VarSite: disease variants and protein structure

VarSite is a web server mapping known disease-associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank (PDB). The analyses are primarily image-based and provide both an overview for each human protein, as well as a report for any specific variant of interest. The information can be useful in assessing whether a given variant might be pathogenic or benign. The structural annotations for each position in the protein include protein secondary structure, interactions with ligand, metal, DNA/RNA, or other protein, and various measures of a given variant's possible impact on the protein's function. The 3D locations of the disease-associated variants can be viewed interactively via the 3dmol.js JavaScript viewer, as well as in RasMol and PyMOL. Users can search for specific variants, or sets of variants, by providing the DNA coordinates of the base change(s) of interest. Additionally, various agglomerative analyses are given, such as the mapping of disease and natural variants onto specific Pfam or CATH domains. The server is freely accessible to all at: https://www.ebi.ac.uk/thornton-srv/databases/VarSite. This article is protected by copyright. All rights reserved

A closed-loop EKF and multi-failure diagnosis approach for cooperative GNSS positioning

Current cooperative positioning with Global Navigation Satellite System (GNSS) for connected vehicle application mainly uses pseudorange measurements. However the positioning accuracy offered cannot meet the requirements for lane-level positioning, collision avoidance and future automatic driving, which needs real-time positioning accuracy of better than 0.5m. Furthermore, there is an apparent lack of research into the integrity issue for these new applications under emerging driverless vehicle applications. In order to overcome those problems, a new Extended Kalman Filter (EKF) and a multi-failure diagnosis algorithm are developed to process both GNSS pseudorange and carrier phase measurements. We first introduce a new closed-loop EKF with partial ambiguity resolution (PAR) as feedback to address the low accuracy issue. Then a multi-failure diagnosis algorithm is proposed to improve integrity and reliability. The core of this new algorithm includes using Carrier phase based Receiver Autonomous Integrity Monitoring (CRAIM) method for failure detection, and the double extended w-test detectors to identify failure. A cooperative positioning experiment was carried out to validate the proposed method. The results show that the proposed closed-loop EKF can provide highly accurate positioning, and the multi-failure diagnosis method is effective in detecting and identifying failures for both code and carrier phase measurements

Moderation of the Association between Media Exposure and Youth Smoking Onset: Race/Ethnicity, and Parent Smoking

This study of youth smoking onset aims to replicate previously published media moderation effects for race/ethnicity in a national longitudinal multiethnic sample of U.S. adolescents. Previous research has demonstrated that associations between media and smoking during adolescence are greater for Whites than Hispanics or Blacks, and for youth living in non-smoking families. In this study, changes in smoking status over 24 months were assessed among 4,511 baseline never-smokers. The incidence of smoking onset was 14.3% by 24 months with no differences by race/ethnicity. Blacks had higher exposure to movie smoking and overall television viewing compared with Whites and Hispanics. Whites responded to movie smoking regardless of parent smoking but more strongly if their parents were non-smokers. In contrast, Black adolescents showed little behavioral response to any media, regardless of parent smoking. Hispanic adolescents responded only to TV viewing and only when their parents did not smoke. In an analysis assessing the influence of the race of smoking characters on smoking behavior of White and Black adolescents, Whites responded to both White and Black movie character smoking, whereas Blacks responded only to smoking by Black movie characters. Taken as a whole, the findings replicate and extend previous findings, suggesting media factors are more influential among adolescents at low to moderate overall risk for smoking. We draw analogies between these low-moderate risk adolescents and “swing voters” in national elections, suggesting that media effects are more apt to influence an adolescent in the middle of the risk spectrum, compared with his peers at either end of it

Multiwavelength Observations of Pulsar Wind Nebulae

The extended nebulae formed as pulsar winds expand into their surroundings provide information about the composition of the winds, the injection history from the host pulsar, and the material into which the nebulae are expanding. Observations from across the electromagnetic spectrum provide constraints on the evolution of the nebulae, the density and composition of the surrounding ejecta, the geometry of the central engines, and the long-term fate of the energetic particles produced in these systems. Such observations reveal the presence of jets and wind termination shocks, time-varying compact emission structures, shocked supernova ejecta, and newly formed dust. Here I provide a broad overview of the structure of pulsar wind nebulae, with specific examples from observations extending from the radio band to very-high-energy gamma-rays that demonstrate our ability to constrain the history and ultimate fate of the energy released in the spin-down of young pulsars.Comment: 20 pages, 11 figures. Invited review to appear in Proc. of the inaugural ICREA Workshop on "The High-Energy Emission from Pulsars and their Systems" (2010), eds. N. Rea and D. Torres, (Springer Astrophysics and Space Science series

What motivates British parents to consent for research? A questionnaire study

BACKGROUND: Informed consent is the backbone of a clinical trial. In children this is given by their parents. There have been many studies in the neonatal population but little is known about the views of the parents of infants and young children from within the United Kingdom. The objectives of this study were to assess what motivates parents to consent to a randomised clinical trial (RCT), their feelings on consent and participation and the factors that would influence their decision to take part in a future study. METHODS: The setting was a multi-centre randomised but non-blinded equivalence trial of oral versus intravenous (IV) treatment for community acquired pneumonia in previously well children aged 6 months to 16 years in the UK (PIVOT Study). Parents were sent a postal questionnaire at the end of the study which included open and closed-ended questions. Fishers Exact Test was used to analyse associations in non parametric categorical data. RESULTS: 243 children were recruited into the PIVOT study. Of a possible 235, 136 questionnaires were returned (response rate 59%). Of those questionnaires returned; 98% of parents remembered consenting, 95% felt they were given enough time to make their decision and 96% felt they received enough information. Major reasons for participation were benefit to other children in the future 31%, contribution to science 27%, benefit to their own child 18%. Most parents (85%) did not feel obliged to participate. 62% felt there was an advantage to taking part and 18% felt there was a disadvantage. 91% of parents said they would take part in a similar study in the future, stating influences on their decision being benefit to their own child (91%) and benefit to all children (89%). CONCLUSION: The major motivation in parents consenting for their previously well child to participate in an RCT of therapy for an acute medical illness was to increase medical knowledge in the future. Most saw an advantage in taking part in the trial and did not feel obliged to participate

Why do women invest in pre-pregnancy health and care? A qualitative investigation with women attending maternity services

Background Despite the importance attributed to good pre-pregnancy care and its potential to improve pregnancy and child health outcomes, relatively little is known about why women invest in pre-pregnancy health and care. We sought to gain insight into why women invested in pre-pregnancy health and care. Methods We carried out 20 qualitative in-depth interviews with pregnant or recently pregnant women who were drawn from a survey of antenatal clinic attendees in London, UK. Interviewees were purposively sampled to include high and low investors in pre-pregnancy health and care, with variation in age, partnership status, ethnicity and pre-existing medical conditions. Data analysis was conducted using the Framework method. Results We identified three groups in relation to pre-pregnancy health and care: 1) The “prepared” group, who had high levels of pregnancy planning and mostly positive attitudes to micronutrient supplementation outside of pregnancy, carried out pre-pregnancy activities such as taking folic acid and making changes to diet and lifestyle. 2) The “poor knowledge” group, who also had high levels of pregnancy planning, did not carry out pre-pregnancy activities and described themselves as having poor knowledge. Elsewhere in their interviews they expressed a strong dislike of micronutrient supplementation. 3) The “absent pre-pregnancy period” group, had the lowest levels of pregnancy planning and also expressed anti-supplement views. Even discussing the pre-pregnancy period with this group was difficult as responses to questions quickly shifted to focus on pregnancy itself. Knowledge of folic acid was poor in all groups. Conclusion Different pre-pregnancy care approaches are likely to be needed for each of the groups. Among the “prepared” group, who were proactive and receptive to health messages, greater availability of information and better response from health professionals could improve the range of pre-pregnancy activities carried out. Among the “poor knowledge” group, better response from health professionals might yield greater uptake of pre-pregnancy information. A different, general health strategy might be more appropriate for the “absent pre-pregnancy period” group. The fact that general attitudes to micronutrient supplementation were closely related to whether or not women invested in pre-pregnancy health and care was an unanticipated finding and warrants further investigation.This report is independent research commissioned and funded by the Department of Health Policy Research Programme Pre-Pregnancy Health and Care in England: Exploring Implementation and Public Health Impact, 006/0068

Anthropometric indices of Gambian children after one or three annual rounds of mass drug administration with azithromycin for trachoma control.

BACKGROUND: Mass drug administration (MDA) with azithromycin, carried out for the control of blinding trachoma, has been linked to reduced mortality in children. While the mechanism behind this reduction is unclear, it may be due, in part, to improved nutritional status via a potential reduction in the community burden of infectious disease. To determine whether MDA with azithromycin improves anthropometric indices at the community level, we measured the heights and weights of children aged 1 to 4 years in communities where one (single MDA arm) or three annual rounds (annual MDA arm) of azithromycin had been distributed. METHODS: Data collection took place three years after treatment in the single MDA arm and one year after the final round of treatment in the annual MDA arm. Mean height-for-age, weight-for-age and weight-for-height z scores were compared between treatment arms. RESULTS: No significant differences in mean height-for-age, weight-for-age or weight-for-height z scores were found between the annual MDA and single MDA arms, nor was there a significant reduction in prevalence of stunting, wasting or underweight between arms. CONCLUSIONS: Our data do not provide evidence that community MDA with azithromycin improved anthropometric outcomes of children in The Gambia. This may suggest reductions in mortality associated with azithromycin MDA are due to a mechanism other than improved nutritional status

Transurethral resection of the prostate in Northern Nigeria, problems and prospects

