiFePO4/carbon and LiFe1-xCoxPO4/carbon (x = 0.02, 0.04, 0.08 and 0.1) composite cathode materials were synthesized by citrate gel technique. X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to study the phase and morphology of un-doped and Co doped lithium iron phosphate/carbon composites. The SEM images revealed that the particles were agglomerated and the particle sizes were almost homogeneously distributed. The particle size was found to be between 200 and 300 nm from transmission electron microscopy. Cyclic voltammetric studies were taken to investigate the electrochemical performance of the prepared composite materials. The high intensity of the anodic and cathodic peaks indicates that Li-ions and electrons were participating actively in redox reactions due to the carbon coating. Charge/discharge studies carried out on a CR2032 coin cell revealed that the carbon coated LiFePO4/carbon composite exhibited an improved discharge capacity of 157 mAh/g at low rates. We found that cobalt doping does not have a favourable effect on the electrochemical performance of lithium iron phosphate cathode materials. © 2008 Elsevier B.V. All rights reserved.

Shanmukaraj, D, Wang, GX, Murugan, R & Liu, HK 2008, 'Ionic conductivity and electrochemical stability of poly(methylmethacrylate)–poly(ethylene oxide) blend-ceramic fillers composites', Journal of Physics and Chemistry of Solids, vol. 69, no. 1, pp. 243-248.
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The role of inorganic ceramic fillers namely nanosized Al2O3 (15-25 nm) and TiO2 (10-14 nm) and ferroelectric filler SrBi4Ti4O15 (SBT CIT) (0.5 μm) synthesized by citrate gel technique (CIT) on the ionic conductivity and electrochemical properties of polymer blend 15 wt% PMMA+PEO8:LiClO4+2 wt% EC/PC electrolytes were investigated. Enhancement in conductivity was obtained with a maximum of 0.72×10-5 S cm-1 at 21 °C for 2 wt% of SrBi4Ti4O15 (SBT CIT) composite polymer electrolyte. The lithium-ion transport number and the electrochemical stability of the composite polymer electrolytes at ambient temperature were analyzed. An enhancement in electrochemical stability was observed for polymer composites containing 2 wt% of SrBi4Ti4O15 (SBT CIT) as fillers. © 2007 Elsevier Ltd. All rights reserved.

Sheldon, CC, Hills, MJ, Lister, C, Dean, C, Dennis, ES & Peacock, WJ 2008, 'Resetting of FLOWERING LOCUS C expression after epigenetic repression by vernalization', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 6, pp. 2214-2219.
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The epigenetic repression of FLOWERING LOCUS C (FLC) in winter-annual ecotypes of Arabidopsis by prolonged cold ensures that plants flower in spring and not during winter. Resetting of the FLC expression level in progeny is an important step in the life cycle of the plant. We show that both the paternally derived and the maternally derived FLC:GUS genes are reset to activity but that the timing of their first expression differs. The paternal FLC:GUS gene in vernalized plants is expressed in the male reproductive organs, the anthers, in both somatic tissue and in the sporogenous pollen mother cells, but there is no expression in mature pollen. In the progeny generation, the paternally derived FLC:GUS gene is expressed in the single-celled zygote (fertilized egg cell) and through embryo development, but not in the fertilized central cell, which generates the endosperm of the progeny seed. FLC:GUS is not expressed during female gametogenesis, with the maternally derived FLC:GUS being first expressed in the early multicellular embryo. We show that FLC activity during late embryo development is a prerequisite for the repressive action of FLC on flowering. © 2008 by The National Academy of Sciences of the USA.

Shi, C, Jin, D & Lou, W 2008, 'Mixed acinar‐endocrine carcinomas of the pancreas: Case report and literature review', Surgical Practice, vol. 12, no. 3, pp. 89-92.
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Acinar cell carcinoma (ACC) of the pancreas is a rare primary tumour of the pancreas with poor prognosis. ACC represent less than 1% of all exocrine tumours of the pancreas. There are no established criteria to differentiate acinar cell carcinomas from non‐functioning neuroendocrine tumours or other malignant exocrine tumours by conventional histological examination. In recent years, some researchers have reported an unusual neoplasm called mixed acinar‐endocrine carcinoma of the pancreas (MAEC) since this entity was first reported in 1982. Until now, there have been less than 20 cases of MAEC reported in the English literature. We report here a case of mixed acinar‐endocrine carcinoma diagnosed and treated in our department and it is the first case of mixed acinar‐endocrine carcinoma ever reported in China.

Siboni, N, Ben Dov E, Sivan A & Kushmaro A 2008, 'Coral-associated ammonium oxidizing crenarchaeota and their role in the coral holobiont nitrogen cycle', Coral Reef Symp, Ft. Lauderdale, Florida, 7-11 July, vol. Session number 8.

Siboni, N, Ben-Dov, E, Sivan, A & Kushmaro, A 2008, 'Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle', ENVIRONMENTAL MICROBIOLOGY, vol. 10, no. 11, pp. 2979-2990.
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Diversity, distribution and genetic comparison of Archaea associated with the surface mucus of corals from three genera, namely Acanthastrea sp., Favia sp. and Fungia sp., from the Gulf of Eilat, Israel and from Heron Island, Australia were studied. Sequencing of the 16S rRNA gene of the coral-associated Archaea revealed dominance of Crenarchaeota (79%, on average). In this phylum, 87% of the sequences were similar (≥ 97%) to the Thermoprotei, with 76% of these being similar (≥ 97%) to the ammonium oxidizer, Nitrosopumilus maritimus. Most of the coral-associated euryarchaeotal sequences (69%) were related to marine group II, while other euryarchaeotal clades were found to be related to anaerobic methanotrophs (8%), anaerobic nitrate reducers (i.e. denitrification, 15%) and marine group III (8%). Most of the crenarchaeotal and euryarchaeotal coral-associated 16S rRNA gene sequences from Heron Island (61%) and from the Gulf of Eilat (71%) were closely related (≥ 97%) to sequences previously derived from corals from the Virgin Islands. Analysis of archaeal amoA sequences obtained from the fungiid coral, Fungia granulosa, divided into three clades, all related to archaeal sequences previously obtained from the marine environment. These sequences were distantly related to amoA sequences previously found in association with other coral species. Preliminary experiments suggest that there is active oxidation of ammonia to nitrite in the mucus of F. granulosa. Thus, coral-associated Archaea may contribute to nitrogen recycling in the holobiont, presumably by acting as a nutritional sink for excess ammonium trapped in the mucus layer, through nitrification and denitrification processes. © 2008 The Authors.

Sihvola, A & Lapine, M 2008, 'Editorial', Metamaterials, vol. 2, no. 2-3, pp. 53-53.
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Simpson, AM 2008, 'Gene Therapy Reverse Diabetes', Australasian Science, vol. April, pp. 23-25.

Simpson, AM & O'Brien, BA 2008, 'Diabetes therapy by lentiviral hepatic insulin gene expression without transformation of liver. Reply to Elsner M, Jorns A, Lenzen S [letter]', DIABETOLOGIA, vol. 51, no. 4, pp. 696-696.
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Sintic, PJ, E, W, Ou, Z, Shao, J, McDonald, JA, Cai, Z-L, Kadish, KM, Crossley, MJ & Reimers, JR 2008, 'Control of the site and potential of reduction and oxidation processes in pi-expanded quinoxalinoporphyrins', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, no. 4, pp. 515-527.
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Quinoxalino[2,3-b′]porphyrins are π-expanded porphyrins, having a quinoxaline fused to a β,β′-pyrrolic position of the porphyrin. They are used as components in systems proposed as 'molecular wires'. Knowledge of their redox properties is of value in the design of electron- or hole-conduction systems. In particular, the location of the charge density in the radical anions of quinoxalinoporphyrins can be modulated by peripheral functionalization. New theoretical treatments of electrochemical potentials are developed that identify the site of reduction in both the anions and the dianions of 33 quinoxalinoporphyrins. These molecules include free-base and metallated macrocycles substituted on the quinoxaline with electron-withdrawing groups (NO2, Cl, Br) and/or electron-donating groups (NH2, OCH3). Spectroelectrochemistry, density-functional theory calculations, and substituent-parameter models are used to verify the analysis. Five distinct patterns are observed for the locations of the first and second reductions; some of these patterns involve delocalized charges. Nitroquinoxalinoporphyrins with the nitro groups at the 5- and 6-quinoxaline positions are found to have quite different properties owing to distortions caused by peri interactions that force the nitro group of the 5-nitro regioisomer out of conjugation. Charge localization on the nitroquinoxaline fragment is found for some molecules, and this is attributed to ion-pairing with the 0.1 M tetrabutylammonium perchlorate electrolyte used, leading to the verified prediction that electron-paramagnetic resonance spectra of these molecules taken without the electrolyte yield delocalized anions. These properties enable the control of conduction through molecular wires synthesised from quinoxalinoporphyrins. © the Owner Societies.

Sintic, PJ, E, W, Ou, Z, Shao, J, McDonald, JA, Cai, Z-L, Kadish, KM, Crossley, MJ & Reimers, JR 2008, 'Control of the site and potential of reduction and oxidation processes in pi-expanded quinoxalinoporphyrins (vol 10, pg 268, 2008)', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, no. 48, pp. 7328-7328.

Sintic, PJ, Wenbo, E, Ou, Z, Shao, J, McDonald, JA, Cai, ZL, Kadish, KM, Crossley, MJ & Reimers, JR 2008, 'Back matter', Physical Chemistry Chemical Physics, vol. 10, no. 48, pp. 7324-7324.
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Sintic, PJ, Wenbo, E, Ou, Z, Shao, J, McDonald, JA, Cai, Z-L, Kadish, KM, Crossley, MJ & Reimers, JR 2008, 'Control of the site and potential of reduction and oxidation processes in pi-expanded quinoxalinoporphyrins', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, no. 2, pp. 515-527.
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Quinoxalino[2,3-b’]porphyrins are π-expanded porphyrins, having a quinoxaline fused to a β,β'-pyrrolic position of the porphyrin. They are used as components in systems proposed as ‘molecular wires’. Knowledge of their redox properties is of value in the design of electron- or hole-conduction systems. In particular, the location of the charge density in the radical anions of quinoxalinoporphyrins can be modulated by peripheral functionalization. New theoretical treatments of electrochemical potentials are developed that identify the site of reduction in both the anions and the dianions of 33 quinoxalinoporphyrins. These molecules include free-base and metallated macrocycles substituted on the quinoxaline with electron-withdrawing groups (NO2, Cl, Br) and/or electron-donating groups (NH2, OCH3). Spectroelectrochemistry, density-functional theory calculations, and substituent-parameter models are used to verify the analysis. Five distinct patterns are observed for the locations of the first and second reductions; some of these patterns involve delocalized charges. Nitroquinoxalinoporphyrins with the nitro groups at the 5- and 6-quinoxaline positions are found to have quite different properties owing to distortions caused by peri interactions that force the nitro group of the 5-nitro regioisomer out of conjugation. Charge localization on the nitroquinoxaline fragment is found for some molecules, and this is attributed to ion-pairing with the 0.1 M tetrabutylammonium perchlorate electrolyte used, leading to the verified prediction that electron-paramagnetic resonance spectra of these molecules taken without the electrolyte yield delocalized anions. These properties enable the control of conduction through molecular wires synthesised from quinoxalinoporphyrins. © the Owner Societies.

