Publications

Larkum, AWD, Orth, RJ & Duarte, CM 2006, SEAGRASSES: BIOLOGY, ECOLOGYAND CONSERVATION, Springer Netherlands.
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Seagrasses are unique plants; the only group of flowering plants to recolonise the sea. They occur on every continental margin, except Antarctica, and form ecosystems which have important roles in fisheries, fish nursery grounds, prawn fisheries, habitat diversity and sediment stabilisation. Over the last two decades there has been an explosion of research and information on all aspects of seagrass biology. However the compilation of all this work into one book has not been attempted previously. In this book experts in 26 areas of seagrass biology present their work in chapters which are state-of-the-art and designed to be useful to students and researchers alike. The book not only focuses on what has been discovered but what exciting areas are left to discover. The book is divided into sections on taxonomy, anatomy, reproduction, ecology, physiology, fisheries, management, conservation and landscape ecology. It is destined to become the chosen text on seagrasses for any marine biology course. © 2006/2007 Springer. All Rights Reserved.

Platen, E & Heath, D 2006, A Benchmark Approach to Quantitative Finance, 1st, Springer Berlin Heidelberg, Berlin, Germany.
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The benchmark approach provides a general framework for financial market modeling, which extends beyond the standard risk-neutral pricing theory. It permits a unified treatment of portfolio optimisation, derivative pricing, integrated risk managemetn and insurance risk modeling. Th existence of an equivalent risk-neutral pricing measure is not required.Instead, it leads to pricing formulae with respect to the real-world probability measure. This yields important modeling freedom which turns out to be necessary for the derivation of realistic, parsimonious market models. The first part of the book describes the necessary tools fromprobability theory, statistics, stochastic calculus and the theory of stochastic differential equations with jumps. The second part of devoted to financial modeling by the benchmark approach. Various quajtitative methods for the real-world pricing and hedging of derivatives are explained. The general framework is used to provide an understanding of the nature of stochastic volatility. The book is intended for a wide audience that includes quantitative analysts, postgraduate students and practitioners in finance, economics and insurance. It aims to be a self- contained, accessible but methematically rigorous introduction to quantitative finance for readers that have a reasonable mathematical or quantitative background. Finally, the book hsould stimulate inetrest in the benchmark approach by describing some of its power and wide applicability.

Baladandayuthapani, V, Holmes, CC, Mallick, BK & Carroll, RJ 2006, 'Modeling Nonlinear Gene Interactions Using Bayesian MARS' in Bayesian Inference for Gene Expression and Proteomics, Cambridge University Press, pp. 116-136.
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Ben-Nissan, B & Ylänen, HO 2006, 'Bioactive Glasses and Glass Ceramics' in Metin Akay (ed), Wiley Encyclopedia of Biomedical Engineering, Wiley, United States, pp. 0-0.
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Abstract Glasses and glass ceramics are widely investigated and produced as biomaterials with CaO and P 2 O 5 additions to their base compositions. One of the main advantages of phosphate‐based materials is their chemical relationship with carbonate hydroxyapatite, one of the main constituents of bone and teeth. Although bioglass was invented in the 1960s, glass has been known to humankind for thousands of years and widely used in building and engineering applications. In this chapter, we review general definitions of glass, glass types presently available, production methods, properties, and their biomedical use. Classification of biomaterials and bioactivity will be introduced to cover the development and progress of the commercially available and currently investigated bioglasses and glass ceramics. Their chemistry, structure, bioactivity, theories behind their bonding within a physiological environment and their interfacial strengths, their synthesis methods, and some of their applications in the biomedical field will be covered.

BILIĆ, A, REIMERS, JR & HUSH, NS 2006, 'FUNCTIONALIZATION OF SEMICONDUCTOR SURFACES BY ORGANIC LAYERS: CONCERTED CYCLOADDITION VERSUS STEPWISE FREE-RADICAL REACTION MECHANISMS' in Properties of Single Organic Molecules on Crystal Surfaces, PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., pp. 333-360.
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In the age when the miniaturization trend that has driven the semiconductor industry is reaching its limits, organic modification of semiconductors is emerging as a field that could give much-needed impetus. We review the current state of understanding of the functionalization of C(100), Si(100), and Ge(100) surfaces through chemisorption of alkenes and alkynes, focusing on adsorbate structural control. While reactions on C(100) show most of the properties expected for concerted cycloaddition reactions such as [2+2] and [4+2] (Diels–Alder) processes, reactions on Si(100) present a wide range of variant behavior, including in some cases the prominence of non-cycloaddition products. More general stepwise free-radical addition processes are seen to provide a better description of reactions on Si(100), their prominence being attributed to either the non-existence or ineffectiveness of π bonding within surface silicon dimers. The investigations of these systems provide not only insight into driving mechanisms for chemisorption but also motivation for the development of new techniques of organic functionalization on semiconductors.

Dalton, JP, Caffrey, CR, Sajid, M, Stack, C, Donnelly, S, Loukas, A, Don, T, McKerrow, J, Halton, DW & Brindley, PJ 2006, 'Proteases in trematode biology.' in Parasitic flatworms: molecular biology, biochemistry, immunology and physiology, CABI, pp. 348-368.
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This chapter discusses the following topics: trematode gut, blood as a source of amino acids, prevention of ingested blood clotting in the gut, lysis of blood cells, peptidases involved in the digestion of blood and tissue proteins in schistosomes and liver flukes, regulation of the digestive process, non-feeding functions attributed to peptidases (invasion and migration through host tissue, excystment of juvenile parasites, hatching of eggs), phylogeny of proteases (cathepsin B, cathepsins L and F, aspartic proteases), gene structure analysis, orthology and molecular evolution.

Dickman, CR & Murray, B 2006, 'Species interactions: complex effects' in Attiwell, P & Wilson, B (eds), Ecology: An Australian Perspective, Oxford University Press, South Melbourne, Australia, pp. 317-334.
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Interactions within ecological communities usually involve many species and pose intriguing challenges for ecologists who wish to map and disentangle them. To simplify this task we often assume that the interactions do not change in strength or direction and that the identities of the key species remain the same. Species can be 'pigeon-holed' into convenient categories such as 'pollinator', 'competitor', 'pest' or even 'redundant' using these assumptions. This makes programs of conservation or pest management easier to implement, but is also ignores an emerging body of evidence that interactions between species vary between situations, places and times. In this chapter we will explore the complexity of effects that arise from changes in tereactions between species. We also consider how such effects may be modelled and predicted,a nd illustrate how ecological insight can be used to guide management decisions.

Harry, E, Monahan, L & Thompson, L 2006, 'Bacterial Cell Division: The Mechanism and Its Precison' in Jeon, KW (ed), International Review of Cytology, Elsevier, The netherlands, pp. 27-94.
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The recent development of cell biology techniques for bacteria to allow visualization of fundamental processes in time and space, and their use in synchronous populations of cells, has resulted in a dramatic increase in our understanding of cell division and its regulation in these tiny cells. The first stage of cell division is the formation of a Z ring, composed of a polymerized tubulin-like protein, FtsZ, at the division site precisely at midcell. Several membrane-associated division proteins are then recruited to this ring to form a complex, the divisome, which causes invagination of the cell envelope layers to form a division septum. The Z ring marks the future division site, and the timing of assembly and positioning of this structure are important in determining where and when division will take place in the cell. Z ring assembly is controlled by many factors including negative regulatory mechanisms such as Min and nucleoid occlusion that influence Z ring positioning and FtsZ accessory proteins that bind to FtsZ directly and modulate its polymerization behavior. The replication status of the cell also influences the positioning of the Z ring, which may allow the tight coordination between DNA replication and cell division required to produce two identical newborn cells. © 2006 Elsevier Inc. All rights reserved.

Larkum, AWD, Drew, EA & Ralph, PJ 2006, 'Photosynthesis and Metabolism in Seagrasses at the Cellular Level' in Larkum, AWD, Orth, RJ & Dyarte, CM (eds), SEAGRASSES: BIOLOGY, ECOLOGYAND CONSERVATION, Springer Netherlands, Dordrecht, The Netherlands, pp. 323-345.
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Seagrasses are marine angiosperms from the Families Potamagetonaceae and Hydrocharitaceae (Chapter 1). These are by origin land plants that developed both aerial photosynthesis and aerial flowering and then returned to a successful fully submerged marine habitat, from where their algal forbears derived. Following the evolution of land plants there have been few developments in terms of photosynthesis: the only outstanding developments being adaptations to arid conditions, such as the development of C4 photosynthesis in semi-arid plants and Crassulacean Acid Metabolism (CAM) in plants from desert regions (Bowes et al. 2002). © 2006/2007 Springer. All Rights Reserved.

Pitman, MR & Menz, RI 2006, 'Methods for Protein Homology Modelling' in Applied Mycology and Biotechnology, Elsevier, pp. 37-59.
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Ralph, PJ, Tomasko, D, Moore, K, Seddon, S & Macinnis-Ng, CMO 2006, 'Human Impacts on Seagrasses: Eutrophication, Sedimentation, and Contamination' in Larkum, AWD, Orth, RJ & Duarte, CM (eds), SEAGRASSES: BIOLOGY, ECOLOGYAND CONSERVATION, Springer Netherlands, The Netherlands, pp. 567-593.
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Growth of human populations along coastal environments, as well as poor water management practices have resulted in the complete loss of seagrass meadows (Kemp et al., 1983; Larkum and West, 1990; Short and Wyllie-Echeverria, 1996; Peters et al., 1997). For example, the catastrophic loss of seagrasses clearly illustrated in Fig. 1 is linked to coastal development and associated reduction in water quality. © 2006/2007 Springer. All Rights Reserved.

Rashid, I, Brown, BE, van Reyk, DM & Davies, MJ 2006, 'The Roles of Protein Glycation, Glycoxidation, and Advanced Glycation End-Product Formation in Diabetes-Induced Atherosclerosis' in Kaur Sukhinder, C (ed), Biochemistry of Atherosclerosis, Springer US, New York, USA, pp. 247-283.
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Diabetes is known to induce a range of micro-and macrovascular compliacations with the latter resutling in premature and accelerated atherosclerosis. Thus people with diabetes have a 2-4 fold increased risk of developing cardiovascular diseases which is responsible for ca. 50% of deaths amongst people with diabetes. The mechanisms behind this elevated risk are still not fully understood, though there is now increasing evidence for a role of glycation and clycoxidation reactions induced by hyperglycemia. This article reviews current knowledge of the role that these reactions play in diabetes-induced atherosclerosis with particular emphasis on the molecular reactions that result in the modification of lipoproteins, and the consequences of these reactions on cellular metabolism.

Rice, SA & Kjelleberg, S 2006, 'Bacterial biofilm formation, adaptation and fitness' in Microbial Ecology of Aerial Plant Surfaces, pp. 67-82.

SPEER, MS & LESLIE, LM 2006, 'LOCAL TO LONG-RANGE DUST TRANSPORT OVER CENTRAL EASTERN AUSTRALIA' in Volume 5: Oceans and Atmospheres, World Scientific Publishing Co. Pte. Ltd., pp. 29-40.
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© 2006 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. A climatology of dust reporting days from 1995 to February 2004 has been prepared for the central eastern Australia region. The climatology reveals a total of 55 "dust days," consisting of 43 dust days associated with fronts. Of these 24 were classified as being embedded in the zonal westerlies in the Great Australian Bight (GAB) or in westerlies produced by from low-pressure systems in the GAB. The remaining 19 were associated with fronts over eastern Australia where high pressure systems in the GAB generated postfrontal south to southeast winds. Two case studies of dust storm generation and transport were modeled using an integrated wind erosion prediction system. The model predictions were broadly consistent with both satellite images highlighting dust and with the synoptic observations that reported dust.

Whitchurch, CB 2006, 'Biogenesis and Function of Type IV Pili in Pseudomonas Species' in Ramos, JL & Levesque, RC (eds), Pseudomonas, Springer US, Netherlands, pp. 139-188.
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Type IV pili or fimbriae are non-flagellar, filamentous surface appendages that are associated with a number of biological activities in bacteria. These processes include a form of surface translocation termed twitching motility; bacteriophage sensitivity; attachment to biotic (bacteria, plant, animal) and abiotic surfaces; biofilm development; and the uptake of naked DNA by natural transformation. Many of these biological functions are reliant on the ability of these structures to extend and retract.

Abel, J, Schares, G, Orzeszko, K, Gasser, RB & Ellis, JT 2006, 'Hammondia isolated from dogs and foxes are genetically distinct', PARASITOLOGY, vol. 132, no. 2, pp. 187-192.
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Hammondia heydorni is regarded as a protozoan parasite that uses canids, e.g. dogs and foxes, as definitive hosts, but clinical signs of infection are rare. This study therefore took advantage of the opportunity to study an oocyst population from the faeces of a dog suffering from intermittent bouts of diarrhoea. Oocysts from the naturally infected dog were shown to be H. heydorni by using the polymerase chain reaction combined with DNA sequencing as a diagnostic tool.† A comparison of the first internal transcribed spacer (ITS1) sequence of ribosomal DNA obtained with those from other dog and fox oocysts, previously regarded as H. heydorni, showed these oocysts contained identical ITS1 sequences. However, the oocyst DNA from the fox and dog differed by the presence/absence of a 9 bp insertion/deletion within intron 1 of the alpha tubulin gene, and this difference was conserved across a number of different oocyst populations from the 2 species of host. A PCR assay was established that takes advantage of this insertion/deletion and is able to differentiate between the 2 oocyst populations. This study therefore provides evidence that H. heydorni oocysts from dogs and foxes represent 2 distinct genetic lineages that can be differentiated using a PCR, which targets the alpha tubulin locus. © 2005 Cambridge University Press.

Aktan, F, Henness, S, Tran, V, Duke, C, Roufogalis, B & Ammit, A 2006, 'Gingerol Metabolite and a Synthetic Analogue Capsarol™ Inhibit Macrophage NF-κB-Mediated iNOS Gene Expression and Enzyme Activity', Planta Medica, vol. 72, no. 8, pp. 727-734.
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Alquezar, R, Markich, SJ & Booth, DJ 2006, 'Effects of metals on condition and reproductive output of the smooth toadfish in Sydney estuaries, south-eastern Australia', ENVIRONMENTAL POLLUTION, vol. 142, no. 1, pp. 116-122.
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This study determined the condition and reproductive output of a common estuarine toadfish, Tetractenos glaber, in two metal contaminated and two reference estuaries near Sydney, Australia. Female toadfish from metal contaminated estuaries were smaller and younger than in reference estuaries; however, it could not be resolved whether these differences were due to direct effects of metal contamination or differences in nutritional value of prey. Lipid content in liver and gonad tissues was inversely related with levels of As, Pb, Cd and Co in sediment. In contrast, protein content in liver, gonad and muscle tissues was positively related to sediment levels of Ni and Co. Increased levels of Pb in gonads were associated with decreased oocyte diameter and density. This suggests a reduction in egg size and fecundity, which ultimately may lead to a decline in female reproductive output. Changes in fish health and reproduction caused by chemical pollutants may alter fish population and community structure. © 2005 Elsevier Ltd. All rights reserved.

Alquezar, R, Markich, SJ & Booth, DJ 2006, 'Metal accumulation in the smooth toadfish, Tetractenos glaber, in estuaries around Sydney, Australia', ENVIRONMENTAL POLLUTION, vol. 142, no. 1, pp. 123-131.
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This study determined the metal levels in sediments and tissues of a common estuarine fish, Tetractenos glaber (smooth toadfish), from two metal contaminated and two reference estuaries near Sydney, Australia. Metal levels were highest in sediments and fish from contaminated estuaries. Gonads contained the highest metal levels followed by muscle, gill and liver. Metal accumulation was gender-dependant (e.g. male gonads were >20 times higher in As than females; female gills were >30 times higher than males for Pb). Cadmium, Pb and Ni levels in fish tissues reflected sediment levels, indicating sediment and/or dietary metal uptake. Levels of As, Co, Cd & Pb in gills showed similar patterns to other tissues, suggesting that metals may have been taken up by gills through contaminated water. Similar metal patterns in tissues and sediments suggest more than one uptake pathway. This study indicates that multiple factors influence metal accumulation in fish. © 2005 Elsevier Ltd. All rights reserved.

Amarasinghe, BHRR, Faivre-Nitschke, E, Wu, Y, Udall, JA, Dennis, ES, Constable, G & Llewellyn, DJ 2006, 'Genomic approaches to the discovery of promoters for sustained expression in cotton (Gossypium hirsutum L.) under field conditions: expression analysis in transgenic cotton and Arabidopsis of a Rubisco small subunit promoter identified using EST sequence analysis and cDNA microarrays', Plant Biotechnology, vol. 23, no. 5, pp. 437-450.
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Biotechnology requires robust and predictable expression of transgenes. Most commercial Genetically Modified (GM) crops contain the viral 35S promoter to drive insecticide and herbicide resistance genes. In cotton there have been reductions in efficacy of Bacillus thuringiensis toxin (Bt) expressing plants late in the season that have been attributed to reductions in promoter activity. We have used genomic approaches to identify cotton genes whose expression remains high during the season to find promoters that might better maintain expression of transgenes in the field. A cDNA library from young late season leaves was used to generate about 2000 ESTs. Clustering of ESTs was used to determine relative transcript abundance and identify the most highly-expressed genes. These were primarily photosynthetic and housekeeping genes and some metabolic genes. The ESTs were printed to a small cDNA microarray and probed with both early- and late-season leaf mRNAs. Absolute fluorescence levels were used to rank genes and confirm the EST abundance data. Candidate genes, including the small subunit of Rubisco (RbcS) were selected. An RbcS promoter (Genbank Accession DQ648074) was isolated and analysed in both Arabidopsis and cotton linked to a GUS reporter gene. Expression of the reporter gene was consistently high in green tissues throughout the life cycle of cotton in the glasshouse, and in the field. A number of other candidate promoters have been identified that may be useful in a variety of biotechnology applications. Copyright © 2006 The Japanese Society for Plant Cell and Molecular Biology.

Arnold, MD 2006, 'An efficient solution for scattering by a perfectly conducting strip grating', JOURNAL OF ELECTROMAGNETIC WAVES AND APPLICATIONS, vol. 20, no. 7, pp. 891-900.
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An efficient implementation of a Wiener-Hopf solution for complementary strip gratings is presented. Acceleration of the required infinite product is achieved via a hybrid approach involving a gamma function expression for the infinite product of Taylor approximated terms. The efficiency of the accelerated method is compared to the brute-force method as a function of system parameters.

Asatryan, AA, Botten, LC, Nicorovici, NA, McPhedran, RC & de Sterke, CM 2006, 'Frequency shift of sources embedded in finite two-dimensional photonic clusters', WAVES IN RANDOM AND COMPLEX MEDIA, vol. 16, no. 2, pp. 151-165.
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The frequency (Lamb) shift and local density of states (LDOS) in two-dimensional photonic crystals composed of a cluster of infinitely long circular cylinders is calculated classically using the radiation reaction mechanism. We investigate the frequency shift and LDOS as a function of the size of the cluster and show that, at the edges of the band gap, both quantities can be large and increase in magnitude with cluster size. We explain this in terms of poles of a scattering operator and also show that both the Lamb shift and LDOS are sensitive functions of the shape of the cluster.

Ashmore, J, Bishop, R, Craig, DC & Scudder, ML 2006, 'Inclusion of polyhalomethanes by a tetrahalogenated diquinoline host', CrystEngComm, vol. 8, no. 12, pp. 923-923.
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B Whitchurch, C 2006, 'Complexity in ?2-component? signal transduction systems', Microbiology Australia, vol. 27, no. 3, pp. 128-128.
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The ?2-component? regulatory systems of bacteria are the predominant signal transduction mechanisms that bacteria utilise to modulate behaviours and metabolism in response to environmental changes. These systems classically involve two proteins ? a membrane bound sensor histidine kinase and a soluble response regulator.

Barbosa, HA, Huete, AR & Baethgen, WE 2006, 'A 20-year study of NDVI variability over the Northeast Region of Brazil', JOURNAL OF ARID ENVIRONMENTS, vol. 67, no. 2, pp. 288-307.
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The natural ecosystems of the Northeast Region of Brazil (NEB) have experienced persistent drought episodes and environmental degradation during the past two decades. In this study, we examined the spatial heterogeneity and temporal dynamics of the NEB using a 20-year time series of Normalized Difference Vegetation Index (NDVI) observations, derived from the National Oceanographic and Atmospheric Administration (NOAA)-Advanced Very High Resolution Radiometer (AVHRR) instrument. A set of 12 000 spatially distributed NDVI values was analysed to investigate significant deviations from the mean-monthly values of the base period (1982-2001) in the study area. Various statistical analyses involving minimum, mean and maximum values, coefficient of variation (CV), standardized anomalies (Z-scores), and 36-month running mean were applied to monthly NDVI values to identify spatial and temporal variations in vegetation dynamics. We found strong seasonal oscillations in the vegetation-growing season (February-May) over the NEB study area, with maximum NDVI observed in April-May and seasonal variations, expressed by the CV, ranging from 14% to 32%. In addition, a consistent upward trend in vegetation greenness occurred over the period 1984-1990, and was strongly reversed in the subsequent period 1991-1998. These upward and downward trends in vegetation greenness followed an inter-annual oscillation of ∼7-8 years. We also found that dry season peak (September) latitudinal variations in NDVI were 20-25% greater in 1991-1999 than 1982-1990 across the study region. The results of this study suggest that patterns in NEB vegetation variability were a result of the impact of enhanced aridity occurring over the last decade of the 20th century. © 2006 Elsevier Ltd. All rights reserved.

Barraud, N, Hassett, DJ, Hwang, S-H, Rice, SA, Kjelleberg, S & Webb, JS 2006, 'Involvement of Nitric Oxide in Biofilm Dispersal of Pseudomonas aeruginosa', Journal of Bacteriology, vol. 188, no. 21, pp. 7344-7353.
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ABSTRACT Bacterial biofilms at times undergo regulated and coordinated dispersal events where sessile biofilm cells convert to free-swimming, planktonic bacteria. In the opportunistic pathogen Pseudomonas aeruginosa , we previously observed that dispersal occurs concurrently with three interrelated processes within mature biofilms: (i) production of oxidative or nitrosative stress-inducing molecules inside biofilm structures, (ii) bacteriophage induction, and (iii) cell lysis. Here we examine whether specific reactive oxygen or nitrogen intermediates play a role in cell dispersal from P. aeruginosa biofilms. We demonstrate the involvement of anaerobic respiration processes in P. aeruginosa biofilm dispersal and show that nitric oxide (NO), used widely as a signaling molecule in biological systems, causes dispersal of P. aeruginosa biofilm bacteria. Dispersal was induced with low, sublethal concentrations (25 to 500 nM) of the NO donor sodium nitroprusside (SNP). Moreover, a P. aeruginosa mutant lacking the only enzyme capable of generating metabolic NO through anaerobic respiration (nitrite reductase, Δ nirS ) did not disperse, whereas a NO reductase mutant (Δ norCB ) exhibited greatly enhanced dispersal. Strategies to induce biofilm dispersal are of interest due to their potential to prevent biofilms and biofilm-related infections. We observed that exposure to SNP (500 nM) greatly enhanced the efficacy of antimicrobial compounds (tobramycin, hydrogen peroxide, and sodium dodecyl sulfate) in the removal of established P. ae...

Barrett, BS, Leslie, LM & Fiedler, BH 2006, 'An Example of the Value of Strong Climatological Signals in Tropical Cyclone Track Forecasting: Hurricane Ivan (2004)', Monthly Weather Review, vol. 134, no. 5, pp. 1568-1577.
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Abstract Since 1970, tropical cyclone (TC) track forecasts have improved steadily in the Atlantic basin. This improvement has been linked primarily to advances in numerical weather prediction (NWP) models. Concurrently, with few exceptions, the development and operational use of statistical track prediction schemes have experienced a relative decline. Statistical schemes provided the most accurate TC track forecasts until approximately the late 1980s. In this note, it is shown that increased reliance on the global NWP models does not always guarantee the best forecast. Here, Hurricane Ivan is used from the 2004 Atlantic TC season as a classical example, and reminder, of how strong climatological signals still can add substantial value to TC track forecasts, in the form of improved accuracy and increased timeliness at minimal computational cost. In an 8-day period in early September 2004, Hurricane Ivan was repeatedly, and incorrectly, forecast by 12 operational NWP models to move with a significant northward (poleward) component. It was found that the mean 24-h trajectory forecasts of a consensus of five commonly used NWP track prediction aids had a statistically significant right-of-track bias. Furthermore, the official track forecasts, which relied heavily on erroneous numerical guidance over this period, were also found to have significant poleward trajectory errors. At the same time, a climatology-based prediction technique, drawn entirely from the historical record of motion characteristics of TCs in geographical locations similar to Ivan, correctly and consistently indicated a more westward motion component, had a small directional spread, and was supported by a large number of archived cases. This climatological signal was in conflict with the deterministic NWP model output, and it is suggested that the large errors in the official track forecast for TC Ivan could hav...

Ben-Dov, E, Shapiro, OH, Siboni, N & Kushmaro, A 2006, 'Advantage of using inosine at the 3 ' termini of 16S rRNA gene universal primers for the study of microbial diversity', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, no. 11, pp. 6902-6906.
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To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3′ termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively to Proteobacteria (95.8%). Sequences belonging to Firmicutes (42.6%) and Thermotogae (9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing temperature of 54°C, while Proteobacteria sequences were more frequent (62.7%) in a library obtained at 50°C, somewhat resembling the result obtained using the original primer set. The increased diversity revealed by using primers 8F-I/907R-I confirms the usefulness of primers with inosine at the 3′ termini in studying the microbial diversity of environmental samples. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Ben-Nissan, B & Choi, AH 2006, 'Sol-gel production of bioactive nanocoatings for medical applications. Part 1: an introduction', Nanomedicine, vol. 1, no. 3, pp. 311-319.
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Coatings offer the possibility of modifying the surface properties of surgical-grade materials to achieve improvements in performance, reliability and biocompatibility. Sol-gel-derived coatings demonstrate promise owing to their relative ease of production, ability to form a physically and chemically pure and uniform coating over complex geometric shapes and potential to deliver exceptional mechanical properties owing to their nanocrystalline structure. Other advantages unique to sol-gel include the production of a homogeneous material, since mixing takes place on the atomic scale, and its relatively low processing temperature avoids decomposition of the coating materials and limits the damage to metallic substrate materials as a result of exposure to elevated temperatures. A range of materials can be adapted easily for a number of biomedical and engineering applications.

Benson, S, Lennard, C, Maynard, P & Roux, C 2006, 'Forensic applications of isotope ratio mass spectrometry—A review', Forensic Science International, vol. 157, no. 1, pp. 1-22.
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The key role of a forensic scientist is to assist in determining whether a crime has been committed, and if so, assist in the identification of the offender. Many people hold the belief that a particular item can be conclusively linked to a specific person, place or object. Unfortunately, this is often not achievable in forensic science. In performing their role, scientists develop and test hypotheses. The significance of those hypotheses that cannot be rejected upon completion of all available examinations/analyses is then evaluated. Although one can generally identify the substances present using available techniques, it is generally not possible to distinguish one source of the same substance from another. In such circumstances, although a particular hypothesis cannot be rejected, it cannot be conclusively proven, i.e. the samples could still have originated from different sources. This limitation of not being able to distinguish between sources currently extends to the analysis of other forensic samples including, but not limited to, ignitable liquids, paints, adhesives, textile fibres, plastics, and illicit drugs. Stable isotope ratio mass spectrometry (IRMS) is an additional technique that can be utilised to test a given hypothesis. This technique shows the potential to be able to individualise a range of materials of forensic interest. This paper provides a brief description of the technique, followed by a review of the various applications of IRMS in different scientific fields. The focus of this summary is on forensic applications of IRMS, in particular the analysis of explosives, ignitable liquids and illicit drugs. © 2005 Elsevier Ireland Ltd. All rights reserved.

Bezuglyi, S, Dooley, AH & Kwiatiowski, J 2006, 'Topologies on the group of homeomorphisms of a Cantor set', TOPOLOGICAL METHODS IN NONLINEAR ANALYSIS, vol. 27, no. 2, pp. 299-331.

Bezuglyi, S, Dooley, AH & Kwiatkowski, J 2006, 'Topologies on the group of Borel automorphisms of a standard Borel space', TOPOLOGICAL METHODS IN NONLINEAR ANALYSIS, vol. 27, no. 2, pp. 333-385.

Bilic, A, Reimers, JR, Hush, NS, Hoft, RC & Ford, MJ 2006, 'Adsorption of benzene on copper, silver, and gold surfaces', JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 2, no. 4, pp. 1093-1105.
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The adsorption of benzene on the Cu(111), Ag(111), Au(111), and Cu(110) surfaces at low coverage is modeled using density-functional theory (DFT) using periodic-slab models of the surfaces as well as using both DFT and complete-active-space self-consistent field theory with second-order Møller-Plesset perturbation corrections (CASPT2) for the interaction of benzene with a Cu13 cluster model for the Cu(110) surface. For the binding to the (111) surfaces, key qualitative features of the results such as weak physisorption, the relative orientation of the adsorbate on the surface, and surface potential changes are in good agreement with experimental findings. Also, the binding to Cu(110) is predicted to be much stronger than that to Cu(111) and much weaker than that seen in previous calculations for Ni(110), as observed. However, a range of physisorptive-like and chemisorptive-like structures are found for benzene on Cu(110) that are roughly consistent with observed spectroscopic data, with these structures differing dramatically in geometry but trivially in energy. For all systems, the bonding is found to be purely dispersive in nature with minimal covalent character. As dispersive energies are reproduced very poorly by DFT, the calculated binding energies are found to dramatically underestimate the observed ones, while CASPT2 calculations indicate that there is no binding at the Hartree-Fock level and demonstrate that the expected intermolecular correlation (dispersive) energy is of the correct order to explain the experimental binding-energy data. DFT calculations performed for benzene on Cu(110) and for benzene on the model cluster indicate that this cluster is actually too reactive and provides a poor chemical model for the system. © 2006 American Chemical Society.

Bishop, MJ, Kelaher, BP, Smith, MPL, York, PH & Booth, DJ 2006, 'Ratio-dependent response of a temperate Australian estuarine system to sustained nitrogen loading', OECOLOGIA, vol. 149, no. 4, pp. 701-708.
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Classical resource- and the less studied ratio-dependent models of predator-prey relationships provide divergent predictions as to the sustained ecological effects of bottom-up forcing. While resource-dependent models, which consider only instantaneous prey density in modelling predator responses, predict community responses that are dependent on the number of trophic levels in a system, ratio-dependent models, which consider the number of prey per consumer, predict proportional increase in each level irrespective of chain length. The two models are only subtly different for systems with two or three trophic levels but in the case of four trophic levels, predict opposite effects of enrichment on primary producers. Despite the poor discriminatory power of tests of the models in systems with two or three trophic levels, field tests in estuarine and marine systems with four trophic levels have been notably absent. Sampling of phytoplankton, macroinvertebrates, invertebrate-feeding fishes, piscivorous fishes in Kooloonbung Creek, Hastings River estuary, eastern Australia, subject to over 20 years of sewage discharge, revealed increased abundances in all four trophic levels at the disturbed location relative to control sites. Increased abundance of phytoplankton at the disturbed site was counter to the predictions of resource-dependent models, which posit a reduction in the first trophic level in response to enrichment. By contrast, the increase in abundance of this first trophic level and the proportionality of increases in abundances of each of the four trophic groups to nitrogen loading provided strong support for ratio dependency. This first evidence of ratio dependence in an estuarine system with four trophic levels not only demonstrates the applicability of ecological theory which seeks to simplify the complexity of systems, but has implications for management. Although large nutrient inputs frequently induce mortality of invertebrates and fish, we hav...

Booth, DJ & Skene, C 2006, 'Rapid assessment of endocrine disruption: vitellogenin (Vtg) expression in male estuarine toadfish (Tetratenos glaber Tetraodontiformes)', Australasian Journal of Ecotoxicology, vol. 12, no. 1, pp. 3-8.
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Increased contamination of waterways has lead to many impacts on organisms, including effects on reproduction. A suite of endocrine-disruptive chemicals (DECs) has been shown to mimic sex hormones in vertebrates and their presence is an important bioindicator of environmental degradation. We examined expression of vitellogenin (Vtg, a female yolk protein) in male toadfish (Tetratenos glaber), as an indicator of EDC presence in estuaries around Sydney, Australia. First we demonstrated induction of Vtg in males from unpolluted estuarine sites through injection of 17beta-oestradiol. Second, serum of fish from polluted and unpolluted estuaries was collected and examined by reducing-polyacryamide gel electrophoresis (SDS-PAGE). While females from polluted (downstream from sewage treatment plants, and subject to urban runoff) and less polluted sites all expressed Vtg in blood serum, males from less polluted sites showed little or no evidence of Vtg expression. however, most males from heavilty polluted sites showed moderate to high levels of vtg expression indicating that EDCs were present and affecting normal endocrine function in males. We suggest that simple biochemical examinations of EDS effects, such as vtg induction in males, are useful rapid assessment methods wich can provide evidence upon which further, more detailed studies may be undertaken.

Botten, LC, Dossou, KB, Wilcox, S, McPhedran, RC, De Sterke, CM, Nicorovici, NA & Asatryan, AA 2006, 'Highly Accurate Modelling of Generalized Defect Modes in Photonic Crystals using the Fictitious Source Superposition Method', International Journal of Microwave and Optical Technology, vol. 1, no. 1, pp. 133-145.
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We present an exact theory for modelling the modes of two-dimensional photonic crystals with a truly infinite cladding. It builds on our previous implementation of the fictitious source superposition method for simple point defects that is based on three key ideas: the use of fictitious sources to modify response fields so defects can be introduced; the representation of the defect mode as a superposition of solutions of quasiperiodic field problems; and the reduction of the twodimensional superposition to a highly efficient, one-dimensional average. Here we describe an elegant extension to model a compound, multiple scatterer, defect in a given layer, and then build on this to construct an arbitrary defect from multiple layers of compound defects. We demonstrate the method's accuracy and efficiency, and present two-and three-dimensional results. We also demonstrate the strengths of the method for difficult problems, such as where a mode is highly extended near cutoff.

Botten, LC, Hansen, RA & de Sterke, CM 2006, 'Supermodes in multiple coupled photonic crystal waveguides', OPTICS EXPRESS, vol. 14, no. 1, pp. 387-396.
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We analyze the supermodes in multiple coupled photonic crystal waveguides for long-wavelengths. In the tight-binding limit we obtain analytic results that agree with fully numerical calculations. We find that when the field flips sign after a single photonic crystal period, and there is an odd number of periods between adjacent waveguides, the supermode order is reversed, compared to that in conventional coupled waveguides, generalizing earlier results obtained for two coupled waveguides. © 2006 Optical Society of America.

Botten, LC, White, TP, de Sterke, CM & McPhedran, RC 2006, 'Wide-angle coupling into rod-type photonic crystals with ultralow reflectance', PHYSICAL REVIEW E, vol. 74, no. 2, pp. 1-10.
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We describe the surprising phenomenon of near-perfect coupling from free space into uniform two-dimensional rod-type photonic crystals over a wide range of incident angles. This behavior is shown to be a generic feature of many rod-type photonic crystal structures that is related to strong forward scattering resonances of the individual cylinders. We explain these results using both semianalytic analysis and two-dimensional numerical calculations and identify the conditions under which efficient, wide-angle coupling can occur. The results may lead to more efficient designs for in-band photonic crystal devices such as superprisms and self-collimation based photonic circuits. © 2006 The American Physical Society.

Brooks, SJ, Gale, PA & Light, ME 2006, 'Anion-binding modes in a macrocyclic amidourea', Chemical Communications, no. 41, pp. 4344-4344.
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Brown, BE, Mahroof, FM, Cook, NL, van Reyk, DM & Davies, MJ 2006, 'Hydrazine compounds inhibit glycation of low-density lipoproteins and prevent the in vitro formation of model foam cells from glycolaldehyde-modified low-density lipoproteins', DIABETOLOGIA, vol. 49, no. 4, pp. 775-783.
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Aims/hypothesis: Previous studies have shown that glycation of LDL by methylglyoxal and glycolaldehyde, in the absence of significant oxidation, results in lipid accumulation in macrophage cells. Such foam cells are a hallmark of atherosclerosis. In this

Brown, D, Craddock, M, Culshaw, R, Fendel, D & Wu, HH 2006, 'Serge lang and the HIV consensus [3]', Notices of the American Mathematical Society, vol. 53, no. 9, p. 1006.

Brown, J, Abbott, O & Diamond, I 2006, 'Dependence in the 2001 One-Number Census Project', Journal of the Royal Statistical Society Series A: Statistics in Society, vol. 169, no. 4, pp. 883-902.
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SummaryThe one-number census approach was developed by the Office for National Statistics to adjust the counts from the 2001 census of England and Wales for underenumeration. The method is underpinned by an assumption of independence between the count of the population that was given by the 2001 census and the count that was given by the Census Coverage Survey. Some dependence was, however, detected, and the paper describes the strategy that was used to measure dependence and to adjust the 2001 census population estimates.

Bruti-Liberati, N & Platen, E 2006, 'Approximation of Jump Diffusions in Finance and Economics', Computational Economics, vol. 29, no. 3-4, pp. 283-312.
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In finance and economics the key dynamics are often specified via stochastic differential equations (SDEs) of jump-diffusion type. The class of jump-diffusion SDEs that admits explicit solutions is rather limited. Consequently, discrete time approximations are required. In this paper we give a survey of strong and weak numerical schemes for SDEs with jumps. Strong schemes provide pathwise approximations and therefore can be employed in scenario analysis, filtering or hedge simulation. Weak schemes are appropriate for problems such as derivative pricing or the evaluation of risk measures and expected utilities. Here only an approximation of the probability distribution of the jump-diffusion process is needed. As a framework for applications of these methods in finance and economics we use the benchmark approach. Strong approximation methods are illustrated by scenario simulations. Numerical results on the pricing of options on an index are presented using weak approximation methods.

Bruti-Liberati, N, Nikitopoulos-Sklibosios, C & Platen, E 2006, 'First Order Strong Approximations of Jump Diffusions', Monte Carlo Methods and Applications, vol. 12, no. 3, pp. 191-209.
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This paper presents new results on strong numerical schemes, which are appropriate for scenario analysis, filtering and hedge simulation, for stochastic differential equations (SDEs) of jump-diffusion type. It provides first order strong approximations for jump-diffusion SDEs driven by Wiener processes and Poisson random measures. The paper covers first order derivative-free, drift-implicit and jump-adapted strong approximations. Moreover, it provides a commutativity condition under which the computational effort of first order strong schemes is independent of the total intensity of the jump measure. Finally, a numerical study on the accuracy of several strong schemes applied to the Merton model is presented. © VSP 2006.

Bruti-Liberati, N, Nikitopoulos-Sklibosios, C & Platen, E 2006, 'First Order Strong Approximations of Jump Diffusions', Monte Carlo Methods and Applications, vol. 12, no. 3.
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BURGESS, J, OLIVER, B, PONIRIS, M, GE, Q, BOUSTANY, S, COX, N, MOIR, L, JOHNSON, P & BLACK, J 2006, 'A phosphodiesterase 4 inhibitor inhibits matrix protein deposition in airways in vitro', Journal of Allergy and Clinical Immunology, vol. 118, no. 3, pp. 649-657.
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Background: Airway smooth muscle (ASM) cells may contribute to airway remodeling through the release of growth factors, cytokines, and extracellular matrix (ECM) proteins. The effect of current asthma therapies on this release is not known. Objective: We

Burnett, TA, Dinkla, K, Rohde, M, Chhatwal, GS, Uphoff, C, Srivastava, M, Cordwell, SJ, Geary, S, Liao, X, Minion, FC, Walker, MJ & Djordjevic, SP 2006, 'P159 is a proteolytically processed, surface adhesin ofMycoplasma hyopneumoniae: defined domains of P159 bind heparin and promote adherence to eukaryote cells', Molecular Microbiology, vol. 60, no. 3, pp. 669-686.
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SummaryMycoplasma hyopneumoniae, the causative agent of porcine enzootic pneumonia, colonizes the respiratory cilia of affected swine causing significant economic losses to swine production worldwide. Heparin is known to inhibit adherence ofM. hyopneumoniaeto porcine respiratory epithelial cilia.M. hyopneumoniaecells bind heparin but the identity of the heparin‐binding proteins is limited. Proteomic analysis ofM. hyopneumoniaelysates identified 27 kDa (P27), 110 kDa (P110) and 52 kDa (P52) proteins representing different regions of a 159 kDa (P159) protein derived from mhp494. These cleavage fragments were surface located and present at all growth stages. Following purification of four recombinant proteins spanning P159 (F1P159, F2P159, F3P159and F4P159), only F3P159and F4P159bound heparin in a dose‐dependent manner (Kdvalues 142.37 ± 22.01 nM; 75.37 ± 7.34 nM respectively). Scanning electron microscopic studies showedM. hyopneumoniaebound intimately to porcine kidney epithelial‐like cells (PK15 cells) but these processes were inhibited by excess heparin and F4P159. Similarly, latex beads coated with F2P159and F4P159adhered to and entered PK15 cells, but heparin, F2P159and F4P159was inhibitory. These findings indicate that P159 is a post‐translationally cleaved, glycosaminoglycan‐binding adhesin ofM. hyopneumoniae.

Burrage, K, Burrage, P, Higham, DJ, Kloeden, PE & Platen, E 2006, 'Comment on “Numerical methods for stochastic differential equations”', Physical Review E, vol. 74, no. 6.
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Cadotte, MW, Murray, BR & Lovett-Doust, J 2006, 'Ecological patterns and biological invasions: Using regional species inventories in macroecology', BIOLOGICAL INVASIONS, vol. 8, no. 4, pp. 809-821.
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Macroecology depends heavily on a comparative methodology in order to identify large-scale patterns and to test alternative hypotheses that might generate such patterns. With the advent and accessibility of large electronic databases of species and their life history and ecological attributes, ecologists have begun seeking generalities, and examining large-scale ecological hypotheses involving core themes of range, abundance and diversity. For example, combinations of ecological, life history and phylogenetic data have been analysed using large species sets to test hypotheses in invasion biology. Analysis of regional species inventories can contribute cogently to our understanding of invasions. Here we examine several ways in which database analysis is effective. We review 19 studies of comparative invasions biology, each using >100 species of plants in their analyses, and show that invader success is linked to seven correlates: short life cycle, abiotic (mostly wind) dispersal, large native range size, non-random taxonomic patterns (emphasizing certain families or orders), presence of clonal organs, occupying disturbed habitats, and earlier time of introduction. These phylogenetically influenced, comparative analyses using regional species inventories are only just beginning and have much potential. © Springer 2006.

Cai, Z-L, Crossley, MJ, Reimers, JR, Kobayashi, R & Amos, RD 2006, 'Density functional theory for charge transfer: The nature of the N-bands of porphyrins and chlorophylls revealed through CAM-B3LYP, CASPT2, and SAC-CI calculations', JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, no. 31, pp. 15624-15632.
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Canfield, P, Dahlbom, MG, Hush, NS & Reimers, JR 2006, 'Density-functional geometry optimization of the 150 000-atom photosystem-I trimer', JOURNAL OF CHEMICAL PHYSICS, vol. 124, no. 2.
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Cantwell, MM, Millen, AE, Carroll, R, Mittl, BL, Hermansen, S, Brinton, LA & Potischman, N 2006, 'A debriefing session with a nutritionist can improve dietary assessment using food diaries.', JOURNAL OF NUTRITION, vol. 136, no. 2, pp. 440-445.

Carraro, R & Gladstone, W 2006, 'Habitat preferences and site fidelity of the ornate wobbegong shark (Orectolobus ornatus) on rocky reefs of New South Wales', PACIFIC SCIENCE, vol. 60, no. 2, pp. 207-223.
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Habitat and microhabitat preferences and site fidelity of Orectolobus ornatus were assessed between September 2002 and August 2003 to assess potential suitability of marine reserves for its conservation. Of six rocky reef habitats available in the study area (sponge gardens, artificial structures, barren boulders, sand, sea grass, macroalgae), O. ornatus exhibited a significant preference for sponge gardens, artificial structures, and barren boulders habitats. Habitat preferences of males and females, and individuals <1 m and >1 m, did not differ. Orectolobus ornatus selected daytime resting positions with a high topographic complexity and crevice volume and did not select on the basis of prey availability. Habitat and microhabitat preferences may be related to the need for predator avoidance. Regular monitoring of 40 individually identified O. ornatus revealed that none was a permanent resident of the study area. Seven individuals exhibited short-term temporary fidelity to the study area; they were resighted frequently for part of an intensive 100-day survey. Remaining individuals were temporary visitors; they were resighted at most once after initial identification or returning after extended absences. Monthly population surveys confirmed the turnover of O. ornatus in the study area. The lack of long-term site fidelity suggests that small marine reserves will be ineffective as a conservation strategy for O. ornatus.

Carroll, RJ, Midthune, D, Freedman, LS & Kipnis, V 2006, 'Seemingly Unrelated Measurement Error Models, with Application to Nutritional Epidemiology', Biometrics, vol. 62, no. 1, pp. 75-84.
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Summary Motivated by an important biomarker study in nutritional epidemiology, we consider the combination of the linear mixed measurement error model and the linear seemingly unrelated regression model, hence Seemingly Unrelated Measurement Error Models. In our context, we have data on protein intake and energy (caloric) intake from both a food frequency questionnaire (FFQ) and a biomarker, and wish to understand the measurement error properties of the FFQ for each nutrient. Our idea is to develop separate marginal mixed measurement error models for each nutrient, and then combine them into a larger multivariate measurement error model: the two measurement error models are seemingly unrelated because they concern different nutrients, but aspects of each model are highly correlated. As in any seemingly unrelated regression context, the hope is to achieve gains in statistical efficiency compared to fitting each model separately. We show that if we employ a “full” model (fully parameterized), the combination of the two measurement error models leads to no gain over considering each model separately. However, there is also a scientifically motivated “reduced” model that sets certain parameters in the “full” model equal to zero, and for which the combination of the two measurement error models leads to considerable gain over considering each model separately, e.g., 40% decrease in standard errors. We use the Akaike information criterion to distinguish between the two possibilities, and show that the resulting estimates achieve major gains in efficiency. We also describe theoretical and serious practical problems with the Bayes information criterion in this context.

Charles, AL, Markich, SJ & Ralph, P 2006, 'Toxicity of uranium and copper individually, and in combination, to a tropical freshwater macrophyte (Lemna aequinoctialis)', CHEMOSPHERE, vol. 62, no. 8, pp. 1224-1233.
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Copper (Cu) and uranium (U) are of potential ecotoxicological concern to tropical freshwater biota in northern Australia, as a result of mining activities. Few data are available on the toxicity of U, and no data are available on the toxic interaction of Cu and U, to freshwater biota. This study determined the toxicity of Cu and U individually, and in combination, to a tropical freshwater macrophyte, Lemna aequinoctialis (duckweed), in a synthetic soft water (27°C; pH, 6.5; hardness, 40 mg CaCO3 l-1, alkalinity, 16 mg CaCO3 l-1), typical of many fresh surface waters in coastal northern Australia. The growth rate of L. aequinoctialis decreased with increasing Cu or U concentrations, with the concentration of Cu inhibiting growth by 50% (EC50) being 16 ± 1.0 μg l-1, with a minimum detectable effect concentration (MDEC) of 3.2 μg l-1. The concentration of U inhibiting growth by 50% (EC50) was 758 ± 35 μg l-1 with a MDEC of 112 μg l-1. The EC50 value for the exposure of L. aequinoctialis to equitoxic mixtures of Cu and U was significantly (P ≤ 0.05) higher than one toxic unit (1.35; 95% confidence interval, 1.18-1.52), indicating that the combined effects of Cu and U are less than additive (antagonistic). Therefore, inhibition of the growth rate of L. aequinoctialis was reduced when Cu and U were present in equitoxic mixtures, relative to individual metal exposures. Since non-additive (e.g. antagonistic) interactions of metal mixtures cannot be predicted using current mixture models, these results have important potential implications for the protection of freshwater ecosystems through the derivation of national water quality guidelines. © 2005 Elsevier Ltd. All rights reserved.

