Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database

Inter-cultural differences in response to a computer-based anti-bullying intervention

Background and purpose: Many holistic anti-bullying interventions have been attempted, with mixed success, while little work has been done to promote a 'self-help' approach to victimisation. The rise of the ICT curriculum and computer support in schools now allows for approaches that benefit from technology to be implemented. This study evaluates the cross-cultural effects of a computer-based anti-bullying intervention on primary school-aged children's knowledge about bullying and relevant coping strategies. Programme description: FearNot! is an interactive computer-based virtual learning environment designed for use as an anti-bullying intervention. It includes interactive virtual agents who assume the most common participant roles found in episodes of bullying. FearNot! was used by children over three consecutive weeks to allow its effectiveness to be evaluated in a longitudinal in situ programme. Sample: Two comparable samples were drawn from the UK and Germany. In the UK, 651 participants (aged 8-11) were recruited from primary schools in Hertfordshire, Coventry and Warwickshire, whereas the 535 German participants (aged 7-10) were sourced from Grundschulen in the Bayern and Hessen regions. Because of lack of parental consent, late joiners and absences/missing responses, data from 908 participants (UK 493; Germany 415) were analysed. Design and methods: A quasi-experimental, pre/post-tests control group design employed pre-published and bespoke questionnaires to collect data. Descriptive and inferential analyses were conducted. Results: UK students possessed higher coping strategy knowledge scores than German participants, but German children's scores improved over time and as a result of the FearNot! intervention. Conclusions: Overall, while not effective at increasing children's coping strategy knowledge in this study, the FearNot! intervention could prove a useful classroom tool to approach the issue of bullying as part of a wider initiative. Cultural differences at baseline and reactions to the intervention are discussed

What are the living conditions and health status of those who don't report their migration status? a population-based study in Chile

BACKGROUND: Undocumented immigrants are likely to be missing from population databases, making it impossible to identify an accurate sampling frame in migration research. No population-based data has been collected in Chile regarding the living conditions and health status of undocumented immigrants. However, the CASEN survey (Caracterizacion Socio- Economica Nacional) asked about migration status in Chile for the first time in 2006 and provides an opportunity to set the base for future analysis of available migration data. We explored the living conditions and health of self-reported immigrants and respondents who preferred not to report their migration status in this survey. METHODS: Cross-sectional secondary analysis of CASEN survey in Chile in 2006. Outcomes: any disability, illness/accident, hospitalization/surgery, cancer/chronic condition (all binary variables); and the number of medical/emergency attentions received (count variables). Covariates: Demographics (age, sex, marital status, urban/rural, ethnicity), socioeconomic status (education level, employment status and household income), and material standard of living (overcrowding, sanitation, housing quality). Weighted regression models were estimated for each health outcome, crude and adjusted by sets of covariates, in STATA 10.0. RESULTS: About 1% of the total sample reported being immigrants and 0.7% preferred not to report their migration status (Migration Status - Missing Values; MS-MV). The MS-MV lived in more deprived conditions and reported a higher rate of health problems than immigrants. Some gender differences were observed by health status among immigrants and the MS-MV but they were not statistically significant. Regressions indicated that age, sex, SES and material factors consistently affected MS-MVs’ chance of presenting poor health and these patterns were different to those found among immigrants. Great heterogeneity in both the MS-MV and the immigrants, as indicated by wide confidence intervals, prevented the identification of other significantly associated covariates. CONCLUSION: This is the first study to look at the living conditions and health of those that preferred not to respond their migration status in Chile. Respondents that do not report their migration status are vulnerable to poor health and may represent undocumented immigrants. Surveys that fail to identify these people are likely to misrepresent the experiences of immigrants and further quantitative and qualitative research is urgently required

Group cognitive analytic music therapy: a quasi-experimental feasibility study conducted in a high secure hospital

This study conducted a feasibility patient preference quasi-experimental study of group cognitive analytic music therapy (G-CAMT) for mentally disordered offenders. Participants either chose or were randomised to 16 sessions of manualised G-CAMT (N = 10) plus treatment as usual (TAU) or TAU alone (N = 10). Self-rated and staff-rated outcomes were assessed at baseline, post-intervention and 8-weeks post-intervention. Residency was assessed at 2-year follow-up. Results indicate that G-CAMT was easily implemented; 9/10 participants completed G-CAMT and attendees had high satisfaction with the approach. Session attendance was high; 4/10 participants attended all sessions. At the 8-week follow-up, 3/9 G-CAMT participants had reliable reductions (i.e. statistically reliable pre to 8-week follow-up change results) in intrusive/possessive behaviours and fear of separation/abandonment. On the staff-rated outcome measure G-CAMT participants as a group were statistically significantly friendlier compared to TAU at 8-week follow-up (U = 0.50, p = 0.009, d = 1.92, CI 0.44 to 3.11). There were no differences between the arms in terms of residency outcomes at 2-year follow-up. The study is discussed in terms of G-CAMT’s theoretical grounding and high acceptability. The study is limited by its small sample size, but indicates the possibility of progressing onto a full trial

Mapping transcription mechanisms from multimodal genomic data

Background Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data. Results We develop a method to identify eQTLs. The method represents eQTLs as information flux between genetic variants and transcripts. We use information theory to simultaneously interrogate SNP and gene expression data, resulting in a Transcriptional Information Map (TIM) which captures the network of transcriptional information that links genetic variations, gene expression and regulatory mechanisms. These maps are able to identify both cis- and trans- regulating eQTLs. The application on a dataset of leukemia patients identifies eQTLs in the regions of the GART, PCP4, DSCAM, and RIPK4 genes that regulate ADAMTS1, a known leukemia correlate. Conclusions The information theory approach presented in this paper is able to infer the dependence networks between SNPs and transcripts, which in turn can identify cis- and trans-eQTLs. The application of our method to the leukemia study explains how genetic variants and gene expression are linked to leukemia.National Human Genome Research Institute (U.S.) (R01HG003354)National Institute of Allergy and Infectious Diseases (U.S.) (U19 AI067854-05)National Heart, Lung, and Blood Institute (grant T32 HL007427-28)National Institutes of Health (U.S.) (grant K99 LM009826

Distinguishing four components underlying physical activity: a new approach to using physical activity questionnaire data in old age

<p>Abstract</p> <p>Background</p> <p>It is evident that physical activity has many benefits, but it often remains unclear which types of activity are optimal for health and functioning in old age. The aim of this methodological study was to propose a method for distinguishing four components underlying self reported physical activity of older adults: intensity, muscle strength, turning actions and mechanical strain.</p> <p>Methods</p> <p>Physical activity was assessed by the validated LAPAQ questionnaire among 1699 older adults of the Longitudinal Aging Study Amsterdam. Based on expert consultation and literature review, the four component scores for several individual daily and sports activities were developed. Factor analysis was performed to confirm whether the developed components indeed measured different constructs of physical activity.</p> <p>Results</p> <p>Based on the factor analyses, three components were distinguished: 1. intensity and muscle strength loaded on the same factor, 2. mechanical strain and 3. turning actions. Analyses in gender, age and activity level subgroups consistently distinguished three factors.</p> <p>Conclusion</p> <p>Future research using these components may contribute to our understanding of how specific daily and sports activities may have a different influence on health and physical functioning in old age.</p

Sentencing drug offenders under the 2003 Criminal Justice Act: Challenges for the probation service

For the most part the 2003 Criminal Justice Act, which came into effect in England and Wales in April 2005, was accepted by the probation service with relatively little opposition. Given the enormity of its impact acquiescence to this degree of change ought to come as something of a surprise. The 2003 Act changed fundamentally the nature of community supervision, it brought to an end the traditional range of non-custodial penalties and replaced them with a single community order to which sentencers could add any of 12 possible requirements. This paper considers the impact of the 2003 legislation on one particular offender group - drug misusers. Drug misusing offenders have the potential to pose serious difficulties for probation officers; the habitual nature of drug addiction and a tendency toward an irregular lifestyle make drug misusers particularly susceptible to breach. Under the new legislation courts have significantly fewer options available to them when responding to incidents of offender non-compliance. This paper argues that many of the provisions of the 2003 Act together with developments elsewhere in the UK are likely to have impacted disproportionately on those groups whose lifestyles are chaotic and whose routines are incompatible with the terms and conditions of modern day probation practice. It concludes that greater flexibility towards non-compliance, supported by regular and consistent judicial review, would encourage improved rates of compliance and retention in treatment and improved outcomes for offenders

Assessing the importance of car meanings and attitudes in consumer evaluations of electric vehicles

This paper reports findings from a research study which assesses the importance of attitudinal constructs related to general car attitudes and the meanings attached to car ownership over evaluations of electric vehicles (EVs). The data are assessed using principal component analysis to evaluate the structure of the underlying attitudinal constructs. The identified constructs are then entered into a hierarchical regression analysis which uses either positive or negative evaluations of the instrumental capabilities of EVs as the dependent variable. Results show that attitudinal constructs offer additional predictive power over socioeconomic characteristics and that the symbolic and emotive meanings of car ownership are as, if not more, effective in explaining the assessment of EV instrumental capability as compared to issues of cost and environmental concern. Additionally, the more important an individual considers their car to be in their everyday life, the more negative their evaluations are of EVs whilst individuals who claim to be knowledgeable about cars in general and EVs in particular have a lower propensity for negative EV attitudes. However, positive and negative EV attitudes are related to different attitudinal constructs suggesting that it is possible for someone to hold both negative and positive assessments at the same time