Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set

Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^>0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations

The clinical profile of tuberous sclerosis complex (TSC) in the United Kingdom: A retrospective cohort study in the Clinical Practice Research Datalink (CPRD)

AbstractBackgroundTuberous Sclerosis Complex (TSC) is a multi-system genetic disorder characterised by the development of benign growths and diverse clinical manifestations, varying in severity, age at onset and with high clinical burden.AimsThis longitudinal study aims to describe the broad spectrum of clinical manifestation profiles in a large, representative cohort of TSC patients in the UK in order to better understand disease complexity.MethodsTSC patients in the Clinical Practice Research Datalink (CPRD) and linked Hospital Episodes Statistics (CPRD-HES) were retrospectively identified between 1987 and 2013. Available history was extracted for each patient and clinical diagnosis, procedure and medication records reviewed. A random selection of patients from the CPRD-HES was used as a Comparator cohort.ResultsThree hundred and thirty-four TSC patients with a mean (SD) age of 30.3 (18.6) years were identified (53% female). TSC was diagnosed at mean age 3.2 (4.2) years. Epilepsy and psychiatric manifestations were reported frequently in paediatric (77% and 55%, respectively) and adult patients (66% and 68%, respectively). The prevalence of manifestations in the TSC cohort was markedly higher versus the Comparator cohort. The majority of paediatric (46%) and adult TSC patients (62%) developed clinical manifestations affecting at least three organ systems and forty-nine distinctive organ system manifestation profiles were identified.ConclusionsTSC patients present with multiple and complex clinical manifestations and profiles that necessitate the co-ordinated action of a multidisciplinary team in order to improve the quality and efficiency of care

Magnetotelluric Data, Mid Valley, Nevada Test Site, Nevada.

The United States Department of Energy (DOE) and the National Nuclear Security Administration (NNSA) at their Nevada Site Office (NSO) are addressing ground-water contamination resulting from historical underground nuclear testing through the Environmental Management (EM) program and, in particular, the Underground Test Area (UGTA) project. One issue of concern is the nature of the somewhat poorly constrained pre-Tertiary geology and its effects on ground-water flow. Ground-water modelers would like to know more about the hydrostratigraphy and geologic structure to support a hydrostratigraphic framework model that is under development for the Rainier Mesa/Shoshone Mountain Corrective Action Unit (CAU) (Bechtel Nevada, 2006). During 2003, the U.S. Geological Survey (USGS), in cooperation with the DOE and NNSA-NSO, collected and processed data at the Nevada Test Site in and near Yucca Flat (YF) to help define the character, thickness, and lateral extent of the pre-tertiary confining units. We collected 51 magnetotelluric (MT) and audio-magnetotelluric (AMT), stations for that research (Williams and others, 2005a, 2005b, 2005c, 2005d, 2005e, 2005f). In early 2005 we extended that research with 26 additional MT data stations (Williams and others, 2006), located on and near Rainier Mesa and Shoshone Mountain (RM-SM). The new stations extended the area of the hydrogeologic study previously conducted in Yucca Flat. This work was done to help refine what is known about the character, thickness, and lateral extent of pre-Tertiary confining units. In particular, a major goal was to define the upper clastic confining unit (UCCU). The UCCU is comprised of late Devonian to Mississippian siliciclastic rocks assigned to the Eleana Formation and Chainman Shale. The UCCU underlies the Yucca Flat area and extends westward towards Shoshone Mountain, southward to Buckboard Mesa, and northward to Rainier Mesa. Late in 2005 we collected another 14 MT stations in Mid Valley and in northern Yucca Flat basin. That work was done to better determine the extent and thickness of the UCCU near the southeastern RM-SM CAU boundary with the southwestern YF CAU, and also in the northern YF CAU. The purpose of this report is to release the MT data at those 14 stations shown in figure 1. No interpretation of the data is included here

Objective measures of strain and subjective muscle soreness differ between positional groups and season phases in American collegiate football.