Chatterjee, N, Spinka, C, Chen, J & Carroll, RJ 2006, 'Comment', Journal of the American Statistical Association, vol. 101, no. 473, pp. 108-111.
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Chen, H, Hansen, MJ, Jones, JE, Vlahos, R, Bozinovski, S, Anderson, GP & Morris, MJ 2006, 'Cigarette Smoke Exposure Reprograms the Hypothalamic Neuropeptide Y Axis to Promote Weight Loss', American Journal of Respiratory and Critical Care Medicine, vol. 173, no. 11, pp. 1248-1254.
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Rationale: Despite irrefutable epidemiologic evidence, cigarette smoking remains the major preventable cause of lung disease morbidity worldwide. The appetite-suppressing effect of tobacco is a major behavioral determinant of smoking, but the underlyingmolecular and neuronal mechanisms are not understood. Neuropeptide Y (NPY) is an orexigenic neuropeptide, whose activity in the hypothalamic paraventricular nucleus governs appetite. Objectives: To compare the effects of smoke exposure and equivalent food restriction on body weight, organ mass, cytokines, and brain NPY in Balb/c mice. Methods: A pair-feeding study design compared smoke exposure (4 wk; 1 cigarette, 3x/d, 5 d/wk) to equivalent food restriction (pair-fed) and sham-exposed control mice. Results: Smoke exposure rapidly induced mild anorexia. After 4 wk, smoke-exposed and pair-fed groups were lighter than control mice (22.0 ± 0.2, 23.2 ± 0.5, 24.9 ± 0.4 g, respectively; p ± 0.05). Brown and white fat masses were only reduced by smoke exposure, relative to control mice. NPY concentration in the paraventricular nucleus was significantly and paradoxically reduced by smoke exposure, despite lower plasma leptin concentrations; this was not observed in the pair-fed group experiencing 19% food restriction. Adipose mRNA expression of uncoupling proteins, inflammatory cytokines interleukin 6 and tumor necrosis factor α, and adipose triglyceride lipase was decreased by smoke exposure, and even lower in pair-fed mice. Conclusions: In contrast to food restriction, smoke exposure caused a reduction in hypothalamic NPY and fat mass, and regulated adipose cytokines. These findings may contribute to understanding weight loss in smoking-related lung disease and in the design of more effective smoking cessation strategies.

Chen, H, Kent, S & Morris, MJ 2006, 'Is the CCK2 receptor essential for normal regulation of body weight and adiposity?', European Journal of Neuroscience, vol. 24, no. 5, pp. 1427-1433.
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AbstractCholecystokinin (CCK) is a gastrointestinal satiety signal released from the duodenum to terminate feeding, via CCK1 receptors. CCK2 receptors are considered to be involved in anxiety. CCK2 receptor knockout mice have increased body weight and food intake. Little is known regarding the effects of CCK2 receptor deficiency on adipose distribution and hypothalamic feeding regulators such as neuropeptide Y (NPY), a powerful stimulator of feeding. Adult (10 week) CCK2 receptor knockout and wild‐type mice were anaesthetized and killed by decapitation. Brain sections, organs and fat tissue were dissected. Plasma leptin, insulin and brain NPY content were measured by radioimmunoassay. Female CCK2 receptor knockout mice weighed more than control mice (22.0 ± 0.2 vs. 19.9 ± 0.4 g, P < 0.05), with this difference being less marked in male mice (26.4 ± 0.4 vs. 25.6 ± 0.6 g). Fat masses in all locations sampled were significantly smaller in CCK2 receptor knockout mice of both genders (P < 0.05), resulting in lower plasma leptin and insulin levels. NPY concentrations were significantly increased in arcuate nucleus and anterior hypothalamus in both male and female CCK2 receptor knockout mice, and total hypothalamic NPY content was increased by 7 and 9% in males and females, respectively (P < 0.05). CCK2 receptor deletion was associated with increased body weight and hypothalamic NPY content, but reduced fat masses and plasma leptin and insulin. Increased NPY might contribute to increased food intake in CCK2 receptor knockout mice. Further work needs to focus on the metabolic changes.

Chen, PPT, Butcher, KSA, Wintrebert-Fouquet, M, Wuhrer, R, Phillips, MR, Prince, KE, Timmers, H, Shrestha, SK & Usher, BF 2006, 'Apparent band-gap shift in InN films grown by remote-plasma-enhanced CVD', JOURNAL OF CRYSTAL GROWTH, vol. 288, no. 2, pp. 241-246.
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The properties of indium nitride grown at various temperatures on c-plane sapphire and glass substrates, using remote plasma-enhanced chemical vapour deposition, have been investigated. The optical absorption spectra show a broad range of apparent band-gap values from approximately 2.3-0.9 eV, depending on the growth temperature. The influence of growth temperature on crystallinity, level of impurity incorporation, stoichiometry, and lattice distortion are analysed. The possible causes of the apparent band-gap shift in indium nitride are discussed. © 2006 Elsevier B.V. All rights reserved.

Cheng, Y, Gamon, JA, Fuentes, DA, Mao, Z, Sims, DA, Qiu, H-L, Claudio, H, Huete, A & Rahman, AF 2006, 'A multi-scale analysis of dynamic optical signals in a Southern California chaparral ecosystem: A comparison of field, AVIRIS and MODIS data', REMOTE SENSING OF ENVIRONMENT, vol. 103, no. 3, pp. 369-378.
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Using field data, Airborne Visible Infrared Imaging Spectrometer (AVIRIS) imagery, and Moderate-Resolution Imaging Spectroradiometer (MODIS) data, a multi-scale analysis of ecosystem optical properties was performed for Sky Oaks, a Southern California chaparral ecosystem in the spectral network (SpecNet) and FLUXNET networks. The study covered a 4-year period (2000-2004), which included a severe drought in 2002 and a subsequent wildfire in July 2003, leading to extreme perturbation in ecosystem productivity and optical properties. Two vegetation greenness indices (Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI)), and a measure of the fraction of photosynthetically active radiation absorbed by vegetation (fPAR), were compared across sampling platforms, which ranged in pixel size from 1 m (tram system in the field) to 1000 m (MODIS satellite sensor). The three MODIS products closely followed the same seasonal trends as the tram and AVIRIS data, but tended to be higher than the tram and AVIRIS values, particularly for fPAR and NDVI. Following a wildfire that removed all green vegetation, the overestimation in MODIS fPAR values was particularly clear. The MODIS fPAR algorithm (version 4 vs. v.4.1) had a significant effect on the degree of overestimation, with v. 4.1 improving the agreement with the other sensors (AVIRIS and tram) for vegetated conditions, but not for low, post-fire values. The differences between MODIS products and the products from the other platform sensors could not be entirely attributed to differences in sensor spectral responses or sampling scale. These results are consistent with several other recently published studies that indicate that MODIS overestimates fPAR and thus net primary production (NPP) for many terrestrial ecosystems, and demonstrates the need for proper validation of MODIS terrestrial biospheric products by direct comparison against optical signals at other spatial scales, as is now p...

Choi, AL, Levy, JI, Dockery, DW, Ryan, LM, Tolbert, PE, Altshul, LM & Korrick, SA 2006, 'Does living near a superfund site contribute to higher polychlorinated biphenyl (PCB) exposure?', ENVIRONMENTAL HEALTH PERSPECTIVES, vol. 114, no. 7, pp. 1092-1098.
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We assessed determinants of cord serum polychlorinated biphenyl (PCB) levels among 720 infants born between 1993 and 1998 to mothers living near a PCB-contaminated Superfund site in Massachusetts, measuring the sum of 51 PCB congeners (∑PCB) and ascertaining maternal address, diet, sociodemographics, and exposure risk factors. Addresses were geocoded to obtain distance to the Superfund site and neighborhood characteristics. We modeled log10(∑PCB) as a function of potential individual and neighborhood risk factors, mapping model residuals to assess spatial correlates of PCB exposure. Similar analyses were performed for light (mono-tetra) and heavy (penta-deca) PCBs to assess potential differences in exposure pathways as a function of relative volatility. PCB-118 (relatively prevalent in site sediments and cord serum) was assessed separately. The geometric mean of ∑PCB levels was 0.40 (range, 0.068-18.14) ng/g serum. Maternal age and birthplace were the strongest predictors of ∑PCB levels. Maternal consumption of organ meat and local dairy products was associated with higher and smoking and previous lactation with lower ∑PCB levels. Infants born later in the study had lower ∑PCB levels, likely due to temporal declines in exposure and site remediation in 1994-1995. No association was found between ∑PCB levels and residential distance from the Superfund site. Similar results were found with light and heavy PCBs and PCB-118. Previously reported demographic (age) and other (lactation, smoking, diet) correlates of PCB exposure, as well as local factors (consumption of local dairy products and Superfund site dredging) but not residential proximity to the site, were important determinants of cord serum PCB levels in the study community.

Choi, MJ, McBean, KE, Wuhrer, R, McDonagh, AM, Maynard, PJ, Lennard, C & Roux, C 2006, 'Investigation into the binding of gold nanoparticles to fingermarks using scanning electron microscopy', Journal of Forensic Identification, vol. 56, no. 1, pp. 24-32.
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For the first time, scanning electron microscopy has been used to investigate the binding of gold nanoparticles to fingermarks placed on nonporous surfaces. The results show that gold nanoparticles, under standard MMDII conditions, bind preferentially to latent fingermark ridges on nonporous surfaces. Variation in surfactant concentration influences background development but does not affect the binding of gold nanoparticles to the ridges, while pH variation influences the binding to ridges but leaves valley regions unaffected.

Choi, MJ, McDonagh, AM, Maynard, PJ, Wuhrer, R, Lennard, C & Roux, C 2006, 'Preparation and evaluation of metal nanopowders for the detection of fingermarks on nonporous surfaces', Journal of Forensic Identification, vol. 56, no. 5, pp. 756-768.
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Gold and silver nanoparticles using oleylamine as a stabilizer have been formulated for developing latent fingermarks on nonporous surfaces. These nanopowders are compared with conventional powders such as black powder, black magnetic powder, aluminum powder, and white powder. Gold nanopowder produced sharp and clear development of latent fingermarks without background staining. Scanning electron microscope images revealed that particles were concentrated in the fingermark ridge areas, with only minor amounts located in the valley regions.

Chowdhury, PR & Heinemann, JA 2006, 'The General Secretory Pathway of Burkholderia gladioli pv. agaricicola BG164R Is Necessary for Cavity Disease in White Button Mushrooms', Applied and Environmental Microbiology, vol. 72, no. 5, pp. 3558-3565.
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ABSTRACT Cavity disease in white button mushrooms is caused by Burkholderia gladioli pv. agaricicola. We describe the isolation and characterization of six mutants of the strain BG164R that no longer cause this disease on mushrooms. The mutations were mapped to genes of the general secretory pathway (GSP). This is the first report of the association of the type II secretion pathway with a disease in mushrooms. Phenotypes of the six avirulent mutants were the following: an inability to degrade mushroom tissue, a highly reduced capacity to secrete chitinase and protease, and a reduced number of flagella. Using these mutants, we also made the novel observation that the factors causing mushroom tissue degradation, thereby leading to the expression of cavity disease, can be separated from mycelium inhibition because avirulent mutants continued to inhibit the growth of actively growing mushroom mycelia. The GSP locus of B. gladioli was subsequently cloned and mapped and compared to the same locus in closely related species, establishing that the genetic organization of the gsp operon of B. gladioli pv. agaricicola is consistent with that of other species of the genus. We also identify the most common indigenous bacterial population present in the mushroom fruit bodies from a New Zealand farm, one of which, Ewingella americana , was found to be an apparent antagonist of B. gladioli pv. agaricicola. While other investigators have reported enhanced disease symptoms due to interactions between endogenous and disease-causing bacteria in other mushroom diseases, to the best of our knowledge this is the first r...

Cifuentes, MP, Powell, CE, Morrall, JP, McDonagh, AM, Lucas, NT, Humphrey, MG, Samoc, M, Houbrechts, S, Asselberghs, I, Clays, K, Persoons, A & Isoshima, T 2006, 'Electrochemical, Spectroelectrochemical, and Molecular Quadratic and Cubic Nonlinear Optical Properties of Alkynylruthenium Dendrimers¹', Journal of the American Chemical Society, vol. 128, no. 33, pp. 10819-10832.
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A combination of cyclic voltammetry (CV), UV-vis-NIR spectroscopy and spectroelectrochemistry, hyper-Rayleigh scattering (HRS) [including depolarization studies], Z-scan and degenerate four-wave mixing (DFWM) [including studies employing an optically transparent thin-layer electrochemical (OTTLE) cell to effect electrochemical switching of nonlinearity], pump-probe, and electroabsorption (EA) measurements have been used to comprehensively investigate the electronic, linear optical, and nonlinear optical (NLO) properties of nanoscopic π-delocalizable electron-rich alkynylruthenium dendrimers, their precursor dendrons, and their linear analogues. CV, UV-vis-NIR spectroscopy, and UV-vis-NIR spectroelectrochemistry reveal that the reversible metal-centered oxidation processes in these complexes are accompanied by strong linear optical changes, 'switching on' low-energy absorption bands, the frequency of which is tunable by ligand replacement. HRS studies at 1064 nm employing nanosecond pulses reveal large nonlinearities for these formally octupolar dendrimers; depolarization measurements are consistent with lack of coplanarity upon π-framework extension through the metal. EA studies at 350-800 nm in a poly(methyl methacrylate) matrix are consistent with the important transitions having a charge-transfer exciton character that increases markedly on introduction of peripheral polarizing substituent. Time-resolved pump-probe studies employing 55 ps, 527 nm pulses reveal absorption saturation, the longest excited-state lifetime being observed for the dendrimer. Z-scan studies at 800 nm employing femtosecond pulses reveal strong two-photon absorption that increases significantly on progression from linear complex to zero- and then first-generation dendrimer with no loss of optical transparency. Both refractive and absorptive nonlinearity for selected alkynylruthenium dendrimers have been reversibly 'switched' by employing the Z-scan technique at 800 and 1180 nm ...

Colbran, SB, Lee, ST, Lonnon, DG, Maharaj, FJD, McDonagh, AM, Walker, KA & Young, RD 2006, 'Covalently Linked Ferrocenyl Quinones:  Proton-Dependent Redox Behavior and Charge Redistribution', Organometallics, vol. 25, no. 9, pp. 2216-2224.
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The proton-dependent redox chemistry of dyads comprised of a ferrocenyl electron donor directly linked to a hydroquinonyl electron donor or to a quinone electron acceptor by a single covalent bond has been characterized. Ferrocenyl-1,4-hydroquinone (2), ferrocenyl-1,4-benzoquinone (3), 3-ferrocenyl-l,2catechol (5), and the precursors ferrocenyl-1,4-dimethoxybenzene (1) and 3-ferrocenyl-l,2-dimethoxybenzene (4) were studied; also the unstable compound 3-ferrocenyl-l,2-benzoquinone (6) was observed in the spectroelectrochemistry of 5. Detailed cyclic voltammetry, coulommetry, and UV-vis-NIR spectroelectrochemistry experiments allied with EPR, NMR, and Mössbauer spectroscopy were used to probe the pH-dependent redox chemistry and electron distribution within the compounds. © 2006 American Chemical Society.

Coleman, VA, Bradby, JE, Jagadish, C & Phillips, MR 2006, 'A Comparison of the Mechanical Properties and the Impact of Contact Induced Damage in a- and c- Axis ZnO Single Crystals', MRS Proceedings, vol. 957.
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ABSTRACTNanoindentation studies were conducted on a-axis oriented ZnO single crystals. The mechanical properties and deformation mechanisms were monitored and compared to previously determined data from c-axis material. Hardness and modulus values reveal that a-axis ZnO is significantly softer than c-axis material (measured hardness of 2 ± 0.2 GPa) and behaves much more plastically. Additionally, the influence of contact induced damage upon the defect structure of a-axis material was also examined using cathodoluminescence spectroscopy and monochromatic imaging to monitor the luminescence from indent sites. Deformation directly under the indent site enhanced the occurrence of red defect luminescence, and was attributed to a native defect in ZnO that has a higher formation energy than the defects responsible for the green and yellow visible defect bands, which were present in the ZnO during growth and were found to cluster to the indent site during annealing.

Coleman, VA, Bradby, JE, Jagadish, C & Phillips, MR 2006, 'Observation of enhanced defect emission and excitonic quenching from spherically indented ZnO', APPLIED PHYSICS LETTERS, vol. 89, no. 8, pp. 1-3.
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The influence of spherical nanoindentation on the band edge and deep level emission of single crystal c-axis ZnO has been studied by cathodoluminescence (CL) spectroscopy and monochromatic imaging. Excitonic emission is quenched at the indent site and defect emission in the range of 450-720 nm is enhanced. Analysis of CL monochromatic images and spectra suggests that at least two different defect states are responsible for the broad defect emission band. Additionally, the indents result in a strong crystallographic dependence of the defect emission, producing a rosette feature with [112̄0] [21̄1̄0], and [12̄10] orientations that reflect the star-shaped luminescence quenching observed at the excitonic peak (390 nm). © 2006 American Institute of Physics.

Coleman, VA, Buda, M, Tan, HH, Jagadish, C, Phillips, MR, Koike, K, Sasa, S, Inoue, M & Yano, M 2006, 'Observation of blue shifts in ZnO/ZnMgO multiple quantum well structures by ion-implantation induced intermixing', SEMICONDUCTOR SCIENCE AND TECHNOLOGY, vol. 21, no. 3, pp. L25-L28.
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Implantation with low-energy (80 keV) oxygen ions and subsequent rapid thermal annealing at 800 °C are used to induce intermixing in a stack of 19 ZnO/Zn0.7Mg0.3O multiple quantum wells grown on sapphire by molecular beam epitaxy. Large blue shifts of more than 300 meV have been observed for doses up to 1 × 1016 cm-2, with no observation of saturation. This process is driven by the creation of defects by implantation which encourage the diffusion of Mg from the barrier layers into the ZnO quantum wells. Although defects are introduced during the implantation process, good recovery of the cathodoluminescence is seen following rapid thermal annealing. The Zn-Mg interdiffusion in this system has also been calculated for the corresponding ion doses, and the diffusion coefficient extracted. This study has significant implications for band gap engineering of ZnO/ZnMgO optoelectronic devices. © 2006 IOP Publishing Ltd.

Coltel, N, Combes, V, Wassmer, SC, Chimini, G & Grau, GE 2006, 'Cell vesiculation and immunopathology: implications in cerebral malaria', Microbes and Infection, vol. 8, no. 8, pp. 2305-2316.
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Combes, V, Coltel, N, Faille, D, Wassmer, SC & Grau, GE 2006, 'Cerebral malaria: role of microparticles and platelets in alterations of the blood–brain barrier', International Journal for Parasitology, vol. 36, no. 5, pp. 541-546.
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Connally, R, Jin, D & Piper, J 2006, 'High intensity solid‐state UV source for time‐gated luminescence microscopy', Cytometry Part A, vol. 69A, no. 9, pp. 1020-1027.
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AbstractBackground.The unique discriminative ability of immunofluorescent probes can be severely compromised when probe emission competes against naturally occurring, intrinsically fluorescent substances (autofluorophores). Luminescence microscopes that operate in the time‐domain can selectively resolve probes with long fluorescence lifetimes (τ > 100 μs) against short‐lived fluorescence to deliver greatly improved signal‐to‐noise ratio (SNR). A novel time‐gated luminescence microscope design is reported that employs an ultraviolet (UV) light emitting diode (LED) to excite fluorescence from a europium chelate immunoconjugate with a long fluorescence lifetime.Methods.A commercial Zeiss epifluorescence microscope was adapted for TGL operation by fitting with a time‐gated image‐intensified CCD camera and a high‐power (100 mW) UV LED. Capture of the luminescence was delayed for a precise interval following excitation so that autofluorescence was suppressed. Giardia cysts were labeled in situ with antibody conjugated to a europium chelate (BHHST) with a fluorescence lifetime >500 μs.Results.BHHST‐labeled Giardia cysts emit at 617 nm when excited in the UV and were difficult to locate within the matrix of fluorescent algae using conventional fluorescence microscopy, and the SNR of probe to autofluorescent background was 0.51:1. However in time‐gated luminescence mode with a gate‐delay of 5 μs, the SNR was improved to 12.8:1, a 25‐fold improvement.Conclusion.In comparison to xenon flashlamps, UV LEDs are inexpensive, easily powered, and extinguish quickly. Furthermore, the spiked emission of the LED enabled removal of spectral filters from the micro...

Connell, KA, Munro, U & Torpy, FR 2006, 'Daytime behaviour of the grey-headed flying fox Pteropus poliocephalus Temminck (Pteropodidae: Megachiroptera) at an autumn/winter roost.', Australian Mammalogy, vol. 28, no. 1, pp. 7-7.
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The grey-headed flying fox (Pteropus poliocephalus Temminck) is a threatened large fruit bat endemic to Australia. It roosts in large colonies in rainforest patches, mangroves, open forest, riparian woodland and, as native habitat is reduced, increasingly in vegetation within urban environments. The general biology, ecology and behaviour of this bat remain largely unknown, which makes it difficult to effectively monitor, protect and manage this species. The current study provides baseline information on the daytime behaviour of P. poliocephalus in an autumn/winter roost in urban Sydney, Australia, between April and August 2003. The most common daytime behaviours expressed by the flying foxes were sleeping (most common), grooming, mating/courtship, and wing spreading (least common). Behaviours differed significantly between times of day and seasons (autumn and winter). Active behaviours (i.e., grooming, mating/courtship, wing spreading) occurred mainly in the morning, while sleeping predominated in the afternoon. Mating/courtship and wing spreading were significantly higher in April (reproductive period) than in winter (non-reproductive period). Grooming was the only behaviour that showed no significant variation between sample periods. These results provide important baseline data for future comparative studies on the behaviours of flying foxes from urban and ?natural? camps, and the development of management strategies for this species.

Cortie, M 2006, 'Antipodean gold', GOLD BULLETIN, vol. 39, no. 3, pp. 92-92.
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Cortie, MB, Maaroof, A, Smith, GB & Ngoepe, P 2006, 'Nanoscale coatings of AuAlx and PtAlx and their mesoporous elemental derivatives', CURRENT APPLIED PHYSICS, vol. 6, no. 3, pp. 440-443.
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A method to produce nanoscale films of AuAlx and PtAlx, and their mesoporous elemental derivatives is described, and the morphology and optical properties of these coatings explored. The color of the AuAlx film is bright purple, in agreement with ab init

Cortie, MB, McBean, KE & Elcombe, MM 2006, 'Fracture mechanics of mollusc shells', PHYSICA B-CONDENSED MATTER, vol. 385, no. 1, pp. 545-547.
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The shape and structure of the shells of molluscs has attracted considerable attention. One aspect of interest is the comparatively high resistance to fracture of these shells. It is known that they are composite structures of aragonite, other calcereous

Cortie, MB, Xu, X & Ford, MJ 2006, 'Effect of composition and packing configuration on the dichroic optical properties of coinage metal nanorods', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 8, no. 30, pp. 3520-3527.
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When nanorods of Au, Ag and some other elements are aligned with a preferred orientation with respect to light, their optical extinction characteristics become dependent on the polarization and angle of incidence of the light. This effect is explored here and it is shown that it could potentially be exploited to produce a 'colour-change coating'. However, particle-particle interactions are also likely to occur in such coatings, with red shifting of extinction spectra occurring for end-on-end configurations of monodisperse rods, and blue shifting for side-by-side configurations. Surprisingly, the particle-particle interactions are attenuated if they are between rods of differing aspect ratios, and this offers a useful new means of control of the optical properties of coatings of nanorods. © the Owner Societies 2006.

Cranfield, CG, Bomzon, Z, Day, D, Gu, M & Cartmell, SH 2006, 'Mechanical Strains Induced in Osteoblasts by Use of Point Femtosecond Laser Targeting.', Int. J. Biomed. Imaging, vol. 2006, pp. 21304:1-21304:1.
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A study demonstrating how ultrafast laser radiation stimulates osteoblasts is presented. The study employed a custom made optical system that allowed for simultaneous confocal cell imaging and targeted femtosecond pulse laser irradiation. When femtosecond laser light was focused onto a single cell, a rise in intracellular Ca 2+ levels was observed followed by contraction of the targeted cell. This contraction caused deformation of neighbouring cells leading to a heterogeneous strain field throughout the monolayer. Quantification of the strain fields in the monolayer using digital image correlation revealed local strains much higher than threshold values typically reported to stimulate extracellular bone matrix production in vitro. This use of point targeting with femtosecond pulse lasers could provide a new method for stimulating cell activity in orthopaedic tissue engineering.

Curtis, TP, Head, IM, Lunn, M, Woodcock, S, Schloss, PD & Sloan, WT 2006, 'What is the extent of prokaryotic diversity?', PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 361, no. 1475, pp. 2023-2037.
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The extent of microbial diversity is an intrinsically fascinating subject of profound practical importance. The term 'diversity' may allude to the number of taxa or species richness as well as their relative abundance. There is uncertainty about both, primarily because sample sizes are too small. Non-parametric diversity estimators make gross underestimates if used with small sample sizes on unevenly distributed communities. One can make richness estimates over many scales using small samples by assuming a species/taxa-abundance distribution. However, no one knows what the underlying taxa-abundance distributions are for bacterial communities. Latterly, diversity has been estimated by fitting data from gene clone libraries and extrapolating from this to taxa-abundance curves to estimate richness. However, since sample sizes are small, we cannot be sure that such samples are representative of the community from which they were drawn. It is however possible to formulate, and calibrate, models that predict the diversity of local communities and of samples drawn from that local community. The calibration of such models suggests that migration rates are small and decrease as the community gets larger. The preliminary predictions of the model are qualitatively consistent with the patterns seen in clone libraries in 'real life'. The validation of this model is also confounded by small sample sizes. However, if such models were properly validated, they could form invaluable tools for the prediction of microbial diversity and a basis for the systematic exploration of microbial diversity on the planet. © 2006 The Royal Society.

Davis, ME, Smith, TJ, Laden, F, Hart, JE, Ryan, LM & Garshick, E 2006, 'Modeling particle exposure in US trucking terminals', ENVIRONMENTAL SCIENCE & TECHNOLOGY, vol. 40, no. 13, pp. 4226-4232.
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Multi-tiered sampling approaches are common in environmental and occupational exposure assessment, where exposures for a given individual are often modeled based on simultaneous measurements taken at multiple indoor and outdoor sites. The monitoring data from such studies is hierarchical by design, imposing a complex covariance structure that must be accounted for in order to obtain unbiased estimates of exposure. Statistical methods such as structural equation modeling (SEM) represent a useful alternative to simple linear regression in these cases, providing simultaneous and unbiased predictions of each level of exposure based on a set of covariates specific to the exposure setting. We test the SEM approach using data from a large exposure assessment of diesel and combustion particles in the U.S. trucking industry. The exposure assessment includes data from 36 different trucking terminals across the United States sampled between 2001 and 2005, measuring PM2.5 and its elemental carbon (EC), organic carbon (OC) components, by personal monitoring, and sampling at two indoor work locations and an outdoor 'background' location. Using the SEM method, we predict the following: (1) personal exposures as a function of work-related exposure and smoking status; (2) work-related exposure as a function of terminal characteristics, indoor ventilation, job location, and background exposure conditions; and (3) background exposure conditions as a function of weather, nearby source pollution, and other regional differences across terminal sites. The primary advantage of SEMs in this setting is the ability to simultaneously predict exposures at each of the sampling locations, while accounting for the complex covariance structure among the measurements and descriptive variables. The statistically significant results and high R 2 values observed from the trucking industry application supports the broader use of this approach in exposure assessment modeling. © 2006 American...

Day, D, Cranfield, CG & Gu, M 2006, 'High-Speed Fluorescence Imaging and Intensity Profiling of Femtosecond-Induced Calcium Transients.', Int. J. Biomed. Imaging, vol. 2006, pp. 93438:1-93438:1.
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We have demonstrated a combined imaging system, where the physiology of biological specimens can be imaged and profiled at 10-20 frames per second whilst undergoing femtosecond laser irradiation. Individual GH3 cells labeled with the calcium fluorophore Fluo-3 were stimulated using a counter-propagating focused femtosecond beam with respect to the imaging system. As a result of the stimulation, calcium waves can be generated in COS cells, and laser-induced calcium oscillations are initiated in the GH3 cells. Single-photon fluorescence images and intensity profiles of the targeted specimens are sampled in real-time using a modified PerkinElmer UltraView LCI microscope. Copyright © 2006 Daniel Day et al.

Day, DM & Wallman, JF 2006, 'A comparison of frozen/thawed and fresh food substrates in development of Calliphora augur (Diptera: Calliphoridae) larvae', International Journal of Legal Medicine, vol. 120, no. 6, pp. 391-394.
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Day, DM & Wallman, JF 2006, 'ERRATUM', Journal of Forensic Sciences, vol. 51, no. 5, pp. 1221-1221.
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Day, DM & Wallman, JF 2006, 'Influence of Substrate Tissue Type on Larval Growth in Calliphora augur and Lucilia cuprina (Diptera: Calliphoridae)^*', Journal of Forensic Sciences, vol. 51, no. 3, pp. 657-663.
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ABSTRACT: The size of fly larvae is an important variable in the use of these insects to estimate postmortem interval. Furthermore, the nutritional intake of larvae is likely to vary subject to the part of a corpse on which they are feeding. A study was therefore conducted to investigate the effect of type of food substrate on larval growth in two species of forensically important Australian blowflies. After collection on sheep's liver in the laboratory, different groups of larvae of Lucilia cuprina (Wiedemann) and Calliphora augur (Fabricius) were grown on sheep's liver, meat, and brains, and their body lengths compared. Results indicated that the development of larvae fed sheep's liver was adversely affected compared with larvae fed meat and brain; they moulted later, reached maximum length more slowly and sometimes produced significantly smaller pupae. These findings, similar to those of another recent study, have obvious implications for postmortem interval determinations. Estimates may be considerably skewed if the site of collection of larvae at a death scene contains tissue types different to those used in reference experiments. We therefore recommend caution in forensic analyses that interpret crime scene data using developmental studies performed with a single type of larval food substrate.

Day, DM & Wallman, JF 2006, 'Width as an alternative measurement to length for post-mortem interval estimations using Calliphora augur (Diptera: Calliphoridae) larvae', Forensic Science International, vol. 159, no. 2-3, pp. 158-167.
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de Bas, BS, Ford, MJ & Cortie, MB 2006, 'Melting in small gold clusters: a density functional molecular dynamics study', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 18, no. 1, pp. 55-74.
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Molecular dynamics simulations of the thermal behaviour of gold clusters containing 7, 13 and 20 atoms have been performed. Total energies and forces at each step of the simulation are calculated from first principles using density functional theory. Ion trajectories are then calculated classically from these forces. In each case the global minimum energy structure and a low-lying isomer are used as the starting structures. In most cases, the clusters do not exhibit a sharp transition from a solid-like phase to a liquid-like phase, but rather pass through a region of transformations between structural isomers that extends over a considerable temperature range. Solid-like behaviour is observed in the atomic trajectories of the simulation at temperatures up to, or above, the bulk melting point. The 20-atom tetrahedral structure is the one exception, showing a sharp transition between solid-like and liquid-like phases at about 1200 K. The starting structure used in the simulation is shown to have a considerable effect upon the subsequent thermal behaviour.

DELA‐CRUZ, J, PRITCHARD, TIM, GORDON, G & AJANI, P 2006, 'The use of periphytic diatoms as a means of assessing impacts of point source inorganic nutrient pollution in south‐eastern Australia', Freshwater Biology, vol. 51, no. 5, pp. 951-972.
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Summary1. Periphytic diatoms are used as indicators of water quality because their ecological tolerances or preferences to environmental variables are thought to be predictable. However, much of the present autecological information for periphytic diatoms has been derived from studies conducted in the northern hemisphere. In this present study we used periphytic diatoms to determine the impacts of inorganic nutrient pollution in a tidal river system in the temperate latitudes of south‐east Australia. In so doing, we assess the suitability of the use of the ‘northern hemisphere’ ecological tolerance/preference data for periphytic diatoms.2. Artificial substrates were used to collect periphytic diatoms at 35 sites, which were positioned along the riverbanks and the middle of the river at various distances upstream and downstream of the sewage outfall. The sampling design took into account tidal excursions and the observed sewage plume dynamics. Periphytic diatoms were collected during the austral winter month of August and the austral spring months of September and October. We deployed the artificial substrates for 4 weeks to allow the periphytic diatoms to recruit and colonise, before identifying and enumerating the assemblages.3. Data analysis included two approaches: multivariate visualisations of combinations of environmental and biological data to investigate shifts in species structure of the periphytic diatom assemblage and multimetric indices based on ecological tolerance/preference data.4. We found that the spatial patterns inferred from multivariate and multimetric analyses were consistent. Temporal variation in the composition of the periphytic diatom assemblage was greater than the spatial variation along horizontal sections of the river (in any one deployment) due mainly to shifts between winter and spring species.5. Outfall effects were most ...

Deller, CA, Franklin, J & Smith, GB 2006, 'Monte Carlo ray-tracing in particle-doped light guides', LIGHTING RESEARCH & TECHNOLOGY, vol. 38, no. 2, pp. 95-108.
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A general Monte Carlo ray-tracing method for light guides with particles randomly dispersed in a matrix material is presented. Previous ray-tracing approaches have been designed for undoped cylindrical light guides, where a propagating ray is deviated by total internal reflection only. These geometrical principles are extended and further developed into a method of ray-tracing suitable for particle-doped systems. Redefining ray direction after deviation by a particle, obtaining ray/ wall intercept points and angles, and calculation of ray reflection angles from a cylindrical surface are described. Simulations of light from a source LED traced through TRIMM-doped (Transparent Refractive Index Matched Micro-Particle) polymethyl methacrylate (PMMA) light guides have been performed. Distributions of the light exiting the walls of two concentrations of TRIMM-doped light guides are given, as an example of an application of the described ray-tracing method.

Deng, C, Gorrie, C, Hayward, I, Elston, B, Venn, M, Mackay‐Sim, A & Waite, P 2006, 'Survival and migration of human and rat olfactory ensheathing cells in intact and injured spinal cord', Journal of Neuroscience Research, vol. 83, no. 7, pp. 1201-1212.
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AbstractIncreasing evidence indicates the potential of olfactory ensheathing cells (OECs) for treating spinal cord injuries. The present study compared proliferation and migration of adult rat and human OECs transplanted into the spinal cord of athymic (immunodeficient) rats. OECs were purified from the nasal lamina propria and prelabeled with a cytoplasmic dye. After OEC injection into the thoracic spinal cord, animals were perfused 4 hr, 24 hr, and 7 days later. Both rat and human OECs showed similar migration. Cells were seen leaving the injection site after 4 hr, and by 7 days both rat and human OECs had migrated approximately 1 mm rostrally and caudally within the cord (rat: 1,400 ± 241 μm rostral, 1,134 ± 262 μm caudal, n = 5; human: 1,337 ± 192 μm rostral, 1,205 ± 148 μm caudal, n = 6). Proliferation of transplanted OECs was evident at 4 hr, but most had ceased dividing by 24 hr. In 10 animals, the spinal cord was injured by a contralateral hemisection made 5 mm rostral to the transplantation site at the time of OEC transplantation. After 7 days, macrophages were numerous both around the injury and at the transplantation site. In the injured cord, rat and human OECs migrated for shorter distances, in both rostral and caudal directions (rat: 762 ± 118 μm rostral, 554 ± 142 μm caudal, n = 4; human: 430 ± 55 μm rostral, 399 ± 161 μm caudal, n = 3). The results show that rat and human OECs rapidly stop dividing after transplantation and have a similar ability to survive and migrate within the spinal cord of immunocompromised hosts. OECs migrated less in animals with a concomitant contralateral hemisection. © 2006 Wiley‐Liss, Inc.

Dennis, ES, Helliwell, CA & Peacock, WJ 2006, 'Vernalization: Spring into flowering', DEVELOPMENTAL CELL, vol. 11, no. 1, pp. 1-2.
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Doblin, MA & Dobbs, FC 2006, 'Setting a size-exclusion limit to remove toxic dinoflagellate cysts from ships' ballast water', MARINE POLLUTION BULLETIN, vol. 52, no. 3, pp. 259-263.
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Dinoflagellate cysts are well-recognized biological constituents of ships ballast tanks. They are present in ballast water, sediments and residual water in drained tanks, and in biofilms formed on interior tank Surfaces. Therefore, cysts have the potenti

Doblin, MA, Baines, SB, Cutter, LS & Cutter, GA 2006, 'Sources and biogeochemical cycling of particulate selenium in the San Francisco Bay estuary', ESTUARINE COASTAL AND SHELF SCIENCE, vol. 67, no. 4, pp. 681-694.
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As part of a study of estuarine selenium cycling, we measured the concentration, chemical form (speciation), and distribution of particulate selenium under various river flow conditions in the North San Francisco Bay (from the Golden Gate to the Sacramen

Doblin, MA, Thompson, PA, Revill, AT, Butler, ECV, Blackburn, SI & Hallegraeff, GM 2006, 'Vertical migration of the toxic dinoflagellate Gymnodinium catenatum under different concentrations of nutrients and humic substances in culture', HARMFUL ALGAE, vol. 5, no. 6, pp. 665-677.
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Vertical migration behaviour by the chainforming dinoflagellate Gymnodinium catenatum Graham was investigated using vertically-stratified laboratory columns. Under surface nutrient-deplete conditions, with nutrients added only at depth, 100% of cells underwent vertical migration (VM), starting downwards migration 3 h before the end of the light period and beginning upwards migration 3 h before the start of the light period. Cells in nutrient-replete columns showed no VM, but they were more dispersed in the upper layer during the dark compared to the light period. When surface layers (S) were nitrate-deplete (-N) and enriched with humic substances (H) contained in Huon River water and bottom waters (B) were nutrient replete (R) (SH-NBR), the pattern of VM was altered-50% of cells underwent migration and 50% remained at the pycnocline. In columns with nitrate-replete and humic-enriched surface layers (SHRBR), Most cells underwent VM, while 30% remained at the surface. Cells in SH-NBR columns showed increased N quotas and intra-cellular nitrate concentrations after 4 days, indicating nitrate uptake by G. catenatum in bottom layers. The concomitant increase in particulate organic nitrogen (PON) with the decrease in external nitrate concentrations in bottom layers provide convincing evidence that VM by G. catenatum facilitates nutrient retrieval at depth. However, addition of humic substances (a potential source of organic nitrogen) to surface layers did not ameliorate G. catenatum N depletion sufficiently to preclude the need for NO3- uptake at depth. Furthermore, there was no detectable pattern of increasing carbon (C) quota during the day (photosynthate accumulation) or increasing N quota during the night (nitrate assimilation).

Donnelly, R, Wang, B & Qu, X 2006, 'Type 2 diabetes in China: partnerships in education and research to evaluate new antidiabetic treatments', British Journal of Clinical Pharmacology, vol. 61, no. 6, pp. 702-705.
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There are 40 million people with diabetes in China, and the projected increase in the rates of obesity and premature cardiovascular disease is alarming. Most patients prefer to combine traditional Chinese medicine with Western medicine, but there is little or no information about the risks and benefits of this approach. Traditional Chinese medicine identifies three patterns of ‘depletion–thirst’ syndrome and therapy is aimed at reversing the deficiency in yin and qi, using a combination of products tailored to the symptoms and clinical features of individual patients. In Western medicine a number of new oral and injectable antidiabetic therapies are likely to enter routine clinical practice over the next 5 years, for example long‐acting GLP‐1 analogues, DPP‐IV inhibitors and dual PPAR‐α, PPAR‐γ agonists. To make best use of these agents in China and to promote diabetes education and health service development, there is a need for improved communication and collaboration between universities and hospitals both inside and outside China; and Western pharmacologists and clinicians need a better understanding of traditional Chinese medicine. There are several examples of institutional cooperation that should further diabetes research in China, for example the Beijing Chaoyang Diabetes Hospital linked with Imperial College, London, and the University of Nottingham, which has a new campus in Ningbo, south of Shanghai.

Dooley, AH & Mortiss, G 2006, 'On the critical dimension and AC entropy for Markov odometers', MONATSHEFTE FUR MATHEMATIK, vol. 149, no. 3, pp. 193-213.
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Dooley, AH & Stenflo, O 2006, 'A criterion for uniqueness in G-measures and perfect sampling', MATHEMATICAL PROCEEDINGS OF THE CAMBRIDGE PHILOSOPHICAL SOCIETY, vol. 140, pp. 545-551.
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DOOLEY, AH & STENFLO, Ö 2006, 'A criterion for uniqueness in $G$-measures and perfect sampling', Mathematical Proceedings of the Cambridge Philosophical Society, vol. 140, no. 03, pp. 545-545.
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Using coupling techniques, we prove uniqueness in G-measures under a weak regularity condition and give estimates of the associated rates of convergence. We also show how to generate a random variable distributed according to the unique G-measure on cylinder sets for any fixed level of precision. © 2006 Cambridge Philosophical Society.

Dooley, AH & Wildberger, NJ 2006, 'Orbital convolution theory for semi-direct products', JOURNAL OF LIE THEORY, vol. 16, no. 4, pp. 743-776.

Dossou, K, Botten, LC, de Sterke, CM, McPhedran, RC, Asatryan, AA, Chen, S & Brnovic, J 2006, 'Efficient couplers for photonic crystal waveguides', OPTICS COMMUNICATIONS, vol. 265, no. 1, pp. 207-219.
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We use two-dimensional simulations to study the design of tapers to provide efficient, low reflection coupling between a waveguide in a two-dimensional photonic crystal (PC) and free space. We find that, largely independent of the PC parameters, or of th

Dossou, K, Byrne, MA & Botten, LC 2006, 'Finite element computation of grating scattering matrices and application to photonic crystal band calculations', JOURNAL OF COMPUTATIONAL PHYSICS, vol. 219, no. 1, pp. 120-143.
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We consider the calculation of the band structure and Bloch mode basis of two-dimensional photonic crystals, modelled as stacks of one-dimensional diffraction gratings. The scattering properties of each grating are calculated using an efficient finite element method (FEM) and allow the complete mode structure to be derived from a transfer matrix method. A range of numerical examples showing the accuracy, flexibility and utility of the method is presented. © 2006 Elsevier Inc. All rights reserved.

Doubell, MJ, Seuront, L, Seymour, JR, Patten, NL & Mitchell, JG 2006, 'High-resolution fluorometer for mapping microscale phytoplankton distributions', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, no. 6, pp. 4475-4478.
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A new high-resolution, in situ profiling fluorometer maps fluorescence distributions with a spatial resolution of 0.5 to 1.5 mm to a depth of 70 m in the open ocean. We report centimeter-scale patterns for phytoplankton distributions associated with gradients exhibiting 10- to 30-fold changes in fluorescence in contrasting marine ecosystems. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Duggin, IG & Bell, SD 2006, 'The chromosome replication machinery of the archaeon Sulfolobus solfataricus', JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 281, no. 22, pp. 15029-15032.
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In the three domains of life, the archaea, bacteria, and eukarya, there are two general lineages of DNA replication proteins: the bacterial and the eukaryal/archaeal lineages. The hyperthermophilic archaeon Sulfolobus solfataricus provides an attractive model for biochemical study of DNA replication. Its relative simplicity in both genomic and biochemical contexts, together with high protein thermostability, has already provided insight into the function of the more complex yet homologous molecules of the eukaryotic domain. Here, we provide an overview of recent insights into the functioning of the chromosome replication machinery of S. solfataricus, focusing on some of the relatively well characterized core components that act at the DNA replication fork.

EAMENS, G, FORBES, W & DJORDJEVIC, S 2006, 'Characterisation of Erysipelothrix rhusiopathiae isolates from pigs associated with vaccine breakdowns', Veterinary Microbiology, vol. 115, no. 4, pp. 329-338.
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Swine erysipelas vaccines are routinely used to protect pigs against peracute and acute/urticarial forms of Erysipelothrix. Between 1995 and 1998, 34 swine herds across four Australian states experienced vaccine failure. Forty-four isolates of Erysipelothrix rhusiopathiae of serovars 2, 1a, 1b and 1b × 21 were recovered from 15 of these 34 vaccine breakdown herds. These isolates were characterised by restriction fragment length polymorphism (RFLP) analyses using RsaI and AluI on whole cell DNA and for the presence of plasmid DNA. Results were compared with those of 20 isolates from 16 herds unaffected by vaccine breakdown and 13 isolates representing 10 reference strains. The majority of breakdown herds possessed isolates of serovar 2 (9/15 herds), followed by serovar 1a (5 herds). No geographic predominance of a single serovar was evident. The identification of 10 RsaI profiles from whole cell DNA among the 44 isolates from 15 breakdown herds indicated that a single, new clonal lineage of E. rhusiopathiae was not responsible for vaccine failure. RsaI RFLP analyses detected a further 14 distinct profiles among 20 field strains unassociated with vaccine breakdowns, and none matched profiles of the 10 serovar reference strains for serovars 1a, 1b, 2 or 21. This technique is recommended for epidemiological studies of E. rhusiopathiae strains.

Egan, TJ, Chen, JY-J, de Villiers, KA, Mabotha, TE, Naidoo, KJ, Ncokazi, KK, Langford, SJ, McNaughton, D, Pandiancherri, S & Wood, BR 2006, 'Haemozoin (β‐haematin) biomineralization occurs by self‐assembly near the lipid/water interface', FEBS Letters, vol. 580, no. 21, pp. 5105-5110.
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Several blood‐feeding organisms, including the malaria parasite detoxify haem released from host haemoglobin by conversion to the insoluble crystalline ferriprotoporphyrin IX dimer known as haemozoin. To date the mechanism of haemozoin formation has remained unknown, although lipids or proteins have been suggested to catalyse its formation. We have found that β‐haematin (synthetic haemozoin) forms rapidly under physiologically realistic conditions near octanol/water, pentanol/water and lipid/water interfaces. Molecular dynamics simulations show that a precursor of the haemozoin dimer forms spontaneously in the absence of the competing hydrogen bonds of water, demonstrating that this substance probably self‐assembles near a lipid/water interface in vivo.

Elder, M, Kambites, M & Ostheimer, G 2006, 'On groups and counter automata', International Journal of Algebra and Computation, vol. 18, pp. 1345-1364.
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We study finitely generated groups whose word problems are accepted bycounter automata. We show that a group has word problem accepted by a blindn-counter automaton in the sense of Greibach if and only if it is virtuallyfree abelian of rank n; this result, which answers a question of Gilman, is ina very precise sense an abelian analogue of the Muller-Schupp theorem. Moregenerally, if G is a virtually abelian group then every group with word problemrecognised by a G-automaton is virtually abelian with growth class boundedabove by the growth class of G. We consider also other types of counterautomata.

