Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling

Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler and illustrate its application to the bacteriophage PhiX174.Comment: 17 pages, 5 figure

Behavioral Health Integration in Primary Care

Behavioral Health Integration in Primary Care Casey Zapata, Depts. of Psychology and English, Demetrius Carter, & MaryKate Crawford, and Samantha Mladen, Emily Donovan, Amber Fox, & Kristen O’Loughlin, Dept. of Psychology Graduate Students, with Dr. Bruce Rybarczyk, Dept. of Psychology Background/Aims: Due to limited access to mental health care, many patients present to primary care with mental health concerns, such as depression and anxiety. Integrated primary care (IPC), an emerging practice model that integrates behavioral health providers with medical providers in primary care, has been demonstrated to improve patient outcomes. This project aims to characterize patients being seen in safety-net IPC, both demographically and clinically. Methods: The data were collected across three safety-net clinics in the Richmond area. The sample consisted of 96 adult patients: 68 female (71%), 24 male (25%), 1 non binary (1%), and 3 not collected (3%); 54 African-American (56%), 29 White (30%), 1 Asian (1%), 1 Other (1%), and 11 not collected (12%). Measures included a patient-completed checklist of patients’ behavioral health concerns, the PHQ-9 for depression, the GAD-7 for anxiety, and clinician-completed chart review for demographic factors. Results: Of the 72 patients who completed the GAD-7, patients reported 13 (18%) severe symptoms of anxiety, 11 (15%) moderate symptoms, 15 (21%) mild symptoms, and 33 (46%) subclinical symptoms. For the 37 patients who completed the PHQ-9, patients reported 7 (19%) severe depressive symptoms, 10 (27%) moderately severe symptoms, 12 (32%) moderate symptoms, 6 (16%) mild symptoms, and 2 (5%) subclinical symptoms. The six most commonly patient-reported problems were stress (n= 73), anxiety (n= 70), depression (n= 65), sleep (n = 55), grief (n = 53), and irritability (n= 53). When asked to rank their top three concerning problems, the five concerns most commonly ranked as top problems were: : (1) anxiety (n = 29), (2) stress (n = 28), (3) depression (n = 27), (4) sleep (n=16), and (5) weight (n=15). Further, 56 (58%) participants reported both depression and anxiety as among their top three concerns. Discussion: Anxiety and depression were reported by the majority of patients, with 33% experiencing at least moderate anxiety and 78% experiencing at least moderate depression. Additionally, anxiety and depression were cited as the third most commonly reported concerns, respectively, as well as ranked within the top three most concerning problems for most participants. Stress, anxiety, depression, and sleep were included in both the most commonly reported problems and the most common top three concerns of participants, suggesting that these concerns are both pervasive and troublesome for participants. Over time, this project will prioritize increasing sample size and tracking longitudinal trends. The continued study of safety-net IPC may allow for increasing access to behavioral health, identifying common behavioral health concerns in primary care, and meeting unmet patient needs.https://scholarscompass.vcu.edu/uresposters/1340/thumbnail.jp

Comparação de métodos para detecção de Ascochyta rabiei em sementes de grão - de - bico

Sautua, Francisco José. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal. Cátedra de Fitopatología. Buenos Aires, Argentina.Casey, Santiago Agustín. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal. Cátedra de Fitopatología. Buenos Aires, Argentina.Zapata, Raúl Lorenzo. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal. Cátedra de Fitopatología. Buenos Aires, Argentina.Scandiani, María Mercedes. Universidad Nacional de Rosario. Centro de Referencia de Micología (CEREMIC). Facultad de Ciencias Bioquímicas y Farmacéuticas. Rosario, Argentina.Carmona, Marcelo Aníbal. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal. Cátedra de Fitopatología. Buenos Aires, Argentina.197-199Seed health is one of the most important factors affecting the quality of chickpea (Cicer arietinum) seeds. The present study aimed to compare and identify the best incubation methods for detecting Ascochyta rabiei associated with chickpea seeds. Four protocols were compared for their sensitivity in detecting A. rabiei: T1) Incubation on paper substrate or filter paper method (blotter test) without surface disinfection, T2) Blotter test through the water restriction technique, T3) PDA plate test, and T4) MEA plate test. Four independent chickpea seed lots, naturally infected with A. rabiei, were sampled from Córdoba Province and other four were sampled from Buenos Aires Province, Argentina. Each treatment was applied to a total of 400 seeds from each locality for the methods to be comparable. T2 and T3 were statistically more sensitive in detecting A. rabiei-infected seeds from Córdoba. Only these two treatments were repeated for seeds from Buenos Aires Province, and T3 proved to be more sensitive; thus, it is recommended for routine sanitary analysis of chickpea seeds

Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups. There was, however, little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 29 siphonophore species analyzed in combination with 14 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose at least twice