Purpose: To assess objective strain and subjective muscle soreness in ‘Bigs’ (Offensive and Defensive Line), ‘Combos’ (Tight Ends, Quarterbacks, Line and Running-Backs) and ‘Skills’ (Wide Receivers and Defensive Backs) American College Football (ACF) players during off-season, fall-camp and in-season phases. Methods: Twenty-three male players were assessed once weekly (3-week off-season, 4-week fall-camp, 3-week in-season) for hydroperoxides (FORT), antioxidant capacity (FORD) and oxidative stress index (OSI)), countermovement jump flight-time, reactive strength index modified (RSImod), and subjective soreness. Linear mixed-models analysed the effect of a two within-subject standard deviation change between predictor and dependent variables. Results: Compared to fall-camp and in-season phases, off-season FORT (P=<.001 and <.001), FORD (P=<.001 and <.001), OSI (P=<.001 and <.001), Flight-time (P=<.001 and <.001), RSImod (P=<.001 and <.001) and soreness (P=<.001 and <.001) were higher for ‘Bigs’, whilst FORT (P=<.001 and <.001) and OSI (P=.02 and <.001) were lower for ‘Combos’. FORT was higher for ‘Bigs’ compared to ‘Combos’ in all phases (P=<.001, .02 and .01). FORD was higher for ‘Skills’ compared to ‘Bigs’ in off-season (P=.02) and ‘Combos’ in-season (P=.01). OSI was higher for ‘Bigs’ compared to ‘Combos’ (P=<.001) and ‘Skills’ (P=.01) during off-season and to ‘Combos’ in-season (P=<.001). Flight-time was higher for ‘Skills’ in fall-camp compared to ‘Bigs’ (P=.04) and to ‘Combos’ in-season (P=.01). RSImod was higher for ‘Skills’ during off-season compared to ‘Bigs’ (P=.02) and ‘Combos’ during fall-camp (P=.03), and in-season (P=.03). Conclusion: Off-season ACF training resulted in higher objective strain and subjective muscle soreness in ‘Bigs’ compared to fall-camp and during in-season compared to ‘Combos’ and ‘Skills’ players

A deep investigation into the structure of carbon dots

Since their discovery, carbon dots (CDs) have been a promising nanomaterial in a variety of fields including nanomedicine. Despite their potential in this area, there are many obstacles to overcome for CDs to be approved for biomedical use. One major hindrance to CDs’ approval is related to their poorly defined structure. Herein a structural study of CDs is presented in order to rectify this shortcoming. The properties of three CDs which have significant promise in biomedical applications, black CDs (B-CDs), carbon nitride dots (CNDs), and yellow CDs (Y-CDs), are compared in order to develop a coherent structural model for each nanosystem. Absorption coefficients were measured for each system and this data gave insight on the level of disorder in each system. Furthermore, extensive structural characterization has been performed in order to derive structural information for each system. This data showed that B-CDs and CNDs are functionalized to a greater degree and are also more disordered and amorphous than Y-CDs. These techniques were used to develop a structural model consistent with the obtained data and what is known for carbonic nanostructures. These models can be used to analyze CD emission properties and to better understand the structure-property relationship in CDs

Mainstreaming domestic and gender-based violence into sociology and the criminology of violence

Sociological and criminological views of domestic and gender-based violencegenerally either dismiss it as not worthy of consideration, or focus on specificgroups of offenders and victims (male youth gangs, partner violence victims). Inthis paper, we take a holistic approach to violence, extending the definition fromthat commonly in use to encompass domestic violence and sexual violence. Weoperationalize that definition by using data from the latest sweep of the CrimeSurvey for England and Wales. By so doing, we identify that violence is currentlyunder-measured and ubiquitous; that it is gendered, and that other forms of violence (family violence, acquaintance violence against women) are equally ofconcern. We argue that violence studies are an important form of activity forsociologists

Interventions that support the creation of dementia friendly environments in health care : protocol for a realist review

© 2016 Handley et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise statedImproving health-care outcomes for people living with dementia when they are admitted to hospital is a policy priority. Dementia friendly interventions in health care promote inclusion of patients and carers in decision-making and adapt practices and environments to be appropriate to the needs of people with cognitive impairment. While there has been a wealth of activity, the number of studies evaluating interventions is limited, and the majority focuses on reporting staff and organisational outcomes. By focusing on patient and carer outcomes, this review will aim to develop an explanatory account of how and in what circumstances dementia friendly environments in health care work for people living with dementia and with what outcomesPeer reviewe

Assessing factors influencing communities' acceptability of mass drug administration for the elimination of lymphatic filariasis in Guyana.