Evans, LS, Gale, PA, Light, ME & Quesada, R 2006, 'Anion binding vs. deprotonation in colorimetric pyrrolylamidothiourea based anion sensors', Chemical Communications, no. 9, pp. 965-965.
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Evans, LS, Gale, PA, Light, ME & Quesada, R 2006, 'Pyrrolylamidourea based anion receptors', New Journal of Chemistry, vol. 30, no. 7, pp. 1019-1019.
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Fatima Shad, K 2006, 'Effect of d-serine on the serotonin receptors of human platelets', Experimental Brain Research, vol. 173, no. 2, pp. 353-356.
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Recent literature and our previous observations indicated the presence of both NMDA and serotonin type 3 receptors in human platelets with very similar ionic currents to that of cultured mammalian neuronal receptors. Baseline electrophysiological data shows similar profile for platelets from both normal and schizophrenic subjects, whereas serotonin receptor studies exhibited the presence of 5-hydroxytryptamine type-3 (5-HT3) currents in both normal and schizophrenic platelets significantly different from each other. The two major differences observed were: first, 5-HT3 receptors present in the platelets of schizophrenic patients were four times more sensitive to serotonin than those present in the platelets of normal subjects and, second, that D: -serine in micro molar concentrations dampens this effect in platelets from schizophrenic patients but increases the sensitivity of serotonin for platelet 5-HT3 receptors of normal subjects. Patch clamp technique was used to measure the whole cell currents passing through serotonin receptors in these two types of human platelets. The currents were found to be 5-HT3 receptor currents as they were abolished by 10 microM D-tubocurarine. Similarly, micromolar concentrations of D: -serine increased the sensitivity of 5HT3 receptor currents in the normal human platelets but decreased it in the platelets of the schizophrenic patients. This effect was reversed when D-amino acid oxidase (0.3 microM) was co applied with 100 microM of D-serine, raising the possibility that D-serine by itself may act as a modulator for platelet 5-HT3 receptor channel currents. These observations raised exciting new questions about the role of platelet serotonin receptors and their regulation by D-serine.

Fergusson, KJ & Platen, E 2006, 'On the distributional characterization of daily log-returns of a world stock index', Applied Mathematical Finance, vol. 13, no. 1, pp. 19-38.
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In this paper distributions are identified which suitably fit log-returns of the world stock index when these are expressed in units of different currencies. By searching for a best fit in the class of symmetric generalized hyperbolic distributions the maximum likelihood estimates appear to cluster in the neighbourhood of those of the Student t distribution. This is confirmed at a high significance level under the likelihood ratio test. Finally, the paper derives the minimal market model, which explains the empirical findings as a consequence of the optimal market dynamics

Ferreira, ME, Ferreira, LG, Huete, AR & Peccinini, AA 2006, 'Análise compararativa dos produtos MODIS Ecologia para o monitoramento biofísico ambiental do bioma cerrado', Revista Brasileira de Geofísica, vol. 24, no. 2, pp. 251-260.
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The Brazilian Cerrado is an extensive and complex biome, characterized by rapid and abrupt land cover changes. Due to its dimensions and physiognomic variations, the Cerrado plays an important role regarding the water, energy, and carbon fluxes at both the regional and global scales. Therefore, the correct understanding of the structure and ecological functioning of this biome, particularly in the temporal domain, is of great importance. With this respect, in this study we compared the seasonal response and land cover discrimination of the major MODIS (MODerate resolution Imaging Spectroradiometer) biophysical indices: the normalized difference vegetation index (NDVI), the enhanced vegetation index (EVI), the leaf area index (LAI), and the fraction of absorbed photosynthetically active radiation (fAPAR). In spite of the fact the four indices showed similar temporal trends, the LAI showed the highest sensitivity to the seasonal variations of the natural and converted landscapes. On the other hand, the NDVI showed the best performance regarding land cover discrimination. Our results suggest a synergistic approach concerning the MODIS biophysical / ecological variables for land cover assessments and environmental monitoring of the Cerrado biome.

Flynn, K, O'Leary, R, Roux, C & Reedy, BJ 2006, 'Forensic analysis of bicomponent fibers using infrared chemical imaging', JOURNAL OF FORENSIC SCIENCES, vol. 51, no. 3, pp. 586-596.
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The application of infrared chemical imaging to the analysis of bicomponent fibers was evaluated. Eleven nominally bicomponent fibers were examined either side-on or in cross-section. In six of the 11 samples, infrared chemical imaging was able to spatia

Ford, M, Cortie, MB, Maclurcan, D & Martin, DK 2006, 'Real world nanotechnology', Materials Australia, vol. 39, no. 3, pp. 10-12.
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There is a degree of uncertainty in the public mind concerning the exact subject matter of nanotechnology. Novels such as Michael Crichtons Prey and the movie Agent Codie Banks have primed many to believe that nanotechnology is about tiny (and rather dangerous) nano-robots. Of course, most technically savvy individuals know better, but because this misconception exists there is an obligation on researchers in this field to communicate a more accurate understanding of the topic to the wider community. The Institute for Nanoscale Technology at the University of Technology, Sydney (UTS) has sought to bridge this gap in understanding.

Ford, M, Masens, CD & Cortie, MB 2006, 'The application of gold surfaces and particles in nanotechnology', Surface Review Letters, vol. 12, no. 2-3, pp. 297-307.
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Gold is widely used in nanotechnology, for example as a substrate in forming self-assembled monolayers or as nanoparticles for their unique optical and chemical properties. In this paper we give an overview of the properties of gold relevant to its potential application in molecular-scale devices and present some of our recent computational predictions. Density functional calculations of molecular adsorption onto gold surfaces were used to investigate the effect of surface symmetry and identify new linking schemes for self-assembled monolayers. Adsorption energies of methythiolate (SCH3) onto the (111), 9100) and (110) surfaces of gold are predicted to be 39.3, 48.4 and 51.1 kcal/mol respectively and demonstrate that selective functionalisation of the surfaces is possible. Phosphine molecules with at least two hydrogen atoms substituted for methyl groups are predicted to form Au-P surface bonds with energies of about 13-20 kcal/mol.

Ford, MJ, Hoft, RC & Gale, JD 2006, 'Adsorption and dimerisation of thiol molecules on Au(111) using a Z-matrix approach in density functional theory', MOLECULAR SIMULATION, vol. 32, no. 15, pp. 1219-1225.
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Th adsorption energies of methanethiolate on Au(111) have been calculated using periodic density functional theory (DFT), based on the SIESTA methodology, with an internal coordination implementation for geometry input and sturcture optimisation. Both molecules are covalently boudn with interaction energies of 1.85 and 1.43 eV for methanethiolate and benzenethiolate, respectively. The preferred binding site is slightly offset from the bridge sire i both cases towards the fcc-hollow. The potential energy durfacces (PES) have depths of 0.36 and 0.22 eV, the hollow sites are local maxima in both cases, and there is not barrier to diffusion ofthe molecule at the bridge site. The corresponding dimers are weakly bound for methanethiolate and benzenthiolate, with binding energies of 0.38 and 0.16eV, respectively, and the preferred binding geometry is with the two sulphur atoms close to adjacent atop sites. The barrier to dissociation of the dimer dimethyl disulphide is estimated to like between 0.3 and 0.35eV.

Ford, MJ, Masens, C & Cortie, MB 2006, 'The application of gold surfaces and particles in nanotechnology', SURFACE REVIEW AND LETTERS, vol. 13, no. 2-3, pp. 297-307.
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Forsyth, CM, Langford, SJ & Lee, KA 2006, '(Z)-Benzyl 2-(hydroxyimino)acetoacetate', Acta Crystallographica Section E Structure Reports Online, vol. 62, no. 12, pp. o5654-o5655.
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Fourment, M & Gibbs, MJ 2006, 'PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change', BMC Evolutionary Biology, vol. 6, no. 1.
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Abstract Background Phylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures. Results PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs. Conclusion The software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at http://biojanus.anu.edu.au/programs/ and requires the Java runtime environment.

Franklin, KA, Lyons, K, Nagler, PL, Lampkin, D, Glenn, EP, Molina-Freaner, F, Markow, T & Huete, AR 2006, 'Buffelgrass (Pennisetum ciliare) land conversion and productivity in the plains of Sonora, Mexico', BIOLOGICAL CONSERVATION, vol. 127, no. 1, pp. 62-71.
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Bufflelgrass (Pennisetum ciliare syn. Cenchrus ciliaris) is an African grass that has been widely introduced in subtropical arid regions of the world to improve rangelands for cattle production. However, it can have a negative effect on the diversity of native plant communities. Buffelgrass was introduced to Sonora, Mexico in the 1970s as a means to bolster the cattle industry. 'Desmonte,' the process by which native desert vegetation is removed in preparation for buffelgrass seeding, alters the land surface such that buffelgrass plots are easily detectable from aerial and Landsat satellite images. We estimated the extent of conversion to buffelgrass in a 1,850,000 ha area centered on Hermosillo, from MSS and TM images from 1973, 1983, 1990 and 2000. We then compared the relative above-ground productivity of buffelgrass to native vegetation using Normalized Difference Vegetation Index values (NDVI) from Landsat and Moderate Resolution Imaging Spectrometer (MODIS) satellite sensor systems. Buffelgrass pastures have increased from just 7700 ha in 1973 to over 140,000 ha in 2000. Buffelgrass pastures now cover 8% of the land surface in the study area. Buffelgrass pastures have lower net primary productivity, estimated by MODIS NDVI values, than unconverted desert land. The desmonte process removes trees and shrubs, while the buffelgrass plantings are often sparse, leading to an apparent net loss in net primary production from land conversion. We recommend that the desmonte process be discontinued until its efficacy and safety for native ecosystems can be established, and that a comprehensive plan for preserving biodiversity while accomodating economic development be established for this region of the Sonoran Desert in Mexico. © 2005 Elsevier Ltd. All rights reserved.

Freedman, LS, Potischman, N, Kipnis, V, Midthune, D, Schatzkin, A, Thompson, FE, Troiano, RP, Prentice, R, Patterson, R, Carroll, R & Subar, AF 2006, 'A comparison of two dietary instruments for evaluating the fat-breast cancer relationship', INTERNATIONAL JOURNAL OF EPIDEMIOLOGY, vol. 35, no. 4, pp. 1011-1021.
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Fu, L, Jain, A, Xie, HK, Cranfield, C & Gu, M 2006, 'Nonlinear optical endoscopy based on a double-clad photonic crystal fiber and a MEMS mirror', OPTICS EXPRESS, vol. 14, no. 3, pp. 1027-1032.
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Fu, LJ, Liu, H, Li, C, Wu, YP, Rahm, E, Holze, R & Wu, HQ 2006, 'Surface modifications of electrode materials for lithium ion batteries', SOLID STATE SCIENCES, vol. 8, no. 2, pp. 113-128.
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Since the birth of the lithium ion battery in the early 1990s, its development has been very rapid and it has been widely applied as power source for a lot of light and high value electronics due to its significant advantages over traditional rechargeable battery systems. Recent research demonstrates the importance of surface structural features of electrode materials for their electrochemical performance, and in this paper the latest progress on this aspect is reviewed. Electrode materials are either anodic or cathodic ones. The former mainly include graphitic carbons, whose surfaces can be modified by mild oxidation, deposition of metals and metal oxides, coating with polymers and other kinds of carbons. P, Through these modifications, the surface structures of the graphitic carbon anodes are improved, and these improvements include: (1) smoothing the active edge surfaces by removing some reactive sites and/or defects on the graphite surface, (2) forming a dense oxide layer on the graphite surface, and (3) covering active edge structures on the graphite surface. Meanwhile, other accompanying changes occur: (1) production of nanochannels/micropores, (2) an increase in the electronic conductivity, (3) an inhibition of structural changes during cycling, (4) a reduction of the thickness of the SEI (solid-electrolyte-interface) layer, and (5) an increase in the number of host sites for lithium storage.

Fu, LJ, Liu, H, Zhang, HP, Li, C, Zhang, T, Wu, YP & Wu, HQ 2006, 'Novel TiO2/C nanocomposites for anode materials of lithium ion batteries', JOURNAL OF POWER SOURCES, vol. 159, no. 1, pp. 219-222.
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Here we reported an effective method to prepare TiO2/C core-shell nanocomposites as active anode materials for lithium ion batteries with markedly ameliorated electrochemical performance. At first, a precursor, polyacrylonitrile coated nano-TiO2 particles, was formed by emulsion polymerization. Then the precursor was heat-treated under argon atmosphere to achieve the nanocomposites. The conductive carbon shell enveloped TiO2 nanoparticles and suppressed the aggregation of nanoparticles during cycling. Meanwhile, it combined closely with the nanocores, significantly enhanced kinetics of lithium intercalation and de-intercalation and diffusion coefficient of lithium ion. This provides a good way to improve the cycling and kinetics of nanoanode materials.

Fu, LJ, Liu, H, Zhang, HP, Li, C, Zhang, T, Wu, YP, Holze, R & Wu, HQ 2006, 'Synthesis and electrochemical performance of novel core/shell structured nanocomposites', ELECTROCHEMISTRY COMMUNICATIONS, vol. 8, no. 1, pp. 1-4.
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A new and effective method to prepare TiO2/C core-shell nanocomposites as active anode materials for lithium ion batteries with markedly ameliorated electrochemical performance is described. Initially a precursor, polyacrylonitrile coated nano-TiO2 particles, is formed by emulsion polymerization. This precursor is heat-treated under argon atmosphere to achieve the nanocomposite. The conductive carbon shell enveloped TiO2 nanoparticles and suppressed the aggregation of the core nanoparticles during cycling. In addition it is attached closely to the nano-cores, and the kinetics of lithium intercalation and de-intercalation, the apparent diffusion coefficient of lithium ions and the consequent cycling behavior are significantly enhanced. This provides a good way to improve cycling and kinetics of nano-anode materials

Fu, WJJ, Hu, JB, Spencer, T, Carroll, R & Wu, GY 2006, 'Statistical models in assessing fold change of gene expression in real-time RT-PCR experiments', COMPUTATIONAL BIOLOGY AND CHEMISTRY, vol. 30, no. 1, pp. 21-26.
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Fujii, M, Koos, C, Poulton, C, Leuthold, J & Freude, W 2006, 'Nonlinear FDTD analysis and experimental verification of four-wave mixing in InGaAsP-InP racetrack microresonators', IEEE Photonics Technology Letters, vol. 18, no. 2, pp. 361-363.
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We demonstrate for the first time a nonlinear finite-difference time-domain (FDTD) analysis of optical parametric four-wave mixing (FWM) in an actual InGaAsP-InP-based racetrack microresonator, and the results are compared with measurements on an experimental prototype. It has been found from the two-dimensional (2-D) and three-dimensional FDTD analyses that the resonance frequencies can be reasonably predicted by an FDTD model by considering the strong material dispersion of the waveguide medium and that the wavelength conversion by FWM is not sensitive to the dimensionality of the model; thus, it is efficiently predicted by the 2-D FDTD model. © 2005 IEEE.

Fujii, M, Koos, C, Poulton, C, Sakagami, I, Leuthold, J & Freude, W 2006, 'A simple and rigorous verification technique for nonlinear fdtd algorithms by optical parametric four-wave mixing', Microwave and Optical Technology Letters, vol. 48, no. 1, pp. 88-91.
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A rigorous quantitative verification technique is presented for nonlinear finite-difference time-domain (FDTD) algorithms by analyzing parametric four-wave mixing (FWM) in an optical Kerr medium without involving other numerical techniques. This technique allows quick and reliable verification of complicated nonlinear FDTD algorithms, hence enhancing the application of nonlinear FDTD analysis to more realistic optical problems. © 2005 Wiley Periodicals, Inc.

Fujii, M, Maitra, A, Poulton, C, Leuthold, J & Freude, W 2006, 'Non-reciprocal transmission and Schmitt trigger operation in strongly modulated asymmetric WBGs', Optics Express, vol. 14, no. 26, pp. 12782-12782.
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We investigate numerically a non-reciprocal switching behavior in strongly modulated waveguide Bragg gratings (WBGs) having a longitudinally asymmetric stopband configuration. The minimum power predicted for a stable switching operation is found to be approximately 77 mW for a realistic waveguide structure made of prospective materials; we assume in this paper a nano-strip InGaAsP/InP waveguide having longitudinally asymmetric modulation of the waveguide width. The analysis has been performed with our in-house nonlinear finite-difference time-domain (FDTD) code adapted to parallel computing. The numerical results clearly show low-threshold Schmitt trigger operation, as well as non-reciprocal transmission property where the switching threshold for one propagation direction is lower than that for the other direction. In addition, we discuss the modulation-like instability phenomena in such nonlinear periodic devices by employing both an instantaneous Kerr nonlinearity and a more involved saturable nonlinearity model. © 2006 Optical Society of America.

Gale, PA 2006, 'Preface', Coordination Chemistry Reviews, vol. 250, no. 23-24, pp. 2917-2917.
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Gale, PA 2006, 'Structural and Molecular Recognition Studies with Acyclic Anion Receptors', Accounts of Chemical Research, vol. 39, no. 7, pp. 465-475.
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Gale, PA & Quesada, R 2006, 'Anion coordination and anion-templated assembly: Highlights from 2002 to 2004', Coordination Chemistry Reviews, vol. 250, no. 23-24, pp. 3219-3244.
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Gale, PA, Light, ME & Quesada, R 2006, 'Formation and X-ray crystal structures of neutral 3D networks by charge-assisted hydrogen bonds between tetrakis(thiourea)platinum(II) complexes and dicarboxylates', Polyhedron, vol. 25, no. 4, pp. 901-909.
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Game, C, Gagnon, MM, Webb, D & Lim, R 2006, 'Endocrine disruption in male mosquitofish (Gambusia holbrooki) inhabiting wetlands in Western Australia', Ecotoxicology, vol. 15, no. 8, pp. 665-672.
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The use of gonopodial indices as potential indicators of endocrine disruption in the mosquitofish Gambusia holbrooki inhabiting south west Australian wetlands was investigated. A minimum of 50 mature makes was collected from each of five water-bodies in the Swan Coastal Plain, Western Australia, in order to measure morphological features related to reproduction. A set of morphological measurements were used to derive the following indices: gonopodium length/ standard body length, pre-anal length/standard body length, the index of elongation and the percentage of male fish with hooks on the distal end of the gonopodium. Indices of male mosquitofish collected from Jack Finney Lake, located in the Curtin University campus, suggest the presence of endocrine disrupting chemicals (EDCs) in this eater-body, while those from Lake Kulinup suggest this is a site of concern. Indices of male fish from the Wagerup wetland, Lake Monger and Loch McNess indicate that fish inhabiting these wetlands are not affected by EDCs. This preliminary study suggests that EDCs may be present ina number of wetlands of the Swan Coastal Plain. Further study using EDC specific markers such as vitellogenin induction in male mosquitofish is required to confirm whether EDCs are present in these water-bodies.

Ganguli, B & Wand, MP 2006, 'Additive models for geo-referenced failure time data', Statistics in Medicine, vol. 25, no. 14, pp. 2469-2482.
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Asthma researchers have found some evidence that geographical variations in susceptibility to asthma could reflect the effect of community level factors such as exposure to violence. Our methodology was motivated by a study of age at onset of asthma among children of inner-city neighbourhoods in East Boston. Cox's proportional hazards model was not appropriate since there was not enough information about the nature of geographical variations so as to impose a parametric relationship. In addition, some of the known risk factors were believed to have non-linear log-hazard ratios. We extend the geoadditive models of Kamman and Wand to the case where the outcome measure is a possibly censored time to event. We reduce the problem to one of fitting a Poisson mixed model by using Poisson approximations in conjunction with a mixed model formulation of generalized additive modelling. Our method allows for low-rank additive modelling, provides likelihood-based estimation of all parameters including the amount of smoothing and can be implemented using standard software. We illustrate our method on the East Boston data. Copyright © 2005 John Wiley & Sons, Ltd.

Gasanov, U, Koina, C, Beagley, KW, Aitken, RJ & Hansbro, PM 2006, 'Identification of the Insulin-Like Growth Factor II Receptor as a Novel Receptor for Binding and Invasion by Listeria monocytogenes', Infection and Immunity, vol. 74, no. 1, pp. 566-577.
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ABSTRACT The gram-positive bacterium Listeria monocytogenes causes a life-threatening disease known as listeriosis. The mechanism by which L. monocytogenes invades mammalian cells is not fully understood, but the processes involved may provide targets to prevent and treat listeriosis. Here, for the first time, we have identified the insulin-like growth factor II receptor (IGFIIR; also known as the cation-independent mannose 6-phosphate receptor CI M6PR or CD222) as a novel receptor for binding and invasion of Listeria species. Random peptide phage display was employed to select a peptide sequence by panning with immobilized L. monocytogenes cells; this peptide sequence corresponds to a sequence within the mannose 6-phosphate binding site of the IGFIIR. All Listeria spp. specifically bound the labeled peptide but not a control peptide, which was demonstrated using fluorescence spectrophotometry and fluorescence-activated cell sorting. Further evidence for binding of the receptor by L. monocytogenes and L. innocua was provided by affinity purification of the bovine IGFIIR from fetal calf serum by use of magnetic beads coated with cell preparations of Listeria spp. as affinity matrices. Adherence to and invasion of mammalian cells by L. monocytogenes was significantly inhibited by both the synthetic peptide and mannose 6-phosphate but not by appropriate controls. These observations indicate a role for the I...

Ghiggino, KP, Hutchison, JA, Langford, SJ, Latter, MJ & Takezaki, M 2006, 'Triaminotriazines—photophysical investigations of a porphyrin‐appended triazine receptor with a naphthalene diimide guest', Journal of Physical Organic Chemistry, vol. 19, no. 8-9, pp. 491-494.
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AbstractA modular synthetic approach to preparing a family of triaminotriazine receptors bearing porphyrin chromophores is described. The porphyrin‐appended triaminotriazines are prepared in a stepwise manner employing either cyanuric chloride or fluoride and 5‐(4′‐aminophenyl)‐10,15,20‐triphenylporphyrin in the first step. Reaction of the porphyrintriazine with excess 1‐pentylamine leads to a triazine core programmed for three‐point hydrogen bonding. Addition of a complementary naphthalene diimide yields a supramolecular donor–acceptor dyad. Photophysical studies in CH2Cl2 solvent show efficient quenching of porphyrin fluorescence within the dyad, consistent with an electron transfer process. Copyright © 2006 John Wiley & Sons, Ltd.

Ghiggino, KP, Hutchison, JA, Langford, SJ, Latter, MJ, Lee, MA-P & Takezaki, M 2006, 'A Simple Dyad Exhibiting Microsecond Charge-Separation in Non-Polar Solvents', Australian Journal of Chemistry, vol. 59, no. 3, pp. 179-179.
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A simple photovoltaic device in which two chromophoric components are assembled by Zn–N coordination yields a charge-separated state with microsecond lifetime upon photoexcitation in non-polar solvents. Characterization of the electron transfer dynamics using time-resolved fluorescence and transient absorption spectroscopy suggests that the unusual longevity is due to charge recombination occurring between states with different electron spin character. Control of electron spin may provide a novel paradigm for optimizing light-induced charge-separation processes.

Ghiggino, KP, Hutchison, JA, Shafiqul Islan, D-M, Araki, Y, Ito, O, Langford, SJ, Lau, V-L & Takezaki, M 2006, 'Metal ion dependent fluorescence quenching in a crown ether bridged porphyrin—fullerene dyad', Photochemical & Photobiological Sciences, vol. 5, no. 12, pp. 1150-1153.
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Gladstone, W, Hacking, N & Owen, V 2006, 'Effects of artificial openings of intermittently opening estuaries on macroinvertebrate assemblages of the entrance barrier', ESTUARINE COASTAL AND SHELF SCIENCE, vol. 67, no. 4, pp. 708-720.
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Gladstone, W, Stanger, R & Phelps, L 2006, 'A Participatory Approach to University Teaching About Partnerships for Biodiversity Conservation', Australian Journal of Environmental Education, vol. 22, no. 2, pp. 21-31.
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Loss of biodiversity and habitats is one of the greatest threats to the environment and education has a critical role to play in addressing this issue. This paper describes a teaching activity for first-year university students studying sustainable resource management at the University of Newcastle which established a partnership between education, government and the community to rehabilitate a nature reserve where biodiversity values were threatened by weed invasion. Students research the problem (weed invasion), quantitatively assess the impacts of weed invasion and management interventions, and work alongside a community-based bushcare group and government agency during on-ground rehabilitation of the reserve. Key outcomes for students have been knowledge and skills relevant to a critical issue for the Australian environment; a more optimistic attitude towards environmental issues and their potential to develop solutions; a positive perspective about the role of community involvement; continued participation in community bushcare groups outside the classroom; and personal involvement in solving a critical environmental issue. © 2003, Cambridge University Press. All rights reserved.

Gladstone, W, Stanger, R & Phelps, L 2006, 'A Participatory Approach to University Teaching About Partnerships for Biodiversity Conservation', Australian Journal of Environmental Education, vol. 22, no. 2, pp. 21-31.
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AbstractLoss of biodiversity and habitats is one of the greatest threats to the environment and education has a critical role to play in addressing this issue. This paper describes a teaching activity for first-year university students studying sustainable resource management at the University of Newcastle which established a partnership between education, government and the community to rehabilitate a nature reserve where biodiversity values were threatened by weed invasion. Students research the problem (weed invasion), quantitatively assess the impacts of weed invasion and management interventions, and work alongside a community-based bushcare group and government agency during on-ground rehabilitation of the reserve. Key outcomes for students have been knowledge and skills relevant to a critical issue for the Australian environment; a more optimistic attitude towards environmental issues and their potential to develop solutions; a positive perspective about the role of community involvement; continued participation in community bushcare groups outside the classroom; and personal involvement in solving a critical environmental issue.

Glasner, JD, Rusch, M, Liss, P, Plunkett, G, Cabot, EL, Darling, A, Anderson, BD, Infield-Harm, P, Gilson, MC & Perna, NT 2006, 'ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.', Nucleic acids research, vol. 34, no. Database issue.
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ASAP is a comprehensive web-based system for community genome annotation and analysis. ASAP is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. New tools, such as the genome alignment program Mauve, have been incorporated into ASAP in order to improve display and analysis of related genomes. Recent improvements to the database and challenges for future development of the system are discussed. ASAP is available on the web at https://asap.ahabs.wisc.edu/asap/logon.php.

Godlewski, M, Phillips, MR, Kazlauskas, K, Czernecki, R, Targowski, G, Perlin, P, Leszczynski, M, Figge, S & Hommel, D 2006, 'Profiling of light emission of GaN-based laser diodes with cathodoluminescence', PHYSICA STATUS SOLIDI A-APPLICATIONS AND MATERIALS SCIENCE, vol. 203, no. 7, pp. 1811-1814.
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Cathodoluminescence is applied for evaluation of in-plane variations of light emission from GaN-based laser diode structures. We demonstrate that potential fluctuations affect significantly emission of laser diodes for e-beam currents above thresholds for a stimulated emission. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.

Gold, DR, Willwerth, BM, Tantisira, KG, Finn, PW, Schaub, B, Perkins, DL, Tzianabos, A, Ly, NP, Schroeter, C, Gibbons, F, Campos, H, Oken, E, Gillman, MW, Palmer, LJ, Ryan, LM & Weiss, ST 2006, 'Associations of cord blood fatty acids with lymphocyte proliferation, IL-13, and IFN-gamma', JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, vol. 117, no. 4, pp. 931-938.
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Background: N-3 and n-6 polyunsaturated fatty acids (PUFAs) have been hypothesized to have opposing influences on neonatal immune responses that might influence the risk of allergy or asthma. However, both n-3 eicosapentaenoic acid (EPA) and n-6 arachidonic acid (AA) are required for normal fetal development. Objective: We evaluated whether cord blood fatty acid levels were related to neonatal immune responses and whether n-3 and n-6 PUFA responses differed. Methods: We examined the relation of cord blood plasma n-3 and n-6 PUFAs (n = 192) to antigen- and mitogen-stimulated cord blood lymphocyte proliferation (n = 191) and cytokine (IL-13 and IFN-γ; n = 167) secretion in a US birth cohort. Results: Higher levels of n-6 linoleic acid were correlated with higher IL-13 levels in response to Bla g 2 (cockroach, P = .009) and Der f 1 (dust mite, P = .02). Higher n-3 EPA and n-6 AA levels were each correlated with reduced lymphocyte proliferation and IFN-γ levels in response to Bla g 2 and Der f 1 stimulation. Controlling for potential confounders, EPA and AA had similar independent effects on reduced allergen-stimulated IFN-γ levels. If neonates had either EPA or AA levels in the highest quartile, their Der f 1 IFN-γ levels were 90% lower (P = .0001) than those with both EPA and AA levels in the lowest 3 quartiles. Reduced AA/EPA ratio was associated with reduced allergen-stimulated IFN-γ level. Conclusion: Increased levels of fetal n-3 EPA and n-6 AA might have similar effects on attenuation of cord blood lymphocyte proliferation and IFN-γ secretion. Clinical implications: The implications of these findings for allergy or asthma development are not yet known. © 2006 American Academy of Allergy, Asthma and Immunology.

Gorkunov, MV, Lapine, MV & Tretyakov, SA 2006, 'Methods of crystal optics for studying electromagnetic phenomena in metamaterials: Review', Crystallography Reports, vol. 51, no. 6, pp. 1048-1062.
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Gorrie, CA, Rodriguez, M, Sachdev, P, Duflou, J & Waite, PME 2006, 'Increased neurofibrillary tangles in the brains of older pedestrians killed in traffic accidents', DEMENTIA AND GERIATRIC COGNITIVE DISORDERS, vol. 22, no. 1, pp. 20-26.
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Background/Aims: Older people are over-represented in pedestrian fatalities, and it has been suggested that the presence of cognitive impairment or dementia in these individuals may contribute to their accidents. Using neuropathological methods, we aimed

Grant, AJ, Trautman, DA, Menz, I & Hinde, R 2006, 'Separation of two cell signalling molecules from a symbiotic sponge that modify algal carbon metabolism', Biochemical and Biophysical Research Communications, vol. 348, no. 1, pp. 92-98.
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Gurisik, E, Warton, K, Martin, DK & Valenzuela, SM 2006, 'An in vitro study of the effects of exposure to a GSM signal in two human cell lines: Monocytic U937 and neuroblastoma SK-N-SH', Cell Biology International, vol. 30, no. 10, pp. 793-799.
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The use of mobile phones is increasing, which also increases the population's exposure to global system of mobile communications (GSM) signals. Questions of safety and possible biological effects are of concern and to date, remain largely unanswered. In

Hall, CA, Reichel, MP & Ellis, JT 2006, 'Performance characteristics and optimisation of cut-off values of two enzyme-linked immunosorbent assays for the detection of antibodies to Neospora caninum in the serum of cattle', VETERINARY PARASITOLOGY, vol. 140, no. 1-2, pp. 61-68.
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Aim: To determine the performance characteristics of two enzyme-linked immunosorbent assays (ELISAs) manufactured by Institut Pourquier (IP) for the detection of antibodies against Neospora caninum in bovine sera. Methods: Sera from 526 cattle were assay

Hall, CA, Reichel, MP & Ellis, JT 2006, 'Prevalence of Neospora caninum infection in Australian (NSW) dairy cattle estimated by a newly validated ELISA for milk', VETERINARY PARASITOLOGY, vol. 142, no. 1-2, pp. 173-178.
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Aim: To determine the performance characteristics of an Institut Pourquier (IP) enzyme-linked immunosorbent assay (ELISA) for the detection of antibodies against Neospora caninum in bovine milk and subsequent determination of the prevalence of N. caninum infection in New South Wales (NSW) dairy cattle. Methods: Matching serum and milk samples from 93 cattle were assayed in two commercially available ELISAs for the detection of anti-N. caninum antibodies. Serum test results of one ELISA (IDEXX) were used to determine the N. caninum infection status of the cattle. Optimised cut-off values for the IP ELISA using milk samples were determined by two-graph receiver operating characteristic (TG-ROC) analysis and then applied to a representative sample of 398 milk samples from dairy herds around NSW. Results: When this ELISA was applied to a representative collection of 398 milk samples from dairy cattle across NSW it demonstrated a 21.1% prevalence of N. caninum infection in those cattle. From the TG-ROC analysis an IP ELISA protocol was derived which suggested a cut-off threshold that would allow milk testing with 97% sensitivity and specificity, respectively, relative to serum testing. Conclusions: The prevalence of N. caninum in NSW dairy cattle was higher than previously believed. When used on individual milk samples this ELISA demonstrated high sensitivity and specificity and so could be used to accurately identify N. caninum infection. TG-ROC analysis of the IP ELISA optimised the protocol and prescribed cut-off values enabling the ELISA to be used for the screening of N. caninum antibodies in the milk of dairy cattle. © 2006 Elsevier B.V. All rights reserved.

Handy, SM, Coyne, KJ, Portune, KJ, Demir, E, Doblin, MA, Hare, CE, Cary, SC & Hutchins, DA 2006, 'Erratum: Evaluating vertical migration behavior of harmful raphidophytes in the Delaware Inland Bays utilizing quantitative real-time PCR (Aquatic Microbial Ecology (2005) 40, (121-132))', Aquatic Microbial Ecology, vol. 42, no. 3, p. 311.

Harris, N, Ford, MJ & Cortie, MB 2006, 'Optimization of plasmonic heating by gold nanospheres and nanoshells', JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, no. 22, pp. 10701-10707.
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Gold nanoparticles have strong and tunable absorption peaks in their optical extinction spectra, a phenomenon that has recently been exploited to generate localized heating in the vicinity of these particles. However the optimum particle geometry and illumination regime to maximize these effects appears not to have been previously examined in any detail. Here we show that the interplay between the particles' absorption cross-sections, volume, and surface area lead to there being specific conditions that can maximize particle temperature and surface heat flux. Optical absorption efficiencies were calculated from the formulation of Mie, and radiative, convective, and conductive heat transfer models were used to model the thermal performance of particles in different situations. Two technologically relevant scenarios for illumination, namely, irradiation by sunlight at 800 W/m2 and by a monochromatic laser source of 50 kW/m2 tuned to the peak absorption wavelength, were considered. For irradiation by sunlight, the resultant heat flux is optimized for an 80 nm diameter nanoshell with an aspect ratio of 0.8, while for irradiation by laser the maximum heat flux is found for 50 nm nanoshells, with an aspect ratio of 0.9. © 2006 American Chemical Society.

Headlam, HA, Gracanin, M, Rodgers, KJ & Davies, MJ 2006, 'Inhibition of cathepsins and related proteases by amino acid, peptide, and protein hydroperoxides', FREE RADICAL BIOLOGY AND MEDICINE, vol. 40, no. 9, pp. 1539-1548.
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Reaction of radicals ill the presence Of O-2, and singlet oxygen, with some amino acids, peptides, and proteins yields hydroperoxides. These species are key intermediates in chain reactions and protein damage. Previously we have shown that peptide and pr

Heath, DP & Platen, E 2006, 'Local volatility function models under a benchmark approach', Quantitative Finance, vol. 6, no. 3, pp. 197-206.
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Without requiring the existence of an equivalent risk-neutral probability measure this paper studies a class of one-factor local volatility function models for stock indices under a benchmark approach. It is assumed that the dynamics for a large diversif

Hebelstrup, KH, Hunt, P, Dennis, E, Jensen, SB & Jensen, EO 2006, 'Hemoglobin is essential for normal growth of Arabidopsis organs', PHYSIOLOGIA PLANTARUM, vol. 127, no. 1, pp. 157-166.
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Helliwell, CA, Wood, CC, Robertson, M, Peacock, WJ & Dennis, ES 2006, 'The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex', PLANT JOURNAL, vol. 46, no. 2, pp. 183-192.
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Henness, S, van Thoor, E, Ge, Q, Armour, CL, Hughes, JM & Ammit, AJ 2006, 'IL-17A acts via p38 MAPK to increase stability of TNF-α-induced IL-8 mRNA in human ASM', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 290, no. 6, pp. L1283-L1290.
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Human airway smooth muscle (ASM) plays an immunomodulatory role in asthma. Recently, IL-17A has become of increasing interest in asthma, being found at elevated levels in asthmatic airways and emerging as playing an important role in airway neutrophilia. IL-17A predominantly exerts its neutrophil orchestrating role indirectly via the induction of cytokines by resident airway structural cells. Here, we perform an in vitro study to show that although IL-17A did not induce secretion of the CXC chemokine IL-8 from ASM cells, IL-17A significantly potentiates TNF-α-induced IL-8 protein secretion and gene expression in a concentration- and time-dependent manner ( P < 0.05). Levels of IL-8 protein produced after 24 h of incubation with TNF-α were enhanced 2.7-fold in the presence of IL-17A, and conditioned media significantly enhanced neutrophil chemotaxis in vitro. As IL-17A had no effect on the activity of NF-κB, a key transcriptional regulator of IL-8 gene expression, we then examined whether IL-17A acts at the posttranscriptional level. We found that IL-17A significantly augmented TNF-α-induced IL-8 mRNA stability. Interestingly, this enhanced stability occurred via a p38 MAPK-dependent pathway. The decay of IL-8 mRNA transcripts proceeded at a significantly faster rate when cells were pretreated with the p38 MAPK inhibitor SB-203580 (−0.05763 ± 0.01964, t1/2= 12.0 h), compared with vehicle (−0.01030 ± 0.007963, t1/2= 67.3 h) [results are expressed as decay constant (means ± SE) and half-life ( t1/2in h): P < 0.05]. Collectively, these results demonstrate that IL-17A amplifies the synthetic function of ASM cells, acting via a p38 MAPK-dependent posttranscriptional pathway to augment TNF-α-induced secretion of the potent neutrophil chemoattractant IL-8 from ASM cells.

Herbert, BR, Grinyer, J, McCarthy, JT, Isaacs, M, Harry, EJ, Nevalainen, H, Traini, MD, Hunt, S, Schulz, B, Laver, M, Goodall, AR, Packer, J, Harry, JL & Williams, KL 2006, 'Improved 2‐DE of microorganisms after acidic extraction', ELECTROPHORESIS, vol. 27, no. 8, pp. 1630-1640.
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Abstract2‐DE separations of protein extracts sometimes have problems with poor resolution and streaking. This problem is particularly apparent with microorganisms, most notably those with a large cell wall. Here we describe a novel, rapid protocol for the extraction of microorganisms in acidic conditions, leading to increased resolution and 2‐D gel quality. The efficiency of the protocol is demonstrated with extracts of bacteria, Escherichia coli and Bacillus subtilis; fungus, Trichoderma harzianum and yeast, Saccharomyces cerevisiae. We also demonstrate using a membrane centrifugal filtration, that large acidic molecules in excess of 100 kDa, probably including cell wall material, are responsible for the separation difficulties. A range of acidic extraction conditions were investigated, and it was found that optimal extraction is achieved using an extraction solution acidified to pH 3 by 80 mM citric acid. These findings have significant implications for the proteomic study of many medically, agriculturally and environmentally significant microorganisms, as the cell walls of these organisms are often considerably more complex than many commonly studied laboratory strains.

Hill, R & Ralph, PJ 2006, 'Photosystern II heterogeneity of in hospite zooxanthellae in scleractinian corals exposed to bleaching conditions', PHOTOCHEMISTRY AND PHOTOBIOLOGY, vol. 82, no. 6, pp. 1577-1585.
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Increased ocean temperatures are thought to be triggering mass coral bleaching events around the world. The intracellular symbiotic zooxanthellae (genus Symbiodinium) are expelled from the coral host, which is believed to be a response to photosynthetic damage within these symbionts. Several sites of impact have been proposed, and here we probe the functional heterogeneity of Photosystem II (PSII) in three coral species exposed to bleaching conditions. As length of exposure to bleaching conditions (32°C and 350 μmol photons m-2 s-1) increased, the QA- reoxidation kinetics showed a rise in the proportion of inactive PSII centers (PSIIX), where QB was unable to accept electrons. PSIIX contributed up to 20% of the total PSII centers in Pocillopora damicornis, 35% in Acropora nobilis and 14% in Cyphastrea serailia. Changes in Fv/Fm and amplitude of the J step along fast induction curves were found to be highly dependent upon the proportion of . PSII X centers within the total pool of PSII reaction centers. Determination of PSII antenna size revealed that under control conditions in the three coral species up to 60% of PSII centers were lacking peripheral light-harvesting complexes (PSIIβ). In P. damicornis, the proportion of PSIIβ increased under bleaching conditions and this could be a photoprotective mechanism in response to excess light. The rapid increases in PSIIX and PSIIβ observed in these corals under bleaching conditions indicates these physiological processes are involved in the initial photochemical damage to zooxanthellae. © 2006 American Society for Photobiology.

Hitchcock, R, Sears, W, Gillies, RM, Milthorpe, B & Walsh, WR 2006, 'In vitro study of shear force on interbody implants', JOURNAL OF SPINAL DISORDERS & TECHNIQUES, vol. 19, no. 1, pp. 32-36.
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The lordosis of the lumbar spine and body weight result in significant shear forces through the lumbosacral elise spaces. These forces result in translational motion across the disc space, which is resisted but not completely abolished by pedicle screw stabilization. It is postulated that this motion may be a factor in the development of nonunion of lumbar interbody fusions. An in vitro study of the micromotion of porcine specimens with serrated or smooth interbody spacers and subjected to shear forces under compressive preload was conducted to determinewhether the surface serrations on vertebral interbody implants significantly resist shear forces and resulting sagittal translation.

Hoft, RC, Ford, MJ & Cortie, MB 2006, 'Prediction of increased tunneling current by bond length stretch in molecular break junctions', CHEMICAL PHYSICS LETTERS, vol. 429, no. 4-6, pp. 503-506.
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We use ab initio calculations of the tunneling current through a 1,4-phenylenedimethanethiol (XYL) molecule adsorbed between Au(1 1 1) electrodes to show that there are circumstances under which tunneling currents can be increased by bond stretching. The effect is dependent upon the geometry of the gold-sulfur bond and does not occur for the physisorbed thiol, that is, a thiol with the hydrogen atom still in place. However, we predict that when the hydrogen atom is removed, causing the sulfur atom to be strongly bound to the gold surface, stretching this bond away from equilibrium will actually increase the tunneling current. © 2006 Elsevier B.V. All rights reserved.

Hoft, RC, Gale, JD & Ford, MJ 2006, 'Implementation of a Z-matrix approach within the SIESTA periodic boundary conditions code and its application to surface adsorption', MOLECULAR SIMULATION, vol. 32, no. 8, pp. 595-600.
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We implement a flexible Z-matrix approach in the density functional theory (DFT) periodic boundary conditions code, SIESTA. This allows a mixture of Z-matrix and Cartesian coordinates to be used for geometry specification and optimisation. In addition, geometry constraints in the form of fixed coordinates and fixed linear relationships between coordinates can be specified. A Z-matrix approach in condensed phase calculations can be advantageous, for example in studying molecular adsorption onto a surface, both in terms of flexibility and efficiency. We demonstrate our implementation for the case of thiol adsorption on the Au(111) surface.

Houseman, EA, Coull, BA & Ryan, LM 2006, 'A functional-based distribution diagnostic for a linear model with correlated outcomes', BIOMETRIKA, vol. 93, no. 4, pp. 911-926.
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In this paper we present an easy-to-implement graphical distribution diagnostic for linear models with correlated errors. Houseman et al. (2004) constructed quantile-quantile plots for the marginal residuals of such models, suitably transformed. We extend the pointwise asymptotic theory to address the global stochastic behaviour of the corresponding empirical cumulative distribution function, and describe a simulation technique that serves as a computationally efficient parametric bootstrap for generating representatives of its stochastic limit. Thus, continuous functionals of the empirical cumulative distribution function may be used to form global tests of normality. Through the use of projection matrices, we generalised our methods to include tests that are directed at assessing the normality of particular components of the error. Thus, tests proposed by Lange & Ryan (1989) follow as a special case. Our method works well both for models having independent units of sampling and for those in which all observations are correlated. © 2006 Biometrika Trust.

Howell, VM, Cardinal, JW, Richardson, A-L, Gimm, O, Robinson, BG & Marsh, DJ 2006, 'Rapid Mutation Screening for HRPT2 and MEN1 Mutations Associated with Familial and Sporadic Primary Hyperparathyroidism', The Journal of Molecular Diagnostics, vol. 8, no. 5, pp. 559-566.
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Huang, DT, Kaplan, J, Menz, RI, Katis, VL, Wake, RG, Zhao, F, Wolfenden, R & Christopherson, RI 2006, 'Thermodynamic Analysis of Catalysis by the Dihydroorotases from Hamster and Bacillus caldolyticus, As Compared with the Uncatalyzed Reaction', Biochemistry, vol. 45, no. 27, pp. 8275-8283.
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Huang, S, Spielmeyer, W, Lagudah, ES, James, RA, Platten, JD, Dennis, ES & Munns, R 2006, 'A sodium transporter (HKT7) is a candidate for Nax1, a gene for salt tolerance in durum wheat', PLANT PHYSIOLOGY, vol. 142, no. 4, pp. 1718-1727.
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Durum wheat (Triticum turgidum subsp. durum) is more salt sensitive than bread wheat (Triticum aestivum). A novel source of Na+ exclusion conferring salt tolerance to durum wheat is present in the durum wheat Line 149 derived from Triticum monococcum C68

Huete, AR, Didan, K, Shimabukuro, YE, Ratana, P, Saleska, SR, Hutyra, LR, Yang, WZ, Nemani, RR & Myneni, R 2006, 'Amazon rainforests green-up with sunlight in dry season', GEOPHYSICAL RESEARCH LETTERS, vol. 33, no. 6.
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Hung, CD, Johnson, K & Torpy, F 2006, 'Liquid culture for efficient micropropagation of Wasabia japonica (Miq.) Matsumura', IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT, vol. 42, no. 6, pp. 548-552.
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Hurt, AC, Hansbro, PM, Selleck, P, Olsen, B, Minton, C, Hampson, AW & Barr, IG 2006, 'Isolation of avian influenza viruses from two different transhemispheric migratory shorebird species in Australia', Archives of Virology, vol. 151, no. 11, pp. 2301-2309.
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Shorebirds on their southerly migration from Siberia to Australia, may pass through Asian regions currently experiencing outbreaks of highly pathogenic H5N1 influenza. To test for the presence of avian influenza viruses in migratory shorebirds arriving in Australia during spring 2004, 173 cloacal swabs were collected from six species. Ten swabs were positive for influenza A, with H4N8 viruses detected in five red-necked stints and H11N9 viruses detected in five sharp-tailed sandpipers. No H5N1 viruses were detected. All isolated viruses were non-pathogenic in domestic chickens. These results further demonstrate the potential for migratory shorebirds to carry and potentially spread influenza viruses.