Non-typeable Haemophilus influenzae and Streptococcus pneumoniae as primary causes of acute otitis media in colombian children: a prospective study

<p>Abstract</p> <p>Background</p> <p>Acute otitis media (AOM) is one of the most frequently encountered bacterial infections in children aged < 5 years; <it>Streptococcus pneumoniae </it>(<it>S. pneumoniae</it>) and non-typeable <it>Haemophilus influenzae </it>(NTHi) are historically identified as primary AOM causes. Nevertheless, recent data on bacterial pathogens causing AOM in Latin America are limited. This prospective study aimed to identify and characterize bacterial etiology and serotypes of AOM cases including antimicrobial susceptibility in < 5 year old Colombian children.</p> <p>Methods</p> <p>From February 2008 to January 2009, children ≥3 months and < 5 years of age presenting with AOM and for whom a middle ear fluid (MEF) sample was available were enrolled in two medical centers in Cali, Colombia. MEF samples were collected either by tympanocentesis procedure or spontaneous otorrhea swab sampling. Bacteria were identified using standard laboratory methods, and antimicrobial resistance testing was performed based on the 2009 Clinical and Laboratory Standards Institute (CLSI) criteria. Most of the cases included in the study were sporadic in nature.</p> <p>Results</p> <p>Of the 106 enrolled children, 99 were included in the analysis. Bacteria were cultured from 62/99 (63%) of samples with <it>S. pneumoniae, H. influenzae, or S. pyogenes</it>. The most commonly isolated bacteria were <it>H. influenzae </it>in 31/99 (31%) and <it>S. pneumoniae </it>in 30/99 (30%) of samples. The majority of <it>H. influenzae </it>episodes were NTHi (27/31; 87%). 19F was the most frequently isolated pneumococcal serotype (10/30; 33%). Of the 30 <it>S. pneumoniae </it>positive samples, 8/30 (27%) were resistant to tetracycline, 5/30 (17%) to erythromycin and 8/30 (27%) had intermediate resistance to penicillin. All <it>H. influenzae </it>isolates tested were negative to beta-lactamase.</p> <p>Conclusions</p> <p>NTHi and <it>S. pneumoniae </it>are the leading causes of AOM in Colombian children. A pneumococcal conjugate vaccine that prevents both pathogens could be useful in maximizing protection against AOM.</p

Measuring the health-related Sustainable Development Goals in 188 countries: a baseline analysis from the Global Burden of Disease Study 2015

BACKGROUND: In September, 2015, the UN General Assembly established the Sustainable Development Goals (SDGs). The SDGs specify 17 universal goals, 169 targets, and 230 indicators leading up to 2030 ..

Acute D3 Antagonist GSK598809 Selectively Enhances Neural Response During Monetary Reward Anticipation in Drug and Alcohol Dependence.

Evidence suggests that disturbances in neurobiological mechanisms of reward and inhibitory control maintain addiction and provoke relapse during abstinence. Abnormalities within the dopamine system may contribute to these disturbances and pharmacologically targeting the D3 dopamine receptor (DRD3) is therefore of significant clinical interest. We used functional magnetic resonance imaging to investigate the acute effects of the DRD3 antagonist GSK598809 on anticipatory reward processing, using the monetary incentive delay task (MIDT), and response inhibition using the Go/No-Go task (GNGT). A double-blind, placebo-controlled, crossover design approach was used in abstinent alcohol dependent, abstinent poly-drug dependent and healthy control volunteers. For the MIDT, there was evidence of blunted ventral striatal response to reward in the poly-drug-dependent group under placebo. GSK598809 normalized ventral striatal reward response and enhanced response in the DRD3-rich regions of the ventral pallidum and substantia nigra. Exploratory investigations suggested that the effects of GSK598809 were mainly driven by those with primary dependence on alcohol but not on opiates. Taken together, these findings suggest that GSK598809 may remediate reward deficits in substance dependence. For the GNGT, enhanced response in the inferior frontal cortex of the poly-drug group was found. However, there were no effects of GSK598809 on the neural network underlying response inhibition nor were there any behavioral drug effects on response inhibition. GSK598809 modulated the neural network underlying reward anticipation but not response inhibition, suggesting that DRD3 antagonists may restore reward deficits in addiction.The research was carried out at the NIHR/Wellcome Trust Imperial Clinical Research Facility, the NIHR/Wellcome Trust Cambridge Research Facility and Clinical Trials Unit at Salford Royal NHS Foundation Trust, and is supported by the North West London, Eastern and Greater Manchester NIHR Clinical Research Networks

