Accounting for Calibration Uncertainties in X-ray Analysis: Effective Areas in Spectral Fitting

While considerable advance has been made to account for statistical uncertainties in astronomical analyses, systematic instrumental uncertainties have been generally ignored. This can be crucial to a proper interpretation of analysis results because instrumental calibration uncertainty is a form of systematic uncertainty. Ignoring it can underestimate error bars and introduce bias into the fitted values of model parameters. Accounting for such uncertainties currently requires extensive case-specific simulations if using existing analysis packages. Here we present general statistical methods that incorporate calibration uncertainties into spectral analysis of high-energy data. We first present a method based on multiple imputation that can be applied with any fitting method, but is necessarily approximate. We then describe a more exact Bayesian approach that works in conjunction with a Markov chain Monte Carlo based fitting. We explore methods for improving computational efficiency, and in particular detail a method of summarizing calibration uncertainties with a principal component analysis of samples of plausible calibration files. This method is implemented using recently codified Chandra effective area uncertainties for low-resolution spectral analysis and is verified using both simulated and actual Chandra data. Our procedure for incorporating effective area uncertainty is easily generalized to other types of calibration uncertainties.Comment: 61 pages double spaced, 8 figures, accepted for publication in Ap

An Introduction to Hard and Soft Data Fusion via Conceptual Spaces Modeling for Space Event Characterization

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework

β-Hydroxybutyrate Oxidation in Exercise Is Impaired by Low-Carbohydrate and High-Fat Availability.

Purpose: In this study, we determined ketone oxidation rates in athletes under metabolic conditions of high and low carbohydrate (CHO) and fat availability. Methods: Six healthy male athletes completed 1 h of bicycle ergometer exercise at 75% maximal power (WMax) on three occasions. Prior to exercise, participants consumed 573 mg·kg bw-1 of a ketone ester (KE) containing a 13C label. To manipulate CHO availability, athletes undertook glycogen depleting exercise followed by isocaloric high-CHO or very-low-CHO diets. To manipulate fat availability, participants were given a continuous infusion of lipid during two visits. Using stable isotope methodology, β-hydroxybutyrate (βHB) oxidation rates were therefore investigated under the following metabolic conditions: (i) high CHO + normal fat (KE+CHO); (ii) high CHO + high fat KE+CHO+FAT); and (iii) low CHO + high fat (KE+FAT). Results: Pre-exercise intramuscular glycogen (IMGLY) was approximately halved in the KE+FAT vs. KE+CHO and KE+CHO+FAT conditions (both p < 0.05). Blood free fatty acids (FFA) and intramuscular long-chain acylcarnitines were significantly greater in the KE+FAT vs. other conditions and in the KE+CHO+FAT vs. KE+CHO conditions before exercise. Following ingestion of the 13C labeled KE, blood βHB levels increased to ≈4.5 mM before exercise in all conditions. βHB oxidation was modestly greater in the KE+CHO vs. KE+FAT conditions (mean diff. = 0.09 g·min-1, p = 0.03; d = 0.3), tended to be greater in the KE+CHO+FAT vs. KE+FAT conditions (mean diff. = 0.07 g·min-1; p = 0.1; d = 0.3) and were the same in the KE+CHO vs. KE+CHO+FAT conditions (p < 0.05; d < 0.1). A moderate positive correlation between pre-exercise IMGLY and βHB oxidation rates during exercise was present (p = 0.04; r = 0.5). Post-exercise intramuscular βHB abundance was markedly elevated in the KE+FAT vs. KE+CHO and KE+CHO+FAT conditions (both, p < 0.001; d = 2.3). Conclusion: βHB oxidation rates during exercise are modestly impaired by low CHO availability, independent of circulating βHB levels

A New Single-Step PCR Assay for the Detection of the Zoonotic Malaria Parasite Plasmodium knowlesi

Recent studies in Southeast Asia have demonstrated substantial zoonotic transmission of Plasmodium knowlesi to humans. Microscopically, P. knowlesi exhibits several stage-dependent morphological similarities to P. malariae and P. falciparum. These similarities often lead to misdiagnosis of P. knowlesi as either P. malariae or P. falciparum and PCR-based molecular diagnostic tests are required to accurately detect P. knowlesi in humans. The most commonly used PCR test has been found to give false positive results, especially with a proportion of P. vivax isolates. To address the need for more sensitive and specific diagnostic tests for the accurate diagnosis of P. knowlesi, we report development of a new single-step PCR assay that uses novel genomic targets to accurately detect this infection.We have developed a bioinformatics approach to search the available malaria parasite genome database for the identification of suitable DNA sequences relevant for molecular diagnostic tests. Using this approach, we have identified multi-copy DNA sequences distributed in the P. knowlesi genome. We designed and tested several novel primers specific to new target sequences in a single-tube, non-nested PCR assay and identified one set of primers that accurately detects P. knowlesi. We show that this primer set has 100% specificity for the detection of P. knowlesi using three different strains (Nuri, H, and Hackeri), and one human case of malaria caused by P. knowlesi. This test did not show cross reactivity with any of the four human malaria parasite species including 11 different strains of P. vivax as well as 5 additional species of simian malaria parasites.The new PCR assay based on novel P. knowlesi genomic sequence targets was able to accurately detect P. knowlesi. Additional laboratory and field-based testing of this assay will be necessary to further validate its utility for clinical diagnosis of P. knowlesi