Huston, WM, Andrew, CR, Servid, AE, McKay, AL, Leech, AP, Butler, CS & Moir, JWB 2006, 'Heterologous Overexpression and Purification of Cytochromec‘ fromRhodobacter capsulatusand a Mutant (K42E) in the Dimerization Region. Mutation Does Not Alter Oligomerization but Impacts the Heme Iron Spin State and Nitric Oxide Binding Properties', Biochemistry, vol. 45, no. 14, pp. 4388-4395.
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Ikonen, PMT, Lapine, M, Nefedov, IS & Tretyakov, SA 2006, 'VECTOR CIRCUIT THEORY FOR SPATIALLY DISPERSIVE UNIAXIAL MAGNETO-DIELECTRIC SLABS', Progress In Electromagnetics Research, vol. 63, pp. 279-294.
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Jenkins, C, Wilton, JL, Minion, FC, Falconer, L, Walker, MJ & Djordjevic, SP 2006, 'Two Domains within theMycoplasma hyopneumoniaeCilium Adhesin Bind Heparin', Infection and Immunity, vol. 74, no. 1, pp. 481-487.
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ABSTRACTMycoplasma hyopneumoniaeis the causative agent of porcine enzootic pneumonia, a chronic and economically significant respiratory disease that affects swine production worldwide.M. hyopneumoniaeadheres to and adversely affects the function of ciliated epithelial cells of the respiratory tract, and the cilium adhesin (Mhp183, P97) is intricately but not exclusively involved in this process. Although binding of pathogenic bacteria to glycosaminoglycans is a recognized step in pathogenesis, knowledge of glycosaminoglycan-binding proteins inM. hyopneumoniaeis lacking. However, heparin and other sulfated polysaccharides are known to block the binding ofM. hyopneumoniaeto purified swine respiratory cilia. In this study, four regions within the cilium adhesin were examined for the ability to bind heparin. Cilium adhesin fragments comprising 653 amino acids of the N terminus and 301 amino acids of the C terminus (containing two repeat regions, R1 and R2) were cloned and expressed. These fragments bound heparin in a dose-dependent and saturable manner with physiologically significant binding affinities of 0.27 ± 0.02 μM and 1.89 ± 0.33 μM, respectively. Heparin binding of both fragments was strongly inhibited by the sulfated polysaccharides fucoidan and mucin but not by chondroitin sulfate B. When the C-terminal repeat regions R1 and R2 were cloned separately and expressed, heparin-binding activity was lost, suggesting that both regions are required for heparin binding. The ability of the cilium adhesin to bind heparin indicates that this molecule plays a multifunctional role in the adherence ofM. hyopneumoniaeto host respiratory surfaces and therefore has important implications with respect to the pathogenesis of this organism.

Jiang, Z, Huete, AR, Li, J & Chen, Y 2006, 'An analysis of angle-based with ratio-based vegetation indices', IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING, vol. 44, no. 9, pp. 2506-2513.
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Remotely sensed, angle-based vegetation indices that measure vegetation amounts by the angle between an approximated soil line and a simulated vegetation isoline in the rednear-infrared reflectance space were developed and evaluated in this paper. Ünsalan and Boyer previously proposed an angle-based vegetation index, 0 (denoted as 0NDVI in this paper), based on the normalized difference vegetation index (NDVI) with the objective of overcoming the saturation problem in the NDVI. However, θNDVI did not consider strong soil background influences present in the NDVI. To reduce soil background noise, an angle-based vegetation index, θSAVI, based on the soil-adjusted vegetation index (SAVI), was derived using trigonometric analysis. The performance of θNDVI and θSAVI was evaluated and compared with their corresponding vegetation indices, NDVI and SAVI. The soil background influence on θNDVI was found to be as significant as that on the NDVI. θNDVI was found to be more sensitive to vegetation amount than the NDVI at low vegetation density levels, but less sensitive to vegetation fraction at high vegetation density levels. Thus, the saturation effect at high vegetation density levels encountered in the NDVI was not mitigated by θNDVI. By contrast, θSAVI exhibited insignificant soil background effects and weaker saturation, as in SAVI, but also improved upon the dynamic range of SAVI. Analyses and evaluation suggest that θSAVI is an optimal vegetation index to assess and monitor vegetation cover across the entire range of vegetation fraction density levels and over a wide variety of soil backgrounds. © 2006 IEEE.

Jiang, ZY, Huete, AR, Chen, J, Chen, YH, Li, J, Yan, GJ & Zhang, XY 2006, 'Analysis of NDVI and scaled difference vegetation index retrievals of vegetation fraction', REMOTE SENSING OF ENVIRONMENT, vol. 101, no. 3, pp. 366-378.
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The normalized difference vegetation index (NDVI) is the most widely used vegetation index for retrieval of vegetation canopy biophysical properties. Several studies have investigated the spatial scale dependencies of NDVI and the relationship between NDVI and fractional vegetation cover, but without any consensus on the two issues. The objectives of this paper are to analyze the spatial scale dependencies of NDVI and to analyze the relationship between NDVI and fractional vegetation cover at different resolutions based on linear spectral mixing models. Our results show strong spatial scale dependencies of NDVI over heterogeneous surfaces, indicating that NDVI values at different resolutions may not be comparable. The nonlinearity of NDVI over partially vegetated surfaces becomes prominent with darker soil backgrounds and with presence of shadow. Thus, the NDVI may not be suitable to infer vegetation fraction because of its nonlinearity and scale effects. We found that the scaled difference vegetation index (SDVI), a scale-invariant index based on linear spectral mixing of red and near-infrared reflectances, is a more suitable and robust approach for retrieval of vegetation fraction with remote sensing data, particularly over heterogeneous surfaces. The proposed method was validated with experimental field data, but further validation at the satellite level would be needed. © 2006 Elsevier Inc. All rights reserved.

Jin, D, Connally, R & Piper, J 2006, 'Long-lived visible luminescence of UV LEDs and impact on LED excited time-resolved fluorescence applications', Journal of Physics D: Applied Physics, vol. 39, no. 3, pp. 461-465.
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Jones, H, Ostrowski, M & Scanlan, DJ 2006, 'A Suppression Subtractive Hybridization Approach Reveals Niche-Specific Genes That May Be Involved in Predator Avoidance in Marine Synechococcus Isolates', Applied and Environmental Microbiology, vol. 72, no. 4, pp. 2730-2737.
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ABSTRACT Picocyanobacteria of the genus Synechococcus are important contributors to marine primary production and are ubiquitous in the world's oceans. This genus is genetically diverse, and at least 10 discrete lineages or clades have been identified phylogenetically. However, little if anything is known about the genetic attributes which characterize particular lineages or are unique to specific strains. Here, we used a suppression subtractive hybridization (SSH) approach to identify strain- and clade-specific genes in two well-characterized laboratory strains, Synechococcus sp. strain WH8103 (clade III) and Synechococcus sp. strain WH7803 (clade V). Among the genes that were identified as potentially unique to each strain were genes encoding proteins that may be involved in specific predator avoidance, including a glycosyltransferase in strain WH8103 and a permease component of an ABC-type polysaccharide/polyol phosphate export system in WH7803. During this work the genome of one of these strains, WH7803, became available. This allowed assessment of the number of false-positive sequences (i.e., sequences present in the tester genome) present among the SSH-enriched sequences. We found that approximately 9% of the WH8103 sequences were potential false-positive sequences, which demonstrated that caution should be used when this technology is used to assess genomic differences in genetically similar bacterial strains.

Kanchanawong, P, Dahlbom, MG, Treynor, TP, Reimers, JR, Hush, NS & Boxer, SG 2006, 'Charge delocalization in the special-pair radical cation of mutant reaction centers of Rhodobacter sphaeroides from stark spectra and nonadiabatic spectral simulations', JOURNAL OF PHYSICAL CHEMISTRY B, vol. 110, no. 37, pp. 18688-18702.
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Kealley, C, Ben-Nissan, B, van Riessen, A & Elcombe, M 2006, 'Development of Carbon Nanotube Reinforced Hydroxyapatite Bioceramics', Key Engineering Materials, vol. 309-311, no. 1, pp. 597-602.
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This paper reports development of a production method to produce a composite material that is biocompatible, with high mechanical strength and resilience. The chemical precipitation conditions necessary for the production of synthetic hydroxyapatite (HAp

Kealley, C, Elcombe, M, van Riessen, A & Ben-Nissan, B 2006, 'Development of carbon nanotube-reinforced hydroxyapatite bioceramics', Physica B: Condensed Matter, vol. 385-386, no. SI, pp. 496-498.
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This paper reports development of a production method to create a composite material that is biocompatible, which will have high mechanical strength and resilience, and be able to withstand exposure to the physiological environment. The chemical precipitation conditions necessary for the production of single-phase synthetic hydroxyapatite (HAp) and a HAp and carbon nanotube (CNT) composite material have been optimised. Neutron diffraction patterns collected before and after sintering show that the nanotubes have remained intact within the structure, while most of the remaining soot has burnt off. Small-angle neutron scattering, in conjunction with scanning electron microscopy (SEM), also shows preservation of the CNTs. Hot isostatically pressed samples showed excellent densification. Neutron diffraction data has enabled the positions of the hydroxide bonds to be determined, and shown that the addition of the CNTs has had no effect on the structural parameters of the HAp phase, with the exception of a slight reduction in the unit cell parameter a.

Kher, A, Mulholland, M, Green, E & Reedy, B 2006, 'Forensic classification of ballpoint pen inks using high performance liquid chromatography and infrared spectroscopy with principal components analysis and linear discriminant analysis', Vibrational Spectroscopy, vol. 40, no. 2, pp. 270-277.
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Several varieties of blue ballpoint pen inks were analysed by higher performance liquid chromatography (HPLC) and infrared spectroscopy (IR). The chromatographic data extracted at four wavelengths (254, 279, 370 and 400 nm)was analysed individually and at a combination of these wavelengths by the soft independent modeling of class analogies (SIMCA) technique using principal components analysis (PCA) to estimate the separation between pen samples. Linear discriminant analysis (LDA) measured the probability with which an observation could be assigned to a pen class. The best resolution was obtained by HPLC using data from all four wavelengths together, differentiating 96.4% pen pairs successfully using PCA and 97.9% pen samples by LDA> PCA separated 60.7% of the pen pairs and LDA provided a correct classification of 62.5% of the pends compared to IR. The need to develop a suitable IR method for analysing nlue ball-point pen inks has been emphasised and it is hoped that the development of such a method would indeed providea valuable tool for the non-destrictive analysis of blue ball-point pen ink samples for forensic purposes.

King, E, Walsh, S & Cobbin, D 2006, 'The Testing of Classical Pulse Concepts in Chinese Medicine: Left- and Right-Hand Pulse Strength Discrepancy Between Males and Females and Its Clinical Implications', The Journal of Alternative and Complementary Medicine, vol. 12, no. 5, pp. 445-450.
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Objectives and design: The use of the radial pulse as a diagnostic tool is an important part of the Chinese medicine (CM) clinical evaluation. This study reports the findings of an investigation into inter-arm pulse strength differences in subjects and t

Kjellerup, BV, Gudmonsson, G, Sowers, K & Nielsen, PH 2006, 'Evaluation of analytical methods for determining the distribution of biofilm and active bacteria in a commercial heating system', Biofouling, vol. 22, no. 3, pp. 133-139.
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Kjellerup, BV, Gudmonsson, G, Sowers, K & Nielsen, PH 2006, 'Evaluation of analytical methods for determining the distribution of biofilm and active bacteria in a commercial heating system.', Biofouling, vol. 22, no. 3-4, pp. 145-151.
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Danish district heating systems have good water quality, but continue to suffer from biofouling and biocorrosion. Localisation analyses of bacteria using microautoradiography were performed for one system in order to obtain detailed information for solving these problems. A mass balance showed that 77% of the bacteria were located at surfaces, with 23% in the bulk water, and 9% of the total carbon originated from biomass, while 91% was dissolved in the bulk water. The presence of active bacteria was determined with microautoradiography which showed that biofilms contained 99% and 1% were in the bulk water. A high bacterial functional diversity was observed, with active mesophilic and thermophilic bacteria under aerobic and anaerobic conditions and with potentially corrosive biofilm bacteria present. The study reveals that by applying the activity based approach, the ratio of living and dead bacteria in the biofilm and bulk water in this type of system could be accurately determined. Also, the results emphasise that to minimise biofilm growth and biocorrosion, monitoring should be established focusing on the surfaces, since bulk water parameters do not reflect bacterial activity.

Koos, C, Fujii, M, Poulton, CG, Steingrueber, R, Leuthold, J & Freude, W 2006, 'FDTD-Modelling of Dispersive Nonlinear Ring Resonators: Accuracy Studies and Experiments', IEEE Journal of Quantum Electronics, vol. 42, no. 12, pp. 1215-1223.
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The accuracy of nonlinear finite-difference time-domain (FDTD) methods is investigated by modeling nonlinear optical interaction in a ring resonator. We have developed a parallelized 3-D FDTD algorithm which incorporates material dispersion, χ(3)-nonlinearities and stair-casing error correction. The results of this implementation are compared with experiments, and intrinsic errors of the FDTD algorithm are separated from geometrical uncertainties arising from the fabrication tolerances of the device. A series of progressively less complex FDTD models is investigated, omitting material dispersion, abandoning the stair-casing error correction, and approximating the structure by a 2-D effective index model. We compare the results of the different algorithms and give guidelines as to which degree of complexity is needed in order to obtain reliable simulation results in the linear and the nonlinear regime. In both cases, incorporating stair-casing error correction and material dispersion into a 2-D effective index model turns out to be computationally much cheaper and more effective than performing a fully three-dimensional simulation without these features. © 2006 IEEE.

Kramarsky-Winter, E, Harel, M, Siboni, N, Ben Dov, E, Brickner, I, Loya, Y & Kushmaro, A 2006, 'Identification of a protist-coral association and its possible ecological role', MARINE ECOLOGY PROGRESS SERIES, vol. 317, pp. 67-73.
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Recent investigations of coral-associated microbial communities have revealed that coral surfaces are replete with microorganisms that may play important roles in colony wellbeing. In this study we show that the surfaces of a number of large polyped coral species are covered by a layer of aggregate-like microorganisms. These microorganisms are embedded in the mucus and in the tissue of solitary coral Fungia granulosa and in a number of faviid species. They are found on the coral surface and in the coral tissue. They are dispersed in a patchy distribution, with the highest density occurring in the area of the polyp mouth. Microscopic investigation revealed that the microorganisms found on and in tissues of F. granulosa are approximately 5 to 30 μm in diameter and are made up of unique coccoid bodies of approximately 1 μm in diameter. Transmission electron microscopy (TEM) revealed that they contain a nucleus, mitochondria and golgi, indicating they are eukaryotic in nature. The morphological data lead us to identify these organisms as stramenopile protists. This premise was strengthened by molecular investigation of samples taken from the surface mucus of the coral F. granulosa. The possible role of these protists is discussed. © Inter-Research 2006.

Kriplani, NM, Nackashi, DP, Amsinck, CJ, Di Spigna, NH, Steer, MB, Franzon, PD, Rick, RL, Solomon, GC & Reimers, JR 2006, 'Physically based molecular device model in a transient circuit simulator', CHEMICAL PHYSICS, vol. 326, no. 1, pp. 188-196.
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Langford, SJ, Latter, MJ & Woodward, CP 2006, 'Construction of Multiporphyrin Arrays via Selective Cross-Metathesis', Organic Letters, vol. 8, no. 12, pp. 2595-2598.
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Langford, SJ, Latter, MJ & Woodward, CP 2006, 'Progress in Charge Transfer Systems Utilizing PorphyrinDonors and Simple Aromatic Diimide Acceptor Units', Photochemistry and Photobiology, vol. 82, no. 6, pp. 1530-1530.
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Langford, SJ, Latter, MJ, Lau, V-L, Martin, LL & Mechler, A 2006, 'Organogels Derived from Tetranitrated Crown Ethers', Organic Letters, vol. 8, no. 7, pp. 1371-1373.
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Le, T & Platen, E 2006, 'Approximating the Growth Optimal Portfolio with a Diversified World Stock Index', Journal of Risk Finance, vol. 7, no. 5, pp. 559-574.
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This paper constructs and compares various total return world stock indices based on daily data. Due to diversification these indices are noticeably similar. A diversification theorem identifies any diversified portfolio as a proxy for the growth optimal portfolio. The paper constructs a diversified world stock index that outperforms a number of other indices and argues that it is a good proxy for the growth optimal portfolio. This has applications to derivative pricing and investment management.

Leigh, A, Close, JD, Ball, MC, Siebke, K & Nicotra, AB 2006, 'Research note: Leaf cooling curves: measuring leaf temperature in sunlight', Functional Plant Biology, vol. 33, no. 5, pp. 515-515.
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Despite the obvious benefits of using thermography under field conditions, most infrared studies at the leaf level are generally conducted in the laboratory. One reason for this bias is that accuracy can potentially be compromised in sunlight because reflected radiation from the leaf might affect the calculation of the temperature measurement. We have developed a method for measuring leaf temperature in sunlight by using thermal imagery to generate cooling curves from which the time constant for cooling, τ, can be calculated. The original temperature of the sunlit leaf may be determined by extrapolating backwards in time. In the absence of specular reflection, there is close agreement between the extrapolated sunlit temperature and the sunlit temperature recorded by the camera. However, when reflected radiation is high, the difference between the initial (incorrect) temperature determined from the sunlit image and the temperature extrapolated from the cooling curve can be > 2°C. Notably, our results demonstrate a close agreement between the extrapolated sunlit temperature and the temperature of the leaf approximately 1 s after being shaded, suggesting that this shaded image provides a good estimate of the original sunlit temperature. Thus, our technique provides two means for measuring leaf surface temperature in sunlight.

LEIGH, A, COSGROVE, MJ & NICOTRA, AB 2006, 'Reproductive allocation in a gender dimorphic shrub: anomalous female investment in Gynatrix pulchella?', Journal of Ecology, vol. 94, no. 6, pp. 1261-1271.
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SummaryIn gender dimorphic species, reproductive allocation (RA, the ratio of reproductive to vegetative biomass) is predicted to be greater in female plants than in male plants. Empirical research on dimorphic plant species supports this hypothesis. To date, of 44 dimorphic angiosperms for which RA has been reported in the literature, RA is greater in females than males in 40 species, is equal in four, and in no species is it greater in males.In many instances where differential RA occurs, sexual dimorphism in morphological or physiological traits has been reported. This dimorphism is often attributed to the differing costs of reproduction or to selection to counteract such costs.We investigated RA and other morphological and physiological characters in Gynatrix pulchella, a dimorphic species that we found ranges from dioecious to subdioecious or gynodioecious, depending on season and locality. Our results showed that contrary to our predictions functionally male plants allocated significantly more biomass to reproduction than female plants across three populations. Greater male RA was due to a combination of larger, more numerous flowers and lower leaf biomass per branch than females.There were no detectable costs of greater RA in males in terms of decreased overall growth or increased mortality. Additionally, leaf nitrogen content was greater in males than in females and there were no between‐sex differences in gas exchange.The finding that male plants allocate significantly more resources to reproduction than females in G. pulchella is apparently a unique case. However, equivalent RA for the sexes doe...

Leslie, LM & Buckley, BW 2006, 'Comments on “Scatterometer-Based Assessment of 10-m Wind Analyses from the Operational ECMWF and NCEP Numerical Weather Prediction Models”', Monthly Weather Review, vol. 134, no. 2, pp. 737-742.
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Leslie, LM & Speer, MS 2006, 'Modelling dust transport over central eastern Australia', Meteorological Applications, vol. 13, no. 2, pp. 141-167.
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AbstractA ten‐year climatology has been prepared of dust days for central eastern Australia, from January 1995 to February 2004, using reports from the Australian Bureau of Meteorology's observational network. It was found that there had been a total of 55 dust days during this ten‐year period. Of these, 43 dust days were associated with cold fronts: 24 were classified as embedded in the zonal westerlies in the Great Australian Bight (GAB) or in westerlies derived from low pressure systems in the GAB, whereas the remaining 19 were associated with cold fronts over eastern Australia where high pressure systems in the GAB generated strong post‐frontal south to southeast winds. Three detailed case studies of dust storm generation and transport were modelled using a sophisticated coupled wind erosion prediction system. The model predictions in all three cases were found to be broadly consistent both with satellite images highlighting dust and the synoptic observations that reported dust. Antecedent land surface conditions are found to be critically important in generating dust, and their representation in the integrated prediction system is subsequently important in providing skilful model predictions of dust transport. Copyright © 2006 Royal Meteorological Society.

Levings, RS, Hall, RM, Lightfoot, D & Djordjevic, SP 2006, 'linG , a New Integron-Associated Gene Cassette Encoding a Lincosamide Nucleotidyltransferase', Antimicrobial Agents and Chemotherapy, vol. 50, no. 10, pp. 3514-3515.
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We have identified a second lin gene in a gene cassette. This cassette was recovered from a multiply antibiotic-resistant Salmonella enterica serovar Stanley strain (SRC54) isolated in 2001 from a traveler who had recently returned from Thailand. This strain was resistant to chloramphenicol, gentamicin, kanamycin, spectinomycin, streptomycin, sulfathiazole, and tetracycline but susceptible to ampicillin and nalidixic acid at levels described previously (6). It displayed intermediate resistance to ciprofloxacin. The gene cassette array was amplified by using standard primers (L2 and R1) in the 5' conserved sequence and 3' conserved sequence of class 1 integrons, and the 2.25-kb amplicon was cloned into pPCRscript and sequenced as previously described (see reference 6 for primer details). E. coli strain DH5{alpha} containing pPCR-Script with the cassette array was at least 10-fold more resistant to lincomycin (MIC, ?2,000 µg/ml) than DH5{alpha} containing only pPCR-Script (MIC, 180 µg/ml).

Levings, RS, Lightfoot, D, Elbourne, LDH, Djordjevic, SP & Hall, RM 2006, 'New Integron-Associated Gene Cassette Encoding a Trimethoprim-Resistant DfrB-Type Dihydrofolate Reductase', Antimicrobial Agents and Chemotherapy, vol. 50, no. 8, pp. 2863-2865.
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ABSTRACT A sixth gene cassette containing a dfrB -type gene, dfrB6 , was found in a dfrB6-aadA1 cassette array in class 1 integrons. This array was isolated from several multiply antibiotic-resistant Salmonella enterica serovar Infantis strains that appear to be clonally related. The DfrB6 dihydrofolate reductase conferred resistance to trimethoprim.

Levings, RS, Lightfoot, D, Hall, RM & Djordjevic, SP 2006, 'Aquariums as Reservoirs for Multidrug-resistantSalmonellaParatyphi B', Emerging Infectious Diseases, vol. 12, no. 3, pp. 507-510.
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Lewis, K, Boonyang, U, Evans, L, Siripaisarnpipat, S & Ben-Nissan, B 2006, 'A Comparative Study of Thai and Australian Crocodile Bone for Use as a Potential Biomaterial', Bioceramics 18, Pts 1 And 2, Key Engineering Materials, vol. 309-311, no. 1, pp. 15-18.
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This study aims to characterize the structure and properties of crocodile bone to assess the potential for use in biomedical applications. Crocodile bone samples obtained from Thailand (Crocodylus siamensis) and Australia (Crocodylus porosus), being the

Li, C, Zhang, HP, Fu, LJ, Liu, H, Wu, YP, Ram, E, Holze, R & Wu, HQ 2006, 'Cathode materials modified by surface coating for lithium ion batteries', ELECTROCHIMICA ACTA, vol. 51, no. 19, pp. 3872-3883.
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Recent research results confirm the importance of structural surface features of cathode materials for their electrochemical performance. Modification by coating is an important method to achieve improved electrochemical performance, and the latest progress was reviewed here. When the surface of cathode materials including LiCoO2, LiNiO2, LiMn2O4 and LiMnO2 is coated with oxides such as MgO, Al2O3, SiO2, TiO2, ZnO, SnO2, ZrO2, Li2O center dot 2B(2)O(3)-glass and other materials, the coatings prevent the direct contact with the electrolyte solution, suppress phase transition, improve the structural stability, and decrease the disorder of cations in crystal sites. As a result, side reactions and heat generation during cycling are decreased. Accompanying actions such as suppression of Mn2+ dissolution, increase in conductivity and removal of HF in electrolyte solutions have been observed. Consequently, marked improvement of electrochemical performance of electrode materials including reversible capacity, coulomb efficiency in the first cycle, cycling behavior, rate capability and overcharge tolerance has been achieved. In conclusion, further directions are suggested for the surface modification of electrode materials. With further understanding of the effects of the surface structure of cathode materials on lithium intercalation and de-intercalation, better and/or cheaper cathode materials from surface modification will come up in the near future.

Li, Y & Ryan, L 2006, 'Inference on survival data with covariate measurement error - An imputation-based approach', SCANDINAVIAN JOURNAL OF STATISTICS, vol. 33, no. 2, pp. 169-190.
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We propose a new method for fitting proportional hazards models with error-prone covariates. Regression coefficients are estimated by solving an estimating equation that is the average of the partial likelihood scores based on imputed true covariates. For the purpose of imputation, a linear spline model is assumed on the baseline hazard. We discuss consistency and asymptotic normality of the resulting estimators, and propose a stochastic approximation scheme to obtain the estimates. The algorithm is easy to implement, and reduces to the ordinary Cox partial likelihood approach when the measurement error has a degenerate distribution. Simulations indicate high efficiency and robustness. We consider the special case where error-prone replicates are available on the unobserved true covariates. As expected, increasing the number of replicates for the unobserved covariates increases efficiency and reduces bias. We illustrate the practical utility of the proposed method with an Eastern Cooperative Oncology Group clinical trial where a genetic marker, c-myc expression level, is subject to measurement error. © Board of the Foundation of the Scandinavian Journal of Statistics 2006.

Lin, X & Carroll, RJ 2006, 'Semiparametric Estimation in General Repeated Measures Problems', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 68, no. 1, pp. 69-88.
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SummaryThe paper considers a wide class of semiparametric problems with a parametric part for some covariate effects and repeated evaluations of a nonparametric function. Special cases in our approach include marginal models for longitudinal or clustered data, conditional logistic regression for matched case–control studies, multivariate measurement error models, generalized linear mixed models with a semiparametric component, and many others. We propose profile kernel and backfitting estimation methods for these problems, derive their asymptotic distributions and show that in likelihood problems the methods are semiparametric efficient. Although generally not true, it transpires that with our methods profiling and backfitting are asymptotically equivalent. We also consider pseudolikelihood methods where some nuisance parameters are estimated from a different algorithm. The methods proposed are evaluated by using simulation studies and applied to the Kenya haemoglobin data.

Liu, H, Cao, Q, Fu, LJ, Li, C, Wu, YP & Wu, HQ 2006, 'Doping effects of zinc on LiFePO4 cathode material for lithium ion batteries', ELECTROCHEMISTRY COMMUNICATIONS, vol. 8, no. 10, pp. 1553-1557.
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Alien atom doping has been adopted to modify the electrochemical performance of olivine type LiFePO4 for cathode material of the lithium ion batteries. Here, we first report that zinc-doping can improve the performance of LiFePO4. The effects of zinc-doping have been studied by the measurements of X-ray diffraction pattern, scanning electronic microscopy, electrochemical impedance spectroscopy and cyclic voltammetry. The results indicate that the zinc atoms do not destroy the lattice structure of LiFePO4, and enlarge the lattice volume. During de-intercalation and intercalation process of lithium ions, the doped zinc atoms protect the LiFePO4 crystal from shrinking. This kind of "pillar" effect provides larger space for the movement of lithium ions. Consequently, the conductivity is enhanced and the lithium ion diffusion coefficient is boosted after doping. These favourable changes are beneficial to the improvement of the electrochemical performance of LiFePO4 including discharge capacity and rate capability.

Liu, H, Li, C, Zhang, HP, Fu, LJ, Wu, YP & Wu, HQ 2006, 'Kinetic study on LiFePO4/C nanocomposites synthesized by solid state technique', JOURNAL OF POWER SOURCES, vol. 159, no. 1, pp. 717-720.
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Well-crystallized, homogeneous nanocomposites of lithium iron(H) phosphate and carbon was synthesized by solid state reaction, and the obtained particles are spherical. Measurement of both CV and EIS shows that the lithium ion diffusion coefficient in the nanocomposites is affected by the incorporated carbon, and markedly increases with the carbon content. Meanwhile, the kinetics of lithium intercalation and de-intercalation is greatly ameliorated. These data provide strong evidence of the potential use of this kind of nanocomposite cathode in lithium ion battery.

Liu, J, Cankurtaran, B, Wieczorek, L, Ford, MJ & Cortie, M 2006, 'Anisotropic optical properties of semitransparent coatings of gold nanocaps', ADVANCED FUNCTIONAL MATERIALS, vol. 16, no. 11, pp. 1457-1461.
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An ordered array of cap-shaped gold nanoparticles has been prepared by vapor deposition onto polystyrene nanospheres supported on a glass substrate. The method of fabrication used imparts a significant anisotropy to the geometric and optical properties of the coating. The optical-absorption properties of these deposits have been measured using UV-vis spectrometry and simulated using a code based on the discrete dipole approximation. Because the nanocaps are not interconnected, they interact with incident light as individual particles with a plasmon resonance that depends upon wavelength and the polarization vector of the light. The resulting extinction peaks manifest in the upper visible and near-infrared regions of the electromagnetic spectrum. Surprisingly, varying the angle of incidence of the light (for a fixed polarization) has no effect on the optical properties of individual nanocaps. Calculations show that these phenomena may be readily interpreted in terms of dipole resonances excited across the longitudinal, transverse, and short-transverse directions of the nanocaps. Coatings comprised of arrays of these particles have the potential to serve as angularly and spectrally selective filters. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.

Liu, L, Gu, HY & Xi, YG 2006, 'Heuristic method for job shop scheduling based on decomposed due date', Kongzhi yu Juece/Control and Decision, vol. 21, no. 3, pp. 253-257.
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A heuristic method for job shop scheduling based on decomposed due date to minimize total weighted tardiness is proposed. The initial due date of each operation is determined according to the flow allowance rate of each job, then the job sequences on all machines are obtained by the improved modified operation due date rule based on Giffler-Thompson scheme. And the due date of the critical operation is adjusted to improve the solution quality with considering interactions among jobs at each iteration. The simulation results show that the proposed method can obtain good solutions with acceptable computational efficiency, and can be used to the real job shop scheduling system.

Lord, MS, Cousins, BG, Doherty, PJ, Whitelock, JM, Simmons, A, Williams, RL & Milthorpe, BK 2006, 'The effect of silica nanoparticulate coatings on serum protein adsorption and cellular response', BIOMATERIALS, vol. 27, no. 28, pp. 4856-4862.
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Serum protein adsorption on colloidal silica surfaces was investigated using a quartz crystal microbalance with dissipation (QCM-D) monitoring. The amount of serum proteins adsorbed on colloidal silica-coated surfaces was not significantly different from the control silica surfaces, with the exception of 21 nm colloidal silica which experienced significantly less (P<0.05) fibrinogen adsorption compared with control silica. The adhesion and proliferation of human endothelial cells (C11STH) on nano-scale colloidal silica surfaces were significantly reduced compared with control silica surfaces, suggesting that the conformation of adsorbed proteins on the colloidal silica surfaces plays a role in modulating the amount of cell binding. Fibronectin is one of the main extracellular matrix proteins involved in endothelial cell attachment to biomaterial surfaces. There was reduced binding of a monoclonal anti-fibronectin antibody, that reacted specifically with the cell-binding fragment, to fibronectin-coated colloidal silica surfaces compared with control silica surfaces. This suggests that the fibronectin adsorbed on the colloidal silica-coated surfaces was conformationally changed compared with control silica reducing the availability of the cell-binding domain of fibronectin.

Lord, MS, Modin, C, Foss, M, Duch, M, Simmons, A, Pedersen, FS, Milthorpe, BK & Besenbacher, F 2006, 'Monitoring cell adhesion on tantalum and oxidised polystyrene using a quartz crystal microbalance with dissipation', BIOMATERIALS, vol. 27, no. 26, pp. 4529-4537.
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The quartz crystal microbalance with dissipation (QCM-D) (Q-Sense AB, Sweden) has been established as a useful tool for evaluating interactions between various biological and non-biological systems, and there has been increasing interest in using the QCM-D technique for cell monitoring applications. This study investigated the potential of the QCM-D to characterise the initial adhesion and spreading of cells in contact with protein precoated biocompatible surfaces. The QCM-D technique is attractive for monitoring cell adhesion and spreading as it allows in situ real-time measurements. The adhesion of NIH3T3 (EGFP) fibroblasts to tantalum (Ta) and oxidised polystyrene (PSox) surfaces precoated with serum proteins was examined using the QCM-D for a period of either 2 or 4 h. Time-lapse photography was performed at 30 min intervals to visually examine cell adhesion and spreading in order to relate cell morphology to the QCM-D response. Following adsorption of albumin, fibronectin or newborn calf serum onto the surfaces, QCM-D measurements showed that cells adhered and spread on the fibronectin and serum coated surfaces, while few cells adhered to the albumin coated surfaces. Cells adhered to albumin coated surfaces had a rounded morphology. The responses to fibronectin and serum precoated surfaces were quite different for each of the underlying substrates indicating that the process of cell adhesion and spreading elicits different responses depending on both the protein coating composition and the influence of the underlying substrate. The different response may be due to extracellular matrix remodelling as well as cytoskeletal changes. Frequency (f) and dissipation (D) changes associated with cell adhesion were less than would be expected from the Sauerbrey relation due to the viscoelastic properties of the cells. © 2006 Elsevier Ltd. All rights reserved.

Lord, MS, Stenzel, MH, Simmons, A & Milthorpe, BK 2006, 'Lysozyme interaction with poly(HEMA)-based hydrogel', BIOMATERIALS, vol. 27, no. 8, pp. 1341-1345.
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Lysozyme interaction with an acrylic-based hydrogel, poly(2-hydroxyethyl methacrylate) co-methacrylic acid (P(HEMA-MAA)), was investigated using a combination of quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR) and dual polarisation interferometry (DPI). This combination of techniques demonstrated that lysozyme initially absorbed into the hydrogel matrix and displaced water from the hydrogel while subsequent lysozyme additions were adsorbed onto the surface of the hydrogel material. QCM-D, being sensitive to bound water, showed an overall decrease in mass and stiffening of the layer after lysozyme addition. SPR, a water insensitive technique, showed a net mass increase after addition of lysozyme and buffer rinses. DPI showed that the first exposure of lysozyme to P(HEMA-MAA) was consistent with lysozyme absorption while subsequent lysozyme exposures were consistent with lysozyme adsorption.

Lord, MS, Stenzel, MH, Simmons, A & Milthorpe, BK 2006, 'The effect of charged groups on protein interactions with poly(HEMA) hydrogels', Biomaterials, vol. 27, no. 4, pp. 567-575.
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Proteins, lipids and other biomolecules interact strongly with the acrylic-based biomaterials used for contact lenses. Although hydrogels are nominally resistant to protein fouling, many studies have reported considerable amounts of protein bound to poly(2-hydroxyethylmethacrylate) (PHEMA) lenses. This study examined the binding of a series of biomolecules (tear protein analogues, mucin and cholesterol) to poly(methylmethacrylate) (PMMA) and three HEMA-based hydrogels (PHEMA, HEMA plus methacrylic acid (P(HEMA-MAA)), HEMA plus methacrylic acid plus N-vinylpyrrolidone (P(HEMA-MAA-NVP))) by use of a quartz crystal microbalance with dissipation (QCM-D) monitoring. The QCM-D estimates changes in the mass and viscous constant for the adsorbed layer through measurements of frequency and dissipation. Protein interaction with each of the test materials caused a net increase in mass of the material indicating protein binding except for lysozyme interacting with P(HEMA-MAA). A net decrease in mass was observed for lysozyme interacting with P(HEMA-MAA) which may be ascribed to lysozyme collapsing the hydrogel by expelling water. A net mass decrease was observed for cholesterol interacting with each of the hydrogel materials, while a mass increase was observed on PMMA. © 2005 Elsevier Ltd. All rights reserved.

Lord, MS, Stenzel, MH, Simmons, A & Milthorpe, BK 2006, 'The effect of charged groups on protein interactions with poly(HEMA) hydrogels', BIOMATERIALS, vol. 27, no. 4, pp. 567-575.
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Lou, W, Jin, D, Niu, W, Ni, X & Wu, W 2006, 'Middle segment pancreatectomy for the treatment of benign and low malignant potential pancreatic tumours', Surgical Practice, vol. 10, no. 2, pp. 75-78.
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Background:  Conventional distal pancreatectomy is used for the removal of lesions located at the body and tail of the pancreas. Generally, the spleen is sacrificed. But for benign and low malignant potential tumours in the pancreatic neck and body, this incurs notable loss of normal pancreatic tissue and the unnecessary risk of diabetes mellitus as well as splenic loss.Methods:  We report three cases of middle segment pancreatectomy in an effort to avoid the unnecessary loss of normal pancreatic tissue and the spleen. Two patients were males with a mucinous cystadenoma and non‐cystic mucinous cystadenocarcinoma. The other was a female with a serous cystadenoma. Middle segment pancreatectomy was performed. Two patients were reconstructed with double pancreaticojejunostomy and the third with a pancreaticogastrostomy.Results:  No major complications were observed.Comnclusions:  Middle segment pancreatectomy is a safe and effective procedure for the resection of benign and low malignant potential tumours in the pancreatic neck and body with preservation of normal pancreatic tissue and the spleen in selected patients. This is the first report of middle segment pancreatectomy for pancreatic tumour in China.

Louis, GB, Dukic, V, Heagerty, PJ, Louis, TA, Lynch, CD, Ryan, LM, Schisterman, EF, Trumble, A & Grp, PMW 2006, 'Analysis of repeated pregnancy outcomes', STATISTICAL METHODS IN MEDICAL RESEARCH, vol. 15, no. 2, pp. 103-126.
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Women tend to repeat reproductive outcomes, with past history of an adverse outcome being associated with an approximate two-fold increase in subsequent risk. These observations support the need for statistical designs and analyses that address this clustering. Failure to do so may mask effects, result in inaccurate variance estimators, produce biased or inefficient estimates of exposure effects. We review and evaluate basic analytic approaches for analysing reproductive outcomes, including ignoring reproductive history, treating it as a covariate or avoiding the clustering problem by analysing only one pregnancy per woman, and contrast these to more modern approaches such as generalized estimating equations with robust standard errors and mixed models with various correlation structures. We illustrate the issues by analysing a sample from the Collaborative Perinatal Project dataset, demonstrating how the statistical model impacts summary statistics and inferences when assessing etiologic determinants of birth weight. © 2006 Edward Arnold (Publishers) Ltd.

Ly, NP, Ruiz-Pérez, B, Onderdonk, AB, Tzianabos, AO, Litonjua, AA, Liang, C, Laskey, D, Delaney, ML, DuBois, AM, Levy, H, Gold, DR, Ryan, LM, Weiss, ST & Celedón, JC 2006, 'Mode of delivery and cord blood cytokines: a birth cohort study', Clinical and Molecular Allergy, vol. 4, no. 1.
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AbstractBackgroundThe mechanisms for the association between birth by cesarean section and atopy and asthma are largely unknown.ObjectiveTo examine whether cesarean section results in neonatal secretion of cytokines that are associated with increased risk of atopy and/or asthma in childhood. To examine whether the association between mode of delivery and neonatal immune responses is explained by exposure to the maternal gut flora (a marker of the vaginal flora).MethodsCBMCs were isolated from 37 neonates at delivery, and secretion of IL-13, IFN-γ, and IL-10 (at baseline and after stimulation with antigens [dust mite and cat dander allergens, phytohemagglutinin, and lipopolysaccharide]) was quantified by ELISA. Total and specific microbes were quantified in maternal stool. The relation between mode of delivery and cord blood cytokines was examined by linear regression. The relation between maternal stool microbes and cord blood cytokines was examined by Spearman's correlation coefficients.ResultsCesarean section was associated with increased levels of IL-13 and IFN-γ. In multivariate analyses, cesarean section was associated with an increment of 79.4 pg/ml in secretion of IL-13 by CBMCs after stimulation with dust mite allergen (P < 0.001). Among children born by vaginal delivery, gram-positive anaerobes and total anaerobes in maternal stool were positively correlated with levels of IL-10, and gram-negative aerobic bacteria in maternal stool were negatively correlated with levels of IL-13 and IFN-γ.ConclusionCesarean section is associated with increased levels of IL-13 and IFN-γ, perhaps because of lack of labor and/or reduced exposure t...

Lynch, GW, Turville, S, Carter, B, Sloane, AJ, Chan, A, Muljadi, N, Li, S, Low, L, Armati, P, Raison, R, Zoellner, H, Williamson, P, Cunningham, A & Church, WB 2006, 'Marked differences in the structures and protein associations of lymphocyte and monocyte CD4: Resolution of a novel CD4 isoform', Immunology & Cell Biology, vol. 84, no. 2, pp. 154-165.
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The structures, molecular interactions and functions of CD4 in a subset of T lymphocytes have been well characterized. The CD4 receptors of other cell types have, however, been poorly documented. We have previously shown that lymphocytes and monocytes/macrophages differ in their expression of CD4 monomers and dimers. In the present study, we have shown further significant differences. Variability in the blocking of CD4 mAb binding by sulfated polyanions indicated differences in exofacial CD4 structures. In contrast to the well‐documented 55 kDa monomers in lymphocytic cells, monocytic cells were found to coexpress two monomer isoforms: the 55 kDa form and a novel 59 kDa species. Experimental uncoupling of CD4 disulfides indicated that the oxidized 55 kDa monomer could be converted to the 59 kDa form. This was achieved by chemical reduction of purified native or recombinant CD4, or in cell transfection experiments by mutation of cysteine to alanine in domain 1 (D1) (Cys16 or Cys84) and in domain 4 (D4) (Cys303 or Cys345). All of these modifications promote CD4 distension on SDS–PAGE analysis and indicate that, when CD4 inter‐β‐sheet disulfides in the D1 and D4 Ig folds are disrupted, there is an unravelling of the oxidized form to an extended 59 kDa unfolded state. We hypothesize that this may be a transition‐state, structural‐intermediate in the formation of disulfide‐linked homodimers. Also identified were CD4‐tyrosine kinase dissimilarities in which lymphocyte CD4 associated with Lck, but monocyte CD4 associated with HcK. These findings show that there is complex heterogeneity in structures and interactions in the CD4 of T lymphocytes and monocytes.

Lyon, JL, Alder, SC, Stone, MB, Scholl, A, Reading, JC, Holubkov, R, Sheng, X, Jr, WGL, Hegmann, KT, Anspaugh, L, Hoffman, FO, Simon, SL, Thomas, B, Carroll, R & Meikle, AW 2006, 'Thyroid disease associated with exposure to the Nevada Nuclear Weapons Test Site radiation - A reevaluation based on corrected dosimetry and examination data', EPIDEMIOLOGY, vol. 17, no. 6, pp. 604-614.
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Ma, Y & Carroll, RJ 2006, 'Locally Efficient Estimators for Semiparametric Models With Measurement Error', Journal of the American Statistical Association, vol. 101, no. 476, pp. 1465-1474.
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Malguth, E, Hoffmann, A, Gehlhoff, W, Gelhausen, O, Phillips, MR & Xu, X 2006, 'Structural and electronic properties of Fe3+ and Fe2+ centers in GaN from optical and EPR experiments', PHYSICAL REVIEW B, vol. 74, no. 16, pp. 1-12.
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This work provides a consistent picture of the structural, optical, and electronic properties of Fe-doped GaN. A set of high-quality GaN crystals doped with Fe at concentrations ranging from 5× 1017 cm-3 to 2× 1020 cm-3 is systematically investigated by means of electron paramagnetic resonance and various optical techniques. Fe3+ is shown to be a stable charge state at concentrations from 1× 1018 cm-3. The fine structure of its midgap states is successfully established, including an effective-mass-like state consisting of a hole bound to Fe2+ with a binding energy of 50±10 meV. A major excitation mechanism of the Fe3+ (T14 → A16) luminescence is identified to be the capture of free holes by Fe2+ centers. The holes are generated in a two-step process via the intrinsic defects involved in the yellow luminescence. The Fe3+/2+ charge-transfer level is found 2.863±0.005 eV above the valence band, suggesting that the internal reference rule does not hold for the prediction of band offsets of heterojunctions between GaN and other III-V materials. The Fe2+ (E5 → T25) transition is observed around 390 meV at any studied Fe concentration by means of Fourier transform infrared spectroscopy. Charge-transfer processes and the effective-mass-like state involving both Fe2+ states are observed. At Fe concentrations from 1× 1019 cm-3, additional lines occur in electron paramagnetic resonance and photoluminescence spectra which are attributed to defect complexes involving Fe3+. With increasing Fe concentration, the Fermi level is shown to move from near the conduction band to the Fe3+/2+ charge-transfer level, where it stays pinned for concentrations from 1× 1019 cm-3. Contrary to cubic II-VI and III-V materials, both electronic states are effected by only a weak Jahn-Teller interaction. © 2006 The American Physical Society.

Mallinckrodt, CH, Detke, MJ, Kaiser, CJ, Watkin, JG, Molenberghs, G & Carroll, RJ 2006, 'Comparing onset of antidepressant action using a repeated measures approach and a traditional assessment schedule', Statistics in Medicine, vol. 25, no. 14, pp. 2384-2397.
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Manefield, M, McDougald, D, A Rice, S & Kjelleberg, S 2006, 'Bacterial communication: when does a metabolite become a signal?', Microbiology Australia, vol. 27, no. 3, pp. 115-115.
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Bacterial communication has risen to prominence in microbiology as a dynamic research topic, both because of its role in microbial ecology and evolution and for the opportunity it offers to control pathogenic microbial activity. Bacterial communication has evolved from the metabolic processes of prokaryotic cellular life, in which the biosynthesis and breakdown of chemical compounds in central metabolism generates secondary metabolites with ambiguous utility in natural selection.

Mau, B, Glasner, JD, Darling, AE & Perna, NT 2006, 'Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli', GENOME BIOLOGY, vol. 7, no. 5, pp. 1-12.
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Background: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. Results: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. Conclusion: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events. © 2006 Mau et al.; licensee BioMed Central Ltd.

Mau, B, Glasner, JD, Darling, AE & Perna, NT 2006, 'Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.', Genome Biol, vol. 7, no. 5, p. R44.
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BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events.

McBean, KE, Phillips, MR & Goldys, EM 2006, 'Synthesis and characterization of doped and undoped ZnO nanostructures', MICROSCOPY AND MICROANALYSIS, vol. 12, no. 4, pp. 327-330.
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Zinc oxide (ZnO) nanoparticles have been produced using precipitation methods from ethanolic solution. Rare-earth metal doping was performed, and the effect of lithium codoping on the luminescence properties of the rare-earth doped products was assessed. The resulting particles were characterized using cathodoluminescence and scanning electron microscopy. It was found that lithium significantly enhanced the cathodoluminescence signal from the rare-earth ions, which has been attributed to the increased integration of the rare-earth ions into the ZnO structure. The nanophase ZnO products were also annealed in argon, hydrogen, and oxygen, with hydrogen being the most successful for removing the broad defect emission present in as-grown samples and enhancing the ZnO near band edge emission. © Microscopy Society of America 2006.