Smith, ADAC & Wand, MP 2008, 'Streamlined variance calculations for semiparametric mixed models', Statistics in Medicine, vol. 27, no. 3, pp. 435-448.
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AbstractSemiparametric mixed model analysis benefits from variability estimates such as standard errors of effect estimates and variability bars to accompany curve estimates. We show how the underlying variance calculations can be done extremely efficiently compared with the direct naïve approach. These streamlined calculations are linear in the number of subjects, representing a two orders of magnitude improvement. Copyright © 2007 John Wiley & Sons, Ltd.

Smith, GB, Maaroof, AI & Cortie, MB 2008, 'Percolation in nanoporous gold and the principle of universality for two-dimensional to hyperdimensional networks', PHYSICAL REVIEW B, vol. 78, no. 16, pp. 1-1.
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Percolation in nanoporous gold can be achieved with as little as 8% by volume of gold. Samples of nanoporous gold of various morphologies are analyzed with a combination of electrical and optical data. Growing thin films and complex multiply connected th

Sotirchos, IM, Hudson, AL, Ellis, J & Davey, MW 2008, 'Thioredoxins of a parasitic nematode: Comparison of the 16- and 12-kDA thioredoxins from Haemonchus contortus', FREE RADICAL BIOLOGY AND MEDICINE, vol. 44, no. 12, pp. 2026-2033.
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Thioredoxins are a family of small proteins conserved through evolution, which are essential for the maintenance of cellular homeostasis. The classic thioredoxin, identified in most species, is a 12-kDa protein with a Cys-Pro-Gly-Cys (CPGC) active site.

Speer, MS 2008, 'On the late twentieth century decrease in Australian east coast rainfall extremes', Atmospheric Science Letters, vol. 9, no. 3, pp. 160-170.
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AbstractA change from negative to positive circulation anomalies over New South Wales (NSW) during the 1970s resulted in a decrease in east coastal low‐pressure systems and accompanying rain. Negative pressure anomalies over eastern Australia, anomalous onshore low‐level winds and larger NSW rainfall totals since 1950, occur in the cool phase of the IPO rather than the warm phase (post‐1976). Larger NSW extreme annual rainfall totals occurred prior to 1977 and were characterized by negative mean sea level pressure (MSLP) anomalies over eastern Australia. In contrast, extreme annual rainfall totals from 1977 were smaller and characterized by positive MSLP anomalies. Copyright © 2008 Royal Meteorological Society

Srinivasan, GV, Unnikrishnan, KP, Rema Shree, AB & Balachandran, I 2008, 'HPLC estimation of berberine in <i> Tinospora cordifolia</i> and <i> Tinospora sinensis</i>', Indian Journal of Pharmaceutical Sciences, vol. 70, no. 1, pp. 96-96.
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Stack, CM, Caffrey, CR, Donnelly, SM, Seshaadri, A, Lowther, J, Tort, JF, Collins, PR, Robinson, MW, Xu, W, McKerrow, JH, Craik, CS, Geiger, SR, Marion, R, Brinen, LS & Dalton, JP 2008, 'Structural and functional relationships in the virulence-associated cathepsin L proteases of the parasitic liver fluke, Fasciola hepatica', JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 283, no. 15, pp. 9896-9908.
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The helminth parasite Fasciola hepatica secretes cysteine proteases to facilitate tissue invasion, migration, and development within the mammalian host. The major proteases cathepsin L1 (FheCL1) and cathepsin L2 (FheCL2) were recombinantly produced and biochemically characterized. By using site-directed mutagenesis, we show that residues at position 67 and 205, which lie within the S2 pocket of the active site, are critical in determining the substrate and inhibitor specificity. FheCL1 exhibits a broader specificity and a higher substrate turnover rate compared with FheCL2. However, FheCL2 can efficiently cleave substrates with a Pro in the P2 position and degrade collagen within the triple helices at physiological pH, an activity that among cysteine proteases has only been reported forhuman cathepsin K. The 1.4-Å three-dimensional structure of the FheCL1 was determined by x-ray crystallography, and the three-dimensional structure of FheCL2 was constructed via homology-based modeling. Analysis and comparison of these structures and our biochemical data with those of human cathepsins L and Kprovided an interpretation of the substrate-recognition mechanisms of these major parasite proteases. Furthermore, our studies suggest that a configuration involving residue 67 and the 'gatekeeper' residues 157 and 158 situated at the entrance of the active site pocket create a topology that endows FheCL2 with its unusual collagenolytic activity. The emergence of a specialized collagenolytic function in Fasciola likely contributes to the success of this tissue-invasive parasite. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Stark, D, Phillips, O, Peckett, D, Munro, U, Marriott, D, Harkness, J & Ellis, J 2008, 'Gorillas are a host for Dientamoeba fragilis: An update on the life cycle and host distribution', VETERINARY PARASITOLOGY, vol. 151, no. 1, pp. 21-26.
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Dientamoeba fragilis is a gastrointestinal protozoan that has a workldwide distribution and is emerging as a common caise of diarrhea. As D. fragilis has a propensity to cause chronic illness with symptoms similar to irritable bowel syndrome (IBS) it is not surprising that some patients with D. fragilis are misidagnosed as having IBS. In contrast to mosrt other pethogenic protozoa verylittle is known about its life ycle, epidemiology and mode of transmission. What role animal reservoirs play in the transmission pf this parasite s unknown.

Stark, D, van Hal, S, Fotedar, R, Butcher, A, Marriott, D, Ellis, J & Harkness, J 2008, 'Comparison of stool antigen detection kits to PCR for diagnosis of amebiasis', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 46, no. 5, pp. 1678-1681.
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The present study was conducted to compare two stool antigen detection kits with PCR for the diagnosis of Entamoeba histolytica infections by using fecal specimens submitted to the Department of Microbiology at St. Vincent's Hospital, Sydney, and the Ins

Stelzer-Braid, S, Escott, R, Baleriola, C, Kirkland, P, Robertson, P, Catton, M & Rawlinson, WD 2008, 'Proficiency of Nucleic Acid Tests for Avian Influenza Viruses, Australasia', Emerging Infectious Diseases, vol. 14, no. 7, pp. 1126-1128.
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Stelzer-Braid, S, Wong, B, Robertson, P, Lynch, GW, Laurie, K, Shaw, R, Barr, I, Selleck, PW, Baleriola, C, Escott, R, Katsoulotos, G & Rawlinson, WD 2008, 'A commercial ELISA detects high levels of human H5 antibody but cross-reacts with influenza A antibodies', Journal of Clinical Virology, vol. 43, no. 2, pp. 241-243.
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Background and objectives: Commercial serological assays to determine influenza A H5N1 infection are available, although the accuracy and reproducibility of these are not reported in detail. This study aimed to assess the validity of a commercial ELISA H5 hemagglutinin (HA) antibody kit. Study design: A commercial ELISA for detection of antibodies towards influenza A H5 HA was evaluated using human sera from vaccinated individuals. The ELISA was used to screen 304 sera with elevated influenza A complement fixation titres collected between the period 1995-2007. Results and conclusions: The ELISA was found to be accurate for sera with high levels of anti-H5 antibodies, and would be useful in clinical settings where a rapid result is required. Thirteen of the stored sera were positive using the ELISA, but were confirmed as negative for H5N1 exposure using further serological tests. Absorption studies suggested that antibodies towards seasonal H3N2 and H1N1 influenza may cross-react with H5 antigen, giving false positive results with the ELISA. © 2008 Elsevier B.V. All rights reserved.

Stocker, R, Seymour, JR, Samadani, A, Hunt, DE & Polz, MF 2008, 'Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 11, pp. 4209-4214.
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Because ocean water is typically resource-poor, bacteria may gain significant growth advantages if they can exploit the ephemeral nutrient patches originating from numerous, small sources. Although this interaction has been proposed to enhance biogeochemical transformation rates in the ocean, it remains questionable whether bacteria are able to efficiently use patches before physical mechanisms dissipate them. Here we show that the rapid chemotactic response of the marine bacterium Pseudoalteromonas haloplanktis substantially enhances its ability to exploit nutrient patches before they dissipate. We investigated two types of patches important in the ocean: nutrient pulses and nutrient plumes, generated for example from lysed algae and sinking organic particles, respectively. We used microfluidic devices to create patches with environmentally realistic dimensions and dynamics. The accumulation of P. haloplanktis in response to a nutrient pulse led to formation of bacterial hot spots within tens of seconds, resulting in a 10-fold higher nutrient exposure for the fastest 20% of the population compared with nonmotile cells. Moreover, the chemotactic response of P. haloplanktis was >10 times faster than the classic chemotaxis model Escherichia coli, leading to twice the nutrient exposure. We demonstrate that such rapid response allows P. haloplanktis to colonize nutrient plumes for realistic particle sinking speeds, with up to a 4-fold nutrient exposure compared with nonmotile cells. These results suggest that chemotactic swimming strategies of marine bacteria in patchy nutrient seascapes exert strong influence on carbon turnover rates by triggering the formation of microscale hot spots of bacterial productivity. © 2008 by The National Academy of Sciences of the USA.

Su, Y-C, Rolph, MS, Hansbro, NG, Mackay, CR & Sewell, WA 2008, 'Granulocyte-Macrophage Colony-Stimulating Factor Is Required for Bronchial Eosinophilia in a Murine Model of Allergic Airway Inflammation', The Journal of Immunology, vol. 180, no. 4, pp. 2600-2607.
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Abstract GM-CSF plays an important role in inflammation by promoting the production, activation, and survival of granulocytes and macrophages. In this study, GM-CSF knockout (GM-CSF−/−) mice were used to investigate the role of GM-CSF in a model of allergic airway inflammation. In allergic GM-CSF−/− mice, eosinophil recruitment to the airways showed a striking pattern, with eosinophils present in perivascular areas, but almost completely absent in peribronchial areas, whereas in wild-type mice, eosinophil infiltration appeared in both areas. In the GM-CSF−/− mice, mucus production in the airways was also reduced, and eosinophil numbers were markedly reduced in the bronchoalveolar lavage (BAL)3 fluid. IL-5 production was reduced in the lung tissue and BAL fluid of GM-CSF−/− mice, but IL-4 and IL-13 production, airway hyperresponsiveness, and serum IgE levels were not affected. The presence of eosinophils in perivascular but not peribronchial regions was suggestive of a cell migration defect in the airways of GM-CSF−/− mice. The CCR3 agonists CCL5 (RANTES) and CCL11 (eotaxin-1) were expressed at similar levels in GM-CSF−/− and wild-type mice. However, IFN-γ mRNA and protein were increased in the lung tissue and BAL fluid in GM-CSF−/− mice, as were mRNA levels of the IFN-γ-inducible chemokines CXCL9 (Mig), CXCL10 (IP-10), and CXCL11 (I-Tac). Interestingly, these IFN-γ-inducible chemokines are natural antagonists of CCR3, suggesting that their overproduction in GM-CSF−/− mice contributes to the lack of airway eosinophils. These findings demonstrate distinctive abnormalities to a model of allergic asthma in the absence of GM-CSF.

