846 research outputs found

    Influences of transversely isotropic rheology and translational diffusion on the stability of active suspensions

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    Suspensions of self-motile, elongated particles are a topic of significant current interest, exemplifying a form of ‘active matter’. Examples include self-propelling bacteria, algae and sperm, and artificial swimmers. Ericksen's model of a transversely isotropic fluid (Ericksen 1960 Colloid Polym. Sci.173, 117–122 (doi:10.1007/bf01502416)) treats suspensions of non-motile particles as a continuum with an evolving preferred direction; this model describes fibrous materials as diverse as extracellular matrix, textile tufts and plant cell walls. Director-dependent effects are incorporated through a modified stress tensor with four viscosity-like parameters. By making fundamental connections with recent models for active suspensions, we propose a modification to Ericksen's model, mainly the inclusion of self-motility; this can be considered the simplest description of an oriented suspension including transversely isotropic effects. Motivated by the fact that transversely isotropic fluids exhibit modified flow stability, we conduct a linear stability analysis of two distinct cases, aligned and isotropic suspensions of elongated active particles. Novel aspects include the anisotropic rheology and translational diffusion. In general, anisotropic effects increase the instability of small perturbations, while translational diffusion stabilizes a range of wave-directions and, in some cases, a finite range of wavenumbers, thus emphasizing that both anisotropy and translational diffusion can have important effects in these systems.C. R. Holloway, G. Cupples, D. J. Smith, J. E. F. Green, R. J. Clarke and R. J. Dyso

    The SPHERE Study. Secondary prevention of heart disease in general practice: protocol of a randomised controlled trial of tailored practice and patient care plans with parallel qualitative, economic and policy analyses. [ISRCTN24081411]

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    BACKGROUND: The aim of the SPHERE study is to design, implement and evaluate tailored practice and personal care plans to improve the process of care and objective clinical outcomes for patients with established coronary heart disease (CHD) in general practice across two different health systems on the island of Ireland. CHD is a common cause of death and a significant cause of morbidity in Ireland. Secondary prevention has been recommended as a key strategy for reducing levels of CHD mortality and general practice has been highlighted as an ideal setting for secondary prevention initiatives. Current indications suggest that there is considerable room for improvement in the provision of secondary prevention for patients with established heart disease on the island of Ireland. The review literature recommends structured programmes with continued support and follow-up of patients; the provision of training, tailored to practice needs of access to evidence of effectiveness of secondary prevention; structured recall programmes that also take account of individual practice needs; and patient-centred consultations accompanied by attention to disease management guidelines. METHODS: SPHERE is a cluster randomised controlled trial, with practice-level randomisation to intervention and control groups, recruiting 960 patients from 48 practices in three study centres (Belfast, Dublin and Galway). Primary outcomes are blood pressure, total cholesterol, physical and mental health status (SF-12) and hospital re-admissions. The intervention takes place over two years and data is collected at baseline, one-year and two-year follow-up. Data is obtained from medical charts, consultations with practitioners, and patient postal questionnaires. The SPHERE intervention involves the implementation of a structured systematic programme of care for patients with CHD attending general practice. It is a multi-faceted intervention that has been developed to respond to barriers and solutions to optimal secondary prevention identified in preliminary qualitative research with practitioners and patients. General practitioners and practice nurses attend training sessions in facilitating behaviour change and medication prescribing guidelines for secondary prevention of CHD. Patients are invited to attend regular four-monthly consultations over two years, during which targets and goals for secondary prevention are set and reviewed. The analysis will be strengthened by economic, policy and qualitative components

    An Intact Kidney Slice Model to Investigate Vasa Recta Properties and Function in situ

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    Background: Medullary blood flow is via vasa recta capillaries, which possess contractile pericytes. In vitro studies using isolated descending vasa recta show that pericytes can constrict/dilate descending vasa recta when vasoactive substances are present. We describe a live kidney slice model in which pericyte-mediated vasa recta constriction/dilation can be visualized in situ. Methods: Confocal microscopy was used to image calcein, propidium iodide and Hoechst labelling in ‘live’ kidney slices, to determine tubular and vascular cell viability and morphology. DIC video-imaging of live kidney slices was employed to investigate pericyte-mediated real-time changes in vasa recta diameter. Results: Pericytes were identified on vasa recta and their morphology and density were characterized in the medulla. Pericyte-mediated changes in vasa recta diameter (10–30%) were evoked in response to bath application of vasoactive agents (norepinephrine, endothelin-1, angiotensin-II and prostaglandin E2) or by manipulating endogenous vasoactive signalling pathways (using tyramine, L-NAME, a cyclo-oxygenase (COX-1) inhibitor indomethacin, and ATP release). Conclusions: The live kidney slice model is a valid complementary technique for investigating vasa recta function in situ and the role of pericytes as regulators of vasa recta diameter. This technique may also be useful in exploring the role of tubulovascular crosstalk in regulation of medullary blood flow

    Statin prescription initiation and lifestyle behaviour: A primary care cohort study

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    BACKGROUND: Statin prescribing and healthy lifestyles contribute to declining cardiovascular disease mortality. Recent guidelines emphasise the importance of giving lifestyle advice in association with prescribing statins but adherence to healthy lifestyle recommendations is sub-optimal. However, little is known about any change in patients’ lifestyle behaviours when starting statins or of their recall of receiving advice. This study aimed to examine patients’ diet and physical activity (PA) behaviours and their recall of lifestyle advice following initiation of statin prescribing in primary care. METHOD: In 12 general practices, patients with a recent initial prescription of statin therapy, were invited to participate. Those who agreed received a food diary by post, to record food consumed over 4 consecutive days and return to the researcher. We also telephoned participants to administer brief validated questionnaires to assess typical daily diet (DINE) and PA level (Godin). Using the same methods, food diaries and questionnaires were repeated 3 months later. At both times participants were asked if they had changed their behaviour or received advice about their diet or PA. RESULTS: Of 384 invited, 122 (32 %) participated; 109 (89.3 %) completed paired datasets; 50 (45.9 %) were male; their mean age was 64 years. 53.2 % (58/109) recalled receiving lifestyle advice. Of those who did, 69.0 % (40/58) reported having changed their diet or PA, compared to 31.4 % (16/51) of those who did not recall receiving advice. Initial mean daily saturated fat intake (12.9 % (SD3.5) of total energy) was higher than recommended; mean fibre intake (13.8 g/day (SD5.5)), fruit/vegetable consumption (2.7 portions/day (SD1.3)) and PA levels (Godin score 7.1 (SD13.9)) were low. Overall, although some individuals showed evidence of behaviour change, there were no significant changes in the proportions who reported high or medium fat intake (42.2 % v 49.5 %), low fibre (51.4 % v 55.0 %), or insufficient PA (80.7 % v 83.5 %) at 3-month follow-up. CONCLUSION: Whilst approximately half of our cohort recalled receiving lifestyle advice associated with statin prescribing this did not translate into significant changes in diet or PA. Further research is needed to explore gaps between people’s knowledge and behaviours and determine how best to provide advice that supports behaviour change. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12875-016-0471-6) contains supplementary material, which is available to authorized users

    A machine learning pipeline for quantitative phenotype prediction from genotype data

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    <p>Abstract</p> <p>Background</p> <p>Quantitative phenotypes emerge everywhere in systems biology and biomedicine due to a direct interest for quantitative traits, or to high individual variability that makes hard or impossible to classify samples into distinct categories, often the case with complex common diseases. Machine learning approaches to genotype-phenotype mapping may significantly improve Genome-Wide Association Studies (GWAS) results by explicitly focusing on predictivity and optimal feature selection in a multivariate setting. It is however essential that stringent and well documented Data Analysis Protocols (DAP) are used to control sources of variability and ensure reproducibility of results. We present a genome-to-phenotype pipeline of machine learning modules for quantitative phenotype prediction. The pipeline can be applied for the direct use of whole-genome information in functional studies. As a realistic example, the problem of fitting complex phenotypic traits in heterogeneous stock mice from single nucleotide polymorphims (SNPs) is here considered.</p> <p>Methods</p> <p>The core element in the pipeline is the L1L2 regularization method based on the naïve elastic net. The method gives at the same time a regression model and a dimensionality reduction procedure suitable for correlated features. Model and SNP markers are selected through a DAP originally developed in the MAQC-II collaborative initiative of the U.S. FDA for the identification of clinical biomarkers from microarray data. The L1L2 approach is compared with standard Support Vector Regression (SVR) and with Recursive Jump Monte Carlo Markov Chain (MCMC). Algebraic indicators of stability of partial lists are used for model selection; the final panel of markers is obtained by a procedure at the chromosome scale, termed ’saturation’, to recover SNPs in Linkage Disequilibrium with those selected.</p> <p>Results</p> <p>With respect to both MCMC and SVR, comparable accuracies are obtained by the L1L2 pipeline. Good agreement is also found between SNPs selected by the L1L2 algorithms and candidate loci previously identified by a standard GWAS. The combination of L1L2-based feature selection with a saturation procedure tackles the issue of neglecting highly correlated features that affects many feature selection algorithms.</p> <p>Conclusions</p> <p>The L1L2 pipeline has proven effective in terms of marker selection and prediction accuracy. This study indicates that machine learning techniques may support quantitative phenotype prediction, provided that adequate DAPs are employed to control bias in model selection.</p

    Nonsteroidal anti-inflammatory drug use and Alzheimer's disease risk: the MIRAGE Study

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    BACKGROUND: Nonsteroidal anti-inflammatory drugs (NSAID) use may protect against Alzheimer's disease (AD) risk. We sought examine the association between NSAID use and risk of AD, and potential effect modification by APOE-ε4 carrier status and ethnicity. METHODS: The MIRAGE Study is a multi-center family study of genetic and environmental risk factors for AD. Subjects comprised 691 AD patients (probands) and 973 family members enrolled at 15 research centers between 1996 and 2002. The primary independent and dependent variables were prior NSAID use and AD case status, respectively. We stratified the dataset in order to evaluate whether the association between NSAID use and AD was similar in APOE-ε4 carriers and non-carriers. Ethnicity was similarly examined as an effect modifier. RESULTS: NSAID use was less frequent in cases compared to controls in the overall sample (adjusted OR = 0.64; 95% CI = 0.38–1.05). The benefit of NSAID use appeared more pronounced among APOE-ε4 carriers (adjusted OR = 0.49; 95% CI = 0.24–0.98) compared to non-carriers, although this association was not statistically significant. The pattern of association was similar in Caucasian and African Americans. CONCLUSIONS: NSAID use is inversely associated with AD and may be modified by APOE genotype. Prospective studies and clinical trials of sufficient power to detect effect modification by APOE-ε4 carrier status are needed

    Drug-gene interactions of antihypertensive medications and risk of incident cardiovascular disease: a pharmacogenomics study from the CHARGE consortium

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    Background Hypertension is a major risk factor for a spectrum of cardiovascular diseases (CVD), including myocardial infarction, sudden death, and stroke. In the US, over 65 million people have high blood pressure and a large proportion of these individuals are prescribed antihypertensive medications. Although large long-term clinical trials conducted in the last several decades have identified a number of effective antihypertensive treatments that reduce the risk of future clinical complications, responses to therapy and protection from cardiovascular events vary among individuals. Methods Using a genome-wide association study among 21,267 participants with pharmaceutically treated hypertension, we explored the hypothesis that genetic variants might influence or modify the effectiveness of common antihypertensive therapies on the risk of major cardiovascular outcomes. The classes of drug treatments included angiotensin-converting enzyme inhibitors, beta-blockers, calcium channel blockers, and diuretics. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, each study performed array-based genome-wide genotyping, imputed to HapMap Phase II reference panels, and used additive genetic models in proportional hazards or logistic regression models to evaluate drug-gene interactions for each of four therapeutic drug classes. We used meta-analysis to combine study-specific interaction estimates for approximately 2 million single nucleotide polymorphisms (SNPs) in a discovery analysis among 15,375 European Ancestry participants (3,527 CVD cases) with targeted follow-up in a case-only study of 1,751 European Ancestry GenHAT participants as well as among 4,141 African-Americans (1,267 CVD cases). Results Although drug-SNP interactions were biologically plausible, exposures and outcomes were well measured, and power was sufficient to detect modest interactions, we did not identify any statistically significant interactions from the four antihypertensive therapy meta-analyses (Pinteraction &gt; 5.0×10−8). Similarly, findings were null for meta-analyses restricted to 66 SNPs with significant main effects on coronary artery disease or blood pressure from large published genome-wide association studies (Pinteraction ≥ 0.01). Our results suggest that there are no major pharmacogenetic influences of common SNPs on the relationship between blood pressure medications and the risk of incident CVD

    Decolonial education and geography: Beyond the 2017 Royal Geographical Society with the Institute of British Geographers annual conference

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    This review is inspired by the recent resurgence of grassroots movements aimed at the decolonisation of education. The departure point of the paper are the numerous, recent academic responses to campaigns such as Rhodes Must Fall, Why is My Curriculum White?, Why Isn't My Professor Black?, and #LiberateMyDegree. Following from there, the narrative is divided into two sections. The first part reviews theoretical approaches to decolonial education, especially those rooted in the modernity/coloniality/decoloniality paradigm. The second part analyses the ways in which geographers have applied these ideas to our discipline. The review pays particular attention to the 2017 Royal Geographical Society with the Institute of British Geographers annual conference, curated under the “Decolonising geographical knowledges” theme. I argue that as geographers, we have to continue reflecting on the meaning of decolonial praxis, especially in relation to geographical education, beyond the recent conference. To these ends, the review concludes with seven specific questions for geographers to consider in the near future
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