Prediction of HLA class II alleles using SNPs in an African population

BACKGROUND: Despite the importance of the human leukocyte antigen (HLA) gene locus in research and clinical practice, direct HLA typing is laborious and expensive. Furthermore, the analysis requires specialized software and expertise which are unavailable in most developing country settings. Recently, in silico methods have been developed for predicting HLA alleles using single nucleotide polymorphisms (SNPs). However, the utility of these methods in African populations has not been systematically evaluated. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we investigate prediction of HLA class II (HLA-DRB1 and HLA-DQB1) alleles using SNPs in the Wolaita population, southern Ethiopia. The subjects comprised 297 Ethiopians with genome-wide SNP data, of whom 188 had also been HLA typed and were used for training and testing the model. The 109 subjects with SNP data alone were used for empirical prediction using the multi-allelic gene prediction method. We evaluated accuracy of the prediction, agreement between predicted and HLA typed alleles, and discriminative ability of the prediction probability supplied by the model. We found that the model predicted intermediate (two-digit) resolution for HLA-DRB1 and HLA-DQB1 alleles at accuracy levels of 96% and 87%, respectively. All measures of performance showed high accuracy and reliability for prediction. The distribution of the majority of HLA alleles in the study was similar to that previously reported for the Oromo and Amhara ethnic groups from Ethiopia. CONCLUSIONS/SIGNIFICANCE: We demonstrate that HLA class II alleles can be predicted from SNP genotype data with a high level of accuracy at intermediate (two-digit) resolution in an African population. This finding offers new opportunities for HLA studies of disease epidemiology and population genetics in developing countrie

The series Bi2Sr2Ca(n-1) Cu(n)O(2n+4) (1 less than or equal to n less than or equal to 5): Phase stability and superconducting properties

Phase relations at 850 and 870 C, melting transitions in air, oxygen, and helium were studied for Bi(2.1)Sr(1.9) CuO6 and for the Bi2Sr2Ca(n-1) Cu(n)O(2n+4) for n = 1, 2, 3, 4, 5, and infinity (CaCuO2). Up to 870 C, the n = 2 composition resides in the compatibility tetrahedron bounded by Bi(2+x)(Sr,Ca)(3-y) Cu2O8, (Sr,Ca)14 Cu24O41, Ca2CuO3, and a Bi-Sr-Ca-O phase. The n is greater than or equal to 3 compositions reside in the compatibility tetrahedron Bi(2+x)(Sr,Ca)(3-y) Cu2O8 - (Sr,Ca)14 Cu24O41 - Ca2CuO3 - CuO up to 850 C. However, Bi(2+x)Sr(4-y) Cu3O10 forms for n is greater than or equal to 3 after extended heating at 870 C. Bi(2+x)Sr(2-y) CuO6 and Bi(2+x)(Sr,Ca)(3-y) Cu2O8 melt in air at 914 C and 895 C respectively. During melting, all of the compositions studied lose 1 to 2 percent by weight of oxygen from the reduction of copper. Bi(2+x)Sr(2-y) CuO6, Bi(2+n)(Sr,Ca)(3-y) Cu2O8, and Bi(2+x)(Sr,Ca)(4-y) Cu3O10 exhibit crystallographic alignment in a magnetic field, with the c-axes orienting parallel to the field

Building Modern Cloud Accessible Tools for Materials Simulations

In recent years, commercial computer systems have grown more user friendly, allowing for new users to quickly and easily make contributions. Unfortunately, this trend is not as apparent in the field of computational materials simulations. The tools used by researchers in this field have remained just as esoteric as the systems of the past. While the methods used in materials simulations continue to grow in complexity and accuracy, the user experience has been neglected entirely. This project aims to eliminate the need for hours spent adjusting file formats and searching for preexisting code, and instead allow researchers to focus on analyzing outputs. Such an endeavor requires the use of online repositories, nanoHUB simulations, and various analysis tools demonstrating materials simulations and making use of molecular dynamics, density functional theory and continuum simulations. Given input files following current LAMMPS standards, this tool can calculate the Radial Distribution Function, X Ray Diffraction, and Vibrational Density of States of the system in question while anticipating issues that will lead to erroneous results. Rather than leaving the user to decide much of the fine customization that goes into these types of analysis, the tool implements a series of robust defaults that provide valid results for most systems. While the tool does not provide the user with This tool also offers a high degree of modularity, allowing for easy integration of additional analysis code

Fast Neutron Breeder

One of the fundamental reasons for developing methods of power generation utilizing nuclear fission as the heat source is to extend the world\u27s supply of energy resources beyond those available in the conventional fuels; coal, oil and gas. The only naturally occurring isotope which can sustain a chain reaction is U-235. In the fertile materials U-238 and Th-232, there is a possibility of magnifying the supply of nuclear energy by several orders of magnitude. In certain types of reactors, it is possible to produce more fissionable material than is consumed in the production of heat. This phenomenon is called breeding and is the main reason for the effort to develop fast reactors. It is the purpose of this paper to discuss some of the distinguishing characteristics of a fast reactor using as illustration the reactor being developed by Atomic Power Development Associates, Inc. (APDA) for construction by Power Reactor Development Corporation (PRDC) at the Enrico Fermi Atomic Power Plant near Monroe, Michigan

