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CSIRO PUBLISHING is an Australian-based science and technology publisher. CSIRO PUBLISHING is the publishing branch of the Commonwealth Scientific and Industrial Research Organisation. They cover a range of scientific disciplines including agriculture, chemistry, plant and animal science, natural history and environmental management. They publish research journals, books, magazines and email newsletters. They also produce videos and multimedia content for students and training. Wikipedia.


Rubinov M.,University of New South Wales | Rubinov M.,Queensland Institute of Medical Research | Rubinov M.,CSIRO | Sporns O.,Indiana University Bloomington
NeuroImage | Year: 2010

Brain connectivity datasets comprise networks of brain regions connected by anatomical tracts or by functional associations. Complex network analysis-a new multidisciplinary approach to the study of complex systems-aims to characterize these brain networks with a small number of neurobiologically meaningful and easily computable measures. In this article, we discuss construction of brain networks from connectivity data and describe the most commonly used network measures of structural and functional connectivity. We describe measures that variously detect functional integration and segregation, quantify centrality of individual brain regions or pathways, characterize patterns of local anatomical circuitry, and test resilience of networks to insult. We discuss the issues surrounding comparison of structural and functional network connectivity, as well as comparison of networks across subjects. Finally, we describe a Matlab toolbox (http://www.brain-connectivity-toolbox.net) accompanying this article and containing a collection of complex network measures and large-scale neuroanatomical connectivity datasets. © 2009 Elsevier Inc.


Manners J.M.,CSIRO
Advances in Botanical Research | Year: 2011

Sugarcane is an established source of sugar and is the current benchmark first-generation feedstock for efficient biofuel production. Sugarcane improvement has traditionally focused on sucrose-yield traits. In the future, energycanes with higher yields of fermentable sugars and fibre (bagasse) for biofuel and electricity applications will be developed. Commercial sugarcane cultivars are poly-aneuploid interspecific hybrids and contain in excess of a hundred chromosomes. Genetic maps linking DNA markers and traits have been developed, but marker-assisted breeding is in its infancy in sugarcane, and genome sequencing has just commenced. Substantial resources are available for the sugarcane transcriptome, and both specific and overlapping gene expression patterns for many traits have been established. Gene silencing and over-expression show promise as tests for gene function in sugarcane, and progress has been made in dissecting sucrose accumulation pathways. Commercial interest in genetically modified sugarcane will initially exploit input traits proven in GM maize but is also stimulating research into novel traits, and molecular tools, from sugarcane. Understanding the unique biological attributes of sugarcane through functional genomics will provide innovative plant improvement applications that can underpin future, carbon-neutral, bioenergy and biomaterial industries. © 2011 Elsevier Ltd.


Vegetation restoration in fragmented regions is constrained by limited supplies of high quality seed and an understanding of the scale over which seed can be moved without causing negative outcomes. 'Local' seed is often prescribed for restoration but in fragmented landscapes this restricts collecting to small, inbred populations. Six polymorphic microsatellites were used to examine genetic diversity and population genetic structure in seed collected from 18 fragmented natural populations and three restored populations of the wind-pollinated and dispersed tree Allocasuarina verticillata, a key restoration species. Smaller populations produced seed crops with significantly fewer alleles, lower allelic richness and less gene diversity. Most of the populations assessed, including the restored sites, produce genetically diverse seed crops suitable for restoration but smaller populations (<30 plants) should be augmented with seed from larger populations. Principal coordinate analysis, graph-theory and Bayesian analyses found little evidence of spatially predictable genetic structure across the study region, which probably reflects long distance gene dispersal preventing the development of strong spatial structure. The absence of strong spatial patterns suggests that seed can be moved beyond current 550-km limits while being mindful of strong selection gradients or conditions that might indicate locally adapted populations. © 2011 CSIRO.


Edgar J.A.,CSIRO | Molyneux R.J.,University of Hawaii at Hilo | Colegate S.M.,U.S. Department of Agriculture
Chemical Research in Toxicology | Year: 2015

Large outbreaks of acute food-related poisoning, characterized by hepatic sinusoidal obstruction syndrome, hemorrhagic necrosis, and rapid liver failure, occur on a regular basis in some countries. They are caused by 1,2-dehydropyrrolizidine alkaloids contaminating locally grown grain. Similar acute poisoning can also result from deliberate or accidental consumption of 1,2-dehydropyrrolizidine alkaloid-containing herbal medicines, teas, and spices. In recent years, it has been confirmed that there is also significant, low-level dietary exposure to 1,2-dehydropyrrolizidine alkaloids in many countries due to consumption of common foods such as honey, milk, eggs, salads, and meat. The level of 1,2-dehydropyrrolizidine alkaloids in these foods is generally too low and too intermittent to cause acute toxicity. However, these alkaloids are genotoxic and can cause slowly developing chronic diseases such as pulmonary arterial hypertension, cancers, cirrhosis, and congenital anomalies, conditions unlikely to be easily linked with dietary exposure to 1,2-dehydropyrrolizidine alkaloids, especially if clinicians are unaware that such dietary exposure is occurring. This Perspective provides a comprehensive review of the acute and chronic toxicity of 1,2-dehydropyrrolizidine alkaloids and their potential to initiate certain chronic diseases, and suggests some associative considerations or indicators to assist in recognizing specific cases of diseases that may have resulted from dietary exposure to these hazardous natural substances. If it can be established that low-level dietary exposure to 1,2-dehydropyrrolizidine alkaloids is a significant cause of some of these costly and debilitating diseases, then this should lead to initiatives to reduce the level of these alkaloids in the food chain. © 2014 American Chemical Society.


Mckimm-Breschkin J.L.,CSIRO
Influenza and other Respiratory Viruses | Year: 2013

There are two major classes of antivirals available for the treatment and prevention of influenza, the M2 inhibitors and the neuraminidase inhibitors (NAIs). The M2 inhibitors are cheap, but they are only effective against influenza A viruses, and resistance arises rapidly. The current influenza A H3N2 and pandemic A(H1N1)pdm09 viruses are already resistant to the M2 inhibitors as are many H5N1 viruses. There are four NAIs licensed in some parts of the world, zanamivir, oseltamivir, peramivir, and a long-acting NAI, laninamivir. This review focuses on resistance to the NAIs. Because of differences in their chemistry and subtle differences in NA structures, resistance can be both NAI- and subtype specific. This results in different drug resistance profiles, for example, the H274Y mutation confers resistance to oseltamivir and peramivir, but not to zanamivir, and only in N1 NAs. Mutations at E119, D198, I222, R292, and N294 can also reduce NAI sensitivity. In the winter of 2007-2008, an oseltamivir-resistant seasonal influenza A(H1N1) strain with an H274Y mutation emerged in the northern hemisphere and spread rapidly around the world. In contrast to earlier evidence of such resistant viruses being unfit, this mutant virus remained fully transmissible and pathogenic and became the major seasonal A(H1N1) virus globally within a year. This resistant A(H1N1) virus was displaced by the sensitive A(H1N1)pdm09 virus. Approximately 0·5-1·0% of community A(H1N1)pdm09 isolates are currently resistant to oseltamivir. It is now apparent that variation in non-active site amino acids can affect the fitness of the enzyme and compensate for mutations that confer high-level oseltamivir resistance resulting in minimal impact on enzyme function. © 2012 Blackwell Publishing Ltd.


Furbank R.T.,Australian National University | Furbank R.T.,CSIRO
Journal of Experimental Botany | Year: 2016

The year 2016 marks 50 years since the publication of the seminal paper by Hatch and Slack describing the biochemical pathway we now know as C4 photosynthesis. This review provides insight into the initial discovery of this pathway, the clues which led Hatch and Slack and others to these definitive experiments, some of the intrigue which surrounds the international activities which led up to the discovery, and personal insights into the future of this research field. While the biochemical understanding of the basic pathways came quickly, the role of the bundle sheath intermediate CO2 pool was not understood for a number of years, and the nature of C4 as a biochemical CO2 pump then linked the unique Kranz anatomy of C4 plants to their biochemical specialization. Decades of "grind and find biochemistry" and leaf physiology fleshed out the regulation of the pathway and the differences in physiological response to the environment between C3 and C4 plants. The more recent advent of plant transformation then high-throughput RNA and DNA sequencing and synthetic biology has allowed us both to carry out biochemical experiments and test hypotheses in planta and to better understand the evolution-driven molecular and genetic changes which occurred in the genomes of plants in the transition from C3 to C4. Now we are using this knowledge in attempts to engineer C4 rice and improve the C4 engine itself for enhanced food security and to provide novel biofuel feedstocks. The next 50 years of photosynthesis will no doubt be challenging, stimulating, and a drawcard for the best young minds in plant biology. © 2016 The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved.


Chang L.Y.,Monash University | Barnard A.S.,CSIRO | Gontard L.C.,Technical University of Denmark | Dunin-Borkowski R.E.,Technical University of Denmark
Nano Letters | Year: 2010

Accurate understanding of the structure of active sites is fundamentally important in predicting catalytic properties of heterogeneous nanocatalysts. We present an accurate determination of both experimental and theoretical atomic structures of surface monatomic steps on industrial platinum nanoparticles. This comparison reveals that the edges of nanoparticles can significantly alter the atomic positions of monatomic steps in their proximity, which can lead to substantial deviations in the catalytic properties compared with the extended surfaces. © 2010 American Chemical Society.


Pownceby M.I.,CSIRO
International Journal of Mineral Processing | Year: 2014

Ilmenite concentrates from the Murray Basin region of southeastern Australia are contaminated with chromium impurities that must be removed for the ilmenite to become a satisfactory feedstock for the sulphate route to titania pigment production. The chromia is present primarily as discrete, compositionally variable, chrome-rich spinel grains with a smaller amount as intra-grain chromia distributed as coatings in fractures and pores of weathered ilmenite grains. Characterisation of chromia deportment through a simulated acid sulphate digestion process showed a small but non-negligible solubility of the spinels. Most spinels were resistant to dissolution with the exception of those containing high Fe(Al,Cr)2O4 and magnetite (Fe3O4) components. Intra grain chromia was highly soluble. Processing to achieve lowbulk chromia using amagnetising roast proceduremust ensure that well crystallised rutile is not produced because of its insolubility in the sulphate process. It is also important that the roast conditions do not substantially increase the magnetite content of the spinels making them more susceptible to dissolution. This work highlights the importance of characterising all spinel composition types within ilmenite concentrates in addition to the level of intra-grain chromia associated with the ilmenite when considering the suitability of Murray Basin primary ilmenites as a feedstock to sulphate route titania pigment plants. ©.


The need to process low-grade and/or complex chalcopyrite-containing ores that cannot be concentrated is the main driver for the development of hydrometallurgical processes. The ferric sulfate-sulfuric acid system, with or without the assistance of microorganisms, has been studied extensively because it comprises the most promising, low-cost process route. Alternative oxidants to ferric ion are known but, as yet, their superior oxidation strengths have not been exploited other than at laboratory scale, probably due to their higher costs. Hybrid sulfate-chloride and sulfate-nitrate systems were included because they may offer specific advantages in some instances. The aims of this review were to summarise current knowledge in respect of these systems and highlight potentially rewarding areas for future research. © 2013 Published by Elsevier B.V.


Effect of heterogeneous oxidation of the thick-film Cu0.4Ru 3.4O7 + RuO2 sensing electrode (SE) of the planar potentiometric dissolved oxygen (DO) sensor on its electrochemical properties has been investigated by field emission beam scanning electron microscopy (FIB-SEM), X-ray photoelectron spectroscopy (XPS), cyclic voltametry (CV) and electrochemical impedance spectroscopy (EIS) techniques. It was found that the most of heterogeneous oxidation has occurred during the first week of SE exposure to the aqueous environment leading to the partial oxidation Ru IV to RuIII occurred mostly on the grain boundaries of SE. The presence of the "inner" active surfaces in the bulk of the developed complex oxide SE has been reaffirmed. It was also found that heterogeneous oxidation caused the increase of the Cu 2p peaks intensity on the surface of SE after the water treatment for one month, which has been confirmed by XPS measurement. Crown Copyright © 2011 Published by Elsevier B.V. All rights reserved.


Murphy A.B.,CSIRO
Journal of Physics D: Applied Physics | Year: 2013

The presence of metal vapour in gas-metal arc welding has been shown to have two strong effects on the arc plasma: a decrease in temperature throughout the arc, and the formation of a local temperature minimum near the arc axis. These effects have been attributed, on the basis of different computational models, to either the increased radiative emission associated with the presence of metal vapour in the arc plasma, or the influence of the metal vapour influx on convective flow in the arc. This question is investigated using a three-dimensional computational model in which the production and the transport of metal vapour are taken into account self-consistently. Parameters relevant to welding of thin sheets of aluminum are examined. For these conditions, it is found that the first effect (the decrease in temperature throughout the arc) is due to both the increased radiative emission and the influence of the metal vapour influx on flow. The second effect (the local temperature minimum, which in this case occurs just below the wire electrode) is a consequence of the influence of aluminum vapour produced from the wire electrode on flow in the arc. By examining published results and the energy balance in the plasma, it is shown that for welding of steel with higher arc currents, the increased radiative emission can lead to a local temperature minimum at a greater distance from the wire electrode. © 2013 IOP Publishing Ltd.


Strange A.D.,CSIRO
Journal of Geophysics and Engineering | Year: 2013

The fundamental performance of ground penetrating radar (GPR) is linked to the ability to measure the signal time-of-flight in order to provide an accurate radar-to-target range estimate. Having knowledge of the actual time range and timing nonlinearities of a trace is therefore important when seeking to make quantitative range estimates. However, very few practical methods have been formally reported in the literature to characterize GPR time-range performance. This paper describes a method to accurately measure the true time range of a GPR to provide a quantitative assessment of the timing system performance and detect and quantify the effects of timing nonlinearity due to timing jitter. The effect of varying the number of samples per trace on the true time range has also been investigated and recommendations on how to minimize the effects of timing errors are described. The approach has been practically applied to characterize the timing performance of two commercial GPR systems. The importance of the method is that it provides the GPR community with a practical method to readily characterize the underlying accuracy of GPR systems. This in turn leads to enhanced target depth estimation as well as facilitating the accuracy of more sophisticated GPR signal processing methods. © 2013 Sinopec Geophysical Research Institute.


Rochester I.J.,CSIRO
Nutrient Cycling in Agroecosystems | Year: 2011

Improving the efficiency of nitrogen (N) fertiliser use is one means of reducing greenhouse gas emissions, particularly in irrigated crops such as cotton (Gossypium hirsutum L.). Internal crop N use efficiency (iNUE) was measured within two N fertiliser rate experiments that covered a wide range of N fertility over six cropping seasons. Crop iNUE was determined by dividing lint yield by crop N uptake. No nutrients other than N limited cotton growth or yield and the crops were irrigated to avoid drought stress. The optimal N fertiliser rates were determined from fitted quadratic functions that related lint yields with N fertiliser rates for each cropping system in each year. When the optimal N fertiliser rate was applied, crop iNUE averaged 12.5 ± 0.2 kg lint/kg crop N uptake. The crop iNUE was then used to determine the degree to which N fertiliser was under or over-applied, with respect to the economic optimum N fertiliser rate. Low iNUE values were associated with excessive N fertiliser application. Crop iNUE was determined in 82 commercial cotton crops in six valleys over the final 4 years of this study. The crop iNUE value was high in 8 fields (10%), optimal in 9 fields (11%) and low in 65 fields (79%). Crop N uptake averaged 247 kg N/ha, yield 2,273 kg lint/ha and crop iNUE 10.1 kg lint/kg crop N uptake for these sites. Averaged over all sites and years, about 49 kg N/ha too much N fertiliser was applied. Apparent N fertiliser recovery by cotton in the N rate experiments ranged from <20% in N-fertile treatments where legume crops had been grown, to more than 60% following winter cereal crops. Information on crop iNUE will enable cotton producers to assess their N fertiliser management and adjust N fertiliser rates for future crops. This study has demonstrated that there is scope to substantially reduce N fertiliser inputs to Australian cotton fields without reducing yields. © 2010 Springer Science+Business Media B.V.


Filarioid nematodes (Nematoda: Filarioidea) parasitic in Australasian monotremes, marsupials and murid rodents are described from three genera, Breinlia (Breinlia), Pelecitus and Sprattia. New host and geographic records are presented for 24 previously described species from these genera, a second subgenus, Breinlia (Johnstonema) and an additional three genera, Cercopithifilaria, Monanema and Pelecitus. Nine species are described as new, B. (B.) beveridgei sp. nov. from the peritoneal cavity of Macropus parryi Bennett, B. (B.) bigenera sp. nov. from the peritoneal and pleural cavities of Aepyprymnus rufescens (Gray), Onychogalea fraenata (Gould), O. unguifera (Gould) and possibly Antechinus swainsonii (Waterhouse), B. (B.) dorcopsis sp. nov. from the peritoneal cavity of Dorcopsis hageni Heller and D. luctuosa (D'Albertis), B. (B.) melomyos sp. nov. from the peritoneal cavity of Melomys cf. burtoni, B. (B.) oweni sp. nov. from the peritoneal cavity of Dactylopsila trivirgata Gray, B. (B.) presidentei sp. nov. from the peritoneal cavity of Mesembriomys gouldii (Gray), M. macrurus (Peters) and the pleural and peritoneal cavities of Conilurus penicillatus (Gould), B. (B.) tricondylus sp. nov. from the peritoneal cavity of Macropus rufogriseus banksianus (Quoy & Gaimard), B. (B.) zyzomyos sp. nov. from the peritoneal cavity of Zyzomys woodwardi (Thomas) and Z. arguurus (Thomas), and Sprattia spearei sp. nov. from the lung (probably blood vessels) of Isoodon macrourus (Gould) . The female of B. (J.) woerlei from the pulmonary artery, right ventricle and lung cysts of Petrogale brachyotis (Gould) is described for the first time. Breinlia (J.) andersoni Spratt & Varughese, 1975 from the subcutaneous connective tissues of Macropus rufus (Desmarest), M. giganteus Shaw, M. robustus erubescens Sclater and Wallabia bicolor (Desmarest) is placed as a synonym of B. (J.) annulipapillata (Johnston & Mawson, 1938) from the subcutaneous connective tissues of M. dorsalis (Gray), O. fraenata and W. bicolor. In general, filarioids predominate in macropodoid hosts and in the north of Australia. Copyright © 2011 . Magnolia Press.


The responses to root zone salinity (0, 25 and 50mM NaCl) by 40 citrus rootstock genotypes introduced from the People's Republic of China, measured as shoot chloride (Cl-) and sodium (Na+) ion accumulation, growth and dry matter accumulation, were investigated under glasshouse conditions. Two experiments, one using aerated nutrient solutions and the other irrigated sand cultures, were conducted with plants grown from rooted cuttings taken from representative trees of different mandarin (Citrus reticulata Blanco and C. erythrosa Hort. ex Tan.), yuzu (C. junos Sieb. ex Tan.), Ichang papeda (C. ichangensis Swing.), sour orange (C. aurantium L.) and trifoliate orange (Poncirus trifoliata (L.) Raf.) genotypes. Two standard genotypes, viz. Rangpur lime (Citrus x limonia Osbeck.) and William's trifoliate orange were included in the experiments as reference controls.After 56days, plant growth and shoot Cl- and Na+ concentrations varied significantly between genotypes within salt treatments in both experiments. There were significant differences between genotypes for relative tolerance indices, expressed as ratios of growth at 25 and 50mM NaCl to growth at 0mM, but the relative rankings did not change between root zone salt concentrations. Although there were some correlations between plant growth and tolerance indices with shoot ion concentrations, these were generally poor.As the plant material was clonal, estimates of broad sense heritability from intra-class correlation coefficients indicated that the genotypes investigated could prove to be valuable parents in breeding for new salt excluding rootstocks. Of particular interest were strains of trifoliate orange that accumulated low concentrations of Cl- and Na+ in shoot tissues. Since P. trifoliata is normally a poor Cl- excluder, but a major source of disease resistance, these results suggested that progeny testing should be conducted to investigate the value of these strains for future rootstock breeding. © 2011.


Krzikalla F.,Stanford University | Muller T.M.,CSIRO
Geophysics | Year: 2011

Elastic upscaling of thinly layered rocks typically is performed using the established Backus averaging technique. Its poroelastic extension applies to thinly layered fluid-saturated porous rocks and enables the use of anisotropic effective medium models that are valid in the low- and high-frequency limits for relaxed and unrelaxed pore-fluid pressures, respectively. At intermediate frequencies, wave-induced interlayer flow causes attenuation and dispersion beyond that described by Biot's global flow and microscopic squirt flow. Several models quantify frequency-dependent, normal-incidence P-wave propagation in layered poroelastic media but yield no prediction for arbitrary angles of incidence, or for S-wave-induced interlayer flow. It is shown that generalized models for P-SV-wave attenuation and dispersion as a result of interlayer flow can be constructed by unifying the anisotropic Backus limits with existing P-wave frequency-dependent interlayer flow models. The construction principle is exact and is based on the symmetry properties of the effective elastic relaxation tensor governing the pore-fluid pressure diffusion. These new theories quantify anisotropic P- and SV-wave attenuation and velocity dispersion. The maximum SV-wave attenuation is of the same order of magnitude as the maximum P-wave attenuation and occurs prominently around an angle of incidence of 45 °. For the particular case of a periodically layered medium, the theoretical predictions are confirmed through numerical simulations. © 2011 Society of Exploration Geophysicists.


Whitehouse M.E.A.,CSIRO
Agricultural Systems | Year: 2011

Integrated Pest Management (IPM) aims to maintain pests below an economic threshold to avoid yield loss without resorting to unnecessary insecticide applications, rather than eradicate all pests in a crop. However, convincing growers to spray only if pest numbers exceed a threshold can be difficult, especially if the threshold changes in response to external factors, as in the case of mirids. The aim of this work was to establish if the mirid thresholds were adhered to by growers, and if not, when they were relaxed. The results showed that pest managers in this survey were following the guidelines recommended for mirid management, but in a conservative manner. Pest managers accepted the threshold for mirid numbers developed for visual surveys, but not the threshold developed for beatsheets. When retention rate and mirid numbers were low, the fruit retention threshold was used to trigger a spray application; but there was no evidence that high retention rates were used to withhold a spray application. There was a high reliance on Fipronil (Regent) to control mirids. This chemical accounted for 63% of the insecticides in the 2006/2007 survey, and was often applied multiple times to fields at low rates. There was no cost to yield in following the mirid thresholds, vindicating the recommended thresholds for mirids. The ultimate aim of this work is to support the further development of IPM in cotton. A discussion of IPM revealed that the cotton industry in Australia is well positioned to support and further develop IPM in cotton, especially given its policy to develop Best Management Practice (BMP). However, differences in interpretive knowledge by the stakeholders appeared to be inhibiting the development of mirid IPM. This common problem in multi-disciplined groups may account for the reluctance of pest managers to adjust their mirid threshold in respect to sampling method. © 2010.


Species of the genus Scolothrips are re-assessed based on examination of type material together with many other specimens, and a key is provided to identify the 14 species recognised. The possibility is discussed that the three North American species, hoodi, pallidus and sexmaculatus are colour variants of a single species. Three apparently Old World species, dilongicornis, longicornis and takahashii, cannot be distinguished satisfactorily. Three new synonyms are established: quadrinotata is a synonym of asura; hartwigi is a synonym of brevipilis; priesneri is a synonym of takahashii. Two species from the Canary Islands are considered nomina dubia: quadrimaculatus and lanzarotensis. Two species are here recorded for the first time from Australia, latipennis and rhagebianus, and Australian records of sexmaculatus are considered to be based on misidentifications. © 2011.


Understanding nanodiamond functionalisation is of great importance for biological and medical applications. Here we examine the stabilities of oxygen, hydroxyl, and water functionalisation of the nanodiamonds using the self-consistent charge density functional tight-binding simulations. We find that the oxygen and hydroxyl termination are thermodynamically favourable and form strong C-O covalent bonds on the nanodiamond surface in an O2 and H2 gas reservoir, which confirms previous experiments. Yet, the thermodynamic stabilities of oxygen and hydroxyl functionalisation decrease dramatically in a water vapour reservoir. In contrast, H2O molecules are found to be physically adsorbed on the nanodiamond surface, and forced chemical adsorption results in decomposition of H2O. Moreover, the functionalisation efficiency is found to be facet dependent. The oxygen functionalisation prefers the {100} facets as opposed to alternative facets in an O2 and H2 gas reservoir. The hydroxyl functionalisation favors the {111} surfaces in an O2 and H2 reservoir and the {100} facets in a water vapour reservoir, respectively. This facet selectivity is found to be largely dependent upon the environmental temperature, chemical reservoir, and morphology of the nanodiamonds.


Trought M.C.T.,The New Zealand Institute for Plant and Food Research Ltd | Bramley R.G.V.,CSIRO
Australian Journal of Grape and Wine Research | Year: 2011

Background and Aims: Previous work has demonstrated that vineyards are spatially variable and that this variability can be understood in terms of the underlying characteristics of the land (soils, topography) supporting the vineyard. Selectively harvesting blocks in response to such variability may be highly profitable. While it has also been shown that crop maturation is spatially variable, there may also be temporal variations in the rate of maturation. Integrating knowledge of how spatial variation in fruit composition may be moderated in time has not previously been attempted and is the key objective in this work. Methods and Results: We used a proximal sensor to map vine vigour at high spatial resolution in a 5.9-ha Marlborough vineyard planted with Sauvignon Blanc. Vigour measurements were also related to fruit-soluble solids (SS), titratable acidity (TA) and pH - key indices of crop maturity. Knowledge of crop phenology and maturation was used to predict how these indices changed with time. The pooled opinions of over 50 Marlborough winemakers on the optimum juice SS, pH and TA at harvest to produce a 'typical Marlborough Sauvignon Blanc' were used to develop a juice index (JI), which in turn was mapped in space and time at the study site. The JI showed marked spatial and temporal variation. Conclusions: In addition to being spatially variable, grape quality in vineyards also changed with time. Thus, the optimisation of decisions about harvest timing requires knowledge of spatial variability. Conversely, strategies such as selective harvesting cannot be properly optimized without knowledge of crop phenology, the maturation of fruit and their implications for fruit quality - which are all also spatially variable. In this study, we have shown that, by integrating knowledge of crop phenology with an understanding of vineyard variability and winemaker objectives through the construction of a JI, it is possible for the optimum harvest decision to be made such that fruit destined for a particular end use are harvested at the right time and from the right place. Significance of the Study: This is the first study in which knowledge of both spatial and temporal vineyard variation has been integrated. It demonstrates that in order to be optimal, strategies such as selective harvesting need to incorporate knowledge of crop phenology rather than rely on knowledge of spatial variation alone. © 2011 New Zealand Institute for Plant and Food Research Ltd.


Ostrikov K.,CSIRO | Ostrikov K.,University of Sydney
Journal of Physics D: Applied Physics | Year: 2011

Plasma nanoscience is an emerging multidisciplinary research field at the cutting edge of a large number of disciplines including but not limited to physics and chemistry of plasmas and gas discharges, materials science, surface science, nanoscience and nanotechnology, solid-state physics, space physics and astrophysics, photonics, optics, plasmonics, spintronics, quantum information, physical chemistry, biomedical sciences and related engineering subjects. This paper examines the origin, progress and future perspectives of this research field driven by the global scientific and societal challenges. The future potential of plasma nanoscience to remain a highly topical area in the global research and technological agenda in the age of fundamental-level control for a sustainable future is assessed using a framework of the five Grand Challenges for Basic Energy Sciences recently mapped by the US Department of Energy. It is concluded that the ongoing research is very relevant and is expected to substantially expand to competitively contribute to the solution of all of these Grand Challenges. The approach to controlling energy and matter at nano- and subnanoscales is based on identifying the prevailing carriers and transfer mechanisms of the energy and matter at the spatial and temporal scales that are most relevant to any particular nanofabrication process. Strong accent is made on the competitive edge of the plasma-based nanotechnology in applications related to the major socio-economic issues (energy, food, water, health and environment) that are crucial for a sustainable development of humankind. Several important emerging topics, opportunities and multidisciplinary synergies for plasma nanoscience are highlighted. The main nanosafety issues are also discussed and the environment- and human health-friendly features of plasma-based nanotech are emphasized. © 2011 IOP Publishing Ltd.


The effectiveness of managing fisheries through the allocation of catch rights, including Individual Transferrable Quota's (ITQs), has been the subject of a number of recent reviews. Inspection of these reviews suggests that the effectiveness of ITQ and similar catch rights schemes in meeting single species sustainability objectives differs from their effectiveness in meeting broader Ecosystem Based Fisheries Management objectives, especially in terms of managing effects on associated and dependent species and habitats. This should not be a surprise, given the attributes of rights-based neoliberal market policy instruments, as discussed here. © 2009 Elsevier Ltd. All rights reserved.


Aplin K.P.,CSIRO | Helgen K.M.,Smithsonian Institution
Bulletin of the American Museum of Natural History | Year: 2010

Large collections of fragmentary animal bones excavated from archaeological contexts in East Timor between 1968 and 2002 provide new material referable to the recently extinct, gigantic murine genus Coryphomys. We document the upper and lower dentition and palatal anatomy of C. buehleri Schaub, 1937, and identify and name a second species of Coryphomys, based on differences in molar size and morphology and skeletal robusticity. Alternative interpretations of the observed morphological and metric variability (sexual dimorphism, resource-based polymorphism, sample heterochroneity) are each carefully assessed and rejected, and we conclude that the genus comprised two species of approximately similar body size. Preserved cranial elements of both species of Coryphomys feature a high degree of anatomical specialization, including an unusual elaboration of the maxillary sinus complex. Though the specialized anatomy of Coryphomys invites consideration of its phylogenetic relationships, this exercise is hindered by a demonstrable high level of homoplasy (i.e., multiple, independent evolutionary losses and gains) in many of the key craniodental features traditionally surveyed within Murinae, while other features are insufficiently well surveyed for broad-scale analysis. Nevertheless, our comparisons highlight two potentially related lineages among the geographically proximate Murinaethe Philippine Phloeomyini and the Australo-Papuan Hydromyini. The remains of Coryphomys are relatively scarce in all the archaeological samples, but distributional evidence suggests that both species of Coryphomys were found primarily in upland habitats. Late Pleistocene samples document their former presence at lower elevations, possibly reflecting cooler climatic conditions at that time. © 2010 American Museum of Natural History.


Barnard A.S.,CSIRO | Chang L.Y.,Monash University
ACS Catalysis | Year: 2011

The development of the next generation of nanosized heterogeneous catalysts requires precise control of the size, shape, and structure of individual components in a variety of chemical environments. Recent reports show that the density of catalytically active defects on Pt nanoparticles is intrinsically linked to performance, such as edges, corners, steps, and kinks, which may be introduced postsynthesis. To optimize the synthesis of nanoparticles decorated by these defects and to understand the structural stability of the final product, multiscale thermodynamic modeling has been used to predict the size and temperature dependence of these steps and to show how this directly relates to catalytic reactivity. The results show that relatively modest annealing can promote the formations of surface steps and kinks and can more than double the reactivity of particles at industrially relevant sizes. © 2011 American Chemical Society.


Murphy A.B.,CSIRO
Journal of Physics D: Applied Physics | Year: 2011

The development of a three-dimensional computational model of gas-metal arc welding is described. The wire electrode, arc plasma and weld pool are included in the computational domain self-consistently. The model takes into account the motion of the electrode, flow in the weld pool, deformation of the weld-pool surface and the influence of metal droplet transfer. Results are presented for welding of an aluminium alloy. The current density distribution at the interface between the arc and the weld pool is strongly dependent on the surface profile of the weld pool. This in turn affects the temperature distribution in the weld pool. The momentum transferred by the droplet affects the direction of flow in the weld pool, and together with the energy transfer, increases the weld-pool depth. The results demonstrate the importance of including the arc plasma in the computational domain. Fair agreement is found between a measured weld profile and the predictions of the model. Inclusion of the influence of metal vapour in the model is expected to improve the agreement. © 2011 IOP Publishing Ltd.


