Fast computing of scattering maps of nanostructures using graphical processing units

Scattering maps from strained or disordered nano-structures around a Bragg reflection can either be computed quickly using approximations and a (Fast) Fourier transform, or using individual atomic positions. In this article we show that it is possible to compute up to 4.10^10 $reflections.atoms/s using a single graphic card, and we evaluate how this speed depends on number of atoms and points in reciprocal space. An open-source software library (PyNX) allowing easy scattering computations (including grazing incidence conditions) in the Python language is described, with examples of scattering from non-ideal nanostructures.Comment: 7 pages, 4 figure

Predictors of timely linkage-to-ART within universal test and treat in the HPTN 071 (PopART) trial in Zambia and South Africa: findings from a nested case-control study.

INTRODUCTION: HPTN 071 (PopART) is a three-arm community randomized trial in Zambia and South Africa evaluating the impact of a combination HIV prevention package, including universal test and treat (UTT), on HIV incidence. This nested study examined factors associated with timely linkage-to-care and ART initiation (TLA) (i.e. within six-months of referral) in the context of UTT within the intervention communities of the HPTN 071 (PopART) trial. METHODS: Of the 7572 individuals identified as persons living with HIV (PLWH) (and not on antiretroviral treatment (ART)) during the first year of the PopART intervention provided by Community HIV-care Providers (CHiPs) through door-to-door household visits, individuals who achieved TLA (controls) and those who did not (cases), stratified by gender and community, were randomly selected to be re-contacted for interview. Standardized questionnaires were administered to explore factors potentially associated with TLA, including demographic and behavioural characteristics, and participants' opinions on HIV and related services. Odds ratios comparing cases and controls were estimated using a multi-variable logistic regression. RESULTS: Data from 705 participants (333 cases/372 controls) were analysed. There were negligible differences between cases and controls by demographic characteristics including age, marital or socio-economic position. Prior familiarity with the CHiPs encouraged TLA (aOR of being a case: 0.58, 95% CI: 0.39 to 0.86, p = 0.006). Participants who found clinics overcrowded (aOR: 1.51, 95% CI: 1.08 to 2.12, p = 0.006) or opening hours inconvenient (aOR: 1.63, 95% CI: 1.06 to 2.51, p = 0.02) were less likely to achieve TLA, as were those expressing stronger feelings of shame about having HIV (ptrend  = 0.007). Expressing "not feeling ready" (aOR: 2.75, 95% CI: 1.89 to 4.01, p < 0.001) and preferring to wait until they felt sick (aOR: 2.00, 95% CI: 1.27 to 3.14, p = 0.02) were similarly indicative of being a case. Worrying about being seen in the clinic or about how staff treated patients was not associated with TLA. While the association was not strong, we found that the greater the number of self-reported lifetime sexual partners the more likely participants were to achieve TLA (ptrend  = 0.06). There was some evidence that participants with HIV-positive partners on ART were less likely to be cases (aOR: 0.75, 95% CI: 0.53 to 1.06, p = 0.07). DISCUSSION: The lack of socio-demographic differences between cases and controls is encouraging for a "universal" intervention that seeks to ensure high coverage across whole communities. Making clinics more "patient-friendly" could enhance treatment uptake further. The finding that those with higher risk behaviour are more actively engaging with UTT holds promise for treatment-as-prevention

Fruit intake and abdominal aortic calcification in elderly women: A prospective cohort study

© 2016 by the authors; licensee MDPI, Basel, Switzerland. Cardiovascular disease (CVD) is the leading cause of death worldwide. There is a consistent inverse relationship between fruit intake with CVD events and mortality in cross-sectional and prospective observational studies, but the relationship of fruit intake with measurements of atherosclerosis in humans is less clear. Nutritional effects on abdominal aortic calcification (AAC), a marker for subclinical intimal and medial atherosclerotic vascular disease, have not been studied previously. The aim of this study was to examine the cross-sectional relationship of total and individual fruit (apple, pear, orange and other citrus, and banana) intake with AAC, scored between 0 and 24. The current study assessed baseline data for a cohort of 1052 women over 70 years of age who completed both a food frequency questionnaire assessing fruit intake, and underwent AAC measurement using dual energy X-ray absorptiometry. AAC scores were significantly negatively correlated with total fruit and apple intakes (p 0.25). In multivariable-adjusted logistic regression, each standard deviation (SD; 50 g/day) increase in apple intake was associated with a 24% lower odds of having severe AAC (AAC score >5) (odd ratio OR): 0.76 (0.62, 0.93), p = 0.009). Total and other individual fruit intake were not associated with increased odds of having severe AAC. Apple but not total or other fruit intake is independently negatively associated with AAC in older women

