2,414 research outputs found

    Pathway-Based Genomics Prediction using Generalized Elastic Net.

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    We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach

    Associations of Adiponectin with Adiposity, Insulin Sensitivity, and Diet in Young, Healthy, Mexican Americans and Non-Latino White Adults.

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    Low circulating adiponectin levels may contribute to higher diabetes risk among Mexican Americans (MA) compared to non-Latino whites (NLW). Our objective was to determine if among young healthy adult MAs have lower adiponectin than NLWs, independent of differences in adiposity. In addition, we explored associations between adiponectin and diet. This was an observational, cross-sectional study of healthy MA and NLW adults living in Colorado (U.S.A.). We measured plasma total adiponectin, adiposity (BMI, and visceral adipose tissue), insulin sensitivity (IVGTT), and self-reported dietary intake in 43 MA and NLW adults. Mean adiponectin levels were 40% lower among MA than NLW (5.8 ± 3.3 vs. 10.7 ± 4.2 µg/mL, p = 0.0003), and this difference persisted after controlling for age, sex, BMI, and visceral adiposity. Lower adiponectin in MA was associated with lower insulin sensitivity (R² = 0.42, p < 0.01). Lower adiponectin was also associated with higher dietary glycemic index, lower intake of vegetables, higher intake of trans fat, and higher intake of grains. Our findings confirm that ethnic differences in adiponectin reflect differences in insulin sensitivity, but suggest that these are not due to differences in adiposity. Observed associations between adiponectin and diet support the need for future studies exploring the regulation of adiponectin by diet and other environmental factors

    Ten Years after 9/11: The Changing Terrorist Threat

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    Panel 3: Emerging Issues in Competition Law and Health Care

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    Supervised and unsupervised language modelling in Chest X-Ray radiological reports

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    Chest radiography (CXR) is the most commonly used imaging modality and deep neural network (DNN) algorithms have shown promise in effective triage of normal and abnormal radiograms. Typically, DNNs require large quantities of expertly labelled training exemplars, which in clinical contexts is a major bottleneck to effective modelling, as both considerable clinical skill and time is required to produce high-quality ground truths. In this work we evaluate thirteen supervised classifiers using two large free-text corpora and demonstrate that bi-directional long short-term memory (BiLSTM) networks with attention mechanism effectively identify Normal, Abnormal, and Unclear CXR reports in internal (n = 965 manually-labelled reports, f1-score = 0.94) and external (n = 465 manually-labelled reports, f1-score = 0.90) testing sets using a relatively small number of expert-labelled training observations (n = 3,856 annotated reports). Furthermore, we introduce a general unsupervised approach that accurately distinguishes Normal and Abnormal CXR reports in a large unlabelled corpus. We anticipate that the results presented in this work can be used to automatically extract standardized clinical information from free-text CXR radiological reports, facilitating the training of clinical decision support systems for CXR triage
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