Diversity starts early: notharctid primates from the Sandcouleean (Early Eocene) of the Powder River Basin, Wyoming, USA

<p>Abundant specimens, mostly isolated teeth, of the Primate family Notharctidae occur in the Early Eocene rocks of the Powder River Basin of northeastern Wyoming, USA. Very early in the North American history of the family, the notharctid species diversified and this diversity may have been widespread, and not restricted to more southerly areas in the Rocky Mountains. The diversity is shown by detailed analysis of the molar dentition. Two new genera are established: <i>Megaceralemur</i> with <i>Megaceralemur trigonodus</i> as its type and <i>Megaceralemur matthewi</i> <b>sp. nov</b><i>.</i> as a Sandcouleean species and <i>Pinolophus,</i> with <i>Pinolophus meikei</i> <b>sp. nov</b>. as its type, for a form with an entoconid notch on lower molar 1. <i>Megaceralemur</i> has a prominent nannopithex-fold which dominates the posterior cingulum of upper molars 1–2 and a cristid obliqua on lower molar 1 which attaches to the metaconid, not the metalophid as it does in <i>Cantius</i> and other genera. A small species, <i>Cantius lohseorum</i> <b>sp. nov.</b>, is named for a derived lineage the size of <i>Cantius torresi</i>.</p> <p>urn:lsid:zoobank.org:pub:066DC515-A2DD-40AF-AD8A-3834E2AFD0FB</p

Additional file 5 of Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods

Prediction of Human Phenotype Ontology terms: detailed experimental results using UA integrated network. (PDF 92.3 kb

Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants - Supplementary Information

This is the Supplementary information of the paper:<br>M. Schubach, M. Re, P.N. Robinson and G. Valentini <a href="http://dx.doi.org/10.1038/s41598-017-03011-5" target="_blank"> Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants</a>, <br> <i>Scientific Reports, Nature Publishing</i>, 7:2959, 201

Additional file 1 of Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

Supplementary figures and tables. The following additional data are available with the online version of this paper. Additional data file 1 contains an explanatory figure for duplication levels as well as figures and tables for additional analyses including duplication rate plots, examples for mapping artifacts, 5’ end coverage around motif centered binding sites, cross-correlation plots, qfrag-length distributions, scatterplots of signal scores of overlapping peaks and corresponding IDR plots, as well as two tables containing the total numbers of overlapping peaks and overlapping peaks with IDR ≤ 0.01 for all pairs of biological replicates. (PDF 3840 kb

Additional file 1 of Alternate-locus aware variant calling in whole genome sequencing

Online supplemental material. A file with 26 figures, five tables, and two algorithms. (PDF 24300 kb

Table_1_Advances in risk predictive performance of pre-symptomatic type 1 diabetes via the multiplex Antibody-Detection-by-Agglutination-PCR assay.xlsx

IntroductionAchieving early diagnosis of pre-symptomatic type 1 diabetes is critical to reduce potentially life-threatening diabetic ketoacidosis (DKA) at symptom onset, link patients to FDA approved therapeutics that can delay disease progression and support novel interventional drugs development. The presence of two or more islet autoantibodies in pre-symptomatic type 1 diabetes patients indicates high-risk of progression to clinical manifestation.MethodHerein, we characterized the capability of multiplex ADAP assay to predict type 1 diabetes progression. We obtained retrospective coded sera from a cohort of 48 progressors and 44 non-progressors from the NIDDK DPT-1 study.ResultThe multiplex ADAP assay and radiobinding assays had positive predictive value (PPV)/negative predictive value (NPV) of 68%/92% and 67%/66% respectively. The improved NPV stemmed from 12 progressors tested positive for multiple islet autoantibodies by multiplex ADAP assay but not by RBA. Furthermore, 6 out of these 12 patients tested positive for multiple islet autoantibodies by RBA in subsequent sampling events with a median delay of 2.8 years compared to multiplex ADAP assay.DiscussionIn summary, multiplex ADAP assay could be an ideal tool for type 1 diabetes risk testing due to its sample-sparing nature (4µL), non-radioactiveness, compatibility with widely available real-time qPCR instruments and favorable risk prediction capability.</p

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns

Poster presentation at the International Conference on Biomedical Ontology (ICBO) 2017, Newcastle, UK

Deep phenotyping for patients by patients: a lay-friendly version of the Human Phenotype Ontology

<div>The Human Phenotype Ontology (HPO) has become the de facto standard representation of clinical “deep phenotype” data for computational comparison of abnormalities and for use in genetic disease diagnostics. The HPO enables non-exact matching of sets of phenotypic features (phenotype profile) against known diseases, other patients, and model organisms. The algorithms have been implemented into many variant prioritization tools and are used by the 100,000 Genomes project, the NIH Undiagnosed Diseases Program/Network, and thousands of other clinics, labs, tools, and databases. </div><div><br></div><div>Patients themselves are an eager and untapped source of accurate information about symptoms and phenotypes - some of which may go unnoticed by the clinician. However, medical terminology is often perplexing to patients, making it difficult to use resources like the HPO. Here, we systematically added layperson synonyms with approximately 60% being translatable into layperson terminology. Analyses suggest that the lay-HPO has the features required to be useful in a diagnostic setting, in that lay terms are: a) sufficiently specific and, b) well-represented in our disease-to-phenotype database that is utilized by the aforementioned tools for differential diagnostics. A new patient-centered tool aims to help patients assist clinicians in creating robust computational phenotype profiles to improve molecular diagnostic rates and be active participants in their diagnostic odysseys. </div

Request for Community partnership in data resource licensing planning

<p>We write an open letter to the NIH Data Research Council to initiate a dialog regarding NIH decisions on data use agreements and licenses. We are members of NIH-funded research groups that collect and/or integrate biomedical data from diverse sources for the purpose of advancing diagnosis, prognosis, treatment selection, and mechanistic discovery. </p><p><br></p><p>We welcome additional signatories here:</p><p>https://docs.google.com/document/d/1fbwKxnPu5f1YXlMM6UMyfBqHx_Inz86tKzwRFO4W8jQ<br></p><br><p>Summary:</p><br><ul><li><p>The current diversity of data use agreements and licenses significantly hampers the ability to reuse and redistribute data in various informatics contexts.</p></li><li><p>We believe that any mandatory data licensing policy must also include a plan for ensuring access, sustainability, and data quality. </p></li><li><p>We request community partnership with NIH to develop common licensing and data reuse plans. </p></li></ul