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’.