Associations between HIV stigma and health-related quality-of-life among people living with HIV: cross-sectional analysis of data from HPTN 071 (PopART)

People living with HIV (PLHIV) report lower health-related quality-of-life (HRQoL) than HIV-negative people. HIV stigma may contribute to this. We explored the association between HIV stigma and HRQoL among PLHIV. We used cross-sectional data from 3991 randomly selected PLHIV who were surveyed in 2017–2018 for HPTN 071 (PopART), a cluster randomised trial in Zambia and South Africa. Participants were 18–44 years, had laboratory-confirmed HIV infection, and knew their status. HRQoL was measured using the EuroQol-5-dimensions-5-levels (EQ-5D-5L) questionnaire. Stigma outcomes included: internalised stigma, stigma experienced in the community, and stigma experienced in healthcare settings. Associations were examined using logistic regression. Participants who had experienced community stigma (n = 693/3991) had higher odds of reporting problems in at least one HRQoL domain, compared to those who had not (adjusted odds ratio, aOR: 1.51, 95% confidence interval, 95% Cl: 1.16–1.98, p = 0.002). Having experienced internalised stigma was also associated with reporting problems in at least one HRQoL domain (n = 552/3991, aOR: 1.98, 95% CI: 1.54–2.54, p < 0.001). However, having experienced stigma in a healthcare setting was less common (n = 158/3991) and not associated with HRQoL (aOR: 1.04, 95% CI: 0.68–1.58, p = 0.850). A stronger focus on interventions for internalised stigma and stigma experienced in the community is required

Mean muscle attenuation correlates with severe acute pancreatitis unlike visceral adipose tissue and subcutaneous adipose tissue

Background: Acute pancreatitis (AP) is a frequent disorder with considerable morbidity and mortality. Obesity has previously been reported to influence disease severity. Objective The aim of this study was to investigate the association of adipose and muscle parameters with the severity grade of AP. Methods: In total 454 patients were recruited. The first contrast-enhanced computed tomography of each patient was reviewed for adipose and muscle tissue parameters at L3 level. Associations with disease severity were analysed through logistic regression analysis. The predictive capacity of the parameters was investigated using receiver operating characteristic (ROC) curves. Results: No distinct variation was found between the AP severity groups in either adipose tissue parameters (visceral adipose tissue and subcutaneous adipose tissue) or visceral muscle ratio. However, muscle mass and mean muscle attenuation differed significantly with p-values of 0.037 and 0.003 respectively. In multivariate analysis, low muscle attenuation was associated with severe AP with an odds ratio of 4.09 (95% confidence intervals: 1.61-10.36, p-value 0.003). No body parameter presented sufficient predictive capability in ROC-curve analysis. Conclusions: Our results demonstrate that a low muscle attenuation level is associated with an increased risk of severe AP. Future prospective studies will help identify the underlying mechanisms and characterise the influence of body composition parameters on AP.Peer reviewe

Finding meaning: HIV self-management and wellbeing among people taking antiretroviral therapy in Uganda

© 2016 Russell et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in anymedium, provided the original author and source are credited. The health of people living with HIV (PLWH) and the sustained success of antiretroviral therapy (ART) programmes depends on PLWH's motivation and ability to self-manage the condition over the long term, including adherence to drugs on a daily basis. PLWH's selfmanagement of HIV and their wellbeing are likely to be interrelated. Successful self-management sustains wellbeing, and wellbeing is likely to motivate continued self-management. Detailed research is lacking on PLWH's self-management processes on ART in resourcelimited settings. This paper presents findings from a study of PLWH's self-management and wellbeing in Wakiso District, Uganda. Thirty-eight PLWH (20 women, 18 men) were purposefully selected at ART facilities run by the government and by The AIDS Support Organisation in and around Entebbe. Two in-depth interviews were completed with each participant over three or four visits. Many were struggling economically, however the recovery of health and hope on ART had enhanced wellbeing and motivated self-management. The majority were managing their condition well across three broad domains of self-management. First, they had mobilised resources, notably through good relationships with health workers. Advice and counselling had helped them to reconceptualise their condition and situation more positively and see hope for the future, motivating their work to self-manage. Many had also developed a new network of support through contacts they had developed at the ART clinic. Second, they had acquired knowledge and skills to manage their health, a useful framework to manage their condition and to live their life. Third, participants were psychologically adjusting to their condition and their new 'self': They saw HIV as a normal disease, were coping with stigma and had regained self-esteem, and were finding meaning in life. Our study demonstrates the centrality of social relationships and other nonmedical aspects of wellbeing for self-management which ART programmes might explore further and encourage

Individual and community-level risk factors for HIV stigma in 21 Zambian and South African communities: analysis of data from the HPTN071 (PopART) study.

