‘Who? Me. A Memoir’ Donald Leslie Shaw (1930–2017)

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Symbolic and analytic techniques for resource analysis of Java bytecode

Recent work in resource analysis has translated the idea of amortised resource analysis to imperative languages using a program logic that allows mixing of assertions about heap shapes, in the tradition of separation logic, and assertions about consumable resources. Separately, polyhedral methods have been used to calculate bounds on numbers of iterations in loop-based programs. We are attempting to combine these ideas to deal with Java programs involving both data structures and loops, focusing on the bytecode level rather than on source code

The cost of youth homelessness in Australia study: snapshot report 1

Overview: This is the first national Australian longitudinal study investigating the economic, personal and social costs of youth homelessness over time across a broad range of locations. Too many young Australians are without any form of safe and secure accommodation. It is estimated that approximately 44,000 Australians under the age of 25 are homeless, but the actual number is likely to be higher. Homeless young people comprise some 42 per cent of the Australian homeless population. Participants have been tracked by researchers over a three year period to see what kind of issues young homeless people face: changes in their circumstances, health and quality of life; how many used services; the types of services they accessed; and whether or not they transitioned from homelessness to permanent accommodation

Understanding the Dynamics of Gene Regulatory Systems : Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms

Peer reviewedPublisher PD

Youthworx media: youth media and social enterprise as intervention and innovation

This research explores the impact of Youthworx, a community-based cross-sector response to the problem of youth marginalisation and social exclusion. Preface Youthworx is a successful model of a practical, community-based, cross-sector response to the problem of youth marginalisation and social exclusion. It combines professional expertise, networks and material resources across social service delivery agencies (Salvation Army and Youth Development Australia (YDA)), youth-run community media (SYN Media), an educational provider (North Melbourne Institute of Technology TAFE (NMIT)) and research organisations (the ARC Centre of Excellence for Creative Industries and Innovation (CCI), at the Swinburne Institute for Social Research (SISR)). Media training and production is used to build capacity to re-engage with learning, education and employment. After some years in development between 2008, when Youthworx effectively began operations, and 2013, the program has provided open access multimedia workshops, accredited training and, more recently, paid traineeships for more than 400 youth disconnected from formal learning, with experience of homelessness, juvenile justice or alcohol and drug abuse. Participants broadcast and distribute their works through SYN Media, local festivals and screenings, as well as online. They also make commissioned creative products for external clients and not-for-profit organisations. Research undertaken by Swinburne University’s SISR between 2005 and 2013 explored impact of Youthworx on these young people and the broader lessons for debates on social innovation, community media and creative economies, informal learning, opportunity and enterprise. The integrated R&D is a unique element of Youthworx, allowing documentation, analysis and capacity-building. It combined longitudinal on-site research, a comparative study of best practices across parallel international youth media initiatives, and mobilisation of established academic and industry networks. Although our findings to date have appeared in a range of publications, this document offers the first comprehensive report on the project. It discusses the development of Youthworx and the results of the 2008-13 period. The presented findings draw on a qualitative fieldwork at Youthworx and semistructured follow-up interviews with a group of Youthworx graduates who participated in the program between 2009-2011. In combination, this material is used to document and explore the specific institutional structure and cultural context in which Youthworx’s media training and production took place, the ways in which young people experienced, engaged with and valued the project, as well as the project’s social outcomes. The longitudinal account of Youthworx presented here integrates and summarises multiple voices, including industry partners, service organisations, practitioners, researchers and, importantly, young people themselves. It reflects arguments developed across the team, including material previously published

The burden of mental health in lymphatic filariasis.

BACKGROUND Neglected Tropical Diseases (NTDs) afflict around one billion individuals in the poorest parts of the world with many more at risk. Lymphatic filariasis is one of the most prevalent of the infections and causes significant morbidity in those who suffer the clinical conditions, particularly lymphedema and hydrocele. Depressive illness has been recognised as a prevalent disability in those with the disease because of the stigmatising nature of the condition. No estimates of the burden of depressive illness of any neglected tropical disease have been undertaken to date despite the recognition that such diseases have major consequences for mental health not only for patients but also their caregivers. METHODS We developed a mathematical model to calculate the burden of Disability- Adjusted Life Years (DALY) attributable to depressive illness in lymphatic filariasis and that of their caregivers using standard methods for calculating DALYs. Estimates of numbers with clinical disease was based on published estimates in 2012 and the numbers with depressive illness from the available literature. RESULTS We calculated that the burden of depressive illness in filariasis patients was 5.09 million disability-adjusted life years (DALYs) and 229,537 DALYs attributable to their caregivers. These figures are around twice that of 2.78 million DALYs attributed to filariasis by the Global Burden of Disease study of 2010. CONCLUSIONS Lymphatic filariasis and other neglected tropical diseases, notably Buruli Ulcer, cutaneous leishmaniasis, leprosy, yaws, onchocerciasis and trachoma cause significant co morbidity associated with mental illness in patients. Studies to assess the prevalence of the burden of this co-morbidity should be incorporated into any future assessment of the Global Burden of neglected tropical diseases. The prevalence of depressive illness in caregivers who support those who suffer from these conditions is required. Such assessments are critical for neglected tropical diseases which have such a huge global prevalence and thus will contribute a significant burden of co-morbidity attributable to mental illness

The effectiveness of incarceration-based drug treatment on criminal behavior.