McCarty, KM, Houseman, EA, Quamruzzaman, Q, Rahman, M, Mahiuddin, G, Smith, T, Ryan, L & Christiani, DC 2006, 'The impact of diet and betel nut use on skin lesions associated with drinking-water arsenic in Pabna, Bangladesh', ENVIRONMENTAL HEALTH PERSPECTIVES, vol. 114, no. 3, pp. 334-340.
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An established exposure-response relationship exists between water arsenic levels and skin lesions. Results of previous studies with limited historical exposure data, and laboratory animal studies suggest that diet may modify arsenic metabolism and toxicity. In this study, we evaluated the effect of diet on the risk of arsenic-related skin lesions in Pabna, Bangladesh. Six hundred cases and 600 controls loosely matched on age and sex were enrolled at Dhaka Community Hospital, Bangladesh, in 2001-2002. Diet, demographic data, and water samples were collected. Water samples were analyzed for arsenic using inductively coupled plasma mass spectroscopy. Betel nut use was associated with a greater risk of skin lesions in a multivariate model [odds ratio (OR) = 1.67; 95% confidence interval (CI), 1.18-2.36]. Modest decreases in risk of skin lesions were associated with fruit intake 1-3 times/month (OR = 0.68; 95%CI, 0.51-0.89) and canned goods at least 1 time/month (OR = 0.41; 95% CI, 0.20-0.86). Bean intake at least 1 time/day (OR = 1.89; 95% CI, 1.11-3.22) was associated with increased odds of skin lesions. Betel nut use appears to be associated with increased risk of developing skin lesions in Bangladesh. Increased intake of fruit and canned goods may be associated with reduced risk of lesions. Increased intake of beans may be associated with an increased risk of skin lesions. The results of this study do not provide clear support for a protective effect of vegetable and overall protein consumption against the development of skin lesions, but a modest benefit cannot be excluded.

McDougald, D, Lin, WH, Rice, SA & Kjelleberg, S 2006, 'The role of quorum sensing and the effect of environmental conditions on biofilm formation by strains ofVibrio vulnificus', Biofouling, vol. 22, no. 3, pp. 161-172.
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McNevin, D, von Caemmerer, S & Farquhar, G 2006, 'Determining RuBisCO activation kinetics and other rate and equilibrium constants by simultaneous multiple non-linear regression of a kinetic model', Journal of Experimental Botany, vol. 57, no. 14, pp. 3883-3900.
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McNevin, DB, Badger, MR, Kane, HJ & Farquhar, GD 2006, 'Measurement of (carbon) kinetic isotope effect by Rayleigh fractionation using membrane inlet mass spectrometry for CO₂-consuming reactions.', Functional plant biology : FPB, vol. 33, no. 12, pp. 1115-1128.
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Methods for determining carbon isotope discrimination, Δ, or kinetic isotope effects, α, for CO₂-consuming enzymes have traditionally been cumbersome and time-consuming, requiring careful isolation of substrates and products and conversion of these to CO₂ for measurement of isotope ratio by mass spectrometry (MS). An equation originally derived by Rayleigh in 1896 has been used more recently to good effect as it only requires measurement of substrate concentrations and isotope ratios. For carboxylation reactions such as those catalysed by d-ribulose-1,5-bisphosphate carboxylase / oxygenase (RuBisCO, EC 4.1.1.39) and PEP carboxylase (PEPC, EC 4.1.1.31), this has still required sampling of reactions at various states of completion and conversion of all inorganic carbon to CO₂, as well as determining the amount of substrate consumed. We introduce a new method of membrane inlet MS which can be used to continuously monitor individual CO₂ isotope concentrations, rather than isotope ratio. This enables the use of a simplified, new formula for calculating kinetic isotope effects, based on the assumptions underlying the original Rayleigh fractionation equation and given by.

McNevin, DB, Badger, MR, Kane, HJ & Farquhar, GD 2006, 'Measurement of (carbon) kinetic isotope effect by Rayleigh fractionation using membrane inlet mass spectrometry for CO2-consuming reactions', Functional Plant Biology, vol. 33, no. 12, pp. 1115-1115.
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Methods for determining carbon isotope discrimination, Δ, or kinetic isotope effects, α, for CO2-consuming enzymes have traditionally been cumbersome and time-consuming, requiring careful isolation of substrates and products and conversion of these to CO2 for measurement of isotope ratio by mass spectrometry (MS). An equation originally derived by Rayleigh in 1896 has been used more recently to good effect as it only requires measurement of substrate concentrations and isotope ratios. For carboxylation reactions such as those catalysed by d-ribulose-1,5-bisphosphate carboxylase / oxygenase (RuBisCO, EC 4.1.1.39) and PEP carboxylase (PEPC, EC 4.1.1.31), this has still required sampling of reactions at various states of completion and conversion of all inorganic carbon to CO2, as well as determining the amount of substrate consumed. We introduce a new method of membrane inlet MS which can be used to continuously monitor individual CO2 isotope concentrations, rather than isotope ratio. This enables the use of a simplified, new formula for calculating kinetic isotope effects, based on the assumptions underlying the original Rayleigh fractionation equation and given by: --> The combination of inlet membrane MS and this formula yields measurements of discrimination in less than 1 h. We validate our method against previously measured values of discrimination for PEP carboxylase and RuBisCO from several species.

Meakin, GE, Jepson, BJN, Richardson, DJ, Bedmar, EJ & Delgado, MJ 2006, 'The role of Bradyrhizobium japonicum nitric oxide reductase in nitric oxide detoxification in soya bean root nodules', Biochemical Society Transactions, vol. 34, no. 1, pp. 195-196.
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The identification of nitric oxide-bound leghaemoglobin within soya bean nodules has led to the question of how Bradyrhizobium japonicum bacteroids overcome the toxicity of this nitric oxide. It has previously been shown that one candidate for nitric oxide detoxification, the respiratory nitric oxide reductase, is expressed in soya bean nodules from plants supplied with nitrate [Mesa, de Dios Alché, Bedmar and Delgado (2004) Physiol. Plant. 120, 205–211]. In this paper, the role of this enzyme in nitric oxide detoxification is assessed and discussion is provided on other possible B. japonicum nitric oxide detoxification systems.

Meeker, JD, Ryan, L, Barr, DB & Hauser, R 2006, 'Exposure to nonpersistent insecticides and male reproductive hormones', EPIDEMIOLOGY, vol. 17, no. 1, pp. 61-68.
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Meier, PC & Rogers, C 2006, 'Reporting Traditional Chinese Medicine morbidity - A University of Technology, Sydney, project with an emphasis on developing standards for testing and reporting data', JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, vol. 12, no. 6, pp. 529-534.
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Objectives: Morbidity in Traditional Chinese Medicine (TCM) research is an emerging field. Few studies have been published, and there is a lack of international standards for data collection and reporting. Based on the experience of developing a computerized system for patient data collection at the University of Technology, Sydney, (UTS) Acupuncture Clinic (Sydney, Australia), and reporting results from that database, a start can be made toward developing guidelines for reporting similar results from TCM clinical audits. Methods: This study reports on data relating to 5735 patients who had undergone 29,697 treatments. Patient information is collected by a computerized database recording International Classification of Primary Care (ICPC) reason for encounter (RFE) and symptom for encounter (SFE) data and TCM tongue, pulse, diagnostic, and treatment data. Data coding is automated, and systems for reliability testing and error reporting were developed. Results: UTS data has a 2.7% error rate and is within international standards of 5% error. Sixty-one-point-three percent (61.3%) of patients were female and of these, 59.45 were 25-44 years of age. Musculoskeletal disorders are the most common presentation (41.4%) of all RFE, followed by general disorders (13.1%) and digestive disorders (8.1%). Conclusions: International standards must be set for TCM morbidity data collection methods and reporting. It is hoped that the methods described and reported in this paper are an initial step in the setting of such standards and that they will be adopted by other researchers. In particular, methods for testing and reporting data reliability must be adopted if TCM morbidity studies are to maintain any credibility. © Mary Ann Liebert, Inc.

Meier, PC, Ballinger, S, Hoi, B & Vickland, V 2006, 'Neurophysiological Effects of Harmonisation : The effect of Harmanization on Hearth Rate Variability, Respiratory Rate and Electroencephalograph', Subtle Energies & Energy Medicine, vol. 17, no. 1, pp. 73-89.
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Harmonization is a prctice whereby the harmoniser who is centered in silent prayer, opens and nourishes the subjects' chakrasm using touch. This technique has been widely used since 1983, with substantial anecdotal evidence wbout its benefits, but no published peer-reviewed data. This preliminary study aimed to discover if standard physiological measuring techniques can detect any significant changes in the central and autonomic nervous system and the cardiopulmonary system during harmonisation. A simple, comparative design was used, with one experimental group of 20 self-selecting, healthy women, naive to harmonisation. The results were compared with reference data, matched for age and gender, from non-intervention control studies conducted by the same experimeners in the same neurophysiological laboratory. An 80-minute recording session determined baseline, intervention and stabilisation measurements on electroencephalographic, electrocardiographic and respiratory data. A significant lowering of brain activity was found during theopening phase of harmonisation, implying a state of increased mental focus coupled with a sense of calmness and relaxation, while significant changes to heartbeat/respiration ratios were observed during the nourishing phase. This suggests that different physiological processes affecting the central and autonomic nervous system and the cardiopulmonary system may occur during different phases of harmonisation.

Michie, KA, Monahan, LG, Beech, PL & Harry, EJ 2006, 'Trapping of a spiral-like intermediate of the bacterial cytokinetic protein FtsZ', JOURNAL OF BACTERIOLOGY, vol. 188, no. 5, pp. 1680-1690.
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The earliest stage in bacterial cell division is the formation of a ring, composed of the tubulin-like protein FtsZ, at the division site. Tight spatial and temporal regulation of Z-ring formation is required to ensure that division occurs precisely at midcell between two replicated chromosomes. However, the mechanism of Z-ring formation and its regulation in vivo remain unresolved. Here we identify the defect of an interesting temperature-sensitive ftsZ mutant (ts1) of Bacillus subtilis. At the nonpermissive temperature, the mutant protein, FtsZ(Ts1), assembles into spiral-like structures between chromosomes. When shifted back down to the permissive temperature, functional Z rings form and division resumes. Our observations support a model in which Z-ring formation at the division site arises from reorganization of a long cytoskeletal spiral form of FtsZ and suggest that the FtsZ(Ts1) protein is captured as a shorter spiral-forming intermediate that is unable to complete this reorganization step. The ts1 mutant is likely to be very valuable in revealing how FtsZ assembles into a ring and how this occurs precisely at the division site. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Mitrovic, SM, Chessman, BC, Bowling, LC & Cooke, RH 2006, 'Modelling suppression of cyanobacterial blooms by flow management in a lowland river', River Research and Applications, vol. 22, no. 1, pp. 109-114.
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AbstractGrowth and dominance of the cyanobacterium Anabaena circinalis in weir pools of the Barwon–Darling River, Australia, are related to persistent vertical thermal stratification between October and March, when discharge is low. We determined critical velocities and discharges required to suppress bloom formation at three sites, and modelled the occurrence of sub‐critical discharges in order to predict the frequency of blooms under different management scenarios. Our model suggests that the frequency of blooms was about double that expected under near‐natural flows (without major impoundment or water extraction) for 1990–2000. Flow management, through Environmental Water Provisions that limit water extraction when river levels are low, has been in place since July 2000. Our model suggests that these provisions are unlikely to have had an effect on bloom frequency for 2000–2003. In the longer term, however, they could reduce bloom frequency at some sites by up to one‐third. Copyright © 2006 John Wiley & Sons, Ltd.

Miura, T, Huete, A & Yoshioka, H 2006, 'An empirical investigation of cross-sensor relationships of NDVI and red/near-infrared reflectance using EO-1 hyperion data', REMOTE SENSING OF ENVIRONMENT, vol. 100, no. 2, pp. 223-236.
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Long term observations of global vegetation from multiple satellites require much effort to ensure continuity and compatibility due to differences in sensor characteristics and product generation algorithms. In this study, we focused on the bandpass filter differences and empirically investigated cross-sensor relationships of the normalized difference vegetation index (NDVI) and reflectance. The specific objectives were: 1) to understand the systematic trends in cross-sensor relationships of the NDVI and reflectance as a function of spectral bandpasses, 2) to examine/identify the relative importance of the spectral features (i.e., the green peak, red edge, and leaf liquid water absorption regions) in and the mechanism(s) of causing the observed systematic trends, and 3) to evaluate the performance of several empirical cross-calibration methods in modeling the observed systematic trends. A Level 1A Hyperion hyperspectral image acquired over a tropical forest-savanna transitional region in Brazil was processed to simulate atmospherically corrected reflectances and NDVI for various bandpasses, including Terra Moderate Resolution Imaging Spectroradiometer (MODIS), NOAA-14 Advanced Very High Resolution Radiometer (AVHRR), and Landsat-7 Enhanced Thematic Mapper Plus (ETM+). Data were extracted from various land cover types typically found in tropical forest and savanna biomes and used for analyses. Both NDVI and reflectance relationships among the sensors were neither linear nor unique and were found to exhibit complex patterns and bandpass dependencies. The reflectance relationships showed strong land cover dependencies. The NDVI relationships, in contrast, did not show land cover dependencies, but resulted in nonlinear forms. From sensitivity analyses, the green peak (∼550 nm) and red-NIR transitional (680-780 nm) features were identified as the key factors in producing the observed land cover dependencies and nonlinearity in cross-sensor relationships. In ...

Moore, CM, Suggett, DJ, Hickman, AE, Kim, Y-N, Tweddle, JF, Sharples, J, Geider, RJ & Holligan, PM 2006, 'Phytoplankton photoacclimation and photoadaptation in response to environmental gradients in a shelf sea', Limnology and Oceanography, vol. 51, no. 2, pp. 936-949.
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Variability in the photosynthetic performance of natural phytoplankton communities, due to both taxonomic composition and the physiological acclimation of these taxa to environmental conditions, was assessed at contrasting sites within a temperate shelf

Morales, KH, Ibrahim, JG, Chen, CJ & Ryan, LM 2006, 'Bayesian model averaging with applications to benchmark dose estimation for arsenic in drinking water', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 101, no. 473, pp. 9-17.
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An important component of quantitative risk assessment involves characterizing the dose-response relationship between an environmental exposure and adverse health outcome and then computing a benchmark dose, or the exposure level that yields a suitably low risk. This task is often complicated by model choice considerations, because risk estimates depend on the model parameters. We propose using Bayesian methods to address the problem of model selection and derive a model-averaged version of the benchmark dose. We illustrate the methods through application to data on arsenic-induced lung cancer from Taiwan. © 2006 American Statistical Association.

Morgan, SW & Phillips, MR 2006, 'Gaseous scintillation detection and amplification in variable pressure scanning electron microscopy', JOURNAL OF APPLIED PHYSICS, vol. 100, no. 7, pp. 1-16.
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This work investigates the generation and detection of gaseous scintillation signals produced in variable pressure scanning electron microscopy through electron-gas molecule excitation reactions. Here a gaseous scintillation detection (GSD) system is developed to efficiently detect photons produced via excitation reactions in electron cascades. Images acquired using GSD are compared to those obtained using conventional gaseous secondary electron detection (GSED) and demonstrate that images rich in secondary electron (SE) contrast can be achieved using the gaseous scintillation signal. A theoretical model, based on existing Townsend theories, is developed. It describes the production and amplification of photon signals generated by cascading SEs, high energy backscattered electrons, and primary beam electrons. Photon amplification (the total number of photons produced per sample emissive electron) is then investigated and compared to conventional electronic amplification over a wide range of microscope operating parameters, scintillating imaging gases, and photon collection geometries. These studies revealed that argon gas exhibited the largest GSD gain, followed by nitrogen then water vapor, exactly opposite to the trend observed for electron amplification data. It was also found that detected scintillation signals exhibit larger SE signal-to-background levels compared to those of conventional electronic signals detected via GSED. Finally, dragging the electron cascade towards the light pipe assemblage of GSD systems, or electrostatic focusing, dramatically increases the collection efficiency of photons. © 2006 American Institute of Physics.

Morgan, SW & Phillips, MR 2006, 'Transient analysis of gaseous electron-ion recombination in the environmental scanning electron microscope', JOURNAL OF MICROSCOPY-OXFORD, vol. 221, no. 3, pp. 183-202.
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Most of the work carried out in relation to contrast mechanisms and signal formation in an environmental scanning electron microscope has yet to consider the time dependent aspects of image generation at a quantitative level. This paper quantitatively describes gaseous electron-ion recombination (also known as 'signal scavenging') in an environmental scanning electron microscope at a transient level by utilizing the dark shadows/streaks seen in gaseous secondary electron detector images of alumina (Al2O3) immediately after a region of enhanced secondary electron emission is encountered by a scanning electron beam. The investigation firstly derives a theoretical model of gaseous electron-ion recombination that takes into consideration transients caused by the time constant of the gaseous secondary electron detector electronics and external circuitry used to generate images. Experimental data of pixel intensity versus time of the streaks are then simulated using the model enabling the relative magnitudes of (i) ionization and recombination rates, (ii) recombination coefficients and (iii) electron drift velocities, as well as absolute values of the total time constant of the gaseous secondary electron detection system and external circuitry, to be determined as a function of microscope operating parameters such as gaseous secondary electron detector bias, sample-electrode separation, imaging gas pressure, and scan speed. The results revealed, for the first time, the exact dependence that the effects of secondary electron-ion recombination on signal formation has on reduced electric field and time in an environmental scanning electron microscope. Furthermore, the model implicitly demonstrated that signal loss as a consequence of field retardation due to ion space charges, although obviously present, is not the foremost phenomenon causing streaking in images, as previously thought. © 2006 The Royal Microscopical Society.

Morris, JS & Carroll, RJ 2006, 'Wavelet-based Functional Mixed Models', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 68, no. 2, pp. 179-199.
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SummaryIncreasingly, scientific studies yield functional data, in which the ideal units of observation are curves and the observed data consist of sets of curves that are sampled on a fine grid. We present new methodology that generalizes the linear mixed model to the functional mixed model framework, with model fitting done by using a Bayesian wavelet-based approach. This method is flexible, allowing functions of arbitrary form and the full range of fixed effects structures and between-curve covariance structures that are available in the mixed model framework. It yields nonparametric estimates of the fixed and random-effects functions as well as the various between-curve and within-curve covariance matrices. The functional fixed effects are adaptively regularized as a result of the non-linear shrinkage prior that is imposed on the fixed effects’ wavelet coefficients, and the random-effect functions experience a form of adaptive regularization because of the separately estimated variance components for each wavelet coefficient. Because we have posterior samples for all model quantities, we can perform pointwise or joint Bayesian inference or prediction on the quantities of the model. The adaptiveness of the method makes it especially appropriate for modelling irregular functional data that are characterized by numerous local features like peaks.

Morris, JS, Arroyo, C, Coull, BA, Ryan, LM, Herrick, R & Gortmaker, SL 2006, 'Using wavelet-based functional mixed models to characterize population heterogeneity in accelerometer profiles: A case study', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 101, no. 476, pp. 1352-1364.
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We present a case study illustrating the challenges of analyzing accelernmetcr data taken from a sample of children participating in an intervention study designed to increase physical activity. An aceelerometer is a small device worn on the hip that records the minute-by-minute activity levels throughout the day for each day it is worn. The resulting data are irregular functions characterized by many peaks representing short bursts of intense activity. We model these data using the wavelet-based functional mixed model. This approach incorporates multiple fixed-effects and random-effects functions of arbitrary form, the estimates of which are adaptively regularised using wavelet shrinkage. The method yields posterior samples for all functional quantities of the model, which can be used to perform various types of Bayesian inference and prediction, in our case study, a high proportion of the daily activity profiles are incomplete (i.e., have some portion of the profile missing), and thus cannot he modeled directly using the previously described method. We present a new method for stochastically imputing the missing data that allows us to incorporate these incomplete profiles in our analysis. Our approach borrows strength from both the observed measurements within the incomplete profiles and from other profiles, from the same child as well as from other children with similar covariutc levels, while appropriately propagating the uncertainty of the imputation throughout all subsequent inference. We apply this method to our case study, revealing some interesting insights into children's activity patterns. We point out some strengths and limitations of using this approach to analyze accelerometer data. © 2006 American Statistical Association.

Murray, BR, Hose, GC, Eamus, D & Licari, D 2006, 'Valuation of groundwater-dependent ecosystems: a functional methodology incorporating ecosystem services', AUSTRALIAN JOURNAL OF BOTANY, vol. 54, no. 2, pp. 221-229.
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Groundwater-dependent ecosystems (GDEs) are ecosystems that must have access to groundwater to maintain their ecological structure and function. Rapidly expanding numbers of humans are placing increased demands on groundwater for consumption, industry and agriculture. These demands alter groundwater regimes of GDEs that have evolved over millennia, resulting in the degradation of ecosystem health. As a consequence, the goods and services (ecosystem services) that GDEs provide for humans, which include food production and water purification, are at serious risk of being lost. Effective management of GDEs and their ecosystem services requires prioritisation of the most valuable ecosystems, given that increasing human demands and limited time and money preclude complete protection of all GDEs. Here, we provide an eight-step method for the valuation and initial prioritisation of GDEs. The proposed methodology improves on previous, primarily subjective methods for the valuation of GDEs by employing both economic valuation of the ecosystem services provided by GDEs, and ecological valuation of significant environmental attributes of GDEs. We apply the eight-step method to a hypothetical case study in order to demonstrate its applicability to a catchment containing a range of GDEs of different sizes, each possessing its own suite of threatened taxa. The major benefit of the valuation methodology presented here is that it can be used at three levels of complexity: (1) a full-desktop study, (2) a semi-desktop study requiring stakeholder consultation, and (3) a full field-based study, according to the time and money available for initial prioritisation efforts. © CSIRO 2006.

Murray, S, Hoppenrath, M, Larsen, J & Patterson, DJ 2006, 'Bysmatrum teres sp nov., a new sand-dwelling dinotlagellate from north-western Australia', PHYCOLOGIA, vol. 45, no. 2, pp. 161-167.
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Murray, S, Hoppenrath, M, Preisfeld, A, Larsen, J, Yoshimatsu, S, Toriumi, S & Patterson, DJ 2006, 'Phylogenetics of Rhinodinium broomeense gen. et sp nov., a peridinioid, sand-dwelling dinoflagellate (Dinophyceae)', JOURNAL OF PHYCOLOGY, vol. 42, no. 4, pp. 934-942.
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Musicki, K, Briscoe, H, Tran, S, Britton, WJ & Saunders, BM 2006, 'DifferentialRequirements for Soluble and Transmembrane Tumor Necrosis Factor in theImmunological Control of Primary and SecondaryListeria monocytogenesInfection', Infection and Immunity, vol. 74, no. 6, pp. 3180-3189.
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ABSTRACTThe relative contributions of transmembrane tumor necrosis factor (memTNF) and soluble tumor necrosis factor (solTNF) in innate and adaptive immunity are poorly defined. We examined the capacities of wild-type (WT) mice, TNF−/−mice, and memTNF mice, which express only transmembrane TNF, to control primary and secondaryListeria monocytogenesinfections. Soluble TNF was not required for induction or maintenance of protective immunity against a low-dose (200-CFU)Listeriainfection. In contrast to TNF−/−mice, both WT and memTNF mice cleared the bacilli within 10 days and were fully protected against rechallenge with a lethal infective dose. Furthermore, T cells transferred from immune mice, but not from naïve, WT, and memTNF mice, protected TNF−/−recipients against an otherwise lethal infection. By contrast, infection with a higher dose ofListeria(2,000 CFU) clearly demonstrated that solTNF is required to coordinate an optimal protective inflammatory response. memTNF mice were more susceptible to a high-dose infection, and they exhibited delayed bacterial clearance, increased inflammation, and necrosis in the liver that resulted in 55% mortality. The dysregulated inflammation was accompanied by prolonged elevated expression of mRNAs for several chemokines as well as the macrophage effector molecules inducible nitric oxide synthase and LRG-47 in the livers of memTNF mice but not in the livers of WT mice. These data demonstrated that memTNF is sufficient for establishing protective immunity against a primary low-doseListeriainfection but that solTNF is required for optimal control of cellular inflammation and resistance to a primary high-dose infection. By contrast, memTNF alone is sufficient for resolution of a secondary, high-dose infection and for t...

Myers, GSA, Rasko, DA, Cheung, JK, Ravel, J, Seshadri, R, DeBoy, RT, Ren, Q, Varga, J, Awad, MM, Brinkac, LM, Daugherty, SC, Haft, DH, Dodson, RJ, Madupu, R, Nelson, WC, Rosovitz, MJ, Sullivan, SA, Khouri, H, Dimitrov, GI, Watkins, KL, Mulligan, S, Benton, J, Radune, D, Fisher, DJ, Atkins, HS, Hiscox, T, Jost, BH, Billington, SJ, Songer, JG, McClane, BA, Titball, RW, Rood, JI, Melville, SB & Paulsen, IT 2006, 'Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens', Genome Research, vol. 16, no. 8, pp. 1031-1040.
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Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique “genomic islands” identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.

Nixon, KL, Vos, M, Bowles, C & Ford, MJ 2006, 'Measuring the electronic structure of disordered overlayers by electron momentum spectroscopy: the Cu/Si interface', SURFACE AND INTERFACE ANALYSIS, vol. 38, no. 8, pp. 1236-1241.
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The Cu-Si interface was studied by electron momentum spectroscopy. A thick disordered interface is formed if one material is deposited on the other. Electron momentum spectroscopy measures intensity as a function of binding energy and target electron momentum. Momentum resolution is demonstrated to be very helpful in interpreting the data, even for these disordered interfaces. The interface layer has a well-defined electronic structure, different from either Si or Cu, and consistent with silicide formation. Information is obtained about the total bandwidth of the interface compound, effective Brillouin zone size and Fermi radius. No clear differences are observed in the electronic structure of the interface layer for Si deposited on Cu or Cu deposited on Si. Copyright © 2006 John Wiley & Sons, Ltd.

O'Brien, BA, Geng, X, Orteu, CH, Huang, Y, Ghoreishi, M, Zhang, Y, Bush, JA, Li, G, Finegood, DT & Dutz, JP 2006, 'A deficiency in the in vivo clearance of apoptotic cells is a feature of the NOD mouse', Journal of Autoimmunity, vol. 26, no. 2, pp. 104-115.
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Deficiencies in apoptotic cell clearance have been linked to autoimmunity. Here we examined the time-course of peritoneal macrophage phagocytosis of dying cells following the direct injection of apoptotic thymocytes into the peritoneum of NOD mice and BALB/c controls. Macrophages from NOD mice demonstrated a profound defect in the phagocytosis of apoptotic thymocytes as compared to control macrophages. Nonobese diabetic mice also demonstrated a decrease in the clearance of apoptotic cell loads following an apoptotic stimulus to thymocytes (dexamethasone) when compared to BALB/c or NOR controls. Further, NOD mice demonstrated an increase in apoptotic cell load following an apoptotic stimulus to keratinocytes (ultraviolet light, UVB) when compared to control strains. Animals deficient in macrophage phagocytosis of apoptotic debris often manifest an autoimmune phenotype characterized by the production of antinuclear autoantibodies (ANA). We determined whether increased apoptotic cell loads (through repeated exposure to UVB irradiation) could accelerate such autoimmune phenomena in young NOD mice. Following repeated UVB irradiation, NOD mice, but not BALB/c or NOR controls, developed ANA. We propose that abnormalities in apoptotic cell clearance by macrophages predispose NOD mice to autoimmunity.

Oliver, BG & Black, JL 2006, 'Airway Smooth Muscle and Asthma', Allergology International, vol. 55, no. 3, pp. 215-223.
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The airway smooth muscle is the key determinant of airway narrowing in asthma but its function in the absence of disease is unknown. Evidence for an intrinsic abnormality in the muscle in asthma is only just emerging. The airway smooth muscle is not merely a contractile cell, but also one which determines the composition of, and interacts with the extracellular matrix, and which may participate in inflammatory and allergic reactions and viral infections. The reason for the differences which have been observed in the in vitro properties of airway smooth muscle derived from asthmatic individuals may result from an inherent "supercontractility", an increased tendency to proliferate due to the absence of an inhibitory transcription factor C/EBP-α, the influence of an altered extracellular matrix and/or a decrease in release of factors such as PGE2 which would under normal circumstances inhibit both proliferation and contraction. Although long acting beta agonists and corticosteroids are successful treatments for inflammation and bronchoconstriction, the structural changes which constitute airway remodelling may require additional therapeutic intervention, the nature of which will be determined by thorough investigation of the mechanisms underlying the asthmatic phenotype. ©2006 Japanese Society of Allergology.

Oliver, BGG, Johnston, SL, Baraket, M, Burgess, JK, King, NJC, Roth, M, Lim, S & Black, JL 2006, 'Increased proinflammatory responses from asthmatic human airway smooth muscle cells in response to rhinovirus infection', Respiratory Research, vol. 7, no. 1, pp. 1-11.
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Background: Exacerbations of asthma are associated with viral respiratory tract infections, of which rhinoviruses (RV) are the predominant virus type. Airway smooth muscle is important in asthma pathogenesis, however little is known about the potential interaction of RV and human airway smooth muscle cells (HASM). We hypothesised that rhinovirus induction of inflammatory cytokine release from airway smooth muscle is augmented and differentially regulated in asthmatic compared to normal HASM cells. Methods: HASM cells, isolated from either asthmatic or non-asthmatic subjects, were infected with rhinovirus. Cytokine production was assayed by ELISA, ICAM-1 cell surface expression was assessed by FACS, and the transcription regulation of IL-6 was measured by luciferase activity. Results: RV-induced IL-6 release was significantly greater in HASM cells derived from asthmatic subjects compared to non-asthmatic subjects. This response was RV specific, as 5% serum- induced IL-6 release was not different in the two cell types. Whilst serum stimulated IL-8 production in cells from both subject groups, RV induced IL-8 production in only asthmatic derived HASM cells. The transcriptional induction of IL-6 was differentially regulated via C/EBP in the asthmatic and NF-κB + AP-1 in the non-asthmatic HASM cells. Conclusion: This study demonstrates augmentation and differential transcriptional regulation of RV specific innate immune response in HASM cells derived from asthmatic and non-asthmatics, and may give valuable insight into the mechanisms of RV-induced asthma exacerbations. © 2006 Oliver et al; licensee BioMed Central Ltd.

O'REILLY, LC, INGLIS, TJJ & UNICOMB, L 2006, 'Australian multicentre comparison of subtyping methods for the investigation of Campylobacter infection', Epidemiology and Infection, vol. 134, no. 4, pp. 768-779.
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In order to identify subtyping methods able to contribute to the surveillance or investigation of Australian Campylobacter infection, six genotypic and three phenotypic subtyping methods were evaluated on a collection of 84 clinical isolates collected over a 30-month period from one region in Australia. The aim was to compare the logistics of various subtyping methods and examine their ability to assist in finding outbreaks or common sources of sporadic infection. The genotypic subtyping methods used were sequencing of the short variable region of the flaA gene, two methods using restriction fragment length polymorphism (RFLP) of the flaA gene using either DdeI or EcoRI with PstI, automated ribotyping, pulsed field gel electrophoresis and multilocus sequence typing. The phenotypic methods employed included Laboratory of Enteric Pathogens serotyping, Lior biotyping and antibiotic resistotyping. The level of agreement between subtyping results was determined. Phenotypic methods showed little agreement whereas genotypic typing methods showed a high level of agreement. Using the premise that five of the six genotypic typing methods were in agreement 15 genotypic groupings were identified. Sequencing of the short variable region of the flaA gene, RFLP of the flaA gene or automated ribotyping in conjunction with multilocus sequence typing best identified genotypic groupings. An alternative combination of RFLP of the flaA gene followed by ribotyping was equally satisfactory. RFLP of the flaA gene appeared to be suitable as a preliminary typing method based on ease of operation, equipment availability and cost.

Oren, A, Pri-El, N, Shapiro, O & Siboni, N 2006, 'Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds', Saline Systems, vol. 2, no. 1.
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Abstract Background Possession of gas vesicles is generally considered to be advantageous to halophilic archaea: the vesicles are assumed to enable the cells to float, and thus reach high oxygen concentrations at the surface of the brine. Results We studied the possible ecological advantage of gas vesicles in a dense community of flat square extremely halophilic archaea in the saltern crystallizer ponds of Eilat, Israel. We found that in this environment, the cells' content of gas vesicles was insufficient to provide positive buoyancy. Instead, sinking/floating velocities were too low to permit vertical redistribution. Conclusion The hypothesis that the gas vesicles enable the square archaea to float to the surface of the brines in which they live was not supported by experimental evidence. Presence of the vesicles, which are mainly located close to the cell periphery, may provide an advantage as they may aid the cells to position themselves parallel to the surface, thereby increasing the efficiency of light harvesting by the retinal pigments in the membrane.

Orwell, RL, Wood, RA, Burchett, MD, Tarran, J & Torpy, F 2006, 'The potted-plant microcosm substantially reduces indoor air VOC pollution: II. Laboratory study', WATER AIR AND SOIL POLLUTION, vol. 177, no. 1-4, pp. 59-80.
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Indoor air-borne loads of volatile organic compounds (VOCs) are usually significantly higher than those outdoors, and chronic exposures can cause health problems. Our previous laboratory studies have shown that the potted-plant microcosm, induced by an initial dose, can eliminate high air-borne VOC concentrations, the primary removal agents being potting-mix microorganisms, selected and maintained in the plant/root-zone microcosm. Our office field-study, reported in the preceding paper, showed that, when total VOC (TVOC) loads in reference offices (0 plants) rose above about 100 ppb, levels were generally reduced by up to 75% (to < 100 ppb) in offices with any one of three planting regimes. The results indicate the induction of the VOC removal mechanism at TVOC levels above a threshold of about 100 ppb. The aims of this laboratory dose-response study were to explore and analyse this response. Over from 5 to 9 days, doses of 0.2, 1.0, 10 and 100 ppm toluene and m-xylene were applied and replenished, singly and as mixtures, to potted-plants of the same two species used in the office study. The results confirmed the induction of the VOC removal response at the lowest test dosage, i.e in the middle of the TVOC range found in the offices, and showed that, with subsequent dosage increments, further stepwise induction occurred, with rate increases of several orders of magnitude. At each dosage, with induction, VOC concentrations could be reduced to below GC detection limits (< 20 ppb) within 24 h. A synergistic interaction was found with the binary mixtures, toluene accelerating m-xylene removal, at least at lower dosages. The results of these two studies together demonstrate that the potted-plant microcosm can provide an effective, self-regulating, sustainable bioremediation or phytoremediation system for VOC pollution in indoor air. © 2006 Springer Science+Business Media, Inc.

OSEIKUMAH, A, AMMIT, A, SMITH, R, GE, Q & CLIFTON, V 2006, 'Inflammatory Mediator Release in Normal Bronchial Smooth Muscle Cells is Altered by Pregnant Maternal and Fetal Plasma Independent of Asthma☆', Placenta, vol. 27, no. 8, pp. 847-852.
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Palenik, B, Ren, Q, Dupont, CL, Myers, GS, Heidelberg, JF, Badger, JH, Madupu, R, Nelson, WC, Brinkac, LM, Dodson, RJ, Durkin, AS, Daugherty, SC, Sullivan, SA, Khouri, H, Mohamoud, Y, Halpin, R & Paulsen, IT 2006, 'Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 103, no. 36, pp. 13555-13559.
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Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments. © 2006 by The National Academy of Sciences of the USA.

Parker, D, Kennan, RM, Myers, GS, Paulsen, IT, Songer, JG & Rood, JI 2006, 'Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus', JOURNAL OF BACTERIOLOGY, vol. 188, no. 13, pp. 4801-4811.
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Type IV fimbriae are expressed by several bacterial pathogens and are essential for virulence in Dichelobacter nodosus, which causes ovine footrot. We have identified a two-component signal transduction system (PilR/S) and an alternative sigma factor (σ54) that were shown by insertional inactivation to be required for the regulation of fimbrial biogenesis in D. nodosus. Western blots showed that in both pilR and rpoN mutants, fimbrial subunit production was significantly reduced by a process that was shown to occur at a PilR- and σ54-dependent promoter. The mutants lacked surface fimbriae, which were shown to be required for the adherence of D. nodosus cells to tissue culture monolayers. The reduction in fimbrial subunit production in these mutants also resulted in a concomitant loss of the ability to secrete extracellular proteases. A maltose binding protein-PilR fusion protein was purified and was shown to bind specifically to a region located 234 to 594 bp upstream of the fimA transcriptional start point. To determine additional targets of PilR and σ54, genome-wide transcriptional profiling was performed using a whole-genome oligonucleotide microarray. The results indicated that PilR and σ54 regulated genes other fimA; these genes appear to encode surface-exposed proteins whose role in virulence is unknown. In conclusion, this study represents a significant advancement in our understanding of how the ability of D. nodosus to cause ovine footrot is regulated, as we have shown that the biogenesis of type IV fimbriae in D. nodosus is regulated by a σ54-dependent PilR/S system that also indirectly controls protease secretion. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Patten, NL, Seymour, JR & Mitchell, JG 2006, 'Flow cytometric analysis of virus-like particles and heterotrophic bacteria within coral-associated reef water', JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, vol. 86, no. 3, pp. 563-566.
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Using flow cytometry, two distinct populations of virus-like particles (VLP) and heterotrophic bacteria were defined within the 12 cm water layer immediately overlying healthy, diseased and dead acroporid corals. Bacterial abundances were similar in overlying water for all coral types, however, VLP were 30% higher above diseased corals than healthy or dead corals. Mean virus to bacteria ratios (VBR) were up to 30% higher above diseased corals than above healthy or dead coral or in distant water. Concomitant with increasing VLP concentrations within 5 cm of coral surfaces, VBR distributions were generally highest above healthy and diseased coral and depressed above dead coral. These results suggest fundamental shifts in the VLP and bacterial community in water associated with diseased corals.

Pauc, N, Phillips, MR, Aimez, V & Drouin, D 2006, 'Carrier diffusion processes near threading dislocations in GaN and GaN : Si characterized by low voltage cathodoluminescence', SUPERLATTICES AND MICROSTRUCTURES, vol. 40, no. 4-6, pp. 557-561.
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We present a low temperature study of GaN epilayers by means of low voltage cathodoluminescence (CL). We show that lowering the primary electrons accelerating voltage down to 1 kV allows imaging of single threading dislocations. By using monochromatic or panchromatic low voltage CL microscopy, it is possible to extract different diffusion lengths related to free excitons, bound excitons or donor-to-acceptor pair transitions. © 2006 Elsevier Ltd. All rights reserved.

Pauc, N, Phillips, MR, Aimez, V & Drouin, D 2006, 'Carrier recombination near threading dislocations in GaN epilayers by low voltage cathodoluminescence', Applied Physics Letters, vol. 89, no. 16, pp. 161905-161905.
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The authors present a low voltage cathodoluminescence (CL) study of as grown GaN and GaN:Si epilayers on sapphire. At 1kV they resolve individual threading dislocations on the sample surface at low temperature (5K), which appear as correlated dark spots. Analysis of CL intensity profiles across individual dislocation cores provides a direct measurement of the exciton and minority carrier diffusion lengths. Using this approach at 5K, an exciton diffusion length of 62±28nm was found for GaN:Si (∼3×1018cm−3) compared with 81±20nm for a nominally undoped n-type GaN (∼1×1016cm−3).

Paul, NA, Cole, L, De Nys, R & Steinberg, PD 2006, 'ULTRASTRUCTURE OF THE GLAND CELLS OF THE RED ALGA ASPARAGOPSIS ARMATA (BONNEMAISONIACEAE)¹', Journal of Phycology, vol. 42, no. 3, pp. 637-645.
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Localization of natural products in the gland cells of the tetrasporophyte of Asparagopsis armata Harvey was examined using light microscopy, epifluorescence microscopy, and TEM. A. armata produces a range of halogenated metabolites that deter herbivores and inhibit bacterial fouling. The halogenated metabolites accumulate as a refractile inclusion inside specialized gland cells and this inclusion was no longer produced when the alga was cultured without bromine. Gland cells are formed soon after the apical division and can occupy a large portion of the algal volume, up to 10% of some parts of the filament. TEM was carried out on cryofixed and freeze‐substituted samples. Ultrastructure studies revealed that gland cells are positioned inside the pericentral cell, originating from the axial cell wall. The refractile inclusion of these gland cells is comprised of numerous electron‐translucent vacuoles enclosed by an electron‐opaque matrix. Some contents of the inclusion autofluoresced under UV excitation by epifluorescence microscopy. Light microscopy further revealed that stalk‐like structures connected the gland cell to the outer wall of the pericentral cell. These stalk‐like structures may provide the mechanism for metabolite transfer to the algal surface. Gland cell walls are relatively thin, which in turn would aid the transfer of metabolites to the stalk‐like structure. These features of the gland cells provide essential clues to the production and storage of the halogenated metabolites in A. armata and offer new insights into a possible mechanism for their release.

Pearce, ND & Wand, MP 2006, 'Penalized Splines and Reproducing Kernel Methods', The American Statistician, vol. 60, no. 3, pp. 233-240.
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Two data analytic research areas - penalized splines and reproducing kernel methods - have become very vibrant since the mid-1990s. This article shows how the former can be embedded in the latter via theory for reproducing kernel Hilbert spaces. This connection facilitates cross-fertilization between the two bodies of research. In particular, connections between support vector machines and penalized splines are established. These allow for significant reductions in computational complexity, and easier incorporation of special structure such as additivity. © 2006 American Statistical Association.

Pernice, M, Deutsch, JS, Andouche, A, Boucher-Rodoni, R & Bonnaud, L 2006, 'Unexpected variation of Hox genes' homeodomains in cephalopods', MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 40, no. 3, pp. 872-879.
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Peters, PC, Thoni, C & Harry, EJ 2006, 'Unexpected photobleaching of Alexa 488 in a fixed bacterial sample during 2-photon excitation', BIOTECHNIC & HISTOCHEMISTRY, vol. 81, no. 2-3, pp. 105-106.
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A sample of fixed bacterial cells was examined by immunofluorescence microscopy using an Alexa 488 conjugated secondary antibody for visualization. Excitation using visible light confirmed the expected photostability of this fluorophore; however, when using 2-photon excitation, Alexa 488 was rapidly and substantially photobleached. The unexpected instability of Alexa 488 under certain conditions may have deleterious consequences if not anticipated and accommodated in experimental protocols.

Phillips, MR 2006, 'Cathodoluminescence microscopy and spectroscopy of opto-electronic materials', MICROCHIMICA ACTA, vol. 155, no. 1-2, pp. 51-58.
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Cathodoluminescence (CL) microscopy and spectroscopy are enabling techniques for the microcharacterisation of technologically important materials. Recent advances in SEM instrumentation have considerably expanded the microanalytical capabilities of the CL technique. In this paper, following a brief overview of the principles and practice of CL microscopy and spectroscopy, a number of examples are presented that demonstrate the utility of the technique for the microcharacterisation of advanced opto-electronic materials.

Phyu, YL, Warne, MSJ & Lim, RP 2006, 'Toxicity and bioavailability of atrazine and molinate to the freshwater fish (Melanotenia fluviatilis) under laboratory and simulated field conditions', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 356, no. 1-3, pp. 86-99.
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Pissuwan, D, Valenzuela, SM & Cortie, MB 2006, 'Therapeutic possibilities of plasmonically heated gold nanoparticles', TRENDS IN BIOTECHNOLOGY, vol. 24, no. 2, pp. 62-67.
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Nanoparticles of gold, which are in the size range 10-100 nm, undergo a plasmon resonance with light. This is a process whereby the electrons of the gold resonate in response to incoming radiation causing them to both absorb and scatter light. This effect can be harnessed to either destroy tissue by local heating or release payload molecules of therapeutic importance. Gold nanoparticles can also be conjugated to biologically active moieties, providing possibilities for targeting to particular tissues. Here, we review the progress made in the exploitation of the plasmon resonance of gold nanoparticles in photo-thermal therapeutic medicine. © 2005 Elsevier Ltd. All rights reserved.

Platen, E 2006, 'A benchmark approach to finance', MATHEMATICAL FINANCE, vol. 16, no. 1, pp. 131-151.
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This paper derives a unified framework for portfolio optimization, derivative pricing, financial modeling, and risk measurement. It is based on the natural assumption that investors prefer more rather than less, in the sense that given two portfolios with the same diffusion coefficient value, the one with the higher drift is preferred. Each such investor is shown to hold an efficient portfolio in the sense of Markowitz with units in the market portfolio and the savings account. The market portfolio of investable wealth is shown to equal a combination of the growth optimal portfolio (GOP) and the savings account. In this setup the capital asset pricing model follows without the use of expected utility functions, Markovianity, or equilibrium assumptions. The expected increase of the discounted value of the GOP is shown to coincide with the expected increase of its discounted underlying value. The discounted GOP has the dynamics of a time transformed squared Bessel process of dimension four. The time transformation is given by the discounted underlying value of the GOP. The squared volatility of the GOP equals the discounted GOP drift, when expressed in units of the discounted GOP. Risk-neutral derivative pricing and actuarial pricing are generalized by the fair pricing concept, which uses the GOP as numeraire and the real-world probability measure as pricing measure. An equivalent risk-neutral martingale measure does not exist under the derived minimal market model. © 2006 Blackwell Publishing Inc.

Platen, E 2006, 'Portfolio selection and asset pricing under a benchmark approach', PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, vol. 370, no. 1, pp. 23-29.
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The paper presents classical and new results on portfolio optimization, as well as the fair pricing concept for derivative pricing under the benchmark approach. The growth optimal portfolio is shown to be a central object in a market model. It links asset pricing and portfolio optimization. The paper argues that the market portfolio is a proxy of the growth optimal portfolio. By choosing the drift of the discounted growth optimal portfolio as parameter process, one obtains a realistic theoretical market dynamics. © 2006 Elsevier B.V. All rights reserved.

Platen, E & Heath, D 2006, 'Currency derivatives under a minimal market model', ICFAI Journal of Derivatives Markets, vol. 3, pp. 68-86.

Platten, JD, Cotsaftis, O, Berthomieu, P, Bohnert, H, Davenport, RJ, Fairbairn, DJ, Horie, T, Leigh, RA, Lin, H-X, Luan, S, Maeser, P, Pantoja, O, Rodriguez-Navarro, A, Schachtman, DP, Schroeder, JI, Sentenac, H, Uozumi, N, Very, A-A, Zhu, J-K, Dennis, ES & Tester, M 2006, 'Nomenclature for HKT transporters, key determinants of plant salinity tolerance', TRENDS IN PLANT SCIENCE, vol. 11, no. 8, pp. 372-374.
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Potas, JR, Zheng, Y, Moussa, C, Venn, M, Gorrie, CA, Deng, C & Waite, PME 2006, 'Augmented locomotor recovery after spinal cord injury in the athymic nude rat', JOURNAL OF NEUROTRAUMA, vol. 23, no. 5, pp. 660-673.
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The immune response contributes to ongoing secondary tissue destruction following spinal cord injury (SCI). Although infiltrating neutrophils and monocytes have been well studied in this process, T-cells have received less attention. The objective of thi

Poulton, CG, Koos, C, Fujii, M, Pfrang, A, Schimmel, T, Leuthold, J & Freude, W 2006, 'Radiation Modes and Roughness Loss in High Index-Contrast Waveguides', IEEE Journal of Selected Topics in Quantum Electronics, vol. 12, no. 6, pp. 1306-1321.
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We predict the scattering loss in rectangular high index-contrast waveguides, using a new variation of the classical approach of coupled-mode theory. The loss predicted by this three-dimensional (3-D) model is considerably larger than that calculated using previous treatments that approximate the true 3-D radiation modes with their two-dimensional counterparts. The 3-D radiation modes of the ideal waveguide are expanded in a series of cylindrical harmonics, and the coupling between the guided and radiation modes due to the sidewall perturbation is computed. The waveguide attenuation can then be calculated semianalytically. It is found that the dominant loss mechanism is radiation rather than reflection, and that the transverse electric polarization exhibits much larger attenuation than transverse magnetic polarization. The method also gives simple rules that can be used in the design of low-loss optical waveguides. The structural properties of sidewall roughness of an InGaAs/InP pedestal waveguide are measured using atomic force microscopy, and the measured attenuation is found to compare well with that predicted by the model. © 2006 IEEE.