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

Crop Updates 2008 - Cereals

This session covers twenty four papers from different authors: WHEAT AGRONOMY 1. Wheat variety performance in the Northern Agricultural Region in 2007, Christine Zaicou, Department of Agriculture and Food 2. Wheat variety performance on the Central Agricultural Region in 2007, Shahajahan Miyan, Department of Agriculture and Food 3. Response of wheat varieties to sowing time in the Great Southern and Lakes Region in 2007, Brenda Shackley and Steve Penny, Department of Agriculture and Food 4. Wheat variety performance in the South Coastal Region in 2007, Sarah Ellis, Department of Agriculture and Food 5. Flowering dates of wheat varieties in Western Australia in 2007, Darshan Sharma, Brenda Shackley and Christine Zaicou, Department of Agriculture and Food BARLEY AGRONOMY 6. Barley variety options for Western Australia, Blakely Paynter, Andrea Hills and Jeff Russell, Department of Agriculture and Food 7. Vlaming A – the newest malting barley variety, Blakely Paynter, Jeff Russell and Andrea Hills, Department of Agriculture and Food 8. Barley yields higher in wide rows with stubble retained in a very dry season at Merredin, Glen Riethmuller, Bill Bowden and Paul Blackwell, Department of Agriculture and Food HERBICIDE TOLERANCE 9. Herbicide tolerance of current/new wheat varieties, Dr Harmohinder Dhammu, Department of Agriculture and Food 10. Herbicide tolerance of new oat varieties, Dr Harmohinder Dhammu, Vince Lambert, and Chris Roberts,Department of Agriculture and Food NUTRITION 11. Managing nitrogen inputs in malting barley, Andrea Hills and Blakely Paynter, Department of Agriculture and Food 12. Decision tools for optimal N on cereal crops, David and Sally Cox, Jeremy Lemon* and Andrea Hills*, *Department of Agriculture and Food 13. Wheat varieties respond differently to potassium application on potassium responsive soils, Paul Damon and Zed Rengel, Faculty of Natural and Agricultural Sciences, University of Western Australia DISEASES 14. Leaf disease management in continuous barley in the northern and central grainbelt of WA, Geoff Thomas, Ciara Beard, Anne Smith, Kith Jayasena and Sean Kelly, Department of Agriculture and Food 15. Temperature and moisture requirements of leaf, stem and stripe rusts of wheat, Geoff Thomas, Rob Loughman and Bill MacLeod, Department of Agriculture and Food 16. Fungicide options for controlling diseases in oats, Raj Malik and Blakely Paynter, Department of Agriculture and Food 17. Survey of wheat root diseases under intensive cereal production in Western Australia during 2005-2007, Ravjit Khangura, William MacLeod, Vivien Vanstone, Colin Hanbury, Mehreteab Aberra, Gordon MacNish and Robert Loughman, Department of Agriculture and Food 18. Epidemiology studies on Wheat Streak Mosaic Virus in 2007, Brenda Coutts, Geoff Strickland, Monica Kehoe, Dustin Severtson and Roger Jones, Department of Agriculture and Food 19. Bacterial diseases that affect WA export hay quality, Dominie Wright and Megan Jordan, Department of Agriculture and Food SOIL 20. Hardpan penetration ability of drought-stressed wheat under pot and field conditions, Xinhua He1, Eli Manyol1, Song-Ai Nio1, Imran Malik1, Tina Botwright-Acuña1,2and Len Wade1,3,1School of Plant Biology, University of Western Australia, 2Tasmanian Institute of Agricultural Research, University of Tasmania, TAS, 3E.H. Graham Centre, Charles Sturt University, NSW HARVEST MANAGEMENT 21. Calculating the risk – the SEPWA Harvest Calculator, Nigel Metz, South East Premium Wheat Growers Association 22. The relationship between grain moisture and atmospheric conditions in cereal crop harvesting on the South Coast of WA, Nigel Metz, South East Premium Wheat Growers Association (SEPWA) MARKETS 23. Varietal accreditation for Australian Barley, Linda Price, Barley Australia STATISTICAL METHODS 24. Applying data mining tools to improve grain quality for growers, Dean Diepeveen1, Leisa Armstrong2, Peter Clarke1, Doug Abrecht1, Rudi Appels2 and Matthew Bellgard3,1Department of Agriculture and Food, Western Australia 2Edith Cowan University, Western Australia, 3Centre of Comparative Genomics, Murdoch Universit

Dreams and nightmares of liberal international law: capitalist accumulation, natural rights and state hegemony

This article develops a line of theorising the relationship between peace, war and commerce and does so via conceptualising global juridical relations as a site of contestation over questions of economic and social justice. By sketching aspects of a historical interaction between capitalist accumulation, natural rights and state hegemony, the article offers a critical account of the limits of liberal international law, and attempts to recover some ground for thinking about the emancipatory potential of international law more generally

Low-frequency variation near common germline susceptibility loci are associated with risk of Ewing sarcoma

Background: Ewing sarcoma (EwS) is a rare, aggressive solid tumor of childhood, adolescence and young adulthood associated with pathognomonic EWSR1-ETS fusion oncoproteins altering transcriptional regulation. Genome-wide association studies (GWAS) have identified 6 common germline susceptibility loci but have not investigated low-frequency inherited variants with minor allele frequencies below 5% due to limited genotyped cases of this rare tumor. Methods We investigated the contribution of rare and low-frequency variation to EwS susceptibility in the largest EwS genome-wide association study to date (733 EwS cases and 1,346 unaffected controls of European ancestry). Results We identified two low-frequency variants, rs112837127 and rs2296730, on chromosome 20 that were associated with EwS risk (OR = 0.186 and 2.038, respectively;P-value < 5x10(-8)) and located near previously reported common susceptibility loci. After adjusting for the most associated common variant at the locus, only rs112837127 remained a statistically significant independent signal (OR = 0.200, P-value = 5.84x10(-8)). Conclusions: These findings suggest rare variation residing on common haplotypes are important contributors to EwS risk. Impact Motivate future targeted sequencing studies for a comprehensive evaluation of low-frequency and rare variation around common EwS susceptibility loci