Suggett, DJ, Warner, ME, Smith, DJ, Davey, P, Hennige, S & Baker, NR 2008, 'PHOTOSYNTHESIS AND PRODUCTION OF HYDROGEN PEROXIDE BY SYMBIODINIUM (PYRRHOPHYTA) PHYLOTYPES WITH DIFFERENT THERMAL TOLERANCES¹', Journal of Phycology, vol. 44, no. 4, pp. 948-956.
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Occurrences whereby cnidaria lose their symbiotic dinoflagellate microalgae (Symbiodinium spp.) are increasing in frequency and intensity. These so‐called bleaching events are most often related to an increase in water temperature, which is thought to limit certain Symbiodinium phylotypes from effectively dissipating absorbed excitation energy that is otherwise used for photochemistry. Here, we examined photosynthetic characteristics and hydrogen peroxide (H2O2) production, a possible signal involved in bleaching, from two Symbiodinium types (a thermally “tolerant” A1 and “sensitive” B1) representative of cnidaria–Symbiodinium symbioses of reef‐building Caribbean corals. Under steady‐state growth at 26°C, a higher efficiency of PSII photochemistry, rate of electron turnover, and rate of O2 production were observed for type A1 than for B1. The two types responded very differently to a period of elevated temperature (32°C): type A1 increased light‐driven O2 consumption but not the amount of H2O2 produced; in contrast, type B1 increased the amount of H2O2 produced without an increase in light‐driven O2 consumption. Therefore, our results are consistent with previous suggestions that the thermal tolerance of Symbiodinium is related to adaptive constraints associated with photosynthesis and that sensitive phylotypes are more prone to H2O2 production. Understanding these adaptive differences in the genus Symbiodinium will be crucial if we are to interpret the response of symbiotic associations, including reef‐building corals, to environmental change.

Suglia, SF, Ryan, L & Wright, RJ 2008, 'Creation of a Community Violence Exposure Scale: Accounting for What, Who, Where, and How Often', JOURNAL OF TRAUMATIC STRESS, vol. 21, no. 5, pp. 479-486.
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Previous research has used the Rasch model, a method for obtaining a continuous scale from dichotomous survey items measuring a single latent construct, to create a scale of community violence exposure. The authors build upon previous work and describe the application of a Rasch model using the continuation ratio model to create an exposure to community violence (ETV) scale including event circumstance information previously shown to modify the impact of experienced events. They compare the Rasch ETV scale to a simpler sum ETV score, and estimate the effect of ETV on child posttraumatic stress symptoms. Incorporating detailed event circumstance information that is grounded in traumatic stress theory may reduce measurement error in the assessment of children's community violence exposure. © 2008 International Society for Traumatic Stress Studies.

Suglia, SF, Ryan, L, Laden, F, Dockery, DW & Wright, RJ 2008, 'Violence exposure, a-chronic psychosocial stressor, and childhood lung function', PSYCHOSOMATIC MEDICINE, vol. 70, no. 2, pp. 160-169.
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OBJECTIVE: Chronic psychosocial stressors, including violence, and neuropsychological and behavioral development in children as well as physiologic alterations that may lead to broader health effects. METHODS: We studied the relationship between violence and childhood lung function in a prospective birth cohort of 313 urban children (age range = 6-7 years). Mothers reported on their child's lifetime exposure to community violence (ETV) and interparental conflict in the home (Conflict Tactics Scale (CTS)) within 1 year of the lung function assessment. RESULTS: In linear regression analyses, adjusting for maternal education, child's age, race, birthweight, tobacco smoke exposure, and medical history, girls in the highest CTS verbal aggression tertile had a 5.5% (95% confidence interval (CI) = -9.6, -1.5) decrease in percent predicted forced expiratory volume (FEV1) and a 5.4% (95% CI = -9.7, -1.1) decrease in forced vital capacity (FVC) compared with girls in the lowest tertile. The CTS verbal aggression subscale was associated with lung function among boys in the same direction, albeit this was not statistically significant. Boys in the highest ETV tertile had a 3.4% (95% CI = -8.0, 1.1) lower FEV1 and 5.3% lower FVC (95% CI = -10.2, -0.4) compared with boys in the lowest tertile. The ETV score was not a significant predictor of girls' lung function. CONCLUSIONS: Interparental conflict, specifically verbal aggression, and ETV were associated with decreased childhood lung function independent of socioeconomic status, tobacco smoke exposure, birthweight, and respiratory illness history. Gender differences were noted based on the type of violence exposure, which may warrant further exploration. Copyright © 2008 by American Psychosomatic Society.

Supansomboon, S, Maaroof, A & Cortie, MB 2008, ''Purple glory': The optical properties and technology of AuAl2 coatings', GOLD BULLETIN, vol. 41, no. 4, pp. 296-304.
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"Purple glory": the optical properties and technology of AuAi2 coatings

Surkan, PJ, Kawachi, I, Ryan, LM, Berkman, LF, Vieira, C & Peterson, KE 2008, 'Maternal depressive symptoms, parenting self-efficacy, and child growth', AMERICAN JOURNAL OF PUBLIC HEALTH, vol. 98, no. 1, pp. 125-132.
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Objectives. We assessed whether maternal depressive symptoms and parenting self-efficacy were associated with child growth delay. Methods. We collected data from a random sample of 595 low-income mothers and their children aged 6 to 24 months in Teresina, Piauí, Brazil, including information on sociodemographic characteristics, mothers' depressive symptoms and parenting self-efficacy, and children's anthropometric characteristics. We used adjusted logistic regression models in our analyses. Results. Depressive symptoms among mothers were associated with 1.8 times higher odds (95% confidence interval [CI]=1.1, 2.9) of short stature among children. Parenting self-efficacy was not associated with short stature, nor did it mediate or modify the relationship between depressive symptoms and short stature. Maternal depressive symptoms and self-efficacy were not related to child underweight. Conclusions. Our results showed that among low-income Brazilian families maternal depressive symptoms, but not self-efficacy, were associated with short stature in children aged 6 to 24 months after adjustment for known predictors of growth.

Swift, PD, Lawlor, R, Smith, GB & Gentle, A 2008, 'Rectangular-section mirror light pipes', SOLAR ENERGY MATERIALS AND SOLAR CELLS, vol. 92, no. 8, pp. 969-975.
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Using an integrated-ray approach an expression for the transmission of rectangular section mirror light pipe (MLP) has been derived for the case of collimated light input. The transmittance and the irradiance distribution at the exit aperture of rectangu

Tan, YP, Giffard, PM, Barry, DG, Huston, WM & Turner, MS 2008, 'Random Mutagenesis Identifies Novel Genes Involved in the Secretion of Antimicrobial, Cell Wall-Lytic Enzymes by Lactococcus lactis', Applied and Environmental Microbiology, vol. 74, no. 24, pp. 7490-7496.
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ABSTRACT Lactococcus lactis is a gram-positive bacterium that is widely used in the food industry and is therefore desirable as a candidate for the production and secretion of recombinant proteins. Previously, we generated a L. lactis strain that expressed and secreted the antimicrobial cell wall-lytic enzyme lysostaphin. To identify lactococcal gene products that affect the production of lysostaphin, we isolated and characterized mutants generated by random transposon mutagenesis that had altered lysostaphin activity. Out of 35,000 mutants screened, only one with no lysostaphin activity was identified, and it was found to contain an insertion in the lysostaphin expression cassette. Ten mutants with higher lysostaphin activity contained insertions in only four different genes, which encode an uncharacterized putative transmembrane protein (llmg_0609) (three mutants), an enzyme catalyzing the first step in peptidoglycan biosynthesis ( murA2 ) (five mutants), a putative regulator of peptidoglycan modification ( trmA ) (one mutant), and an uncharacterized enzyme possibly involved in ubiquinone biosynthesis (llmg_2148) (one mutant). These mutants were found to secrete larger amounts of lysostaphin than the control strain (MG1363[ lss ]), and the greatest increase in secretion was 9.8- to 16.1-fold, for the llmg_0609 mutants. The lysostaphin-oversecreting llmg_0609, murA2 , and trmA mutants were also found to secrete larger amounts of another cell wall-lytic enzyme (the Listeria monocytogenes bacteriophage endolysi...

Taylor, D & Eamus, D 2008, 'Coordinating leaf functional traits with branch hydraulic conductivity: resource substitution and implications for carbon gain', TREE PHYSIOLOGY, vol. 28, no. 8, pp. 1169-1177.
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We studied relationships among branch hydraulic conductivity, xylem embolism, stomatal conductance (gs), foliar nitrogen (N) concentration and specific leaf area (SLA) of seven tree species growing at four temperate woodland sites spanning a 464-1350 mm rainfall gradient. Specifically, we examined the question: are gs and foliar N concentration coordinated with branch hydraulic conductivity and, if so, what are the implications for carbon assimilation? Area-based, light-saturated photosynthetic rate (Aa) was uniquely and positively correlated with gs and foliar N concentration. Multiple regression analyses showed that, when variability in SLA was controlled for, the (positive) partial slope for each predictor remained significant. In contrast, there was a negative correlation between gs and foliar N concentration such that, for any given Aa, leaves with a high gs allocated less N to foliage than leaves with a low gs. Foliar N concentration was negatively correlated with branch hydraulic conductivity, whereas gs was positively correlated with branch hydraulic conductivity. These relationships were also significant when variability in leaf area to sapwood area ratio, gs and SLA were controlled for in a multiple regression, suggesting that the relationships were unique and independent of other confounding factors. Trees with low water transport capacity were able to support a high Aa by increasing investment in foliar N. Resource substitution occurred such that there was a trade-off between gs and foliar N in relation to branch hydraulic conductivity. High Aa could be sustained through either a high branch hydraulic conductivity and hence high gs and a low allocation to foliar N, or the effect of a low branch hydraulic conductivity and hence low gs could be offset by a high allocation to foliar N. The results are discussed in relation to mechanisms for minimizing the negative effects of limited water availability on carbon gain. © 2008 Heron Publishing.

Taylor, SR, Ung, AT & Pyne, SG 2008, 'ChemInform Abstract: Synthesis of Benzo[c]chromen‐6‐one via Novel Cyclic Aryl—Pd(II)—Ester Enolate Intermediates.', ChemInform, vol. 39, no. 6.
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AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Thomas, CR, Hose, GC, Warne, MS & Lim, RP 2008, 'Effects of river water and salinity on the toxicity of deltamethrin to freshwater shrimp, cladoceran, and fish', ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY, vol. 55, no. 4, pp. 610-618.
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Deltamethrin is a pyrethroid insecticide used extensively to control invertebrate pests on cotton and other crops. It is acutely toxic to nontarget aquatic organisms, but existing toxicity data are mostly from toxicity tests using purified laboratory wat

Thomas, T, Evans, FF, Schleheck, D, Mai-Prochnow, A, Burke, C, Penesyan, A, Dalisay, DS, Stelzer-Braid, S, Saunders, N, Johnson, J, Ferriera, S, Kjelleberg, S & Egan, S 2008, 'Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment', PLOS ONE, vol. 3, no. 9.
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Background: Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. Methodology/Principal Findings: To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. Conclusions/Significance: The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associa...