Booth T.H.,CSIRO
Forest Ecology and Management | Year: 2013

Eucalypts are grown in plantations in more than 90 countries, so it is important to assess their vulnerability to climate change. Global mean annual temperature over land has already increased by about 0.9°C in the last century and many countries have agreed that urgent action should be taken to limit the increase in global mean temperature below 2°C. Unfortunately, as emissions are currently tracking at higher levels than the worst case scenario envisaged by the Intergovernmental Panel on Climate Change it appears increasingly unlikely that temperature increase can be limited to 2°C. This paper assesses the vulnerability of eucalypt plantations to climate change. Vulnerability is a function of potential impact, which is related to exposure and sensitivity, and adaptive capacity. Eucalypt plantations total more than 20million hectares and are grown in many countries around the world, so have significant exposure to climate change. About 41% of more than 800 eucalypt taxa grow naturally in Australia within narrow climatic ranges of less than 2°C, so are potentially sensitive to climatic change. Fortunately, the small number of commercially important species tend to have much wider climatic tolerances, but genetic selection to improve growth may well be reducing their climatic adaptability. Efforts have been made to simulate eucalypt growth under changing climatic and atmospheric conditions. If photosynthesis and water use efficiency are increased by increasing atmospheric carbon dioxide levels then some plantations may enjoy significant yield increases. However, recent results from eucalypts growing under elevated CO2 conditions in whole tree chambers suggest there is little if any 'fertilisation effect' on photosynthesis, though water use efficiency is increased. Consequently, productivity may increase in some plantations and decrease in others. Fortunately, the adaptive capacity of eucalypt plantations is high. Many eucalypts are grown on short rotations of less than ten years, so changing silvicultural practices and planting different genotypes to match changing climatic conditions is relatively easy. While the vulnerability of eucalypt plantations is only at a medium level it is concluded that sharing information about where particular eucalypt genotypes are grown, identifying potentially marginal climatic areas and recommending genotypes suitable for changing conditions would help to further reduce potential vulnerability. The development of a eucalypt database and mapping system is proposed as a major collaborative project to help to protect one of global forestry's most valuable resources. © 2012 .


In vernalized Arabidopsis, the extent of FLC repression and promotion of flowering are correlated with the length of winter (low temperature exposure), but how plants measure the duration of winter is unknown. Repression of FLC occurs in two phases: establishment and maintenance. This study investigates the early events in the transition between establishment and maintenance of repression. Initial repression was rapid but transient; within 24 h of being placed at low temperatures FLC transcription was reduced by 40% and repression was complete after 5 days in the cold. The extent to which repression was maintained depended on the length of the cold treatment. Occupancy of the +1 nucleosome in FLC chromatin increased in a time-dependent manner over a 4-week low temperature treatment concomitant with decreased histone acetylation and increased trimethylation of histone H3 lysine 27 (H3K27me3). Mutant analyses showed that increased nucleosome occupancy occurred independent of histone deacetylation and increased H3K27me3, suggesting that it is an early step in the switch between transient and stable repression. Both altered histone composition and deacetylation contributed to increased nucleosome occupancy. The time-dependency of the steps required for the switch between transient and stable repression suggests that the duration of winter is measured by the chromatin state at FLC. A chromatin-based switch is consistent with finding that each FLC allele in a cell undergoes this transition independently. Significance Statement In vernalized Arabidopsis, the extent of FLC repression and promotion of flowering are correlated with the length of winter, but how plants measure the duration of winter is unknown. This study shows that there is a time-dependent increase in the stability of the first nucleosome in the FLC gene that correlates with both the length of cold and stable FLC repression, suggesting that plants measure the duration of winter at the level of FLC chromatin. © 2015 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.


O'Hara T.D.,Museum Victoria | Rowden A.A.,NIWA - National Institute of Water and Atmospheric Research | Bax N.J.,CSIRO
Current Biology | Year: 2011

The large-scale spatial distribution of seafloor fauna is still poorly understood. In particular, the bathyal zone has been identified as the key depth stratum requiring further macroecological research [1], particularly in the Southern Hemisphere [2]. Here we analyze a large biological data set derived from 295 research expeditions, across an equator-to-pole sector of the Indian, Pacific, and Southern oceans, to show that the bathyal ophiuroid fauna is distributed in three broad latitudinal bands and not primarily differentiated by oceanic basins as previously assumed. Adjacent faunas form transitional ecoclines rather than biogeographical breaks. This pattern is similar to that in shallow water despite the order-of-magnitude reduction in the variability of environmental parameters at bathyal depths. A reliable biogeography is fundamental to establishing a representative network of marine reserves across the world's oceans [1, 3]. © 2011 Elsevier Ltd.


Scattered trees are highly visible reminders of lost vegetation in many intensively managed agricultural landscapes globally. Despite fragmentation, these trees provide important ecosystem services but are rapidly declining and expected to disappear within 200. years. Consequently, natural regeneration and restoration are required to maintain ecosystem services. But seed sourced for older restoration projects was often collected from too few individuals or small, inbred sites. Consequently, restored sites may have insufficient genetic diversity to underpin genetic and demographic processes and facilitate adaptation to climate change. Yellow Box (Eucalyptus melliodora) is a key species in endangered Box-Gum Grassy Woodlands in southeastern Australia that often now exists as scattered trees. This community has been restored for >20. years and it is now prudent to determine whether plantings that will persist over time have been created. Genetic diversity, mating system and pollen dispersal parameters were evaluated in scattered and restored trees and restored tree seed crops. Although within-site variability was evident, overall genetic diversity was significantly lower in restored trees. Significant genetic differentiation between restored and scattered trees indicated that seed was not necessarily sourced locally. Local (250. m) and distant (1. km) pollen sources were detected in the seed crops but these were often dominated by 3-5 nearby scattered trees. The persistence of some of these Yellow Box sites may be constrained by inbreeding once scattered trees are lost from the surrounding landscape. It is unclear how pervasive these responses are in restoration efforts and further information is needed to prevent the presence of restored sites being equated with persistence. © 2013 Elsevier Ltd.


Li Y.,CSIRO | Li J.,CAS Institute of Atmospheric Physics | Feng J.,CAS Institute of Atmospheric Physics
Journal of Climate | Year: 2012

Rainfall in both southwest Western Australia (SWWA) and North China (NC) has been declining substantially since the mid-1960s, which has led to a series of droughts in both regions since then. Using observed rainfall datasets in China and Australia and the NCEP reanalysis dataset during 1951-2008, it is found that the decline ofSWWArainfall occurs in early austral winter [May-July (MJJ)] while the reduction ofNCrainfall is in late boreal summer [July-September (JAS)]. The relationship between SWWA MJJ rainfall and NC JAS rainfall during 1951-2008 is then examined, and it is found that a significant link exists between these two rainfall series with a correlation of 0.43 and this link remains after the data are detrended. In particular, this relationship accounts for up to 62% variance on interdecadal time scales, and seems to be driven by the poleward shift of the southern subtropical high ridge (SSHR) and the northern subtropical high ridge (NSHR) over longitudes 1108-1508E. The poleward shift of the SSHR may induce an anomalous anticyclone centered near the south Australian coast, resulting in anomalous easterlies of dry air to SWWA, while the poleward shift of the NSHR is associated with an anomalous anticyclone in East Asia near NC causing anomalous northeasterlies of dry air to NC. The poleward shift of SSHR/NSHR may be linked to the warming sea surface temperatures (SSTs) in the tropical Indian-western Pacific. The results herein suggest that the poleward shifts of the SSHR and the NSHR instigated by the warming SSTs in the tropical Indian-western Pacific may have partially contributed to the rainfall reduction in both regions. © 2012 American Meteorological Society.


Lin Z.,CAS Institute of Atmospheric Physics | Li Y.,CSIRO
Journal of Climate | Year: 2012

Rainfall in North West Australia (NWA) has been increasing over the past decades, occurring mainly in the austral summer season (December-March).Arange of factors such as decreased land albedo in Australia and increasing anthropogenic aerosols in the Northern Hemisphere, identified using simulations from climate models, have been implicated in this wetting trend. However, the impact of land albedo and aerosols on Australian rainfall remains unclear. In addition, previous studies showed that dominant sea surface temperature (SST) signals in the Pacific-Indian Ocean including El Niño-Southern Oscillation (ENSO), ENSO Modoki, and the Indian Ocean dipole mode have no significant impact on the NWA rainfall trend. The present study proposes another viewpoint on the remote influence of tropical Atlantic atmospheric vertical motion on the observed rainfall variability and trend in NWA. It is found that, with the atmospheric ascent instigated by the warming of SST over the tropical Atlantic, a Rossby wave train is emanating southeastward from off the west coast of subtropical South America to the midlatitudes of the South Atlantic Ocean. It then travels eastward embedded in the westerly jet waveguide over the South Atlantic and South Indian Oceans. The eastward-propagated Rossby wave induces an anticyclonic anomaly in the upper troposphere over Australia, which is at the exit of the westerly jet waveguide. This leads to an in situ upper-tropospheric divergence, ascending motion and a lower-tropospheric convergence, and the associated increase in rainfall in NWA. Thus, the increasing trend in atmospheric upward motion induced by the warming trend of SST in the tropical Atlantic may partially explain the observed rainfall trend in NWA. © 2012 American Meteorological Society.


Bradford S.A.,U.S. Department of Agriculture | Torkzaban S.,CSIRO
Langmuir | Year: 2012

A simple modeling approach was developed to calculate colloid adhesive parameters for chemically heterogeneous porous media. The area of the zone of electrostatic influence between a colloid and solid-water interface (A z) was discretized into a number of equally sized grid cells to capture chemical heterogeneity within this region. These cells were divided into fractions having specific zeta potentials (e.g., negative or positive values). Mean colloid adhesive parameters such as the zeta potential, the minimum and maximum in the interaction energy, the colloid sticking efficiency (α), and the fraction of the solid surface area that contributes to colloid immobilization (Sf) were calculated for possible charge realizations within Az. The probability of a given charge realization in A z was calculated using a binomial mass distribution. Probability density functions (PDFs) for the colloid adhesive parameters on the heterogeneous surface were subsequently calculated at the representative elementary area (REA) scale for a porous medium. This approach was applied separately to the solid-water interface (SWI) and the colloid, or jointly to both the SWI and colloid. To validate the developed model, the mean and standard deviation of the interaction energy distribution on a chemically heterogeneous SWI were calculated and demonstrated to be consistent with published Monte Carlo simulation output using the computationally intensive grid surface integration technique. Our model results show that the PDFs of colloid adhesive parameters at the REA scale were sensitive to the size of the colloid and the heterogeneity, the charge and number of grid cells, and the ionic strength. © 2012 American Chemical Society.


Maeda N.,CSIRO
Review of Scientific Instruments | Year: 2014

A High Pressure Automated Lag Time Apparatus (HP-ALTA) can measure gas hydrate formation probability distributions from water in a glass sample cell. In an HP-ALTA gas hydrate formation originates near the edges of the sample cell and gas hydrate films subsequently grow across the water-guest gas interface. It would ideally be desirable to be able to measure gas hydrate formation probability distributions of a single water droplet or mist that is freely levitating in a guest gas, but this is technically challenging. The next best option is to let a water droplet sit on top of a denser, immiscible, inert, and wall-wetting hydrophobic liquid to avoid contact of a water droplet with the solid walls. Here we report the development of a second generation HP-ALTA which can measure gas hydrate formation probability distributions of a water droplet which sits on a perfluorocarbon oil in a container that is coated with 1H,1H,2H,2H-Perfluorodecyltriethoxysilane. It was found that the gas hydrate formation probability distributions of such a quasi-free water droplet were significantly lower than those of water in a glass sample cell. © 2014 AIP Publishing LLC.


Lagudah E.S.,CSIRO
Euphytica | Year: 2011

Over 150 resistance genes that confer resistance to either leaf rust, stripe rust or stem rust have been catalogued in wheat or introgressed into wheat from related species. A few of these genes from the 'slow-rusting' adult plant resistance (APR) class confer partial resistance in a race non-specific manner to one or multiple rust diseases. The recent cloning of two of these genes, Lr34/Yr18, a dual APR for leaf rust and stripe rust, and Yr36, a stripe rust APR gene, showed that they differ from other classes of plant resistance genes. Currently, seven Lr34/Yr18 haplotypes have been identified from sequencing the encoding ATP Binding Cassette transporter gene from diverse wheat germplasm of which one haplotype is commonly associated with the resistance phenotype. The paucity of well characterised APR genes, particularly for stem rust, calls for a focused effort in developing critical genetic stocks to delineate quantitative trait loci, construct specific BAC libraries for targeted APR genes to facilitate robust marker development for breeding applications, and the eventual cloning of the encoding genes. © 2011 Springer Science+Business Media B.V.


Saghafi A.,CSIRO
Australian Journal of Earth Sciences | Year: 2014

A new site-specific (Tier 3) method has been developed to determine greenhouse gas emissions from open coal mining. The Tier 3 method presented here is based on extensive measurement of gas emissions from open-cut coal mines and the physics of gas desorption from coal. It was adopted by Australian National Greenhouse and Energy Reporting in 2009 and since 2012 formed the scientific basis for the Australian Government guidelines on calculating greenhouse gas emissions from open cut mines. The main strength of this method is its site-specific nature and accuracy, as well as its ability to be integrated with routine coal exploration programs. New concepts were produced for the model: a coal mine is regarded as a 'gas reservoir,' with coal seam gas being emitted from a 'gas release zone' that consists of sedimentary geological units (emission layers) above and below the base of the mine. The primary data required for the method are the in situ gas content and gas composition of the coal and carbonaceous rocks contained within the gas-release zone. These data are obtained through direct measurement of gas desorption from bore cores. To reduce gas drilling, a mine lease is compartmentalised into 'gas zones' of similar gas content and reservoir properties. The outputs of the method are emission density (the potential volume of gas emitted from mining site per unit area of the ground surface) and emission factor (the gas volume emitted per tonne of raw coal extracted). Owing to spatial variability and errors of measurement, the estimate of emissions is associated with uncertainty. A simple method of calculating uncertainty of emissions is presented in this work. © 2013 © 2013 CSIRO.


Burke-Spolaor S.,California Institute of Technology | Burke-Spolaor S.,Jet Propulsion Laboratory | Bannister K.W.,CSIRO
Astrophysical Journal | Year: 2014

We report the detection of a dispersed fast radio burst (FRB) in archival intermediate-latitude Parkes Radio Telescope data. The burst appears to be of the same physical origin as the four purported extragalactic FRBs reported by Thornton et al. This burst's arrival time precedes the Thornton et al. bursts by 10 years. We consider that this survey, and many other archival low-latitude (|gb| < 30°) pulsar surveys, have been searched for FRBs but produced fewer detections than the comparatively brief Thornton et al. search. Such a rate dependence on Galactic position could provide critical supporting evidence for an extragalactic origin for FRBs. To test this, we form an analytic expression to account for Galactic position and survey setup in FRB rate predictions. Employing a sky temperature, scattering, and dispersion model of the Milky Way, we compute the expected number of FRBs if they are isotropically distributed on the sky with respect to the Galactic position (i.e., local), and if they are of extragalactic origin. We demonstrate that the relative detection rates reject a local origin with a confidence of 99.96% (∼3.6σ). The extragalactic predictions provide a better agreement; however, there are still strong discrepancies with the low-latitude detection rate at a confidence of 99.69% (∼2.9σ). However, for the extragalactic population, the differences in predicted versus detected population may be accounted for by a number of factors, which we discuss. © 2014. The American Astronomical Society. All rights reserved.


Assuming without evidence that magnetic sources are magnetised parallel to the geomagnetic field can seriously mislead interpretation and can result in drill holes missing their targets. This article reviews methods that are available for estimating, directly or indirectly, the natural remanent magnetisation (NRM) and total magnetisation of magnetic sources, noting the strengths and weaknesses of each approach. These methods are: (i) magnetic property measurements of samples; (ii) borehole magnetic measurements; (iii) inference of properties from petrographic/petrological information, supplemented by palaeomagnetic databases; (iv) constrained modelling/inversion of magnetic sources; (v) direct inversions of measured or calculated vector and gradient tensor data for simple sources; (vi) retrospective inference of magnetisation of a mined deposit by comparing magnetic data acquired pre- and post-mining; (vii) combined analysis of magnetic and gravity anomalies using Poissonstate SAs theorem; (viii) using a controlled magnetic source to probe the susceptibility distribution of the subsurface; (ix) Helbig-type analysis of gridded vector components, gradient tensor elements, and tensor invariants; (x) methods based on reduction to the pole and related transforms; and (xi) remote in situ determination of NRM direction, total magnetisation direction and Koenigsberger ratio by deploying dual vector magnetometers or a single combined gradiometer/magnetometer to monitor local perturbation of natural geomagnetic variations, operating in base station mode within a magnetic anomaly of interest. Characterising the total and remanent magnetisations of sources is important for several reasons. Knowledge of total magnetisation is often critical for accurate determination of source geometry and position. Knowledge of magnetic properties such as magnetisation intensity and Koenigsberger ratio constrains the likely magnetic mineralogy (composition and grain size) of a source, which gives an indication of its geological nature. Determining the direction of a stable ancient remanence gives an indication of the age of magnetisation, which provides useful information about the geological history of the source and its environs.


Binns R.A.,CSIRO | Binns R.A.,Australian National University
Economic Geology | Year: 2014

The 2.7 m Bikpela chimney differs from sulfide-rich chimneys at PACMANUS, eastern Manus basin, by virtue of high silica content, a stromatolite-like layered structure, and the presence of a large internal collapse cavity. Its interior is dominated by 5-to 10-mm-thick primary laminae of opal-A-dominated fronds clouded by submicroscopic sphalerite inclusions, set between thin subhorizontal growth borders. Larger sphalerites with sulfosalt-galena intergrowths at frond ends project into discoid cavities under the growth borders. A steeper, second-order lamination reflects arrested expansion of the 50-cm-high internal collapse cavity. Underlying the cavity floor an axial breccia pipe contains distorted fragments of laminated interior modified by dissolution and then redeposition of opal and further growth of pyrite and sphalerite. Beneath a thin Mn oxide crust, a hard outer sphalerite-barite carapace ∼5 cm thick and devoid of opal is banded parallel to the chimney exterior.At least three stages of chimney growth are evident, beginning with repetitive deposition of opaline frond layers probably developed from microbial mat precursors by overgrowth of hydrothermal opal and fine sphalerite. Next, with rising fluid temperatures, hydrothermal Fe-poor sphalerite with Pb sulfosalts and galena deposited at frond ends and under growth borders and, via lateral diffusion and mixing with seawater, formed abundantly in the outer carapace of the chimney. Passage of hot, more acid fluids into the chimney axial zone then caused dissolution of primary opal and consequent formation of the collapse cavity and underlying breccia pipe, together with deposition of Fe-rich sphalerite and pyrite in second-order fractures and cavities related to the collapse. Finally, conductive cooling during or after this latter stage produced films and spherules of clear opal coating pores and grain margins throughout the structure, apart from in the carapace.Bikpela contains significant gold and silver (avg: 8.7 ppm Au, 250 ppm Ag; n = 9), but it is low overall in Cu (up to 0.5 wt % in the pipe) and Pb (up to 0.7 wt % in the carapace). Its carapace is relatively rich in Zn (up to 54 wt %), Ag, As, and Sb, with one sample containing 0.12 wt % silver. © 2014 by Economic Geology.


Pinetown K.L.,CSIRO
Australian Journal of Earth Sciences | Year: 2014

Basin modelling has been used to improve understanding of the origin and temporal evolution of coal seam gas in the Hunter Coalfield of the Sydney Basin. Burial history models were produced based on data from seven boreholes located in the southern, eastern, central and western areas of the coalfield. Mean random vitrinite reflectance (Rv,r) data, derived from measurements of mean maximum reflectance (Rv,max), were used for calibration of the models. A qualitative sensitivity analysis of one model shows that varying the paleoheat flow has a greater influence on calculated Rv,r than varying the eroded overburden thickness.The differences between the constructed models are significant enough to provide plausible explanations for regional gas distribution in the Hunter Coalfield. Coals in the south of the coalfield appear to have the greatest potential for thermogenic gas generation. Modelling has shown that areas that have low gas contents and decreased permeability have been uplifted more, and buried less, compared with areas that have high gas contents. Burial history modelling shows noticeable variations in the extent of burial and uplift, and, consequently, in thermal maturities and potential for thermogenic gas generation; together with the assessment of other coal and gas property data, it appears that present-day gas contents may partially reflect coal ranks and adsorption capacities, with late-stage biogenic gas generation replenishing CH4 volumes that were lost following uplift during the Late Cretaceous. © 2014 © 2014 CSIRO.


Biodosimetric methods for determining exposure dose in individuals following a radiation accident are important for the health management of the exposed cohort and prioritisation of high dose exposure cases to receive emergency medical treatment. This brief review provides a succinct outline of (i) the current status of standard cytogenetic methods used in radiation biodosimetry; (ii) development of high-throughput systems for current standard cytogenetic methods; (iii) emerging minimally invasive methods; (iv) the impact of nutrition and genotype on observed dose-response relationships and (v) new frontiers in biodosimetry using molecular biology techniques such as transcriptomics and proteomics. © 2011 Elsevier Ltd. All rights reserved.


Chen D.,University of Melbourne | Caruso R.A.,University of Melbourne | Caruso R.A.,CSIRO
Advanced Functional Materials | Year: 2013

Recent progress in the fabrication and application of diverse spherical titania nanostructures, including mesoporous spheres, spherical flaky assemblies, and dendritic particles of variable diameter and monodispersity in size, is summarized in this article. Utilizing different synthesis strategies, spherical titania nanostructures with tailored polymorphs (including amorphous, anatase, rutile, brookite and TiO2-B), particle sizes (from tens of nanometers to millimeters), monodispersity, porosity, and variable surface properties have been produced. Such spherical titania nanostructures show realized and potential applications in the areas of chromatographic separation, lithium-ion batteries, dye-sensitized solar cells, photocatalytic oxidation and water splitting, photoluminescence, electrorheological fluids, catalysis, gas sensing, and anticancer intracellular drug delivery. Gaining further understanding of both synthesis design and application of these materials will promote the commercialization of such spherical titania nanostructures in the future. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Du Y.,CAS South China Sea Institute of Oceanology | Cai W.,CSIRO | Wu Y.,CAS South China Sea Institute of Oceanology
Journal of Climate | Year: 2013

The tropical Indian Ocean dipole/zonal mode (IOD) is phase locked with the austral winter and spring seasons. This study describes three types of the IOD in terms of their peak time and duration. In particular, the authors focus on a new type that develops in May-June and matures in July-August, which is distinctively different from the canonical IOD, which may develop later and peak in September-November or persist from June to November. Such "unseasonable" IOD events are only observed since the mid-1970s, a period after which the tropical Indian Ocean has a closer relationship with the Pacific Ocean. The unseasonable IOD is an intrinsic mode of the Indian Ocean and occurs without an ensuing El Nĩo. A change in winds along the equator is identified as a major forcing. The wind change is in turn related to a weakening Walker circulation in the Indian Ocean sector in austral winter, which is in part forced by the rapid Indian Ocean warming. Thus, although the occurrence of the unseasonable IOD may be partially influenced by oceanic variability, the authors' results suggest an influence from the Indian Ocean warming. This suggestion, however, awaits further investigation using fully coupled climate models. © 2013 American Meteorological Society.


Electronic noses (E-noses) use various types of electronic gas sensors that have partial specificity. This review focuses on commercial and experimental E-noses that use metal oxide semi-conductors. The review covers quality control applications to food and beverages, including determination of freshness and identification of contaminants or adulteration. Applications of E-noses to a wide range of foods and beverages are considered, including: meat, fish, grains, alcoholic drinks, non-alcoholic drinks, fruits, milk and dairy products, olive oils, nuts, fresh vegetables and eggs. © 2010 by the authors.


Ants are a prominent invertebrate group used to assess ecological change in response to disturbance. Their application as a bioindicator group has been particularly widespread in Australia, and a recent comprehensive review of their responses to environmental disturbance identified a range of consistent and predictable patterns. Here I conduct a literature review of the responses of ants to grazing globally, and specifically test whether key patterns identified in the review of ant responses to disturbance in Australia apply globally. The patterns tested were (1) soil and vegetation type are primary determinants of ant community composition, and often have a far greater effect on ant community composition than disturbance, (2) disturbance induces species compositional change, but does not necessarily affect overall species richness or abundance, (3) a species' response is not necessarily consistent across habitats because of variation in inherent habitat suitability, and (4) approximately one quarter to one half of species that are common enough for statistical analysis have significant responses to disturbance. All these patterns were found to hold true for grazing studies worldwide. All but three studies sampling multiple soils/vegetation types found the influence of these variables to override grazing effects. Community composition changed consistently, yet the responses of total ant abundance and species richness were highly inconsistent. All studies that analysed species-level data on multiple soils/vegetation types, showed mixed responses to grazing across habitats. On average, 33% of tested species had statistically significant differences across treatments. This is the first such formulation of global patterns for any terrestrial invertebrate group for their use in bioindication, and provides valuable support to the use of ants as indicators of ecological disturbance. The challenge now is to provide a predictive understanding of this context dependency, as well as to improve the precision of the predictive responses. The confirmation of global patterns to grazing presented here represents a first step in developing the valuable contribution that ants can provide to rangeland monitoring systems. © 2009 Elsevier Ltd. All rights reserved.


Walsh K.,University of Melbourne | Lavender S.,CSIRO | Scoccimarro E.,Instituto Nazionale Of Geofisica E Vulcanologia | Murakami H.,Japan Agency for Marine - Earth Science and Technology
Climate Dynamics | Year: 2013

Detection of tropical lows is performed in a suite of climate model simulations using objectively-determined detection thresholds that are resolution-dependent. It is found that there is some relationship between model resolution and tropical cyclone formation rate even after the resolution-dependent tropical cyclone detection threshold is applied. The relationship is investigated between model-simulated tropical cyclone formation and a climate-based tropical cyclone Genesis Potential Index (GPI). It is found that coarser-resolution models simulate the GPI better than they simulate formation of tropical cyclones directly. As a result, there appears to be little relationship from model to model between model GPI and the directly-simulated cyclone formation rate. Statistical analysis of the results shows that the main advantage of increasing model resolution is to give a considerably better pattern of cyclone formation. Finer resolution models also simulate a slightly better pattern of GPI, and for these models there is some relationship between the pattern of GPI simulated by each model and that model's pattern of simulated tropical cyclone formation. © 2012 Springer-Verlag.


Butt C.R.M.,CSIRO | Cluzel D.,CNRS Matter and Environment Multidisciplinary Research
Elements | Year: 2013

Nickel laterite ores account for over 60% of global nickel supply. They are the product of intensive deep weathering of serpentinites under humid tropical conditions. Nickel is concentrated to over 1.0 wt% and is hosted in a variety of secondary oxides, hydrous Mg silicates and smectites. The formation, mineralogy and grade of the deposits are controlled by the interplay of lithology, tectonics, climate and geomorphology. Most deposits have a multi-phase development, evolving as their climatic and/or topographic environment change. The richest deposits (>3 wt% Ni) formed where oxide-rich regoliths were uplifted and Ni leached downwards to concentrate in neo-formed silicates in the saprolite.


The present-day stress field in the Gediz Graben is characterized by vertical maximum and horizontal 105°N-trending intermediate and 015°N-trending minimum principal stress axes. Stress gradients are 23.4, 18.6 and 15.3MPa/km for maximum, intermediate and minimum stresses, respectively. This stress tensor aligns well with the observed fault pattern of the graben and confirms the ∼N-S-oriented extension. The strike\dip of optimum planes with highest slip tendency is 105°\60°S and 285°\60°N and highest dilation tendency is on 105°N-trending vertical fractures. Faults in the graben fill have near normal frictional strength with friction coefficient of (μ) 0.48. Pore pressure is generally hydrostatic but local overpressure elevated to pore-fluid factor (λ) of 0.71 was observed in close proximity to the master bounding fault of the graben. Data and geological evidence suggest that this fault is a major conduit for mantle degassing and plays a significant role in fluid circulation. The hot CO2-rich fluids ascending through the fault system could be locally trapped to form overpressured CO2 pockets as observed in the shale-rich Alaşehir Formation which is suitable to form clay smears and clay-matrix fault gouges with high seal potential. High temperature and CO2 content is also favorable for healing and sealing of the fractures by carbonate precipitation to re-establish fault cohesion. Temporary fault seal breaching may occur due to shear reactivation of the faults and could relieve excess pore pressure. This may also lead to surface discharge of CO2-rich fluids with hydrocarbons generated in the Alaşehir Formation. Projection of the deduced stress field to 6km depth suggests that brittle reactivation of the low-angle segment of the master bounding fault possibly requires combined operation of overpressuring and fault zone weakening. © 2012 Elsevier Ltd.


Determining the effects of compaction-related inclination shallowing of remanence directions is crucial for ascertaining the validity of low palaeolatitudes for Neoproterozoic red beds in South Australia that are central to the debate concerning low-latitude Proterozoic glaciation. The inclination correction (or flattening) factor, f, is defined as tan(ID)/tan(IF), where ID and IF are the inclinations of the measured detrital remanence and the ancient inducing field, respectively. The anisotropy can be estimated using anisotropy of magnetic susceptibility and the anisotropy of high-field isothermal remanence (hf-AIR). The elongation-inclination (E-I) method has also been used to infer inclination shallowing. We add the anisotropy of thermoremanent magnetisation (ATR) to these methods. For the late Cryogenian Elatina Formation arenites, which constitute the bulk of the Elatina data set, the inclination correction using f=0.738 derived from ATR increases the palaeolatitude of the Elatina Formation from 6.5±2.2° to 8.8±3.2°, which confirms that the Elatina glaciation occurred near the palaeoequator. Inclination corrections for the Ediacaran argillaceous Brachina and Wonoka formations, using f=0.35-0.38 derived from ATR, are significantly greater than for the more arenaceous Elatina Formation, which increases their palaeolatitudes from ~12° to ~30°. Carbonates from the basal Ediacaran Nuccaleena Formation yielded f=0.8 from ATR, which represents only a small palaeolatitude correction from 19° to 23°. The anisotropy results imply that the characteristic remanent magnetisations carried by all these units were acquired early as depositional remanent magnetisations, essentially at the time of deposition. The shift of the palaeopoles from argillaceous units indicating significantly higher palaeolatitudes introduces a distinctive loop into the late Cryogenian-Ediacaran-Cambrian pole path for Australia. This loop shows similarities with the North American pole path for this period, for which true polar wander (TPW) has been inferred. However, until ages of Neoproterozoic strata in South Australia are better constrained uncertainty persists on whether the similarities of the Australian and North American pole paths reflect TPW. © 2012.


Barnard A.S.,CSIRO
Crystal Growth and Design | Year: 2013

Self-assembled monolayers (SAMs) are applied to gold nanoparticles to guide growth, increase stability, and provide additional functionality. However, as with any surface coating, the changes to the energetics of the surface can have unanticipated consequences, as well as introducing new opportunities. Understanding the relationship between the efficiency and type of SAMs and the underlying gold nanoparticles is challenging, but can be explored very efficiently using theory and computer simulation. In this paper, the relationship between the density of alkanethiol SAMs with different chain lengths and the shape of gold nanoparticles is reported as a function of size, including the impact of highly under-coordinated sites such as edges and corners. The results show that the most favorable sites for adsorption are on the {111} facets adjacent to the {111}|{111} edges (followed by the corners), but it is the concentration of SAMs on facets themselves that drives variations in the morphology. With the right choice of thiol and control of the SAM efficiency, it will be possible to create gold nanoparticles with a majority of either {111} or {100} facets, as required. © 2013 American Chemical Society.


Morrison M.,CSIRO | Morrison M.,Ohio State University
Current Opinion in Microbiology | Year: 2013

The fields of biomedicine and livestock agriculture share a need for advances in our understanding of microbiology, since the gastrointestinal tracts of all animals support a microbiota (microbial community) and their genomes (microbiome) that serves as a functional and dynamic interface between its genotype, environment, and lifestyle, with commensurate effects on host nutrition and health. Recently, small animal (especially rodent) models have been an invaluable resource with respect to exploring and establishing these relationships, and their relevance, to human health and well-being. By highlighting recent research studies, this review seeks to address how the functional and comparative analyses of the gut microbiome from 'large' animals by metagenomics and related 'metaomic' approaches can provide mutual benefits for livestock agriculture and biomedicine. © 2013.


Hislop G.,CSIRO
Journal of Geophysics and Engineering | Year: 2016

A detailed analytical feasibility study is performed which identifies several important limitations in the problem of layered earth characterization with off-ground GPR in the mono-static or small baseline bistatic configurations. It is shown mathematically that the characterization of layered earth by radar is an ill-posed problem. The permittivity and thickness of the first layer may be estimated. However, for penetrable earth, one may not estimate the first layer's conductivity or the parameters of deeper layers without ambiguity. This problem may be partially circumvented via the use of a priori knowledge and several examples of this, applicable to practical problems, are considered in detail. The feasibility study identifies the limitations in question in the form of a mathematical proof. These limitations are demonstrated using extensive simulated and experimental results. © 2016 Sinopec Geophysical Research Institute.