<p>Abstract</p> <p>Background</p> <p>Benign prostatic hyperplasia (BPH) is the commonest disease of the urinary tract afflicting the ageing male and is the commonest neoplastic disease in men aged 50 years and above.</p> <p>Transurethral prostatectomy (TURP) is the ultimate treatment of choice for benign prostatic hyperplasia (BPH) due mainly to the preference of minimally invasive surgery, long term relief of symptoms and cost effectiveness. It is however not available to the majority of Nigerians in need of prostatic surgery in Public Health Institutions.</p> <p>Methods</p> <p>The records of patients who underwent prostatectomy in Aminu Kano Teaching Hospital, over the period June 2001 to July 2007 were examined. The bio data of patients and laboratory investigations performed were retrieved.</p> <p>Results</p> <p>Five Hundred and forty two patients were operated upon, out of which 40 were excluded due to open prostatectomy (22 patients), bladder neck stenosis (16 patients) or bladder tumour around the trigon (2 patients). The age range of the patients was 47–110 years with a mean of 67.2 years. 289 patients (80.1%) had urethral catheter in situ at presentation and 11 (3%) patients had suprapubic cystostomy of which only 3 (0.85%) had combined urethral stricture and BPH.</p> <p>Only 131 (26%) had their PSA measured which ranged from 2–100 ng/ml out of which 39(29.8% n = 131) patients had more than 4 ng/ml and cancer of the prostate and 1(0.8%, n = 131) patient had a PSA level of 4 ng/ml and malignant prostate.</p> <p>Hospital stay was 1–32 days (mean 7.9) and the mean follow up period was 5.6 months (range 0–60) and there were 17.5% complications comprising of urinary tract infection (UTI) 7.2%, Orchitis 2.2%, urinary incontinence 0.6%, atonic bladder 1%, erectile dysfunction 0.6%, cerebrovascular accident 0.4%, myocardial infarction 0.4%, deep vein thrombosis 0.4% and disseminated intravascular coagulopathy (DIC) 0.6% and 1.2% mortality. The cost of treatment inclusive of pre-admission investigations was US$615.00 (range US$ 300–1,300)</p> <p>Conclusion</p> <p>Despite advances in minimally invasive therapy for LUTH/BPH, TURP is the optimum treatment of choice for the ageing male of sub-Saharan Africa. It is however not available to the majority of patients in this region due to poor health allocation and inadequate facilities and training.</p

What motivates senior clinicians to teach medical students?

BACKGROUND: This study was designed to assess the motivations of senior medical clinicians to teach medical students. This understanding could improve the recruitment and retention of important clinical teachers. METHODS: The study group was 101 senior medical clinicians registered on a teaching list for a medical school teaching hospital (The Canberra Hospital, ACT, Australia). Their motivations to teach medical students were assessed applying Q methodology. RESULTS: Of the 75 participants, 18 (24%) were female and 57 (76%) were male. The age distribution was as follows: 30–40 years = 16 participants (21.3%), 41–55 years = 46 participants (61.3%) and >55 years = 13 participants (17.3%). Most participants (n = 48, 64%) were staff specialists and 27 (36%) were visiting medical officers. Half of the participants were internists (n = 39, 52%), 12 (16%) were surgeons, and 24 (32%) were other sub-specialists. Of the 26 senior clinicians that did not participate, two were women; 15 were visiting medical officers and 11 were staff specialists; 16 were internists, 9 were surgeons and there was one other sub-specialist. The majority of these non-participating clinicians fell in the 41–55 year age group. The participating clinicians were moderately homogenous in their responses. Factor analysis produced 4 factors: one summarising positive motivations for teaching and three capturing impediments for teaching. The main factors influencing motivation to teach medical students were intrinsic issues such as altruism, intellectual satisfaction, personal skills and truth seeking. The reasons for not teaching included no strong involvement in course design, a heavy clinical load or feeling it was a waste of time. CONCLUSION: This study provides some insights into factors that may be utilised in the design of teaching programs that meet teacher motivations and ultimately enhance the effectiveness of the medical teaching workforce

Accounting Problems Under the Excess Profits Tax

DNA vaccines based on subunits from pathogens have several advantages over other vaccine strategies. DNA vaccines can easily be modified, they show good safety profiles, are stable and inexpensive to produce, and the immune response can be focused to the antigen of interest. However, the immunogenicity of DNA vaccines which is generally quite low needs to be improved. Electroporation and co-delivery of genetically encoded immune adjuvants are two strategies aiming at increasing the efficacy of DNA vaccines. Here, we have examined whether targeting to antigen-presenting cells (APC) could increase the immune response to surface envelope glycoprotein (Env) gp120 from Human Immunodeficiency Virus type 1 (HIV- 1). To target APC, we utilized a homodimeric vaccine format denoted vaccibody, which enables covalent fusion of gp120 to molecules that can target APC. Two molecules were tested for their efficiency as targeting units: the antibody-derived single chain Fragment variable (scFv) specific for the major histocompatilibility complex (MHC) class II I-E molecules, and the CC chemokine ligand 3 (CCL3). The vaccines were delivered as DNA into muscle of mice with or without electroporation. Targeting of gp120 to MHC class II molecules induced antibodies that neutralized HIV-1 and that persisted for more than a year after one single immunization with electroporation. Targeting by CCL3 significantly increased the number of HIV-1 gp120-reactive CD8(+) T cells compared to non-targeted vaccines and gp120 delivered alone in the absence of electroporation. The data suggest that chemokines are promising molecular adjuvants because small amounts can attract immune cells and promote immune responses without advanced equipment such as electroporation.Funding Agencies|Research Council of Norway; Odd Fellow</p