Thompson, FE, Kipnis, V, Midthune, D, Freedman, LS, Carroll, RJ, Subar, AF, Brown, CC, Butcher, MS, Mouw, T, Leitzmann, M & Schatzkin, A 2008, 'Performance of a food-frequency questionnaire in the US NIH–AARP (National Institutes of Health–American Association of Retired Persons) Diet and Health Study', Public Health Nutrition, vol. 11, no. 2, pp. 183-195.
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AbstractObjectiveWe evaluated the performance of the food-frequency questionnaire (FFQ) administered to participants in the US NIH–AARP (National Institutes of Health–American Association of Retired Persons) Diet and Health Study, a cohort of 566 404 persons living in the USA and aged 50–71 years at baseline in 1995.DesignThe 124-item FFQ was evaluated within a measurement error model using two non-consecutive 24-hour dietary recalls (24HRs) as the reference.SettingParticipants were from six states (California, Florida, Pennsylvania, New Jersey, North Carolina and Louisiana) and two metropolitan areas (Atlanta, Georgia and Detroit, Michigan).SubjectsA subgroup of the cohort consisting of 2053 individuals.ResultsFor the 26 nutrient constituents examined, estimated correlations with true intake (not energy-adjusted) ranged from 0.22 to 0.67, and attenuation factors ranged from 0.15 to 0.49. When adjusted for reported energy intake, performance improved; estimated correlations with true intake ranged from 0.36 to 0.76, and attenuation factors ranged from 0.24 to 0.68. These results compare favourably with those from other large prospective studies. However, previous biomarker-based studies suggest that, due to correlation of errors in FFQs and self-report reference instruments such as the 24HR, the correlations and attenuation factors observed in most calibration studies, including ours, tend to overestimate FF...

Tong, CC, Quesada, R, Sessler, JL & Gale, PA 2008, 'meso-Octamethylcalix[4]pyrrole: an old yet new transmembrane ion-pair transporter', Chemical Communications, no. 47, pp. 6321-6321.
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Ton-That, C, Foley, M & Phillips, MR 2008, 'Luminescent properties of ZnO nanowires and as-grown ensembles', NANOTECHNOLOGY, vol. 19, no. 41, pp. 1-5.
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Vertically aligned ZnO nanowires were synthesized on a sapphire (1120) substrate by vapour deposition and their light-emitting properties were characterized using photoluminescence and cathodoluminescence spectroscopies. Besides the nanowires, there exists a mosaic ZnO film on the substrate surface. Comparison of the luminescent properties of the as-grown ensemble and the nanowires extracted from it shows that the mosaic film is the major source of the defect-related green emission while the nanowires possess highly crystalline quality with virtually no defects. Photoemission spectroscopy shows that the valence band states associated with O 2p from the as-grown sample are diminished compared with those from the extracted nanowires. These findings suggest that the green emission partly arises from oxygen vacancies located on the surface of the mosaic film. © IOP Publishing Ltd.

Ton-That, C, Foley, M & Phillips, MR 2008, 'Luminescent properties of ZnO nanowires and as-grown ensembles.', Nanotechnology, vol. 19, no. 41, p. 415606.
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Vertically aligned ZnO nanowires were synthesized on a sapphire ([Formula: see text]) substrate by vapour deposition and their light-emitting properties were characterized using photoluminescence and cathodoluminescence spectroscopies. Besides the nanowires, there exists a mosaic ZnO film on the substrate surface. Comparison of the luminescent properties of the as-grown ensemble and the nanowires extracted from it shows that the mosaic film is the major source of the defect-related green emission while the nanowires possess highly crystalline quality with virtually no defects. Photoemission spectroscopy shows that the valence band states associated with O 2p from the as-grown sample are diminished compared with those from the extracted nanowires. These findings suggest that the green emission partly arises from oxygen vacancies located on the surface of the mosaic film.

Ton-That, C, Phillips, MR & Nguyen, T-P 2008, 'Blue shift in the luminescence spectra of MEH-PPV films containing ZnO nanoparticles', JOURNAL OF LUMINESCENCE, vol. 128, no. 12, pp. 2031-2034.
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Luminescence properties of nanocomposites consisting of ZnO nanoparticles in a conjugated polymer, poly [2-methoxy-5-(2′-ethyl hexyloxy)-phenylene vinylene] (MEH-PPV), were investigated. Photoluminescence measurements reveal a blue shift in the emission spectrum of MEH-PPV upon incorporation of ZnO nanoparticles into the polymer film while the emission is increasingly quenched with increasing ZnO concentration. In contrast, the structure of the polymer and its conjugation length are not affected by the presence of ZnO nanoparticles (up to 16 wt% ZnO) as revealed by Raman spectroscopy. The blue shift and photoluminescence quenching are explained by the separation of photogenerated electron-hole pairs at the MEH-PPV/ZnO interface and the charging of the nanoparticles. Crown Copyright © 2008.

Ton-That, C, Phillips, MR, Foley, M, Moody, SJ & Stampfl, APJ 2008, 'Surface electronic properties of ZnO nanoparticles', APPLIED PHYSICS LETTERS, vol. 92, no. 26, pp. 1-3.
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The surface electronic structure of ZnO nanoparticles has been studied with photoemission and x-ray absorption spectroscopies. Contrary to expectation, ZnO:Zn phosphor nanoparticles were found to contain a lower oxygen vacancy density on the surface than undoped ZnO counterparts, but oxygen vacancies are in different chemical environments. Cathodoluminescence shows intense green luminescence from the ZnO:Zn surface, while the undoped nanoparticles exhibit only the near-band-edge emission. The results indicate the roles of surface oxygen vacancies and their environment in the previously unexplained green luminescence from the ZnO:Zn material. © 2008 American Institute of Physics.

Ton-That, C, Stockton, G, Phillips, MR, Nguyen, T-P, Huang, CH & Cojocaru, A 2008, 'Luminescence properties of poly-(phenylene vinylene) derivatives', POLYMER INTERNATIONAL, vol. 57, no. 3, pp. 496-501.
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Background: Conjugated polymers, especially those of the poly(phenylene vinylene) (PPV) family, are promising candidates as emission material in light-emitting devices. The aim of this work was to investigate the dependence of the luminescence properties of PPV-based derivatives on their polymer structure, especially side groups. Results: Three PPV derivatives, BEHPPV, MEHPPV and MEHSPPV, were synthesised and characterised by photoluminescence (PL) and cathodoluminescence (CL) spectroscopies in the temperature range 10-300K. PL and CL spectra of the polymers exhibit similar luminescence peaks, which undergo a blue shift with increasing temperature. The shift in wavelength is accompanied by variations in the relative intensities of emission peaks. Both BEHPPV and MEHPPV display emission characteristics of the PPV backbone, but the peak of MEHPPV shifts to a longer wavelength in comparison with the corresponding peak of BEHPPV at the same temperature. The luminescence spectra of MEHSPPV, which has a sulfanyl incorporated in the side chain, are considerably different from those of the two other derivatives. Conclusions: The results demonstrate that the luminescence properties depend strongly on the chain conformations of the conjugated backbone, which are affected by polymer side chains. © 2007 Society of Chemical Industry.

Treerat, P, Widmer, F, Middleton, PG, Iredell, J & George, AM 2008, 'In vitro interactions of tobramycin with various nonantibiotics against Pseudomonas aeruginosa and Burkholderia cenocepacia', FEMS MICROBIOLOGY LETTERS, vol. 285, no. 1, pp. 40-50.
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Pseudomonas aeruginosa and Burkholderia cepacia are the major pathogens that colonize the airway surface and cause progressive respiratory failure and high mortality, especially in cystic fibrosis (CF) patients. Tobramycin is the treatment of choice, but persistent usage enables the infectious organisms to activate defence mechanisms, making eradication rarely successful. Combinations of antibiotic and nonantibiotic compounds have been tested in vitro against P. aeruginosa and B. cepacia, but with mixed results. Sodium ions interfere with the bacterial tobramycin uptake system, but amiloride partially reverses this antagonism. In this pilot study, we extend previous findings of the effectiveness of tobramycin in combination with amiloride and other nonantibiotics against a P. aeruginosa type strain, and against four P. aeruginosa strains and one Burkholderia cenocepacia strain isolated from CF patients. Significantly, the four clinical P. aeruginosa strains were tobramycin resistant. We also find that Na+ and K+, but not Cl-, are the chief antagonists of tobramycin efficacy. These results suggest that chemotherapy for CF patients might not only be compromised by antibiotic-resistant pathogens alone, but by a lack of penetration of antibiotics caused either by bacterial biofilms or the high sodium flux in the CF lung, or by antagonistic effects of some drug combinations, any of which could allow the persistence of drug-susceptible bacteria.

Ulstrup, KE, Hill, R, van Oppen, MJH, Larkum, AWD & Ralph, PJ 2008, 'Seasonal variation in the photo-physiology of homogeneous and heterogeneous Symbiodinium consortia in two scleractinian corals', MARINE ECOLOGY PROGRESS SERIES, vol. 361, pp. 139-150.
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Seasonal variation in the composition of the algal endosymbiont community and photophysiology was determined in the corals Pocillopora damicornis,w hich show high local fidelity to one symbiont type (Symbiodinium C1) and Acropora valida, with a mixed Symbiodinium synbiont community, compromising members of both clades A and C. The relative abundances of Symbiodinium types varied overtime. A significant decline in symbiont densities in both coral species during the summer of 2005 coincided with a NOAA 'hotspot' warning for Heron Island. This also coincided with a relayiove increase in the presence and dominance of clade A in A. valida particularl in sun-adapted surfaces.

UNICOMB, LE, O'REILLY, LC, KIRK, MD, STAFFORD, RJ, SMITH, HV, BECKER, NG, PATEL, MS & GILBERT, GL 2008, 'Risk factors for infection withCampylobacter jejuni flaAgenotypes', Epidemiology and Infection, vol. 136, no. 11, pp. 1480-1491.
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SUMMARYWe aimed to exploreCampylobactergenotype-specific risk factors in Australia. Isolates collected prospectively from cases recruited into a case-control study were genotyped usingflaArestriction fragment-length polymorphism typing (flaAgenotyping). Exposure information for cases and controls was collected by telephone interview. Risk factors were examined for majorflaAgenotypes using logistic and multinomial regression. FiveflaAgenotypes accounted for 325 of 590 (55%) cases – flaA-6b (n=129),flaA-6 (n=70),flaA-10 (n=48),flaA-2 (n=43),flaA-131 (n=35). In Australia, infections due toflaA-10 andflaA-2 were found to be significantly associated with eating non-poultry meat (beef and ham, respectively) in both case-control and inter-genotype comparisons. All major genotypes apart fromflaA-10 were associated with chicken consumption in the case-control comparisons. Based on several clinical criteria, infections due toflaA-2 were more severe than those due to other genotypes. Thus genotype analysis may reveal genotype-specific niches and differences in virulence and transmission routes.

