Software fault-freeness and reliability predictions

Many software development practices aim at ensuring that software is correct, or fault-free. In safety critical applications, requirements are in terms of probabilities of certain behaviours, e.g. as associated to the Safety Integrity Levels of IEC 61508. The two forms of reasoning - about evidence of correctness and about probabilities of certain failures -are rarely brought together explicitly. The desirability of using claims of correctness has been argued by many authors, but not been taken up in practice. We address how to combine evidence concerning probability of failure together with evidence pertaining to likelihood of fault-freeness, in a Bayesian framework. We present novel results to make this approach practical, by guaranteeing reliability predictions that are conservative (err on the side of pessimism), despite the difficulty of stating prior probability distributions for reliability parameters. This approach seems suitable for practical application to assessment of certain classes of safety critical systems

Evaluation of the Psychometric Properties of a Version of the London Measure of Unplanned Pregnancy for Women’s Partners

BackgroundThe role of women’s partners in pregnancy planning has gained importance with the development of preconception care. The measurement of pregnancy planning/intention has also changed in the last two decades with the development of psychometric measures such as the London Measure of Unplanned Pregnancy (LMUP). This analysis aimed to evaluate the psychometric properties of a version of the LMUP for women’s partners in the UK.&#x0D; MethodsThe LMUP items, adapted for completion by partners, were piloted and included in a survey of (mainly male) partners in three antenatal clinics in London, UK, as part of a study of pre-pregnancy health and care. The psychometric properties of the partner LMUP were assessed according to the principles of Classical Test Theory.&#x0D; ResultsThere were 575 partners of pregnant women in the sample, 573 (99.7%) being men. There were high comple-tion rates for all the LMUP items. The distribution of LMUP scores ranged from 1–12, with a negative skew (biased towards planned/intended pregnancies). In terms of reliability (internal consistency), Cronbach’s alpha was 0.69, item-rest correlations were &gt;0.2 for five items, and all inter-item correlations were positive. In terms of construct validity, principal components analysis showed that measurement was unidimensional, confirmatory factor analysis showed good model fit, and the convergent validity hypothesis of non-perfect, moderate-to-good agreement between couples’ LMUP scores was met.&#x0D; ConclusionsThe partner LMUP performed well in terms of reliability and validity according to internationally-accepted criteria for the performance of psychometric measures and can be used in future research on men and couples. However, we recommend further research relating to the concept of pregnancy planning/inten-tion among partners of all gender identities to understand whether additional content would enhance the measurement of the construct. In particular, we recommend further conceptual exploration with men who have experienced unplanned pregnancies.&#x0D;  </jats:p

Community-onset Staphylococcus aureus infections presenting to general practices in South-eastern Australia

Community-acquired Staphylococcus aureus infections are a public health concern, yet little is known about infections that do not present to hospital. We identified community-onset S. aureus infections via specimens submitted to a community-based pathology service. Referring doctors confirmed eligibility and described infection site, severity and treatment. Isolates were characterized on antibiotic resistance, PFGE, MLST/SCCmec, and Panton–Valentine leukocidin (PVL), representing 106 community-onset infections; 34 non-multiresistant methicillin-resistant S. aureus (nmMRSA) (resistant to <3 non-β-lactam antibiotics), 15 multiply antibiotic-resistant MRSA (mMRSA) and 57 methicillin-sensitive S. aureus (MSSA). Most (93%) were skin and soft tissue infections. PVL genes were carried by 42% of nmMRSA isolates [95% confidence interval (CI) 26–61] and 15% of MSSA (95% CI 8–28). PVL was associated with infections of the trunk, head or neck (56•4% vs. 24•3%, P = 0•005) in younger patients (23 vs. 52 years, P < 0•001), and with boils or abscesses (OR 8•67, 95% CI 2•9–26•2), suggesting underlying differences in exposure and/or pathogenesis

Climate Change in Queensland's Grazing Lands: II. An Assessment of the Impact on Animal Production From Native Pastures