Nutritionally Enhanced Staple Food Crops

Crop biofortification is a sustainable and cost-effective strategy to address malnutrition in developing countries. This review synthesizes the progress toward developing seed micronutrient-dense cereals and legumes cultivars by exploiting natural genetic variation using conventional breeding and/or transgenic technology, and discusses the associated issues to strengthen crop biofortification research and development. Some major QTL for seed iron and zinc, seed phosphorus, and seed phytate in common bean, rice,J;md wheat have been mapped. An iron reductase QTL associated with seed-iron ~QTL is found in common bean where the genes coding for candidate enzymes involved in phytic acid synthesis have also been mapped. Candidate genes for Ipa co segregate with mutant phenotypes identified in rice and soybean. The Gpe-B1 locus in wild emmer wheat accelerates senescence and increases nutrient remobilization from leaves to developing seeds, and another gene named TtNAM-B1 affecting these traits has been cloned. Seed iron-dense common bean and rice in Latin America; seed iron-dense common bean in eastern and southern Africa;....

Healthcare Access and Quality Index based on mortality from causes amenable to personal health care in 195 countries and territories, 1990-2015 : a novel analysis from the Global Burden of Disease Study 2015

Background National levels of personal health-care access and quality can be approximated by measuring mortality rates from causes that should not be fatal in the presence of effective medical care (ie, amenable mortality). Previous analyses of mortality amenable to health care only focused on high-income countries and faced several methodological challenges. In the present analysis, we use the highly standardised cause of death and risk factor estimates generated through the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) to improve and expand the quantification of personal health-care access and quality for 195 countries and territories from 1990 to 2015. Methods We mapped the most widely used list of causes amenable to personal health care developed by Nolte and McKee to 32 GBD causes. We accounted for variations in cause of death certification and misclassifications through the extensive data standardisation processes and redistribution algorithms developed for GBD. To isolate the effects of personal health-care access and quality, we risk-standardised cause-specific mortality rates for each geography-year by removing the joint effects of local environmental and behavioural risks, and adding back the global levels of risk exposure as estimated for GBD 2015. We employed principal component analysis to create a single, interpretable summary measure-the Healthcare Quality and Access (HAQ) Index-on a scale of 0 to 100. The HAQ Index showed strong convergence validity as compared with other health-system indicators, including health expenditure per capita (r= 0.88), an index of 11 universal health coverage interventions (r= 0.83), and human resources for health per 1000 (r= 0.77). We used free disposal hull analysis with bootstrapping to produce a frontier based on the relationship between the HAQ Index and the Socio-demographic Index (SDI), a measure of overall development consisting of income per capita, average years of education, and total fertility rates. This frontier allowed us to better quantify the maximum levels of personal health-care access and quality achieved across the development spectrum, and pinpoint geographies where gaps between observed and potential levels have narrowed or widened over time. Findings Between 1990 and 2015, nearly all countries and territories saw their HAQ Index values improve; nonetheless, the difference between the highest and lowest observed HAQ Index was larger in 2015 than in 1990, ranging from 28.6 to 94.6. Of 195 geographies, 167 had statistically significant increases in HAQ Index levels since 1990, with South Korea, Turkey, Peru, China, and the Maldives recording among the largest gains by 2015. Performance on the HAQ Index and individual causes showed distinct patterns by region and level of development, yet substantial heterogeneities emerged for several causes, including cancers in highest-SDI countries; chronic kidney disease, diabetes, diarrhoeal diseases, and lower respiratory infections among middle-SDI countries; and measles and tetanus among lowest-SDI countries. While the global HAQ Index average rose from 40.7 (95% uncertainty interval, 39.0-42.8) in 1990 to 53.7 (52.2-55.4) in 2015, far less progress occurred in narrowing the gap between observed HAQ Index values and maximum levels achieved; at the global level, the difference between the observed and frontier HAQ Index only decreased from 21.2 in 1990 to 20.1 in 2015. If every country and territory had achieved the highest observed HAQ Index by their corresponding level of SDI, the global average would have been 73.8 in 2015. Several countries, particularly in eastern and western sub-Saharan Africa, reached HAQ Index values similar to or beyond their development levels, whereas others, namely in southern sub-Saharan Africa, the Middle East, and south Asia, lagged behind what geographies of similar development attained between 1990 and 2015. Interpretation This novel extension of the GBD Study shows the untapped potential for personal health-care access and quality improvement across the development spectrum. Amid substantive advances in personal health care at the national level, heterogeneous patterns for individual causes in given countries or territories suggest that few places have consistently achieved optimal health-care access and quality across health-system functions and therapeutic areas. This is especially evident in middle-SDI countries, many of which have recently undergone or are currently experiencing epidemiological transitions. The HAQ Index, if paired with other measures of health-systemcharacteristics such as intervention coverage, could provide a robust avenue for tracking progress on universal health coverage and identifying local priorities for strengthening personal health-care quality and access throughout the world. Copyright (C) The Author(s). Published by Elsevier Ltd.Peer reviewe