Unnikrishnan, KP, Raja, S & Balachandran, I 2008, 'A reverse phase HPLC-UV and HPTLC methods for determination of plumbagin inPlumbago indicaandPlumbago zeylanica', Indian Journal of Pharmaceutical Sciences, vol. 70, no. 6, pp. 844-844.
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Vanamala, J, Glagolenko, A, Yang, P, Carroll, RJ, Murphy, ME, Newman, RA, Ford, JR, Braby, LA, Chapkin, RS, Turner, ND & Lupton, JR 2008, 'Dietary fish oil and pectin enhance colonocyte apoptosis in part through suppression of PPARδ/PGE 2 and elevation of PGE 3', Carcinogenesis, vol. 29, no. 4, pp. 790-796.
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Varganov, SA, Gilbert, ATB, Deplazes, E & Gill, PMW 2008, 'Resolutions of the Coulomb operator', The Journal of Chemical Physics, vol. 128, no. 20, pp. 201104-201104.
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We discuss a generalization of the resolution of the identity by considering one-body resolutions of two-body operators, with particular emphasis on the Coulomb operator. We introduce a set of functions that are orthonormal with respect to 1∕r12 and propose that the resulting “resolution of the Coulomb operator,” r12−1=∣ϕi⟩⟨ϕi∣, may be useful for the treatment of large systems due to the separation of two-body interactions. We validate our approach by using it to compute the Coulomb energy of large systems of point charges.

Vijayakumar, R, Shivaramu, Ramamurthy, N & Ford, MJ 2008, 'Compton scattering study of electron momentum distribution in lithium fluoride using 662 keV gamma radiations', PHYSICA B-CONDENSED MATTER, vol. 403, no. 23-24, pp. 4309-4313.
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Here we report the first ever 137Cs Compton spectroscopy study of lithium fluoride. The spherical average Compton profiles of lithium fluoride are deduced from Compton scattering measurements on poly crystalline sample at gamma ray energy of 662 keV. To compare the experimental data, we have computed the spherical average Compton profiles using self-consistent Hartree-Fock wave functions employed on linear combination of atomic orbital (HF-LCAO) approximation. The directional Compton profiles and their anisotropic effects are also calculated using the same HF-LCAO approximation. The experimental spherical average profiles are found to be in good agreement with the corresponding HF-LCAO calculations and in qualitative agreement with Hartree-Fock free atom values. The present experimental isotropic and calculated directional profiles are also compared with the available experimental isotropic and directional Compton profiles using 59.54 and 159 keV γ-rays. © 2008 Elsevier B.V. All rights reserved.

Wadsworth, KD, Rowland, SL, Harry, EJ & King, GF 2008, 'The divisomal protein DivIB contains multiple epitopes that mediate its recruitment to incipient division sites', Molecular Microbiology, vol. 67, no. 5, pp. 1143-1155.
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SummaryBacterial cytokinesis is orchestrated by an assembly of essential cell division proteins that form a supramolecular structure known as the divisome. DivIB and its orthologue FtsQ are essential members of the divisome in Gram‐positive and Gram‐negative bacteria respectively. DivIB is a bitopic membrane protein composed of an N‐terminal cytoplasmic domain, a single‐pass transmembrane domain, and a C‐terminal extracytoplasmic region comprised of three separate protein domains. A molecular dissection approach was used to determine which of these domains are essential for recruitment of DivIB to incipient division sites and for its cell division functions. We show that DivIB has three molecular epitopes that mediate its localization to division septa; two epitopes are encoded within the extracytoplasmic region while the third is located in the transmembrane domain. It is proposed that these epitopes represent sites of interaction with other divisomal proteins, and we have used this information to develop a model of the way in which DivIB and FtsQ are integrated into the divisome. Remarkably, two of the three DivIB localization epitopes are dispensable for vegetative cell division; this suggests that the divisome is assembled using a complex network of protein–protein interactions, many of which are redundant and likely to be individually non‐essential.

Walsh, SJ, Buckleton, JS, Ribaux, O, Roux, C & Raymond, T 2008, 'Comparing the growth and effectiveness of forensic DNA databases', Forensic Science International: Genetics Supplement Series, vol. 1, no. 1, pp. 667-668.
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Wang, G, Gou, X, Horvat, J & Park, J 2008, 'Facile Synthesis and Characterization of Iron Oxide Semiconductor Nanowires for Gas Sensing Application', The Journal of Physical Chemistry C, vol. 112, no. 39, pp. 15220-15225.
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We report a facile and efficient synthesis technique for the preparation of iron oxide semiconductor nanowires in large quantity by using nitrilotriacetic acid (NTA) as a chelating agent to form polymeric chains, followed by heat treatment. This technique can also be applied for preparing other transition metal oxide nanowires such as MnO2 nanowires and NiO nanowires. The as-prepared α-Fe2O3 nanowires have exhibited a blue shift of bandgap, peculiar magnetic properties, and high sensitivities toward ethanol and acetic acid gases. © 2008 American Chemical Society.

Wang, G, Park, J, Kong, X, Wilson, PR, Chen, Z & Ahn, J-H 2008, 'Facile Synthesis and Characterization of Gallium Oxide (β-Ga₂O₃) 1D Nanostructures: Nanowires, Nanoribbons, and Nanosheets', Crystal Growth & Design, vol. 8, no. 6, pp. 1940-1944.
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β-Ga2O3, one-dimensional (1D) nanostructures including nanowires, nanoribbons and nanosheets were synthesized via a combined carbon thermal reduction and chemical vapor deposition (CVD) approach. All of these nanostructures consist of single-crystalline monoclinic structure, which has been confirmed via high-resolution TEM and electron diffraction analysis. We obtained β-Ga2O3, nanowires at high temperature zone, nanosheets, and nanoribbons at medium temperature zone at low-pressure environments. We found that β-Ga2Q3 nanowires and nanoribbons have diversified different growth directions. The optical properties of β-Ga2O3 nanowires and nanoribbons from UV-vis spectra show that the bandgaps are red-shifted by 0.13 eV. © 2008 American Chemical Society.

Wang, G, Yang, J, Park, J, Gou, X, Wang, B, Liu, H & Yao, J 2008, 'Facile synthesis and characterization of graphene nanosheets', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 112, no. 22, pp. 8192-8195.
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Graphene nanosheets were produced in large quantity via a soft chemistry synthetic route involving graphite oxidation, ultrasonic exfoliation, and chemical reduction. X-ray diffraction and transmission electron microscopy (TEM) observations show that graphene nanosheets were produced with sizes in the range of tens to hundreds of square nanometers and ripple-like corrugations. High resolution TEM (HRTEM) and selected area electron diffraction (SAED) analysis confirmed the ordered graphite crystal structure of graphene nanosheets. The optical properties of graphene nanosheets were characterized by Raman spectroscopy. © 2008 American Chemical Society.

Wang, GX, Park, JS, Park, MS & Gou, XL 2008, 'Synthesis and high gas sensitivity of tin oxide nanotubes', Sensors and Actuators B: Chemical, vol. 131, no. 1, pp. 313-317.
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Semiconductor tin oxide (SnO2) nanotubes have been synthesised in bulk quantities using a sol-gel template (AAO membrane) synthetic technique. The morphology and crystal structure of SnO2 nanotubes were characterised by a field emission scanning electron microscope (FESEM) and a transmission electron microscope (TEM). The as-prepared SnO2 nanotubes are polycrystalline with an outer diameter of 200 nm, an inner diameter of about 150 nm and a length extending to tens of micrometers. SnO2 nanotube sensors exhibited high sensitivity towards ethanol gas. © 2007 Elsevier B.V. All rights reserved.

Wang, J-Z, Chou, S-L, Chen, J, Chew, S-Y, Wang, G-X, Konstantinov, K, Wu, J, Dou, S-X & Liu, HK 2008, 'Paper-like free-standing polypyrrole and polypyrrole–LiFePO4 composite films for flexible and bendable rechargeable battery', Electrochemistry Communications, vol. 10, no. 11, pp. 1781-1784.
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Highly flexible, paper-like, free-standing polypyrrole and polypyrrole-LiFePO4 composite films were prepared using the electropolymerization method. The films are soft, lightweight, mechanically robust and highly electrically conductivity. The electrochemical behavior of the free-standing films was examined against lithium counter electrode. The electrochemical performance of the free-standing pure PPy electrode was improved by incorporating the most promising cathode material, LiFePO4, into the PPy films. The cell with PPy-LiFePO4 composite film had a higher discharge capacity beyond 50 cycles (80 mA h/g) than that of the cell with pure PPy (60 mA h/g). The free-standing films can be used as electrode materials to satisfy the new market demand for flexible and bendable batteries that are suitable for the various types of design and power needs of soft portable electronic equipment. © 2008 Elsevier B.V. All rights reserved.

Wang, L, Smith, NA, Zhang, L, Dennis, ES, Waterhouse, PM, Unrau, PJ & Wang, M-B 2008, 'Synthesis of complementary RNA by RNA-dependent RNA polymerases in plant extracts is independent of an RNA primer', FUNCTIONAL PLANT BIOLOGY, vol. 35, no. 11, pp. 1091-1099.
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RNA-dependent RNA polymerase (RDR) activities were readily detected in extracts from cauliflower and broccoli florets, Arabidopsis thaliana (L.) Heynh callus tissue and broccoli nuclei. The synthesis of complementary RNA (cRNA) was independent of a RNA primer, whether or not the primer contained a 30 terminal 20 -O-methyl group or was phosphorylated at the 50 terminus. cRNA synthesis in plant extracts was not affected by loss-of-function mutations in the DICER-LIKE (DCL) proteins DCL2, DCL3, and DCL4, indicating that RDRs function independently of these DCL proteins. A loss-of-function mutation in RDR1, RDR2 or RDR6 did not significantly reduce the amount of cRNA synthesis. This indicates that these RDRs did not account for the bulk RDR activities in plant extracts, and suggest that either the individual RDRs each contribute a fraction of polymerase activity or another RDR(s) is predominant in the plant extract.

Wang, M-B, Helliwell, CA, Wu, L-M, Waterhouse, PM, Peacock, WJ & Dennis, ES 2008, 'Hairpin RNAs derived from RNA polymerase II and polymerase III promoter-directed transgenes are processed differently in plants', RNA-A PUBLICATION OF THE RNA SOCIETY, vol. 14, no. 5, pp. 903-913.
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RNA polymerase III (Pol III) as well as Pol II (35S) promoters are able to drive hairpin RNA ( hpRNA) expression and induce target gene silencing in plants. siRNAs of 21 nt are the predominant species in a 35S Pol II line, whereas 24- and/or 22-nucleotide (nt) siRNAs are produced by a Pol III line. The 35S line accumulated the loop of the hpRNA, in contrast to full-length hpRNA in the Pol III line. These suggest that Pol II and Pol III-transcribed hpRNAs are processed by different pathways. One Pol III transgene produced only 24- nt siRNAs but silenced the target gene efficiently, indicating that the 24- nt siRNAs can direct mRNA degradation; specific cleavage was confirmed by 59 rapid amplification of cDNA ends (RACE). Both Pol II- and Pol III-directed hpRNA transgenes induced cytosine methylation in the target DNA. The extent of methylation is not correlated with the level of 21-nt siRNAs, suggesting that they are not effective inducers of DNA methylation. The promoter of a U6 transgene was significantly methylated, whereas the promoter of the endogenous U6 gene was almost free of cytosine methylation, suggesting that endogenous sequences are more resistant to de novo DNA methylation than are transgene constructs.