The 160 million ha of grazing land in Queensland support approximately 10 million beef equivalents (9.8 million cattle and 10.7 million sheep) with treed and cleared native pastures as the major forage source. The complexity of these biophysical systems and their interaction with pasture and stock management, economic and social forces limits our ability to easily calculate the impact of climate change scenarios. We report the application of a systems approach in simulating the flow of plant dry matter and utilisation of forage by animals. Our review of available models highlighted the lack of suitable mechanistic models and the potential role of simple empirical relationships of utilisation and animal production derived from climatic and soil indices. Plausible climate change scenarios were evaluated by using a factorial of rainfall (f 10%) * 3260C temperature increase * doubling CO, in sensitivity studies at property, regional and State scales. Simulation of beef cattle liveweight gain at three locations in the Queensland black speargrass zone showed that a *lo% change in rainfall was magnified to be a f 15% change in animal production (liveweight gain per ha) depending on location, temperature and CO, change. Models of 'safe' carrying capacity were developed from property data and expert opinion. Climate change impacts on 'safe' carrying capacity varied considerably across the State depending on whether moisture, temperature or nutrients were the limiting factors. Without the effect of doubling CO,, warmer temperatures and +lo% changes in rainfall resulted in -35 to +70% changes in 'safe' carrying capacity depending on location. With the effect of doubling CO, included, the changes in 'safe' carrying capacity ranged from -12 to +115% across scenarios and locations. When aggregated to a whole-of-State carrying capacity, the combined effects of warmer temperature, doubling CO, and +lo% changes in rainfall resulted in 'safe' carrying capacity changes of +3 to +45% depending on rainfall scenario and location. A major finding of the sensitivity study was the potential importance of doubling CO, in mitigating or amplifying the effects of warmer temperatures and changes in rainfall. Field studies on the impact of CO, are therefore a high research priority. Keywords: climate change, Queensland, simulation, rangelands, beef production, cattle, carrying capacity, CO,, utilisatio

Linking adaptation science to action to build food secure Pacific Island communities

Climate change is a major threat to food security in Pacific Island countries, with declines in food production and increasing variability in food supplies already evident across the region. Such impacts have already led to observed consequences for human health, safety and economic prosperity. Enhancing the adaptive capacity of Pacific Island communities is one way to reduce vulnerability and is underpinned by the extent to which people can access, understand and use new knowledge to inform their decision-making processes. However, effective engagement of Pacific Island communities in climate adaption remains variable and is an ongoing and significant challenge. Here, we use a qualitative research approach to identify the impediments to engaging Pacific Island communities in the adaptations needed to safeguard food security. The main barriers include cultural differences between western science and cultural knowledge, a lack of trust among local communities and external scientists, inappropriate governance structures, and a lack of political and technical support. We identify the importance of adaptation science, local social networks, key actors (i.e., influential and trusted individuals), and relevant forms of knowledge exchange as being critical to overcoming these barriers. We also identify the importance of co-ordination with existing on-ground activities to effectively leverage, as opposed to duplicating, capacity

DNA-binding protein prediction using plant specific support vector machines:validation and application of a new genome annotation tool

There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes

Different bacterial gene expression patterns and attenuated host immune responses are associated with the evolution of low-level vancomycin resistance during persistent methicillin-resistant Staphylococcus aureus bacteraemia

BACKGROUND: Low-level vancomycin resistance in Staphylococcus aureus (vancomycin-intermediate S. aureus (VISA) and hetero-VISA [hVISA]) emerges during persistent infection and failed vancomycin therapy. Up-regulation of genes associated with the "cell wall stimulon" and mutations in the vraSR operon have both been implicated in the development of resistance, however the molecular mechanisms of resistance are not completely understood. To further elucidate the mechanisms leading to resistance transcriptome comparisons were performed using multiple clinical pairs of vancomycin-susceptible S. aureus (VSSA) and hVISA/VISA (n = 5), and three VSSA control pairs from hospitalized patients with persistent bacteraemia that did not develop hVISA/VISA. Based on the transcriptome results multiple genes were sequenced and innate immune system stimulation was assessed in the VSSA and hVISA/VISA pairs. RESULTS: Here we show that up-regulation of vraS and the "cell wall stimulon" is not essential for acquisition of low-level vancomycin resistance and that different transcriptional responses occur, even between closely related hVISA/VISA strains. DNA sequencing of vraSR, saeSR, mgrA, rot, and merR regulatory genes and upstream regions did not reveal any differences between VSSA and hVISA/VISA despite transcriptional changes suggesting mutations in these loci may be linked to resistance in these strains. Enhanced capsule production and reduced protein A expression in hVISA/VISA were confirmed by independent bioassays and fully supported the transcriptome data. None of these changes were observed in the three control pairs that remained vancomycin-susceptible during persistent bacteremia. In a macrophage model of infection the changes in cell surface structures in hVISA/VISA strains were associated with significantly reduced NF-kappaB activation resulting in reduced TNF-alpha and IL-1beta expression. CONCLUSION: We conclude that there are multiple pathways to low-level vancomycin resistance in S. aureus, even among closely related clinical strains, and these can result in an attenuated host immune response. The persistent infections associated with hVISA/VISA strains may be a consequence of changes in host pathogen interactions in addition to the reduced antibiotic susceptibility

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

Abstract Recent reports indicate the emergence of a new carbapenemase producing Klebsiella pneumoniae clone, ST307. Here we show that ST307 emerged in the mid-1990s (nearly 20 years prior to its first report), is already globally distributed and is intimately associated with a conserved plasmid harbouring the bla CTX-M-15 extended-spectrum beta-lactamase (ESBL) gene plus other antimicrobial resistance determinants. Our findings support the need for enhanced surveillance of this widespread ESBL clone in which carbapenem resistance is now emerging