Chen Z.R.,CSIRO
Journal of Petroleum Science and Engineering | Year: 2011

Fluid migration and heat transport result in changes in pore pressure and temperature within a reservoir, which can induce stresses and deformations in the reservoir and the bounding rock system through poroelastic and thermoelastic couplings. Analytical and semi-analytical solutions for investigating the induced stresses and deformations are therefore extremely useful when applied to both predicting and monitoring the reservoir volume changes and associated subsurface and surface deformation. The poroelastic and thermoelastic eigenstrains are used here to characterize the pore pressure change and temperature variation, respectively, in the reservoir. The induced stresses and deformations are then obtained by using the single- and double-inclusion models, and are expressed in terms of the Galerkin vector stress function, which is related to the corresponding eigenstrains in a straightforward way. The difference in mechanical properties between the reservoir and the bounding rocks is accounted for using the theory of inhomogeneous inclusions. The effect of the reservoir shape, elastic properties, and the distribution of pore pressure change within the reservoir on the surface deformation has been investigated. The magnitude and pattern of the induced surface tilt have been compared with those produced by a hydraulic fracture. The analytical expressions obtained here for the displacement and tilt fields can serve as a useful forward model for monitoring and mapping hydraulic fractures, subsurface fluid migration and heat transport associated with injection or production of fluid into or from a reservoir by surface deformation-based monitoring techniques, such as tiltmeter monitoring. © 2011.


Kroon F.J.,CSIRO
Limnology and Oceanography: Methods | Year: 2015

The efficacy of clove oil for anaesthesia was examined on eight species of Australian tropical freshwater fishes: the native Mulgrave goby (Glossogobius bellendenensis, Gobiidae), empire gudgeon (Hypseleotris compressa) and sleepy cod (Oxyeleotris lineolatus) (both Eleotrididae), Eastern rainbowfish (Melanotaenia splendida, Melanotaeniidae), Pacific blue-eye (Pseudomugil signifer, Pseudomugilidae), and eel-tailed catfish (Tandanus tandanus, Plotosidae), and the non-native species spotted tilapia (Pelmatolapia mariae, Cichlidae) and guppy (Poecilia reticulata, Poecilidae). Induction to anaesthesia, recovery from anaesthesia and survival of fish were determined for five concentrations (20 mg/L, 30 mg/L, 40 mg/L, 80 mg/L, and 160 mg/L). A 20 mg/L clove oil concentration was not sufficient to induce a loss of reflex reactivity within 10 min for most individuals (> 85%) in the eight species examined. Effective clove oil concentrations for anaesthesia induction and recovery (40-80 mg/L) for seven out of the eight species examined overlap with those reported for other tropical freshwater fish species. Differences in induction and recovery times among treatments were not always independent of fish size for G. bellendenensis, M. splendida, O. lineolatus, and P. mariae, emphasizing the importance of taking biological and environmental factors into account when determining and applying effective clove oil concentrations for anaesthesia in fish. In contrast, long recovery times and mortality for T. tandanus in even relatively low concentrations suggests that clove oil may not be an appropriate anaesthetic for at least some fish species. © 2015 The Authors Limnology and Oceanography: Methods published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography.


Integrated spatio-temporal assessment and modelling of complex social-ecological systems is required to address global environmental challenges. However, the computational demands of this modelling are unlikely to be met by traditional Geographic Information System (GIS) tools anytime soon. I evaluated the potential of a range of high-performance computing (HPC) hardware and software tools to overcome these computational barriers. Performance advantages were quantified using a synthetic model. Four tests were compared, using: a) an Arc Macro Language (AML) GIS script on a single central processing unit (CPU); b) Python/NumPy on 1-256 CPU cores; c) Python/NumPy on 1-64 graphics processing units (GPUs) with high-level PyCUDA abstraction (GPUArray); and d) Python/NumPy on 1-64 GPUs with low-level PyCUDA abstraction (ElementwiseKernel). The GIS implementation effectively took 15.5 weeks to run. Python/NumPy on a single CPU core led to a speed-up of 59× compared to the GIS. On a single GPU, speed-ups of 1473× were achieved using GPUArray and 4881× using ElementwiseKernel. Parallel processing led to further performance enhancements. At best, the ElementwiseKernel module in parallel over 64 GPUs achieved a speed-up of 63,643×. Open source tools such as Python applied across a spectrum of HPC resources offer transformational and accessible performance improvements for integrated assessment and modelling. By reducing the computational barrier, HPC can lead to a step change in modelling sophistication, including the better representation of uncertainty, and perhaps even new modelling paradigms. However, migration to new hardware and software environments also has significant costs. Costs and benefits of HPC are discussed and code tools are provided to help others migrate to HPC and transform our ability to address global challenges through integrated assessment and modelling. © 2012 Elsevier Ltd.


Ridoutt B.G.,CSIRO | Pfister S.,ETH Zurich
International Journal of Life Cycle Assessment | Year: 2013

Purpose: A complete assessment of water use in life cycle assessment (LCA) involves modelling both consumptive and degradative water use. Due to the range of environmental mechanisms involved, the results are typically reported as a profile of impact category indicator results. However, there is also demand for a single score stand-alone water footprint, analogous to the carbon footprint. To facilitate single score reporting, the critical dilution volume approach has been used to express a degradative emission in terms of a theoretical water volume, sometimes referred to as grey water. This approach has not received widespread acceptance and a new approach is proposed which takes advantage of the complex fate and effects models normally employed in LCA. Methods: Results for both consumptive and degradative water use are expressed in the reference unit H2Oe, enabling summation and reporting as a single stand-alone value. Consumptive water use is assessed taking into consideration the local water stress relative to the global average water stress (0.602). Concerning degradative water use, each emission is modelled separately using the ReCiPe impact assessment methodology, with results subsequently normalised, weighted and converted to the reference unit (H2Oe) by comparison to the global average value for consumptive water use (1.86 × 10-3 ReCiPe points m-3). Results and discussion: The new method, illustrated in a simplified case study, incorporates best practice in terms of life cycle impact assessment modelling for eutrophication, human and eco-toxicity, and is able to assimilate new developments relating to these and any other impact assessment models relevant to water pollution. Conclusions: The new method enables a more comprehensive and robust assessment of degradative water use in a single score stand-alone water footprint than has been possible in the past. © 2012 Springer-Verlag.


Schenk P.M.,University of Queensland | Carvalhais L.C.,University of Queensland | Kazan K.,CSIRO
Trends in Biotechnology | Year: 2012

Plants in their natural habitats are surrounded by a large number of microorganisms. Some microbes directly interact with plants in a mutually beneficial manner whereas others colonize the plant only for their own benefit. In addition, microbes can indirectly affect plants by drastically altering their environments. Understanding the complex nature of plant-microbe interactions can potentially offer new strategies to enhance plant productivity in an environmentally friendly manner. As briefly reviewed here, the emerging area of multi-species transcriptomics holds the promise to provide knowledge on how this can be achieved. We discuss key aspects of how transcriptome analysis can be used to provide a more comprehensive picture of the complex interactions of plants with their biotic and abiotic environments. © 2011.


Anthropogenic activities are having a deleterious effect on biodiversity. To understand the magnitude of this issue, and ultimately temper its pace, requires reproducible biodiversity measurements at suitable spatio-temporal scales. Procuring such data solely by existing approaches is unachievable because of the costs, time and the taxonomic expertise required. High-throughput molecular biodiversity analysis shows great promise, increasing the breadth of biota sampled and accelerating the rate of data collection. In this issue of Molecular Ecology, Yoccoz et al. (2012) use short informative DNA product 'meta-barcodes' to provide an insight into above-ground vascular plant diversity from boreal, temperate and tropical environments. Interestingly, their molecular analysis was derived from the soils and not the plants themselves, with the molecular signatures of the soils not only strongly reflecting current diversity, but also traces of crops not sown for up to one hundred years. Importantly, the research examines the complexities associated with deriving biomass estimates from molecular data and the need to consider biomass turnover. The use of soil-derived meta-barcodes extends beyond estimating vascular plant diversity, with the approach being suited to the range of ecological applications, especially scenarios where DNA may be degraded. © 2012 Blackwell Publishing Ltd.


Leal A.M.M.,Imperial College London | Blunt M.J.,Imperial College London | LaForce T.C.,CSIRO
Geochimica et Cosmochimica Acta | Year: 2014

Chemical equilibrium calculations are essential for many environmental problems. It is also a fundamental tool for chemical kinetics and reactive transport modelling, since these applications may require hundreds to billions equilibrium calculations in a single simulation. Therefore, an equilibrium method for such critical applications must be very efficient, robust and accurate. In this work we demonstrate the potential effectiveness of a novel Gibbs energy minimisation algorithm for reactive transport simulations. The algorithm includes strategies to converge from poor initial guesses; capabilities to specify non-linear equilibrium constraints such as pH of an aqueous solution and activity or fugacity of a species; a rigorous phase stability test to determine the unstable phases; and a strategy to boost the convergence speed of the calculations to quadratic rates, requiring only few iterations to converge. We use this equilibrium method to solve geochemical problems relevant to carbon storage in saline aquifers, where aqueous, gaseous and minerals phases are present. The problems are formulated to mimic the ones found in kinetics and transport simulations, where a sequence of equilibrium calculations are performed, each one using the previous solution as the initial guess. The efficiency and convergence rates of the calculations are presented, which require an average of 1-2 iterations. These results indicate that critical applications such as chemical kinetics and reactive transport modelling can potentially benefit by using this multiphase equilibrium algorithm. © 2014 The Authors.


Chang L.-Y.,Monash University | Sawa E.,Shinshu University | Barnard A.S.,CSIRO
Nanoscale | Year: 2011

A reliable explanation for the underlying mechanism responsible for the persistent aggregation and self-assembly of colloidal 5 nm diamond nanoparticles is critical to the development of nanodiamond-based technologies. Although a number of mechanisms have been proposed, validation has been hindered by the inherent difficulty associated with the identification and characterisation of the inter-particle interfaces. In this paper we present results of high resolution aberration corrected electron microscopy and complementary computer simulations to explicate the features involved, and confirm the electrostatic interaction mechanism as the most probable cause for the formation of agglutinates and agglomerates of primary particles. © 2011 The Royal Society of Chemistry.


Feng M.,CSIRO | McPhaden M.J.,National Oceanic and Atmospheric Administration | Lee T.,Jet Propulsion Laboratory
Geophysical Research Letters | Year: 2010

[1] Historical sea level records reveal that a strengthening of the Pacific subtropical cells (STCs) since the early-1990,s has reversed a multi-decadal weakening tendency. Stronger STCs correspond to a stronger Leeuwin Current in the southeast Indian Ocean (SEIO) and a stronger Indonesian Throughflow, due to dynamic connections of the Pacific and SEIO through equatorial and coastal waveguides. Multi-decadal trends of the STCs and their influence on the SEIO have confounded the detection of human induced global change signals in the short instrumental records of the two circulation systems. Copyright © 2010 by the American Geophysical Union.


Blaber S.J.M.,CSIRO
Estuarine, Coastal and Shelf Science | Year: 2013

Since 2002 there has been an increase in knowledge of many aspects of the biology and ecology of tropical estuarine fishes, as well as significant changes to many estuarine fisheries. Analyses of literature databases (2002-2012) show that: of the c. 600 relevant papers, 52% are primarily related to ecology, 11% to conservation, 11% to anthropogenic and pollution effects on fishes, 9% to fisheries, 7% to aquaculture, 4% to study techniques, and 1% each to fish larvae, effects of fishing, taxonomy, climate change, evolution and genetics. In terms of geographic spread 17% are from North America, 15% from south Asia, 14% from the Caribbean, 13% from Australasia, 12% from Africa and 9% each from South America and SE Asia. Research papers came from 50 countries of which the dominant were USA (15%), India (12%), Australia (11%) and Brazil (7%). Increasing numbers of studies in West Africa, SE and South Asia and South America have increased basic knowledge of the ecology of estuarine fish faunas. Increases in understanding relate to: roles of salinity, turbidity and habitat diversity; connectivity between habitats; water flow; ecological drivers of spatial variability; scale dependent variation; thermal tolerances; movement patterns; food webs; larval adaptations; and the viability of areas heavily impacted by human activities. New reviews both challenge and support different aspects of the estuarine dependence paradigm - still perhaps one of the main research issues - and the protective function of estuaries and mangroves for juvenile fishes has received attention in relation to e.g. predation risks and fisheries. There have also been significant advances in the use of guilds and biodiversity models. Fishing pressures have continued unabated in most tropical estuaries and are summarised and management issues discussed. Understanding of the relationships between fisheries production and mangroves has advanced and significant differences have emerged between Indo-West Pacific and Atlantic systems. The effects of fishing itself have also received attention and research is often related to conservation studies. The effects of anthropogenic activities are reviewed and important advances in mitigation are discussed. Restoration of estuarine habitats, such as mangroves, previously taking place mainly in countries such as Australia and USA, is now occurring in more countries. The design of reserves and the use of protected areas as management tools are gaining credence. Finally, the evidence for actual and potential effects of climate change is discussed. © 2012 Elsevier Ltd.


Bannister K.W.,CSIRO | Madsen G.J.,University of Sydney | Madsen G.J.,University of Cambridge
Monthly Notices of the Royal Astronomical Society | Year: 2014

The recent detection of fast radio bursts has generated strong interest in identifying the origin of these bright, non-repeating, highly dispersed pulses. The principal limitation in understanding the origin of these bursts is the lack of reliable distance estimates; their high dispersion measures imply that they may be at cosmological distances (0.1 < z<1.0). Here, we discuss new distance constraints to the FRB010621 (a.k.a J1852-08) first reported by Keane. We use velocity resolved Hα and Hβ observations of diffuse ionized gas towards the burst to calculate an extinction-corrected emission measure along the line of sight. We combine this emission measure with models of Galactic rotation and of electron distribution to derive a 90 per cent probability of the pulse residing in the Galaxy. However, we cannot differentiate between the two Galactic interpretations of Keane: a neutron star with unusual pulse amplitude distribution or Galactic black hole annihilation. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Fulton E.A.,CSIRO
Journal of Marine Systems | Year: 2010

Ever growing understanding of general ecological, biogeochemical and climatic processes is allowing for the construction of a growing list of end-to-end models. While many of these are taking the form of generic modelling frameworks, no one approach defines end-to-end ecosystem modelling. There is a wide range of scales, resolutions, forcings, components and represented processes. Examples drawn from existing models can be used to give guidance on best practice approaches for creating end-to-end models. In particular, it is clear that defaulting to the finest resolution and greatest complexity in all the dimensions (e.g. spatial, temporal, taxonomic, process detail) is not beneficial. There is also a lot of value, during model development and implementation, in trying different model types, assumptions and formulations; there is no one "best" model. Maintaining a diversity of approaches is important given that end-to-end models are most effective when used as strategic tools, to address questions that are at scales where there is still a lot of uncertainty about how systems function. There are still many challenges facing the end-to-end modelling field, particularly when long simulation periods are called for, but perhaps the greatest ones are: non-stationarity introduced by shifting climate, biodiversity and evolution; representing human responses; and handling uncertainty. © 2009 Elsevier B.V. All rights reserved.


Feng J.,Lanzhou University | Li J.,CAS Institute of Atmospheric Physics | Li Y.,CSIRO
Journal of Climate | Year: 2010

Using the NCEP-NCAR reanalysis, the 40-yr ECMWF Re-Analysis (ERA-40), and precipitation data from the Climate Prediction Center (CPC) Merged Analysis of Precipitation (CMAP) and the Australian Bureau of Meteorology, the variability and circulation features influencing southwest Western Australia (SWWA) winter rainfall are investigated. It is found that the climate of southwest Australia bears a strong seasonality in the annual cycle and exhibits a monsoon-like atmospheric circulation, which is called the southwest Australian circulation (SWAC) because of its several distinct features characterizing a monsoonal circulation: the seasonal reversal of winds, alternate wet and dry seasons, and an evident land-sea thermal contrast. The seasonal march of the SWAC in extended winter (May-October) is demonstrated by pentad data. An index based on the dynamics' normalized seasonality was introduced to describe the behavior and variation of the winter SWAC. It is found that the winter rainfall over SWWA has a significant positive correlation with the SWAC index in both early (May-July) and late (August-October) winter. In weaker winter SWAC years, there is an anticyclonic anomaly over the southern Indian Ocean resulting in weaker westerlies and northerlies, which are not favorable for more rainfall over SWWA, and the opposite combination is true in the stronger winter SWAC years. The SWAC explains not only a large portion of the interannual variability of SWWA rainfall in both early and late winter but also the long-term drying trend over SWWA in early winter. The well-coupled SWAC-SWWA rainfall relationship seems to be largely independent of the well-known effects of large-scale atmospheric circulations such as the southern annular mode (SAM), El Niño-Southern Oscillation (ENSO), Indian Ocean dipole (IOD), and ENSO Modoki (EM). The result offers qualified support for the argument that the monsoon-like circulation may contribute to the rainfall decline in early winter over SWWA. The external forcing of the SWAC is also explored in this study. © 2010 American Meteorological Society.


Lindenmayer D.B.,Australian National University | Cunningham S.A.,CSIRO
Landscape Ecology | Year: 2013

Managing a landscape for its natural resources while attempting to ensure an ecologically sustainable future is a truly complex and challenging task. We present six general principles for sustainable forest landscape management derived from insights in an array of natural and commodity production ecosystems in south-eastern Australia but which are likely to have broad applicability to many forested ecosystems worldwide. These principles are: (1) Landscape management problems are typically underpinned by human-use drivers that over-commit natural resources and undermine the ecosystem services which support the replenishment of those resources. (2) Not all parts of a landscape are equal in their contribution to species persistence and ecological processes. Special steps are needed to secure the ecological integrity of these disproportionately important areas. (3) Managing connectivity is critical, but it is essential to determine what kind of connectivity is desirable, and for what species and processes. (4) Land use practices can produce spatial and temporal cumulative effects with negative impacts on biodiversity and ecological processes. (5) Land use decisions on the land sparing-land sharing spectrum are highly scale and context dependent. (6) Our understanding of landscape-scale processes is shaped by our conceptual model of the landscape. It is therefore important to check if a given mental model is appropriate for a given landscape and the species or ecological processes of concern. These six principles should not be applied uncritically. Rather, it is best to treat them as a checklist of considerations that will help guide our thinking about landscape change, so that we can orient toward more ecologically sustainable landscape management. © 2012 Springer Science+Business Media B.V.


Van Dijk A.I.J.M.,CSIRO
Hydrology and Earth System Sciences | Year: 2010

An appropriately simple event runoff model for catchment hydrological studies was derived. The model was selected from several variants as having the optimum balance between simplicity and the ability to explain daily observations of streamflow from 260 Australian catchments (23-1902 km2). Event rainfall and runoff were estimated from the observations through a combination of baseflow separation and storm flow recession analysis, producing a storm flow recession coefficient (kQF). Various model structures with up to six free parameters were investigated, covering most of the equations applied in existing lumped catchment models. The performance of alternative structures and free parameters were expressed in Aikake's Final Prediction Error Criterion (FPEC) and corresponding Nash-Sutcliffe model efficiencies (NSME) for event runoff totals. For each model variant, the number of free parameters was reduced in steps based on calculated parameter sensitivity. The resulting optimal model structure had two or three free parameters; the first describing the non-linear relationship between event rainfall and runoff (Smax), the second relating runoff to antecedent groundwater storage (CSg), and a third that described initial rainfall losses (Li), but which could be set at 8 mm without affecting model performance too much. The best three parameter model produced a median NSME of 0.64 and outperformed, for example, the Soil Conservation Service Curve Number technique (median NSME 0.30-0.41). Parameter estimation in ungauged catchments is likely to be challenging: 64% of the variance in kQF among stations could be explained by catchment climate indicators and spatial correlation, but corresponding numbers were a modest 45% for CSg, 21% for Smax and none for L i, respectively. In gauged catchments, better estimates of event rainfall depth and intensity are likely prerequisites to further improve model performance.


Schmidt P.W.,CSIRO | Williams G.E.,University of Adelaide
Geophysical Journal International | Year: 2010

We report new palaeomagnetic data for red beds from the Ediacaran Brachina and Wonoka formations in the Adelaide Geosyncline, South Australia, and discuss their place with previously determined poles in the Ediacaran apparent polar wander path for Australia. Both formations behave similarly on thermal demagnetization, displaying high-temperature components that decay to the origin at 680 °C, consistent with haematite being the only magnetic mineral present. Restoring the strata to the palaeohorizontal yielded positive fold tests for both units at 99 per cent confidence, indicating that acquisition of magnetization occurred before the early Palaeozoic Delamerian Orogeny. For the Brachina Formation (N = 91 specimens) the mean direction after unfolding is declination D = 178.2°, inclination I = -22.6° (α95 = 4.4°), indicating a palaeolatitude λ = 11.8 ± 2.5° and a pole position at latitude λp = 46.0°S, longitude φp = 315.4°E, with confidence semi-axes dp = 2.4° and dm = 4.6° The mean direction for the Wonoka Formation after unfolding (N = 70) is D = 255.9°, I = -23.7° (α95 = 6.4°), indicating λ = 12.3 +3.8/-3.4° and a pole position at latitude λp = 5.2°S, longitude φp = 30.5°E (dp = 3.6° and dm = 6.8°). The mean directions for these units and other Ediacaran units in the Adelaide Geosyncline are significantly different from each other, which excludes blanket remagnetization of the units before Delamerian folding and therefore gives strong preference to their magnetization dating from close to the time of deposition. The late Cryogenian-Ediacaran-Cambrian apparent polar wander path for South Australia spans 150 Myr from ∼635 to 490 Ma and places Australia in low palaeolatitudes throughout the interval studied. The poles differ significantly from each other, suggesting Australia underwent continual drift during that time. Whereas the directional difference between the late Cryogenian Elatina Formation and early Ediacaran Nuccaleena Formation is mainly in inclination, for most other contiguous stratigraphic units the differences are mainly in declination with minor inclination differences, indicating Australia was rotating about a nearby Euler pole in low palaeolatitudes. The large and perhaps rapid polar shifts at 615-590 and 575-565 Ma in the Laurentian apparent polar wander path are not evident in the Ediacaran apparent polar wander path for Australia. Because true polar wander should be recorded globally, in the absence of evidence for any major stratigraphic break in the South Australian succession we conclude that large true polar wander did not occur during the Ediacaran. © 2010 CSIRO Journal compilation © 2010 RAS.


Durack P.J.,University of Tasmania | Wijffels S.E.,CSIRO
Journal of Climate | Year: 2010

Using over 1.6 million profiles of salinity, potential temperature, and neutral density from historical archives and the international Argo Program, this study develops the three-dimensional field of multidecadal linear change for ocean-state properties. The period of analysis extends from 1950 to 2008, taking care to minimize the aliasing associated with the seasonal and major global El Niño-Southern Oscillation modes. Large, robust, and spatially coherent multidecadal linear trends in salinity to 2000-dbar depth are found. Salinity increases at the sea surface are found in evaporation-dominated regions and freshening in precipitationdominated regions, with the spatial pattern of change strongly resembling that of the mean salinity field, consistent with an amplification of the global hydrological cycle. Subsurface salinity changes on pressure surfaces are attributable to both isopycnal heave and real water-mass modification of the temperature-salinity relationship. Subduction and circulation by the ocean's mean flow of surface salinity and temperature anomalies appear to account for most regional subsurface salinity changes on isopycnals. Broad-scale surface warming and the associated poleward migration of isopycnal outcrops drive a clear and repeating pattern of subsurface isopycnal salinity change in each independent ocean basin. Qualitatively, the observed global multidecadal salinity changes are thus consonant with both broad-scale surface warming and the amplification of the global hydrological cycle. © 2010 American Meteorological Society.


Bristow C.S.,University of London | Hudson-Edwards K.A.,University of London | Chappell A.,CSIRO
Geophysical Research Letters | Year: 2010

Atmospheric mineral dust plays a vital role in Earth's climate and biogeochemical cycles. The Bodl Depression in Chad has been identified as the single biggest source of atmospheric mineral dust on Earth. Dust eroded from the Bodélé is blown across the Atlantic Ocean towards South America. The mineral dust contains micronutrients such as Fe and P that have the potential to act as a fertilizer, increasing primary productivity in the Amazon rain forest as well as the equatorial Atlantic Ocean, and thus leading to N 2 fixation and CO2 drawdown. We present the results of chemical analysis of 28 dust samples collected from the source area, which indicate that up to 6.5 Tg of Fe and 0.12 Tg of P are exported from the Bodélé Depression every year. This suggests that the Bodl may be a more significant micronutrient supplier than previously proposed. © 2010 by the American Geophysical Union.


Hobday A.J.,CSIRO
Progress in Oceanography | Year: 2010

Changes in the climate due to anthropogenic effects are impacting the global oceans and the constituent biology, particularly through changes in water temperature. Impacts of warming water on oceanic species are most likely to be detected as changes in distribution. Pelagic fishes, in particular, respond to changes in ocean temperature, and modify their distribution on seasonal and interannual timescales, and thus are likely to do so in the future. Global climate models provide insight into possible future conditions, but there is also considerable uncertainty regarding future changes because of differences in model structure and future scenarios. To address some of this uncertainty, I considered output from multiple climate models through an ensemble analysis and examined potential changes in the distribution of large pelagic fishes captured by longline fisheries on the east and west coast of Australia by the year 2100. For the east coast, over 95% of model predictions for 14 pelagic species (tunas and billfishes) suggested that core range would move south, and be smaller than what occurs presently. There was less certainty for the west coast, although the core range for all 14 species moved south and was smaller for 63% and larger for 37% of scenario-model combinations. The overall rate of predicted habitat movement for the suite of pelagic species averaged about 40 km/decade. While relatively coarse, these predictions give some confidence to stakeholders about likely changes in future distribution for these regionally important pelagic fishes. © 2010.


Ma X.,CSIRO
International Journal of Mineral Processing | Year: 2010

The effect of hydrolyzable metal cations, i.e. calcium and magnesium, present in mineral suspensions on starch-kaolinite interactions was studied through zeta potential, adsorption and turbidity measurements. The results demonstrate that hydrolyzable metal cations in mineral suspensions can significantly affect starch adsorption on kaolinite under typical conditions of iron ore flotation and selective flocculation. The effect of calcium and magnesium on starch adsorption on kaolinite surfaces correlates to their abilities to reduce the electrostatic repulsion between the anionic starch molecules and the negatively charged kaolinite particles. The hydrolyzable metal cations cause fast coagulation of kaolinite particles at pH 10.5 by reducing the repulsive electrostatic forces between kaolinite particles, when their concentration is ≥ 0.001 M. The presence of starch further enhances such effect at low dosages, but re-disperses kaolinite particles at high dosages by inducing steric forces between the kaolinite particles coated with starch. © 2010 Elsevier B.V. All rights reserved.


Guo H.,Shanghai University | Xu H.,University of Wisconsin - Madison | Barnard A.S.,CSIRO
Energy and Environmental Science | Year: 2013

Environmental indicators play an important role in assessing the state of the environment and understanding the trend of environmental changes. Iron oxide nanostructures are widespread in multiple ecosystems, and are therefore suitable for providing environmental indicators with measurable physical or chemical properties that are sensitive to the environmental conditions. It has been found that the morphologies of natural hematite (α-Fe 2O3) nanocrystals have large variations depending on thermodynamic and chemical conditions of their formation environments. To assess the applicability of nanomorphology as an environmental indicator, we construct a morphology map of hematite nanocrystals in hydrous environments, characterized with different temperatures, humidity and supersaturation of oxygen. Our model indicates that the fractional surface areas of morphologically significant facets change with humidity and temperature, and can be used to track the variation of these environmental conditions. This journal is © The Royal Society of Chemistry 2013.


I develop and test several new phase-shifting formulas for a Fizeau interferometer, using a spherical cavity of high NA. The associated phase-shift miscalibrations provide a useful range for testing phase-shift error compensation experimentally. After removing the "double-frequency" cyclic phase variation from the error-fringe pattern by wellknown methods, the residual phase oscillations occur mainly at 1 and 3 times the fringe frequency. The latter can be addressed by the theory of characteristic polynomials; the former cannot, but is removed by a variation on known averaging methods, and allows empirical optimization of phase-reconstruction performance, which can then be analyzed with characteristic polynomials again. © 2010 Optical Society of America.


Climate change is now a hot political topic that blurs the boundary between policy relevant and policy prescriptive (as contained for example in the avowed stance of the Intergovernmental Panel on Climate Change). The growing political relevance of climate change science necessarily places a premium on timely advice and on risk assessment and management. What is the role of climate scientists in that new situation? © The Author(s) 2010.


Van Dijk A.I.J.M.,CSIRO
Hydrology and Earth System Sciences | Year: 2010

Daily streamflow data were analysed to assess which climate and terrain factors best explain streamflow response in 183 Australian catchments. Assessed descriptors of catchment response included the parameters of fitted baseflow models, and baseflow index (BFI), average quick flow and average baseflow derived by baseflow separation. The variation in response between catchments was compared with indicators of catchment climate, morphology, geology, soils and land use. Spatial coherence in the residual unexplained variation was investigated using semi-variogram techniques. A linear reservoir model (one parameter; recession coefficient) produced baseflow estimates as good as those obtained using a non-linear reservoir (two parameters) and for practical purposes was therefore considered an appropriate balance between simplicity and explanatory performance. About a third (27-34%) of the spatial variation in recession coefficients and BFI was explained by catchment climate indicators, with another 53% of variation being spatially correlated over distances of 100-150 km, probably indicative of substrate characteristics not captured by the available soil and geology data. The shortest recession half-times occurred in the driest catchments and were attributed to intermittent occurrence of fast-draining (possibly perched) groundwater. Most (70-84%) of the variation in average baseflow and quick flow was explained by rainfall and climate characteristics; another 20% of variation was spatially correlated over distances of 300-700 km, possibly reflecting a combination of terrain and climate factors. It is concluded that catchment streamflow response can be predicted quite well on the basis of catchment climate alone. The prediction of baseflow recession response should be improved further if relevant substrate properties were identified and measured.


Weinberg R.F.,Monash University | Regenauer-Lieb K.,University of Western Australia | Regenauer-Lieb K.,CSIRO
Geology | Year: 2010

Mechanisms proposed to explain efficient melt transport away from hot, ductile source regions are problematic. Brittle-elastic fracturing is a well-known mechanism that allows fast magma migration as dikes through cold crust. Ductile fractures have been propo sed as an alternative for ductile environments, where brittle-elastic diking is inhibited. Ductile fracturing results from rock creep and growth of microscale voids that become interconnected, leading to rock failure. In this paper, we present observations and numerical models supporting the hypothesis that ductile fracture controls early steps in magma migration. We postulate that once developed, ductile fracture dikes may reach a critical length where magma stresses at dike tips overcome fracture toughness and lead to brittle-elastic diking, which subsequently controls magma migration. © 2010 Geological Society of America.


Rickards L.,University of Melbourne | Howden S.M.,CSIRO
Crop and Pasture Science | Year: 2012

Climate change presents the need and opportunity for what the Stern report called 'major, non-marginal change'. Such transformational adaptation is rapidly emerging as a serious topic in agriculture. This paper provides an overview of the topic as it applies to agriculture, focusing on the Australian situation. It does so by first defining transformational adaptation, distinguishing it from other more incremental but overlapping modes of climate change adaptation and positing its emergence in agriculture as a response to both drivers and opportunities. The multiple dimensions of transformational adaptation are highlighted before two types or cases are focussed upon in order to tease out issues and highlight two major examples of transformation in agriculture in the past. Four key issues about climate change adaptation in agriculture particularly pertinent for transformational adaptation are then reviewed: the identification, level, distribution and management of the costs of adaptation; the definition, potential for and need to avoid maladaptation; the capacity demands that this level of adaptation presents; and the role of government in adaptation. Overall, transformational adaptation poses potential great gains but also great risks. It reinforces the realisation that agricultural research can no longer remain insulated from off-farm, non-science or non-agricultural knowledge or processes. Support and guidance of transformational adaptation requires that we understand how Australian agriculture is currently, and could be, positioned within the landscape, rural communities, and broader social, political and cultural environment. © 2012 CSIRO.


Using large-scale variables, in this study we have developed a method for defining monsoon onset/retreat in the Australia-Asian region and used this method to study monsoon activities simulated by global climate models. For this purpose, the method needs to capture fundamental characteristics of monsoon rainfall and circulation seasonal variations and at the same time it can be reasonably simulated by current climate models. We develop the method by using both atmospheric precipitable water and wind conditions in our definition and compared our results using 44-year ERA-40 reanalysis data with some published results in the region. Our results offer similar features to several observational studies, including features in Australia-Asian summer monsoon temporal and spatial evolutions and their interannual variations. Results further show that the observed significant increase in summer rainfall in northwest Australia corresponds to earlier onset and much longer duration of its summer monsoon, with its duration significantly increased. Prolonged summer monsoon duration is also seen in central-east China where upward rainfall trend is observed. Furthermore, the Australian summer monsoon appears to be more affected by ENSO than the Asian monsoon, with delayed onsets and shortened durations during El Nino years. Finally, by analyzing results from an IPCC AR4 model, we have shown that using the two large-scale variables simulated by climate models, it is possible to conduct some detailed studies on monsoon activities in current and future climate. Results from this particular model suggest that global warming could potentially modify some of the monsoon characteristics, including earlier onset in most of the region but different features for changes in duration. In the Australian region, it also displays further southward penetration of its summer monsoon. © 2009 Springer-Verlag.