Webb, JK & Shine, R 2008, 'Differential effects of an intense wildfire on survival of sympatric snakes', JOURNAL OF WILDLIFE MANAGEMENT, vol. 72, no. 6, pp. 1394-1398.
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We analyzed 16 years of mark-recapture data to investigate whether a wildfire influenced survival of an arboreal ambush-forager (broad-headed snake [Hoplocephalus bungaroides]) and a terrestrial active forager (small-eyed snake Cryptophis nigrescens). We predicted that wildfire would cause direct mortality and reduce subsequent survival of both snake species. Contrary to this prediction, wildfire did not affect abundance of broad-headed snakes, but abundance of small-eyed snakes decreased by 48% after the wildfire. Estimated annual survival of small-eyed snakes was 37% lower after fire (s= 0.47, SE = 0.07) than before fire (s = 0.74, SE = 0.05). Prescribed burning may be a suitable tool for creating open habitat mosaics for the endangered broad-headed snake.

Webb, JK, Brown, GP, Child, T, Greenlees, MJ, phillips, BL & Shine, R 2008, 'A native dasyurid predator (common planigale, Planigale maculata) rapidly learns to avoid a toxic invader', AUSTRAL ECOLOGY, vol. 33, no. 7, pp. 821-829.
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Interactions between invasive species and native fauna afford a unique opportunity to examine interspecific encounters as they first occur, without the complications introduced by coevolution. In northern Australia, the continuing invasion of the highly toxic cane toad Bufo marinus poses a threat to many frog-eating predators. Can predators learn to distinguish the novel toxic prey item from native prey (and thus, avoid being poisoned), or are longer-term genetically based changes to attack behaviour needed before predators can coexist with toads? To predict the short-term impact of cane toads on native predators, we need to know the proportion of individuals that will attack toads, the proportion surviving the encounter, and whether surviving predators learn to avoid toads. We quantified these traits in a dasyurid (common planigale, Planigale maculata) that inhabits tropical floodplains across northern Australia. Although 90% of naïve planigales attacked cane toads, 83% of these animals survived because they either rejected the toad unharmed, or killed and consumed the prey snout-first (thereby avoiding the toxin-laden parotoid glands). Most planigales showed one-trial learning and subsequently refused to attack cane toads for long time periods (up to 28 days). Toad-exposed planigales also avoided native frogs for up to 9 days, thereby providing an immediate benefit to native anurans. However, the predators gradually learnt to use chemical cues to discriminate between frogs and toads. Collectively, our results suggest that generalist predators can learn to distinguish and avoid novel toxic prey very rapidly - and hence, that small dasyurid predators can rapidly adapt to the cane toad invasion. Indeed, it may be feasible to teach especially vulnerable predators to avoid cane toads before the toads invade, by deploying low-toxicity baits that stimulate taste-aversion learning. © 2008 The Authors.

Webb, JK, Pike, DA & Shine, R 2008, 'Population ecology of the velvet gecko, Oedura lesueurii in south eastern Australia: Implications for the persistence of an endangered snake', AUSTRAL ECOLOGY, vol. 33, no. 7, pp. 839-847.
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Ecological specialization, such as major dependence upon a single-prey species, can render a predator taxon vulnerable to extinction. In such cases, understanding the population dynamics of that prey type is important for conserving the predator that relies upon it. In eastern Australia, the endangered broad-headed snake Hoplocephalus bungaroides feeds largely on velvet geckos (Oedura lesueurii). We studied growth, longevity and reproduction in a population of velvet geckos in Morton National Park in south-eastern Australia. We marked 458 individual geckos over a 3-year period (1992-1995) and made yearly visits to field sites from 1995-2006 to recapture marked individuals. Female geckos grew larger than males, and produced their first clutch at age 4 years. Males can mature at 2 years, but male-male combat for females probably forces males to delay reproduction until age 3 years. Females lay a single clutch of two eggs in communal nests in November, and up to 22 females deposited eggs in a single nest. Egg hatching success was high (100%), and juveniles had high survival (76%) during their first 6 months of life. Velvet geckos are long-lived, and the mean age of marked animals recaptured after 1995 was 6.1 years (males) and 8.4 years (females). Older females (7.5-9.5 years) were all gravid when last recaptured. Like other temperate-climate gekkonids, O. lesueurii has a 'slow' life history, and population viability could be threatened by any factors that increase egg or adult mortality. Two such factors - the removal of 'bush rocks' for urban gardens, and the overgrowth of rock outcrops by vegetation - could render small gecko populations vulnerable to extinction. In turn, the reliance of predatory broad-headed snakes on this slow-growing lizard species may increase its vulnerability to extinction. © 2008 The Authors.

Wenbo, E, Kadish, KM, Sintic, PJ, Khoury, T, Govenlock, LJ, Ou, Z, Shao, J, Ohkubo, K, Reimers, JR, Fukuzumi, S & Crossley, MJ 2008, 'Control of the orbital delocalization and implications for molecular rectification in the radical anions of porphyrins with coplanar 90 degrees and 180 degrees beta,beta '-fused extensions', JOURNAL OF PHYSICAL CHEMISTRY A, vol. 112, no. 3, pp. 556-570.
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Through-porphyrin electronic communication is investigated using 'linear-type' and 'corner-type' bis(quinoxalino)porphyrins in free-base form and their ZnII, CuII, NiII, and PdII derivatives. These compounds are porphyrins with quinoxalines fused on opposite or adjacent β,β'-pyrrolic positions; they were synthesized from 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)- porphyrin-2,3,12,13- and -2,3,7,8-tetraone, respectively, by reaction with 1,2-phenylenediamine. The degree of electron spin derealization into the fused rings in the π-radical anions of the free-base and metal(II) bisquinoxalinoporphyrins was elucidated by electrochemistry, UV-vis absorption, and electron spin resonance (ESR) spectra of the singly reduced species and density functional theory calculations. Hyperfine splitting patterns in the ESR spectra of the π-radical anions show that symmetric molecules have delocalized electron spin, indicating that significant inter-quinoxaline interactions are mediated through the central porphyrin unit, these interactions being sufficient to guarantee throughmolecule conduction. However, when molecular symmetry is broken by tautomeric exchange of the inner nitrogen hydrogens in the free-base porphyrin with a corner-type quinoxaline substitution pattern, the π-radical anion becomes confined so that one quinoxaline group is omitted from spin derealization. This indicates the appearance of a unidirectional barrier to through-molecule conduction, suggesting a new motif for chemically controlled rectification. © 2008 American Chemical Society.

West, PJ, Zareie, HM & McDonagh, AM 2008, 'Synthesis and characterization of anthracene-2,6-dithioacetate: a rigid, conjugated molecule for the formation of monolayers on gold', AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 61, no. 10, pp. 758-761.
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The synthesis and characterization of a new photoswitchable anthracene compound, anthracene-2,6-dithioacetate, is presented. The compound dimerizes in solution on irradiation with UV light, and thin films can be formed on gold surfaces from both the monomer and photodimer. © CSIRO 2008.

White, TP, Botten, LC, de Sterke, CM, Dossou, KB & McPhedran, RC 2008, 'Efficient slow-light coupling in a photonic crystal waveguide without transition region', OPTICS LETTERS, vol. 33, no. 22, pp. 2644-2646.
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We consider the coupling into a slow mode that appears near an inflection point in the band structure of a photonic crystal waveguide. Remarkably, the coupling into this slow mode, which has a group index ng > 1000, can be essentially perfect without any transition region. We show that this efficient coupling occurs thanks to an evanescent mode in the slow medium, which has appreciable amplitude and helps satisfy the boundary conditions but does not transport any energy. © 2008 Optical Society of America.

Whitley, R, Zeppel, M, Armstrong, N, Macinnis-Ng, C, Yunusa, I & Eamus, D 2008, 'A modified Jarvis-Stewart model for predicting stand-scale transpiration of an Australian native forest', PLANT AND SOIL, vol. 305, no. 1-2, pp. 35-47.
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Rates of water uptake by individual trees in a native Australian forest were measured on the Liverpool Plains, New South Wales, Australia, using sapflow sensors. These rates were up-scaled to stand transpiration rate (expressed per unit ground area) using sapwood area as the scalar, and these estimates were compared with modelled stand transpiration. A modified Jarvis-Stewart modelling approach (Jarvis 1976), previously used to calculate canopy conductance, was used to calculate stand transpiration rate. Three environmental variables, namely solar radiation, vapour pressure deficit and soil moisture content, plus leaf area index, were used to calculate stand transpiration, using measured rates of tree water use to parameterise the model. Functional forms for the model were derived by use of a weighted non-linear least squares fitting procedure. The model was able to give comparable estimates of stand transpiration to those derived from a second set of sapflow measurements. It is suggested that short-term, intensive field campaigns where sapflow, weather and soil water content variables are measured could be used to estimate annual patterns of stand transpiration using daily variation in these three environmental variables. Such a methodology will find application in the forestry, mining and water resource management industries where long-term intensive data sets are frequently unavailable.

Willcox, MDP, Zhu, H, Conibear, TCR, Hume, EBH, Givskov, M, Kjelleberg, S & Rice, SA 2008, 'Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis', Microbiology, vol. 154, no. 8, pp. 2184-2194.
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Williams, DBG & Lawton, MC 2008, 'Highly atom efficient aluminium triflate catalysed acetal formation', Green Chemistry, vol. 10, no. 9, pp. 914-914.
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Williams, DBG & Pretorius, M 2008, 'Synthesis and evaluation of phosphine–N ligands in transition metal-catalysed CC bond forming reactions', Journal of Molecular Catalysis A: Chemical, vol. 284, no. 1-2, pp. 77-84.
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Williams, DBG, Shaw, ML, Green, MJ & Holzapfel, CW 2008, 'Aluminum Triflate as a Highly Active and Efficient Nonprotic Cocatalyst in the Palladium‐Catalyzed Methoxycarbonylation Reaction', Angewandte Chemie International Edition, vol. 47, no. 3, pp. 560-563.
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Wohlthat, S, Pauly, F & Reimers, JR 2008, 'The conduction properties of alpha,omega-diaminoalkanes and hydrazine bridging gold electrodes', CHEMICAL PHYSICS LETTERS, vol. 454, no. 4-6, pp. 284-288.
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The conduction properties of alpha,omega-diaminoalkanes and hydrazine bridging gold electrodes are investigated using density functional theory in combination with Green's function techniques and group theory. We show that more than 99% of the current at low bias is carried by one channel of A' symmetry whose form is invariant to both the alkane chain length and realistic changes of the injection energy. The total conductance decreases exponentially with a decay constant of 0.73 angstrom(-1) with increasing chain length while the calculated gold- amine contact resistance is ca. 150 k Omega.

Wohlthat, S, Pauly, F & Reimers, JR 2008, 'Two-dimensional, phenanthroline-based, extended pi-conjugated molecules for single-molecule conduction', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 20, no. 29, p. 295208.
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The conduction properties of phenanthroline-terminated, polycyclic extended π-conjugated molecular wires are investigated using density functional theory (DFT) in combination with Green's function techniques and group theory. While these molecules could possibly be thought of as accessible graphene-like fragments, they are calculated to conduct poorly. The decay constant for their exponential decrease of conductance with length is in excess of 0.6 Å-1 for the addition of internal fused quinoxaline groups and in excess of 0.9 Å-1 for the addition of internal pyrazine-fused pyrene groups. Furthermore, while the bidentate phenanthroline connectors adhere strongly to gold, they are sometimes predicted to be less conductive than related monodentate connectors. Careful design is thus required for any graphene-like extended π-system intended for single-molecule conduction applications. © 2008 IOP Publishing Ltd.