Background - Many, if not most, incarcerated offenders have substance abuse problems. Without effective treatment, these substance-abusing offenders are likely to persist in non-drug offending. The period of incarceration offers an opportunity to intervene in the cycle of drug abuse and crime. Although many types of incarceration-based drug treatment programs are available (e.g., therapeutic communities and group counseling), the effectiveness of these programs is unclear. Objectives - The objective of this research synthesis is to systematically review quasi-experimental and experimental (RCT) evaluations of the effectiveness of incarceration-based drug treatment programs in reducing post-release recidivism and drug relapse. A secondary objective of this synthesis is to examine variation in effectiveness by programmatic, sample, and methodological features. In this update of the original 2006 review (see Mitchell, Wilson, and MacKenzie, 2006), studies made available since the original review were included in an effort to keep current with emerging research. Main results - Seventy-four evaluations met our eligibility criteria. The overall average effect of these programs was approximately a 15 to 17% reduction in recidivism and drug relapse. The effectiveness of such programs, however, varied by program type. Therapeutic communities had relatively consistent but modest reductions in recidivism and drug relapse. Counseling and narcotic maintenance programs had mixed effects. Specifically, counseling programs on average reduced recidivism but not drug relapse, narcotic maintenance programs had sizeable reductions in drug relapse but not recidivism, and boot camps had negligible effects on both recidivism and drug relapse. Conclusions - This synthesis of evaluations of incarceration-based drug treatment programs found that such programs are modestly effective in reducing recidivism. These findings most strongly support the effectiveness of therapeutic communities, as these programs produced relatively consistent reductions in recidivism and drug use. Both counseling and incarceration-based narcotic maintenance programs had mixed effects. Counseling programs were associated with reductions in recidivism but not drug use; whereas, incarceration-based narcotic maintenance programs were associated with reductions in drug use but not recidivism. Note that our findings regarding the effectiveness of incarceration-based narcotic maintenance programs differ from a larger review of community-based narcotic maintenance programs (see Egli, Pina, Christensen, Aebi, and Killias, 2009). Finally, boot camp programs for drug offenders had negligible effects on both recidivism and drug use

Quahogs in Eastern North America: Part II, History by Province and State

The northern quahog, Mercenaria mercenaria, ranges along the Atlantic Coast of North America from the Canadian Maritimes to Florida, while the southern quahog, M. campechiensis, ranges mostly from Florida to southern Mexico. The northern quahog was fished by native North Americans during prehistoric periods. They used the meats as food and the shells as scrapers and as utensils. The European colonists copied the Indians treading method, and they also used short rakes for harvesting quahogs. The Indians of southern New England and Long Island, N.Y., made wampum from quahog shells, used it for ornaments and sold it to the colonists, who, in turn, traded it to other Indians for furs. During the late 1600’s, 1700’s, and 1800’s, wampum was made in small factories for eventual trading with Indians farther west for furs. The quahoging industry has provided people in many coastal communities with a means of earning a livelihood and has given consumers a tasty, wholesome food whether eaten raw, steamed, cooked in chowders, or as stuffed quahogs. More than a dozen methods and types of gear have been used in the last two centuries for harvesting quahogs. They include treading and using various types of rakes and dredges, both of which have undergone continuous improvements in design. Modern dredges are equipped with hydraulic jets and one type has an escalator to bring the quahogs continuously to the boats. In the early 1900’s, most provinces and states established regulations to conserve and maximize yields of their quahog stocks. They include a minimum size, now almost universally a 38-mm shell width, and can include gear limitations and daily quotas. The United States produces far more quahogs than either Canada or Mexico. The leading producer in Canada is Prince Edward Island. In the United States, New York, New Jersey, and Rhode Island lead in quahog production in the north, while Virginia and North Carolina lead in the south. Connecticut and Florida were large producers in the 1990’s. The State of Tabasco leads in Mexican production. In the northeastern United States, the bays with large openings, and thus large exchanges of bay waters with ocean waters, have much larger stocks of quahogs and fisheries than bays with small openings and water exchanges. Quahog stocks in certified beds have been enhanced by transplanting stocks to them from stocks in uncertified waters and by planting seed grown in hatcheries, which grew in number from Massachusetts to Florida in the 1980’s and 1990’s

A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number

Motivation: cis-regulatory DNA sequence elements, such as enhancers and silencers, function to control the spatial and temporal expression of their target genes. Although the overall levels of gene expression in large cell populations seem to be precisely controlled, transcription of individual genes in single cells is extremely variable in real time. It is, therefore, important to understand how these cis-regulatory elements function to dynamically control transcription at single-cell resolution. Recently, statistical methods have been proposed to back calculate the rates involved in mRNA transcription using parameter estimation of a mathematical model of transcription and translation. However, a major complication in these approaches is that some of the parameters, particularly those corresponding to the gene copy number and transcription rate, cannot be distinguished; therefore, these methods cannot be used when the copy number is unknown. Results: Here, we develop a hierarchical Bayesian model to estimate biokinetic parameters from live cell enhancer–promoter reporter measurements performed on a population of single cells. This allows us to investigate transcriptional dynamics when the copy number is variable across the population. We validate our method using synthetic data and then apply it to quantify the function of two known developmental enhancers in real time and in single cells

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. Results To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. Conclusions This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations