Adetayo Kasim

FABIA: factor analysis for bicluster acquisition

Motivation: Biclustering of transcriptomic data groups genes and samples simultaneously. It is emerging as a standard tool for extracting knowledge from gene expression measurements. We propose a novel generative approach for biclustering called ‘FABIA: Factor Analysis for Bicluster Acquisition’. FABIA is based on a multiplicative model, which accounts for linear dependencies between gene expression and conditions, and also captures heavy-tailed distributions as observed in real-world transcriptomic data. The generative framework allows to utilize well-founded model selection methods and to apply Bayesian techniques. Results: On 100 simulated datasets with known true, artificially implanted biclusters, FABIA clearly outperformed all 11 competitors. On these datasets, FABIA was able to separate spurious biclusters from true biclusters by ranking biclusters according to their information content. FABIA was tested on three microarray datasets with known subclusters, where it was two times the best and once the second best method among the compared biclustering approaches. Availability: FABIA is available as an R package on Bioconductor (http://www.bioconductor.org). All datasets, results and software are available at http://www.bioinf.jku.at/software/fabia/fabia.html Contact: hochreit@bioinf.jku.at Supplementary information: Supplementary data are available at Bioinformatics online.

A systematic review of the effectiveness of individual, community and societal level interventions at reducing socioeconomic inequalities in obesity amongst children

BackgroundTackling childhood obesity is one of the major contemporary public health policy challenges and vital in terms of addressing socioeconomic health inequalities.We aimed to systematically review studies of the effectiveness of interventions (individual, community and societal) operating via different approaches (targeted or universal) in reducing socio-economic inequalities in obesity-related outcomes amongst children.MethodsNine electronic databases were searched from start date to October 2012 along with website and grey literature searches. The review examined the best available international evidence from interventions that aimed to prevent obesity, treat obesity, or improve obesity-related behaviours (diet and/or physical activity) amongst children (aged 0-18 years) in any setting and country, so long as they provided relevant information and analysis on both socioeconomic status and obesity-related outcomes. Data extraction and quality appraisal were conducted using established mechanisms and narrative synthesis was conducted.ResultsWe located 23 studies that provided the ‘best available’ (strongest methodologically) international evidence. At the individual level (n = 4), there was indicative evidence that screen time reduction and mentoring health promotion interventions could be effective in reducing inequalities in obesity. For the community level interventions (n = 17), evidence was inconclusive - with some studies suggesting that school-based health promotion activities and community-based group-based programmes were effective in reducing obesity - others not. Societal level evaluations were few (n = 1). However, there was no evidence to suggest that any of these intervention types increase inequalities and several studies found that interventions could at least prevent the widening of inequalities in obesity. The majority of studies were from America and were of 6-12 year old children.ConclusionsThe review has found only limited evidence although some individual and community based interventions may be effective in reducing socio-economic inequalities in obesity-related outcomes amongst children but further research is required, particularly of more complex, societal level interventions and amongst adolescents.

A systematic review of the effectiveness of individual, community and societal level interventions at reducing socioeconomic inequalities in obesity amongst adults.

Background:Socioeconomic inequalities in obesity are well established in high-income countries. There is a lack of evidence of the types of intervention that are effective in reducing these inequalities among adults.Objectives:To systematically review studies of the effectiveness of individual, community and societal interventions in reducing socio-economic inequalities in obesity among adults.Methods:Nine electronic databases were searched from start date to October 2012 along with website and grey literature searches. The review examined the best available international evidence (both experimental and observational) of interventions at an individual, community and societal level that might reduce inequalities in obesity among adults (aged 18 years or over) in any setting and country. Studies were included if they reported a body fatness-related outcome and if they included a measure of socio-economic status. Data extraction and quality appraisal were conducted using established mechanisms and narrative synthesis was conducted.Results:The ‘best available’ international evidence was provided by 20 studies. At the individual level, there was evidence of the effectiveness of primary care delivered tailored weight loss programmes among deprived groups. Community based behavioural weight loss interventions and community diet clubs (including workplace ones) also had some evidence of effectiveness—at least in the short term. Societal level evaluations were few, low quality and inconclusive. Further, there was little evidence of long term effectiveness, and few studies of men or outside the USA. However, there was no evidence to suggest that interventions increase inequalities.Conclusions:The best available international evidence suggests that some individual and community-based interventions may be effective in reducing socio-economic inequalities in obesity among adults in the short term. Further research is required particularly of more complex, multi-faceted and societal-level interventions.

Community pharmacy-delivered interventions for public health priorities: a systematic review of interventions for alcohol reduction, smoking cessation and weight management, including meta-analysis for smoking cessation

Objectives To systematically review the effectiveness of community pharmacy-delivered interventions for alcohol reduction, smoking cessation and weight management. Design Systematic review and meta-analyses. 10 electronic databases were searched from inception to May 2014. Eligibility criteria for selecting studies Study design: randomised and non-randomised controlled trials; controlled before/after studies, interrupted times series. Intervention: any relevant intervention set in a community pharmacy, delivered by the pharmacy team. No restrictions on duration, country, age, or language. Results 19 studies were included: 2 alcohol reduction, 12 smoking cessation and 5 weight management. Study quality rating: 6 ‘strong’, 4 ‘moderate’ and 9 ‘weak’. 8 studies were conducted in the UK, 4 in the USA, 2 in Australia, 1 each in 5 other countries. Evidence from 2 alcohol-reduction interventions was limited. Behavioural support and/or nicotine replacement therapy are effective and cost-effective for smoking cessation: pooled OR was 2.56 (95% CI 1.45 to 4.53) for active intervention vs usual care. Pharmacy-based interventions produced similar weight loss compared with active interventions in other primary care settings; however, weight loss was not sustained longer term in a range of primary care and commercial settings compared with control. Pharmacy-based weight management interventions have similar provider costs to those delivered in other primary care settings, which are greater than those delivered by commercial organisations. Very few studies explored if and how sociodemographic or socioeconomic variables moderated intervention effects. Insufficient information was available to examine relationships between effectiveness and behaviour change strategies, implementation factors, or organisation and delivery of interventions. Conclusions Community pharmacy-delivered interventions are effective for smoking cessation, and demonstrate that the pharmacy is a feasible option for weight management interventions. Given the potential reach, effectiveness and associated costs of these interventions, commissioners should consider using community pharmacies to help deliver public health services.

Annual Review of Competence Progression (ARCP) performance of doctors who passed Professional and Linguistic Assessments Board (PLAB) tests compared with UK medical graduates: national data linkage study.

Objective To determine whether use of the Professional and Linguistic Assessments Board (PLAB) examination system used to grant registration for international medical graduates results in equivalent postgraduate medical performance, as evaluated at Annual Review of Competence Progression (ARCP), between UK based doctors who qualified overseas and those who obtained their primary medical qualification from UK universities. Design Observational study linking ARCP outcome data from the UK deaneries with PLAB test performance and demographic data held by the UK General Medical Council (GMC). Setting Doctors in postgraduate training for a medical specialty or general practice in the UK and doctors obtaining GMC registration via the PLAB system. Participants 53 436 UK based trainee doctors with at least one competency related ARCP outcome reported during the study period, of whom 42 017 were UK medical graduates and 11 419 were international medical graduates who were registered following a pass from the PLAB route. Main outcome measure Probability of obtaining a poorer versus a more satisfactory category of outcome at ARCP following successful registration as a doctor in the UK. Results International medical graduates were more likely to obtain a less satisfactory outcome at ARCP compared with UK graduates. This finding persisted even after adjustment for the potential influence of sex, age, years of UK based practice, and ethnicity and exclusion of outcomes associated with postgraduate examination failure (odds ratio 1.63, 95% confidence interval 1.30 to 2.06). However, international medical graduates who scored in the highest twelfth at part 1 of the PLAB (at least 32 points above the pass mark) had ARCP outcomes that did not differ significantly from those of UK graduates. Conclusions These findings suggest that the PLAB test used for registration of international medical graduates is not generally equivalent to the requirements for UK graduates. The differences in postgraduate performance, as captured at ARCP, following the two routes to registration might be levelled out by raising the standards of English language competency required as well as the pass marks for the two parts of the PLAB test. An alternative might be to introduce a different testing system.

Diet and physical activity interventions to prevent or treat obesity in South Asian children and adults: a systematic review and meta-analysis.

Background and Aims: The metabolic risks associated with obesity are greater for South Asian populations compared with White or other ethnic groups, and levels of obesity in childhood are known to track into adulthood. Tackling obesity in South Asians is therefore a high priority. The rationale for this systematic review is the suggestion that there may be differential effectiveness in diet and physical activity interventions in South Asian populations compared with other ethnicities. The research territory of the present review is an emergent, rather than mature, field of enquiry, but is urgently needed. Thus the aim of this systematic review and meta-analysis was to assess the effectiveness of diet and physical activity interventions to prevent or treat obesity in South Asians living in or outside of South Asia and to describe the characteristics of effective interventions. Methods: Systematic review of any type of lifestyle intervention, of any length of follow-up that reported any anthropometric measure for children or adults of South Asian ethnicity. There was no restriction on the type of comparator; randomised controlled trials, controlled clinical trials, and before-after studies were included. A comprehensive search strategy was implemented in five electronic databases: ASSIA, Cochrane Controlled Trials Register, Embase, Medline and Social Sciences Citation Index. The search was limited to English language abstracts published between January 2006 and January 2014. References were screened; data extraction and quality assessment were carried out by two reviewers. Results are presented in narrative synthesis and meta-analysis. Results: Twenty-nine studies were included, seven children, 21 adult and one mixed age. No studies in children under six were identified. Sixteen studies were conducted in South Asia, ten in Europe and three in USA. Effective or promising trials include physical activity interventions in South Asian men in Norway and South Asian school-children in the UK. A home-based, family-orientated diet and physical activity intervention improved obesity outcomes in South Asian adults in the UK, when adjusted for baseline differences. Meta-analyses of interventions in children showed no significant difference between intervention and control for body mass index or waist circumference. Meta-analyses of adult interventions showed significant improvement in weight in data from two trials adjusted for baseline differences (mean difference −1.82 kgs, 95% confidence interval −2.48 to −1.16) and in unadjusted data from three trials following sensitivity analysis (mean difference −1.20 kgs, 95% confidence interval −2.23 to −0.17). Meta-analyses showed no significant differences in body mass index and waist circumference for adults. Twenty of 24 intervention groups showed improvements in adult body mass index from baseline to follow-up; average change in high quality studies (n = 7) ranged from 0.31 to −0.8 kg/m2. There was no evidence that interventions were more or less effective according to whether the intervention was set in South Asia or not, or by socio-economic status. Conclusions: Meta-analysis of a limited number of controlled trials found an unclear picture of the effects of interventions on body mass index for South Asian children. Meta-analyses of a limited number of controlled trials showed significant improvement in weight for adults but no significant differences in body mass index and waist circumference. One high quality study in South Asian children found that a school-based physical activity intervention that was delivered within the normal school day which was culturally sensitive, was effective. There is also evidence of culturally appropriate approaches to, and characteristics of, effective interventions in adults which we believe could be transferred and used to develop effective interventions in children.

The positive pharmacy care law: an area-level analysis of the relationship between community pharmacy distribution, urbanity and social deprivation in England

Objectives To: (1) determine the percentage of the population in England that have access to a community pharmacy within 20 min walk; (2) explore any relationship between the walking distance and urbanity; (3) explore any relationship between the walking distance and social deprivation; and (4) explore any interactions between urbanity, social deprivation and community pharmacy access. Design This area level analysis spatial study used postcodes for all community pharmacies in England. Each postcode was assigned to a population lookup table and lower super output area (LSOA). The LSOA was then matched to urbanity (urban, town and fringe or village, hamlet and isolated dwellings) and deprivation decile (using the Index of Multiple Deprivation score). Primary outcome measure Access to a community pharmacy within 20 min walk. Results Overall, 89.2% of the population is estimated to have access to a community pharmacy within 20 min walk. For urban areas, that is 98.3% of the population, for town and fringe, 79.9% of the population, while for rural areas, 18.9% of the population. For areas of lowest deprivation (deprivation decile 1) 90.2% of the population have access to a community pharmacy within 20 min walk, compared to 99.8% in areas of highest deprivation (deprivation decile 10), a percentage difference of 9.6% (8.2, 10.9). Conclusions Our study shows that the majority of the population can access a community pharmacy within 20 min walk and crucially, access is greater in areas of highest deprivation—a positive pharmacy care law. More research is needed to explore the perceptions and experiences of people—from various levels of deprivation—around the accessibility of community pharmacy services.

Access all areas? An area-level analysis of accessibility to general practice and community pharmacy services in England by urbanity and social deprivation

Objectives (1) To determine the percentage of the population in England that has access to a general practitioner (GP) premises within a 20 min walk (the accessibility); (2) explore the relationship between the walking distance to a GP premises and urbanity and social deprivation and (3) compare accessibility of a GP premises to that of a community pharmacy—and how this may vary by urbanity and social deprivation. Design This area-level analysis spatial study used postcodes for all GP premises and community pharmacies in England. Each postcode was assigned to a population lookup table and Lower Super Output Area (LSOA). The LSOA was then matched to urbanity (urban, town and fringe, or village, hamlet and isolated dwellings) and deprivation decile (using the Index of Multiple Deprivation score 2010). Primary outcome measure Living within a 20 min walk of a GP premises. Results Overall, 84.8% of the population is estimated to live within a 20 min walk of a GP premises: 81.2% in the most affluent areas, 98.2% in the most deprived areas, 94.2% in urban and 19.4% in rural areas. This is consistently lower when compared with the population living within a 20 min walk of a community pharmacy. Conclusions Our study shows that the vast majority of the population live within a 20 min walk of a GP premises, with higher proportions in the most deprived areas—a positive primary care law. However, more people live within a 20 min walk of a community pharmacy compared with a GP premises, and this potentially has implications for the commissioning of future services from these healthcare providers in England.

Prospective pilot evaluation of the effectiveness and cost-utility of a ‘health first’ case management service for long-term Incapacity Benefit recipients

BACKGROUND In line with the NICE guidance, an NHS-commissioned case management intervention was provided for individuals receiving Incapacity Benefit payments for ≥3 years in the North East of England. The intervention aimed to improve the health of the participants. METHODS A total of 131 participants receiving the intervention were compared over 9 months with a (non-equivalent) comparison group of 229 receiving Incapacity Benefit payments and usual care. Health was measured using EQ-5D, EQ-VAS, SF-8, HADS and the Nordic Musculoskeletal questionnaire. Socio-demographic and health behaviour data were also collected. Fixed-effects linear models with correlated errors were used to compare health changes between groups over time. A preliminary cost-utility analysis was also conducted. RESULTS The comparison group measures of health were stable over time. Starting from comparatively poor initial levels, case-management group generic (EQ5D, EQ-VAS) and mental health (HADS-A, HADS-D and SF8-MCS) measures improved within 6 months to similar levels found in the comparison group. Musculoskeletal (Nordic 2) and health behaviours did not improve. Tentative estimates of cost-utility suggest an intervention cost in the region of £16 700-£23 500 per QALY. CONCLUSIONS Case management interventions may improve the health of Incapacity Benefit recipients. Further research is required to help confirm these pilot findings.

The impact of gender and physical environment on the handwashing behaviour of university students in Ghana

Objectives  To establish levels of handwashing after defecation among students at the University of Cape Coast in Ghana, and to test hypotheses that gender and washroom environment affect handwashing behaviour.