Wressnig, A & Booth, DJ 2008, 'Patterns of seagrass biomass removal by two temperate Australian fishes (Monacanthidae)', MARINE AND FRESHWATER RESEARCH, vol. 59, no. 5, pp. 408-417.
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Despite the global significance of nearshore seagrass beds, little is known of their trophodynamic processes. Herbivory by seagrass fishes is thought to be significant but some species previously suspected to be herbivores may be largely detritivorous. Patterns of grazing on the seagrass Posidonia australis by two abundant monacanthid fishes, Meuschenia freycineti and Meuschenia trachylepis, were determined by calculating the removal of seagrass biomass in three Australian estuaries over 14 months. M. freycineti removed significantly more seagrass biomass than M. trachylepis but seagrass biomass removed by both species varied widely across the three estuaries over time. Median amounts of seagrass removal were generally low for all sites compared with standing stock biomass of P. australis leaves and its epiphytes. Nevertheless, grazing by the two species caused high localised rates of removal (up to 90 mg dry weight of P. australis with epibiota per m2) in winter, the season when seagrass growth is least. Such removal rates are far greater than those reported for any other fish grazer in P. australis. These two fish species directly affect seagrass biomass and potentially alter the trophodynamics of P. australis seagrass beds, especially when grazing intensity is high during the season of lowest seagrass growth. © CSIRO 2008.

Wu, J, Wang, G, Jin, D, Yuan, J, Guan, Y & Piper, J 2008, 'Luminescent europium nanoparticles with a wide excitation range from UV to visible light for biolabeling and time-gated luminescence bioimaging', Chem. Commun., no. 3, pp. 365-367.
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Wuhrer, R, Moran, K & Phillips, MR 2008, 'Multi-Detector X-Ray Mapping and Generation of Correction Factor Images for Problem Solving', Microscopy and Microanalysis, vol. 14, no. S2, pp. 1108-1109.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008

Wynne, O, Horvat, J, Smith, R, Hansbro, P, Clifton, V & Hodgson, D 2008, '64. Impact of neonatal infection on adult hippocampal glucocorticoid receptor and mineralocorticoid receptor abundance', Brain, Behavior, and Immunity, vol. 22, no. 4, pp. 19-19.
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Xia, L & Gu, HY 2008, 'SOM-based approach for addressing multi-criteria scheduling problems', Jisuanji Jicheng Zhizao Xitong Computer Integrated Manufacturing Systems CIMS, vol. 14, no. 4, pp. 757-820.
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To solve the posterior multi-criteria scheduling problems, a new method based on Self-Organization feature Map neural network (SOM) was presented to generate approximate Pareto boundaries. Firstly, Lagrange relaxation algorithm was applied to obtain several Pareto optima which were exploited to divide the search space into several domains. For each domain, two simultaneously running SOM were constructed to explore the remaining Pareto optima. According to the characteristics of multi-criteria scheduling, a new definition of neighbor for neural network training was proposed. Numerical experiments demonstrated the feasibility and the effectiveness of this algorithm.

Xie, M, Simpson, DG & Carroll, RJ 2008, 'Semiparametric analysis of heterogeneous data using varying-scale generalized linear models', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 103, no. 482, pp. 650-660.
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Xu, J, Zhong, Y, Jin, D, Zhang, H & Wu, Z 2008, 'Effect of Dietary Fiber and Growth Hormone on Colonic Adaptation in Short Bowel Syndrome Treated by Enteral Nutrition', World Journal of Surgery, vol. 32, no. 8, pp. 1832-1839.
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AbstractBackgroundColon adaptation can partially compensate for the reduced capacity of nutrient absorption in patients with short bowel syndrome (SBS).ObjectiveThe aim of this study was to assess the effect of combined treatment with enteral nutrition (EN), dietary fiber, and recombinant human growth hormone (rhGH) on promoting colonic adaptation.MethodsA group of 40 male Sprague‐Dawley rats undergoing up to 80% to 85% small intestine resection were randomly assigned to four groups of 10 rats each: enteral nutrition (EN, the control); enteral nutrition/dietary fiber (EF); enteral nutrition/rhGH (EG); and enteral nutrition/dietary fiber/rhGH (EFG). All groups received isonitrogenous, isocaloric enteral feeding for 21 days. Body weight, daily nitrogen balance, colonic morphology, DNA, insulin‐like growth factor‐1/IGF‐1 receptor (IGF‐1)/IGF‐1R) expression were determined.ConclusionMorphologic adaptation of the colon (including increased mucosal thickness and plica height, enlarged surface area, increased hyditloid cells) was observed on postoperative day 21. GH is superior to fiber in several aspects: increasing colon diameters (0.46 ± 0.03 vs. 0.38 ± 0.02 cm, P < 0.05), villous height (356 ± 23 vs. 307 ± 21 μm, P < 0.05) and total surface area (15,222 ± 1344 vs. 13,178 ± 1727 μm2, P < 0.05). Increased DNA content—1.66 ± 0.13 (EG) and 1.71 ± 0.13 (EGF) vs. 1.28 ± 0.11(EF), P < 0.05—in the colon was also found in the EG and EGF groups. GH administration led to a significant increase in plasma IGF‐1 (439.6 ± 88.3 ng/ml in the EG group, 455.4 ± 107.4 ng/ml in the EGF ...

Yanetz, R, Carroll, RJ, Dodd, KW, Subar, AF, Schatzkin, A & Freedman, LS 2008, 'Using Biomarker Data to Adjust Estimates of the Distribution of Usual Intakes for Misreporting: Application to Energy Intake in the US Population', Journal of the American Dietetic Association, vol. 108, no. 3, pp. 455-464.
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Yang, J, Li, S, Li, ZW, McBean, K & Phillips, MR 2008, 'Origin of excitonic emission suppression in an individual ZnO nanobelt', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 112, no. 27, pp. 10095-10099.
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The near band edge emissions of an individual ZnO nanobelt were investigated by cathodoluminescence spectroscopy, which has unique advantages in higher spatial resolution, orientation, and environmental independence over the conventional photoluminescence spectroscopy. The results show that the presence of a large surface-to-volume ratio is the determinant to suppress the formation of excitons in ZnO nanobelts. Ab initio calculations show that a drastic decrease of density-of-state in the conduction band and increase in the valence band upon size reduction are the key consequence of the large surface-to-volume ratio, revealing the possible fundamental physical origin of exciton suppression. The weak exciton polarity also reduces the likelihood for an exciton to couple with longitudinal phonons. This causes a reduction in the first longitudinal phonon replica intensity and then a complete suppression of the second replica. Understanding the effect of large surface ratio upon the physical properties of ZnO nanomaterials may provide new insights into the fundamental science of nanotechnology for the development of optoelectronics. © 2008 American Chemical Society.

Yang, J, Wang, G, Liu, H, Park, J, Gou, X & Cheng, X 2008, 'Solvothermal synthesis and characterization of ZnSe nanoplates', JOURNAL OF CRYSTAL GROWTH, vol. 310, no. 15, pp. 3645-3648.
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ZnSe nanoplates were synthesized by a solvothermal method using ethylenediamine (EN) as the liganding solvent. The crystal structures, morphologies and optical properties of the precursor and ZnSe products were systematically characterized. Results reveal that precursor ZnSe(en)1/2 with a layered structure was initially obtained through solvothermal synthesis, which can be converted into hexagonal wurtzite structured ZnSe by heat-treatment in Ar atmosphere. The as-prepared ZnSe was composed of stacked nanoplates. The field emission scanning electron microscope (FESEM) and transmission electron microscope (TEM) results reveal that every nanoplate was made up of plenty of tiny single crystals. The room temperature ultraviolet-visible (UV/vis) measurements indicate that the bandgap of the obtained ZnSe is 2.7 eV and a large blue shift about 1.3 eV was observed in precursor ZnSe(en)1/2. © 2008 Elsevier B.V. All rights reserved.

Yousef Mohamad, K, Rekiki, A, Myers, G, Bavoil, PM & Rodolakis, A 2008, 'Identification and characterisation of coding tandem repeat variants in incA gene of Chlamydophila pecorum.', Vet Res, vol. 39, no. 6, p. 56.
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Bacteria of the family Chlamydiaceae are obligate intracellular pathogens of human and animals. Chlamydophila pecorum is associated with different pathological conditions in ruminants, swine and koala. To characterize a coding tandem repeat (CTR) identified at the 3' end of incA gene of C. pecorum, 51 strains of different chlamydial species were examined. The CTR were observed in 18 of 18 tested C. pecorum isolates including symptomatic and asymptomatic animals from diverse geographical origins. The CTR were also found in two strains of C. abortus respectively isolated from faeces from a healthy ewe and from a goat belonging to asymptomatic herds, but were absent in C. abortus strains isolated from clinical disease specimens, and in tested strains of C. psittaci, C. caviae, C. felis and C. trachomatis. The number of CTR repeats is variable and encode several motifs that are rich in alanine and proline. The CTR-derived variable structure of incA, which encode the Chlamydiaceae-specific type III secreted inclusion membrane protein, IncA, may be involved in the adaptation of C. pecorum to its environment by allowing it to persist in the host cell.