The Coorong is a choked coastal lagoon in South Australia that forms part of the terminal lake system at the end of the River Murray, Australia's major river. It is an inverse estuary with a constricted channel connection to the sea at one end and extends parallel to the coast for more than 100 km away from this inlet. The present paper considers the physical dynamics of the Coorong, particularly its ecologically important salinity and water level regimes, and how these respond to connectedness with the ocean, barrage flows and meteorological conditions. The approach combines hydrodynamic modelling with measurements and considers temporal variation in the system ranging from seasonal to multi-decadal timescales.The Coorong is relatively unusual in that the major freshwater input occurs through barrages much closer to the estuary mouth than to its head. Thus, the barrage flows only 'flush' the Coorong between the barrages and the sea. Over most of its length, salt accumulating through evapo-concentration mixes back out of the system by fluctuating water motions caused by sea level variations propagating through the inlet channel and by wind. By scouring the inlet channel on a seasonal basis, barrage flows facilitate the penetration of sea level variations into the Coorong leading to enhanced along-lagoon mixing. Further, barrage flows freshen the waters near the seaward end of the system causing water of lower salt content than sea water to replace evaporative losses in its interior. By increasing the water depth in the system, barrage flows facilitate the exchange between the North and South Lagoons of the Coorong which are its two major basins.The modelling supported by measurements shows how the salinity regime in the Coorong appears to have responded to multi-year cycles of variation in discharge of the River Murray over the last 50 years. Even before the present drought, which has seen salinity in the South Lagoon exceed four times sea water, the lagoon was dominantly hypersaline. The modelling suggests that the significant reductions in freshwater inflows to the Coorong due to water resource development would have caused the South Lagoon to evolve from a state of being usually brackish to marine into its present hypersaline state. The conceptual understanding of the Coorong's physical dynamics and their encapsulation in a hydrodynamic model are enabling strategies to be evaluated for alleviation of its present degraded condition, and for its improved future management. © 2010.


Poulsen B.A.,CSIRO
International Journal of Rock Mechanics and Mining Sciences | Year: 2010

A method for calculating the load acting on a pillar of coal in a bord-and-pillar mine is described for the purpose of back analysing pillar failure or assessing the stability of a panel of pillars. The method is applicable to pillars of arbitrary plan shape and accounts for the spatial position of the pillar with respect to the other pillars, un-mined coal, and the network of roadways. Calculation of the extraction ratio within the pillar's zone of influence defined by the depth dependent load transfer distance accounts for the pillar's spatial position in the mine layout. An advantage of this approach is its suitability for computer programming for the automated analysis of hundreds of pillars. In this paper, pillars are analysed by the new method, and by tributary area theory, with the results from the new method comparing favourably to elastic three dimensional numerical analysis. Finally, an example of coal mine pillar failure from the literature that neither could be satisfactorily back-analysed by the traditional factor of safety approach nor by two-dimensional numerical modelling is considered. With the proposed, approach 42 of the 54 pillars in the observed failed pillar region are predicted to have a safety factor below the recommended value for long term stability and of these, three pillars are predicted to have an FoS of 1.18. With tributary area theory every pillar, including all those outside the failed pillar region, is predicted to have an FoS less than 1.2. © 2010.


Lucas C.,CSIRO
Australian Meteorological and Oceanographic Journal | Year: 2010

The creation of a national historical fire weather data-set, extending from 1973 to 2008, is described. For this purpose, fire weather is described using the McArthur Forest Fire Danger Index (FFDI). A detailed deconstruction of the FFDI and its sensitivities is presented. To create the data-set, meteorological measurements of air temperature, relative humidity, wind speed and rainfall are required. A total of 77 stations are used. At many of these stations, the input data are non-homogeneous. A particularly concerning issue for the fire weather data-set here is the inhomogeneity of the wind measurements, largely a consequence of different measurement instrumentation and methodologies implemented over the decades. Monte Carlo techniques are used to investigate the sensitivity of the distribution of the FFDI to changes in the distribution of the wind. The mean wind speed is shown to have the largest effect. A method for estimating the magnitude of the errors introduced is presented.


Luhar A.K.,CSIRO
Boundary-Layer Meteorology | Year: 2010

Information concerning the average wind speed and the variances of lateral and longitudinal wind velocity fluctuations is required by dispersion models to characterise turbulence in the atmospheric boundary layer. When the winds are weak, the scalar average wind speed and the vector average wind speed need to be clearly distinguished and both lateral and longitudinal wind velocity fluctuations assume equal importance in dispersion calculations. We examine commonly-used methods of estimating these variances from wind-speed and wind-direction statistics measured separately, for example, by a cup anemometer and a wind vane, and evaluate the implied relationship between the scalar and vector wind speeds, using measurements taken under low-wind stable conditions. We highlight several inconsistencies inherent in the existing formulations and show that the widely-used assumption that the lateral velocity variance is equal to the longitudinal velocity variance is not necessarily true. We derive improved relations for the two variances, and although data under stable stratification are considered for comparison, our analysis is applicable more generally. © Springer Science+Business Media B.V. 2010.


Provision of independent scientific advice is central to the operation of regional fisheries management organizations (RFMOs) even though RFMOs are largely policy (and political) instruments. Political pressures and intervention in science and crossing of the boundaries between scientific and political processes, however, appear to be relatively common. A case study is presented to illustrate some ways in which this occurs. It involves a paper that was withdrawn from scientific meetings of two RFMOs as a result of largely political (rather than scientific) concerns. The details involved in this incident are important for understanding the ways in which political intervention in independent scientific process can and does occur. Moreover, unless one is directly involved in actions of this kind, it is impossible from the reports of RFMOs' scientific bodies to assess whether, and the extent to which, there has been political intervention in the scientific process. It is argued that the nature of the working arrangements in these scientific committees can engender deliberate or inadvertent crossing of the boundaries between scientific independence and the political processes of RFMOs, both of which are important components of RFMO operation. Further, there is very little documentation or assessment of the generic extent of such problems. No simple solutions or reforms exist for isolating scientific advice from political agenda in the processes of RFMOs but it is suggested that increased discussion of the problem along with better understanding and clarity of the role of science in the management process may lead to improved recognition of the importance of independent scientific analyses and advice. © 2011 Elsevier Ltd.


Zhang X.,University of Melbourne | Maeda N.,CSIRO
Journal of Physical Chemistry C | Year: 2011

We previously reported formation of spherical-cap-shaped nanobubbles and a quasi-two-dimensional gas layer (micropancakes) on highly oriented pyrolytic graphite (HOPG) surfaces by the solvent-exchange protocol. Here we report that the same protocol is capable of inducing gaseous micropancakes as well as nanobubbles on two other crystalline surfaces: molybdenum disulfide (MoS 2) and talc in water. The maximum height of gaseous micropancakes in atomic force microscopy (AFM) images was found to correlate well with the maximum height of nanobubbles on the same surface. In contrast, the same protocol was unable to induce spherical-cap-shaped nanobubbles or gaseous micropancakes on amorphous (glassy) carbon or on trimethylchlorosilane-coated silicon surfaces, which had a similar contact angle of water as the crystalline surfaces. It appears that formation of these interfacial gaseous states requires the presence of adequate nucleation sites on the surfaces (in addition to local supersaturation of gases created during the solvent exchange). The layered structure of the surfaces and concomitant presence of atomic steps appeared to have facilitated the formation of gaseous micropancakes. © 2010 American Chemical Society.


Barnard A.S.,CSIRO
Energy and Environmental Science | Year: 2011

The design of optimal nanoparticle photocatalysts requires a detailed understanding of how materials parameters relate to photoactivity. To make these devices safe the same information is needed to assess the potential for nanotoxicity from free radicals. In this study a structure-property map for predicting the efficiency for free radical production of titania nanoparticles as a function of particle size and the thermal/chemical environment is presented. The results, which account for the size- and temperature-dependent anatase-to-rutile phase transition and changes in shape, show an increase in activity/toxicity at around 33 nm, in agreement with previously reported experimental results. © 2011 The Royal Society of Chemistry.


Jasinge D.,Monash University | Ranjith P.G.,Monash University | Choi S.K.,CSIRO
Fuel | Year: 2011

One of the key issues with geological sequestration of carbon dioxide in coal seams is change of permeability caused by carbon dioxide (CO2) injection, and especially any resulting reduction in injectivity. Injection causes changes in pressure and effective stress, with further changes caused by coal matrix swelling associated with adsorption of CO2. In this paper we aim to study how the change in effective stress and coal swelling may influence the gas permeability in brown coal using natural coal and reconstituted coal specimens. Tests were conducted at different confining pressures to represent conditions at different depths. Different gas injection pressures were also employed at each confining stress stage. The test results clearly depicted an exponential reduction of coal permeability to CO2 gas when effective stress increases. Based on the experimental results, an empirical correlation to represent the effect of stress on permeability was developed. The results also showed that increase in pore pressure can induce further swelling of the coal specimens, and this can lead to further decrease in permeability which can have important impact on field injectivity. Test results for natural brown coal specimens were compared with results of tests on reconstituted coal specimens made from compaction of coal particles obtained from crushing of blocks of natural coal. Observed permeability behaviour of gas in reconstituted coal was similar to the natural coal specimen permeability trend, when effective stress increases. © 2010 Elsevier Ltd. All rights reserved.


Bt cotton has been gradually released and adopted by Australian growers since 1996. It was initially deployed in Australia primarily to control the polyphagous pest Helicoverpa armigera (Hübner), which in the 1990s became increasingly difficult to control due to widespread resistance to synthetic chemical insecticides. Bt-cotton has become a key tool in a program of integrated pest management for the production system that reduces pesticide dependence and the problems associated with its use. Herein we overview the deployment of Bt cotton in Australia including its performance and the approaches used to prolong the evolution of resistance to it by H. armigera. An integral component of this approach is monitoring resistance in this pest. We outline resistance screening methods, as well as the characteristics of resistant strains of H. armigera that have been isolated from field populations, or selected in the laboratory. We then highlight the successes and challenges for Bt cotton in Australia by way of discussing adaptive resistance management in light of potential changes in resistance.


Lim E.-P.,Center for Australian Weather and Climate Research | Hendon H.H.,Center for Australian Weather and Climate Research | Rashid H.,CSIRO
Journal of Climate | Year: 2013

has traditionally been considered to be low because the SAM is regarded as an internal mode of variability with a typical decorrelation time of about 10 days. However, the association of the SAM with El Niño-Southern Oscillation (ENSO) suggests the potential for making seasonal predictions of the SAM. In this study the authors explore seasonal predictability and the predictive skill of SAM using observations and retrospective forecasts (hindcasts) from the Australian Bureau of Meteorology dynamical seasonal forecast system [the Predictive Ocean and Atmosphere Model for Australia, version 2 (POAMA2)]. Based on the observed seasonal relationships of the SAM with tropical sea surface temperatures, two distinctive periods of high seasonal predictability are suggested: austral late autumn to winter and late spring to early summer. Predictability of the SAM in the austral cold seasons stems from the association of the SAM with warm-pool (or Modoki/central Pacific) ENSO, whereas predictability in the austral warm seasons stems from the association of the SAM with cold-tongue (or eastern Pacific) ENSO. Using seasonal hindcasts for 1980-2010 from POAMA2, it is shown that the observed relationship between SAM and ENSO is faithfully depicted and SST variations associated with ENSO are skillfully predicted. Consequently, POAMA2 can skillfully predict the phase and amplitude of seasonal anomalies of the SAM in early summer and early winter for at least one season in advance. Zero-lead monthly forecasts of theSAMare furthermore shown to be highly skillful in almost all months, which is ascribed to predictability stemming from observed atmospheric initial conditions. © 2013 American Meteorological Society.


Understanding the emergence and sustainability of cooperation is a fundamental problem in evolutionary biology and is frequently studied in the framework of evolutionary game theory. A very powerful mechanism to promote cooperation is network reciprocity, where the interaction patterns and opportunities for strategy spread of agents are constrained to limited sets of permanent interactions partners. Cooperation survives because it is possible for close-knit communities of cooperation to be shielded from invasion by defectors. Here we show that parameter ranges in which cooperation can survive are strongly expanded if game play on networks is skewed towards more frequent interactions with more successful neighbours. In particular, if agents exclusively select neighbors for game play that are more successful than themselves, cooperation can even dominate in situations in which it would die out if interaction neighbours were chosen without a bias or with a preference for less successful opponents. We demonstrate that the "selecting fitter neighbours" strategy is evolutionarily stable. Moreover, it will emerge as the dominant strategy out of an initially random population of agents. Copyright © 2011 EPLA.


Min S.-K.,CSIRO | Son S.-W.,Seoul National University
Journal of Geophysical Research: Atmospheres | Year: 2013

It has been suggested that the Hadley cell has been widening during the past three decades in both hemispheres, but attribution of its cause(s) remains challenging. By applying an optimal fingerprinting technique to 7 modern reanalyses and 49 coupled climate models participating in the CMIP3 and CMIP5, here we detect an influence of human-induced stratospheric ozone depletion on the observed expansion of the Hadley cell in the Southern Hemisphere (SH) summer. The detected signal is found to be separable from other external forcings that include greenhouse gases (GHGs), confirming a dominant role of stratospheric ozone in the SH summer climate change. Our results are largely insensitive to observational and model uncertainties, providing additional evidence for a human contribution to the atmospheric circulation changes. © 2013. American Geophysical Union. All Rights Reserved.


Nguyen D.T.,University of Tasmania | Negnevitsky M.,University of Tasmania | De Groot M.,CSIRO
IEEE Transactions on Power Systems | Year: 2011

In restructured power systems, there are many independent players who benefit from demand response (DR). These include the transmission system operator (TSO), distributors, retailers, and aggregators. This paper proposes a new concept-demand response eXchange (DRX)-in which DR is treated as a public good to be exchanged between DR buyers and sellers. Buyers need DR to improve the reliability of their own electricity-dependent businesses and systems. Sellers have the capacity to significantly modify electricity demand on request. Microeconomic theory is applied to model the DRX in the form of a pool-based market. In this market, a DRX operator (DRXO) collects DR bids and offers from the buyers and sellers, respectively. It then clears the market by maximizing the total market benefit subject to certain constraints including: demand-supply balance, and assurance contracts related to individual buyer contributions for DR. The DRX model is also tested on a small power system, and its efficiency is reported. © 2011 IEEE.


Species of Apelaunothrips are fungus-feeders on dead leaves, particularly in leaf-litter, and they are recorded across the Old World tropics from Africa to northern Australia and southern Japan. All species in this genus have the maxillary stylets 4-6 microns in diameter, considerably broader than the 2-3 micron diameter that is typical among Phlaeothripinae. The species are largely uniform in structure, but in four species the larger males have fore femora enlarged with a conspicuous tubercle on the inner margin at the base. In one of these species, the males are dimorphic, with no intermediates between large and small individuals, in contrast to the continuous variation in structure found in many polymorphic Phlaeothripidae. A key is provided to the 37 recognised species of Apelaunothrips, including the following: A. desleyae sp.n. from northern Australia; A. bogor sp.n. from Java; A. gombak sp.n. from Peninsular Malaysia. Copyright © 2013 Magnolia Press.


Abouna S.,CSIRO
International Journal of Mining Science and Technology | Year: 2014

This study discusses a method of quantifying emissions from surface coal mining that has been trialled in Australia. The method is based on direct measurement of surface emissions from uncovered coal seams in mine pits, concurrent measurement of residual gas content of blasted coal in mine pits, and measurement of pre-mining gas content of the same seam from cores retrieved from exploration boreholes drilled away from active mining. The results from one of the mines studied are presented in this paper. In this mine, the pre-mining gas content of the target seam was measured using cores from an exploration borehole away from active mining. Gas content varied from 0.7 to 0.8 m 3/t and gas composition varied from 16% to 21% CH4 (84-79% CO2). In-pit measurements included seam surface emissions and residual gas content of blasted and ripped coal. Residual gas content varied from 0.09 to 0.15 m3/t, less than twofold across the mine pit. Composition of the residual gas was in general 90% CO2 and 10% CH4, with slight variation between samples. Coal seam surface emissions varied from 1.03 to 7.50 mL of CO2-e per minute and per square meter of the coal seam surface, a sevenfold variation across the mine pit. © 2014 Published by Elsevier B.V. on behalf of China University of Mining & Technology.


Su F.,South China University of Technology | Miao M.,CSIRO
Electrochimica Acta | Year: 2014

We present a simple design and a fabrication method for a high-performance, flexible, two-ply yarn supercapacitor based on irradiated CNT yarn and conductive polymer Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT/PSS). The CNT yarn is treated with gamma irradiation and the yarn surface is coated with the PEDOT/PSS to improve the energy storage capacitance of the as-spun yarn supercapacitor. A layer of PVA gel is coated on the surfaces of the CNT yarn and the composite yarn to form a separation layer containing electrolyte. The results show that the gamma irradiation greatly increases the electrical conductivity and improved the gram capacitance of the as-spun CNT two-ply yarn supercapacitor. The coating of PEDOT/PSS on the surface of the pure and irradiated CNT yarns further significantly improves the capacitance of the supercapacitors. The two-ply yarn supercapacitor constructed from the irradiation CNT yarn coated by PEDOT/PSS exhibits the large capacitance and high cyclic charge-discharge stability. Moreover, these two-ply yarn supercapacitors with fine diameters are highly flexible and can be easily woven or knitted into textile fabrics for uses in wearable electronics. © 2014 Elsevier Ltd.


Moad G.,CSIRO
Progress in Polymer Science (Oxford) | Year: 2011

Processes for chemical transformation of starch by extrusion processing (reactive extrusion, REX) are reviewed with a focus on non-food applications. The scope, advantages, limitations and specificity of various REX processes for are examined in this context. The processes covered include: the grafting of monomers from starch as single units, such as ring-opening of epoxides, esterification (with lactones, anhydrides, acids, halides or vinyl esters) phosphorylation and silylation; graft polymerization from starch by radical-induced grafting or the ring-opening polymerization of lactones; reactive compatibilization with polyesters and polyolefins by grafting to or from starch; crosslinking of starch with epichlorohydrin or by phosphorylation; and the degradation of starch thermally or catalyzed by acid or enzymes. © 2010 Elsevier Ltd. All rights reserved.


Chen Z.W.,Xiamen University | Chen Z.W.,Hong Kong Polytechnic University | Xu Y.L.,Hong Kong Polytechnic University | Wang X.M.,CSIRO
Journal of Structural Engineering (United States) | Year: 2012

Long-span suspension bridges carrying both highway and railway have been built in wind-prone regions. The estimation of fatigue damage of such bridges under the long-term combined action of railway, highway, and wind loading represents a challenging task in consideration of randomness in multiple types of loading. This study presents a framework for fatigue reliability analysis of multiloading long-span suspension bridges equipped with structural health monitoring systems (SHMS), and the Tsing Ma suspension bridge in Hong Kong is taken as a case study. A limit-state function in the daily sum of m-power stress ranges is first defined for fatigue reliability analysis. Probabilistic models of railway, highway, and wind loading are established on the basis of the measurement data acquired from the SHMS. The daily stochastic stress responses induced by the multiple types of loading are simulated at the fatigue-critical locations of the bridge deck by using the finite-element method and Monte Carlo simulation (MCS) together with the loading probabilistic models established. The probability distribution of the daily sum of m-power stress ranges is estimated on the basis of the daily stochastic stress responses. The probability distribution of the sum of m-power stress ranges for a given time period is then evaluated in consideration of future traffic growth patterns. Finally, the fatigue failure probabilities of the bridge at the fatigue-critical locations are calculated for different time periods. The results demonstrate that the health condition of the Tsing Ma Bridge at the end of its design life will be satisfactory under current traffic conditions without growth but that attention should be paid to future traffic growth because it may lead to a much greater fatigue failure probability. © 2012 American Society of Civil Engineers.


Ananda J.,La Trobe University | Proctor W.,CSIRO
Ecological Economics | Year: 2013

Despite the popularity and rhetoric of collaborative approaches, the successes of such initiatives are not widespread and remain elusive. Some commentators argue that without 'the noise of participation', a return to centralised governance should be reconsidered. Whilst this conclusion may be premature given the lack of rigorous analysis of collaborative approaches, it calls for a closer examination of contexts and processes that are conducive to the success of collaborative initiatives. This paper evaluates the scope of collaborative watershed management and planning in the Howard River Catchment in northern Australia. The findings depict the challenges of collaborative planning in a nested hierarchy with multiple institutions. The existing institutional apparatus can potentially constrain the collaborative initiatives to water planning. They include the norms of agency authority, administrative inflexibility and power structures in a nested institutional hierarchy. Delegating decision making responsibility to decentralized structures should be backed up by the development of the capacity of such structures. Considerable transaction costs exist in overlaying collaborative approaches across a nested hierarchy of multiple institutions. © 2012 Elsevier B.V.


Alteration and associated impurity element enrichment in detrital ilmenites from the Murray Basin in southeastern Australia was examined using electron-beam imaging and analysis techniques. A database of over 15 000 analyses from 22 deposits (16 coarse grained, six fine grained) showed a broad spectrum of alteration products from primary ilmenite through to pseudorutile, hydroxylian pseudorutile and minor leucoxene. Impurity element levels were strongly affected by the degree of alteration. Ilmenites from fine-grained deposits were less altered than their coarse-grained equivalents. Regional analysis of the data showed an increase in the degree of alteration towards the northern margins of the basin. Two types of ilmenite alteration were observed: a continuous process in which ilmenite alters to pseudorutile and then leucoxene (Type I) plus a second type of alteration which converts ilmenite directly to hydroxylian pseudorutile (Type II). Type I alteration was present throughout all deposits and occurred prior to final emplacement under acidic oxygenated conditions. Type II alteration was restricted to deposits in the more northern sectors of the basin. Conditions for the formation of Type II alteration are unknown but textural evidence indicates alteration was in situ. The Murray Basin ilmenites represent the final products of multi-stage alteration processes. © 2010 Geological Society of Australia.


Allen J.I.,Plymouth Marine Laboratory | Fulton E.A.,CSIRO
Progress in Oceanography | Year: 2010

The paper by Hannah et al. (this volume) invokes foodweb theory and the ideas of complexity theory to guide the construction of models of intermediate complexity, which sacrifice explicit process detail to increase the number of interacting components of the system and simulate the web of feedback loops. This approach has its merits, if best practice modelling guidelines are followed and the method is used well. However, if this is not the case then the fundamental weakness of the intermediate model approach is that it may end up producing models that are over general and therefore not useful. To make the most of the intermediate complexity approach it is essential to keep the tenets of the middle-out approach in mind. Under the middle-out approach computational models are constructed and tested at the levels where we have the most detailed information, building on our existing knowledge and data and coupling a hierarchy of models rather than being swamped in a morass of detail or missing key feedbacks through over-generality. © 2009 Elsevier Ltd.


One of the aims of developing new climate projections is to better address the requirements of stakeholders-particularly those who require less uncertainty and/or probabilistic information to work with. Projections are continually updated over time as more, and newer, climate model simulations of the future become available but this can introduce problems when it comes to interpreting large samples with differing results. Regional projections of rainfall are characterised by a high level of uncertainty, partly because of different sensitivities of the different models. Some models can be demonstrated to perform relatively poorly when assessed by their ability to simulate present-day means and variability and here we show that the uncertainty in model projections can potentially be reduced when the projection from these models are either discounted or ignored entirely. When applied to the Murray Darling Basin of south east Australia, it is possible to demonstrate a clustering of the results from the better performing models. These indicate that the rainfall changes to be expected as a result of increased greenhouse gas concentrations into the future are more likely to be at the drier end of the full set of model results. This occurs because the better performing models indicate decreases in winter and spring which are significantly different to the changes indicated by the other models. These results suggest that there are compelling reasons for discounting, if not entirely dismissing, some model results based on their failure to satisfy some basic performance criteria. © 2009 Springer Science+Business Media B.V.


Corujeira Gallo S.,CSIRO | Dong H.,University of Birmingham
Scripta Materialia | Year: 2012

Low-temperature active-screen plasma nitriding is an effective surface engineering technology to improve the wear and corrosion resistance of austenitic stainless steel through the formation of expanded austenite. The material sputtered from the active screen and redeposited on the specimens has been suggested to play an important role in the nitriding mechanism involved. This paper reports a patterned deposition layer, which is in correlation with the grain orientation of polycrystalline specimens. This has provided new insights into the nitriding mechanism. © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


A new genus of oribatid mite, Spineremaeus is erected and its type species, S. smithi sp. nov., is described from Norfolk Island, as well as three new species belonging to the genus Scapheremaeus. Spineremaeus is morphologically closest to the Emarginatus species-group of Scapheremaeus, found in Australia, Java and New Zealand. Scapheremaeus pinguis sp. nov. is closest morphologically to S. emarginatus from New Zealand. Scapheremaeus pacificus sp. nov. and S. tumidus sp. nov., members of the Carinatus species-group, are closest morphologically to each other and to S. insularis, also from New Zealand. Thus all four cymbaeremaeid species from Norfolk Island show strongest biogeographical affinities with the oribatid fauna of New Zealand rather than Australia. Copyright © 2011 Magnolia Press.


Xia J.,University of Oklahoma | Luo Y.,University of Oklahoma | Wang Y.-P.,CSIRO | Hararuk O.,University of Oklahoma
Global Change Biology | Year: 2013

Biogeochemical models have been developed to account for more and more processes, making their complex structures difficult to be understood and evaluated. Here, we introduce a framework to decompose a complex land model into traceable components based on mutually independent properties of modeled biogeochemical processes. The framework traces modeled ecosystem carbon storage capacity (Xss) to (i) a product of net primary productivity (NPP) and ecosystem residence time (τE). The latter τE can be further traced to (ii) baseline carbon residence times (τ′E), which are usually preset in a model according to vegetation characteristics and soil types, (iii) environmental scalars (ξ), including temperature and water scalars, and (iv) environmental forcings. We applied the framework to the Australian Community Atmosphere Biosphere Land Exchange (CABLE) model to help understand differences in modeled carbon processes among biomes and as influenced by nitrogen processes. With the climate forcings of 1990, modeled evergreen broadleaf forest had the highest NPP among the nine biomes and moderate residence times, leading to a relatively high carbon storage capacity (31.5 kg cm-2). Deciduous needle leaf forest had the longest residence time (163.3 years) and low NPP, leading to moderate carbon storage (18.3 kg cm-2). The longest τE in deciduous needle leaf forest was ascribed to its longest τ′E (43.6 years) and small ξ (0.14 on litter/soil carbon decay rates). Incorporation of nitrogen processes into the CABLE model decreased Xss in all biomes via reduced NPP (e.g., -12.1% in shrub land) or decreased τE or both. The decreases in τE resulted from nitrogen-induced changes in τ′E (e.g., -26.7% in C3 grassland) through carbon allocation among plant pools and transfers from plant to litter and soil pools. Our framework can be used to facilitate data model comparisons and model intercomparisons via tracking a few traceable components for all terrestrial carbon cycle models. Nevertheless, more research is needed to develop tools to decompose NPP and transient dynamics of the modeled carbon cycle into traceable components for structural analysis of land models. © 2013 Blackwell Publishing Ltd.


The integration of social and ecological knowledge has been identified as one of the key issues and research priorities in landscape ecology. However, research into the tools and processes that support knowledge integration for planning sustainable land- and sea-scapes is largely lacking. To fill this gap, Bohnet and Smith (Landsc Urban Plan 80:137-152, 2007) developed a social-ecological planning framework based on a holistic landscape concept which I applied in the Tully-Murray basin to test the framework's transferability and effectiveness for knowledge integration in a water quality improvement planning context in the Great Barrier Reef (GBR) region, Australia. In this paper I present the context in which the Tully Water Quality Improvement Plan (WQIP) was developed, the tools and processes applied during the three planning stages to achieve knowledge integration, and the results from this exercise. I then discuss the transferability and effectiveness of the framework using criteria identified to assess collaborative planning processes, outputs and outcomes, such as collaborative science and social and political capital. While many social outcomes such as the creation of partnerships between multiple-stakeholders, including Traditional Owners, local farmers, industry, government, community groups, schools, and the wider public, have been achieved, the research also highlights some of the challenges related to multiple-stakeholder relations. Further research into the roles and responsibilities of multiple-stakeholders for knowledge integration in developing and managing sustainable land- and sea-scapes is recommended. © 2010 Springer Science+Business Media B.V.


Cox S.J.D.,CSIRO
Semantic Web | Year: 2016

We have extended OWL-Time to support the encoding of temporal position in a range of reference systems, in addition to the Gregorian calendar and conventional clock. Two alternative implementations are provided: as a pure extension or OWL-Time, or as a replacement, both of which preserve the same representation for the cases originally supported by OWL-Time. The combination of the generalized temporal position encoding and the temporal interval topology from OWL-Time support a range of applications in a variety of cultural and technical settings. These are illustrated with examples involving non-Gregorian calendars, Unix-time, and geologic time using both chronometric and stratigraphic timescales. © 2016 - IOS Press and the authors. All rights reserved.


Gardner J.L.,Australian National University | Peters A.,Max Planck Institute for Ornithology (Radolfzell) | Peters A.,Monash University | Kearney M.R.,University of Melbourne | And 2 more authors.
Trends in Ecology and Evolution | Year: 2011

A recently documented correlate of anthropogenic climate change involves reductions in body size, the nature and scale of the pattern leading to suggestions of a third universal response to climate warming. Because body size affects thermoregulation and energetics, changing body size has implications for resilience in the face of climate change. A review of recent studies shows heterogeneity in the magnitude and direction of size responses, exposing a need for large-scale phylogenetically controlled comparative analyses of temporal size change. Integrative analyses of museum data combined with new theoretical models of size-dependent thermoregulatory and metabolic responses will increase both understanding of the underlying mechanisms and physiological consequences of size shifts and, therefore, the ability to predict the sensitivities of species to climate change. © 2011 Elsevier Ltd.


Robson B.J.,CSIRO
Environmental Modelling and Software | Year: 2014

This systematic review considers how water quality and aquatic ecology models represent the phosphorus cycle. Although the focus is on phosphorus, many of the observations and discussion points here relate to aquatic ecosystem models in general. The review considers how models compare across domains of application, the degree to which current models are fit for purpose, how to choose between multiple alternative formulations, and how models might be improved. Lake and marine models have been gradually increasing in complexity, with increasing emphasis on inorganic processes and ecosystems. River models have remained simpler, but have been more rigorously assessed. Processes important in less eutrophic systems have often been neglected: these include the biogeochemistry of organic phosphorus, transformations associated with fluxes through soils and sediments, transfer rate-limited phosphorus uptake, and responses of plants to pulsed nutrient inputs. Arguments for and against increasing model complexity, physical and physiological realism are reviewed. © 2014 The Author.


Cruz M.G.,CSIRO | Cruz M.G.,Bushfire Cooperative Research Center | Alexander M.E.,University of Alberta
Environmental Modelling and Software | Year: 2013

The degree of accuracy in model predictions of rate of spread in wildland fires is dependent on the model's applicability to a given situation, the validity of the model's relationships, and the reliability of the model input data. On the basis of a compilation of 49 fire spread model evaluation datasets involving 1278 observations in seven different fuel type groups, the limits on the predictability of current operational models are examined. Only 3% of the predictions (i.e. 35 out of 1278) were considered to be exact predictions according to the criteria used in this study. Mean percent error varied between 20 and 310% and was homogeneous across fuel type groups. Slightly more than half of the evaluation datasets had mean errors between 51 and 75%. Under-prediction bias was prevalent in 75% of the 49 datasets analysed. A case is made for suggesting that a ±35% error interval (i.e. approximately one standard deviation) would constitute a reasonable standard for model performance in predicting a wildland fire's forward or heading rate of spread. We also found that empirical-based fire behaviour models developed from a solid foundation of field observations and well accepted functional forms adequately predicted rates of fire spread far outside of the bounds of the original dataset used in their development. © 2013.