BACKGROUND: Guyana is one of four countries in the Latin American Region where lymphatic filariasis (LF) remains endemic. In preparation for the introduction of a new triple drug therapy regimen (ivermectin, diethylcarbamazine, and albendazole (IDA)) in 2019, an acceptability study was embedded within sentinel site mapping in four regions to assess mass drug administration (MDA) coverage and compliance, acceptability, and perceptions about treatment and disease. The results from this survey would inform the rollout of IDA in Guyana in 2019. METHODS: Data collection for the study occurred in August 2019, using a validated questionnaire administered by trained enumerators. Across all regions, a total of 1,248 participants were sampled by the Filarial Mapping team. Four-hundred and fifty-one participants aged over 18 years were randomly selected for participation in an expanded acceptability questionnaire. All data were captured in Secure Data Kit (SDK). RESULTS: Acceptability was measured using a mean acceptability score. Unadjusted mean scores ranged from 24.6 to 29.3, with 22.5 as the threshold of acceptability. Regional variation occurred across many indicators of interest: self-rated understanding about LF, mechanisms of LF transmission, LF drug safety and history of treatment during MDA. Region IV (Georgetown) recorded higher knowledge about LF, but lower compliance and acceptability. Number of pills was not perceived as a concern. CONCLUSION: Acceptability of MDA was good across all four regions under study. Results from this study set a baseline level for key indicators and acceptability, from which the acceptability of IDA can be measured. Regional variations across indicators suggest that localized approaches should be considered for social mobilization and MDA delivery to capture these contextual differences

Individual and Contextual Factors Associated with Low Childhood Immunisation Coverage in Sub-Saharan Africa: A Multilevel Analysis

Background: In 2010, more than six million children in sub-Saharan Africa did not receive the full series of three doses of the diphtheria-tetanus-pertussis vaccine by one year of age. An evidence-based approach to addressing this burden of un-immunised children requires accurate knowledge of the underlying factors. We therefore developed and tested a model of childhood immunisation that includes individual, community and country-level characteristics. Method and Findings: We conducted multilevel logistic regression analysis of Demographic and Health Survey data for 27,094 children aged 12–23 months, nested within 8,546 communities from 24 countries in sub-Saharan Africa. According to the intra-country and intra-community correlation coefficient implied by the estimated intercept component variance, 21% and 32% of the variance in unimmunised children were attributable to country- and community-level factors respectively. Children born to mothers (OR 1.35, 95%CI 1.18 to 1.53) and fathers (OR 1.13, 95%CI 1.12 to 1.40) with no formal education were more likely to be unimmunised than those born to parents with secondary or higher education. Children from the poorest households were 36% more likely to be unimmunised than counterparts from the richest households. Maternal access to media significantly reduced the odds of children being unimmunised (OR 0.94, 95%CI 0.94 to 0.99). Mothers with health seeking behaviours were less likely to have unimmunised children (OR 0.56, 95%CI 0.54 to 0.58). However, children from urban areas (OR 1.12, 95% CI 1.01 to 1.23), communities with high illiteracy rates (OR 1.13, 95% CI 1.05 to 1.23), and countries with high fertility rates (OR 4.43, 95% CI 1.04 to 18.92) were more likely to be unimmunised. Conclusion: We found that individual and contextual factors were associated with childhood immunisation, suggesting that public health programmes designed to improve coverage of childhood immunisation should address people, and the communities and societies in which they live

Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine-Related Metabolic Pathways

Riboswitches are regulatory elements modulating gene expression in response to specific metabolite binding. It has been recently reported that riboswitch agonists may exhibit antimicrobial properties by binding to the riboswitch domain. Guanine riboswitches are involved in the regulation of transport and biosynthesis of purine metabolites, which are critical for the nucleotides cellular pool. Upon guanine binding, these riboswitches stabilize a 5′-untranslated mRNA structure that causes transcription attenuation of the downstream open reading frame. In principle, any agonistic compound targeting a guanine riboswitch could cause gene repression even when the cell is starved for guanine. Antibiotics binding to riboswitches provide novel antimicrobial compounds that can be rationally designed from riboswitch crystal structures. Using this, we have identified a pyrimidine compound (PC1) binding guanine riboswitches that shows bactericidal activity against a subgroup of bacterial species including well-known nosocomial pathogens. This selective bacterial killing is only achieved when guaA, a gene coding for a GMP synthetase, is under the control of the riboswitch. Among the bacterial strains tested, several clinical strains exhibiting multiple drug resistance were inhibited suggesting that PC1 targets a different metabolic pathway. As a proof of principle, we have used a mouse model to show a direct correlation between the administration of PC1 and the reduction of Staphylococcus aureus infection in mammary glands. This work establishes the possibility of using existing structural knowledge to design novel guanine riboswitch-targeting antibiotics as powerful and selective antimicrobial compounds. Particularly, the finding of this new guanine riboswitch target is crucial as community-acquired bacterial infections have recently started to emerge