Pushpamalar, V, Langford, SJ, Ahmad, M & Lim, YY 2006, 'Optimization of reaction conditions for preparing carboxymethyl cellulose from sago waste', Carbohydrate Polymers, vol. 64, no. 2, pp. 312-318.
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Qi, L, Leslie, LM & Speer, MS 2006, 'Climatology of cyclones over the southwest Pacific: 1992–2001', Meteorology and Atmospheric Physics, vol. 91, no. 1-4, pp. 201-209.
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Queck, S, Weitere, M, Moreno, AM, Rice, SA & Kjelleberg, S 2006, 'The role of quorum sensing mediated developmental traits in the resistance of Serratia marcescens biofilms against protozoan grazing', Environmental Microbiology, vol. 8, no. 6, pp. 1017-1025.
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SummaryResistance against protozoan grazers is a crucial factor that is important for the survival of many bacteria in their natural environment. However, the basis of resistance to protozoans and how resistance factors are regulated is poorly understood. In part, resistance may be due to biofilm formation, which is known to protect bacteria from environmental stress conditions. The ubiquitous organism Serratia marcescens uses quorum sensing (QS) control to regulate virulence factor expression and biofilm formation. We hypothesized that the QS system of S. marcescens also regulates mechanisms that protect biofilms against protozoan grazing. To investigate this hypothesis, we compared the interactions of wild‐type and QS mutant strains of S. marcescens biofilms with two protozoans having different feeding types under batch and flow conditions. Under batch conditions, S. marcescens forms microcolony biofilms, and filamentous biofilms are formed under flow conditions. The microcolony‐type biofilms were protected from grazing by the suspension feeder, flagellate Bodo saltans, but were not protected from the surface feeder, Acanthamoeba polyphaga. In contrast, the filamentous biofilm provided protection against A. polyphaga. The main findings presented in this study suggest that (i) the QS system is not involved in grazing resistance of S. marcescens microcolony‐type biofilms; (ii) QS in S. marcescens regulates antiprotozoan factor(s) that do not interfere with the grazing efficiency of the protozoans; and (iii) QS‐controlled, biofilm‐specific differentiation of filaments and cell chains in biofilms of S. marcescens provides an effici...

Rawson, CA, Lim, RP, Warne, MS & Doyle, CJ 2006, 'The effect of 17 beta-estradiol on the development of modified hemal spines in early-life stage Gambusia holbrooki', ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY, vol. 51, no. 2, pp. 253-262.
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The morphologic development of the gonopodium of male mosquitofish, Gambusia holbrooki, is essential for proper reproductive function and has previously been used as a biomarker for the presence of endocrine-disrupting chemicals (EDCs) in freshwater systems. The development of the gonopodium is accompanied by the modification of the hemal spines on the 14th, 15th, and 16th vertebrae. These form an anchor for the movement of the gonopodium, and their normal development is therefore critical. This development is under hormonal control. It has been hypothesized that the modification of the hemal spines may be used as an end point for understanding the effects of exposure of early-life stage fish to EDCs and to add to the understanding of the differential sensitivities of different life stages. Larval fish were exposed to concentrations (0, 20, 100, and 500 ng/L) of 17β-estradiol (E2) in two experiments using a flow-through system for 8 and 12 weeks. There was a general delay in the development of the three hemal spines when exposed to high concentrations of E2. However, this delay was not observed for all end points on a particular spine nor across all spines. Fish examined at 8 weeks postpartum showed a more extensive delay at high concentrations than those examined at 12 weeks postpartum, suggesting that later in the life cycle, high levels of exogenous E2 may be overcome by increasing levels of endogenous androgen. There was a decrease in the number of phenotypic male fish present in the 500-ng/L treatment at 12 weeks postpartum and an apparent decrease in the degree of sexual differentiation at high levels of E2 exposure. The results suggest that effects of EDC exposure begin very early in a fish's life cycle. © 2006 Springer Science+Business Media, Inc.

Reichel, MP & Ellis, JT 2006, 'If control of Neospora caninum infection is technically feasible does it make economic', VETERINARY PARASITOLOGY, vol. 142, no. 1-2, pp. 23-34.
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Recent work on Neospora caninum, a protozoan parasite that causes abortions in dairy cattle has focused on a number of different control options. Modelling has suggested the most effective options for control but the present paper argues that the most effective option might not necessarily be optimal from an economic point of view. Decision trees, using published quantitative data, were constructed to choose between four different control strategies. The costs of these interventions, such as 'test and cull', therapeutic treatment with a pharmaceutical, vaccination or 'doing nothing' were compared, and modelled, in the first instance, on the New Zealand and Australian dairy situation. It is argued however, that the relative costs in other countries might be similar and that only the availability of a registered vaccine will change the decision tree outcomes, as does the within-herd prevalence of N. caninum infection. To 'do nothing' emerged as the optimal economic choice for N. caninum infections/abortions up to a within-herd prevalence of 18%, when viewed over a 1-year horizon, or 21% when costs were calculated over a 5 years horizon. For a higher (≥21%) within-herd prevalence of N. caninum infection vaccination provided the best (i.e. most economic) strategy. Despite being the most efficacious solutions, 'test and cull' or therapeutic treatment never provided a viable economic alternative to vaccination or 'doing nothing'. Decision tree analysis thus provided clear outcomes in terms of economically optimal strategies. The same approach is likely to be applicable to other countries and the beef industry, with only minor changes expected in the relationships of decisions versus within-herd prevalence of N. caninum infection. © 2006 Elsevier B.V. All rights reserved.

Reimers, JR, Solomon, GC, Cai, Z-L, Hush, NS, Gagliardi, A, Frauenheim, T, Pecchia, A & Di Carlo, A 2006, 'Application of DFTB in molecular electronics', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 232, pp. 263-263.

Reimers, JR, Ulstrup, J, Meyer, TJ & Solomon, GC 2006, 'Preface - 'The molecules and methods of chemical, biochemical, and nanoscale electron transfer'', CHEMICAL PHYSICS, vol. 326, no. 1, pp. 1-2.
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Reimers, JR, Ulstrup, J, Meyer, TJ & Solomon, GC 2006, ''The molecules and methods of chemical, biochemical, and nanoscale electron transfer' - Preface', CHEMICAL PHYSICS, vol. 324, no. 1, pp. 1-2.
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Rodgers, KJ, Hume, PM, Morris, JGL & Dean, RT 2006, 'Evidence for L-dopa incorporation into cell proteins in patients treated with levodopa', JOURNAL OF NEUROCHEMISTRY, vol. 98, no. 4, pp. 1061-1067.
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Levodopa (L-dopa) is the most widely used agent for the symptomatic relief of Parkinson's disease. There is concern that chronic L-dopa treatment may be detrimental, with some studies suggesting that L-dopa may be neurotoxic. A potentially important mech

Rodgers, KJ, Watkins, DJ, Miller, AL, Chan, PY, Karanam, S, Brissette, WH, Long, CJ & Jackson, CL 2006, 'Destabilizing role of cathepsin S in murine atherosclerotic plaques', ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, vol. 26, no. 4, pp. 851-856.
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Objective - Lysosomal proteinases have been implicated in a number of pathologies associated with extracellular matrix breakdown. Therefore, we investigated the possibility that the lysosomal proteinase cathepsin S may be involved in atherosclerotic plaq

Rose, RM, Carruthers, A, Stauber, JL, Lim, RP & Blockwell, S 2006, 'Development of an acute toxicity test with the marine copepod acartia sinjiensis', Australasian Journal of Ecotoxicology, vol. 12, pp. 67-75.
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Few toxicity test protocols with tropical marine species are currently available in Australasia. In this study, an acute 48h immobilisation toxicity test was developed with an native marine copepod Acartia sinjiensis. This species is widley distributed in tropical and sub-tropical brackish waters in Australia and is an important component of marine food webs. A comparison of its sensitivity to other species shwoed that this copepod was amongst the most sensitive Australian species to copper

Ryan, KG, Hegseth, EN, Martin, A, Davy, SK, O'Toole, R, Ralph, PJ, McMinn, A & Thorn, CJ 2006, 'Comparison of the microalgal community within fast ice at two sites along the Ross Sea coast, Antarctica', ANTARCTIC SCIENCE, vol. 18, no. 4, pp. 583-594.
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Diverse microbial communities survive within the sea ice matrix and are integral to the energy base of the Southern Ocean. Here we describe initial findings of a four season survey (between 1999-2004) of community structure and biomass of microalgae within the sea ice and in the underlying water column at Cape Evans and Cape Hallett, in the Ross Sea, Antarctica as part of the Latitudinal Gradient Project. At Cape Evans, bottom-ice chlorophyll a levels ranged from 4.4 to 173 mg Chl a m-2. Dominant species were Nitzschia stellata, N. lecointei, and Entomoneis kjellmanii, while the proportion of Berkeleya adeliensis increased steadily during spring. Despite being obtained later in the season, the Cape Hallett data show considerably lower standing stocks of chlorophyll ranging from 0.11 to 36.8 mg Chl a m-2. This difference was attributed to a strong current, which may have ablated much of the bottom ice biomass and provided biomass to the water below. This loss of algae from the bottom of the ice may explain why the ice community contributed only 2% of the standing stock in the total water column. Dominant species at Cape Hallett were Nitzschia stellata, Fragilariopsis curta and Cylindrotheca closterium. The low biomass at Cape Hallett and the prevalence of smaller-celled diatoms in the bottom ice community indicate that the ice here is more typical of pack ice than fast ice. Further data will allow us to quantify and model the extent to which ice-driven dynamics control the structure and function of the sea ice ecosystem and to assess its resilience to changing sea ice conditions. © Antarctic Science Ltd.

Sabatti, C 2006, 'Comment', Journal of the American Statistical Association, vol. 101, no. 473, pp. 104-106.
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Sanchez-Camara, J, Booth, DJ, Murdoch, J, Watts, D & Turon, X 2006, 'Density, habitat use and behaviour of the weedy seadragon Phyllopteryx taeniolatus (Teleostei : Syngnathidae) around Sydney, New SouthWales, Australia', MARINE AND FRESHWATER RESEARCH, vol. 57, no. 7, pp. 737-745.
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The vulnerability of marine fish species, particularly those inhabiting coastal waters, is an increasingly important issue in marine conservation. Although the weedy seadragon Phyllopteryx taeniolatus (Lacepede, 1804), a syngnathid fish endemic to southern Australia, is legally protected in New South Wales, there are no studies on population density, habitat use and behaviour to support this protection. We investigated the abundance, sex ratios and distribution of the weedy seadragon at three sites near Sydney, Australia. The distribution, density and sex ratios of seadragons were temporally stable, suggesting no large-scale seasonal migrations. Estimated population densities varied among sites from 10 individuals per ha to 65 individuals per ha, with sex ratios close to 1:1. Survival rates from one encounter to the next (approximately weekly) were high, being slightly lower for males (0.985 ± 0.006, mean ± se) and females (0.987 ± 0.005) compared with juveniles (1.000 ± 0.000). All size classes and both sexes were most common near the border of kelp and sand except when exhibiting hiding behaviour, when they were more often found in kelp beds. Kelp beds were the least-used habitat when feeding. Pregnant males tended to hide more often than other groups and therefore were more frequently found in kelp and kelp patches. Seadragons tended to be solitary, although pairing and grouping behaviour was also observed. Results of the present study show that weedy seadragons are resident in the same area throughout the year and have a strong affinity with heavily weeded rock and/or sand habitat. It is therefore recommended that the current species-based protection laws be used in concert with habitat-protection zones as a necessary measure to ensure the conservation of weedy seadragon populations. © CSIRO 2006.

Sastraruji, T, Jatisatienr, A, Issakul, K, Pyne, SG, Ung, AT, Lie, W & Williams, MC 2006, 'Phytochemical studies on Stemona plants: Isolation of new tuberostemonine and stemofoline alkaloids', NATURAL PRODUCT COMMUNICATIONS, vol. 1, no. 10, pp. 813-818.
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Six new stemofoline alkaloids, (2`R)-hydroxystemofoline (5), (3`R)-stemofolenol (6), (3`S)-stemofolenol (7), 1`,2`-didehydrostemofoline-N-oxide (8), the first C19 stemofoline alkaloid, methylstemofoline (9), and the first glycosidated Stemona alkaloid, stemofolinoside (10), and three known alkaloids, (2`S)-hydroxystemofoline (2), (11Z)-1`,2`-didehydrostemofoline (3), and (11E)-1`,2`-didehydrostemofoline (4), have been isolated from a root extract of an unidentified Stemona species. The structure and relative configuration of these new alkaloids have been determined by spectral data interpretation and from semisynthetic studies.

Schael, S, Barate, R, Bruneliere, R, Buskulic, D, De Bonis, I, Decamp, D, Ghez, P, Goy, C, Jezequel, S, Lees, JP, Lucotte, A, Martin, F, Merle, E, Minard, MN, Nief, JY, Odier, P, Pietrzyk, B, Trocme, B, Bravo, S, Casado, MP, Chmeissani, M, Comas, P, Crespo, JM, Fernandez, E, Fernandez-Bosman, M, Garrido, L, Grauges, E, Juste, A, Martinez, M, Merino, G, Miquel, R, Mir, LM, Orteu, S, Pacheco, A, Park, IC, Perlas, J, Riu, I, Ruiz, H, Sanchez, F, Colaleo, A, Creanza, D, De Filippis, N, de Palma, M, Iaselli, G, Maggi, G, Maggi, M, Nuzzo, S, Ranieri, A, Raso, G, Ruggieri, F, Selvaggi, G, Silvestris, L, Tempesta, P, Tricomi, A, Zito, G, Huang, X, Lin, J, Ouyang, Q, Wang, T, Xie, Y, Xu, R, Xue, S, Zhang, J, Zhang, L, Zhao, W, Abbaneo, D, Bazarko, A, Becker, U, Boix, G, Bird, F, Blucher, E, Bonvicini, B, Bright-Thomas, P, Barklow, T, Buchmuller, O, Cattaneo, M, Cerutti, F, Ciulli, V, Clerbaux, B, Drevermann, H, Forty, RW, Frank, M, Greening, TC, Hagelberg, R, Halley, AW, Gianotti, F, Girone, M, Hansen, JB, Harvey, J, Jacobsen, R, Hutchcroft, DE, Janot, R, Jost, B, Knobloch, J, Kado, M, Lehraus, I, Lazeyras, P, Maley, R, Mato, P, May, J, Moutussi, A, Pepe-Altarelli, M, Ranjard, F, Rolandi, L, Schlatter, D, Schmitt, B, Schneider, O, Tejessy, W, Teubert, F, Tomalin, IR, Tournefier, E, Veenhof, R, Valassi, A, Wiedenmann, W, Wright, AE, Ajaltouni, Z, Badaud, F, Chazelle, G, Deschamps, O, Dessagne, S, Falvard, A, Ferdi, C, Fayolle, D, Gay, P, Guicheney, C, Henrard, P, Jousset, J, Michel, B, Monteil, S, Montret, JC, Pallin, D, Pascolo, JM, Perret, P, Podlyski, F, Bertelsen, H, Fernley, T, Hansen, JD, Hansen, JR, Hansen, PH, Kraan, AC, Lindahl, A, Mollerud, R, Nilsson, BS, Rensch, B, Waananen, A, Daskalakis, G, Kyriakis, A, Markou, C, Simopoulou, E, Siotis, I, Vayaki, A, Zachariadou, K, Blondel, A, Bonneaud, G, Brient, JC, Machefert, E, Rouge, A, Rumpf, M, Swynghedauw, M, Tanaka, R, Verderi, M, Videau, H, Ciulli, V, Focardi, E, Parrini, G, Zachariadou, K, Corden, M, Georgiopoulos, C, Antonelli, A, Antonelli, M, Bencivenni, G, Bologna, G, Bossi, F, Campana, P, Capon, G, Cerutti, F, Chiarella, V, Felici, G, Laurelli, P, Mannocchi, G, Murtas, GP, Passalacqua, L, Picchi, P, Colrain, P, Ten Have, I, Hughes, IS, Kennedy, J, Knowles, IG, Lynch, JG, Morton, WT, Negus, P, O'Shea, V, Raine, C, Reeves, P, Scarr, JM, Smith, K, Thompson, AS, Turnbull, RM, Wasserbaech, S & et al. 2006, 'Precision electroweak measurements on the Z resonance', PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, vol. 427, no. 5-6, pp. 257-454.
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Sedger, LM, Osvath, SR, Xu, X-M, Li, G, Chan, FK-M, Barrett, JW & McFadden, G 2006, 'Poxvirus Tumor Necrosis Factor Receptor (TNFR)-Like T2 Proteins Contain a Conserved Preligand Assembly Domain That Inhibits Cellular TNFR1-Induced Cell Death', Journal of Virology, vol. 80, no. 18, pp. 9300-9309.
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ABSTRACTThe poxvirus tumor necrosis factor receptor (TNFR) homologue T2 has immunomodulatory properties; secreted myxoma virus T2 (M-T2) protein binds and inhibits rabbit TNF-α, while intracellular M-T2 blocks virus-induced lymphocyte apoptosis. Here, we define the antiapoptotic function as inhibition of TNFR-mediated death via a highly conserved viral preligand assembly domain (vPLAD). Jurkat cell lines constitutively expressing M-T2 were generated and shown to be resistant to UV irradiation-, etoposide-, and cycloheximide-induced death. These cells were also resistant to human TNF-α, but M-T2 expression did not alter surface expression levels of TNFRs. Previous studies indicated that T2's antiapoptotic function was conferred by the N-terminal region of the protein, and further examination of this region revealed a highly conserved N-terminal vPLAD, which is present in all poxvirus T2-like molecules. In cellular TNFRs and TNF-α-related apoptosis-inducing ligand (TRAIL) receptors (TRAILRs), PLAD controls receptor signaling competency prior to ligand binding. Here, we show that M-T2 potently inhibits TNFR1-induced death in a manner requiring the M-T2 vPLAD. Furthermore, we demonstrate that M-T2 physically associates with and colocalizes with human TNFRs but does not prevent human TNF-α binding to cellular receptors. Thus, M-T2 vPLAD is a species-nonspecific dominant-negative inhibitor of cellular TNFR1 function. Given that the PLAD is conserved in all known poxvirus T2-like molecules, we predict that it plays an important function in each of these proteins. Moreover, that the vPLAD confers an important antiapoptotic function confirms this domain as a potential target in the development of the next generation of TNF-α/TNFR therapeutics.

Seery, CR, Gunthorpe, L & Ralph, PJ 2006, 'Herbicide impact on Hormosira banksii gametes measured by fluorescence and germination bioassays', ENVIRONMENTAL POLLUTION, vol. 140, no. 1, pp. 43-51.
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The innovative bioassay described here involves chlorophyll a fluorescence measurements of gametes from the macroalgae, Hormosira banksii, where gametes (eggs) were exposed to Diuron, Irgarol and Bromacil. Response was assessed as percent inhibition from control of effective quantum yield (ΔF/Fm′) of photosystem II, herein referred to as % PSII Inhibition. This was measured with the dual-channelled pulse amplitude modulated (PAM) fluorometer, ToxY-PAM. The fluorescence bioassay was run simultaneously with an established H. banksii germination bioassay to compare sensitivity, precision, and time-to-result. The fluorescence bioassay gave highly sensitive results evidenced by EC 50s (% PSII Inhibition) for Diuron, Irgarol and Bromacil being three, four and three orders of magnitude (respectively) lower than EC50s generated from the germination bioassays. Precision of the fluorescence bioassay was demonstrated with low coefficient of variations (<30%) for all three toxicants. With regard to time, the fluorescence bioassay gave results within 6 h, as opposed to more than 50 h for the germination bioassay. © 2005 Elsevier Ltd. All rights reserved.

Sekiya, M, Mulcahy, G, Irwin, JA, Stack, CM, Donnelly, SM, Xu, W, Collins, P & Dalton, JP 2006, 'Biochemical characterisation of the recombinant peroxiredoxin (FhePrx) of the liver fluke, Fasciola hepatica', FEBS LETTERS, vol. 580, no. 21, pp. 5016-5022.
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The parasitic helminth Fasciola hepatica secretes a 2-Cys peroxiredoxin (Prx) that may play important functions in host-parasite interaction. Recombinant peroxiredoxin (FhePrx) prevented metal-catalyzed oxidative nicking of plasmid DNA and detoxified hydrogen peroxide when coupled with Escherichia coli thioredoxin and thioredoxin reductase (kcat/Km = 5.2 × 105 M-1 s-1). Enzyme kinetic analysis revealed that the catalytic efficiency of FhePrx is similar to other 2-Cys peroxiredoxins; the enzyme displayed saturable enzyme Michaelis-Menten type kinetics with hydrogen peroxide, cumene hydroperoxide and t-butyl hydroperoxide, and is sensitive to concentrations of hydrogen peroxide above 0.5 mM. Like the 2-Cys peroxiredoxins from a related helminth, Schistosoma mansoni, steady-state kinetics indicate that FhePrx exhibits a saturable, single displacement-like reaction mechanism rather than non-saturable double displacement (ping-pong) enzyme substitution mechanism common to other peroxiredoxins. However, unlike the schistosome Prxs, FhePrx could not utilise reducing equivalents supplied by glutathione or glutathione reductase. © 2006 Federation of European Biochemical Societies.

Sessler, JL, Gross, DE, Cho, W-S, Lynch, VM, Schmidtchen, FP, Bates, GW, Light, ME & Gale, PA 2006, 'Calix[4]pyrrole as a Chloride Anion Receptor:  Solvent and Countercation Effects', Journal of the American Chemical Society, vol. 128, no. 37, pp. 12281-12288.
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Sessler, JL, Pantos, GD, Gale, PA & Light, ME 2006, 'Synthesis and Anion Binding Properties of N,N‘-Bispyrrol-2-yl-2,5-diamidopyrrole', Organic Letters, vol. 8, no. 8, pp. 1593-1596.
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Seymour, JR, Seuront, L, Doubell, M, Waters, RL & Mitchell, JG 2006, 'Microscale patchiness of virioplankton', JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, vol. 86, no. 3, pp. 551-561.
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The microscale spatial distributions of viruses were investigated in three contrasting environments including oligotrophic open ocean, eutrophic coastal and estuarine habitats. The abundances of two discrete populations of both viruses and heterotrophic bacteria were measured at spatial resolutions of between 1 and 5 cm using purpose-designed microscale sampling equipment and flow cytometric sample analysis. Within open water samples, virus distributions were characterized by non-normal distributions and by `hotspots' in abundance where concentrations varied by up to 17-fold. In contrast to patterns generally observed at larger spatiotemporal scales, there was no correlation between bacterial and viral abundance or correspondence between bacteria and virus hotspots within these samples. Consequently, strong hotspots and gradients in the virus:bacteria ratio (VBR) were also apparent within samples. Within vertical pro¢les taken from above the sediment water interface within a temperate mangrove estuary, distributions of planktonic viruses were characterized by gradients in abundance, with highest concentrations observed within the 1-2 cm immediately above the sediment surface, and virus distributions were correlated to bacterial abundance (P50.01). The patterns observed in these contrasting habitats indicate that microscale patchiness of virus abundance may be a common feature of the marine environment. This form of heterogeneity may have important implications for virus^host dynamics and subsequently in£uence microbial trophodynamics and nutrient cycling in the ocean.

Sharkhuu, T, Matthaei, KI, Forbes, E, Mahalingam, S, Hogan, SP, Hansbro, PM & Foster, PS 2006, 'Mechanism of interleukin‐25 (IL‐17E)‐induced pulmonary inflammation and airways hyper‐reactivity', Clinical & Experimental Allergy, vol. 36, no. 12, pp. 1575-1583.
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SummaryBackground IL‐25, a novel member of the IL‐17 cytokine family, promotes CD4+ T‐helper 2 lymphocyte‐like (Th type‐2) inflammatory responses in the lung. Although IL‐25 up‐regulates IL‐13 in the lung, the contribution of this and other type 2 cytokine signalling pathways to the induction and persistence of airways hyper‐reactivity (AHR) and allergic inflammation are unclear.Objective To determine the downstream factors employed by IL‐25 to induce Th type‐2 pulmonary inflammation and AHR.Methods IL‐25 was delivered to the airways of BALB/c mice by intra‐tracheal (i.t.) instillation and AHR and Th type‐2 inflammatory responses were characterized in wild type (WT) and Th type‐2‐cytokine and ‐signalling pathway‐deficient (−/−) mice.Results IL‐25 treatment resulted in AHR, eosinophilic inflammation, mucus hypersecretion and a progressive increase in the production of Th type‐2 cytokines in the lungs. Levels of arginase‐I (arg‐I) and eotaxin were also elevated by IL‐25 treatment. A significant reduction in AHR, and attenuation of mucus production was observed in IL‐25‐treated IL‐13−/−, IL‐4 receptor alpha (IL‐4Rα−/−)‐ and signal‐transducer‐and‐activator‐of‐transcription‐factor‐6 (STAT6−/−)‐deficient mice. AHR was also inhibited in IL‐4−/−‐ and IL‐5/eotaxin(1)−/−‐ deficient mice treated with IL‐25, however, mucus hypersecretion was not completely ablated. IL‐25 promoted Th type‐2 responses by directly acting on naïve T cells.Conclusion IL‐25 potently (single dose) induces sustained AHR and acute pulmonary inflammation with eosinophilia. IL‐25‐induced AHR is dependent on the production of Th...

Sheldon, CC, Finnegan, EJ, Dennis, ES & Peacock, WJ 2006, 'Quantitative effects of vernalization on FLC and SOC1 expression', PLANT JOURNAL, vol. 45, no. 6, pp. 871-883.
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Shemon, AN, Sluyter, R, Fernando, SL, Clarke, AL, Dao-Ung, L-P, Skarratt, KK, Saunders, BM, Tan, KS, Gu, BJ, Fuller, SJ, Britton, WJ, Petrou, S & Wiley, JS 2006, 'A Thr357 to Ser Polymorphism in Homozygous and Compound Heterozygous Subjects Causes Absent or Reduced P2X7 Function and Impairs ATP-induced Mycobacterial Killing by Macrophages', Journal of Biological Chemistry, vol. 281, no. 4, pp. 2079-2086.
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The P2X7 receptor is a ligand-gated cation channel that is highly expressed on mononuclear leukocytes and that mediates ATP-induced apoptosis and killing of intracellular pathogens. There is a wide variation in P2X7 receptor function between subjects, explained in part by four loss-of-function polymorphisms (R307Q, E496A, I568N, and a 5′-intronic splice site polymorphism), as well as rare mutations. In this study, we report the allele frequencies of 11 non-synonymous P2X7 polymorphisms and describe a fifth loss-of-function polymorphism in the gene (1096C → G), which changes Thr357 to Ser (T357S) with an allele frequency of 0.08 in the Caucasian population. P2X7 function was measured by ATP-induced ethidium+ influx into peripheral blood lymphocytes and monocytes and, when compared with wild-type subjects, was reduced to 10-65% in heterozygotes, 1-18% in homozygotes, and 0-10% in compound heterozygotes carrying T357S and a second loss-of-function polymorphism. Overexpression of the T357S mutant P2X7 in either HEK-293 cells or Xenopus oocytes gave P2X7 function of ∼50% that of wild-type constructs. Differentiation of monocytes to macrophages, which also up-regulates P2X 7, restored P2X7 function to near normal in cells heterozygous for T357S and to a value 50-65% of wild-type in cells homozygous for T357S or compound heterozygous for T357S/E496A. However, macrophages from subjects that are compound heterozygous for either T357S/R307Q or T357S/stop codon had near-to-absent P2X7 function. These functional deficits induced by T357S were paralleled by impaired ATP-induced apoptosis and mycobacteria killing in macrophages from these subjects. Lymphocytes, monocytes, and macrophages from subjects homozygous for T357S or compound heterozygous for T357S and a second loss-of-function allele have reduced or absent P2X 7 receptor function. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

Sherman, M, Apanasovich, TV & Carroll, RJ 2006, 'On estimation in binary autologistic spatial models', Journal of Statistical Computation and Simulation, vol. 76, no. 2, pp. 167-179.
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Siegle, JS, Hansbro, N, Herbert, C, Yang, M, Foster, PS & Kumar, RK 2006, 'Airway Hyperreactivity in Exacerbation of Chronic Asthma Is Independent of Eosinophilic Inflammation', American Journal of Respiratory Cell and Molecular Biology, vol. 35, no. 5, pp. 565-570.
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We have developed an animal model to investigate the mechanisms underlying an acute exacerbation of chronic asthma. Sensitized BALB/c mice were exposed to aerosolized ovalbumin, either as chronic low-level challenge (mass concentration ≈ 3 mg/m3) for 4 wk, a single moderate-level challenge (≈ 30 mg/m3), or chronic low-level followed by single moderate-level challenge (the acute exacerbation group). Compared with animals receiving chronic challenge alone, mice in the acute exacerbation group exhibited a more marked inflammatory response, with involvement of intrapulmonary airways and lung parenchyma, and increased numbers of lymphocytes and eosinophils in bronchoalveolar lavage fluid. They also developed airway hyperreactivity (AHR) to methacholine, demonstrable as increased transpulmonary resistance and decreased compliance. This pattern of AHR was absent in chronically challenged animals, but was also present in animals given single moderate-level challenge. However, compared with animals receiving a single moderate-level challenge, inflammation and AHR were induced more rapidly in the acute exacerbation group. Eosinophil-deficient GATA1 Δdbl mice exhibited undiminished AHR in the acute exacerbation model. We conclude that in mice with pre-existing airway lesions resembling mild chronic asthma, exposure to a moderately high concentration of inhaled antigen induces features of an acute exacerbation. The inflammatory response involves distal airways and is associated with a distinct pattern of AHR, which develops independent of the enhanced eosinophilic inflammation.

Skelding, KA, Hickey, DK, Horvat, JC, Bao, S, Roberts, KG, Finnie, JM, Hansbro, PM & Beagley, KW 2006, 'Comparison of intranasal and transcutaneous immunization for induction of protective immunity against Chlamydia muridarum respiratory tract infection', Vaccine, vol. 24, no. 3, pp. 355-366.
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Skrobot, M, Godlewski, M, Guziewicz, E, Kopalko, K & Phillips, MR 2006, 'Tuning of Color Chromaticity of Light Emission from ZnSe Films Grown on a GaAs Substrate by Atomic Layer Epitaxy', Acta Physica Polonica A, vol. 110, no. 3, pp. 359-367.
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Sloan, WT, Lunn, M, Woodcock, S, Head, IM, Nee, S & Curtis, TP 2006, 'Quantifying the roles of immigration and chance in shaping prokaryote community structure', ENVIRONMENTAL MICROBIOLOGY, vol. 8, no. 4, pp. 732-740.
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Naturally occurring populations of bacteria and archaea are vital to life on the earth and are of enormous practical significance in medicine, engineering and agriculture. However, the rules governing the formation of such communities are still poorly understood, and there is a need for a usable mathematical description of this process. Typically, microbial community structure is thought to be shaped mainly by deterministic factors such as competition and niche differentiation. Here we show, for a wide range of prokaryotic communities, that the relative abundance and frequency with which different taxa are observed in samples can be explained by a neutral community model (NCM). The NCM, which is a stochastic, birth-death immigration process, does not explicitly represent the deterministic factors and therefore cannot be a complete or literal description of community assembly. However, its success suggests that chance and immigration are important forces in shaping the patterns seen in prokaryotic communities. © 2005 Society for Applied Microbiology and Blackwell Publishing Ltd.

Solina, D, Lott, D, Tietze, U, Frank, O, Leiner, V & Schreyer, A 2006, 'The new neutron reflectometer NERO', Physica B: Condensed Matter, vol. 385-386, pp. 1167-1169.
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The year 2005 saw the opening of the new NEutron ReflectOmeter (NERO) at the GKSS research centre in Geesthacht, Germany for the investigation of magnetic and non-magnetic systems as well as soft matter nano-structures. NERO operates with a monochromatic beam of neutrons of wavelength 0.433 nm with a resolution better than 2%. An angular range of -20°<2θ<100° allows for both reflectometry and high-angle diffraction measurements to be made. NERO has both a position-sensitive detector and a pencil detector installed for flexibility when making specular and diffuse measurements. NERO has been designed to accommodate heavy-sample environments such as cryo-furnaces and various kinds of magnets. Polarization analysis is available for the investigation of magnetic nano-structures. A supermirror stack with a wide angular-acceptance range will be available in 2006 for time-efficient measurements of magnetic diffuse reflectivity. Further information and proposal forms can be obtained online at http//:genf.gkss.de. © 2006 Elsevier B.V. All rights reserved.

Solomon, GC, Gagliardi, A, Pecchia, A, Frauenheim, T, Di Carlo, A, Reimers, JR & Hush, NS 2006, 'Molecular origins of conduction channels observed in shot-noise measurements', NANO LETTERS, vol. 6, no. 11, pp. 2431-2437.
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Solomon, GC, Gagliardi, A, Pecchia, A, Frauenheim, T, Di Carlo, A, Reimers, JR & Hush, NS 2006, 'The symmetry of single-molecule conduction', JOURNAL OF CHEMICAL PHYSICS, vol. 125, no. 18.
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Solomon, GC, Gagliardi, A, Pecchia, A, Frauenheim, T, Di Carlo, A, Reimers, JR & Hush, NS 2006, 'Understanding the inelastic electron-tunneling spectra of alkanedithiols on gold', JOURNAL OF CHEMICAL PHYSICS, vol. 124, no. 9.
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Spatafora, JW, Sung, G-H, Johnson, D, Hesse, C, O'Rourke, B, Serdani, M, Spotts, R, Lutzoni, F, Hofstetter, V, Miadlikowska, J, Reeb, V, Gueidan, C, Fraker, E, Lumbsch, T, Lucking, R, Schmitt, I, Hosaka, K, Aptroot, A, Roux, C, Miller, AN, Geiser, DM, Hafellner, J, Hestmark, G, Arnold, AE, Budel, B, Rauhut, A, Hewitt, D, Untereiner, WA, Cole, MS, Scheidegger, C, Schultz, M, Sipman, H & Schoch, CL 2006, 'A five-gene phylogeny of Pezizomycotina', Mycologia, vol. 98, no. 6, pp. 1018-1028.
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Stark, D, Beebe, N, Marriott, D, Ellis, J & Harkness, J 2006, 'Evaluation of three diagnostic methods, including real-time PCR, for detection of Dientamoeba fragilis in stool specimens', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 44, no. 1, pp. 232-235.
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Dientamoeba fragilis is a protozoan parasite of humans that infects the mucosa of the large intestine and is associated with gastrointestinal disease. We developed a 5′ nuclease (TaqMan)-based real-time PCR assay, targeting the small subunit rRNA gene, for the detection of D. fragilis in human stool specimens and compared its sensitivity and specificity to conventional PCR and microscopic examination by a traditional modified iron-hematoxylin staining procedure. Real-time PCR exhibited 100% sensitivity and specificity. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Stark, DJ, Beebe, N, Marriott, D, Ellis, JT & Harkness, J 2006, 'Dientamoebiasis: clinical importance and recent advances', TRENDS IN PARASITOLOGY, vol. 22, no. 2, pp. 92-96.
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Dientamoeba fragilis, an unusual single-celled parasite that was described first in 1918, is found worldwide in the gastrointestinal tract of humans. D. fragilis has emerged from obscurity recently because it is now recognized as a common cause of chronic diarrhoea and is treatable with drugs. Recent molecular studies have described D. fragilis as having two genotypes. Diagnostic tests, based on conventional and real-time PCR, have been developed that will provide a rapid, sensitive and specific diagnosis of D. fragilis. These tests will also aid the elucidation of the host distribution and the life cycle of this pathogen. © 2005 Elsevier Ltd. All rights reserved.

Stark, DJ, Fotedar, R, Ellis, JT & Harkness, JL 2006, 'Locally acquired infection with Entamoeba histolytica in men who have sex with men in Australia', MEDICAL JOURNAL OF AUSTRALIA, vol. 185, no. 8, pp. 417-417.
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To the Editor: We report three cases of locally acquired Entamoeba histolytica infection in men who have sex with men (MSM) in Sydney, New South Wales. E. histolytica is an invasive pathogenic amoeba that can cause invasive intestinal and extraintestinal amoebiasis. Entamoeba dispar is morphologically identical but is considered non-pathogenic and non-invasive.1 The three patients presented with a 1â3-week history of diarrhoea and abdominal pain. Routine bacterial cultures were negative for pathogens. Ova, cyst and parasite investigations showed cysts and trophozoites of E. histolytica/dispar complex in permanently stained, fixed faecal smears. Stool samples were tested for E. histolytica and E. dispar by polymerase chain reaction (PCR), using a previously described method.2 All three patients were positive for E. histolytica by PCR; sequencing of the amplicons verified the presence of E. histolytica DNA.

Stelzer, S, Egan, S, Larsen, MR, Bartlett, DH & Kjelleberg, S 2006, 'Unravelling the role of the ToxR-like transcriptional regulator WmpR in the marine antifouling bacterium Pseudoalteromonas tunicata', Microbiology, vol. 152, no. 5, pp. 1385-1394.
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The dark-green-pigmented marine bacterium Pseudoalteromonas tunicata produces several target-specific compounds that act against a range of common fouling organisms, including bacteria, fungi, protozoa, invertebrate larvae and algal spores. The ToxR-like regulator WmpR has previously been shown to regulate expression of bioactive compounds, type IV pili and biofilm formation phenotypes which all appear at the onset of stationary phase. In this study a comparison of survival under starvation or stress between the wild-type P. tunicata strain and a wmpR mutant (D2W2) does not suggest a role for WmpR in regulating starvation- and stress-resistant phenotypes such as those that may be required in stationary phase. Both proteomic [2-dimensional PAGE (2D-PAGE)] and transcriptomic (RNA arbitrarily primed PCR) studies were used to discover members of the WmpR regulon. 2D-PAGE identified 11 proteins that were differentially expressed by WmpR. Peptide sequence data were obtained for six of these proteins and identified using the draft P. tunicata genome as being involved in protein synthesis, amino acid transamination and ubiquinone biosynthesis, as well as hypothetical proteins. The transcriptomic analysis identified three genes significantly up-regulated by WmpR, including a TonB-dependent outer-membrane protein, a non-ribosomal peptide synthetase and a hypothetical protein. Under iron-limitation the wild-type showed greater survival than D2W2, indicating the importance of WmpR under these conditions. Results from these studies show that WmpR controls the expression of genes encoding proteins involved in iron acquisition and uptake, amino acid metabolism and ubiquinone biosynthesis in addition to a number of proteins with as yet unknown functions.

Stevens, JR & Wallman, JF 2006, 'The evolution of myiasis in humans and other animals in the Old and New Worlds (part I): phylogenetic analyses', Trends in Parasitology, vol. 22, no. 3, pp. 129-136.
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Stevens, JR, Wallman, JF, Otranto, D, Wall, R & Pape, T 2006, 'The evolution of myiasis in humans and other animals in the Old and New Worlds (part II): biological and life-history studies', Trends in Parasitology, vol. 22, no. 4, pp. 181-188.
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Stones, RW, Padmadas, SS, Guo, S, Brown, JJ, Zhao, F & Li, B 2006, 'Dyspareunia, Urinary Sensory Symptoms, and Incontinence Among Young Chinese Women', Archives of Sexual Behavior, vol. 35, no. 5, pp. 561-567.
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This study examined the prevalence of dyspareunia, urinary sensory symptoms, and urinary incontinence and explored their associations among sexually active Chinese women aged 1534 years. Data from 3,150 women were analyzed from a survey undertaken during 2003 in 30 counties in China as part of the United Nations Population Fund Country Program. The overall prevalence of dyspareunia was 4.7%. Urinary pain, burning or frequency was reported by 8.5%, 6.2% reported urinary incontinence, and 2.3% reported both sets of urinary symptoms. The prevalence of urinary incontinence, both alone and in combination with sensory symptoms, increased in a linear manner with age. Dyspareunia was associated with early sexual debut, primary level of education, and membership of minority ethnic communities. Urinary sensory symptoms and incontinence were more common among those reporting early sexual debut, those with less schooling, and women engaged in agricultural and manual unskilled occupations. Urinary incontinence was more common among women who had had a previous vaginal delivery compared to nulliparous women. Dyspareunia was strongly associated with the presence of urinary symptoms, particularly among those with both sensory symptoms and incontinence (26.8%). Nearly a quarter of women who had dyspareunia had sought treatment but fewer had done so for urinary incontinence. Dyspareunia and urinary symptoms show distinct but overlapping patterns of association with demographic variables. The findings indicate unmet need for assessment and advice about these symptoms in womens reproductive health programs.

Suggett, DJ, Maberly, SC & Geider, RJ 2006, 'Gross photosynthesis and lake community metabolism during the spring phytoplankton bloom', Limnology and Oceanography, vol. 51, no. 5, pp. 2064-2076.
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Daily productivity determinations of linear photosynthetic electron transfer and of net and gross inorganic CO2 uptake were determined in situ throughout a 6-week sampling period of the spring phytoplankton bloom in Esthwaite Water in the English Lake Di

Suggett, DJ, Moore, CM, Marañón, E, Omachi, C, Varela, RA, Aiken, J & Holligan, PM 2006, 'Photosynthetic electron turnover in the tropical and subtropical Atlantic Ocean', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 53, no. 14-16, pp. 1573-1592.
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Photosynthetic electron transport directly generates the energy required for carbon fixation and thus underlies the aerobic metabolism of aquatic systems. We determined photosynthetic electron turnover rates, ETRs, from ca. 100 FRR fluorescence water-column profiles throughout the subtropical and tropical Atlantic during six Atlantic Meridional Transect cruises (AMT 6, MayJune 1998, to AMT 11, SeptemberOctober 2000). Each FRR fluorescence profile yielded a water-column ETR-light response from which the maximum electron turnover rate (ETRRCIImax), effective absorption (s PSII) and light saturation parameter (E k) specific to the concentration of photosystem II reaction centres (RCIIs) were calculated. ETRRCIImax and E k increased whilst s PSII decreased with mixed-layer depth and the daily integrated photosynthetically active photon flux when all provinces were considered together. These trends suggested that variability in maximum ETR can be partly attributed to changes in effective absorption. Independent bio-optical measurements taken during AMT 11 demonstrated that s PSII variability reflects taxonomic and physiological differences in the phytoplankton communities. ETRRCIImax and Ek, but not sPSII, remained correlated with mixed-layer depth and daily integrated photosynthetically active photon flux when data from each oceanic province were considered separately, indicating a decoupling of electron turnover and carbon fixation rates within each province. Comparison of maximum ETRs with 14C-based measurements of Pmax further suggests that light absorption and C fixation are coupled to differing extents for the various oligotrophic Atlantic provinces. We explore the importance of quantifying RCII concentration for determination of ETRs and interpretation of ETR-C fixation coupling.

Sukparungsee, S & Novikov, A 2006, 'On EWMA procedure for detection of a change in observation via Martingale approach', KMITL Science Journal, vol. 6, no. 2a, pp. 373-380.
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Using martingale technique wepresent analytic approximation and exact lower bounds for the expectation of the first passage times of an Exponentially Weighted Moving Average (EWMA) procedure used for monitoring changes in distributions. Based on these results, a simple numericalprocedure for finding optimal parameters of EWMA for small changes in the means of observation processes is established.

Sun, N, Carroll, RJ & Zhao, H 2006, 'Bayesian error analysis model for reconstructing transcriptional regulatory networks', Proceedings of the National Academy of Sciences, vol. 103, no. 21, pp. 7988-7993.
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Transcription regulation is a fundamental biological process, and extensive efforts have been made to dissect its mechanisms through direct biological experiments and regulation modeling based on physical–chemical principles and mathematical formulations. Despite these efforts, transcription regulation is yet not well understood because of its complexity and limitations in biological experiments. Recent advances in high throughput technologies have provided substantial amounts and diverse types of genomic data that reveal valuable information on transcription regulation, including DNA sequence data, protein–DNA binding data, microarray gene expression data, and others. In this article, we propose a Bayesian error analysis model to integrate protein–DNA binding data and gene expression data to reconstruct transcriptional regulatory networks. There are two unique aspects to this proposed model. First, transcription is modeled as a set of biochemical reactions, and a linear system model with clear biological interpretation is developed. Second, measurement errors in both protein–DNA binding data and gene expression data are explicitly considered in a Bayesian hierarchical model framework. Model parameters are inferred through Markov chain Monte Carlo. The usefulness of this approach is demonstrated through its application to infer transcriptional regulatory networks in the yeast cell cycle.

Swift, PD, Smith, GB & Franklin, J 2006, 'Authors’ response to IR Edmonds and DJ Carter', Lighting Research & Technology, vol. 38, no. 1, pp. 30-31.
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Swift, PD, Smith, GB & Franklin, J 2006, 'Hotspots in cylindrical mirror light pipes: description and removal', LIGHTING RESEARCH & TECHNOLOGY, vol. 38, no. 1, pp. 19-31.
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The transmittance and irradiance distribution at the exit aperture of a cylindrical mirror light pipe (MLP) have been measured and calculated for the cases of collimated and diffuse inputs. MLPs are an example of a nonimaging optical system that can concentrate light, which may give rise to problematic hotspots and glare either on any diffuser used at the exit aperture or in the illuminated room. It is shown in this work that use of a diffuser at the entrance aperture overcomes these problems without a marked reduction in transmission of a typical MLP. © The Chartered Institute of Building Services Engineers 2006.

Szymańska, I, Radecka, H, Radecki, J, Gale, PA & Warriner, CN 2006, 'Ferrocene-substituted calix[4]pyrrole modified carbon paste electrodes for anion detection in water', Journal of Electroanalytical Chemistry, vol. 591, no. 2, pp. 223-228.
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Thompson, LS & Harry, EJ 2006, 'Alternative sigma factors: the master regulators', MICROBIOLOGY AUSTRALIA, vol. 27, no. 3, pp. 118-120.

Thompson, LS, Beech, PL, Real, G, Henriques, AO & Harry, EJ 2006, 'Requirement for the Cell Division Protein DivIB in Polar Cell Division and Engulfment during Sporulation inBacillus subtilis', Journal of Bacteriology, vol. 188, no. 21, pp. 7677-7685.
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ABSTRACTDuring spore formation inBacillus subtilis, cell division occurs at the cell pole and is believed to require essentially the same division machinery as vegetative division. Intriguingly, although the cell division protein DivIB is not required for vegetative division at low temperatures, it is essential for efficient sporulation under these conditions. We show here that at low temperatures in the absence of DivIB, formation of the polar septum during sporulation is delayed and less efficient. Furthermore, the polar septa that are complete are abnormally thick, containing more peptidoglycan than a normal polar septum. These results show that DivIB is specifically required for the efficient and correct formation of a polar septum. This suggests that DivIB is required for the modification of sporulation septal peptidoglycan, raising the possibility that DivIB either regulates hydrolysis of polar septal peptidoglycan or is a hydrolase itself. We also show that, despite the significant number of completed polar septa that form in this mutant, it is unable to undergo engulfment. Instead, hydrolysis of the peptidoglycan within the polar septum, which occurs during the early stages of engulfment, is incomplete, producing a similar phenotype to that of mutants defective in the production of sporulation-specific septal peptidoglycan hydrolases. We propose a role for DivIB in sporulation-specific peptidoglycan remodelling or its regulation during polar septation and engulfment.