Ooi T.C.,Fortescue Metals | Lu L.,CSIRO
Chemosphere | Year: 2011

The sintering of iron ore is presently a significant industrial source of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) worldwide owing to the fundamental requirement of the operation of a high temperature process to pre-treat fines and to recycle plant by-products arising from the integrated iron and steelworks. The process is a noteworthy contributor of PCDD/F indirectly due to decreasing PCDD/F releases from municipal solid waste incineration. Commonly PCDD/F formation from the process is associated with the addition of oily mill scales although raw material containing a combination of C, Cl and specific metal catalyst has been shown to drastically increase PCDD/F formation in the process. The degenerate graphitic structure of carbon present in coke fuel and soot formed and the chemistry of catalytic metals and Cl are important factors.A review on PCDD/F emission in this process has been carried out, including examination of its formation mechanism, congener distribution, contributing factors and mitigation strategies, with emphasis on the use of inhibiting compound to achieve suppression. A detailed analysis of the de novo and precursor theories of formation and the contributing factor is given since the subject of PCDD/F formation is still controversial. The de novo formation pathway identified in sinter plants and controlled studies performed in the laboratory as well as at pilot-scale are discussed; where appropriate, a comparison is drawn between sintering and other thermal processes emitting PCDD/Fs. Summary of the latest developments in PCDD/F downstream abatement strategies presently employed in full scale industrial plants is provided. Potential inhibiting compounds are discussed in terms of their mode of action and merits under sintering conditions. © 2011 Elsevier Ltd.


Murphy A.B.,CSIRO
Chemical Physics | Year: 2012

Calculated values of the viscosity, thermal conductivity and electrical conductivity of nitrogen and mixtures of nitrogen and hydrogen, including ammonia and hydrazine, at high temperatures are presented. Combined ordinary, pressure, temperature and electric field diffusion coefficients are also given for the mixtures. The calculations, which assume local thermodynamic equilibrium, are performed for plasmas in the temperature range from 300 to 30,000 K and the pressure range from 0.1 to 5 atm. The results are compared with those of previously published studies. Reasonable and in some cases very good agreement is found; those discrepancies that exist are attributed to the improved values of the some of the collision integrals used here. Different mixing rules are tested, with two found to give very good results: that of Yun et al. [K.-S. Yun, S. Weissman, E.A. Mason, Phys. Fluids 5 (1962) 672] for the viscosity and thermal conductivity, and a simple interpolation weighted by mole fraction for the electrical conductivity. © 2011 Elsevier B.V. All rights reserved.


Magnetic hysteresis curves of bulk amorphous ferromagnet alloys of composition Nd60Fe30Al10, Nd 60Fe20Co10Al10 and Pr 58Fe24Al18 have been measured in applied magnetic fields up to 9 T at temperatures in the range 10350 K. The behaviour of the demagnetisation curve in the first quadrant is interpreted using a mean field interaction model as proposed by Callen et al. [Phys. Rev. B 16 (1977) 263], which extends the StonerWohlfarth model [Philos. Trans. Roy. Soc. A 240 (1948) 599] for a random distribution of non-interacting uniaxial grains. Application of the mean field interaction model enables the determination of the saturation magnetisation Ms, anisotropy field Ha, and interaction parameter d, and from these other magnetic parameters, such as the anisotropy constant, K, are deduced. For the three alloys, the temperature dependent behaviour of Ms, Ha, d and K over the range 20350 K are found to be qualitatively similar, though there are quantitative differences. In all cases Ms increases with decreasing temperature, both Ha and K increase with decreasing temperature, reaching a peak in the range 75120 K, and then decreasing, and d decreases approximately linearly as the temperature decreases. The physical mechanisms responsible for coercivity in these materials are discussed in the context of random anisotropy and a strong pinning model of domain walls. © 2011 Elsevier B.V. All rights reserved.


Kovalyshen Y.,CSIRO
International Journal of Non-Linear Mechanics | Year: 2014

In search for the root cause of stick-slip, a mode of torsional vibrations of a drilling assembly, a linear stability analysis of coupled axial-torsional vibrations has been carried out. It has been shown that in a rotary drilling system with axial and torsional degree of freedom two distinct modes of self-excited vibrations are present: axial and torsional. These axial (torsional) modes of vibrations are due to resonance between the cutting forces acting at the bit and the axial (torsional) natural modes of drillstring vibrations. It has been demonstrated that although axial and torsional modes of vibrations do affect each other the underlying mechanisms driving these modes of vibrations are completely different. In particular, the only driving mechanism of the axial vibrations is the regenerative effect, while there are two distinct mechanisms that drive the torsional vibrations: (i) the cutting action of the bit, and (ii) the wearflat/rock interaction. Moreover, in the case of the torsional vibrations the regenerative effect plays only a secondary role. The results of the present study indicate that the axial compliance can play a stabilizing role. In particular, the stabilizing role of the axial compliance increases as the ratio of the torsional to the axial natural frequency of the drillstring vibrations decreases. Crown Copyright © 2014 Published by Elsevier Ltd. All rights reserved.


Koribalski B.S.,CSIRO
Publications of the Astronomical Society of Australia | Year: 2012

Here I will outline successes and challenges for finding spectral line sources in large data cubes that are dominated by noise. This is a 3D challenge as the sources we wish to catalog are spread over several spatial pixels and spectral channels. While 2D searches can be applied, e.g. channel by channel, optimal searches take into account the 3-dimensional nature of the sources. In this overview I will focus on Hi 21-cm spectral line source detection in extragalactic surveys, in particular HIPASS, the Hi Parkes All-Sky Survey and WALLABY, the ASKAP Hi All-Sky Survey. I use the original HIPASS data to highlight the diversity of spectral signatures of galaxies and gaseous clouds, both in emission and absorption. Among others, I report the discovery of a 680kms-1 wide Hi absorption trough in the megamaser galaxy NGC 5793. Issues such as source confusion and baseline ripples, typically encountered in single-dish Hi surveys, are much reduced in interferometric Hi surveys. Several large Hi emission and absorption surveys are planned for the Australian Square Kilometre Array Pathfinder (ASKAP): here we focus on WALLABY, the 21-cm survey of the sky (+30; z0.26) which will take about one year of observing time with ASKAP. Novel phased array feeds ('radio cameras') will provide 30deg2 instantaneous field-of-view. WALLABY is expected to detect more than 500 000 galaxies, unveil their large-scale structures and cosmological parameters, detect their extended, low-surface-brightness disks as well as gas streams and filaments between galaxies. It is a precursor for future Hi surveys with SKA Phase I and II, exploring galaxy formation and evolution. The compilation of highly reliable and complete source catalogs will require sophisticated source-finding algorithms as well as accurate source parametrisation. Journal compilation © Australian Mammal Society 2012.


NGO S.N.T.,University of Adelaide | Williams D.B.,University of South Australia | Head R.J.,CSIRO
Critical Reviews in Food Science and Nutrition | Year: 2011

Colorectal cancer is the second leading cause of cancer death in Australia. Nutrition, particularly intake of vegetables and certain plant components, has been reported to have a major role in cancer risk reduction. Recently, there has been a growing research interest in rosemary, a common household plant grown in many parts of the world. This study aims to review scientific evidence from all studies, published from 1996 to March 2010 that examined the protective effects of rosemary on colorectal cancer and other types of cancer. Literature evidence from animal and cell culture studies demonstrates the anticancer potential of rosemary extract, carnosol, carnosic acid, ursolic acid, and rosmarinic acid. No evidence for other rosemary constituents was found. The reported anticancer properties were found to arise through the molecular changes in the multiple-stage process of cancer development, which are dose related and not tissue or species specific. This is evidenced by the ability of rosemary to suppress the development of tumors in several organs including the colon, breast, liver, stomach, as well as melanoma and leukemia cells. The results suggested that the different molecular targets modulated by rosemary and its active constituents are useful indicators of success in clinical cancer chemo-prevention trials. © Taylor and Francis Group, LLC.


Furbank R.T.,CSIRO | Tester M.,University of Adelaide
Trends in Plant Science | Year: 2011

Global agriculture is facing major challenges to ensure global food security, such as the need to breed high-yielding crops adapted to future climates and the identification of dedicated feedstock crops for biofuel production (biofuel feedstocks). Plant phenomics offers a suite of new technologies to accelerate progress in understanding gene function and environmental responses. This will enable breeders to develop new agricultural germplasm to support future agricultural production. In this review we present plant physiology in an 'omics' perspective, review some of the new high-throughput and high-resolution phenotyping tools and discuss their application to plant biology, functional genomics and crop breeding. © 2011.


Jurek R.,CSIRO
Publications of the Astronomical Society of Australia | Year: 2012

The spectral line datacubes obtained from the Square Kilometre Array (SKA) and its precursors, such as the Australian SKA Pathfinder (ASKAP), will be sufficiently large to necessitate automated detection and parametrisation of sources. Matched filtering is widely acknowledged as the best possible method for the automated detection of sources. This paper presents the Characterised Noise Hi (cnhi) source finder, which employs a novel implementation of matched filtering. This implementation is optimised for the 3-D nature of the Hi spectral line observations of the planned Wide-field ASKAP Legacy L-band All-sky Blind surveY (WALLABY). The cnhi source finder also employs a novel sparse representation of 3-D objects, with a high compression rate, to implement the Lutz one-pass algorithm on datacubes that are too large to process in a single pass. WALLABY will use ASKAP's phenomenal 30 square degree field of view to image ∼70% of the sky. It is expected that WALLABY will find 500000Hi galaxies out to z∼0.2. Journal compilation © Australian Mammal Society 2012.


Craig P.D.,CSIRO
Ecological Modelling | Year: 2010

Both observational and modelling studies of the natural environment are characterised by their 'grain' and 'extent', the smallest and largest scales represented in time and space. These are imposed scales that should be chosen to ensure that the natural scales of the system are captured in the study. A simple cellular automata model of habitat represents only the presence or absence of vegetation, with global and local interactions described by four empirical parameters. Such a model can be formulated as a nonlinear Markov equation for the habitat probability. The equation produces inherent space and time scales that may be considered as transition scales or the scales for recovery from disturbance. However, if the resolution of the model is changed, the empirical parameters must be changed to preserve the properties of the system. Further, changes in the spatial resolution lead to different interpretations of the spatial structure. In particular, as the resolution is reduced, the apparent dominance of one habitat type over the other increases. The model provides an ability to compare both field and model investigations conducted at different resolutions in time and space. © 2010.


Marshall N.A.,CSIRO
Global Environmental Change | Year: 2010

Resource-dependent industries are particularly vulnerable to climate change, and their ability to adapt will be as critical to society as to the natural systems upon which they rely. More than ever, resource-users will need to anticipate, and prepare for, climate-related changes, and institutions will need to be particularly supportive, if resource industries and the extended social systems dependent on them are to be sustained. I examine the capacity of cattle-graziers in Australia to cope and adapt to climate variability as a precursor for understanding their vulnerability to climate change by assessing: (i) their perception of risk, (ii) their capacity to plan, learn and reorganise, (iii) their proximity to the thresholds of coping, and (iv) their level of interest in adapting to change. Graziers perceived themselves to be resilient to climate variability in their perceptions of climate risk, reorganising capacity, coping, and interest in adapting. Their dependency on the grazing resource and use of seasonal climate forecasts were significant influences, suggesting that resilience could be enhanced. Facilitated collaborative learning amongst graziers and other stakeholders may assist to develop strategic skills, increasing climate awareness, developing financial security and adopt climate tools such as seasonal climate forecasts. Enhanced strategies for coping with climate variability will provide a way for encouraging gradual, incremental adjustments for climate adaptation. Crown Copyright © 2009.


Through the interconnectedness of global business, the local consumption of products and services is intervening in the hydrological cycle throughout the world to an unprecedented extent. In order to address the unsustainable use of global freshwater resources, indicators are needed which make the impacts of production systems and consumption patterns transparent. In this paper, a revised water footprint calculation method, incorporating water stress characterisation factors, is presented and demonstrated for two case study products, Dolmio® pasta sauce and Peanut M&M's® using primary production data. The method offers a simple, yet meaningful way of making quantitative comparisons between products, production systems and services in terms of their potential to contribute to water scarcity. As such, capacity is created for change through public policy as well as corporate and individual action. This revised method represents an alternative to existing volumetric water footprint calculation methods which combine green and blue water consumption from water scarce and water abundant regions such that they give no clear indication about where the actual potential for harm exists. © 2009 Elsevier Ltd. All rights reserved.


Rowe K.C.,University of California at Berkeley | Rowe K.C.,Southern Cross University of Australia | Aplin K.P.,CSIRO | Baverstock P.R.,Southern Cross University of Australia | Moritz C.,University of California at Berkeley
Systematic Biology | Year: 2011

Recent and rapid radiations provide rich material to examine the factors that drive speciation. Most recent and rapid radiations that have been well-characterized involve species that exhibit overt ecomorphological differences associated with clear partitioning of ecological niches in sympatry. The most diverse genus of rodents, Rattus (66 species), evolved fairly recently, but without overt ecomorphological divergence among species. We used multilocus molecular phylogenetic data and five fossil calibrations to estimate the tempo of diversification in Rattus, and their radiation on Australia and New Guinea (Sahul, 24 species). Based on our analyses, the genus Rattus originated at a date centered on the Pliocene-Pleistocene boundary (1.84-3.17 Ma) with a subsequent colonization of Sahul in the middle Pleistocene (0.85-1.28 Ma). Given these dates, the per lineage diversification rates in Rattus and Sahulian Rattus are among the highest reported for vertebrates (1.1-1.9 and 1.6-3.0 species per lineage per million years, respectively). Despite their rapid diversification, Rattus display little ecomorphological divergence among species and do not fit clearly into current models of adaptive radiations. Lineage through time plots and ancestral state reconstruction of ecological characters suggest that diversification of Sahulian Rattus was most rapid early on as they expanded into novel ecological conditions. However, rapid lineage accumulation occurred even when morphological disparity within lineages was low suggesting that future studies consider other phenotypes in the diversification of Rattus. [Adaptive radiation; Australia; chromosomal rearrangements; Molecular systematics; Murinae; New Guinea.] © 2011 The Author(s).


Alexander M.E.,University of Alberta | Cruz M.G.,CSIRO
International Journal of Wildland Fire | Year: 2013

This paper constitutes a digest and critique of the currently available information pertaining to the influence of live fuel or foliar moisture content (FMC) on the spread rate of crown fires in conifer forests and shrublands. We review and discuss the findings from laboratory experiments and field-based fire behaviour studies. Laboratory experimentation with single needles or leaves and small conifer trees has shown an unequivocal effect of FMC on flammability metrics. A much less discernible effect of FMC on crown fire rate of spread was found in the existing set of experimental crown fires carried out in conifer forests and similarly with the far more robust database of experimental fires conducted in shrubland fuel complexes. The high convective and radiant heat fluxes associated with these fires and the lack of appropriate experimental design may have served to mask any effect of FMC or live fuel moisture on the resulting spread rate. Four theoretical functions and one empirical function used to adjust rate of fire spread for the effect of foliar or live fuel moisture were also concurrently examined for their validity over a wide range of FMC conditions with varying outcomes and relevancy. None of these model functions was found suitable for use with respect to dead canopy foliage. © 2013 IAWF.


Tucker M.R.,University of Adelaide | Koltunow A.M.G.,CSIRO
Current Opinion in Plant Biology | Year: 2014

The formation of female gametes in plants occurs within the ovule, a floral organ that is also the precursor of the seed. Unlike animals, plants lack a typical germline separated from the soma early in development and rely on positional signals, including phytohormones, mobile mRNAs and sRNAs, to direct diploid somatic precursor cells onto a reproductive program. In addition, signals moving between plant cells must overcome the architectural limitations of a cell wall which surrounds the plasma membrane. Recent studies have addressed the molecular and histological signatures of young ovule cells and indicate that dynamic cell wall changes occur over a short developmental window. These changes in cell wall properties impact signal flow and ovule cell identity, thereby aiding the establishment of boundaries between reproductive and somatic ovule domains. © 2013 Elsevier Ltd.


Ekstrom M.,CSIRO
Environmental Modelling and Software | Year: 2016

Dynamical downscaling attempts to provide regional detail to climate change projections that subsequently can be used as input to climate change impact models. However, unlike forecasts by numerical weather prediction models, downscaled projections cannot be tested for skill because the future of interest is decades away. Nevertheless, models can be tested in terms of how well they simulate current weather or climate, thus giving an indication of skill in representing the process of interest. Here, six configurations using different combinations of three microphysics and two planetary boundary layer schemes are assessed on their skill to simulate desired characteristics in daily rainfall fields from three two week simulations in southeast Australia; 'desired' meaning desirable in relation to the intended application. Of different metrics and analysis assessed, a metric based on variography analysis, summarising characteristics about spatial variability and dissimilarity, is shown to provide the most informative guidance relative to the desirable characteristics. © 2016 Elsevier Ltd.


Day L.,CSIRO
Trends in Food Science and Technology | Year: 2013

Increasing utilisation of plant protein is required to support the production of protein-rich foods that can replace animal proteins in the human diet so as to reduce the strain that intensive animal husbandry poses to the environment. From a nutritional standpoint, with the right combination, plant proteins can supply sufficient amounts of essential amino acids for human health requirements. In addition to their role as a macronutrient, proteins play an integral role in structural formation of foods through processes such as emulsification, foaming, gelation and dough formation. This review aims to provide an overview of the major sources of plant proteins, their physiochemical functionalities and nutritional properties, with emphasis on the research needed to support technology innovation for more plant protein to meet world nutritional requirements and as food sources to feed the growing world population. © 2013.


Alexander M.E.,University of Alberta | Cruz M.G.,CSIRO
Environmental Modelling and Software | Year: 2013

Evaluation is a crucial component for model credibility and acceptance by researchers and resource managers. The nature and characteristics of free-burning wildland fires pose challenges to acquiring the kind of quality data necessary for adequate fire behaviour model evaluation. As a result, in some circles it has led to a research culture that tends to avoid evaluating model performance. Operational fire modelling systems commonly used in western North America have been shown to exhibit an underprediction bias when employed to determine the threshold conditions necessary for the onset of crowning and the associated spread rate of active crown fires in conifer forest stands. This pronouncement was made a few years ago after at least a decade of model misapplication in fire and fuel management simulation modelling stemming from a lack of model evaluation. There are signs that the same situation may be repeated with developing physics-based models that simulate potential wildland fire behaviour; these models have as yet undergone limited testing against observations garnered from planned and/or accidental wildland fires. We propose a broad co-operative project encompassing modellers and experimentalists is needed to define and acquire the benchmark fire behaviour data required for model calibration and evaluation. © 2012 Elsevier Ltd.


Nuttall S.D.,CSIRO
Methods in molecular biology (Clifton, N.J.) | Year: 2012

Immunoglobulin new antigen receptors (IgNARs) from sharks are a distinct class of immune receptors, consisting of homodimers with no associated light chains. Antigen binding is encapsulated within single VNAR immunoglobulin domains of 13-14 kDa in size. This small size and single domain format means that they exhibit considerable stability and are readily produced in heterologous protein expression systems. In this chapter, I describe the history and discovery of IgNARs, the development of VNAR biotechnology, and highlight important factors in VNAR protein production.


Johnston P.,Monash University | Braybrook C.,CSIRO | Saito K.,Monash University
Chemical Science | Year: 2012

Solid-state topochemical polymerization is one way to synthesize novel macromolecular architectures with stereoregular chain structures. Topochemical reactions are attractive, "green" synthetic pathways in material design, since they occur in solvent-free conditions and in response to external stimuli, such as heat and light. For the first time, we have used the reversible [2π + 2π]-cycloaddition of a bioinspired bis-thymine monomer to topochemically synthesize a polymer. The polymer can be fully photo-depolymerized to the monomer and then reversibly and repeatedly photo-polymerized and photo-depolymerized. This is the first demonstration of complete photo-depolymerization and subsequent monomer recycling using this mechanism. This journal is © The Royal Society of Chemistry 2012.


Brede M.,CSIRO
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2010

In this paper, we consider spatial networks that realize a balance between an infrastructure cost (the cost of wire needed to connect the network in space) and communication efficiency, measured by average shortest path length. A global optimization procedure yields network topologies in which this balance is optimized. These are compared with network topologies generated by a competitive process in which each node strives to optimize its own cost-communication balance. Three phases are observed in globally optimal configurations for different cost-communication trade offs: (i) regular small worlds, (ii) starlike networks, and (iii) trees with a center of interconnected hubs. In the latter regime, i.e., for very expensive wire, power laws in the link length distributions P (w) w-α are found, which can be explained by a hierarchical organization of the networks. In contrast, in the local optimization process the presence of sharp transitions between different network regimes depends on the dimension of the underlying space. Whereas for d=∞ sharp transitions between fully connected networks, regular small worlds, and highly cliquish periphery-core networks are found, for d=1 sharp transitions are absent and the power law behavior in the link length distribution persists over a much wider range of link cost parameters. The measured power law exponents are in agreement with the hypothesis that the locally optimized networks consist of multiple overlapping suboptimal hierarchical trees. © 2010 The American Physical Society.


Falcaro P.,CSIRO | Furukawa S.,Kyoto University
Angewandte Chemie - International Edition | Year: 2012

Space division with red cubes: Doping metal-organic frameworks with another metal component gives a further opportunity to tune their properties. Recent work successfully introduced europium into the inorganic nodes of frameworks. Although the doping element does not affect the framework topology, highly improved emissive performance was measured thanks to the intrinsic red emission of europium.


Henery M.L.,CSIRO
Agricultural and Forest Entomology | Year: 2011

High productivity in plantations of exotic tree species is achieved by management for fast growth in the absence of the full complex of co-evolved insect herbivores. In the case of Eucalyptus, silvicultural selection for desirable wood traits is concomitant with a trade-off against defence and a reduction of chemical and genetic diversity. These factors, combined with accidental introductions, rapid insect evolution and the emergence of new pests, increase the likelihood that future plantations will need insect pest management to maintain productivity. Forestry researchers have suggested that selecting for resistant genotypes may be beneficial in insect control. There are, however, significant differences between long-lived trees and annual crops that make this approach unlikely to be successful. This is illustrated using several examples of research into resistance to insect herbivores in trees. Selection for resistance to insects in trees requires an assessment of trial plantations for heritable variation in insect damage and then a determination of the effect of variation in resistance on insect population parameters. Identifying rare resistant genotypes using markers is difficult because many factors interact to produce a resistant phenotype, and phytophagous insects have less intimate relationships with their host than pathogens, resulting in weak associations with genetic loci. If resistant genotypes are identified, their widespread deployment in plantations might not provide satisfactory management of insect pests when the use of extensive monocultures is continued. In this paper, experiments are suggested that would explore the effectiveness of polycultures or chemotype mixtures with respect to ameliorating the damage of insects on plantation productivity. In addition, mitigating the effects of some insects on plantation productivity by maintaining vigour of fast-growing eucalypts should be considered. © 2010 CSIRO. Agricultural and Forest Entomology © 2010 The Royal Entomological Society.


Stacey F.D.,CSIRO
Reports on Progress in Physics | Year: 2010

Applications of elementary thermodynamic principles to the dynamics of the Earth lead to robust, quantitative conclusions about the tectonic effects that arise from convection. The grand pattern of motion conveys deep heat to the surface, generating mechanical energy with a thermodynamic efficiency corresponding to that of a Carnot engine operating over the adiabatic temperature gradient between the heat source and sink. Referred to the total heat flux derived from the Earth's silicate mantle, the efficiency is 24% and the power generated, 7.7 × 1012 W, causes all the material deformation apparent as plate tectonics and the consequent geological processes. About 3.5% of this is released in seismic zones but little more than 0.2% as seismic waves. Even major earthquakes are only localized hiccups in this motion. Complications that arise from mineral phase transitions can be used to illuminate details of the motion. There are two superimposed patterns of convection, plate subduction and deep mantle plumes, driven by sources of buoyancy, negative and positive respectively, at the top and bottom of the mantle. The patterns of motion are controlled by the viscosity contrasts (>104 : 1) at these boundaries and are self-selected as the least dissipative mechanisms of heat transfer for convection in a body with very strong viscosity variation. Both are subjects of the thermodynamic efficiency argument. Convection also drives the motion in the fluid outer core that generates the geomagnetic field, although in that case there is an important energy contribution by compositional separation, as light solute is rejected by the solidifying inner core and mixed into the outer core, a process referred to as compositional convection. Uncertainty persists over the core energy balance because thermal conduction is a drain on core energy that has been a subject of diverse estimates, with attendant debate over the need for radiogenic heat in the core. The geophysical approach to thermal physics, especially thermal expansion and the Grüneisen parameter, invokes insights that have disappeared from view in 'mainstream' physics. © 2010 IOP Publishing Ltd.


Murphy A.B.,CSIRO
Plasma Chemistry and Plasma Processing | Year: 2015

The state-of-the-art on arc welding research is considered, with unresolved questions and future directions highlighted. Both diagnostics and modelling are discussed. The focus is on the arc plasma, and its interactions with the electrode and workpiece, in tungsten–inert-gas and metal–inert-gas welding. Areas in which the need for further work is identified include development of techniques to measure current density distributions, calculation of the distribution of different gasses in the arc plasma (for example vapours of different metallic elements when welding alloys), computational methods for modelling metal transfer, and treatments of the sheath regions. It is shown that a thorough understanding of the arc is important in welding research and development. For example, reliable calculation of the heat flux to the workpiece requires the interactions between the arc and electrodes to be considered. Computational models of welding that take into account these interactions can already predict the shape and depth of the weld pool. Extensions of these methods would enable the determination of important properties of the welded metal, such as microstructure, residual stress and distortion, raising the possibility of the development of a “virtual manufacturing” capability. © 2015, Springer Science+Business Media New York.


Leech P.W.,CSIRO
Materials and Design | Year: 2014

The effect of laser surface melting (LSM) on the microscopic morphology of a complex high alloy steel has been examined in single track experiments. Different combinations of power (1-4kW) and scan speed (500-1000mmmin-1) were selected in order to obtain a range of depths of melt penetration. An increase in the depth of melt penetration has correlated with rise in the estimated surface temperature induced by laser melting. Within the strongly refined structure of the laser melted alloy, the interdendritic spacing, λ varied from 0.29μm to 0.97μm with increase in the depth of melt penetration. The microhardness in the laser surface melted region has been shown to decrease linearly with λ-0.5. © 2013 Elsevier Ltd.


Santoso A.,University of New South Wales | England M.H.,University of New South Wales | Cai W.,CSIRO
Journal of Climate | Year: 2012

The impact of Indo-Pacific climate feedback on the dynamics of El Niñ o-Southern Oscillation (ENSO) is investigated using an ensemble set of Indian Ocean decoupling experiments (DCPL), utilizing a millennial integration of a coupled climate model. It is found that eliminating air-sea interactions over the Indian Oceanresults in various degrees of ENSO amplification across DCPL simulations, with a shift in the underlying dynamics toward a more prominent thermocline mode. The DCPLexperiments reveal that the net effect of the Indian Ocean in the control runs (CTRL) is a damping of ENSO. The extent of this damping appears to be negatively correlated to the coherence between ENSO and the Indian Ocean dipole (IOD). This type of relationship can arise from the long-lasting ENSO events that the model simulates, such that developing ENSO often coincides with Indian Ocean basin-wide mode (IOBM) anomalies during non-IOD years. As demonstrated via AGCM experiments, the IOBM enhances western Pacific wind anomalies that counteract the ENSO-enhancing winds farther east. In the recharge oscillator framework, this weakens the equatorial Pacific air-sea coupling that governs the ENSO thermocline feedback. Relative to the IOBM, the IOD is more conducive for ENSO growth. The net damping by the Indian Ocean in CTRL is thus dominated by the IOBM effect which is weaker with stronger ENSO-IOD coherence. The stronger ENSO thermocline mode in DCPL is consistent with the absenceof any IOBM anomalies. This study supports the notion that the Indian Ocean should be viewed as an integral part of ENSO dynamics. © 2012 American Meteorological Society.


Hunt B.G.,CSIRO
Climate Dynamics | Year: 2012

A multi-millennial run of the CSIRO Mark2 coupled climatic model has been used to investigate megadroughts and megafloods during the Indian summer monsoon (June-September). These extreme events were defined as having rainfall anomalies at least two standard deviations from normal. More than ten megafloods and more than twenty megadroughts, so-defined, were found to occur in a 5,000-year period of the simulation. The simulation replicated most of the major features of the observed summer monsoon, but a comparison of observed and simulated probability density functions suggests that the limited observed rainfall time series to date does not adequately sample the possible range of Indian monsoonal rainfall. An investigation of causal mechanisms of Indian rainfall variability reproduced the observed negative correlation with ENSO events, but it was found that neither extreme ENSO events or extremes of a range of other climatic phenomena coincided with the simulated, extreme megadroughts and megafloods. This disconnect between these events is succinctly illustrated with examples related to ENSO events in particular. Autoregressive and FFT analysis of observed and simulated Indian summer monsoon rainfall time series revealed them to consist of white noise. Since these time series therefore consist of random outcomes, it is apparent that these Indian megadroughts and megafloods are the consequence of stochastic influences. Thus, it is concluded that the interannual variability of Indian summer monsoonal rainfall cannot be predicted in general, nor can megadroughts and megafloods in particular. © 2012 Springer-Verlag.


Asseng S.,CSIRO | Foster I.,Locked Bag 4 | Turner N.C.,University of Western Australia
Global Change Biology | Year: 2011

With current annual production at over 600 million tonnes, wheat is the third largest crop in the world behind corn and rice, and an essential source of carbohydrates for millions of people. While wheat is grown over a wide range of environments, it is common in the major wheat-producing countries for grain filling to occur when soil moisture is declining and temperature is increasing. Average global temperatures have increased over the last decades and are predicted to continue rising, along with a greater frequency of extremely hot days. Such events have already been reported for major wheat growing regions in the world. However, the direct impact of past temperature variability and changes in averages and extremes on wheat production has not been quantified. Attributing changes in observed yields over recent decades to a single factor such as temperature is not possible due to the confounding effects of other factors. By using simulation modelling, we were able to separate the impact of temperature from other factors and show that the effect of temperature on wheat production has been underestimated. Surprisingly, observed variations in average growing-season temperatures of ±2°C in the main wheat growing regions of Australia can cause reductions in grain production of up to 50%. Most of this can be attributed to increased leaf senescence as a result of temperatures >34°C. Temperature conditions during grain filling in the major wheat growing regions of the world are similar to the Australian conditions during grain filling. With average temperatures and the frequency of heat events projected to increase world-wide with global warming, yield reductions due to higher temperatures during the important grain-filling stage alone could substantially undermine future global food security. Adaptation strategies need to be considered now to prevent substantial yield losses in wheat from increasing future heat stress. © 2010 Blackwell Publishing Ltd.


Tomkins K.M.,CSIRO
Hydrological Processes | Year: 2014

Discharge time series' are one of the core data sets used in hydrological investigations. Errors in the data mainly occur through uncertainty in gauging (measurement uncertainty) and uncertainty in determination of the stage-discharge relationship (rating curve uncertainty). Thirty-six flow gauges from the Namoi River catchment, Australia, were examined to explore how rating curve uncertainty affects gauge reliability and uncertainty of observed flow records. The analysis focused on the deviations in gaugings from the rating curves because standard (statistical) uncertainty methods could not be applied. Deviations of greater/lesser than 10% were considered significant to allow for a measurement uncertainty threshold of 10%, determined from quality coding of gaugings and operational procedures. The deviations in gaugings were compared against various factors to examine trends and identify major controls, including stage height, date, month, rating table, gauging frequency and quality, catchment area and type of control. The analysis gave important insights into data quality and the reliability of each gauge, which had previously not been recognized. These included identification of more/less reliable periods of record, which varied widely between gauges, and identification of more/less reliable parts of the hydrograph. Most gauges showed significant deviations at low stages, affecting the determination of low flows. This was independent of the type of gauge control, with many gauges experiencing problems in the stability of the rating curve, likely as a result of sediment flux. The deviations in gaugings also have widespread application in modelling, for example, informing suitable calibration periods and defining error distributions. This paper demonstrates the value and importance of undertaking qualitative analyses of observed records. © 2012 John Wiley & Sons, Ltd.


Robson B.J.,CSIRO
Environmental Modelling and Software | Year: 2014

This article considers how aquatic systems modelling has changed since 1995 and how it must change in future if we are to continue to advance. A distinction is made between mechanistic and statistical models, and the relative merits of each are considered. The question of "when do aquatic systems models provide accurate and useful predictions?" is addressed, implying some guidelines for model development. It is proposed that, in general, ecological models only provide management-relevant predictions of the behaviour of real systems when there are strong physical (as opposed to chemical or ecological) drivers. Developments over the past 15 years have included changes in technology, changes in the modelling community and changes in the context in which modelling is conducted: the implications of each are briefly discussed. Current trends include increased uptake of best practice guidelines, increasing integration of models, operationalisation, data assimilation, development of improved tools for skill assessment, and application of models to new management questions and in new social contexts. Deeper merging of statistical and mechanistic modelling approaches through such techniques as Bayesian Melding, Bayesian Hierarchical Modelling and surrogate modelling is identified as a key emerging area. Finally, it is suggested that there is a need to systematically identify areas in which our current models are inadequate. We do not yet know for which categories of problems well-implemented aquatic systems models can (or cannot) be expected to accurately predict observational data and system behaviour. This can be addressed through better modelling and publishing practices. © 2014 Elsevier Ltd.


