Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Developing ethical identities in young offenders through restorative justice practice in Australia

Restorative justice is firmly established in Australian juvenile justice. While the official language used to describe restorative initiatives varies across states and territories, the most common form is a meeting or conference between young offenders and their victims (most commonly known as a family group or youth justice conference). During the past decade, an impressive amount of empirical research has examined how the restorative justice process affects offenders, victims and other participants (such as supporters for young offenders and victims). Results from this line of research are remarkably consistent and show that participants generally regard restorative conferences as procedurally fair and that they are satisfied with the outcomes (eg what young offenders agree to do to make up for their offending behaviour, such as offer a sincere apology or perform work for the victim or the community). What is less common, however, is the perception among participants that restorative conferences achieve the key aim of restoration.By ‘restoration’ we refer to encounters where ‘offenders apologise, their apologies are accepted, victims offer forgiveness,and conferences conclude with a feeling of mutual good will’.

Soil carbon sequestration rates and associated economic costs for farming systems of south-eastern Australia

Soil organic carbon (C) sequestration rates based on the Intergovernmental Panel for Climate Change (IPCC) methodology were combined with local economic data to simulate the economic potential for C sequestration in response to conservation tillage in the six agro-ecological zones within the Southern Region of the Australian grains industry. The net C sequestration rate over 20 years for the Southern Region (which includes discounting for associated greenhouse gases) is estimated to be 3.6 or 6.3 Mg C/ha after converting to either minimum or no-tillage practices, respectively, with no-till practices estimated to return 75% more carbon on average than minimum tillage. The highest net gains in C per ha are realised when converting from conventional to no-tillage practices in the high-activity clay soils of the High Rainfall and Wimmera agro-ecological zones. On the basis of total area available for change, the Slopes agro-ecological zone offers the highest net returns, potentially sequestering an additional 7.1 Mt C under no-tillage scenario over 20 years. The economic analysis was summarised as C supply curves for each of the 6 zones expressing the total additional C accumulated over 20 years for a price per t C sequestered ranging from zero to AU$200. For a price of $50/Mg C, a total of 427 000 Mg C would be sequestered over 20 years across the Southern Region, <5% of the simulated C sequestration potential of 9.1 Mt for the region. The Wimmera and Mid-North offer the largest gains in C under minimum tillage over 20 years of all zones for all C prices. For the no-tillage scenario, for a price of $50/Mg C, 1.74 Mt C would be sequestered over 20 years across the Southern Region, <10% of the simulated C sequestration potential of 18.6 Mt for the region over 20 years. The Slopes agro-ecological zone offers the best return in C over 20 years under no-tillage for all C prices. The Mallee offers the least return for both minimum and no-tillage scenarios. At a price of $200/Mg C, the transition from conventional tillage to minimum or no-tillage practices will only realise 19% and 33%, respectively, of the total biogeochemical sequestration potential of crop and pasture systems of the Southern Region over a 20-year period.

Access and Quality of Heart Failure Management Programs in Australia

Background/aim In response to the high burden of disease associated with chronic heart failure (CHF), in particular the high rates of hospital admissions, dedicated CHF management programs (CHF-MP) have been developed. Over the past five years there has been a rapid growth of CHF-MPs in Australia. Given the apparent mismatch between the demand for, and availability of CHF-MPs, this paper has been designed to discuss the accessibility to and quality of current CHF-MPs in Australia. Methods The data presented in this report has been combined from the research of the co-authors, in particular a review of the inequities in access to chronic heart failure which utilised geographical information systems (GIS) and the survey of heterogeneity in quality and service provision in Australian. Results Of the 62 CHF-MPs surveyed in this study 93% (58) centres had been located areas that are rated as Highly Accessible. This result indicated that most of the CHF-MPs have been located in capital cities or large regional cities. Six percent (4 CHF-MPs) had been located in Accessible areas which were country towns or cities. No CHF-MPs had been established outside of cities to service the estimated 72,000 individuals with CHF living in rural and remote areas. 16% of programs recruited NYHA Class I patients and of these 20% lacked confirmation (echocardiogram) of their diagnosis. Conclusion Overall, these data highlight the urgent need to provide equitable access to CHF-MP's. When establishing CHF-MPs consideration of current evidence based models to ensure quality in practice.