Barriers/Drivers of Diverse Perennial Systems: Policy Recommendations

Despite growing documentation of perennial- and grass-based systems’ importance in addressing many ecological, infrastructural, farmer profitability, and climate concerns, these systems do not predominate on most United States farm and ranch lands. To better understand what impedes their wider adoption, we undertook four focus groups of diverse current and potential farmers using perennial systems. We were especially interested in how these farmers access, or don’t, insurance, credit, and federal programs, identifying patterns among farmers embracing more sustainable practices. Our virtual focus groups comprised 16 farmers in ten states, transecting climate zones and representing both rural and urban production systems and diversity in ethnicity, gender, and farm size. We committed to maintaining participants’ anonymity and paid them a modest stipend. Some clear trends emerged as motivations for adopting perennial farming systems, including their ecosystem benefits to farms and to society, relative simplicity and ease of implementation, and lesser capital requirements for entry. Participants described numerous barriers to adoption, including woody perennials’ longer establishment period before becoming productive and cash-flow challenges during that period. Some farmers experienced a lack of understanding of perennials by federal agency staff and challenges accessing federal programs. Some desired easy-to-access support in navigating agency options and an easier process to appeal agency decisions. Many participants perceived perennials to be inherently risk-reducing, but few considered federal crop insurance useful. Similarly, challenges in accessing credit required many participants to self-finance or grow their operations slowly. Federal conservation programs had served some participants, but farmers of color reported difficulty in accessing them, partly due to agency staff’s restricted hours. Direct markets were easier for some perennial farmers, although time-consuming, but processing delays and impediments could be problematic, including for meat animals grown on managed pasture. Many farmers would profit from technical assistance and nationally-available reliable information on perennial production systems

Parental engagement in preventive parenting programs for child mental health: a systematic review of predictors and strategies to increase engagement

Background. Child mental health problems are now recognised as a key public health concern. Parenting programs have been developed as one solution to reduce children's risk of developing mental health problems. However, their potential for widespread dissemination is hindered by low parental engagement, which includes intent to enrol, enrolment, and attendance. To increase parental engagement in preventive parenting programs, we need a better understanding of the predictors of engagement, and the strategies that can be used to enhance engagement. Method. Employing a PRISMA method, we conducted a systematic review of the predictors of parent engagement and engagement enhancement strategies in preventive parenting programs. Key inclusion criteria included: (1) the intervention is directed primarily at the parent, (2) parent age >18 years, the article is (3) written in English and (4) published between 2004-2016, Stouffer's method of combining p-values was used to determine whether associations between variables were reliable. Results. Twenty-three articles reported a variety of predictors of parental engagement and engagement enhancement strategies. Only one of eleven predictors (child mental health symptoms) demonstrated a reliable association with enrolment (Stouffer's p < .01). Discussion. There was a lack of consistent evidence for predictors of parental engagement. Nonetheless, preliminary evidence suggests that engagement enhancement strategies modelled on theories, such as the Health Belief Model and Theory of Planned Behaviour, may increase parents' engagement

Identifying patients at risk of emergency admission for colorectal cancer.

BACKGROUND: Patients whose colorectal cancer is treated after an emergency admission tend to have late-stage cancer and a poor prognosis. We identified risk factors for an emergency admission by linking data from the National Bowel Cancer Audit (NBCA) and the English Hospital Episode Statistics (HES), an administrative database of all admissions to English National Health Service hospitals, which includes data on mode of admission. METHODS: We identified all adults included in the NBCA with a primary diagnosis of bowel cancer, excluding cancer of the appendix, between August 2007 and July 2011 whose record could be linked to HES. Multivariable logistic regression was used to estimate adjusted odds ratios (OR) for an emergency admission for colorectal cancer. All risk factors were adjusted for cancer site and calendar year. RESULTS: 97,909 adults were identified with a primary diagnosis of bowel cancer and 82,777 patients could be linked to HES. Patients who were older, female, of a non-white ethnic background, and more socioeconomically deprived, and those with dementia or cardiac, neurologic and liver disease had an increased risk of presenting as an emergency admission. The strongest risk factors were age (90 compared with 70 years: OR 2.99, 95% CI 2.84 to 3.15), dementia (OR 2.46, 2.18 to 2.79), and liver disease (OR 1.87, 1.69 to 2.08). CONCLUSIONS: Our study identifies risk factors that may impair health-seeking behaviour and access to healthcare. An earlier recognition of symptoms in patients with these risk factors may contribute to better outcomes