A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

The Patient Care Ownership Scale: External Validation of an Instrument that Measures Patient Care Ownership Among Internal Medicine Trainees—a Multi-Institutional Study

BackgroundPatient care ownership improves accountability, clinical skills, and quality of patient care among resident physicians, but appears to be gradually eroding. Research is limited by the lack of a reliable, objective measure of ownership.ObjectiveTo validate the Patient Care Ownership Scale, an instrument that measures decision ownership among internal medicine residents.DesignMulti-institutional, cross-sectional study using a 66-item, online survey that queried residents on ownership's key constructs (advocacy, responsibility, accountability, follow-through, knowledge, communication, initiative, continuity of care, autonomy, self-efficacy, and perceived ownership) as well as mood and burnout.ParticipantsInternal medicine residents in five geographically diverse residency programs completing an inpatient rotation.Main measuresWe performed exploratory and confirmatory factor analysis in two randomly split groups to evaluate for subscales and inform item reduction. We conducted reliability testing with Cronbach's α. We performed bivariate analyses to examine construct validity and identify correlates of ownership.Key resultsOf the 785 eligible residents, 625 completed the survey (80% response rate); we included responses from 563 in the analysis. We identified three factors corresponding to assertiveness, conscientiousness, and confidence or perceived competence. After iterative item reduction, the 13-item ownership scale demonstrated good reliability (Cronbach's α = 0.82). Convergent validity was supported by a significant association with perceived ownership (eliminated from the final scale) (r = 0.67, p < 0.001). There was a positive association between ownership and training level (p < 0.01) and prior experience in the intensive care unit (p < 0.001). There were significant, inverse relationships between ownership and self-defined burnout (r = - 0.24, p < 0.001), depression (r = - 0.22, p < 0.001), detachment (r = - 0.26, p < 0.001), and frustration (r = - 0.15, p = 0.02), and significant positive associations between ownership and feeling energetic (r = 0.29, p < 0.001), happy (r = 0.33, p < 0.001), and fulfilled (r = 0.34, p < 0.001).ConclusionsThe Patient Care Ownership Scale is valid in diverse residency program settings. Medical educators and investigators can use our scale to assess interventions aimed at fostering ownership

Comment On The Proposed Precedence Of The Specific Name Of Euphryne Obesus Baird, 1859 Over That Of Sauromalus Ater Dumeril, 1856

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Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer

Contains fulltext : 118378.pdf (publisher's version ) (Open Access)HNF1B is overexpressed in clear cell epithelial ovarian cancer, and we observed epigenetic silencing in serous epithelial ovarian cancer, leading us to hypothesize that variation in this gene differentially associates with epithelial ovarian cancer risk according to histological subtype. Here we comprehensively map variation in HNF1B with respect to epithelial ovarian cancer risk and analyse DNA methylation and expression profiles across histological subtypes. Different single-nucleotide polymorphisms associate with invasive serous (rs7405776 odds ratio (OR)=1.13, P=3.1 x 10(-10)) and clear cell (rs11651755 OR=0.77, P=1.6 x 10(-8)) epithelial ovarian cancer. Risk alleles for the serous subtype associate with higher HNF1B-promoter methylation in these tumours. Unmethylated, expressed HNF1B, primarily present in clear cell tumours, coincides with a CpG island methylator phenotype affecting numerous other promoters throughout the genome. Different variants in HNF1B associate with risk of serous and clear cell epithelial ovarian cancer; DNA methylation and expression patterns are also notably distinct between these subtypes. These findings underscore distinct mechanisms driving different epithelial ovarian cancer histological subtypes

A comparison of self-reported risk and protective factors and the death implicit association test in the prediction of future suicide attempts in adolescent emergency department patients

BackgroundConcerns have been raised about the utility of self-report assessments in predicting future suicide attempts. Clinicians in pediatric emergency departments (EDs) often are required to assess suicidal risk. The Death Implicit Association Test (IAT) is an alternative to self-report assessment of suicidal risk that may have utility in ED settings.MethodsA total of 1679 adolescents recruited from 13 pediatric emergency rooms in the Pediatric Emergency Care Applied Research Network were assessed using a self-report survey of risk and protective factors for a suicide attempt, and the IAT, and then followed up 3 months later to determine if an attempt had occurred. The accuracy of prediction was compared between self-reports and the IAT using the area under the curve (AUC) with respect to receiver operator characteristics.ResultsA few self-report variables, namely, current and past suicide ideation, past suicidal behavior, total negative life events, and school or social connectedness, predicted an attempt at 3 months with an AUC of 0.87 [95% confidence interval (CI), 0.84-0.90] in the entire sample, and AUC = 0.91, (95% CI 0.85-0.95) for those who presented without reported suicidal ideation. The IAT did not add significantly to the predictive power of selected self-report variables. The IAT alone was modestly predictive of 3-month attempts in the overall sample ((AUC = 0.59, 95% CI 0.52-0.65) and was a better predictor in patients who were non-suicidal at baseline (AUC = 0.67, 95% CI 0.55-0.79).ConclusionsIn pediatric EDs, a small set of self-reported items predicted suicide attempts within 3 months more accurately than did the IAT