LAND USE AND ITS RELATIONSHIP TO RIPARIAN ZONE ORGANIC CARBON STORAGE ON THE UPPER HUNTER RIVER

Anthropogenic influences and land use practices in eastern Australia over the past 200 years have resulted in vastly altered channel and catchment conditions. This has not only reduced geomorphic diversity but also vegetation diversity and ecological functioning. As such, identifying the impact of various land use regimes is highly important when developing future riparian zone management strategies. To investigate the influence land use (specifically grazing) has on the riparian zone and river system, 12 in-channel river deposits were studied on the Hunter River between Muswellbrook and Aberdeen. Three land use types were selected — i) never grazed, ii) crash grazed and iii) perennially grazed — and samples were taken at three study reaches (Aberdeen, Downstream Aberdeen and Dart Brook Mine). One hundred and eleven (111) soil samples were collected from bars and benches in order to determine organic carbon content and fine sediment retention. The soil samples were analysed using loss-on-ignition (LOI) testing to determine the percentage (%) of organic carbon (OC). The Malvern Mastersizer was used to analyse average grain size and to determine the dominant sediment fraction within each soil sample. Hand sieves (-4 phi and -1 phi) were used to determine the main sediment fractions as a measure of bar variability. Spatial and hydrologic analyses were undertaken to determine historical and recent changes in both vegetation and river geomorphology. Results from the sample analysis showed that sites that had never been grazed had an average increased OC concentration of 6.43% and were also comprised of the finest sediment (FS), at 108.7m. Study locations that had been subjected to controlled grazing (3.02% OC and FS 324.4m) fell on average between permanently grazed (2.68% OC and FS 376.4m) and never-grazed locations across most variables analysed. Riparian zone management is a prevalent and important topic and these results provide guidance for developing management strategies. It has been found that stock may be useful in removing exotic vegetation as part of a larger weed management program, however in doing so they may decrease the amount of carbon sequestered and fine sediment retained. Decreased organic carbon can affect the nutrient cycling and the removal of nitrogen and phosphorus from water prior to entering the stream. In addition, decreased fine sediment retention may result in increased turbidity and therefore decreased light availability throughout the water column. These results may also have implications on global carbon storage through the riparian zone and its associated role in mitigating climate change

Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

peer-reviewedBackground: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience

The Demand for Beef in Indonesia: Implications for Australian Agribusiness

Meat consumption and socio-demographic data from the 1990, 1993 and 1996 SUSENAS Household Food Expenditure and Consumption Surveys were employed to estimate the demand for meats in Indonesia. The focus was on the Provinces of DKI Jakarta and West Java where about one-fourth of the Indonesian population reside. Statistical and econometric procedures were used to aggregate the 16 meat types recorded in the SUSENAS into four Meat Groups. They were then used to estimate the Linear Approximation of the Almost Ideal Demand System (LA/AIDS) model, taking into account zero observations and the restrictions on budget shares. The demand for Meat Group 1 (with the dominant meat, beef) is income-inelastic, whereas for Meat Group 2 (with the dominant meat, commercial and native chicken) it is income-elastic. These two groups comprise nearly 95 per cent of all meat purchases. The estimated own-price elasticity of the beef group is -0.92, while that for the chicken group is -1.09. The cross-price elasticities indicate that all the meat groups are substitute goods, as expected. The results suggest that the current focus of the Indonesian government on strengthening the domestic poultry industry is well placed, as the demand for chicken is likely to respond more quickly to income growth than the demand for beef. Further, consumers seem more likely to adapt their chicken consumption patterns to price changes than they do for beef. However, these differences are relatively minor and there is still a major opportunity for Australian agribusiness firms in the cattle and beef sectors to take advantage of the projected rapid growth in Indonesian beef demand.beef demand, almost ideal demand system, commodity aggregation, Demand and Price Analysis, Food Consumption/Nutrition/Food Safety, Livestock Production/Industries,

Developing an alcohol policy assessment toolkit: application in the western pacific

Objective: To demonstrate the development and feasibility of a tool to assess the adequacy of national policies aimed at reducing alcohol consumption and related problems. Methods: We developed a quantitative tool – the Toolkit for Evaluating Alcohol policy Stringency and Enforcement (TEASE-16) – to assess the level of stringency and enforcement of 16 alcohol control policies. TEASE-16 was applied to policy data from nine study areas in the western Pacific: Australia, China excluding Hong Kong Special Administrative Region (SAR), Hong Kong SAR, Japan, Malaysia, New Zealand, the Philippines, Singapore and Viet Nam. Correlation and regression analyses were then used to examine the relationship between alcohol policy scores and income-adjusted levels of alcohol consumption per capita. Findings: Vast differences exist in how alcohol control policies are implemented in the western Pacific. Out of a possible 100 points, the nine study areas achieved TEASE-16 scores that ranged from 24.1 points for the Philippines to 67.5 points for Australia. Study areas with high policy scores – indicating relatively strong alcohol policy frameworks – had lower alcohol consumption per capita. Sensitivity analyses indicated scores and rankings for each study area remained relatively stable across different weighting schemes, indicating that TEASE-16 was robust. Conclusion: TEASE-16 could be used by international and national regulatory bodies and policy-makers to guide the design, implementation, evaluation and refinement of effective policies to reduce alcohol consumption and related problems

Imposing Observation-Varying Equality Constraints Using Generalised Restricted Least Squares

Linear equality restrictions derived from economic theory are frequently observation-varying. Except in special cases, Restricted Least Squares (RLS) cannot be used to impose such restrictions without either underconstraining or overconstraining the parameter space. We solve the problem by developing a new estimator that collapses to RLS in cases where the restrictions are observation-invariant. We derive some theoretical properties of our so-called Generalised Restricted Least Squares (GRLS) estimator, and conduct a simulation experiment involving the estimation of a constant returns to scale production function. We find that GRLS significantly outperforms RLS in both small and large samples

Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle

peer-reviewedBackground Four traits related to carcass performance have been identified as economically important in beef production: carcass weight, carcass fat, carcass conformation of progeny and cull cow carcass weight. Although Holstein-Friesian cattle are primarily utilized for milk production, they are also an important source of meat for beef production and export. Because of this, there is great interest in understanding the underlying genomic structure influencing these traits. Several genome-wide association studies have identified regions of the bovine genome associated with growth or carcass traits, however, little is known about the mechanisms or underlying biological pathways involved. This study aims to detect regions of the bovine genome associated with carcass performance traits (employing a panel of 54,001 SNPs) using measures of genetic merit (as predicted transmitting abilities) for 5,705 Irish Holstein-Friesian animals. Candidate genes and biological pathways were then identified for each trait under investigation. Results Following adjustment for false discovery (q-value  0.5) with at least one of the four traits. In total, 557 unique bovine genes, which mapped to 426 human orthologs, were within 500kbs of QTL found associated with a trait using the Bayesian approach. Using this information, 24 significantly over-represented pathways were identified across all traits. The most significantly over-represented biological pathway was the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Conclusions A large number of genomic regions putatively associated with bovine carcass traits were detected using two different statistical approaches. Notably, several significant associations were detected in close proximity to genes with a known role in animal growth such as glucagon and leptin. Several biological pathways, including PPAR signaling, were shown to be involved in various aspects of bovine carcass performance. These core genes and biological processes may form the foundation for further investigation to identify causative mutations involved in each trait. Results reported here support previous findings suggesting conservation of key biological processes involved in growth and metabolism

Does evidence influence policy? Resource allocation and the Indigenous Burden of Disease study

Objective The Indigenous Burden of Disease (IBoD) report is the most comprehensive assessment of Indigenous disease burden in Australia. The aim of the present study was to investigate the potential effect of the IBoD report on Australian Indigenous health policy, service expenditure and research funding. Findings have significance for understanding factors that may influence Indigenous health policy. Methods The potential effect of the IBoD report was considered by: (1) conducting a text search of pertinent documents published by the federal government, Council of Australian Governments and the National Health and Medical Research Council of Australia (NHMRC) and observing the quantity and quality of references to IBoD; (2) examining data on government Indigenous healthcare expenditure for trends consistent with the findings and policy implications of the IBoD report; and (3) examining NHMRC Indigenous grant allocation trends consistent with the findings and policy implications of the IBoD report. Results Of 110 government and NHMRC documents found, IBoD was cited in 27. Immediately after publication of the IBoD report, federal and state governments increased Indigenous health spending (relative to non-Indigenous), notably for community health and public health at the state level. Expenditure on Indigenous hospital separations for chronic diseases also increased. These changes are broadly consistent with the findings of the IBoD report on the significance of chronic disease and the need to address certain risk factors. However, there is no evidence that such changes had a causal connection with the IBoD study. After publication of the IBoD report, changes in NHMRC Indigenous research funding showed little consistency with the findings of the IBoD report. Conclusions The present study found only indirect and inconsistent correlational evidence of the potential influence of the IBoD report on Indigenous health expenditure and research funding. Further assessment of the potential influence of the IBoD report on Indigenous health policy will require more targeted research, including interviews with key informants involved in developing health policy. What is known about the topic? There are currently no publications that consider the potential effed of the IBoD study on Indigenous health expenditure and research funding. What does this paper add? This paper offers the first consideration of the potential effect of the IBoD report. It contains analyses of data from readily available sources, examining national expenditures on Indigenous health and NHMRC Indigenous research, before and after the publication of the IBoD report. What are the implications for practitioners? The paper is relevant to analysts interested in drivers of Indigenous health policy. Although it finds correlations between the release of the IBoD report and some subsequent health spending decisions, other factors should be investigated to better understand the complexity of processes that drive government efforts to improve Indigenous health

Geometric algebra and its application to mathematical physics

Clifford algebras have been studied for many years and their algebraic properties are well known. In particular, all Clifford algebras have been classified as matrix algebras over one of the three division algebras. But Clifford Algebras are far more interesting than this classification suggests; they provide the algebraic basis for a unified language for physics and mathematics which offers many advantages over current techniques. This language is called geometric algebra - the name originally chosen by Clifford for his algebra - and this thesis is an investigation into the properties and applications of Clifford's geometric algebra. The work falls into three broad categories: - The formal development of geometric algebra has been patchy and a number of important subjects have not yet been treated within its framework. A principle feature of this thesis is the development of a number of new algebraic techniques which serve to broaden the field of applicability of geometric algebra. Of particular interest are an extension of the geometric algebra of spacetime (the spacetime algebra) to incorporate multiparticle quantum states, and the development of a multivector calculus for handling differentiation with respect to a linear function. - A central contention of this thesis is that geometric algebra provides the natural language in which to formulate a wide range of subjects from modern mathematical physics. To support this contention, reformulations of Grassmann calculus, Lie algebra theory, spinor algebra and Lagrangian field theory are developed. In each case it is argued that the geometric algebra formulation is computationally more efficient than standard approaches, and that it provides many novel insights. - The ultimate goal of a reformulation is to point the way to new mathematics and physics, and three promising directions are developed. The first is a new approach to relativistic multiparticle quantum mechanics. The second deals with classical models for quantum spin-I/2. The third details an approach to gravity based on gauge fields acting in a fiat spacetime. The Dirac equation forms the basis of this gauge theory, and the resultant theory is shown to differ from general relativity in a number of its features and predictions