Ton-That, C, Shard, AG, Dhanak, VR, Shinohara, H, Bendall, JS & Welland, ME 2006, 'Electronic structure of pristine and potassium-doped Y@C-82 metallofullerene', PHYSICAL REVIEW B, vol. 73, no. 20.
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Tooze, JA, Midthune, D, Dodd, KW, Freedman, LS, Krebs-Smith, SM, Subar, AF, Guenther, PM, Carroll, RJ & Kipnis, V 2006, 'A New Statistical Method for Estimating the Usual Intake of Episodically Consumed Foods with Application to Their Distribution', Journal of the American Dietetic Association, vol. 106, no. 10, pp. 1575-1587.
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Trevaskis, B, Hemming, MN, Peacock, WJ & Dennis, ES 2006, 'HvVRN2 responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status', PLANT PHYSIOLOGY, vol. 140, no. 4, pp. 1397-1405.
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Tucker, BJ, Booth, MA, Allan, GL, Booth, D & Fielder, DS 2006, 'Effects of photoperiod and feeding frequency on performance of newly weaned Australian snapper Pagrus auratus', Aquaculture, vol. 258, no. 1-4, pp. 514-520.
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An experiment was done to investigate the interactive effects of photoperiod (12L:12D or 18L:6D) and feeding frequency on the growth of newly weaned Australian snapper (mean weight = 0.14 g fish- 1). Feeding frequency was investigated over 4 levels with 2 feeds delivered during the first half of the daylight period (2FE), 2 feeds during the latter half of the daylight period (2FL), 4 (4F) or 8 (8F) evenly spaced feeds per daylight period. Each treatment combination was replicated in 6 tanks and each tank was stocked with a biomass of 15 g tank- 1 (i.e. approximately 108 fish tank- 1). Snapper were fed a constant ration of 10% BW day- 1 for 32 days, which was adjusted during the experiment according to frequent weight check procedures. Fish that died were counted but not replaced. Photoperiod, feeding frequency and the interaction of these factors significantly affected the individual harvest weight and thermal growth coefficient (TGC) of snapper. Interactions were driven by an increase in the magnitude of individual weight and TGC in snapper fed the 4F and 8F treatments and reared under the 18L:6D photoperiod, compared to snapper fed at the same frequencies but reared under the 12L:12D regime. Weight gain and TGC were best in snapper reared under a 18L:6D photoperiod regime and fed 8 feeds day- 1, however, weight gain did not plateau, suggesting further increases in weight gain may be possible if feeding frequencies greater then 8F are employed. Survival and apparent feed conversion ratio (AFCR) were significantly affected by feeding frequency alone, with significant improvements in snapper fed more frequently and in snapper fed twice daily but later in the same photoperiod (2FE < 2FL < 4F < 8F). Size heterogeneity (measured by the coefficient of variation for individual harvest weight, CVhw) was affected by photoperiod, and decreased significantly in snapper reared under the 18L:6D regime. Size heterogeneity was also affected by feeding frequency, howe...

Udall, JA, Swanson, JM, Haller, K, Rapp, RA, Sparks, ME, Hatfield, J, Yu, YS, Wu, YR, Dowd, C, Arpat, AB, Sickler, BA, Wilkins, TA, Guo, JY, Chen, XY, Scheffler, J, Taliercio, E, Turley, R, McFadden, H, Payton, P, Klueva, N, Allen, R, Zhang, DS, Haigler, C, Wilkerson, C, Suo, JF, Schulze, SR, Pierce, ML, Essenberg, M, Kim, H, Llewellyn, DJ, Dennis, ES, Kudrna, D, Wing, R, Paterson, AH, Soderlund, C & Wendel, JF 2006, 'A global assembly of cotton ESTs', GENOME RESEARCH, vol. 16, no. 3, pp. 441-450.
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Ulstrup, KE, Berkelmans, R, Ralph, PJ & van Oppen, MJH 2006, 'Variation in bleaching sensitivity of two coral species across a latitudinal gradient on the Great Barrier Reef: the role of zooxanthellae', MARINE ECOLOGY PROGRESS SERIES, vol. 314, pp. 135-148.
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The ability of corals to cope with environmental change, such as increased temperature, relies on the physiological mechanisms of acclimatisation and long-term genetic adaptation. We experimentally examined the bleaching sensitivity exhibited by 2 species of coral, Pocillopora damicornis and Turbinaria reniformis, at 3 locations across a latitudinal gradient of almost 6 degrees on the Great Barrier Reef (GBR), Target bleaching temperature was reached by using a ramping rate of 0.2 degrees C/h. We found that the bleaching sensitivity and recovery of both species differed between corals with clade D symbionts and those with clade C. However, in F damicornis bleaching susceptibility corresponded more strongly with latitude than with zooxanthella type and hence, temperature history, suggesting that local adaptation has occurred. The observed bleaching sensitivity was shown by a decrease in photochemical efficiency (F-v/F-m) in both species of coral. The rate of recovery in T reniformis was highest in explants containing clade D symbionts. The occurrence of clade D in the northern section of the GBR may reflect a long-term response to high sea water temperatures, while the presence of clade D in low abundance in T reniformis at Heralds Prong Reef and Percy Island may be a result of recent bleaching events.

Ulstrup, KE, Ralph, PJ, Larkum, AWD & Kuhl, M 2006, 'Intra-colonial variability in light acclimation of zooxanthellae in coral tissues of Pocillopora damicornis', MARINE BIOLOGY, vol. 149, no. 6, pp. 1325-1335.
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Unicomb, LE, Ferguson, J, Stafford, RJ, Ashbolt, R, Kirk, MD, Becker, NG, Patel, MS, Gilbert, GL, Valcanis, M & Mickan, L 2006, 'Low-Level Fluoroquinolone Resistance among Campylobacter jejuni Isolates in Australia', Clinical Infectious Diseases, vol. 42, no. 10, pp. 1368-1374.
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Upadhyaya, NM, Zhu, QH, Zhou, XR, Eamens, AL, Hoque, MS, Ramm, K, Shivakkumar, R, Smith, KF, Pan, ST, Li, SZ, Peng, KF, Kim, SJ & Dennis, ES 2006, 'Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice', THEORETICAL AND APPLIED GENETICS, vol. 112, no. 7, pp. 1326-1341.
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van der Heyde, HC, Nolan, J, Combes, V, Gramaglia, I & Grau, GE 2006, 'A unified hypothesis for the genesis of cerebral malaria: sequestration, inflammation and hemostasis leading to microcirculatory dysfunction', Trends in Parasitology, vol. 22, no. 11, pp. 503-508.
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van Reyk, DM, Brown, AJ, Hult'en, LM, Dean, RT & Jessup, W 2006, 'Oxysterols in biological systems: sources, metabolism and pathophysiological relevance', REDOX REPORT, vol. 11, no. 6, pp. 255-262.
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Oxysterols are the 27-carbon products of cholesterol oxidation by both enzymic and non-enzymic mechanisms. Their roles in cholesterol homeostasis, as well as in diseases in which oxidative damage and lipid peroxidation are implicated (e.g. atherosclerosis), have been investigated extensively. However, there are a number of important considerations regarding the physiological/pathophysiological functions and activities of the different oxysterols. First, in both normal and diseased tissues, the levels of oxysterols are very low when compared to the native sterol. Also, when assessing studies that have measured the levels of oxysterols in biological samples, there must be careful consideration as to the method of sample isolation, storage and sampling. This is because of the potential generation or loss of oxysterols during these procedures. Additionally, the relevance of in vitro studies which examine the effects of oxysterols upon cell function should be judged as to cellular oxysterol content (both in terms of the levels of oxysterol and the degree of esterification) resulting from the oxysterol reatment. We present evidence that the means by which oxysterol is delivered in vitro determines whether the oxysterol content reflects what has been found in vivo. Studies identifying the specific cellular targets of oxysterol indicate that several oxysterols may be regulators of cellular lipid metabolism via control of gene transcription. © W. S. Maney & Son Ltd.

Veal, TD, Piper, LFJ, Phillips, MR, Zareie, MH, Lu, H, Schaff, WJ & McConville, CF 2006, 'Scanning tunnelling spectroscopy of quantized electron accumulation at InxGa1-xN surfaces', PHYSICA STATUS SOLIDI A-APPLICATIONS AND MATERIALS SCIENCE, vol. 203, no. 1, pp. 85-92.
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Electron tunnelling spectroscopy has been used to investigate quantized levels in electron accumulation layers at InGaN surfaces. The tunnelling spectra exhibit a plateau in the normalized conductance which widens with increasing Ga-content, corresponding to the band gap of InGaN. The measured In xGa 1-xN band gaps (between ∼0.65 eV for x = 1 and 1.8 eV for x - 0.43) are consistent with the band gaps determined by previous optical absorption and cathodoluminescence spectroscopy. Additional structures in the spectra reflect the two-dimensional electronic subbands in the surface quantum well. The subband energies depend on Ga-content, bulk doping level and the resultant shape of the surface potential well. The tunnelling spectra are compared with calculations of the potential well, the charge-profile and the subband energies. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Verbout, SM, Brooks, HE, Leslie, LM & Schultz, DM 2006, 'Evolution of the U.S. Tornado Database: 1954–2003', Weather and Forecasting, vol. 21, no. 1, pp. 86-93.
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Abstract Over the last 50 yr, the number of tornadoes reported in the United States has doubled from about 600 per year in the 1950s to around 1200 in the 2000s. This doubling is likely not related to meteorological causes alone. To account for this increase a simple least squares linear regression was fitted to the annual number of tornado reports. A “big tornado day” is a single day when numerous tornadoes and/or many tornadoes exceeding a specified intensity threshold were reported anywhere in the country. By defining a big tornado day without considering the spatial distribution of the tornadoes, a big tornado day differs from previous definitions of outbreaks. To address the increase in the number of reports, the number of reports is compared to the expected number of reports in a year based on linear regression. In addition, the F1 and greater Fujita-scale record was used in determining a big tornado day because the F1 and greater series was more stationary over time as opposed to the F2 and greater series. Thresholds were applied to the data to determine the number and intensities of the tornadoes needed to be considered a big tornado day. Possible threshold values included fractions of the annual expected value associated with the linear regression and fixed numbers for the intensity criterion. Threshold values of 1.5% of the expected annual total number of tornadoes and/or at least 8 F1 and greater tornadoes identified about 18.1 big tornado days per year. Higher thresholds such as 2.5% and/or at least 15 F1 and greater tornadoes showed similar characteristics, yet identified approximately 6.2 big tornado days per year. Finally, probability distribution curves generated using kernel density estimation revealed that big tornado days were more likely to occur slightly earlier in the year and have a narrower distribution than any given tornado day.

Villavedra, M, To, J, Lemke, S, Broady, K, Melrose, J, Birch, D, Wallach, M & Raison, RL 2006, 'Carbohydrate epitopes are immunodominant at the surface of infectious Neoparamoeba spp', GLYCOBIOLOGY, vol. 16, no. 11, pp. 1143-1143.
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Waite, PME, Gorrie, CA, Herath, NP & Marotte, LR 2006, 'Whisker maps in marsupials: Nerve lesions and critical periods', ANATOMICAL RECORD PART A-DISCOVERIES IN MOLECULAR CELLULAR AND EVOLUTIONARY BIOLOGY, vol. 288A, no. 2, pp. 174-181.
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In the wallaby, whisker-related patterns develop over a protracted period of postnatal maturation in the pouch. Afferents arrive simultaneously in the thalamus and cortex from postnatal day (P) 15. Whisker-related patterns are first seen in the thalamus

Wallace, Kunkel, CS, Lennard, CJ, Stoilovic, M & Roux, CP 2006, 'Evaluation of 5-Methylthioninhydrin for the Detection of Fingermarks on Porous Surfaces and Comparison', Identification Canada, vol. 29, no. 1, pp. 4-13.
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The chemical 5-methylthioninhydrin was developed in the early 1990s for treating fingermarks on porous surfaces. Although many researchers showed the promise of this chemical during the years between 1990 and 1997, current research indicates that this reagent is sill not commonly used in casework. The current study assessed the commercially produced 5-methylthioninhydrin and compared it to the more commonly used reagents for detecting fingermarks on porous surfaces. The study found that 5-methylthioninhydrin is superior to ninhydrin; however, 1,2-indanedione produced a much stronger luminescence when used to treat latent fingermarks. Comparable fluorescence was produced with 5-methlthioninhydrin after metal salt treatment to DFO; the high background detracts from the ridge detail, however. The study concludes that although the cost of 5-methylthioninhydrin is higher than for conventional reagents, its use may be justified in some circumstances. The second article begins with an illustrated step-by-step demonstration of the technique for blending two exposures of the same scene. It involves the use of layers within Adobe Photoshop CS and then placing one exposure overtop of another exposure. The best qualities of each exposure are then used in the final print. The article then examines a few applied forensic applications of the blending of two exposures, including a technique for rescuing underexposed images. This issues section on Society Business (Canadian Identification Society) addresses Society awards, the Presidents message,' the 29th CIS Educational Conference, guidelines for authors, a listing of award winners and past presidents, and a listing of staff members

Walsh, CT, Pease, BC, Hoyle, SD & Booth, DJ 2006, 'Variability in growth of longfinned eels among coastal catchments of south‐eastern Australia', Journal of Fish Biology, vol. 68, no. 6, pp. 1693-1706.
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Longfinned eels Anguilla reinhardtii were captured by both fishery‐dependent and independent sampling methods from three rivers in New South Wales, south‐eastern Australia. Growth rates were examined in two zones (fresh water and tidal) in the Hacking, Hawkesbury and Clarence Rivers. Mean annual growth increments of sampled longfinned eels ranged from 30 to 60 mm year−1 using age‐length analyses and up to 167 mm year−1 based on tag‐recapture model estimates (GROTAG), with both methods showing high intra‐ and inter‐population variability. Growth was significantly faster in younger (5–15 years) fish than older (>15 years) fish, with females growing an average 10 mm year−1 faster than males of similar age and capture location. Longfinned eels found in tidal areas grew significantly faster than those in non‐tidal freshwater areas as a result of longer growing seasons in the highly productive estuarine habitats. Other possible factors influencing variability in growth rates for this species include habitat preference, density and fishing pressure.

Wassmer, SC, Cianciolo, GJ, Combes, V & Grau, GE 2006, 'LMP-420, un nouvelle approche thérapeutique pour le paludisme cérébral ?', médecine/sciences, vol. 22, no. 4, pp. 343-345.
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Wassmer, SC, Combes, V, Candal, FJ, Juhan-Vague, I & Grau, GE 2006, 'Platelets Potentiate Brain Endothelial Alterations Induced byPlasmodium falciparum', Infection and Immunity, vol. 74, no. 1, pp. 645-653.
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ABSTRACTBrain lesions of cerebral malaria (CM) are characterized by a sequestration ofPlasmodium falciparum-parasitized red blood cells (PRBC) and platelets within brain microvessels, as well as by blood-brain barrier (BBB) disruption. In the present study, we evaluated the possibility that PRBC and platelets induce functional alterations in brain endothelium. In a human brain endothelial cell line, named HBEC-5i, exhibiting most of the features demanded for a pathophysiological study of BBB, tumor necrosis factor (TNF) or lymphotoxin α (LT-α) reduced transendothelial electrical resistance (TEER), enhanced the permeability to 70-kDa dextran, and increased the release of microparticles, a recently described indicator of disease severity in CM patients. In vitro cocultures showed that platelets or PRBC can have a direct cytotoxic effect on activated, but not on resting, HBEC-5i cells. Platelet binding was required, as platelet supernatant had no effect. Furthermore, platelets potentiated the cytotoxicity of PRBC for TNF- or LT-α-activated HBEC-5i cells when they were added prior to these cells on the endothelial monolayers. This effect was not observed when platelets were added after PRBC. Both permeability and TEER were strongly affected, and the apoptosis rate of HBEC-5i cells was dramatically increased. These findings provide insights into the mechanisms by which platelets can be deleterious to the brain endothelium during CM.

Webb, JK, Shine, R & Christian, KA 2006, 'The adaptive significance of reptilian viviparity in the tropics: Testing the maternal manipulation hypothesis', EVOLUTION, vol. 60, no. 1, pp. 115-122.
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Phylogenetic transitions from oviparity to viviparity in reptiles generally have occurred in cold climates, apparently driven by selective advantages accruing from maternal regulation of incubation temperature. But why, then, are viviparous reptiles so successful in tropical climates? Viviparity might enhance fitness in the tropics via the same pathway as in the temperate zone, if pregnant female reptiles in the tropics maintain more stable temperatures than are available in nests (Shine's maternal manipulation hypothesis). Alternatively, viviparity might succeed in the tropics for entirely different reasons than apply in the temperate zone. Our data support the maternal manipulation hypothesis. In a laboratory thermal gradient, pregnant death adders (Acanthophis praelongus) from tropical Australia maintained less variable body temperatures (but similar mean temperatures) than did nonpregnant females. Females kept at a diel range of 25-31°C (as selected by pregnant females) gave birth earlier and produced larger offspring (greater body length and head size) than did females kept at 23-33°C (as selected by nonpregnant snakes). Larger body size enhanced offspring recapture rates (presumably reflecting survival rates) in the field. Thus, even in the tropics, reproducing female reptiles manipulate the thermal regimes experienced by their developing embryos in ways that enhance the fitness of their offspring. This similarity across climatic zones suggests that a single general hypothesis - maternal manipulation of thermal conditions for embryogenesis - may explain the selective advantage of viviparity in tropical as well as cold-climate reptiles. © 2006 The Society for the Study of Evolution. All rights reserved.

White, R, Phillips, MR, Thomas, P & Wuhrer, R 2006, 'In-situ investigation of discolouration processes between historic oil paint pigments', MICROCHIMICA ACTA, vol. 155, no. 1-2, pp. 319-322.
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Discolouring interactions between paint pigments have been observed since the mid 19th century. The source of some of these discolourations is the production of copper sulfides from an interaction between cadmium sulfide pigments and copper containing pigments. In this work, the discolouring interaction between cadmium yellow and malachite pigments was observed dynamically using the environmental scanning electron microscope (ESEM).

Wilhelm, SW, Carberry, MJ, Eldridge, ML, Poorvin, L, Saxton, MA & Doblin, MA 2006, 'Marine and freshwater cyanophages in a Laurentian Great Lake: Evidence from infectivity assays and molecular analyses of g20 genes', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, no. 7, pp. 4957-4963.
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While it is well established that viruses play an important role in the structure of marine microbial food webs, few studies have directly addressed their role in large lake systems. As part of an ongoing study of the microbial ecology of Lake Erie, we have examined the distribution and diversity of viruses in this system. One surprising result has been the pervasive distribution of cyanophages that infect the marine cyanobacterial isolate Synechococcus sp. strain WH7803. Viruses that lytically infect this cyanobacterium were identified throughout the western basin of Lake Erie, as well as in locations within the central and eastern basins. Analyses of the gene encoding the g20 viral capsid assembly protein (a conservative phylogenetic marker for the cyanophage) indicate that these viruses, as well as amplicons from natural populations and the ballast of commercial ships, are related to marine cyanophages but in some cases form a unique clade, leaving questions concerning the native hosts of these viruses. The results suggest that cyanophages may be as important in freshwater systems as they are known to be in marine systems. Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Williams, DBG & Lawton, M 2006, 'Aluminium triflate: an efficient recyclable Lewis acid catalyst for the aminolysis of epoxides', Tetrahedron Letters, vol. 47, no. 37, pp. 6557-6560.
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Williams, DBG, Ajam, M & Ranwell, A 2006, 'Highly Selective Metathesis of 1-Octene in Ionic Liquids', Organometallics, vol. 25, no. 12, pp. 3088-3090.
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Wood, CC, Robertson, M, Tanner, G, Peacock, WJ, Dennis, ES & Helliwell, CA 2006, 'The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 103, no. 39, pp. 14631-14636.
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In Arabidopsis thaliana, the promotion of flowering by cold temperatures, vernalization, is regulated via a floral-repressive MAIDS box transcription factor, FLOWERING LOCUS C (FLC). Vernalization leads to the epigenetic repression of FLC expression, a p

Wood, RA, Burchett, MD, Alquezar, R, Orwell, RL, Tarran, J & Torpy, F 2006, 'The potted-plant microcosm substantially reduces indoor air VOC pollution: I. Office field-study', WATER AIR AND SOIL POLLUTION, vol. 175, no. 1-4, pp. 163-180.
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Volatile organic compounds (VOCs) are major contaminants of indoor air, with concentrations often several times higher than outdoors. They are recognized as causative agents of 'building-related illness' or 'sick-building syndrome'. Our previous laboratory test-chamber studies have shown that the potted-plant/root-zone microorganism microcosm can eliminate high concentrations of air-borne VOCs within 24 hours, once the removal response has been induced by an initial dose. However, the effectiveness of the potted-plant microcosm in 'real-world' indoor spaces has never previously been tested experimentally. This paper reports the results of a field-study on the effects of potted-plant presence on total VOC (TVOC) levels, measured in 60 offices (12 per treatment), over two 5-9 week periods, using three planting regimes, with two 'international indoor-plant' species. Fourteen VOCs were identified in the office air. When TVOC loads in reference offices rose above 100 ppb, large reductions, of from 50 to 75% (to <100 ppb), were found in planted offices, under all planting regimes The results indicate that air-borne TVOC levels above a threshold of about 100 ppb stimulate the graded induction of an efficient metabolic VOC-removal mechanism in the microcosm. Follow-up laboratory dose-response experiments, reported in the following paper, confirm the graded induction response, over a wide range of VOC concentrations. The findings together demonstrate that potted-plants can provide an efficient, self-regulating, low-cost, sustainable, bioremediation system for indoor air pollution, which can effectively complement engineering measures to reduce indoor air pollution, and hence improve human wellbeing and productivity. © Springer 2006.

Woodcock, S, Curtis, TP, Head, IM, Lunn, M & Sloan, WT 2006, 'Taxa-area relationships for microbes: the unsampled and the unseen', ECOLOGY LETTERS, vol. 9, no. 7, pp. 805-812.
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The recent observation of a power-law relationship, S ∝ Az, between number of taxa, S, and area, A, for microbial eukaryotes and bacteria suggests that this is one of the few generic relationships in ecology, applicable to plants, animals and microbes. However, the rate of increase in the number of species with area varies from approximately the fourth (z = 0.26) to as little as the 50th root (z = 0.0019) in microbes. This is an enormous range for which no quantitative explanation has been proffered. We show by sampling from synthetic populations that the disparity between sample and community sizes in microbial community surveys means z can be considerably underestimated and accrual of rare taxa with increasing area will not be detectable. Significant microbial taxa-area relationships will only be observed when changes in community structure within samples correlate with area. Thus, the very low z values observed recently cannot be used as the sole evidence in support of any particular community theory of community assembly. More generally, this suggests that our search for patterns and laws in the microbial world will be profoundly influenced and, potentially distorted by the sample sizes that are typical of microbial community surveys. © 2006 Blackwell Publishing Ltd/CNRS.

Wu, X, Fang, W, Yamilov, A, Chabanov, AA, Asatryan, AA, Botten, LC & Cao, H 2006, 'Random lasing in weakly scattering systems', PHYSICAL REVIEW A, vol. 74, no. 5.
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Wu, YR, Machado, AC, White, RG, Llewellyn, DJ & Dennis, ES 2006, 'Expression profiling identifies genes expressed early during lint fibre initiation in cotton', PLANT AND CELL PHYSIOLOGY, vol. 47, no. 1, pp. 107-127.
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Wu, Z, Li, Y & Murray, BR 2006, 'Insular shifts in body size of rice frogs in the Zhoushan Archipelago, China', JOURNAL OF ANIMAL ECOLOGY, vol. 75, no. 5, pp. 1071-1080.
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1. Differences in body size between mainland and island populations have been reported for reptiles, birds and mammals. Despite widespread recognition of insular shifts in body size in these taxa, there have been no reports of such body size shifts in amphibians. 2. We provide the first evidence of an insular shift in body size for an amphibian species, the rice frog Rana limnocharis. We found significant increases in body size of rice frogs on most sampled islands in the Zhoushan archipelago when compared with neighbouring mainland China. 3. Large body size in rice frogs on islands was significantly related to increased population density, in both breeding and non-breeding seasons. Increases in rice frog density were significantly related to higher resource availability on islands. Increased resource availability on islands has led to higher carrying capacities, which has subsequently facilitated higher densities and individual growth rates, resulting in larger body size in rice frogs. We also suggest that large body size has evolved on islands, as larger individuals are competitively superior under conditions of harsh intraspecific competition at high densities. 4. Increases in body size in rice frogs were not related to several factors that have been implicated previously in insular shifts in body size in other taxa. We found no significant relationships between body size of rice frogs and prey size, number of larger or smaller frog species, island area or distance of islands from the mainland. 5. Our findings contribute to the formation of a broad, repeatable ecological generality for insular shifts in body size across a range of terrestrial vertebrate taxa, and provide support for recent theoretical work concerning the importance of resource availability for insular shifts in body size. © 2006 The Authors.

Xu, X & Cortie, MB 2006, 'Shape change and color gamut in gold nanorods, dumbbells, and dog bones', ADVANCED FUNCTIONAL MATERIALS, vol. 16, no. 16, pp. 2170-2176.
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It is shown here that deviations from a prolate ellipsoidal shape have a significant effect on the optical properties of gold nanorods. Transitions from rods to 'dumbbell'- or 'phi'-shaped particles lead to a shift in the longitudinal plasmon peak in the

Xu, X, Gibbons, TH & Cortie, MB 2006, 'Spectrally-selective gold nanorod coatings for window glass', GOLD BULLETIN, vol. 39, no. 4, pp. 156-165.
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The unique optical properties of gold nanorods, which exhibit tuneable absorption asa function of their aspect ratio, suggest that they might have potential applications in coatings for solar control on windows. Here we explore the properties of coatings produced by attaching gold nanorods to the surface of glass. Such coatings can attenuate solar radiation effectively, even at very low gold contents, but the figure-of-merit of our experimental coatings was close to unit, indicating that theyr are not spectrally selective. however, calculations are presented to show how coatings comprised of a blend of rods with aspect ratios of greater than 3 can produce coatings of up to 1.4. The maximum avlue possible for perfectly spectrally-selective coating in sunlight is 2.08. Unfortunately, the practical realisation of such coatings requires the further development of reliable methods to scale up the production of gold nanorods of longer aspect ratios.

Yang, M, Mattes, J, Hansbro, PM & Foster, PS 2006, 'Employment of microRNA profiles and RNA interference and antagomirs for the characterization and treatment of respiratory disease', Drug Discovery Today: Therapeutic Strategies, vol. 3, no. 3, pp. 325-332.
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The complex etiology and heterogeneity of respiratory diseases have made it difficult to design pharmacological reagents that show good efficacy across a diseased population. The discovery of small 'non-coding' RNA molecules (small interfering (si)- and micro-RNAs) that regulate the function of a gene or clusters of genes and the design of synthetic analogues of these molecules may provide new directions for the treatment and characterization of respiratory disorders. © 2006 Elsevier Ltd. All rights reserved.

York, PH, Booth, DJ, Glasby, TM & Pease, BC 2006, 'Fish assemblages in habitats dominated by Caulerpa taxifolia and native seagrasses in south-eastern Australia', MARINE ECOLOGY PROGRESS SERIES, vol. 312, pp. 223-234.
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Seagrass beds in estuaries are important habitats and nursery grounds for a great variety of fishes, including many economically important species. The introduction of the invasive green alga Caulerpa taxifolia could potentially threaten the seagrasses of south-eastern Australia. This study examined the implications of the spread of C. taxifolia on ichthyofauna in 2 estuaries in central New South Wales. Fish assemblages were compared among adjacent habitats of C. taxifolia and 2 seagrass species (Posidonia australis and Zostera capricorni). Fish were sampled using a small beam trawl to test for differences among habitats in (1) the species composition of the fish assemblages, (2) total abundance and species richness of fishes, and (3) abundances of major fish families. Fish assemblages separated into 3 significantly distinct groupings based on habitat. Total abundances of fishes were similar among habitats; however, species richness was lower in C. taxifolia. The fish assemblages in C. taxifolia were largely characterised by high abundances of gobiid fishes, similar to those in Z. capricorni, and few or no syngnathid and monacanthid species when compared to seagrass fish assemblages. This suggests that if C. taxifolia competitively replaces native seagrass beds in the estuaries of New South Wales, the resulting change in habitat may also cause a change in fish assemblages. This could reduce the abundances of some protected and economically important fish species but may also increase abundances of other opportunistic fishes. © Inter-Research 2006.

Yunusa, IAM, Eamus, D, DeSilva, DL, Murray, BR, Burchett, MD, Skilbeck, GC & Heidrich, C 2006, 'Fly-ash: An exploitable resource for management of Australian agricultural soils', FUEL, vol. 85, no. 16, pp. 2337-2344.
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Agricultural soils in Australia have inherent limitations of structural and nutritional nature that pose major constraints to crop productivity. These soils are still productive due to intensive management that involves routine treatments with lime and gypsum at significant costs both to the farmer and the environment. Production costs associated with these inputs average about 30% of the total cost of soil treatment. Furthermore, reserves of gypsum are under pressure. There is therefore an opportunity for the more than 13 million tonnes of coal combustion products (CCPs) produced annually by coal-fired power stations to be utilised in the management of agricultural soils. At present, about 70% of the ash is emplaced within landfills. In this paper we briefly describe the main constraints of major agricultural soils that could be ameliorated with fly-ash. We used a model to estimate that application of fine (<20 μm) fly-ash to the top 0.15 m coarse textured (sandy) soil would reduce hydraulic conductivity by 25% and so improve water-holding capacity. The same treatment of fine textured clayey soil with coarse (>20 μm) fly-ash would increase conductivity by up to 20%. We cite examples of studies that have shown beneficial use of coal-ash for crop production, including our ongoing glasshouse study in which fly-ash was found to increase early growth vigour and seed yield by 20% for canola (Brassica napus). There are several issues, including costs and regulation, and knowledge-gaps that need to be addressed before adoption of CCP for routine soil management. © 2006 Elsevier Ltd. All rights reserved.

Zareie, HM, McDonagh, AM, Edgar, J, Ford, MJ, Cortie, MB & Phillips, MR 2006, 'Controlled assembly of 1,4-phenylenedimethanethiol molecular nanostructures', CHEMISTRY OF MATERIALS, vol. 18, no. 9, pp. 2376-2380.
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We present here the first high-resolution scanning tunneling microscope images showing that 1,4-phenylenedimethanethiol forms mono- and multilayers on gold(111) substrates under particular solution-deposition conditions. The high-resolution images show that the deposition conditions strongly influence the type of surface structure formed. The molecular structures were also probed using molecular-etching techniques and through deposition and imaging of gold nanoparticles. The current-voltage (I-V) characteristics of the multilayer structures are significantly different from those of monolayers. For the first time, scanning electron microscopy experiments were used to investigate the homogeneity of larger surface areas of the surface structures. © 2006 American Chemical Society.

Zareie, MH, Barber, J & McDonagh, AM 2006, 'Structural Changes in Self-Assembled Monolayers Initiated by Ultraviolet Light', The Journal of Physical Chemistry B, vol. 110, no. 32, pp. 15951-15954.
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Self-assembled monolayers of 2-anthracenethiol and 2-naphthalenethiol on gold (111) were irradiated with low-power UV light. Scanning tunneling microscope images recorded in situ show unusual structural changes. In the case of 2-anthracenethiol, structur

Zeng, J, Dunlop, RA, Rodgers, KJ & Davies, MJ 2006, 'Evidence for inactivation of cysteine proteases by reactive carbonyls via glycation of active site thiols', BIOCHEMICAL JOURNAL, vol. 398, no. 2, pp. 197-206.
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Hyperglycaemia, triose phosphate decomposition and oxidation reactions generate reactive aldehydes in vivo. These compounds react non-enzymatically with protein side chains and N-terminal amino groups to give adducts and cross-links, and hence modified proteins. Previous studies have shown that free or protein-bound carbonyls inactivate glyceraldehyde-3-phosphate dehydrogenase with concomitant loss of thiol groups [Morgan, Dean and Davies (2002) Arch. Biochem. Biophys. 403, 259-269]. It was therefore hypothesized that modification of lysosomal cysteine proteases (and the structurally related enzyme papain) by free and protein-bound carbonyls may modulate the activity of these components of the cellular proteolytic machinery responsible for the removal of modified proteins and thereby contribute to a decreased removal of modified proteins from cells. It is shown that MGX (methylglyoxal), GO (glyoxal) and glycolaldehyde, but not hydroxyacetone and glucose, inhibit catB (cathepsin B), catL (cathepsin L) and catS (cathepsin S) activity in macrophage cell lysates, in a concentration-dependent manner. Protein-bound carbonyls produced similar inhibition with both cell lysates and intact macrophage cells. Inhibition was also observed with papain, with this paralleled by loss of the active site cysteine residue and formation of the adduct species S-carboxymethylcysteine, from GO, in a concentration-dependent manner. Inhibition of autolysis of papain by MGX, along with cross-link formation, was detected by SDS/PAGE. Treatment of papain and catS with the dialdehyde o-phthalaldehyde resulted in enzyme inactivation and an intramolecular active site cysteine-lysine cross-link. These results demonstrate that reactive aldehydes inhibit cysteine proteases by modification of the active site cysteine residue. This process may contribute to the accumulation of modified proteins in tissues of people with diabetes and age-related pathologies, including atherosclerosis, catar...

Zhang, HY, Gu, HY & Xi, YG 2006, 'Planning algorithm for WCDMA base station location problem based on cluster decomposition', Kongzhi yu Juece/Control and Decision, vol. 21, no. 2, pp. 213-216.
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An algorithm based on cluster decomposition is presented for large scale WCDMA base station positioning problem. A data matrix based on the signal gain of cellular networks and some criterion functions are designed for K means clustering. In the algorithm, the original problem is firstly decomposed into K sub-problems by K means clustering. Each sub-problem is then solved by integer programming. Finally, the solutions of K sub-problems are coordinated to form an approximate solution of the global problem. Simulation result shows the validity of this algorithm.

Zhao, Y, Staudenmayer, J, Coull, BA & Wand, MP 2006, 'General Design Bayesian Generalized Linear Mixed Models', Statistical Science, vol. 21, no. 1, pp. 35-51.
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Linear mixed models are able to handle an extraordinary range ofcomplications in regression-type analyses. Their most common use is to accountfor within-subject correlation in longitudinal data analysis. They are also thestandard vehicle for smoothing spatial count data. However, when treated infull generality, mixed models can also handle spline-type smoothing and closelyapproximate kriging. This allows for nonparametric regression models (e.g.,additive models and varying coefficient models) to be handled within the mixedmodel framework. The key is to allow the random effects design matrix to havegeneral structure; hence our label general design. For continuous responsedata, particularly when Gaussianity of the response is reasonably assumed,computation is now quite mature and supported by the R, SAS and S-PLUSpackages. Such is not the case for binary and count responses, wheregeneralized linear mixed models (GLMMs) are required, but are hindered by thepresence of intractable multivariate integrals. Software known to us supportsspecial cases of the GLMM (e.g., PROC NLMIXED in SAS or glmmML in R) or relieson the sometimes crude Laplace-type approximation of integrals (e.g., the SASmacro glimmix or glmmPQL in R). This paper describes the fitting of generaldesign generalized linear mixed models. A Bayesian approach is taken and Markovchain Monte Carlo (MCMC) is used for estimation and inference. In thisgeneralized setting, MCMC requires sampling from nonstandard distributions. Inthis article, we demonstrate that the MCMC package WinBUGS facilitates soundfitting of general design Bayesian generalized linear mixed models in practice.

Zhu, Q-H, Ramm, K, Eamens, AL, Dennis, ES & Upadhyaya, NM 2006, 'Transgene structures suggest that multiple mechanisms are involved in T-DNA integration in plants', PLANT SCIENCE, vol. 171, no. 3, pp. 308-322.
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To gain further understanding of the mechanisms involved in Agrobacterium-mediated genetic transformation and T-DNA integration, we analysed 156 T-DNA/rice, 69 T-DNAfr-DNA and 11T-DNA/vector backbone (VB) junctions, which included 171 left borders (LB) a

ZUO, Y 2006, 'Modified bottleneck-based procedure for large-scale flow-shop scheduling problems with bottleneck', Chinese Journal of Mechanical Engineering (English Edition), vol. 19, no. 03, pp. 356-356.
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Zuo, Y, Gu, HY & Xi, YG 2006, 'Bottleneck-based decomposition algorithm for large-scale flow shop scheduling problems', Kongzhi yu Juece/Control and Decision, vol. 21, no. 4, pp. 425-429.
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A bottleneck-based decomposition heuristic algorithm is proposed for dealing with computational complexity in large-scale flow shop scheduling problems. Based on the characteristic of bottleneck, the flow shop is decomposed into bottleneck and non-bottleneck machines. A single-machine scheduling problem with release time and delivery time is built for the bottleneck machine, which is solved optimally, while simple priority rules are used for scheduling the non-bottlenecks. The correlations between the bottleneck and non-bottleneck machines are coordinated by adjusting the release time and delivery time of jobs on the bottleneck machine. Simulation results show that the heuristic algorithm can obtain better solution in quite short time and be suitable to large-scale problems.

ZWIENIECKI, MA, STONE, HA, LEIGH, A, BOYCE, CK & HOLBROOK, NM 2006, 'Hydraulic design of pine needles: one‐dimensional optimization for single‐vein leaves', Plant, Cell & Environment, vol. 29, no. 5, pp. 803-809.
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ABSTRACTSingle‐vein leaves have the simplest hydraulic design possible, yet even this linear water delivery system can be modulated to improve physiological performance. We determined the optimal distribution of transport capacity that minimizes pressure drop per given investment in xylem permeability along the needle for a given length without a change in total water delivery, or maximizes needle length for a given pressure difference between petiole and needle tip. This theory was tested by comparative analysis of the hydraulic design of three pine species that differ in the length of their needles [Pinus palustris (Engl.) Miller, ∼50 cm; Pinus ponderosa Lawson & Lawson, ∼20 cm and Pinus rigida Miller, ∼5 cm]. In all three species, the distribution of hydraulic permeability was similar to that predicted by the optimum solution. The needles of P. palustris showed an almost perfect match between predicted and actual hydraulic optimum solution, providing evidence that vein design is a significant factor in the hydraulic design of pine leaves.

Akhavan, A, Mahmodi, H & Akhshani, A 1970, 'A New Image Encryption Algorithm Based on One-Dimensional Polynomial Chaotic Maps', COMPUTER AND INFORMATION SCIENCES - ISCIS 2006, PROCEEDINGS, 21st International Symposium on Computer and Information Sciences (ISCIS 2006), Springer Berlin Heidelberg, Istanbul, TURKEY, pp. 963-971.
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Akhshani, A, Mahmodi, H & Akhavan, A 1970, 'A Novel Block Cipher Based on Hierarchy of One-Dimensional Composition Chaotic Maps', 2006 International Conference on Image Processing, 2006 International Conference on Image Processing, IEEE.
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Allotta, A, Messaike, E, Smith, NF, Torpy, FR, Sutisno, M & Sztynda, T 1970, 'The Human Ear - An Adjunct for Identification', 18th Symposium on the Forensic Sciences, Fremantle, Australia, Fremantle, Australia.

Arnold, MD & Blaikie, RJ 1970, 'Modeling surface plasmon enhanced contact lithography', Bulletin American Physical Society: March meeting 2006, American Physical Society March Meeting 2006, American Physical Society, Baltimore, USA, p. G16.00006.

BENN, DE, RICHARDSON, AL, MARSH, DJ & ROBINSON, BG 1970, 'Genetic Testing in Pheochromocytoma‐ and Paraganglioma‐Associated Syndromes', Annals of the New York Academy of Sciences, 1st International Symposium on Pheochromocytoma, Wiley, Bethesda, MD, pp. 104-111.
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Abstract:  Genetic understanding of pheochromocytoma (PHEO) and paraganglioma (PGL) syndromes has recently expanded with the identification of the involvement of the mitochondrial complex II peptides, namely the succinate dehydrogenase subunit B (SDHB), subunit C (SDHC), and subunit D (SDHD). In patients with PHEO and/or PGL genetic testing for germline mutations in SDHD and SDHB has been recommended, in addition to the PHEO susceptibility genes VHL and RET. After careful clinical assessment of the patient, suspected familial disease may direct the clinician to the appropriate gene for testing. In the absence of obvious features of familial disease, the decision regarding the appropriate gene for testing is more difficult. Such testing can be costly and time consuming, but a rational prioritization of gene testing can streamline the process. Therefore in order to achieve this for apparently sporadic cases we propose a decision matrix based on site of tumor, functionality, and age at presentation.

Berry, K, Ferguson, J, Cobbin, DM, Zaslawski, CJ, Walsh, SP & Meier, PC 1970, 'Acupuncture and the treatment of alcohol and other drug addiction', WFAS World Conference on Acupuncture.

Berry, K, Ferguson, J, Cobbin, DM, Zaslawski, CJ, Walsh, SP & Meier, PC 1970, 'Integration fo CAM in Public Helath Care Services - A reflection on soem of the experiences from the UTS Alcohol and Other Drugs Clinical Placement Program as Rozelle Hospital', AACMA Annual Conference, Adelaide.

Blaber, M, Harris, N, Ford, M & Cortie, M 1970, 'Optimisation of absorption efficiency for varying dielectric spherical nanoparticles', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, QLD Australia, pp. 556-559.
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In this paper we compare the optical absorption for nanospheres made from a range of transition and alkali metals from Li (A=3) to Au (A=79). Numerical solutions to Mie theory were used to calculate the absorption efficiency, Q abs, for nanospheres varying in radii between 5 nm and 100 nm in vacuum. We show that, although gold is the most commonly used nanoparticle material, its absorption efficiency at the plasmon resonance is not as strong as materials such as the alkali metals. Of all the materials tried, potassium spheres with a radius of 21 nm have an optimum absorption efficiency of 14.7. In addition we also show that, unlike gold, the wavelength of the plasmon peak in other materials is sensitive to the sphere radius. In potassium the peak position shifts by 100 nm for spheres ranging from 5 nm to 65 nm, the shift is less than 10 nm for gold spheres. © 2006 IEEE.

Blaber, MG, Harris, N, Ford, MJ, Cortie, MB & IEEE 1970, 'Optimisation of absorption efficiency for varying dielectric spherical nanoparticles', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 61-64.

Botten, L, Hansen, R & de Sterke, CM 1970, 'Tight binding analysis of coupled photonic crystal waveguides', ACOFT/AOS 2006 - Australian Conference on Optical Fibre Technology/Australian Optical Society, 2006 Australian Conference on Optical Fibre Technology (ACOFT), IEEE, pp. 109-111.
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We apply a novel tight-binding analysis, not involving overlap integrals, to coupled photonic crystal waveguides. Our results show that the mode order can be the reverse of that for conventional guides, consistent with exact results.

Botten, LC, Asatryan, AA, Nicorovici, NA, Byme, MA, Dossou, KB, Norton, AH, McPhedran, RC, de Sterke, CM & White, TP 1970, 'Strengths and applications of semi-analytic techniques for photonic crystal modelling', NUSOD '06: PROCEEDINGS OF THE 6TH INTERNATIONAL CONFERENCE ON NUMERICAL SIMULATION OF OPTOELECTRONIC DEVICES, 6th International Conference on Numerical Simulation of Optoelectronic Devices, IEEE, Nanyang Technol Univ, Singapore, SINGAPORE, pp. 101-102.
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Botten, LC, Hansen, RA & De Sterke, CM 1970, 'Tight binding analysis of coupled photonic crystal waveguides', Optics InfoBase Conference Papers, Australian Conference on optical firbe technology & meeting f the Australian Optical Society, IEEE, Melbourne, pp. 109-111.
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We apply a novel tight-binding analysis to coupled PC waveguides. Our results do not involve overlap integrals and shows the mode order can be the reverse of that for conventional guides, consistent with exact results. © 2005 Optical Society of America.

Botten, LC, Hansen, RA & De, SC 1970, 'Tight binding analysis of coupled photonic waveguides', ACIFT/AOS 2006 - Proceedings, 2006 Conference on Lasers and Electro-Optics and 2006 Quantum Electronics and Laser Science Conference, IEEE, Sydney, Australia.
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We apply a novel tight-binding analysis to coupled PC waveguides. Our results do not involve overlap integrals and shows the mode order can be the reverse of that for conventional guides, consistent with exact results. © 2005 Optical Society of America.

Botten, LC, McPhedran, RC, Byrne, MA, Asatryan, AA, Nicorovici, NA, Norton, AH & De Sterke, CM 1970, 'The modelling of fano resonances in photonic crystal slabs', Optics InfoBase Conference Papers.
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A Bloch mode theory for diffraction of plane waves by planar PC slabs is outlined. The theory provides physical insight into the origin of Fano resonances, allowing a simple pole model to be deduced rigorously. © 2006 Optical Society of America.

Botten, LC, McPhedran, RC, Byrne, MA, Asatryan, AA, Nicorovici, NA, Norton, AH & de Sterke, CM 1970, 'The Modelling of Fano Resonances in Photonic Crystal Slabs', Photonic Metamaterials: From Random to Periodic, Photonic Metamaterials: From Random to Periodic, OSA.
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A Bloch mode theory for diffraction of plane waves by planar PC slabs is outlined. The theory provides physical insight into the origin of Fano resonances, allowing a simple pole model to be deduced rigorously. © 2006 Optical Society of America.

Bruti Liberati, N & Platen, E 1970, 'On the weak approximation of jump-diffusion processes with applications in finance', Proceedings of the VII Workshop on Quantitative Finance, VII Workshop on Quantitative Finance, University of Perugia, Italy, Perugia, Italy, pp. 1-96.

Bruti Liberati, N & Platen, E 1970, 'Predictor-corrector schemes for jump-diffusion processes.', International Conference on Numerical Methods for Finance, Dublin, Ireland.

Bruti Liberati, N & Platen, E 1970, 'Weak predictor-corrector methods for jump diffusions in finance', 5th National Symposium on Financial Mathematics, Melbourne, Australia.

Bruti Liberati, N, Nikitopoulos Sklibosios, C & Platen, E 1970, 'Heath Jarrow Morton equation for jump-diffusions under the benchmark approach', 2nd International Symposium on Economic Theory, Policy & Applications, 2nd International Symposium on Economic Theory, Policy & Applications, -, Athens, Greece.

Bruti Liberati, N, Nikitopoulos Sklibosios, C & Platen, E 1970, 'On the strong approximation of jump-diffusion processes', Stochastic Calculus and its Applications to Quantitative Finance and Electrical Engineering, Calgary, Canada.

Bruti-Liberati, N & Platen, E 1970, 'On Weak Predictor-Corrector Schemes for Jump-Diffusion Processes in Finance', Quantitative Methods in Finance 2007 Conference, Quantitative Methods in Finance 2006 Conference, -, Sydney, Australia.
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Event-driven uncertainties such as corporate defaults, operational failures or central bank announcements are important elements in the modelling of financial quantities. Therefore, stochastic differential equations (SDEs) of jump-diffusion type are often used in finance. We consider in this paper weak discrete time approximations of jump-diffusion SDEs which are appropriate for problems such as derivative pricing and the evaluation of risk measures. We present regular and jump-adapted predictor-corrector schemes with first and second order of weak convergence. The regular schemes are constructed on regular time discretizations that do not include jump times, while the jump-adapted schemes are based on time discretizations that include all jump times. A numerical analysis of the accuracy of these schemes when applied to the jump-diffusion Merton model is provided.