Thornton P.K.,CGIAR Research Programme on Climate Change | Ericksen P.J.,Kenya International Livestock Research Institute | Herrero M.,CSIRO | Challinor A.J.,University of Leeds
Global Change Biology | Year: 2014

The focus of the great majority of climate change impact studies is on changes in mean climate. In terms of climate model output, these changes are more robust than changes in climate variability. By concentrating on changes in climate means, the full impacts of climate change on biological and human systems are probably being seriously underestimated. Here, we briefly review the possible impacts of changes in climate variability and the frequency of extreme events on biological and food systems, with a focus on the developing world. We present new analysis that tentatively links increases in climate variability with increasing food insecurity in the future. We consider the ways in which people deal with climate variability and extremes and how they may adapt in the future. Key knowledge and data gaps are highlighted. These include the timing and interactions of different climatic stresses on plant growth and development, particularly at higher temperatures, and the impacts on crops, livestock and farming systems of changes in climate variability and extreme events on pest-weed-disease complexes. We highlight the need to reframe research questions in such a way that they can provide decision makers throughout the food system with actionable answers, and the need for investment in climate and environmental monitoring. Improved understanding of the full range of impacts of climate change on biological and food systems is a critical step in being able to address effectively the effects of climate variability and extreme events on human vulnerability and food security, particularly in agriculturally based developing countries facing the challenge of having to feed rapidly growing populations in the coming decades. © 2014 The Authors.


Vaze J.,NSW Office of Water | Teng J.,CSIRO
Hydrological Processes | Year: 2011

This paper describes the rainfall-runoff modelling for New South Wales (NSW) and Australian Capital Territory (ACT) under historical climate and the likely changes to runoff around the year 2030 for the Intergovernmental Panel on Climate Change (IPCC) SRES A1B global warming scenario. Results show that the mean annual historical rainfall and runoff, averaged over the entire region, are 516 and 55 mm, respectively. There is considerable uncertainty in the global climate modelling (GCM) of rainfall response in the region to global warming. The majority of GCMs show a decrease in the mean annual rainfall and the median estimate indicates that future mean annual runoff in the region in 2030 relative to 1990 will be lower by 0-20% in the southern parts, no change to a slight reduction in the eastern parts and higher by 0-20% in the northwest corner. Averaged across the entire region, the median estimate is a 5% decrease in the mean annual runoff and the extreme estimates range from a 14% decrease to a 10% increase in mean annual runoff. This is the first comprehensive study on the hydrological impacts of climate change done in NSW that covers the entire state. Outputs from this study are being used to underpin the hydrology for a number of major climate change impact studies that are presently underway across NSW. The results and output datasets from this study will be available through a web interface and they can be used by all state government agencies and industries in NSW to plan for and adapt to the impacts of climate change © 2010 John Wiley & Sons, Ltd.


Risbey J.S.,CSIRO
Regional Environmental Change | Year: 2011

Water resources in Australia are sensitive to changes in rainfall. Ongoing droughts in south-west and south-east Australia are stressing water resources in the major cities and in agricultural regions. Climate change scenarios for Australia include reasonable prospects of long-term drying, which would exacerbate these issues. The dryer scenarios would entail major readjustments and costs on natural and human systems. © 2010 Springer-Verlag.


Barnes S.J.,CSIRO | Fiorentini M.L.,University of Western Australia
Economic Geology | Year: 2012

Komatiites are found in most Archean granite-greenstone terranes, but sulfide Ni mineralization associated with these rocks has a very biased distribution. The global endowment of sulfides Ni in Archean komatiites is overwhelmingly dominated by the Kalgoorlie terrane of the Eastern Goldfields Superterrane in the Yilgarn Craton. The question of whether the Kalgoorlie terrane komatiites possess any exceptional attributes which could explain this bias is addressed through an exhaustive compilation of geochemical data from this terrane and a number of others: the southeastern Youanmi terrane of the Yilgarn Craton; the eastern terranes of the Eastern Goldfields superterrane (Kurnalpi, Burtville and others); and the Abitibi greenstone belt of the Superior province. High MgO komatiite magmas, with MgO in the 25 to 30% range, are found in all the terranes sampled, but the proportion of these compositions appears to be higher in the Kalgoorlie terrane, and the abundance of strongly adcumulate olivine cumulates is much higher. Crustal contamination is apparently more extensive and advanced in the Kalgoorlie terrane than in all the others, but there is no systematic difference in the lithophile trace element (LILE) characteristics and degree of source depletion evident in the most primitive magmas from all the terranes. Consideration of variable-valency transition metals V and Cr indicates there are no systematic variations in oxidation state between the terranes and komatiites uniformly evolved close to the quartz-fayalite-magnetite buffer. Platinum-group element (PGE) variations imply that komatiites in all the terranes were emplaced sulfide undersaturated and were derived from sources with remarkably similar PGE contents. There is no evidence that the Kalgoorlie terrane magmas were in any way exceptional. The Forrestania and Lake Johnston Belts of the Youanmi terrane include the only known examples of Al-depleted komatiites hosting significant Ni sulfide resources, and they are also the only komatiites of this type that form adcumulate dunite bodies. The presence of adcumulate dunites, formed by high magma fluxes in central conduits, is the common feature between these belts and the Kalgoorlie terrane. Coupled with evidence for higher degrees of contamination in the Kalgoorlie terrane, and the availability of accessible crustal S sources, it appears that magma flux, rather than primitive magma composition, is the critical factor, and that craton-scale deep lithospheric structure is the ultimate control on the rate of magma supply between mantle source and crustal emplacement site. The Kalgoorlie terrane komatiites were emplaced at exceptionally high rates, giving rise to well-developed long-lived magma conduits, either lava tubes or subvolcanic channelized sills, which are interpreted to be the essential condition for forming large deposits. © 2012 Society of Economic Geologists, Inc.


Brede M.,CSIRO
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2010

In this Rapid Communication we investigate spatially constrained networks that realize optimal synchronization properties. After arguing that spatial constraints can be imposed by limiting the amount of "wire" available to connect nodes distributed in space, we use numerical optimization methods to construct networks that realize different trade offs between optimal synchronization and spatial constraints. Over a large range of parameters such optimal networks are found to have a link length distribution characterized by power-law tails P (l) l-α, with exponents α increasing as the networks become more constrained in space. It is also shown that the optimal networks, which constitute a particular type of small world network, are characterized by the presence of nodes of distinctly larger than average degree around which long-distance links are centered. © 2010 The American Physical Society.


Specific products and their relative abundances observed in gas-phase collision-induced dissociation experiments for [amine-H + CO2 + H2O]- reflect the behaviour of the bulk aqueous amines in the presence of CO2. © 2013 The Royal Society of Chemistry.


Werkmeister J.A.,CSIRO
Biomedical materials (Bristol, England) | Year: 2012

New biological materials for tissue engineering are now being developed using common genetic engineering capabilities to clone and express a variety of genetic elements that allow cost-effective purification and scaffold fabrication from these recombinant proteins, peptides or from chimeric combinations of these. The field is limitless as long as the gene sequences are known. The utility is dependent on the ease, product yield and adaptability of these protein products to the biomedical field. The development of recombinant proteins as scaffolds, while still an emerging technology with respect to commercial products, is scientifically superior to current use of natural materials or synthetic polymer scaffolds, in terms of designing specific structures with desired degrees of biological complexities and motifs. In the field of tissue engineering, next generation scaffolds will be the key to directing appropriate tissue regeneration. The initial period of biodegradable synthetic scaffolds that provided shape and mechanical integrity, but no biological information, is phasing out. The era of protein scaffolds offers distinct advantages, particularly with the combination of powerful tools of molecular biology. These include, for example, the production of human proteins of uniform quality that are free of infectious agents and the ability to make suitable quantities of proteins that are found in low quantity or are hard to isolate from tissue. For the particular needs of tissue engineering scaffolds, fibrous proteins like collagens, elastin, silks and combinations of these offer further advantages of natural well-defined structural scaffolds as well as endless possibilities of controlling functionality by genetic manipulation.


Turning commercial lab automation into a high-throughput centre requires an underlying process, and implementing checks to ensure that the process is working as it should. At the Collaborative Crystallisation Centre (C3), protein samples from local, national and international groups are set up in crystallisation screening and optimisation experiments with two thousand 96 well plates being set up each year. During its five years of operation, the C3 has implemented a series of enabling protocols - from simple 'reality checks' to determine if a screen has evaporated during storage to more sophisticated systems such as a sample labelling and tracking system. The most important - and perhaps surprising - lesson has been how much effort is required to effectively communicate between the centre and its clients, as well as between the centre's staff members. It is easy to confuse the concept of 'high throughput' in any field with the idea of setting up an experiment quickly. Although automation can be used to set up a single experiment more rapidly than can be done by hand, the distinguishing feature of a high throughput technology is the sustainability of the increased rate. © 2011 Elsevier Inc.


DNA damage at the base-sequence, epigenome and chromosome level is a fundamental cause of developmental and degenerative diseases. Multiple micronutrients and their interactions with the inherited and/or acquired genome determine DNA damage and genomic instability rates. The challenge is to identify for each individual the combination of micronutrients and their doses (i.e. the nutriome) that optimises genome stability and DNA repair. In this paper I describe and propose the use of high-throughput nutrient array systems with high content analysis diagnostics of DNA damage, cell death and cell growth for defining, on an individual basis, the optimal nutriome for DNA damage prevention and cancer growth control. © 2010 Fenech; licensee BioMed Central Ltd.


Cordes J.M.,Cornell University | Shannon R.M.,Cornell University | Shannon R.M.,CSIRO
Astrophysical Journal | Year: 2012

We assess the detectability of a nanohertz gravitational wave (GW) background in a pulsar timing array (PTA) program by considering the shape and amplitude of the cross-correlation function summed over pulsar pairs. The distribution of correlation amplitudes is found to be non-Gaussian and highly skewed, which significantly influences detection and false-alarm probabilities. When only white noise combines with GWs in timing data, our detection results are consistent with those found by others. Contamination by red noise from spin variations and from any uncorrected interstellar plasma effects significantly increases the false-alarm probability. The number of arrival times (and thus the observing cadence) is important only as long as the residuals are dominated by white noise. When red noise and GWs dominate, the statistical significance of the correlation estimate can be improved only by increasing the number of pulsars. We characterize plausible detection regimes by evaluating the number of millisecond pulsars (MSPs) that must be monitored in a high-cadence, five-year timing program to detect a GW background spectrum hc (f) = A(f/f 0)-2/3 with f 0 = 1yr-1 and A = 10-15. Our results indicate that a sample of 20 super-stable MSPs - those with rms timing residuals σr ≲ 20 ns(A/10 -15) from red-noise contributions over a five-year span - will allow detection of the GW background and study of its spectrum. However, a timing program on ≳ 50-100 MSPs is likely needed for a complete PTA program, particularly if red noise is generally present in MSPs. © 2012. The American Astronomical Society. All rights reserved.


March T.L.,Flinders University | Johnston M.R.,Flinders University | Duggan P.J.,CSIRO
Organic Letters | Year: 2012

(R)-2-Phenylglycine ethyl ester was found to be a cheap and effective auxiliary for the preparation of aliphatic α,α-difluoro- β 3-amino esters via a Reformatsky reaction performed under sonication conditions. The products were obtained in good to high yield and ≥96:4 dr, thus providing a new stereoselective route to this under-represented class of compounds. A facile one-pot removal of the phenylglycine moiety and concomitant Boc protection subsequently afforded the corresponding Boc-protected β 3-amino esters in excellent yield. © 2011 American Chemical Society.


Parr C.L.,University of Liverpool | Lehmann C.E.R.,Macquarie University | Lehmann C.E.R.,University of Edinburgh | Bond W.J.,University of Cape Town | And 2 more authors.
Trends in Ecology and Evolution | Year: 2014

Tropical grassy biomes (TGBs) are globally extensive, provide critical ecosystem services, and influence the earth-atmosphere system. Yet, globally applied biome definitions ignore vegetation characteristics that are critical to their functioning and evolutionary history. Hence, TGB identification is inconsistent and misinterprets the ecological processes governing vegetation structure, with cascading negative consequences for biodiversity. Here, we discuss threats linked to the definition of TGB, the Clean Development Mechanism (CDM) and Reducing Emissions from Deforestation and Forest Degradation schemes (REDD+), and enhanced atmospheric CO2, which may facilitate future state shifts. TGB degradation is insidious and less visible than in forested biomes. With human reliance on TGBs and their propensity for woody change, ecology and evolutionary history are fundamental to not only the identification of TGBs, but also their management for future persistence. © 2014 Elsevier Ltd.


Murray L.,CSIRO
IEEE Transactions on Parallel and Distributed Systems | Year: 2012

We consider the use of commodity graphics processing units (GPUs) for the common task of numerically integrating ordinary differential equations (ODEs), achieving speedups of up to 115-fold over comparable serial CPU implementations, and 15-fold over multithreaded CPU code with SIMD intrinsics. Using Lorenz '96 models as a case study, single and double precision benchmarks are established for both the widely used DOPRI5 method and computationally tailored low-storage RK4(3)5[2R+]C. A range of configurations are assessed on each, including multithreading and SIMD intrinsics on the CPU, and GPU kernels parallelized over both the dimensionality of the ODE system and number of trajectories. On the GPU, we draw particular attention to the problem of variable task-length among threads of the same warp, proposing a lightweight strategy of assigning multiple data items to each thread to reduce the prevalence of redundant operations. A simple analysis suggests that the strategy can draw performance close to that of ideal parallelism, while empirical results demonstrate up to a 10 percent improvement over the standard approach. © 2006 IEEE.


McVicar T.R.,CSIRO | Korner C.,University of Basel
Oecologia | Year: 2013

Effective communication regarding distance in the vertical dimension is critical for many ecological, climatological and broader geophysical studies of the Earth. Confusion exists regarding the definition of three English words commonly used to describe the vertical dimension: (1) elevation; (2) altitude; and (3) height. While used interchangeably in "everyday" non-technical English, here we provide explicit definitions and strongly recommend their use in scientific literature. We briefly discuss the likely origins of the sub-optimal use of these three words due to translations between languages. Finally, we provide examples of how using these terms, as explicitly defined herein, improves scientific communication. © 2012 Springer-Verlag.


Young A.G.,CSIRO | Pickup M.,University of Toronto
Journal of Applied Ecology | Year: 2010

Summary: The role of genetic factors in species decline and extinction is the subject of a long-running controversy, with demographical factors often seen as more important for the immediate persistence of populations and species. One gene system that directly links genetic diversity with reproduction, through its influence on fertilization success, is the self-incompatibility (SI) locus in angiosperm plants. Despite the potential importance of SI allele diversity for demographical function, there are few direct measures of S-allele numbers in multiple populations, and no studies have simultaneously measured reproductive output, mate availability, S-allele diversity and pollinator service.We used diallel crosses to estimate S-allele number and mate availability in seven populations of the forb Rutidosis leptorrhynchoides ranging in size from 5 to 100 000 plants. Seed set and correlated paternity were assessed from open-pollinated inflorescences to examine reproductive output and variance in female and male fitness. To assess whether populations were receiving adequate pollinator service, the amount of pollen deposited on open-pollinated stigmas was quantified.3. We found that small populations (<100 plants) of R. leptorrhynchoides have low S-allele diversity and mate availability and exhibit significant reductions in seed set relative to large populations (>1000 plants) with higher numbers of S-alleles, despite the maintenance of pollinator service. Greater variance in seed set among plants and higher correlated paternity in small populations suggest that low S-allele numbers are directly limiting mate availability and causing the observed reproductive failure.. Synthesis and applications. Our work demonstrates that the loss of genetic diversity at the SI locus can have immediate detrimental effects on reproductive performance, despite the maintenance of pollinator service. These results highlight the importance of genetic factors in determining demographical outcomes when clear links between genotype and individual fitness exist, even when populations are not ecologically constrained. This result is important for the conservation and management of many plant species as approximately half of all angiosperm families contain species with genetically controlled SI and the loss of genetic diversity through habitat loss and fragmentation is an ever-increasing reality for plant species worldwide. © 2010 The Authors. Journal compilation © 2010 British Ecological Society.


Udikovic-Kolic N.,Ruder Boskovic Institute | Scott C.,CSIRO | Martin-Laurent F.,CNRS Agroecology Lab
Applied Microbiology and Biotechnology | Year: 2012

Since their first introduction in the mid 1950s, manmade s-triazine herbicides such as atrazine have extensively been used in agriculture to control broadleaf weed growth in different crops, and thus contributed to improving crop yield and quality. Atrazine is the most widely used s-triazine herbicide for the control of weeds in crops such as corn and sorghum. Although atrazine was initially found to be slowly and partially biodegradable, predominantly by nonspecific P450 monoxygenases which do not sustain microbial growth, microorganisms gradually evolved as a result of repeated exposure, started using it as a growth substrate and eventually succeeded in mineralizing it. Within three decades, an entirely new hydrolase-dependent pathway for atrazine mineralization emerged and rapidly spread worldwide among genetically different bacteria. This review focuses on the enzymes involved in atrazine mineralization and their evolutionary histories, the genetic composition of microbial populations involved in atrazine degradation and the biotechnologies that have been developed, based on these systems, for the bioremediation of atrazine contamination in the environment. © Springer-Verlag Berlin Heidelberg 2012.


Davis T.J.,CSIRO | Davis T.J.,Melbourne Center For Nanofabrication | Hendry E.,University of Exeter
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

We show theoretically that localized surface plasmons can generate optical fields with a chirality exceeding that of circularly polarized light by a factor of 50. This superchiral optical field can be formed from linearly polarized light incident on nonchiral metal structures. We identify three mechanisms that lead to large optical chirality involving the coupling between the incident light and the evanescent fields of the surface plasmons. Two of these mechanisms create superchiral regions with nonzero average chirality suitable for the excitation of chiral molecules in solution. © 2013 American Physical Society.


Chattopadhyay M.,CSIRO
Electricity Journal | Year: 2012

India's high renewable target might be achievable but it comes at a significant cost, given the nation's already-stressed power system. That's why it is important to get the policy design right from the beginning. The starting point should be a climate data analysis to assess the resource potential and its spatial and seasonal distribution. © 2012 Elsevier Inc..


Brede M.,CSIRO
Artificial Life | Year: 2011

We study the evolution of cooperation in the prisoner's dilemma game on time-invariant heterogeneous payoff landscapes on regular and heterogeneous networks. Correlations in the landscape structure and their implications for the evolution of cooperation are investigated. On regular networks we find that negatively and neutrally correlated payoff landscapes strongly enhance cooperation, while positively correlated landscapes may suppress the evolution of cooperation. On heterogeneous networks, cooperation is facilitated if payoff stochasticity is positively correlated withnetwork heterogeneity and may be suppressed otherwise. © 2011 Massachusetts Institute of Technology.


Barnard A.S.,CSIRO
Accounts of Chemical Research | Year: 2012

Under a given set of conditions, nanomaterials can crystallize into structures that are entirely inconsistent with the bulk material and may adopt a range of faceted morphologies that depend on the particle size. A size-dependent phase diagram, a graphical representation of the chemical equilibrium, offers a convenient way to describe this relationship among the size, morphology, and thermodynamic environment. Although creating such a diagram from conventional experiments is extremely challenging (and costly), theory and simulation allow us to use virtual experiments to control the temperature, pressure, size, structure and composition independently.Although the stability and morphology of gold nanoparticles has been add-ressed numerous times in recent years, a critical examination of the literature reveals a number of glaring contradictions. Typically gold nanoparticles present as multiply-twinned structures, such as icosahedra and decahedra, or faceted monocrystalline (fcc) shapes, such as truncated octahedra and cuboctahedra. All of these shapes are dominated by various fractions of {111} and {100} facets, which have different surface atom densities, electronic structure, bonding, chemical reactivities, and thermodynamic properties. Although many of the computational (and theoretical) studies agree on the energetic order of the different motifs and shapes, they do not necessarily agree with experimental observations. When discrepancies arise between experimental observations and thermodynamic modeling, they are often attributed to kinetics. But only recently could researchers analytically compare the kinetics and thermodynamics of faceted nanoparticles.In this Account, we follow a theoretical study of the size, shape, and structure of nanogold. We systematically explore why certain shapes are expected at different sizes and (more importantly) why others are actually observed. Icosahedra are only thermodynamically preferred at small sizes, but we find that they are the most frequently observed structures at larger sizes because they are kinetically stable (and coarsen more rapidly). In contrast, although the phase diagram correctly predicts that other motifs will emerge at larger sizes, it overestimates the frequency of those observations. These results suggest either a competition or collaboration between the kinetic and thermodynamic influences.We can understand this interaction between influences if we consider the change in shape and the change in size over time. We then use the outputs of the kinetic model as inputs for the thermodynamic model to plot the thermodynamic stability as a function of time. This comparison confirms that decahedra emerge through a combination of kinetics and thermodynamics, and that the fcc shapes are repressed due to an energetic penalty associated with the significant departure from the thermodynamically preferred shape. The infrequent observation of the fcc structures is governed by thermodynamics alone. © Published 2012 by the American Chemical Society.


Guo H.,Shanghai University | Barnard A.S.,CSIRO
Journal of Materials Chemistry A | Year: 2013

The widespread nanostructures of iron oxides and oxyhydroxides are important reagents in many biogeochemical processes in many parts of our planet and ecosystem. Their functions in various aspects are closely related to their shapes, sizes, and thermodynamic surroundings, and there is much that we can learn from these natural relationships. This review covers these subjects of several phases (ferrihydrite, goethite, hematite, magnetite, maghemite, lepidocrocite, akaganéite and schwertmannite) commonly found in water, soils and sediments. Due to surface passivation by ubiquitous water in aquatic and most terrestrial environments, the difference in formation energies of bulk phases can decrease substantially or change signs at the nanoscale because of the disproportionate surface effects. Phase transformations and the relative abundance are sensitive to changes in environmental conditions. Each of these phases (except maghemite) displays characteristic morphologies, while maghemite appears frequently to inherit the precursor's morphology. We will see how an understanding of naturally occurring iron oxide nanostructures can provide useful insight for the production of synthetic iron oxide nanoparticles in technological settings. © 2013 The Royal Society of Chemistry.


McKay M.R.,Hong Kong University of Science and Technology | Collings I.B.,CSIRO | Tulino A.M.,Alcatel - Lucent
IEEE Transactions on Information Theory | Year: 2010

This paper investigates the achievable sum rate of multiple-input multiple-output (MIMO) wireless systems employing linear minimum mean-squared error (MMSE) receivers. We present a new analytic framework which exploits an interesting connection between the achievable sum rate with MMSE receivers and the ergodic mutual information achieved with optimal receivers. This simple but powerful result enables the vast prior literature on ergodic MIMO mutual information to be directly applied to the analysis of MMSE receivers. The framework is particularized to various Rayleigh and Rician channel scenarios to yield new exact closed-form expressions for the achievable sum rate, as well as simplified expressions in the asymptotic regimes of high and low signal-to-noise ratios (SNRs). These expressions lead to the discovery of key insights into the performance of MIMO MMSE receivers under practical channel conditions. © 2009 IEEE.


Smajgl A.,CSIRO
Environmental Modelling and Software | Year: 2010

A critical challenge for science in times of increasingly depleted natural resources is how policy and management can be improved to attain a pathway to sustainability. This paper argues that facilitating a learning experience for decision makers by employing participatory modelling and explicitly considering multiple tiers of governance can effectively contribute to achieve sustainable outcomes. Decision makers operate on different scales and respond to decisions made on other scales. However, shared beliefs can vary and policy interventions from different levels can be incompatible due to a lack of cross-sectoral and cross-scale coordination. Sustainability is determined by conditions defined by this process of interactive decision-making, and across various tiers of governance. To improve understanding at one scale in isolation with constant assumptions of the responses at other scales is likely to lead to unsustainable unintended side effects. Based on applied research in Indonesia, consequences for research design, methodological aspects of modelling and the process of decision support are discussed. The agent-based analysis links household livelihoods, deforestation, and fuel price changes. Focused on process-related aspects, this work identifies the effectiveness of participatory modelling to challenge shared beliefs and, therefore, facilitate a potentially valuable learning experience for decision makers. © 2010 Elsevier Ltd.


Cheney N.P.,CSIRO
Conservation Science Western Australia | Year: 2010

Wildfire burnt 27 700 ha of jarrah (Eucalyptus marginata) forest in the Pickering Brook area of the Perth hills during January 2005. Fuels in the area ranged from 1 year-old to 22 year-old in a broad mosaic. A detailed reconstruction of the spread over two days allowed the testing of fire-spread prediction models and the examination of the effects of prescribed burning on fire behaviour. The Forest Fire Behaviour Tables for Western Australia grossly under-predicted fire spread when a wind ratio of 5:1 was used to convert open wind speed to in-forest wind speed. Using a wind ratio of 3:1, the tables predicted reasonably well at low to moderate wind speeds but over-predicted at high wind speeds. The fire spread equations based on Project Vesta experiments predicted fire spread reasonably well over the full range of fuel loads and wind speeds. However, the data suggested the need for better models to predict fuel moisture content, particularly after a day of low humidity Comparison of predicted and observed rates of spread indicated that reducing fuel load by prescribed burning reduced the rate of spread below the rate predicted in 20 year-old fuel loads for at least 8 years. Fire in 3 year-old fuel spread six times slower and was 20 times less intense than fire in 20 year-old fuel In the absence of a prescribed burning program and assuming the area had not been burnt for 20 years it was estimated the fire would have burnt into the outer suburbs of Perth with the potential for extensive property damage. The final burnt area could have exceeded 100 000ha, or more than three times the area actually burnt. © The Government of Western Australia.


Indicators of trawl exposure were developed for 837 bycatch and benthos species, assemblages and habitats on the Great Barrier Reef shelf, by analysing their spatial distributions (mapped by a previous study) in relation to management zones, overlap with trawl grounds, and the intensity of trawl effort - and estimating the proportion of their distributions exposed to trawling. Exposure to trawl intensity as a swept-coverage was a more sensitive indicator than exposure to trawled grounds or exposure as permitted by management zones. Few habitats and assemblages were highly exposed. About 33 species had high exposure to trawl effort, whereas approximately 70% of the 837 species had low exposure. The indicators for species were extended, using relative catch rates, to estimate the proportion of populations caught annually (exploitation rate). Five species had high estimated exploitation rates and 28 were intermediate, whereas most (>800) species had low exploitation rates. The productivity potential of species to counter the incidental catch was assessed using recovery scores from life history traits. This qualitative approach indicated species at higher relative risk due to trawling. A quantitative indicator of absolute sustainability was estimated using available natural mortality rates to calculate the proportion of fishing mortality at maximum sustainable yield (FMSY). Three species exceeded a limit reference point (≅1.0×FMSY), one species exceeded a first conservative reference point (≅0.8×FMSY) and two others exceeded a second conservative reference point (≅0.6×FMSY). While few species were assessed at high risk, there were uncertainties in the distributions, relative catch rates, and natural mortality rates that required a precautionary response, including considering additional species with high indicator values. The species identified as high risk by the quantitative sustainability indicator and by the qualitative productivity scores corresponded poorly. This raises concerns about the reliability of qualitative approaches often used to conduct risk assessments for data-poor species. © 2013 Elsevier B.V.


Haverd V.,CSIRO | Cuntz M.,Max Planck Institute For Biogeochemie
Journal of Hydrology | Year: 2010

We present a new isotopically enabled hydrologic scheme, "Soil-Litter-Iso", suitable for use as part of an isotopically enabled land surface model. Soil-Litter-Iso is a one-dimensional model for coupled transport of heat, water and stable isotopes (HDO and H218O) in soil and litter. It is sufficiently efficient for use at regional scale, yet includes the complexity of coupled heat and water transport enabling decomposition of the total moisture flux into liquid and vapour components. The numerical implementation is based on Ross' fast solution to the Richards equation (Ross, 2003). This, combined with the explicit solution of the energy and moisture equations at the soil/air interface, permit the isotopic calculations to be performed with thick soil layers and large times steps, resulting in significantly improved computational efficiency compared with existing isotopically-enabled soil models of similar complexity. We demonstrate the model's numerical accuracy by conducting a series of established test-cases and comparing predictions of steady-state isotopic concentration profiles with corresponding analytical solutions. We also demonstrate the model's operation within a land surface model by performing simulations for the forested flux site at Tumbarumba in south-eastern Australia. These simulations show that the total evapotranspiration (ET) flux, its components and their isotopic signatures are very sensitive to the inclusion of litter, and that the model is a useful tool for assessing when the isotopic signatures of the ET components are sufficiently distinct to be useful for flux partitioning. Crown Copyright © 2010.


Lu X.,Huazhong University of Science and Technology | Naidis G.V.,RAS Joint Institute for High Temperatures | Laroussi M.,Old Dominion University | Ostrikov K.,CSIRO | Ostrikov K.,University of Sydney
Physics Reports | Year: 2014

This review focuses on one of the fundamental phenomena that occur upon application of sufficiently strong electric fields to gases, namely the formation and propagation of ionization waves-streamers. The dynamics of streamers is controlled by strongly nonlinear coupling, in localized streamer tip regions, between enhanced (due to charge separation) electric field and ionization and transport of charged species in the enhanced field. Streamers appear in nature (as initial stages of sparks and lightning, as huge structures-sprites above thunderclouds), and are also found in numerous technological applications of electrical discharges. Here we discuss the fundamental physics of the guided streamer-like structures-plasma bullets which are produced in cold atmospheric-pressure plasma jets. Plasma bullets are guided ionization waves moving in a thin column of a jet of plasma forming gases (e.g.,He or Ar) expanding into ambient air. In contrast to streamers in a free (unbounded) space that propagate in a stochastic manner and often branch, guided ionization waves are repetitive and highly-reproducible and propagate along the same path-the jet axis. This property of guided streamers, in comparison with streamers in a free space, enables many advanced time-resolved experimental studies of ionization waves with nanosecond precision. In particular, experimental studies on manipulation of streamers by external electric fields and streamer interactions are critically examined. This review also introduces the basic theories and recent advances on the experimental and computational studies of guided streamers, in particular related to the propagation dynamics of ionization waves and the various parameters of relevance to plasma streamers. This knowledge is very useful to optimize the efficacy of applications of plasma streamer discharges in various fields ranging from health care and medicine to materials science and nanotechnology. © 2014 Elsevier B.V.


Braun R.,CSIRO
Astrophysical Journal | Year: 2012

Galaxy disks are shown to contain a significant population of atomic clouds of 100pc linear size which are self-opaque in the 21cm transition. These objects have H I column densities as high as 1023cm-2 and contribute to a global opacity correction factor of 1.34 ± 0.05 that applies to the integrated 21cm emission to obtain a total H I mass estimate. High-resolution, opacity-corrected images of the nearest external galaxies have been used to form a robust redshift zero distribution function of H I, f(N H I, X, z = 0), the probability of encountering a specific H I column density along random lines of sight per unit comoving distance. This is contrasted with previously published determinations of f(N H I, X) at z = 1 and 3. A systematic decline of moderate column density (18 < log(N H I) < 21) H I is observed with decreasing redshift that corresponds to a decline in surface area of such gas by a factor of five since z = 3. The number of equivalent Damped Lyman Alpha absorbers (log(N H I)>20.3) has also declined systematically over this redshift interval by a similar amount, while the cosmological mass density in such systems has declined by only a factor of two to its current, opacity-corrected value of ΩDLA H I(z = 0) = 5.4 ± 0.9 × 10-4. We utilize the tight but strongly nonlinear dependence of 21cm absorption opacity on column density at z = 0 to transform our high-resolution H I images into ones of 21cm absorption opacity. These images are used to calculate distribution and pathlength functions of integrated 21cm opacity. We suggest that that this z = 0 calibration may also apply at higher redshift. In this case, the incidence of deep 21cm absorption systems is predicted to show very little evolution with redshift, while that of faint absorbers should decline by a factor of 5 between z = 3 and the present. We explicitly consider the effects of H I absorption against background sources that are extended relative to the 100pc intervening absorber size scale. Extended background sources result in dramatically altered distribution and pathlength functions which are insensitive to the predicted redshift evolution. Future surveys of 21cm absorption will require very high angular resolution, of about 15mas, for their unambiguous interpretation. © © 2012. The American Astronomical Society. All rights reserved..