Yousef Mohamad, K, Roche, SM, Myers, G, Bavoil, PM, Laroucau, K, Magnino, S, Laurent, S, Rasschaert, D & Rodolakis, A 2008, 'Preliminary phylogenetic identification of virulent Chlamydophila pecorum strains', Infection, Genetics and Evolution, vol. 8, no. 6, pp. 764-771.
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Yu, J, Cheng, YY, Tao, Q, Wong, YP, Tian, L, Jin, H, Leung, WK, Chan, FKL & Sung, JJY 2008, 'M1619 Methylated Protocadherin 10 Is Identified As a Target of Epigenetic Silencing and a Prognostic Predictor in Gastric Cancer', Gastroenterology, vol. 134, no. 4, pp. A-383.
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Yu, J, Tao, Q, Cheng, YY, Tian, L, Cheung, KF & Sung, JJY 2008, 'M1615 Aberrant Methylation of Dkk-3 in Gastric Cancer Associated with Poor Outcome', Gastroenterology, vol. 134, no. 4.
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Yu, J, Tao, Q, Cheung, KF, Jin, H, Poon, FF, Wang, X, Li, H, Cheng, YY, Röcken, C, Ebert, MPA, Chan, ATC & Sung, JJY 2008, 'Epigenetic identification of ubiquitin carboxyl‐terminal hydrolase L1 as a functional tumor suppressor and biomarker for hepatocellular carcinoma and other digestive tumors†', Hepatology, vol. 48, no. 2, pp. 508-518.
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Yu, J, Tao, Q, Jin, H, Poon, FF, Wang, X, Li, H, Cheng, YY, Ebert, MPA, Röcken, C, Chan, AW & Sung, JJY 2008, 'M1616 Functional Significance of a Putative Tumor Suppressor, the Ubiquitin Carboxyl-Terminal Hydrolase L1 Gene, in Multiple Digestive Tumors', Gastroenterology, vol. 134, no. 4, pp. A-383.
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Yunusa, IAM, Manoharan, V, DeSilva, DL, Eamus, D, Murray, BR & Nissanka, SP 2008, 'Growth and elemental accumulation by canola on soil amended with coal fly ash', JOURNAL OF ENVIRONMENTAL QUALITY, vol. 37, no. 3, pp. 1263-1270.
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To explore the agronomic potential of an Australian coal fly ash, we conducted two glasshouse experiments in which we measured chlorophyll fluorescence, CO2 assimilation (A), transpiration, stomacal conductance, biomass accumulation, seed yield, and elemental uptake for canola (Brassica napus) grown on soil amended with an alkaline fly ash. In Experiment 1, application of up to 25 Mg/ha of fly ash increased A and plant weight early in the season before flowering and seed yield by up to 21%. However, at larger rates of ash application A, plant growth, chlorophyll concentration, and yield were all reduced. Increases in early vigor and seed yield were associated with enhanced uptake of phosphorus (P) by the plants treated with fly ash. Fly ash application did not influence accumulation of B, Cu, Mo, or Zn in the stems at any stage of plant growth or in the seed at harvest, except Mo concentration, which was elevated in the seed. Accumulation of these elements was mostly in the leaves, where concentrations of Cu and Mo increased with any amount of ash applied while that of B occurred only with ash applied at 625 Mg/ha. In Experiment 2, fly ash applied at 500 Mg/ha and mixed into die whole 30 cm soil core was detrimental to growth and yield of canola, compared with restricting mixing to 5 or 15 cm depth. In contrast, application of ash at 250 Mg/ha with increasing depth of mixing increased A and seed yield. We concluded that fly ash applied at not more than 25 Mg/ha and mixed into the top 10 to 15 cm of soil is sufficient to obtain yield benefits. Copyright © 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Yunusa, IAM, Nuberg, IK, Fuentes, S, Lu, P & Eamus, D 2008, 'A simple field validation of daily transpiration derived from sapflow using a porometer and minimal meteorological data', PLANT AND SOIL, vol. 305, no. 1-2, pp. 15-24.
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Heat-pulse techniques are routinely used to estimate transpiration from canopies of woody plants typically without any local calibration, mainly because of the difficulty of doing so in the field and, frequently, lack of detailed weather data. This is de

Yunusa, IAM, Nuberg, IK, Fuentes, S, Lu, P & Eamus, D 2008, 'A simple field validation of daily transpiration derived from sapflow using a porometer and minimal meteorological data (vol 305, pg 15, 2008)', PLANT AND SOIL, vol. 310, no. 1-2, pp. 269-269.
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Zareie, HM, Morgan, SW, Moghaddam, M, Maaroof, AI, Cortie, MB & Phillips, MR 2008, 'Nanocapacitive circuit elements', ACS NANO, vol. 2, no. 8, pp. 1615-1619.
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'Natural' lithography was used to prepare arrays of nanoscale capacitors on silicon. The capacitance was verified by a novel technique based on the interaction of a charged substrate with the electron beam of a scanning electron microscope. The 'nanocapacitors' possessed a capacitance of ∼1 × 10-16F and were observed to hold charge for over an hour. Our results indicate that fabricating nanostructures using natural lithography may provide a viable alternative for future nanoelectronic devices. © 2008 American Chemical Society.

Zaslawski, CJ 2008, 'Acupuncture for Persistent Allergic Rhinitis', Australian Journal of Acupuncture and Chinese Medicine, vol. 3, no. 1, pp. 56-56.

Zaslawski, CJ, Zheng, Z & Smith, C 2008, 'The Status and Future of Acupuncture Research:10 Years Post NIH Consensus Conference', Australian Journal of Acupuncture and Chinese Medicine, vol. 3, pp. 66-67.

Zeppel, M & Eamus, D 2008, 'Coordination of leaf area, sapwood area and canopy conductance leads to species convergence of tree water use in a remnant evergreen woodland', AUSTRALIAN JOURNAL OF BOTANY, vol. 56, no. 2, pp. 97-108.
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Zeppel, M, Macinnis-Ng, C, Palmer, A, Taylor, D, Whitley, R, Fuentes, S, Yunusa, I, Williams, M & Eamus, D 2008, 'An analysis of the sensitivity of sap flux to soil and plant variables assessed for an Australian woodland using a soil-plant-atmosphere model', FUNCTIONAL PLANT BIOLOGY, vol. 35, no. 6, pp. 509-520.
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Daily and seasonal patterns of tree water use were measured for the two dominant tree species, Angophora bakeri E.C.Hall (narrow-leaved apple) and Eucalyptus sclerophylla (Blakely) L.A.S. Johnson & Blaxell (scribbly gum), in a temperate, open, evergreen woodland using sap flow sensors, along with information about soil, leaf, tree and micro-climatological variables. The aims of this work were to (a) validate a soil-plant-atmosphere (SPA) model for the specific site; (b) determine the total depth from which water uptake must occur to achieve the observed rates of tree sap flow; (c) examine whether the water content of the upper soil profile was a significant determinant of daily rates of sap flow; and (d) examine the sensitivity of sap flow to several biotic factors. It was found that (a) the SPA model was able to accurately replicate the hourly, daily and seasonal patterns of sap flow; (b) water uptake must have occurred from depths of up to 3 m; (c) sap flow was independent of the water content of the top 80 cm of the soil profile; and (d) sap flow was very sensitive to the leaf area of the stand, whole tree hydraulic conductance and the critical water potential of the leaves, but insensitive to stem capacitance and increases in root biomass. These results are important to future studies of the regulation of vegetation water use, landscape-scale behaviour of vegetation, and to water resource managers, because they allow testing of large-scale management options without the need for large-scale manipulations of vegetation cover. © CSIRO 2008.

Zeppel, M, Macinnis-Ng, CMO, Ford, CR & Eamus, D 2008, 'The response of sap flow to pulses of rain in a temperate Australian woodland', PLANT AND SOIL, vol. 305, no. 1-2, pp. 121-130.
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In water-limited systems, pulses of rainfall can trigger a cascade of plant physiological responses. However, the timing and size of the physiological response can vary depending on plant and environmental characteristics, such as rooting depth, plant size, rainfall amount, or antecedent soil moisture. We investigated the influence of pulses of rainfall on the response of sap flow of two dominant evergreen tree species, Eucalyptus crebra (a broadleaf) and Callitris glaucophylla (a needle leaved tree), in a remnant open woodland in eastern Australia. Sap flow data were collected using heat-pulse sensors installed in six trees of each species over a 2 year period which encompassed the tail-end of a widespread drought. Our objectives were to estimate the magnitude that a rainfall pulse had to exceed to increase tree water use (i.e., define the threshold response), and to determine how tree and environmental factors influenced the increase in tree water use following a rainfall pulse. We used data filtering techniques to isolate rainfall pulses, and analysed the resulting data with multivariate statistical analysis. We found that rainfall pulses less than 20 mm did not significantly increase tree water use (P>0.05). Using partial regression analysis to hold all other variables constant, we determined that the size of the rain event (P<0.05, R 2=0.59), antecedent soil moisture (P<0.05, R 2=0.29), and tree size (DBH, cm, P<0.05, R 2=0.15), all significantly affected the response to rainfall. Our results suggest that the conceptual Threshold-Delay model describing physiological responses to rainfall pulses could be modified to include these factors. We further conclude that modelling of stand water use over an annual cycle could be improved by incorporating the T-D behaviour of tree transpiration.

Zeppel, MJB, Macinnis-Ng, CMO, Yunusa, IAM, Whitley, RJ & Eamus, D 2008, 'Long term trends of stand transpiration in a remnant forest during wet and dry years', Journal of Hydrology, vol. 349, no. 1-2, pp. 200-213.
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Daily and annual rates of stand transpiration in a drought year and a non-drought year are compared in order to understand the adaptive responses of a remnant woodland to drought and predict the effect of land use change. Two methods were used to estimat

Zhang, D-Y, Ma, Z-F, Wang, G, Chen, J, Wallace, GC & Liu, H-K 2008, 'Preparation of Low Loading Pt/C Catalyst by Carbon Xerogel Method for Ethanol Electrooxidation', Catalysis Letters, vol. 122, no. 1-2, pp. 111-114.
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Low platium loading Pt/C catalyst was prepared by direct Pt-embedded carbon xerogel method. The Pt content of the as-prepared Pt/C is about 4.32 wt% and has a typical polycrystalline phase. Textural and structural characteristics of the catalysts were characterized by XRD, EDS and BET. Pt-embedded in carbon xerogel increases the specific surface area and pore volume of the X-Pt/C during carbon gelation and the carbonization process. Electrochemical characteristics of the catalysts for ethanol electrooxidation were measured. The results indicated that the as-prepared 4.32 wt% Pt/C has higher mass current density in ethanol electrooxidation as compared to the 20 wt% Pt/C. This may be due to the high roughness of the Pt surface that is formed during the carbon gelation and carbonization process. © 2007 Springer Science+Business Media, LLC.

Zhang, W-G & Wang, Y-L 2008, 'An analytic derivation of admissible efficient frontier with borrowing', European Journal of Operational Research, vol. 184, no. 1, pp. 229-243.
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Zheng, L, Wayper, PJ, Gibbs, AJ, Fourment, M, Rodoni, BC & Gibbs, MJ 2008, 'Accumulating Variation at Conserved Sites in Potyvirus Genomes Is Driven by Species Discovery and Affects Degenerate Primer Design', PLoS ONE, vol. 3, no. 2, pp. e1586-e1586.
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Zhou, L, Huang, JZ & Carroll, RJ 2008, 'Joint modelling of paired sparse functional data using principal components', Biometrika, vol. 95, no. 3, pp. 601-619.
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Zhou, L, Powell, CA, Li, W, Irey, M & Duan, Y 2008, 'Prophage-Mediated Dynamics of ‘Candidatus Liberibacter asiaticus’ Populations, the Destructive Bacterial Pathogens of Citrus Huanglongbing', PLoS ONE, vol. 8, no. 12, pp. e82248-e82248.
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Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and p

Zuo, Y, Gu, H & Xi, Y 2008, 'Study on constraint scheduling algorithm for job shop problems with multiple constraint machines', INTERNATIONAL JOURNAL OF PRODUCTION RESEARCH, vol. 46, no. 17, pp. 4785-4801.
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This paper focuses on a job-shop scheduling problem with multiple constraint machines (JSPMC). A constraint scheduling method for the JSPMC is proposed. It divides the machines in the shop into constraint and non-constraint machines based on a new identification method, and formulates a reduced problem only for constraint machines while replacing the operations of non-constraint machines with time lags. The constraint machines are scheduled explicitly by solving the reduced problem with an efficient heuristic, while the non-constraint machines are scheduled by the earliest operation due date (EODD) dispatching rule. Extensive computational results indicate that the proposed constraint scheduling algorithm can obtain a better trade-off between solution quality and computation time compared with various versions of the shifting bottleneck (SB) methods for the JSPMC.