OBJECTIVE: To describe the prevalence and determinants of HIV stigma in 21 communities in Zambia and South Africa. DESIGN: Analysis of baseline data from the HPTN 071 (PopART) cluster-randomized trial. HIV stigma data came from a random sample of 3859 people living with HIV. Community-level exposures reflecting HIV fears and judgements and perceptions of HIV stigma came from a random sample of community members not living with HIV (n = 5088), and from health workers (HW) (n = 851). METHODS: We calculated the prevalence of internalized stigma, and stigma experienced in the community or in a healthcare setting in the past year. We conducted risk-factor analyses using logistic regression, adjusting for clustering. RESULTS: Internalized stigma (868/3859, prevalence 22.5%) was not associated with sociodemographic characteristics but was less common among those with a longer period since diagnosis (P = 0.043). Stigma experienced in the community (853/3859, 22.1%) was more common among women (P = 0.016), older (P = 0.011) and unmarried (P = 0.009) individuals, those who had disclosed to others (P < 0.001), and those with more lifetime sexual partners (P < 0.001). Stigma experienced in a healthcare setting (280/3859, 7.3%) was more common among women (P = 0.019) and those reporting more lifetime sexual partners (P = 0.001) and higher wealth (P = 0.003). Experienced stigma was more common in clusters wherever community members perceived higher levels of stigma, but was not associated with the beliefs of community members or HW. CONCLUSION: HIV stigma remains unacceptably high in South Africa and Zambia and may act as barrier to HIV prevention and treatment. Further research is needed to understand its determinants

Corrigendum to: community-based health workers implementing universal access to HIV testing and treatment: lessons from South Africa and Zambia-HPTN 071 (PopART).

In the originally published version of this manuscript, the spelling of the co-author’s name was incorrect. The name should be “Mubekapi-Musadaidzwa” but is listed as “Mubekapi-Muzadaidzwa”. This error has now been corrected online

Impact of gene variants on sex-specific regulation of human Scavenger receptor class B type 1 (SR-BI) expression in liver and association with lipid levels in a population-based study

<p>Abstract</p> <p>Background</p> <p>Several studies have noted that genetic variants of <it>SCARB1</it>, a lipoprotein receptor involved in reverse cholesterol transport, are associated with serum lipid levels in a sex-dependent fashion. However, the mechanism underlying this gene by sex interaction has not been explored.</p> <p>Methods</p> <p>We utilized both epidemiological and molecular methods to study how estrogen and gene variants interact to influence <it>SCARB1 </it>expression and lipid levels. Interaction between 35 <it>SCARB1 </it>haplotype-tagged polymorphisms and endogenous estradiol levels was assessed in 498 postmenopausal Caucasian women from the population-based Rancho Bernardo Study. We further examined associated variants with overall and <it>SCARB1 </it>splice variant (SR-BI and SR-BII) expression in 91 human liver tissues using quantitative real-time PCR.</p> <p>Results</p> <p>Several variants on a haplotype block spanning intron 11 to intron 12 of <it>SCARB1 </it>showed significant gene by estradiol interaction affecting serum lipid levels, the strongest for rs838895 with HDL-cholesterol (p = 9.2 × 10^-4) and triglycerides (p = 1.3 × 10^-3) and the triglyceride:HDL cholesterol ratio (p = 2.7 × 10^-4). These same variants were associated with expression of the SR-BI isoform in a sex-specific fashion, with the strongest association found among liver tissue from 52 young women <45 years old (p = 0.002).</p> <p>Conclusions</p> <p>Estrogen and <it>SCARB1 </it>genotype may act synergistically to regulate expression of <it>SCARB1 </it>isoforms and impact serum levels of HDL cholesterol and triglycerides. This work highlights the importance of considering sex-dependent effects of gene variants on serum lipid levels.</p