Bryan B.A.,CSIRO
Environmental Science and Policy | Year: 2013

Incentive schemes are increasingly used to motivate the supply of ecosystem services from agro-ecosystems through changes in land use and management. Here, I synthesize the complex effects of incentives on ecosystem services through their influence on land use and management. Linkages between incentives and land use change, and between land use change and ecosystem services can be one-to-many, many-to-one, and many-to-many. Change in land use and management can affect multiple ecosystem services, with both co-benefits and trade-offs. Incentives can motivate multiple changes in land use and management and multiple incentives often interact with both synergies and tensions in their effect upon ecosystem services. These vary over both space and time, and can be non-linear. Depending on incentive design, changes in ecosystem service supply can also have a feedback effect on incentive prices. I suggest that continued quantitative development is required to further explore these linkages: in the influence of incentives on land use change; in the impact of land use change on ecosystem services, and; in ecosystem service supply feedbacks on incentive prices. Quantifying and understanding these linkages is essential to progress more comprehensive analyses of the impact of incentives on ecosystem services, and the design of incentives capable of realizing synergies and avoiding tensions. © 2012 Elsevier Ltd.


Hobbs G.,CSIRO | Lyne A.G.,University of Manchester | Kramer M.,University of Manchester
Monthly Notices of the Royal Astronomical Society | Year: 2010

We provide an analysis of timing irregularities observed for 366 pulsars. Observations were obtained using the 76-m Lovell radio telescope at the Jodrell Bank Observatory over the past 36 years. These data sets have allowed us to carry out the first large-scale analysis of pulsar timing noise over time-scales of >10 yr, with multiple observing frequencies and for a large sample of pulsars. Our sample includes both normal and recycled pulsars. The timing residuals for the pulsars with the smallest characteristic ages are shown to be dominated by the recovery from glitch events, whereas the timing irregularities seen for older pulsars are quasi-periodic. We emphasize that previous models that explained timing residuals as a low-frequency noise process are not consistent with observation. © 2009 The Authors. Journal compilation © 2009 RAS.


Groundwater discharge constitutes a significant proportion of the total flow volume in most rivers. The exchange flux between surface and groundwater greatly impacts the surface as well as the groundwater balance with serious implications on ecosystem health especially during low flow conditions. There is a move towards conjunctive river-aquifer management with the integration of surface-groundwater exchange fluxes into surface and groundwater models to manage water as a single resource. Groundwater-Surface water (GW-SW) exchange fluxes are seldom integrated into river operation and planning models. The time lags associated with the impacts of groundwater processes on nearby rivers can greatly compromise the forecasting capacity of river models especially during low flow conditions.This paper presents a conceptual framework for integrating GW-SW exchange fluxes into the new generation river operation-planning model 'Source Integrated Modelling System'. The proposed GW-SW Link Module adopts a simple pragmatic approach for estimating the exchange fluxes between a river reach and the underlying aquifer using explicit analytical solutions. This flux becomes an inflow/outflow to that river reach and forms part of the routing and calibration processes. The exchange flux comprises four components: (1) natural exchange flux resulting from river stage fluctuations during low flow conditions, within bank and overbank fluctuations; (2) flux due to groundwater extraction; (3) flux due to changes in aquifer recharge; and (4) flux due to changes in evapotranspiration. The sum of those components during every time step dictates whether the river loses water to or gains water from the aquifer.The proposed analytical solutions were found to provide flux predictions that agree favourably with those derived from a numerical groundwater model. Recognising that the simplifying assumptions that underpin the explicit analytical solution are likely to be violated in the natural world, a suite of criteria was recommended for their use under many violating conditions related to boundary conditions, head gradients, and aquifer heterogeneity. Low flow indices were adopted to demonstrate the critical role of GW-SW exchange flux when predicting river low flows. Explicit accounting of GW-SW interactions into river operation and planning models greatly enhances their forecasting capacity during low flow conditions. © 2011 Elsevier Ltd.


Lima P.C.,CSIRO
Fish & shellfish immunology | Year: 2013

Aquatic animal diseases are one of the most significant constraints to the development and management of aquaculture worldwide. As a result, measures to combat diseases of fish and shellfish have assumed a high priority in many aquaculture-producing countries. RNA interference (RNAi), a natural mechanism for post-transcriptional silencing of homologous genes by double-stranded RNA (dsRNA), has emerged as a powerful tool not only to investigate the function of specific genes, but also to suppress infection or replication of many pathogens that cause severe economic losses in aquaculture. However, despite the enormous potential as a novel therapeutical approach, many obstacles must still be overcome before RNAi therapy finds practical application in aquaculture, largely due to the potential for off-target effects and the difficulties in providing safe and effective delivery of RNAi molecules in vivo. In the present review, we discuss the current knowledge of RNAi as an experimental tool, as well as the concerns and challenges ahead for the application of such technology to combat infectious disease of farmed aquatic animals. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.


Barnard A.S.,CSIRO
Reports on Progress in Physics | Year: 2010

As we learn more about the physics, chemistry and engineering of materials at the nanoscale, we find that the development of a complete understanding is not (in general) possible using one technique alone. Computer simulations provide a very valuable addition to our scientific repertoire, but it is not immediately intuitive which of the many methods available are right for a given problem. In this paper, various computational approaches are described as they apply to the study of the structure and formation of discrete inorganic nanoparticles. To illustrate how these methods are best used, results of studies from many research groups are reviewed, and informal case studies are constructed on carbon, titania and gold nanoparticles. © 2010 IOP Publishing Ltd.


Walker P.J.,CSIRO | Winton J.R.,U.S. Geological Survey
Veterinary Research | Year: 2010

The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. Aquaculture is now integral to the economies of many countries. It has provided employment and been a major driver of socio-economic development in poor rural and coastal communities, particularly in Asia, and has relieved pressure on the sustainability of the natural harvest from our rivers, lakes and oceans. However, the rapid growth of aquaculture has also been the source of anthropogenic change on a massive scale. Aquatic animals have been displaced from their natural environment, cultured in high density, exposed to environmental stress, provided artificial or unnatural feeds, and a prolific global trade has developed in both live aquatic animals and their products. At the same time, over-exploitation of fisheries and anthropogenic stress on aquatic ecosystems has placed pressure on wild fish populations. Not surprisingly, the consequence has been the emergence and spread of an increasing array of new diseases. This review examines the rise and characteristics of aquaculture, the major viral pathogens of fish and shrimp and their impacts, and the particular characteristics of disease emergence in an aquatic, rather than terrestrial, context. It also considers the potential for future disease emergence in aquatic animals as aquaculture continues to expand and faces the challenges presented by climate change. © 2010 INRA, EDP Sciences.


Brede M.,CSIRO
Physica D: Nonlinear Phenomena | Year: 2010

The synchronization transition of correlated ensembles of coupled Kuramoto oscillators on sparse random networks is investigated. Extensive numerical simulations show that correlations between the native frequencies of adjacent oscillators on the network systematically shift the critical point as well as the critical exponents characterizing the transition. Negative correlations imply an onset of synchronization for smaller coupling, whereas positive correlations shift the critical coupling towards larger interaction strengths. For negatively correlated oscillators the transition still exhibits critical behaviour similar to that of the all-to-all coupled Kuramoto system, while positive correlations change the universality class of the transition depending on the correlation strength. Crucially, the paper demonstrates that the synchronization behaviour is not only determined by the coupling architecture, but also strongly influenced by the oscillator placement on the coupling network. Crown Copyright © 2010 Published by Elsevier B.V. All rights reserved.


Goodall J.L.,University of South Carolina | Robinson B.F.,CSIRO | Castronova A.M.,University of South Carolina
Environmental Modelling and Software | Year: 2011

Service-oriented computing is a software engineering paradigm that views complex software systems as an interconnected collection of distributed computational components. Each component has a defined web service interface that allows it to be loosely-coupled with client applications. The service-oriented paradigm presents an attractive way of modeling multidisciplinary water resource systems because it allows a diverse community of scientists and engineers to work independently on components of a larger modeling system. While a service-oriented paradigm has been successfully applied for integrating water resource data, this paper considers service-oriented computing as an approach for integrating water resource models. We present an interface design for exposing water resource models as web services and demonstrate how it can be used to simulate a rainfall/runoff event within a watershed system. We discuss the advantages and disadvantages of using service-oriented computing for modeling water resource systems, and conclude with future work needed to advance the application of service-oriented computing for modeling water resource systems. © 2010 Elsevier Ltd.


Walker B.,CSIRO | Westley F.,Institute for Complexity and Innovation
Ecology and Society | Year: 2011

We present some insights on the use and interpretation of resilience ideas that arose in a conference on "Society's Resilience in Withstanding Disaster." Three points in particular have relevance for those interested in resilience in social-ecological systems: (1) Time as a threshold vs. avoiding quick fixes; (2) Trading risks: specified vs. general resilience; (3) Response origination: building local general resilience, and general resilience in central agencies. In the latter the need is to allow improvisation, and failure, during times of crisis. © 2011 by the author(s).


Gallant J.C.,CSIRO | Hutchinson M.F.,Australian National University
Water Resources Research | Year: 2011

Analysis of the behavior of specific catchment area in a stream tube leads to a simple nonlinear differential equation describing the rate of change of specific catchment area along a flow path. The differential equation can be integrated numerically along a flow path to calculate specific catchment area at any point on a digital elevation model without requiring the usual estimates of catchment area and width. The method is more computationally intensive than most grid-based methods for calculating specific catchment area, so its main application is as a reference against which conventional methods can be tested. This is the first method that provides a benchmark for more approximate methods in complex terrain with both convergent and divergent areas, not just on simple surfaces for which analytical solutions are known. Preliminary evaluation of the D8, M8, digital elevation model networks (DEMON), and D methods indicate that the D method is the best of those methods for estimating specific catchment area, but all methods overestimate in divergent terrain.© 2011 by the American Geophysical Union.


White R.G.,CSIRO | Barton D.A.,University of Sydney
Journal of Experimental Botany | Year: 2011

Actin and myosin are components of the plant cell cytoskeleton that extend from cell to cell through plasmodesmata (PD), but it is unclear how they are organized within the cytoplasmic sleeve or how they might behave as regulatory elements. Early work used antibodies to locate actin and myosin to PD, at the electron microscope level, or to pitfields (aggregations of PD in the cell wall), using immunofluorescence techniques. More recently, a green fluorescent protein (GFP)-tagged plant myosin VIII was located specifically at PD-rich pitfields in cell walls. Application of actin or myosin disrupters may modify the conformation of PD and alter rates of cell-cell transport, providing evidence for a role in regulating PD permeability. Intriguingly, there is now evidence of differentiation between types of PD, some of which open in response to both actin and myosin disrupters, and others which are unaffected by actin disrupters or which close in response to myosin inhibitors. Viruses also interact with elements of the cytoskeleton for both intracellular and intercellular transport. The precise function of the cytoskeleton in PD may change during cell development, and may not be identical in all tissue types, or even in all PD within a single cell. Nevertheless, it is likely that actin-and myosin-associated proteins play a key role in regulating cell-cell transport, by interacting with cargo and loading it into PD, and may underlie the capacity for one-way transport across particular cell and tissue boundaries. © 2011 The Author.


Marshall N.A.,CSIRO
Society and Natural Resources | Year: 2011

Climate change is altering the quality and availability of natural resources with far-reaching implications for resource users and the extensive social and economic systems that they support. Those who are particularly dependent on a climate sensitive resource will be especially sensitive to climate changes. Measuring resource dependency is key to understanding the sensitivity of resource users to climate change. I assessed 100 cattle-graziers in Queensland, Australia, for their dependency on grazing lands. I assessed their (i) attachment to place, (ii) attachment to occupation, (iii) family circumstances, (iv) employability, (v) networks, (vi) financial circumstances, (vii) business characteristics, (viii) local knowledge and skills, and (ix) attitudes and behavior. Results indicate that graziers are highly resource dependent, socially and economically. Understanding dependency in its entirety may provide the foundations for developing strategic efforts to reduce climate vulnerability and assist resource users to cope and adapt. © 2011 Crown copyright.


Acquisition of magnetic gradient tensor data is likely to become routine in the near future. New methods for inverting gradient tensor surveys to obtain source parameters have been developed for several elementary, but useful, models. These include point dipole (sphere), vertical line of dipoles (narrow vertical pipe), line of dipoles (horizontal cylinder), thin dipping sheet, and contact models. A key simplification is the use of eigenvalues and associated eigenvectors of the tensor. The normalised source strength (NSS), calculated from the eigenvalues, is a particularly useful rotational invariant that peaks directly over 3D compact sources, 2D compact sources, thin sheets and contacts, and is independent of magnetisation direction. In combination the NSS and its vector gradient determine source locations uniquely. NSS analysis can be extended to other useful models, such as vertical pipes, by calculating eigenvalues of the vertical derivative of the gradient tensor. Inversion based on the vector gradient of the NSS over the Tallawang magnetite deposit obtained good agreement between the inferred geometry of the tabular magnetite skarn body and drill hole intersections. Besides the geological applications, the algorithms for the dipole model are readily applicable to the detection, location and characterisation (DLC) of magnetic objects, such as naval mines, unexploded ordnance, shipwrecks, archaeological artefacts, and buried drums. © 2012 ASEG.


Lacey J.,CSIRO | Lamont J.,University of Queensland
Journal of Cleaner Production | Year: 2014

The emerging coal seam gas (CSG) industry has been commercially active in Australia since the mid 1990s. More recently however, the development of the CSG industry has escalated rapidly with its trajectory predicted to grow into the future as gas supplies become a major and important fuel source in the transition to a lower carbon future. However, the industry has been the subject of significant social opposition. Coordinated citizen action groups taking direct action against CSG operations have delayed and even stopped CSG projects progressing. In response, the industry has recognised the importance of establishing its social licence to operate. While conflicts around CSG development tend to incorporate a combination of environmental, social, economic and technological concerns, the ethical aspects of these disagreements are rarely made explicit or explored in any depth. However, some of these more implicit ethical assumptions have begun to be formalised in the concept of social licence. The idea that a social licence represents a social contract between companies and communities is instructive. Because social contract theory describes the nature and purpose of agreement-making among members of an organised society, there are clear implications for understanding the social sustainability of those arrangements. This paper explores how consent-based and justice-based forms of social contract provide an ethical framework for the way CSG companies and communities interact. © 2013 Elsevier Ltd. All rights reserved.


Pettolino F.A.,CSIRO | Walsh C.,University of Melbourne | Fincher G.B.,University of Adelaide | Bacic A.,University of Melbourne
Nature Protocols | Year: 2012

The plant cell wall is a chemically complex structure composed mostly of polysaccharides. Detailed analyses of these cell wall polysaccharides are essential for our understanding of plant development and for our use of plant biomass (largely wall material) in the food, agriculture, fabric, timber, biofuel and biocomposite industries. We present analytical techniques not only to define the fine chemical structures of individual cell wall polysaccharides but also to estimate the overall polysaccharide composition of cell wall preparations. The procedure covers the preparation of cell walls, together with gas chromatographyg-mass spectrometry (GC-MS)-based methods, for both the analysis of monosaccharides as their volatile alditol acetate derivatives and for methylation analysis to determine linkage positions between monosaccharide residues as their volatile partially methylated alditol acetate derivatives. Analysis time will vary depending on both the method used and the tissue type, and ranges from 2 d for a simple neutral sugar composition to 2 weeks for a carboxyl reduction/methylation linkage analysis. © 2012 Nature America, Inc. All rights reserved.


Asseng S.,University of Florida | Asseng S.,CSIRO | Pannell D.J.,University of Western Australia
Climatic Change | Year: 2013

The Western Australian wheat-belt has experienced more rainfall decline than any other wheat-cropping region in Australia. Future climate change scenarios suggest that the Western Australian wheat-belt is likely to see greater future reductions in rainfall than other regions, together with a further increase in temperatures. While these changes appear adverse for water-limited rain-fed agriculture, a close analysis of the changes and their impacts reveals a more complex story. Twentieth century changes in rainfall, temperature and atmospheric CO2 concentration have had little or no overall impact on wheat yields. Changes in agricultural technology and farming systems have had much larger impacts. Contrary to some claims, there is no scientific or economic justification for any immediate actions by farmers to adapt to long-term climate change in the Western Australian wheat-belt, beyond normal responses to short-term variations in weather. Rather than promoting current change, the most important policy response is research and development to enable farmers to facilitate future adaptation to climate change. Research priorities are proposed. © 2012 Springer Science+Business Media Dordrecht.


Some of the most productive plants on the planet use a variant of photosynthesis known as the C 4 pathway. This photosynthetic mechanism uses a biochemical pump to concentrate CO 2 to levels up to 10-fold atmospheric in specialized cells of the leaf where Rubisco, the primary enzyme of C 3 photosynthesis, is located. The basic biochemical pathways underlying this process, discovered more than 40 years ago, have been extensively studied and, based on these pathways, C 4 plants have been subdivided into two broad groups according to the species of C 4 acid produced in the mesophyll cells and into three groups according to the enzyme used to decarboxylate C 4 acids in the bundle sheath to release CO 2. Recent molecular, biochemical, and physiological data indicate that these three decarboxylation types may not be rigidly genetically determined, that the possibility of flexibility between the pathways exists and that this may potentially be both developmentally and environmentally controlled. This evidence is synthesized here and the implications for C 4 engineering discussed. © 2011 The Author.


Miao M.,CSIRO
Carbon | Year: 2011

The porosity of multi-walled carbon nanotube yarns can be varied over a wide range by adjusting the yarn construction, resulting in a dramatic change in yarn electrical conductivity. When the yarn electrical conductivity is converted into specific conductivity, its value remains approximately constant irrespective of the changes in yarn construction and porosity. The process of carbon nanotube yarn production involves two key steps, the formation of a network of carbon nanotube bundles spliced together by the entanglement of individual nanotubes and the compaction of the network into a cylindrical yarn. The splices formed from entangled individual nanotubes play a much greater role in electrical conduction than the cross-over contact formed between CNT bundles by compaction during spinning. © 2011 Elsevier Ltd. All rights reserved.


Borges P.V.K.,CSIRO | Izquierdo E.,University of London
IEEE Transactions on Circuits and Systems for Video Technology | Year: 2010

Automated fire detection is an active research topic in computer vision. In this paper, we propose and analyze a new method for identifying fire in videos. Computer vision-based fire detection algorithms are usually applied in closed-circuit television surveillance scenarios with controlled background. In contrast, the proposed method can be applied not only to surveillance but also to automatic video classification for retrieval of fire catastrophes in databases of newscast content. In the latter case, there are large variations in fire and background characteristics depending on the video instance. The proposed method analyzes the frame-to-frame changes of specific low-level features describing potential fire regions. These features are color, area size, surface coarseness, boundary roughness, and skewness within estimated fire regions. Because of flickering and random characteristics of fire, these features are powerful discriminants. The behavioral change of each one of these features is evaluated, and the results are then combined according to the Bayes classifier for robust fire recognition. In addition, a priori knowledge of fire events captured in videos is used to significantly improve the classification results. For edited newscast videos, the fire region is usually located in the center of the frames. This fact is used to model the probability of occurrence of fire as a function of the position. Experiments illustrated the applicability of the method. © 2010 IEEE.


Griffin G.J.,CSIRO
Journal of Fire Sciences | Year: 2010

The use of mathematical models to predict the thermal resistance of polymer-based, intumescent coatings are reviewed and their limitations are discussed. A mathematical model is derived to describe the developing temperature profile across an intumescent coating when exposed to a radiant heat source. The model includes the effects of: the endothermic and exothermic reactions; convective heat transfer as degradation gases are transported through the coating; radiation heat transfer across the developing porous solid; and the increase in thermal resistance as gases are formed and the coating expands. The model predictions are compared with experimental data from the heating of epoxy-based and vinyl acetate-based intumescent coatings in a cone calorimeter. A sensitivity analysis is performed to show the effect of the thermal characteristics of the coating on the thermal resistance of the material. The application of the model to newly developed intumescent coatings is discussed. © 2010 SAGE Publications.


Background Auxin is a versatile plant hormone with important roles in many essential physiological processes. In recent years, significant progress has been made towards understanding the roles of this hormone in plant growth and development. Recent evidence also points to a less well-known but equally important role for auxin as a mediator of environmental adaptation in plants. Scope This review briefly discusses recent findings on how plants utilize auxin signalling and transport to modify their root system architecturewhen responding to diverse biotic and abiotic rhizosphere signals, includingmacro- and micro-nutrient starvation, cold and water stress, soil acidity, pathogenic and beneficial microbes, nematodes and neighbouring plants. Stress-responsive transcription factors and microRNAs that modulate auxin- and environment- mediated root development are also briefly highlighted. Conclusions The auxin pathway constitutes an essential component of the plant's biotic and abiotic stress tolerance mechanisms. Further understanding of the specific roles that auxin plays in environmental adaptation can ultimately lead to the development of crops better adapted to stressful environments. © The Author 2013.


Radcliffe J.C.,CSIRO
Water Science and Technology | Year: 2010

The prolonged Australian drought which commenced in 2002, and the agreement between Australia's Commonwealth and States/Territories governments to progress water reform through the National Water Initiative, has resulted in many new recycling projects in Australia's capital cities. Dual reticulation systems are being advanced in new subdivision developments in Sydney, Melbourne and Adelaide. Brisbane has installed three large Advanced Water Treatment Plants that are designed to send indirect potable recycled water to the Wivenhoe Dam which is Brisbane's principal water reservoir. Numerous water recycling projects are serving industry and agriculture. Experimental managed aquifer recharge is being undertaken with wetland-treated stormwater in Adelaide and reverse osmosis treated wastewater in Perth. New National Water Quality Management Strategy recycled water guidelines have been developed for managing environmental risks, for augmentation of drinking water supplies, for managed aquifer recharge and for stormwater harvesting and reuse. Many recent investments are part-supported through Commonwealth government grants. Desalination plants are being established in Melbourne and Adelaide and a second one in Perth in addition to the newly-operational plants in Perth, South-East Queensland and Sydney. Despite there being numerous examples of unplanned indirect potable recycling, most governments remain reluctant about moving towards planned potable recycling. There is evidence of some policy bans still being maintained by governments but the National Water Commission continues to reinforce the necessity of an even-handed objective consideration of all water supply options. © IWA Publishing 2010.


There is a current debate about development of the river and wetland systems of tropical Australia. Aboriginal and non-Aboriginal residents of tropical river catchment areas have complex values for these systems which are difficult for decision-makers to accommodate. Aboriginal Australians are a large and growing proportion of the population and are also significant landowners, yet there is little information about the impacts of potential development scenarios on the welfare of Aboriginal Australians that can be used in benefit-cost analyses. This paper reports the application of a choice experiment to assess the potential impact of development/management strategies for three tropical rivers in Australia, and explores the differences between the preferences of Aboriginal and non-Aboriginal Australians living in the catchment areas. Most respondents preferred healthy river systems that are managed under conservation schemes even if this comes at a private cost. The willingness-to-pay of Aboriginal Australians was significantly higher than that of non-Aboriginal Australians for some river attributes, particularly those related to cultural values. Aboriginal respondents were also indifferent towards the extraction of water for irrigated agriculture while non-Aboriginal respondents preferred moderate rather than large or small scale use. © 2010 Elsevier B.V.


Rand D.A.J.,CSIRO
Journal of Solid State Electrochemistry | Year: 2011

As the nations of the world continue to develop, their industrialization and growing populations will require increasing amounts of energy. Yet, global energy consumption, even at present levels, has already given rise to major concerns over the security of future supplies, together with the attendant twin problems of environmental degradation and climate change. Accordingly, countries are examining a whole range of new policies and technology issues to make their energy futures 'sustainable', that is, to maintain economic growth and cultural values whilst providing energy security and environmental protection. A step in the right direction is to place electrochemical power sources-serviceable, efficient and clean technology-at the cutting edge of energy strategies, regardless of the relatively low price of such traditional fuels as coal, mineral oil and natural gas. Following a chronicle of the events that led up to the discovery of batteries and fuel cells, the paper discusses the application of these devices as important technology for shifting primary energy demand away from fossil fuels and towards renewable sources that are more abundant, less expensive and/or more environmentally benign. Finally, consideration is given to the idea of introducing hydrogen as the universal vector for conveying renewable forms of energy and also as the ultimate non-polluting fuel. Fuel cells are the key enabling technology for a hydrogen economy. As requested, the paper opens with a brief account of the circumstances by which the author joined others on a fascinating journey on the electrochemical road to sustainability. © 2011 Springer-Verlag.


Chemical and sensory characterisation of whole and fractionated myrosinase-free extracts from selected Australian-grown, raw Brassica vegetables (broccoli, cauliflower, Brussels sprouts and red cabbage) was carried out to determine the contribution of key phytochemicals (i.e. glucosinolates, free sugars, phenolics) to the taste profiles of these vegetables. Glucosinolate (GS) and phenolic profiles were determined by liquid chromatography coupled with photodiode array detection and mass spectrometry. Ten glucosinolates (GS) were quantified across the vegetables investigated. Brussels sprouts (186.3 μg g(-1) FW) followed by broccoli (164.1 μg g(-1) FW) were found to contain the most GS. The phenolic profiles of all samples were dominated by hydroxycinnamic acid derivatives. As expected, red cabbage was the only vegetable with a significant anthocyanin signal (574.0 μg g(-1) FW). Red cabbage (26.7 mg g(-1) FW) and cauliflower (18.7 mg g(-1) FW) were found to contain a higher concentration of free sugars than Brussels sprouts (12.6 mg g(-1) FW) and broccoli (10.2 mg g(-1) FW). Descriptive sensory analysis of the whole extracts found sweetness (cauliflower and red cabbage sweeter than broccoli and Brussels sprouts) and bitterness (Brussels sprouts more bitter than others) as the most discriminating attributes. A hydrophilic fraction with sweetness, umami and saltiness as the main attributes was the most taste active fraction across all Brassica whole extracts. Sub-fractionation showed that this fraction was also bitter but the presence of sugars counteracted bitterness. Several components within each extract were found to contribute to the bitterness of whole Brassica extracts. The total and individual GS content alone could not explain the perceived bitterness of these extracts. Phenolics and/or other components are likely to be contributing to the bitterness associated with these vegetables.


Torkzaban S.,CSIRO | Bradford S.A.,U.S. Department of Agriculture
Water Research | Year: 2016

This paper examines the critical role of surface roughness (both nano- and micro-scale) on the processes of colloid retention and release in porous media under steady-state and transient chemical conditions. Nanoscale surface roughness (NSR) in the order of a few nanometers, which is common on natural solid surfaces, was incorporated into extended-DLVO calculations to quantify the magnitudes of interaction energy parameters (e.g. the energy barrier to attachment, δΦa, and detachment, δΦd, from a primary minimum). This information was subsequently used to explain the behavior of colloid retention and release in column and batch experiments under different ionic strength (IS) and pH conditions. Results demonstrated that the density and height of NSR significantly influenced the interaction energy parameters and consequently the extent and kinetics of colloid retention and release. In particular, values of δΦa and δΦd significantly decreased in the presence of NSR. Therefore, consistent with findings of column experiments, colloid retention in the primary minimum was predicted to occur at some specific locations on the sand surface, even at low IS conditions. However, NSR yielded a much weaker primary minimum interaction compared with that of smooth surfaces. Colloid release from primary minima upon decreasing IS and increasing pH was attributed to the impact of NSR on the values of δΦd Pronounced differences in the amount of colloid retention in batch and column experiments indicated that primary minimum interactions were weak even at high IS conditions. Negligible colloid retention in batch experiments was attributed to hydrodynamic torques overcoming adhesive torques, whereas significant colloid retention in column experiments was attributed to nano- and micro-scale roughness which would dramatically alter the lever arms associated with hydrodynamic and adhesive torques. © 2015 Elsevier Ltd.


The Nothridae of Australia hitherto consisted of the semi-cosmopolitan Nothrus anauniensis, Novonothrus flagellatus and an un-named Novonothrus species. This paper contains additional records of N. anauniensis and descriptions of five new species of Novonothrus, including immatures (N. barringtonensis sp. nov., N. coronospinosus sp. nov., N. glabriseta sp. nov., N. nothofagii sp. nov. and N. silvanus sp. nov.), a genus known from Australia, New Zealand and Chile. A key to Novonothrus is provided and the genus redefined. A second species of Trichonothrus (T. hallidayi sp. nov.), is described, representing a new generic record for Australia: Trichonothrus was previously known only from South Africa. Supplementary descriptions are given for Novonothrus flagellatus Hammer, 1966 and Trichonothrus austroafricanus Mahunka, 1986. The Australian record of the former species is based on a misidentification of the species described herein as N. glabriseta sp. nov. and N. flagellatus appears to be confined to New Zealand. Three species groups are proposed for Novonothrus: Barringtonensis (N. barringtonensis, N. nothofagii and N. silvanus) from central New South Wales and Victoria; Puyehue (N. glabriseta from Tasmania, N. puyehue, N. covarrubiasi and N. kethleyi from Valdivian temperate rain forest in Chile) and Flagellatus (N. coronospinosus from northern New South Wales and N. flagellatus from native forest, including Nothofagus, in New Zealand). Novonothrus and Trichonothrus show a relict Gondwanan distribution and are associated with indigenous wet forests. In Australia, members of these genera have been recorded mostly from cool tem-perate Nothofagus rain forest. The relatively high diversity of sexual species of Nothrina in Australian temperate rain forests is contrasted with high diversity of thelytokous parthenogenetic species in temperate Northern Hemisphere localities and is discussed in relation to differences in palaeoclimate and environmental history. Copyright © 2011 • Magnolia Press.


Beckett S.J.,CSIRO
Journal of Stored Products Research | Year: 2011

Insect and mite control by sufficient drying and cooling of commodities would satisfy growing market desire for pesticide-free storage and help control increased insect resistance, particularly to phosphine. The response of insects and mites to such conditions, as opposed to those specifically targeted for disinfestation, is reviewed. The responses to temperatures at various humidities within the range 9-55 °C are examined which include those that induce individual mortality, those at the threshold for population growth, and those where rates of growth are slow. Drying is examined mainly in terms of an enhancement to the detrimental effects of temperature. A 10 °C range in minimum threshold temperature for population growth was found among the insect and mite species examined. A substantial level of protection was seen at temperatures just above these thresholds. At conditions roughly 6 °C below the threshold for population growth, >99% mortality of major coleopteran species is possible after 9 months at 45% r.h. Insect mortality at moderately elevated grain temperatures (35-55 °C) is examined as an opportunity to disinfest grain during drying. Several coleopteran and psocopteran species were found to suffer at least 99% mortality at 50 °C after 2.5 h. The extent of variation among species is discussed in terms of targeting particular susceptibilities to moderately low or high temperatures at low humidities as an alternative to chemical treatments. © 2011 Elsevier Ltd.


Hemer M.A.,CSIRO | Fan Y.,Princeton University | Mori N.,Kyoto University | Semedo A.,Escola Naval | And 2 more authors.
Nature Climate Change | Year: 2013

Future changes in wind-wave climate have broad implications for the operation and design of coastal, near- and off-shore industries and ecosystems, and may further exacerbate the anticipated vulnerabilities of coastal regions to projected sea-level rise. However, wind waves have received little attention in global assessments of projected future climate change. We present results from the first community-derived multi-model ensemble of wave-climate projections. We find an agreed projected decrease in annual mean significant wave height (H S) over 25.8% of the global ocean area. The area of projected decrease is greater during boreal winter (January-March, mean; 38.5% of the global ocean area) than austral winter (July-September, mean; 8.4%). A projected increase in annual mean H S is found over 7.1% of the global ocean, predominantly in the Southern Ocean, which is greater during austral winter (July-September; 8.8%). Increased Southern Ocean wave activity influences a larger proportion of the global ocean as swell propagates northwards into the other ocean basins, observed as an increase in annual mean wave period (T M) over 30.2% of the global ocean and associated rotation of the annual mean wave direction (θ M). The multi-model ensemble is too limited to systematically sample total uncertainty associated with wave-climate projections. However, variance of wave-climate projections associated with study methodology dominates other sources of uncertainty (for example, climate scenario and model uncertainties). © 2013 Macmillan Publishers Limited. All rights reserved.