Byrne, M, Botten, L, Asatryan, A, Nicorovici, N, Norton, A, McPhedran, R & de Sterke, CM 1970, 'Fano resonances of photonic crystal slabs', ACOFT/AOS 2006 - Australian Conference on Optical Fibre Technology/Australian Optical Society, 2006 Australian Conference on Optical Fibre Technology (ACOFT), IEEE, Melbourne, pp. 87-89.
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Cankurtaran, B, Ford, M & Cortie, M 1970, 'Local Electromagnetic Fields Surrounding Gold Nano-Cap Particles', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, Australia, pp. 478-481.
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Using the discrete dipole approximation (DDA) the local electromagnetic fields surrounding gold nano-cap particles are investigated. Suitable k-vectors and polarization vectors of the incident light are used to determine the largest local electric field enhancement. The largest enhancement can be found for the 864 nm dipole resonance; where the field enhancement is approximately 30 000 times the applied field. The electric field contours surrounding the particle are used to assign the order of the surface plasmon resonances. © 2006 IEEE.

Cankurtaran, B, Ford, MJ, Cortie, M & IEEE 1970, 'Local electromagnetic fields surrounding gold nano-cap particles', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 15-18.

Chan, PY, Dunlop, RA & Rodgers, KJ 1970, 'Accumulation of hypochlorite modified LDL by human monocyte-derived macrophages causes a selective increase in expression of the cathepsin S gene.', FREE RADICAL RESEARCH, 13th Biennial Meeting of the Society-for-Free-Radical-Research-International, TAYLOR & FRANCIS LTD, Davos, SWITZERLAND, pp. S107-S107.

Cortie, M & Xu, X 1970, 'Control of Plasmon Resonance in Coatings of Gold Nanorods', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, QLD Australia, pp. 470-473.
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Gold nanorods manifest a tunable plasmon resonance with light in the visible to near-infrared regions of the spectrum, and have been proposed for use in spectrally selective coatings on glass. however, details of shape and packing density have a significant effect onthe optical properties of these nanoparticle coatings. Here we show how these effects can be controlled and exploited to produce a flexible spectral response.

Cortie, M, Laguna, A & Thompson, D 1970, 'Gold 2006 Highlights of 4th International Conference on the Science, Technology and Industrial Applications of Gold', Gold Bulletin, Springer Science and Business Media LLC, pp. 226-235.
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Cortie, M, Maaroof, A & Smith, GB 1970, 'Functional Metamaterials Based on Mesoscale Gold Sponges, Particulate Aggregates, and Their Composites with Dielectric Materials', MRS Proceedings, Springer Science and Business Media LLC, pp. 25-30.
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ABSTRACTThe optical properties of some nanoscale composites may deviate from that expected from a simple law of mixture of their individual components. In these cases the resulting structure can be considered to be a type of “metamaterial”. Here we explore some of the possibilities for nanoscale composite structures comprised of gold and VO2 – the latter being a functional material that undergoes a reversible insulator to metallic phase transition at 68°C. Two microstructures are examined: aggregates of gold nanoparticles surrounded by VO2 as the continuous phase, and its geometric inverse, mesoporous gold sponge with discontinuous VO2 inclusions. A composite, right-angled parallelepiped measuring 40×100×100 nm is taken as representative of the mixture, and calculations of the optical properties performed using the discrete dipole approximation code of Draine and Flatau. The VO2 matrix strongly attenuates the dipole-dipole plasmon resonance of the gold structure, and thermochromic switching of the remaining plasmon resonance occurs

Cortie, M, Maaroof, A, Mortari, A & Wuhrer, R 1970, 'Applications of Nano- and Mesoporous Gold in Electrodes and Electrochemical Sensors', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, QLD Australia, pp. 524-527.
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A nano- or- mesoporous sponge of Au is formed when the intermetallic compound AuAl2 is de-alloyed with NaOH. The large specific surface area of the sponge, and the unique surface chemical properties of Au indicate that this porous material might suefully serve as an electrode in capacitive sensors or other specialised electrochemical cells. Results for some prototype sensor and emergy storage systems are presented, and methods of controlling the nature of the porosity presented.

Coupland, MP & Crawford, K 1970, 'Many dimensions: the complex picture of student encounters with a computer algebra system', Identities Cultures & Learning Spaces, Mathematics Education Research Group of Australasia Inc, Canberra, pp. 155-156.

Davis, M, Smith, T, Laden, F, Hart, J, Ryan, L & Garshick, E 1970, 'Structural equation modeling in exposure assessment', EPIDEMIOLOGY, ISEE/ISEA 2006 Conference, LIPPINCOTT WILLIAMS & WILKINS, Paris, FRANCE, pp. S466-S466.
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de Sterke, CM, White, TP, Botten, LC & McPhedran, RC 1970, 'Low interface reflection of rod-type photonic crystals: a bottom up approach', SPIE Proceedings, Integrated Optoelectronic Devices 2006, SPIE, San Jose, CA.
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Deller, CA, Franklin, JB & Smith, GB 1970, 'Lighting simulations using smoothed LED profiles compared with measured profiles - art. no. 63370X', Sixth International Conference on Solid State Lighting, 6th International Conference on Solid State Lighting, SPIE-INT SOC OPTICAL ENGINEERING, San Diego, CA, pp. X3370-X3370.
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Dowd, A, Johansson, B, Armstrong, N, Ton-That, C & Phillips, M 1970, 'Cathodoluminescence as a method of extracting detailed information from nanophotonics systems: a study of silicon nanocrystals', PHOTONICS: DESIGN, TECHNOLOGY, AND PACKAGING II, Conference on Microelectronics - Design, Technology and Packaging II, SPIE-INT SOC OPTICAL ENGINEERING, Brisbane, AUSTRALIA.
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Drouin, D, Pauc, N, Phillips, M, Poissant, P, Delample, V, Souifi, A, Aimez, V & Beauvais, J 1970, 'SEM characterization of nanodevices and nanomaterials', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 690-+.

Drouin, D, Pauc, N, Phillips, M, Poissant, P, Delample, V, Souifi, A, Aimez, V & Beauvais, J 1970, 'SEM Characterization of Nanodevices and Nanomaterials', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane QLD Australia, pp. 596-599.
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The scanning electron microscope (SEM) can be used to study and characterize a wide variety of materials used in nanoelectronic and photonic applications. Several different techniques make use of this versatile tool. These include voltage contrast in secondary electron imaging, charge collection for semiconductor samples and cathodoluminescence. These techniques are important in device nanofabrication process development and nanomaterials characterization. © 2006 IEEE.

Esposito, V, Luong, B, Fronzi, M & Traversa, E 1970, 'Synthesis, Characterization, and Densification of Samaria Doped Ceria Ultra-Fine Powders', ECS Transactions, The Electrochemical Society, pp. 35-50.
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Nanometric Samaria 20% mol Doped Ceria (SDC20) powders were synthesized by a co-precipitation method. Nano-sized SDC20 powders (crystals size ~ 15 nm) were obtained by calcination at 600 {degree sign}C. The powders were formed by uniaxial pressure and then sintered. Sintering procedures were led both conventionally, at 1500 {degree sign}C for different sintering times (1, 5, 10 hours), and by fast firing process at different temperatures (1200, 1300, 1400, 1500, 1600 {degree sign}C for ~ 0.1 hour). As consequence of the thermal treatments, different resultant microstructures were observed. Electrochemical impedance spectroscopy (EIS) was used to determine total conductivity and to separate bulk and grain boundary impedance contributions. As expected, densification and electrical properties of the conventionally sintered samples showed to be mainly dependent on the average grain size. On the other hand, for the fast fired samples, lattice diffusion mechanism mainly controlled the densification, boundary arrangement and the resultant microstructures at various temperatures.

Ford, MJ, Hoft, RC, Gale, JD & Mcdonagh, AM 1970, 'A new class of self-assembled monolayers on gold using an alkynyl group as a linker', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane QLD, Australia, pp. 645-648.
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The geometry and energetics for adsorption of ethynylbenzene on Au(111) have been studied using Density Functional Theory. The alkynyl group, following removal of the terminal H atom, adsorbs covalently to the surface in the fcc hollow site with a bond energy of about 70 kcal.mol-1. Intermediate adsorption states are also possible via a hydrogen 1,2 shift to form a surface-bound vinylidene, or through the opening of the C-C triple bond without removing the hydrogen atom. © 2006 IEEE.

Ford, MJ, Hoft, RC, Gale, JD, McDonagh, AM & IEEE 1970, 'A new class of self-assembled monolayers on gold using an alkynyl group as a linker', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 11-14.

Ford, MJ, Kirkup, L, Gentle, A, Zareie, H & Cortie, M 1970, 'How reliable are scanning tunneling microscopy measurements of electron transport in molecules? - art. no. 603604', BioMEMS and NanoTechnology II, Conference on BioMEMS and Nanotechnology II, Spie-Int Society Optical Engineering, Brisbane, AUSTRALIA, pp. 3604-3604.
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Scanning tunneling microscopy measurements of tunneling through molecules adsorbed on a surface have been simulated using a standard empirical model based upon the Wentzel-Kramer-Brillouin method applied to tunneling through a barrier. The Gaussian noise inherent in these experiments has been added to the model data using a Monte Carlo technique. By generating multiple sets of current-voltage curves and fitting these to the model we have evaluated how reliably barrier height can be determined as a function of noise level. The results suggest that for constant percentage standard deviation in the noise greater than 5% the barrier height cannot be determined reliably. At this level, the standard deviation in the estimate of the barrier height is about 10%. Weighted fits give more reliable estimates of the barrier height. If the height of the tip above the molecule is known, so that the fit is only a single parameter the barrier height can be determined reliably even at percentage noise levels as high as 20%. However, in this case unweighted fits must be used otherwise the estimated value deviates by up to 15% from the true value. Data with constant absolute noise give similar results. The effects of experimental resolution have been evaluated in a similar manner and are shown to have a significant influence on the reliability. At a resolution of about 0.1% of full scale the standard deviation in the estimate of barrier height is only about 2% but increases rapidly to 10% for a resolution of about 1%.

Foulkes, J, Arnold, MD & Blaikie, RJ 1970, 'Fabrication and characterisation of solid-state electrochemical switches', 13th Electronics New Zealand Conference, ENZCON06, Electronics New Zealand Incorporated, Christchurch, New Zealand.

Freeman, D, Madden, S, Luther-Davies, B, Grillet, C, Asatryan, AA, Dossou, K, Byrne, MA & Botten, LC 1970, 'Fabrication of photonic crystal membranes in chalcogenide glasses by focused ion beam milling', Optics InfoBase Conference Papers, Conference on Optoelectronic and Microelectronic Materials and Devices, IEEE, Univ Queensland, Brisbane, AUSTRALIA, pp. 157-160.
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Free-standing films of AMTIR-1 chalcogenide glass have been patterned using a focused ion beam, to produce a photonic crystal. Optical measurements of Fano resonances indicated that the resulting structures had strongly modified guided modes. © 2005 Optical Society of America.

Freude, W, Maitra, A, Wang, J, Koos, C, Poulton, C, Fujii, M & Leuthold, J 1970, 'All-Optical Signal Processing WITH Nonlinear Resonant Devices', 2006 International Conference on Transparent Optical Networks, Proceedings of 2006 8th International Conference on Transparent Optical Networks, IEEE, Nottingham, ENGLAND, pp. 215-+.
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Fu, L, Jain, A, Xie, H, Cranfield, C & Gu, M 1970, 'Integration of a Double-clad Photonic Crystal Fiber, a GRIN Lens and a MEMS Mirror for Nonlinear Optical Endoscopy', Biomedical Optics, Biomedical Topical Meeting, OSA.
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We report on a prototype of a nonlinear optical endoscope based on a doubleclad photonic crystal fiber and a GRIN lens to improve the detection efficiency and a MEMS mirror to steer the beam. © 2006 Optical Society of America.

Fujii, M, Koos, C, Poulton, C, Leuthold, J & Freude, W 1970, 'Nonlinear FDTD Analysis and Experiment of FWM in InGaAsP-InP Optical Microresonator', 2006 International Conference on Numerical Simulation of Semiconductor Optoelectronic Devices, 2006 International Conference on Numerical Simulation of Semiconductor Optoelectronic Devices, IEEE, Nanyang Technol Univ, Singapore, SINGAPORE, pp. 107-+.
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Gagliardi, A, Solomon, GC, Pecchia, A, Di Carlo, A, Frauenheim, T, Reimers, JR & Hush, NS 1970, 'Simulations of inelastic tunnelling in molecular bridges', Nonequilibrium Carrier Dynamics in Semiconductors Proceedings, 14th International Conference on Nonequilibrium Carrier Dynamics in Semiconductors, SPRINGER-VERLAG BERLIN, Chicago, IL, pp. 183-186.

Gentle, A, Maaroof, A, Smith, G & Cortie, M 1970, 'Optical properties and applications to production of plasmonic thin film nanostructures of self-ordered columnar alumina arrays on glass.', PHOTONICS: DESIGN, TECHNOLOGY, AND PACKAGING II, Conference on Photonics - Design, Technology and Packaging II, SPIE, Brisbane, Australia, pp. 3816-3816.
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In this paper we report on new techniques for making self-ordered porous layers of alumina of varying aspect ratios on glass, without the use of lithographic or masking techniques. Use of RF etching in one of the hole forming steps and also when filling the holes with sputtered metal is shown to be advantageous over additional anodisation. These hole arrays have intrinsically interesting optical responses which will be reported, but their main use is for nano-patterning of subsequent deposited layers either as templates or as masks. High resolution images demonstrate the uniformity in nanohole diameter and in the spacing between holes, which can be achieved when care is used in production. While many nanostructured materials can be deposited using these Porous Anodic Alumina (PAA) templates we focus here on filling the vertical cylindrical holes with silver. Etching during hole filling leads to better-controlled structures and more efficient processes. Novel optical data on the resultant conducting columnar rings will be presented. Spectrally much sharper plasmon resonant features are found than those reported for classical and more random silver column and island arrays. The optical properties are analysed from an effective medium perspective using data from spectrophotometry and ellipsometry. Fitting this data gives modelled layer thickness and the vertical profile in close agreement with direct SEM imaging. The effective refractive indices of the silver columnar layer have interesting and potentially useful dispersion characteristics.

Godfrey, CM, Stensrud, DJ & Leslie, LM 1970, 'Soil temperature and moisture errors in Eta model analyses', 86th AMS Annual Meeting.

Grillet, C, Smith, C, Lee, M, Magi, E, Moss, D, Eggleton, B, Freeman, D, Madden, S, Luther-Davies, B, Byrne, M, Asatryan, A & Botten, L 1970, 'Nonlinear photonic crystals in chalcogenide for all-optical processing', ACOFT/AOS 2006 - Australian Conference on Optical Fibre Technology/Australian Optical Society, 2006 Australian Conference on Optical Fibre Technology (ACOFT), IEEE, Melbourne, pp. 109-111.
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We present the first experimental and theoretical results using nonlinear 2D photonic crystals in Chalcogenide. This scheme provides a promising platform to realize low power integrated all-optical switching and logic functions.

Gunning, SJ, Maggio, FJ, Valenzuela, S, Broady, KW, King, GK & Nicholson, GM 1970, 'Pharmacophore mapping of the κ-atracotoxins: selective insect potassium channel blockers that reveal a novel insecticide target', 15th World Congress on Animal, Plant and Microbial Toxins, Glasgow, Scotland.

Hoa, XD, Nicorovici, NA, McPhedran, RC, Botten, LC & Kirk, AG 1970, 'Rigorous modal method for the analysis of lamellar metallic gratings for surface plasmon resonance sensing', 2006 IEEE LEOS Annual Meeting Conference Proceedings, 2006 IEEE LEOS Annual Meeting, IEEE, Montreal, CANADA, pp. 376-+.
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Hoft, RC, Ford, MJ & Cortie, MB 1970, 'Effect of dipole moment on current-voltage characteristics of single molecules', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, QLD Australia, pp. 395-398.
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We perform empirical calculations of the tunneling current through various small organic molecules sandwiched between gold electrodes by using the Wenzel-Kramers-Brillouin (WKB) approximation. The barrier to tunneling is taken to be the work function of gold and calculated from a first principles electronic structure code. The current-voltage characteristics of these molecules are compared in the context of existing first principles and experimental results. In this model the surface dipole moment, induced by the adsorbed molecule, can have a significant effect on the current and hence dipole moments may be an important property for prediction of the conductance characteristics of a molecule. © 2006 IEEE.

Hoft, RC, Ford, MJ, Cortie, MB & IEEE 1970, 'Effect of dipole moment on current-voltage characteristics of single molecules', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 77-80.

Hoft, RC, Liu, J, Cortie, MB & Ford, MJ 1970, 'Electron tunneling through alkanedithiol molecules', BIOMEMS AND NANOTECHNOLOGY II, Conference on BioMEMS and Nanotechnology II, Spie-Int Society Optical Engineering, Brisbane, AUSTRALIA, pp. 3603-3603.
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We report on first principles calculations of the tunneling current across n-alkanedithiol molecules (n = 4,6,8,10,12) sandwiched between two Au {111} electrodes. The conductance drops exponentially with increased chain length with decay parameter βn= 0.9. The results are compared with scanning tunneling microscopy measurements on decanedithiol and with other n-alkanedithiol (n = 6,8,10) results in the literature. The theoretical results are found to be an order of magnitude larger than experimental values but follow the same trend. However, two additional, more realistic, geometries are modeled by changing the bond type and by combining the first-principles results with a Wentzel-Kramer-Brillouin (WKB) expression for tunneling across the air gap that is invariably present during scanning tunneling microscopy (STM) measurements. These results are more compatible with the experimental data.

Hong, MY, Turner, ND, Murphy, ME, Carroll, RJ, Bancroft, LK, Davidson, LA, Chapkin, RS & Lupton, JR 1970, 'Dietary fish oil down‐regulates pro‐inflammatory gene expression in colonocytes', The FASEB Journal, Experimental Biology 2006 Meeting, Wiley, San Francisco, CA, pp. A150-A151.
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Huete, AR, Miura, T, Kim, Y, Didan, K & Privette, J 1970, 'Assessments of multisensor vegetation index dependencies with hyperspectral and tower flux data', REMOTE SENSING AND MODELING OF ECOSYSTEMS FOR SUSTAINABILITY III, Conference on Remote Sensing and Modeling of Ecosystems for Sustainability III, SPIE-INT SOC OPTICAL ENGINEERING, San Diego, CA.
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Huete, AR, Running, S, Myneni, R & IEEE 1970, 'Monitoring Rainforest Dynamics in the Amazon with MODIS Land Products', 2006 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM, VOLS 1-8, IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IEEE, Denver, CO, pp. 263-265.
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Humphreys, WF, Seymour, JR & Mitchell, JG 1970, 'Stratification of microbial communities in an anchialine sinkhole', Romania.

Jin, D, Connally, R & Piper, J 1970, 'UV LED excited time-gated luminescence flow cytometry: concepts and experimental evaluation', Smart Medical and Biomedical Sensor Technology IV, Optics East 2006, SPIE, Boston, MA.
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Kabakova, IV & Sukhorukov, AP 1970, 'Optical beam reflection upon two-frequency noncollinear interaction in photorefractive crystals', Bulletin of the Russian Academy of Sciences: Physics, pp. 2002-2006.
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The effect of nonlinear reflection upon two-frequency noncollinear interaction of optical beams in photorefractive crystals was considered for the first time. Simple expression for the critical reflection angle was found in the geometrical-optics approximation. Numerical simulation confirms the theoretical result. © 2007 by Allerton Press, Inc.

Koos, C, Poulton, C, Jacome, L, Zimmermann, L, Leuthold, J & Freude, W 1970, 'Ideal Trajectory for Ultracompact Low-Loss Waveguide Bends', 2006 European Conference on Optical Communications, 2006 32nd European Conference on Optical Communications - (ECOC 2006), IEEE.
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The ideal trajectory for compact whispering gallery bends is derived analytically and verified by 3D- FDTD simulations and experiments. We predict bend losses below 0.1 dB for SOI waveguides with R=1.5 /urn which is supported experimentally.

Lapine, M, Nefedov, I, Saily, J & Tretyakov, S 1970, 'Artificial lines with exotic dispersion for phase shifters and delay lines', 2006 European Microwave Conference, 2006 European Microwave Conference, IEEE, pp. 427-430.
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We discuss various possibilities to design phase shifters with reduced frequency dispersion using combined sections of forward-wave and backward-wave transmission lines. It is shown that inclusion of backward-wave sections into a single transmission line always increases the total dispersion. On the other hand, we show that dispersion can be reduced by means of lines with positive anomalous dispersion and provide an example of such line. Furthermore, we report the theory and design of a novel phase shifter, based on parallel combined backward-forward transmission lines. The phase shifts, produced by this device, are characterized with negligible frequency dependence in a wide frequency range. We show that for an ideal performance, phase deviation can be less than 1° within a 20% bandwidth while excellent impedance matching is retained. We support these theoretical estimates by microwave circuit simulations and direct measurements, showing that the novel phase shifter can be easily implemented with simple electronic components. © 2006 EuMA.

Lapine, M, Nefedov, IS, Saily, J & Tretyakov, SA 1970, 'Artificial lines with exotic dispersion for phase shifters and delay lines', 2006 EUROPEAN MICROWAVE CONFERENCE, VOLS 1-4, 36th European Microwave Conference, IEEE, Manchester, ENGLAND, pp. 1823-+.

Liptser, R & Novikov, A 1970, 'Tail Distributions of Supremum and Quadratic Variation of Local Martingales', Springer Berlin Heidelberg, pp. 421-432.
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Lupton, DJR, Turner, DND, Braby, DL, Ford, DJ, Carroll, DRJ & Chapkin, DRS 1970, 'A combination of omega-3 fatty acids and a butyrate-producing fiber mitigates colon cancer development', 57th International Astronautical Congress, 57th International Astronautical Congress, American Institute of Aeronautics and Astronautics, pp. 101-110.
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Galactic cosmic radiation-induced cancer risk is a major limitation to long-duration missions, with colon cancer development being a likely target since it is the second leading cause of death from cancer in the United States today and strikes men and women equally. We tested if diet could act as a countermeasure against radiation-enhanced cancer in 560 male rats using a 2×2×2×3 factorial design (+ or - irradiation with 1 Gy, 1 GeV/nucleon Fe ions; 2 fats and 2 fibers; and 3 termination points). All rats were injected with a colon specific carcinogen (azoxymethane). A diet high in fish oil (omega 3 fatty acid source) combined with pectin (a fermentable fiber) was protective against radiation-induced cancer at each stage of the tumorigenic process (initiation, progression, and final tumor development). At the final tumor stage, the fish oil/pectin diet resulted in only 1/3 of the relative risk for tumor development as compared to the corn oil/cellulose or corn oil/pectin diets (P = 0.066). Fecal material was collected from rats during the tumorigenic process and mRNA extracted from exfoliated colon cells. This noninvasive technique (which is tested in humans) can detect changes in gene expression profiles over time, and used for early detection of cancer.

Malguth, E, Hoffmann, A, Phillips, M & Gehlhoff, W 1970, 'Fe-centers in GaN as candidates for spintronics applications', Materials Research Society Symposium Proceedings, Symposium on Progress in Semiconductor Materials V held at the 2005 MRS Fall Meeting, MATERIALS RESEARCH SOC, Boston, MA, pp. 219-224.
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The potential use of Fe doped GaN for spintronics applications requires a complete understanding of the electronic structure of Fe in all of its charge states. To address these issues, a set of 400 μm thick freestanding HVPE grown GaN:Fe crystals with different Fe-concentration levels ranging from 5×1017 cm-3 to 2×1020 cm -3 was studied by means of photoluminescence, photoluminescence excitation (PLE) and Fourier transform infrared (FTIR) transmission experiments. The Fe3+/2+ charge transfer (CT) level was determined to be at 2.86 ± 0.01 eV above the valence band maximum considerably lower than the previously reported value of 3.17 ± 0.10 eV. A bound state of the form (Fe2+, hVB) with a binding energy of 50 ± 10 meV has been established as an excited state of Fe3+. FTIR transmission measurements revealed an internal (5E - 5T2) transition of Fe2+ around 400 eV which, until now, was believed to be degenerate with the conduction band. Consequently, a second CT band was detected in PLE spectra. © 2006 Materials Research Society.

Malguth, E, Hoffmann, A, Phillips, M & Gehlhoff, W 1970, 'Fe-centers in GaN as candidates for spintronics applications', GaN, AIN, InN and Related Materials, Symposium on GaN, AIN, InN Related Materials, Materials Research Society, Boston, MA, pp. 131-136.
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The potential use of Fe doped GaN for spintronics applications requires a complete understanding of the electronic structure of Fe in all of its charge states. To address these issues, a sel of 400 μm thick freestanding HVPE grown GaN:Fe crystals with different Fe-concentration levels ranging from 5×1017 cm-3 to 2×1020 cm -3 was studied by means of photoluminescence. photoluminescence excitation (PLE) and Fourier transform infrared (FTIR) transmission experiments. The Fe3+/2+ charge transfer (CT) level was determined to be at 2.80 ± 0.01 eV above the valence band maximum considerably lower than the previously reported value of 3.17 ± 0.10 eV. A bound state of the form (Fe2+, l1VB) with a binding energy of 50 ± 10 meV has been established as an excited state of Fe3+, FTIR transmission measurements revealed an internal (5E - 5T2) transition of Fe2+ around 400 eV which, until now, was believed to be degenerate with the conduction band. Consequently, a second CT band was detected in PLE spectra. © 2006 Materials Research Society.

McBean, K, Phillips, M & Drouin, D 1970, 'Effects of Lithium Doping and Post-processing on the Cathodoluminescence of Zinc Oxide Nanoparticles', Microscopy and Microanalysis, Microscopy & Microanalysis, Oxford University Press (OUP), Chicago, USA, pp. 1510-1511.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006

McCracken, J, Diaz, A, Castro, E, Edwards, R, Ryan, L, Schwartz, J, Chowdhury, Z & Smith, KR 1970, 'Biomass smoke exposure among Guatemalan infants participating in a randomized trial of chimney stoves', EPIDEMIOLOGY, ISEE/ISEA 2006 Conference, LIPPINCOTT WILLIAMS & WILKINS, Paris, FRANCE, pp. S35-S36.
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McGinnis, JM, Birt, DF, Brannon, PM, Carroll, RJ, Gibbons, RD, Hazzard, WR, Kamerow, DB, Levin, B, Ntambi, JM, Paneth, N, Rogers, D, Saftlas, AF & Vaughan, W 1970, 'National Institutes of Health State-of-the-Science Conference Statement', Nutrition Today, Ovid Technologies (Wolters Kluwer Health), pp. 196-206.
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National Institutes of Health (NIH) consensus and state-of-the-science statements are prepared by independent panels of health professionals and public representatives on the basis of 1) the results of a systematic literature review prepared under contract with the Agency for Healthcare Research and Quality (AHRQ), 2) presentations by investigators working in areas relevant to the conference questions during a 2-day public session, 3) questions and statements from conference attendees during open discussion periods that are part of the public session, and 4) closed deliberations by the panel during the remainder of the second day and the morning of the third. This statement is an independent report of the panel and is not a policy statement of the NIH or the federal government. The statement reflects the panel's assessment of medical knowledge available at the time the statement was written. Thus, it provides a "snapshot in time" of the state of knowledge on the conference topic. When reading the statement, keep in mind that new knowledge is inevitably accumulating through medical research. © 2006 Lippincott Williams & Wilkins, Inc.

McGinnis, JM, Birt, DF, Brannon, PM, Carroll, RJ, Gibbons, RD, Hazzard, WR, Kamerow, DB, Levin, B, Ntambi, JM, Paneth, N, Rogers, D, Saftlas, AF & Vaughan, W 1970, 'National Institutes of Health State-of-the-Science Conference Statement: Multivitamin/Mineral Supplements and Chronic Disease Prevention', Annals of Internal Medicine, American College of Physicians, pp. 364-364.
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Meier, PC & Rogers, C 1970, 'Setting Standards for Clinical Audits', World Federationof Acupuncture Societies, World Conference on Acupuncture, Indonesia.

Messaike, E, Sutisno, M, Torpy, FR & Sztynda, T 1970, 'Mapping the Human Auricle in Asians Residing in the Sydney Region', 18th Symposium on the Forensic Sciences, Fremantle, Australia March 2006, Fremantle, Australia.

Mokkapati, S, Tan, HH, Jagadish, C, Mcbean, KE & Phillips, MR 1970, 'Integration of Quantum Dot devices by Selective Area Epitaxy', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, Australia, pp. 442-445.
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The results of nucleation of InGaAs and InAs quantum dots by selective area epitaxy are presented. By pre-patterning the substrates with different (SiO2) mask dimensions, the bandgap of the quantum dots can be tuned over a large range. This technique is used to demonstrate a quantum dot laser integrated with a quantum well waveguide. © 2006 IEEE.

Mokkapati, S, Tan, HH, Jagadish, C, McBean, KE & Phillips, MR 1970, 'Integration of quantum dot devices by selective area epitaxy', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 554-+.

Mynttinen, T, Lapine, M, Saily, J, Nefedov, IS & Tretyakov, SA 1970, 'Microwave devices with enhanced phase-compensation principle', 2006 First European Conference on Antennas and Propagation, 2006 1st European Conference on Antennas and Propagation (EuCAP), IEEE.
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We report an advanced phase compensation principle, which employs combined backward-forward transmission lines having similar frequency dispersion. Various applications of this principle to the design of microwave devices allow for an exceptionally low dispersion in a wide frequency range while keeping the structure very compact and simple compared to conventional solutions. To illustrate the idea, we present the performance of (i) phase shifters, (ii) power dividers and (iii) baluns (complete antenna feeders) built on the reported principle. We support the theoretical estimates by microwave circuit simulations and direct measurements, showing that the novel devices can be easily implemented with simple electronic components.

Pauc, N, Phillips, M, Aimez, V & Drouin, D 1970, 'Cathodoluminescence study of GaN and GaN:Si on sapphire', SPIE Proceedings, Integrated Optoelectronic Devices 2006, SPIE, San Jose, CA, pp. A1210-A1210.
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Pecchia, A, Gagliardi, A, Solomon, G, Di Carlo, A, Frauenheim, T & Reimers, JR 1970, 'Incoherent tunneling and heat dissipation in molecular bridges', Progress in Nonequilibrium Green's Functions III, Conference on Progress in Nonequilibrium Greens Functions III, IOP PUBLISHING LTD, Univ Kiel, Kiel, GERMANY, pp. 349-356.
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Phillips, MR & Drouin, D 1970, 'Comparison of Low Voltage Cathodoluminescent Phosphors', Microscopy and Microanalysis, Microscopy & Microanalysis, Oxford University Press (OUP), Chicago, USA, pp. 1526-1527.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Phillips, MR & Morgan, SW 1970, 'Enhanced High Speed SE Imaging in a VPSEM Using a Frisch Grid', Microscopy and Microanalysis, Microscopy & Microanalysis, Oxford University Press (OUP), Chicago, USA, pp. 1480-1481.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Phillips, MR, Drouin, D & Pauc, N 1970, 'Probing Carrier Behavior at the Nanoscale in Gallium Nitride using Low Voltage Cathodoluminescence', Microscopy and Microanalysis, Microscopy & Microanalysis, Oxford University Press (OUP), Chicago USA, pp. 156-157.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Platen, E 1970, 'A benchmark approach to asset management', Stochastic Finance 2004, Stochastic Finance 2004, -, Lisbon, Portugal.
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This paper aims to discuss the optimal selection of investments for the short and long run in a continuous time financial market setting. First, it documents the almost sure pathwise long-run outperformance of all positive portfolios by the growth optimal portfolio. Secondly, it assumes that every investor prefers more rather than less wealth and keeps the freedom to adjust his or her risk aversion at any time. In a general continuous market, a two fund separation result is derived which yields optimal portfolios located on the Markowitz efficient frontier. An optimal portfolio is shown to have a fraction of its wealth invested in the growth optimal portfolio and the remaining fraction in the savings account. The risk aversion of the investor at a given time determines the volatility of her/his optimal portfolio. It is pointed out that it is usually not rational to reduce risk aversion further than is necessary to achieve the maximum growth rate. Assuming an optimal dynamics for a global market, the market portfolio turns out to be growth optimal. The discounted market portfolio is shown to follow a particular time transformed diffusion process with explicitly known transition density. Assuming that the drift of the discounted market portfolio grows exponentially, a parsimonious and realistic model for its dynamics results. It allows for efficient portfolio optimisation and derivative pricing.

Platen, E 1970, 'A Benchmark Approach to Finance', Mathematical Finance, Workshop on Stochastic Analysis and Applications in Finance, -, Leipzig, Germany, pp. 131-151.
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Platen, E 1970, 'A benchmark approach to finance', MATHEMATICAL FINANCE, Workshop on Mathematical Finance and Insurance, WILEY, PEOPLES R CHINA, Yellow Mt, pp. 131-151.
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Platen, E 1970, 'A benchmark approach to portfolio optimization and derivative pricing.', Statistical Modeling in Finance Conference, Statistical Modeling in Finance Conference, Philadelphia, USA.

Platen, E 1970, 'A benchmark approach to portfolio optimization and derivative pricing.', First Conference of Advanced Mathematical Methods for Finance, First Conference of Advanced Mathematical Methods for Finance, Antalya, Turkey.

Platen, E 1970, 'A parsimonious financial market model in a jump diffusion setting', Workshop on Mathematical Finance and Insurance, Lijiang, China.

Platen, E 1970, 'A unified approach to portfolio optimization and derivative pricing.', Conference on Risk Management, Conference on Risk Management, Ascona, Switzerland.

Platen, E 1970, 'Capital asset pricing for markets with intensity based jumps', STOCHASTIC FINANCE, International Conference on Stochastic Finance 2004, SPRINGER, Univ Tecn Lisboa, Inst Super Econ Gestao, Lisbon, PORTUGAL, pp. 157-182.
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DP0343913 This paper proposes a unified framework for portfolio optimization, derivative pricing, modeling and risk measurement in financial markets with security price processes that exhibit intensity based jumps. It is based on the natural assumption that invest

Platen, E 1970, 'On the Pricing and Hedging of Long Dated Zero Coupon Bonds', 5th National Symposium on Financial Mathematics, 5th National Symposium on Financial Mathematics, Melbourne, Australia.
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The pricing and hedging of long dated derivative contracts is a challenging area of research. As a result of utility indifference pricing for general payoffs the growth optimal portfolio turns out to be the appropriate numeraire or benchmark with the real world probability measure as corresponding pricing measure. This concept of real world pricing can be applied for valuing long dated derivatives. An equivalent risk neutral probability measure does not need to exist under this benchmark approach. This paper develops a parsimonious model for a stock index dynamics, which is based on a time transformed squared Bessel process. It uses a diversified world stock index as proxy for the growth optimal portfolio. Surprisingly low prices result for long dated zero coupon bonds that can be replicated using historical data. Such prices and hedges are difficult to explain under the prevailing risk neutral approach.

Platen, E 1970, 'Pricing and hedging of long dated zero coupon bonds.', 2006 DAIWA International Workshop on Financial Engineering, DAIWA International Workshop on Financial Engineering, Tokyo, Japan.

Ratana, P, Huete, AR, Didan, K & IEEE 1970, 'MODIS EVI-based Variability in Amazon Phenology across the Rainforest-Cerrado Ecotone', 2006 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM, VOLS 1-8, IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IEEE, Denver, CO, pp. 1942-1944.
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Salih, A, Wiedenmann, J, Matz, M, Larkum, AW & Cox, G 1970, 'Photoinduced activation of GFP-like proteins in tissues of reef corals', Genetically Engineered Probes for Biomedical Applications, Biomedical Optics 2006, SPIE.
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A variety of fluorescent and chromophoric proteins homologous to the green fluorescent protein (GFP) has been recently discovered and cloned from non-bioluminescent marine animals, such as corals, and now provide a multitude of colors for use in fluorescence imaging applications. Recently, a novel fluorescence imaging methodology has emerged that utilizes the unique photoactivatory property of several GFP-like proteins, which respond to irradiation by altering their optical properties, thereby providing a new spatio-temporal capability to the GFP-based imaging applications. During our studies of GFP-like proteins from the Great Barrier Reef corals, several novel photoactivatable (PA) GFP-like proteins have been discovered. These include fluorescence photo-amplifiers and reversible photoswitchers, similar to PA jelly-fish derived PA-GFP and Dronpa, that greatly increase their emissions following ultraviolet-A (UVA) irradiation; the red-to-green (R-to-G) converters, similar to DsRed, that rapidly change to green color following single- or 2-photon irradiation; the green-to-red (G-to-R) converters, that acquire bright red fluorescence following UV-violet irradiation, similar to Kaede-like proteins; and the kindling GFP-like proteins, that are non fluorescent, but rapidly acquire bright fluorescence after green light irradiation. We report on the various optical characteristics of these coral PA proteins that may be used to expand the scope of the available fluorescence bio-imaging technologies.

Seymour, JR & Stocker, R 1970, 'The causes and implications of microscale patchiness in the ocean studied using microfluidics.', United States.

Shimabukuro, YE, Anderson, LO, Aragao, LEOC, Huete, A & IEEE 1970, 'USING FRACTION IMAGES TO STUDY NATURAL LAND COVER CHANGES IN THE AMAZON', 2006 IEEE INTERNATIONAL GEOSCIENCE AND REMOTE SENSING SYMPOSIUM, VOLS 1-8, IEEE International Geoscience and Remote Sensing Symposium (IGARSS), IEEE, Denver, CO, pp. 2103-2106.
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Shiozawa, N & Rodgers, KJ 1970, 'Comparison of the gene expression profiles of different cell lines in response to oxidatively modified proteins.', FREE RADICAL RESEARCH, 13th Biennial Meeting of the Society-for-Free-Radical-Research-International, TAYLOR & FRANCIS LTD, Davos, SWITZERLAND, pp. S85-S85.

Smith, GB, Maaroof, A, Dowd, A, Gentle, A & Cortie, M 1970, 'Tuning plasma frequency for improved solar control glazing using mesoporous nanostructures - art. no. 61970T', Photonics for Solar Energy Systems, Conference on Photonics for Solar Energy Systems, SPIE-INT SOC OPTICAL ENGINEERING, Strasbourg, FRANCE, pp. T1970-T1970.
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Stocker, R, Seymour, JR & Marcos, M 1970, 'Microfluidics for studying microbial ecology', United States.

Suglia, SF, Ryan, L, Bellinger, D & Wright, R 1970, 'The influence of the social and physical environment on child behavior', EPIDEMIOLOGY, ISEE/ISEA 2006 Conference, LIPPINCOTT WILLIAMS & WILKINS, Paris, FRANCE, pp. S387-S387.
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Suglia, SF, Ryan, L, Bellinger, D & Wright, RJ 1970, 'Violence exposure predicts adverse child behavior: Use of item response theory to characterize violence experience.', AMERICAN JOURNAL OF EPIDEMIOLOGY, 2nd North American Congress of Epidemiology, OXFORD UNIV PRESS INC, Seattle, WA, pp. S233-S233.
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Thompson, FL & Klose, KE 1970, 'Vibrio2005: the First International Conference on the Biology of Vibrios', Journal of Bacteriology, American Society for Microbiology, pp. 4592-4596.
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Thompson, LE, Rice, PM, Delenia, E, Lee, VY, Brock, PJ, Magbitang, TP, Dubois, G, Volksen, W, Miller, RD & Kim, H-C 1970, 'Imaging Thin Films of Nanoporous Low-k Dielectrics: Comparison between Ultramicrotomy and Focused Ion Beam Preparations for Transmission Electron Microscopy', Microscopy and Microanalysis, Oxford University Press (OUP), pp. 156-159.
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Ultramicrotomy, the technique of cutting nanometers-thin slices of material using a diamond knife, was applied to prepare transmission electron microscope (TEM) specimens of nanoporous poly(methylsilsesquioxane) (PMSSQ) thin films. This technique was compared to focused ion beam (FIB) cross-section preparation to address possible artifacts resulting from deformation of nanoporous microstructure during the sample preparation. It was found that ultramicrotomy is a successful TEM specimen preparation method for nanoporous PMSSQ thin films when combined with low-energy ion milling as a final step. A thick, sacrificial carbon coating was identified as a method of reducing defects from the FIB process which included film shrinkage and pore deformation.

Toth, M, Knowles, R, Hartigan, G & Lobo, C 1970, 'Electron Flux Controlled Switching Between Electron Beam Induced Etching and Deposition', Microscopy and Microanalysis, Oxford University Press (OUP), pp. 168-169.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Vella, A, Whitley, RJ, Armstrong, NG, Dowd, AR & Cline, JP 1970, 'Analysis of admixed CeO2 nanoparticles via TEM and x-ray diffraction techniques', 30th Annual Condensed matter and materials meeting, Annual Condensed matter and materials meeting, AIP, Wagga Wagga, pp. 1-4.
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The techniques used to identify nanoparticle size and shape characteristics are o vital importance in the developemnt of functional nanoparticles. Each technique offers different advantages: this work compares the two techniques of transmission electron microscopy (TEM) and x-ray diffraction (XRD) analysis by charactering CeO2 nanoparticle specimens. Whole Powder Pattern Modelling (WPPM) is used to quantify the specimens dislocations and size characteristics from XRD data. Using admixed samples we test and extend the techniques. We show that XRD accurately characterises small crystallite distributions and that larger crystallite distributions necessitate further investigation.

Vorthman, RG & Holt, SA 1970, 'Towards a rational approach to standards for integrated ocean observing systems (IOOS) development', OCEANS 2006, VOLS 1-4, Oceans 2006 Conference, IEEE, Boston, MA, pp. 1330-+.

Webster, J, Holt, S & Dalgliesh, R 1970, 'INTER the chemical interfaces reflectometer on target station 2 at ISIS', Physica B: Condensed Matter, 8th International Conference on Neutron Scattering, Elsevier BV, Sydney, AUSTRALIA, pp. 1164-1166.
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Wilcox, S, Botten, LC, Martijn de Sterke, C, McPhedran, RC, Kuhlmey, BT, Fussell, DP & Tomljenovic-Hanic, S 1970, 'Fundamental mode in index-guided microstructured optical fibers: Long wavelength properties', Optics InfoBase Conference Papers.
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Using a novel computational method, the fundamental mode in index-guided microstructured optical fibers with genuinely infinite cladding is shown to have no cut-off, but its area grows rapidly when the wavelength crosses a transition region. © 2005 Optical Society of America.

Wuhrer, R, Moran, K & Phillips, MR 1970, 'X-Ray Mapping and Post Processing', Microscopy and Microanalysis, Microscopy & Microanalysis, Oxford University Press (OUP), Chicago USA, pp. 1404-1405.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006

Wuhrer, R, Moran, K, Phillips, MR & Davey, P 1970, 'X-Ray Mapping Using a Multiple-EDS (DUAL) Detectors', Microscopy and Microanalysis, Microscopy & Microanalysis, Oxford University Press (OUP), Chicago USA, pp. 1406-1407.
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Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006

Zareie, H, Sarikaya, M, Mcdonagh, A, Barber, J, Cortie, M & Phillips, M 1970, 'Self-Organized Materials: From Organic molecules to Genetically Engineered Gold-Binding Proteins', 2006 International Conference on Nanoscience and Nanotechnology, 2006 International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, Australia, pp. 517-519.
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We present examples of ordered assemblies of organic and biological molecules on gold(111) surfaces. The first example shows how control over mono- or multilayer assemblies of 1,4-phenylenedimethanthiol can be achieved and monitored. The second example shows how monolayers on gold can be prepared using amine groups to anchor aromatic molecules to the surface. A third example shows how ordered assemblies of genetically-engineered inorganic-binding polypeptides can be formed on gold surfaces using a 3-repeat, 14 amino acid gold-binding protein (GBP1). © 2006 IEEE.

Zareie, H, Sarikaya, M, McDonagh, AM, Barber, J, Cortie, M, Phillips, M & IEEE 1970, 'Self-organized materials: From organic molecules to genetically engineered gold-binding proteins', 2006 INTERNATIONAL CONFERENCE ON NANOSCIENCE AND NANOTECHNOLOGY, VOLS 1 AND 2, International Conference on Nanoscience and Nanotechnology, IEEE, Brisbane, AUSTRALIA, pp. 530-532.

Zinder, Y, Singh, G & Weiskircher, R 1970, 'A new method of scheduling UET tasks on parallel machines', IMECS 2006: International Multiconference of Engineers and Computer Scientists, International Multiconference of Engineers and Computer Scientists, International Association Engineers-Iaeng, Kowloon, PEOPLES R CHINA, pp. 796-801.
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The paper describes a new method of scheduling partially ordered unit execution time tasks on parallel machines. The goal is to minimize the largest completion time. It is well known that this scheduling problem is NP-hard in the strong sense, and the co

Craddock, MJ & Lennox, KA Quantitative Finance Research Centre, UTS 2006, Lie Group Symmetries as Integral Transforms of Fundamental Solutions, pp. 1-23, Broadway, NSW.

Reyner, LA, Flatley, D & Brown, JJ Department for Transport 2006, Effectiveness of Motorway Services Areas in Reducing Fatigue-related and other Accidents, pp. 1-80, London.
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INTRODUCTION 'Motorway service stations exist to meet a road safety need by giving drivers somewhere to stop and rest' Lord Whitty. From analyses of road crash investigation reports on a total of over 2,000 roadtraffic collision (RTC) files obtained from UK police forces, we have found that sleepiness is a major cause of serious accidents on monotonous roads in Great Britain, especially motorways. Moreover, compared with RTCs as a whole, we have found that sleep-related crashes (SRCs) are more likely to result in death or serious injury. We have also shown that STATS19 has not been a reliable source of information on SRCs, and we have developed other techniques for identifying them. These techniques are now adopted by over half the police forces and have been successfully 'tested' in many court cases involving death by dangerous driving. Our analyses of SRCs, on behalf of the Department for Transport (DfT), have been the basis of road-crash audits that have also examined the influence of: time of day, day of week, type of driver, road lighting versus no lighting, road-traffic density (e.g. 'Sleep related vehicle accidents on sections of selected trunk roads and motorways in the UK, 1995-1998' - DfT Road Safety Report No. 22, 2001). In these respects, we have found, for example, that in relation to traffic flow rates, proportionately many more SRCs happen during the hours of midnight to 0600h and, typically, drivers causing SRCs are men, usually aged under 30 years. We have also conducted laboratory studies of the processes of falling asleep at the wheel using a realistic, interactive and fully instrumented driving simulator that enables us to monitor and analyse automatically a variety of driving behaviours, as well as the electroencephalographic (EEG) status of the driver. We have used this system to evaluate practical methods that the driver can utilise to overcome sleepiness (findings from which are incorporated in the Highway Code), and we have show...

Bruti Liberati, N & Platen, E 2006, 'On weak predictor-corrector schemes for jump-diffusion processes in finance (QFRC paper #179)', Quantitative Finance Research Centre Working Paper Series.

Heath, D & Platen, E 2006, 'Local volatility function models under a benchmark approach'.

Le, T & Platen, E 2006, 'Approximating the growth optimal portfolio with a diversified world stock index (QFRC paper #184)', Quantitative Finance Research Centre Working Paper Series.

Platen, E 2006, 'On the pricing and hedging of long dated zero coupon bonds (QFRC paper #185)', Quantitative Finance Research Centre Working Paper Series.