Fischer R.A.,CSIRO
Crop and Pasture Science | Year: 2011

This review focuses on recent advances in some key areas of wheat physiology, namely phasic development, determination of potential yield and water-limited potential yield, tolerance to some other abiotic stresses (aluminium, salt, heat shock), and simulation modelling. Applications of the new knowledge to breeding and crop agronomy are emphasized. The linking of relatively simple traits like time to flowering, and aluminium and salt tolerance, in each case to a small number of genes, is being greatly facilitated by the development of molecular gene markers, and there is some progress on the functional basis of these links, and likely application in breeding. However with more complex crop features like potential yield, progress at the gene level is negligible, and even that at the level of the physiology of seemingly important component traits (e.g., grain number, grain weight, soil water extraction, sensitivity to water shortage at meiosis) is patchy and generally slow although a few more heritable traits (e.g. carbon isotope discrimination, coleoptile length) are seeing application. This is despite the advent of smart tools for molecular analysis and for phenotyping, and the move to study genetic variation in soundly-constituted populations. Exploring the functional genomics of traits has a poor record of application; while trait validation in breeding appears underinvested. Simulation modeling is helping to unravel G×E interaction for yield, and is beginning to explore genetic variation in traits in this context, but adequate validation is often lacking. Simulation modelling to project agronomic options over time is, however, more successful, and has become an essential tool, probably because less uncertainty surrounds the influence of variable water and climate on the performance of a given cultivar. It is the ever-increasing complexity we are seeing with genetic variation which remains the greatest challenge for modelling, molecular biology, and indeed physiology, as they all seek to progress yield at a rate greater than empirical breeding is achieving. © CSIRO 2011.


Chakraborty S.,CSIRO | Newton A.C.,Scottish Crop Research Institute
Plant Pathology | Year: 2011

Global food production must increase by 50% to meet the projected demand of the world's population by 2050. Meeting this difficult challenge will be made even harder if climate change melts portions of the Himalayan glaciers to affect 25% of world cereal production in Asia by influencing water availability. Pest and disease management has played its role in doubling food production in the last 40 years, but pathogens still claim 10-16% of the global harvest. We consider the effect of climate change on the many complex biological interactions affecting pests and pathogen impacts and how they might be manipulated to mitigate these effects. Integrated solutions and international co-ordination in their implementation are considered essential. Providing a background on key constraints to food security, this overview uses fusarium head blight as a case study to illustrate key influences of climate change on production and quality of wheat, outlines key links between plant diseases, climate change and food security, and highlights key disease management issues to be addressed in improving food security in a changing climate. © 2011 The Authors. Plant Pathology © 2011 BSPP.


Recognition that climate change could have negative consequences for agricultural production has generated a desire to build resilience into agricultural systems. One rational and cost-effective method may be the implementation of increased agricultural crop diversification. Crop diversification can improve resilience in a variety of ways: by engendering a greater ability to suppress pest outbreaks and dampen pathogen transmission, which may worsen under future climate scenarios, as well as by buffering crop production from the effects of greater climate variability and extreme events. Such benefits point toward the obvious value of adopting crop diversification to improve resilience, yet adoption has been slow. Economic incentives encouraging production of a select few crops, the push for biotechnology strategies, and the belief that monocultures are more productive than diversified systems have been hindrances in promoting this strategy. However, crop diversification can be implemented in a variety of forms and at a variety of scales, allowing farmers to choose a strategy that both increases resilience and provides economic benefits. © 2011 by American Institute of Biological Sciences. All rights reserved.


Smith N.A.,CSIRO
Methods in molecular biology (Clifton, N.J.) | Year: 2012

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main classes of sRNA, the small-interfering RNA (siRNA) and microRNA (miRNA) classes, are well documented and several experimental approaches have been developed to allow for their routine isolation and detection from plant tissues. Here, we describe the current methods used for the isolation of total RNA and the subsequent enrichment of low-molecular-weight (LMW) RNA species, as well as to outline how sRNAs are detected from such nucleic acid preparations.


Savage G.P.,CSIRO
Current Organic Chemistry | Year: 2010

The 1,3-dipolar cycloaddition reaction of nitrile oxides with carbon dipolarophiles is a versatile and powerful synthetic method to prepare isoxazolines. In particular nitrile oxide cycloaddition reactions with exocyclic methylene or alkylidene compounds generally proceed regioselectively leading to spiro heterocyclic compounds. This review deals with progress in the field of nitrile oxide cycloaddition chemistry for the synthesis of spiro isoxazolines. © 2010 Bentham Science Publishers Ltd.


Rahman A.,CSIRO | Verma B.,Central Queensland University
Knowledge-Based Systems | Year: 2013

In this paper, we propose a novel cluster oriented ensemble classifier generation method and a Genetic Algorithm based approach to optimize the parameters. In the proposed method the data set is partitioned into a variable number of clusters at different layers. Base classifiers are trained on the clusters at different layers. Due to the variability of the number of clusters at different layers, the cluster compositions in one layer are different from that in another layer. Due to this difference in cluster contents, the base classifiers trained at different layers are diverse among each other. A test pattern is classified by the base classifier of the nearest cluster at each layer and the decisions from different layers are fused using majority voting. The accuracy of the proposed method depends on the number of layers and the number of clusters at the corresponding layer. A Genetic Algorithm based search is incorporated to obtain the optimal number of layers and clusters. The Genetic Algorithm is evaluated under three different objective functions: optimizing (i) accuracy, (ii) diversity, and (iii) accuracy × diversity. We have conducted a number of experiments to evaluate the effectiveness of the different objective functions. © 2013 Elsevier B.V. All rights reserved.


Walsh K.J.E.,University of Melbourne | McInnes K.L.,CSIRO | McBride J.L.,Center for Australian Weather and Climate Research
Global and Planetary Change | Year: 2012

This paper reviews the current understanding of the effect of climate change on extreme sea levels in the South Pacific region. This region contains many locations that are vulnerable to extreme sea levels in the current climate, and projections indicate that this vulnerability will increase in the future. The recent publication of authoritative statements on the relationship between global warming and global sea level rise, tropical cyclones and the El Niño-Southern Oscillation phenomenon has motivated this review. Confident predictions of global mean sea level rise are modified by regional differences in the steric (density-related) component of sea level rise and changing gravitational interactions between the ocean and the ice sheets which affect the regional distribution of the eustatic (mass-related) contribution to sea level rise. The most extreme sea levels in this region are generated by tropical cyclones. The intensity of the strongest tropical cyclones is likely to increase, but many climate models project a substantial decrease in tropical cyclone numbers in this region, which may lead to an overall decrease in the total number of intense tropical cyclones. This projection, however, needs to be better quantified using improved high-resolution climate model simulations of tropical cyclones. Future changes in ENSO may lead to large regional variations in tropical cyclone incidence and sea level rise, but these impacts are also not well constrained. While storm surges from tropical cyclones give the largest sea level extremes in the parts of this region where they occur, other more frequent high sea level events can arise from swell generated by distant storms. Changes in wave climate are projected for the tropical Pacific due to anthropogenically-forced changes in atmospheric circulation. Future changes in sea level extremes will be caused by a combination of changes in mean sea level, regional sea level trends, tropical cyclone incidence and wave climate. Recommendations are given for research to increase understanding of the response of these factors to climate change. Implications of the results for adaptation research are also discussed. © 2011 Elsevier B.V.


Gonzalez-alvarez I.,CSIRO | Kerrich R.,University of Saskatchewan
Precambrian Research | Year: 2012

The Mesoproterozoic Belt-Purcell Supergroup (BPS) preserves a thickness of 17. km of dominantly siliciclastic rocks deposited between 1470 and 1400. Ma. The total range of Chemical Index of Alteration (CIA) values, corrected for diagenetic K-addition, are 62-88 for argillites and 55-80 for sandstones, with averages of 72 ± 6 and 68 ± 7, respectively. More intense CIA values, in conjunction with low absolute contents of Sr, Ca and Na, and high Rb/Sr ratios (average 4), reflect an intensely weathered provenance in a hot-wet climate with hot-arid intervals resulting in evaporitic sediments. Covariations of CIA-Eu/Eu* and Sr-Eu/Eu* are consistent with a large catchment area including extensive provenance terranes of weathered recycled sedimentary rocks for the most extreme CIA and Eu/Eu* values, with smaller less intensely weathered juvenile terranes represented by lower CIA values. Accordingly, variations of CIA within the BPS stratigraphic sequence may record some combination of shifting catchment terranes and weathering intensity. Stratigraphic trends in CIA within the Appekunny and Grinnell Formations of 80 ± 6 to 66 ± 4 to 79 ± 5 record the variation in this combination with time. Siliciclastic rocks record a first order trend of CIA values from CIA ∼80-100 in the Mesoarchean, through ∼80-90 in the Neoarchean, and ∼70-85 in the Proterozoic, to ∼72 for global Phanerozoic shales. These values reflect progressive drawdown of greenhouse gases that promote silicate weathering by their sequestration into carbonates and black shales, as preserved in the geologic record. Second order secular peaks in CIA values correlate in time with mantle plumes that emit greenhouse gases, which enhance silicate weathering. Some of the more intense CIA values in the BPS may also stem from release of volcanic gases during magmatism that accompanied rifting of Laurentia during breakup of the Supercontinent Columbia at ∼1.4. Ga. Overall, CIA values are within the range of modern humid-temperate and humid-tropical climatic catchment areas drained by large river systems such as the Orinoco, Nile and Amazon rivers. Proterozoic rivers have been viewed as mostly braided systems due to the lack of influence of rooted vegetation, which resulted in fast channel lateral migration, high run-off rates, and low bank stability. Many large-scale Proterozoic siliciclastic basins have been preserved, formed by river systems up to pan-continental scale. However, their significance as archives of continental weathering intensity remains under-explored. This study suggests that BPS CIA values reflect more aggressive chemical weathering, since Proterozoic rivers had less sediment residence times due to a lack of vegetation cover, and therefore faster transport time than their modern counterparts. To achieve high CIA values in shorter periods of time without vegetation cover, more intense chemical weathering conditions must have been present. © 2012.


Liu W.,CSIRO | Migdisov A.,McGill University | Williams-Jones A.,McGill University
Geochimica et Cosmochimica Acta | Year: 2012

Knowledge of the thermodynamic properties of aqueous nickel chloride complexes is important for understanding and quantitatively evaluating nickel transport in hydrothermal systems. In this paper, UV-Visible spectroscopic measurements are reported for dissolved nickel in perchlorate, triflic acid and sodium chloride solutions at temperatures up to 250°C and 100bar. The observed molar absorbance of Ni 2+ in both perchlorate and triflic acid solutions is similar, and the absorbance peak migrates toward lower energy (red-shift) with increasing temperature. The spectra of nickel chloride solutions show a systematic red-shift with increasing temperature and/or chloride concentration. This allowed identification of the nickel chloride species as NiCl +, NiCl 2(aq) and NiCl 3 -, and determination of their formation constants. Based on the experimental data reported in this paper and those of previous experimental studies, formation constants for these nickel chloride complexes have been calculated for temperatures up to 700°C and pressures up to 2000bar. The solubility of millerite (NiS) and pentlandite (Ni 4.5Fe 4.5S 8) calculated using these constants shows that nickel dissolves in significantly higher concentrations in hydrothermal solutions than previously estimated. However, the solubility is considerably lower than for corresponding cobalt sulphide minerals. This may explain why hydrothermal nickel deposits are encountered so much less frequently than hydrothermal deposits of cobalt. © 2012 Elsevier Ltd.


Harman I.N.,CSIRO
Boundary-Layer Meteorology | Year: 2012

Turbulence above and within canopies has characteristics distinct from that over rough surfaces. The vertical transport of momentum and scalars is dominated by coherent structures whose origin is now thought to be the result of the unstable inflexion in the profile of the mean wind speed established by the application of canopy drag. This distinctive property leads to the failure of the standard Monin-Obukhov flux-profile relationships over homogeneous canopies, relationships that are assumed in many surface exchange schemes within numerical weather prediction and general circulation models. A modification of the flux-profile relationships is presented that incorporates the effects of the canopy turbulence. The subsequent impacts on the evolution of the surface energy balance and boundary-layer state are investigated within a simple numerical model for the evolution of the boundary layer and canopy state. By comparing cases with and without the modification it is shown that canopy-generated turbulence can lead, not only to the alteration of the flux-profile relationships above the canopy, but also to a different evolution of the surface energy balance and differences in near-surface conditions that would be significant in numerical weather prediction. More fundamentally, the modifications to the flux-profile relationships imply that parameters such as the roughness length and displacement height for canopies should not be considered as invariant properties, but rather as properties that depend on the flow and hence vary systematically with the diabatic stability of the boundary layer. © 2011 Springer Science+Business Media B.V.


Heterogeneous nucleation probability distributions of gas hydrates on a water droplet that was supported by inert and immiscible perfluorocarbon oil, perfluorodecalin is studied. The guest gas used was a mixture of 90 mol % methane and 10 mol % propane. The probability distribution was measured using a high pressure automated lag time apparatus under the guest gas pressure range of 6.7-12.5 MPa and the cooling rate range of 0.002-0.02 K/s. Nucleation curves were derived for unit area of water surface. The nucleation rate per unit area of water surface that was contained in a glass sample cell, which differed significantly from that on a quasi-free water droplet, is also derived. It is concluded that the nucleation curves in the presence of a solid wall should be normalized to the unit length of the three-phase line at which water, guest gas, and the solid wall meet. © 2015 American Institute of Chemical Engineers.


Moritz C.,Australian National University | Moritz C.,CSIRO | Moritz C.,University of California at Berkeley | Agudo R.,Australian National University
Science | Year: 2013

As climates change across already stressed ecosystems, there is no doubt that species will be affected, but to what extent and which will be most vulnerable remain uncertain. The fossil record suggests that most species persisted through past climate change, whereas forecasts of future impacts predict large-scale range reduction and extinction. Many species have altered range limits and phenotypes through 20th-century climate change, but responses are highly variable. The proximate causes of species decline relative to resilience remain largely obscure; however, recent examples of climate-associated species decline can help guide current management in parallel with ongoing research.


Ross P.J.,CSIRO
Vadose Zone Journal | Year: 2013

Existing methods of estimating spatially varying soil thermal conductivity and diffusivity using harmonic analysis of soil temperatures are applicable only at periodic steady state. This study adopted a more general Fourier analysis which is applicable when transients are present. Two new methods of estimation were compared with existing methods using synthetic data generated by solution of the one-dimensional heat conduction equation in a soil whose water content varied with depth. All methods gave accurate results for the logarithmic derivative of conductivity and the diffusivity at steady state, but only the new methods were accurate when initial temperatures led to transients. Sensitivity to depth spacings and to noise were also investigated. Spatially interpolating the amplitude and phase of the temperature data with filtering for estimating derivatives allowed good results to be obtained in the presence of noise, especially for the diffusivity. Although the methods work best for temperatures at several depths and spacings of 0.05 m or less, errors in diffusivity were less than 8% with only three depths at 0.1 m spacing. © Soil Science Society of America, All rights reserved.


Viscarra Rossel R.A.,CSIRO
Journal of Geophysical Research: Earth Surface | Year: 2011

Clay minerals are the most reactive inorganic components of soils. They help to determine soil properties and largely govern their behaviors and functions. Clay minerals also play important roles in biogeochemical cycling and interact with the environment to affect geomorphic processes such as weathering, erosion and deposition. This paper provides new spatially explicit clay mineralogy information for Australia that will help to improve our understanding of soils and their role in the functioning of landscapes and ecosystems. I measured the abundances of kaolinite, illite and smectite in Australian soils using near infrared (NIR) spectroscopy. Using a model-tree algorithm, I built rule-based models for each mineral at two depths (0-20 cm, 60-80 cm) as a function of predictors that represent the soil-forming factors (climate, parent material, relief, vegetation and time), their processes and the scales at which they vary. The results show that climate, parent material and soil type exert the largest influence on the abundance and spatial distribution of the clay minerals; relief and vegetation have more local effects. I digitally mapped each mineral on a 3 arc-second grid. The maps show the relative abundances and distributions of kaolinite, illite and smectite in Australian soils. Kaolinite occurs in a range of climates but dominates in deeply weathered soils, in soils of higher landscapes and in regions with more rain. Illite is present in varied landscapes and may be representative of colder, more arid climates, but may also be present in warmer and wetter soil environments. Smectite is often an authigenic mineral, formed from the weathering of basalt, but it also occurs on sediments and calcareous substrates. It occurs predominantly in drier climates and in landscapes with low relief. These new clay mineral maps fill a significant gap in the availability of soil mineralogical information. They provide data to for example, assist with research into soil fertility and food production, carbon sequestration, land degradation, dust and climate modeling and paleoclimatic change. Copyright 2011 by the American Geophysical Union.


Barton I.J.,CSIRO
Journal of Atmospheric and Oceanic Technology | Year: 2011

Analyses based on atmospheric infrared radiative transfer simulations and collocated ship and satellite data are used to investigate whether knowledge of vertical atmospheric water vapor distributions can improve the accuracy of sea surface temperature (SST) estimates from satellite data. Initially, a simulated set of satellite brightness temperatures generated by a radiative transfer model with a large maritime radiosonde database was obtained. Simple linear SST algorithms are derived from this dataset, and these are then reapplied to the data to give simulated SST estimates and errors. The concept of water vapor weights is introduced in which a weight is a measure of the layer contribution to the difference between the surface temperature and that measured by the satellite. The weight of each atmospheric layer is defined as the layer water vapor amount multiplied by the difference between the SST and the midlayer temperature. Satellite-derived SST errors are then plotted against the difference in the sum of weights above an altitude of 2.5 km and that below. For the simple two-channel (with typical wavelengths of 11 and 12 μm) analysis, a clear correlation between the weights differences and the SST errors is found. A second group of analyses using ship-released radiosondes and satellite data also show a correlation between the SST errors and the weights differences. The analyses suggest that, for an SST derived using a simple two-channel algorithm, the accuracy may be improved if account is taken of the vertical distribution of water vapor above the ocean surface. For SST estimates derived using algorithms that include data from a 3.7 μm channel, there is no such correlation found. © 2011 American Meteorological Society.


Essington T.E.,University of Washington | Plaganyi E.E.,CSIRO
ICES Journal of Marine Science | Year: 2014

Ecosystem models have been developed for many marine systems to provide guidance on fisheries management strategies that protect key ecological functions. These models are commonly "recycled", i.e. applied to new questions or policy concerns after the initial phase of model development, testing, and application. Because decisions about the model structure are typically based on the intended model use, it is important to recognize limits in the capacity of models to address questions for which they were not specifically designed. Here, we evaluate existing foodweb models in the context of their ability to identify key forage species in foodwebs and to test management strategies for fisheries that target them. We find that the depth and breadth with which predator species are represented are commonly insufficient for evaluating sensitivities of predator populations to forage fish depletion. We demonstrate that aggregating predator species into functional groups creates bias in foodweb metrics such as connectance. Models also varied considerably with respect to the extent that they have been tuned or fitted to retrospective patterns and the degree to which key sensitivities are identified. We use this case study to provide several general recommendations when "recycling" ecosystem and foodweb models. Briefly, we suggest as routine procedure careful scrutiny of structural model attributes, of scales at which ecological processes are included, and quality of fits for key functional groups. © 2013 International Council for the Exploration of the Sea. Published by Oxford University Press. All rights reserved.


Kuehne G.,CSIRO
Agriculture and Human Values | Year: 2013

This paper presents a discussion of my personal experiences of selling a family farm and analyses those experiences using the layered account form of autoethnographic writing. I describe how the cultural influences from family farming led me, a farmer's son, to also become a farmer, why farmers may choose to continue in their occupation sometimes against increasingly negative economic pressures, why I continued farming for as long as I did, and the thoughts and feelings associated with my decision to sell my farm and exit the industry. I discuss the emotions that I experienced and place them in a theoretical context that makes them more understandable to others. Because this paper examines the effects from my decision to retire from farming it makes a contribution to the limited literature on farmers' retirement. © 2012 Springer Science+Business Media B.V.


Precise studies on the structure and behavior of thrips can be particularly difficult, due to their small size and restless behavior. As a result, many "host-plant" records are no more than casual "finding places" with limited biological significance. Definitions of "host-plant" are complicated by situations where a plant species provides an important feeding or behavioral resource, but is not used for breeding. Similarly, failure to clearly define some structures on a thrips body, often due to inadequate technical and microscopy skills, can lead to faulty interpretation of species identities and evolutionary relationships. This article re-examines some of these problems.


Unsworth K.L.,University of Western Australia | Mason C.M.,CSIRO
Journal of Occupational Health Psychology | Year: 2012

This research reports on two field studies which demonstrate that self-leadership training decreases strain via increases in self-efficacy and positive affect. The first, an experimental study, found that strain was reduced in the randomly assigned training group, but not in the control group. The second was a longitudinal study and supported the hypotheses that self-efficacy and positive affect mediated the effect of self-leadership training on strain. Our findings extend both self-leadership and stress management literatures by providing a theoretical framework within which the effects of self-leadership on strain can be understood. Practically speaking, our findings suggest that self-leadership training offers an individual-level preventive approach to stress management. © 2012 American Psychological Association.


Llopiz J.K.,Woods Hole Oceanographic Institution | Hobday A.J.,CSIRO
Deep-Sea Research Part II: Topical Studies in Oceanography | Year: 2015

Scombroid fishes, including tunas, mackerels, and billfishes, constitute some of the most important fisheries in lower latitudes around the world. Though the early life stages of these taxa are relatively well-studied, worldwide patterns in larval feeding dynamics and how such patterns relate to environmental conditions are poorly resolved. We present a synthesis of feeding success (i.e. feeding incidences) and diets of larval scombroids from around the world, and relate these results to water column and sea surface properties for the several regions in which larval feeding studies have been conducted. Feeding success of larval tunas was shown to be distinctly different among regions. In some locations (the Straits of Florida and the Mediterranean Sea), nearly no larvae had empty guts, whereas in other locations (the Gulf of California and off NW Australia) ~40-60% of larvae were empty. Diets were consistently narrow in each region (dominated by cyclopoid copepods, appendicularians, nauplii, and other fish larvae), and were usually, but not always, similar for a given scombroid taxon among regions (though diets differed among taxa). Larval habitat conditions were often similar among the 9 regions examined, but some clear differences included low levels of eddy kinetic energy and cooler waters (at the surface and at depth) in the Mediterranean, and lower chlorophyll concentrations around the Nansei Islands, Japan and off NW Australia where feeding success was low. When observed zooplankton abundances are also taken into account, the compiled results on feeding and environmental conditions indicate a bottom-up influence on feeding success. Moreover, the variability among regions highlights the potential for region-specific mechanisms regulating larval survival and, ultimately, levels of adult recruitment. © 2014 Elsevier Ltd.


Piner B.G.,Whittier College | Pant N.,Whittier College | Edwards P.G.,CSIRO
Astrophysical Journal | Year: 2010

We present 23 new VLBA images of the six established TeV blazars Markarian 421, Markarian 501, H 1426+428, 1ES 1959+650, PKS 2155-304, and 1ES 2344+514, obtained from 2005 to 2009. Most images were obtained at 43 GHz (7 mm), and they reveal the parsec-scale structures of three of these sources (1ES 1959+650, PKS 2155-304, and 1ES 2344+514) at factors of 2-3 higher resolution than has previously been attained. These images reveal new morphological details, including a high degree of jet bending in the inner milliarcsecond in PKS 2155-304. This establishes strong apparent jet bending on VLBI scales as a common property of TeV blazars, implying viewing angles close to the line of sight. Most of the remaining images map the linear polarization structures at a lower frequency of 22 GHz (1 cm). We discuss the transverse structures of the jets as revealed by the highfrequency and polarimetric imaging. The transverse structures include significant limb brightening in Mrk 421, and "spine-sheath" structures in the electric vector position angle and fractional polarization distributions in Mrk 421, Mrk 501, and 1ES 1959+650. We use new measured component positions to update measured apparent jet speeds, in many cases significantly reducing the statistical error over previously published results. With the increased resolution at 43 GHz, we detect new components within 0.1-0.2 mas of the core in most of these sources. No motion is apparent in these new components over the time span of our observations, and we place upper limits on the apparent speeds of the components near the core of <2c. From those limits, we conclude that Γ2 < (Γ1)1/2 at ∼105 Schwarzschild radii, where Γ1 and Γ2 are the bulk Lorentz factors in the TeV emitting and 43 GHz emitting regions, respectively, assuming that their velocity vectors are aligned. © 2010. The American Astronomical Society.


Hunt P.W.,CSIRO
Veterinary Parasitology | Year: 2011

Since 1977, >2000 research papers described attempts to detect, identify and/or quantify parasites, or disease organisms carried by ecto-parasites, using DNA-based tests and 148 reviews of the topic were published. Despite this, only a few DNA-based tests for parasitic diseases are routinely available, and most of these are optional tests used occasionally in disease diagnosis. Malaria, trypanosomiasis, toxoplasmosis, leishmaniasis and cryptosporidiosis diagnosis may be assisted by DNA-based testing in some countries, but there are very few cases where the detection of veterinary parasites is assisted by DNA-based tests. The diagnoses of some bacterial (e.g. lyme disease) and viral diseases (e.g. tick borne encephalitis) which are transmitted by ecto-parasites more commonly use DNA-based tests, and research developing tests for these species makes up almost 20% of the literature. Other important uses of DNA-based tests are for epidemiological and risk assessment, quality control for food and water, forensic diagnosis and in parasite biology research. Some DNA-based tests for water-borne parasites, including Cryptosporidium and Giardia, are used in routine checks of water treatment, but forensic and food-testing applications have not been adopted in routine practice. Biological research, including epidemiological research, makes the widest use of DNA-based diagnostics, delivering enhanced understanding of parasites and guidelines for managing parasitic diseases. Despite the limited uptake of DNA-based tests to date, there is little doubt that they offer great potential to not only detect, identify and quantify parasites, but also to provide further information important for the implementation of parasite control strategies. For example, variant sequences within species of parasites and other organisms can be differentiated by tests in a manner similar to genetic testing in medicine or livestock breeding. If an association between DNA sequence and phenotype has been demonstrated, then qualities such as drug resistance, strain divergence, virulence, and origin of isolates could be inferred by DNA-based tests. No such tests are in clinical or commercial use in parasitology and few tests are available for other organisms. Why have DNA-based tests not had a bigger impact in veterinary and human medicine? To explore this question, technological, biological, economic and sociological factors must be considered. Additionally, a realistic expectation of research progress is needed. DNA-based tests could enhance parasite management in many ways, but patience, persistence and dedication will be needed to achieve this goal. © 2011.


Kovalyshen Y.,CSIRO
Journal of Sound and Vibration | Year: 2013

A simple analytical model of bit whirl is presented. In contrast to the previous works, which consider bottom hole assembly mass imbalance to model bit whirl, the model here takes into account the history-dependent boundary conditions at the bit-rock interface as well as the bit geometry. In particular, an analytical expression for the bit-rock interaction is derived. It is shown that the bit geometry affects the bit-rock interaction only through three dimensionless parameters. Depending on the value of these parameters the system can be stable or undergo forward or backward whirl. © 2013 Published by Elsevier Ltd. All rights reserved.


Golley R.K.,Sansom Institute for Health Research | Hendrie G.A.,CSIRO | McNaughton S.A.,Deakin University
Journal of Nutrition | Year: 2011

Diet quality indices reflect overall dietary patterns better than single nutrients or food groups. The study aims were to develop a measure of adherence with dietary guidelines applicable to child and adolescent populations in Australia and determine the association between index scores and food and nutrient intake, socio-demographic characteristics, and measures of adiposity. Data were analyzed from 4- to 16-y-old participants of the 2007 Australian Children's Nutrition and Physical Activity Survey (n = 3416). The Dietary Guideline Index for Children and Adolescents (DGI-CA) comprises 11 components: 5 core food groups, wholegrain bread, reduced-fat dairy foods, extra foods (nutrient poor and high in fat, salt, and added sugar), healthy fats/oils, water, and diet variety (possible score of 100). The index criteria were age specific. The mean DGI-CA score was low (53.6 ± 0.4), similar between boys and girls, and differed by age; the youngest children scored higher than the oldest children (P<, 0.0001). Higher DGI-CA scores were associated with lower energy intake, energy density, total and saturated fat, and sugar intake; higher protein, carbohydrate, fiber, calcium, iron, vitamin C, vitamin A, folate, phosphorous, magnesium, zinc, and iodine intakes; and a higher polyunsaturated:saturated fat ratio (P<, 0.0001). DGI-CA scores were associated with socio-economic characteristics and measures of family circumstance. Weak positive associations were observed between DGI-CA score and BMI or waist circumference Z-scores in the 4- to 10-y and 12- to 16-y age groups only. This index is the first validated index in Australia and one of the few international indices to describe the diet quality of children and adolescents. © 2011 American Society for Nutrition.


Paterson S.,CSIRO | Bryan B.A.,University of Adelaide
Ecology and Society | Year: 2012

Understanding the effects of payments on the adoption of reforestation in agricultural areas and the associated food-carbon trade-offs is necessary to inform climate change policy. Economic viability of reforestation under payment per hectare and payment per tonne schemes for carbon sequestration was assessed in a region in southern Australia supporting 6.1 Mha of rain-fed agriculture. The results show that under the median scenario, a carbon price of 27 A$/tCO 2-e could make onethird of the study area (nearly 2 Mha) more profitable for reforestation than agriculture, and at 58 A$/tCO 2-e all of the study area could become more profitable. The results were sensitive to variation in carbon risk factor, establishment costs, and discount rates. Pareto-optimal land allocation could realize one-third of the potential carbon sequestration from reforestation (16.35 MtCO 2-e/yr at a carbon risk factor of 0.8) with a loss of less than one-tenth (107.89 A$M/yr) of the agricultural production. Both payment schemes resulted in efficiencies within 1% of the Pareto-optimum. Understanding food-carbon trade-offs and policy efficiencies can inform carbon policy design. © 2012 by the author(s).


Chen S.H.,Australian National University | Pollino C.A.,CSIRO
Environmental Modelling and Software | Year: 2012

Bayesian networks (BNs) are increasingly being used to model environmental systems, in order to: integrate multiple issues and system components; utilise information from different sources; and handle missing data and uncertainty. BNs also have a modular architecture that facilitates iterative model development. For a model to be of value in generating and sharing knowledge or providing decision support, it must be built using good modelling practice. This paper provides guidelines to developing and evaluating Bayesian network models of environmental systems, and presents a case study habitat suitability model for juvenile Astacopsis gouldi, the giant freshwater crayfish of Tasmania. The guidelines entail clearly defining the model objectives and scope, and using a conceptual model of the system to form the structure of the BN, which should be parsimonious yet capture all key components and processes. After the states and conditional probabilities of all variables are defined, the BN should be assessed by a suite of quantitative and qualitative forms of model evaluation. All the assumptions, uncertainties, descriptions and reasoning for each node and linkage, data and information sources, and evaluation results must be clearly documented. Following these standards will enable the modelling process and the model itself to be transparent, credible and robust, within its given limitations. © 2012 Elsevier Ltd.


Mankad A.,CSIRO
Environment International | Year: 2012

The study of emotion has gathered momentum in the field of environmental science, specifically in the context of community resource decision-making. Of particular interest in this review is the potential influence of emotion, risk and threat perception on individuals' decisions to acceptance and adopt decentralised water systems, such as rainwater tanks and greywater systems. The role of message framing is also considered in detail, as well as the influences that different types of framing can have on decision making. These factors are considered as possible predictors for analysing community acceptance of decentralised water in urban environments. Concepts believed to be influenced by emotion, such as trust and framing, are also discussed as potentially meaningful contributors to an overall model of community acceptance of decentralised water. Recommendations are made for how emotion-based concepts, such as risk and threat, can be targeted to facilitate widespread adoption of decentralised systems and how researchers can explore different types of emotions that influence decision making in distinct ways. This review is an important theoretical step in advancing the psycho-social understanding of acceptance and adoption of on-site water sources. Avenues for future research are recommended, including the need for greater theoretical development to encourage future social science research on decentralised systems. © 2012.


Diaz-Pulido G.,Griffith University | Diaz-Pulido G.,University of Queensland | Gouezo M.,University of Queensland | Tilbrook B.,CSIRO | And 2 more authors.
Ecology Letters | Year: 2011

Ecology Letters (2011) 14: 156-162 Space competition between corals and seaweeds is an important ecological process underlying coral-reef dynamics. Processes promoting seaweed growth and survival, such as herbivore overfishing and eutrophication, can lead to local reef degradation. Here, we present the case that increasing concentrations of atmospheric CO2 may be an additional process driving a shift from corals to seaweeds on reefs. Coral (Acropora intermedia) mortality in contact with a common coral-reef seaweed (Lobophora papenfussii) increased two- to threefold between background CO2 (400ppm) and highest level projected for late 21st century (1140ppm). The strong interaction between CO2 and seaweeds on coral mortality was most likely attributable to a chemical competitive mechanism, as control corals with algal mimics showed no mortality. Our results suggest that coral (Acropora) reefs may become increasingly susceptible to seaweed proliferation under ocean acidification, and processes regulating algal abundance (e.g. herbivory) will play an increasingly important role in maintaining coral abundance. © 2010 Blackwell Publishing Ltd/CNRS.


Barnard A.S.,CSIRO
Physical Chemistry Chemical Physics | Year: 2012