Phenotype Prediction Using Regularized Regression on Genetic Data in the DREAM5 Systems Genetics B Challenge

A major goal of large-scale genomics projects is to enable the use of data from high-throughput experimental methods to predict complex phenotypes such as disease susceptibility. The DREAM5 Systems Genetics B Challenge solicited algorithms to predict soybean plant resistance to the pathogen Phytophthora sojae from training sets including phenotype, genotype, and gene expression data. The challenge test set was divided into three subcategories, one requiring prediction based on only genotype data, another on only gene expression data, and the third on both genotype and gene expression data. Here we present our approach, primarily using regularized regression, which received the best-performer award for subchallenge B2 (gene expression only). We found that despite the availability of 941 genotype markers and 28,395 gene expression features, optimal models determined by cross-validation experiments typically used fewer than ten predictors, underscoring the importance of strong regularization in noisy datasets with far more features than samples. We also present substantial analysis of the training and test setup of the challenge, identifying high variance in performance on the gold standard test sets.National Science Foundation (U.S.). Graduate Research Fellowship ProgramNational Defense Science and Engineering Graduate Fellowshi

How are compassion fatigue, burnout, and compassion satisfaction affected by quality of working life? Findings from a survey of mental health staff in Italy

BACKGROUND: Quality of working life includes elements such as autonomy, trust, ergonomics, participation, job complexity, and work-life balance. The overarching aim of this study was to investigate if and how quality of working life affects Compassion Fatigue, Burnout, and Compassion Satisfaction among mental health practitioners. METHODS: Staff working in three Italian Mental Health Departments completed the Professional Quality of Life Scale, measuring Compassion Fatigue, Burnout, and Compassion Satisfaction, and the Quality of Working Life Questionnaire. The latter was used to collect socio-demographics, occupational characteristics and 13 indicators of quality of working life. Multiple regressions controlling for other variables were undertaken to predict Compassion Fatigue, Burnout, and Compassion Satisfaction. RESULTS: Four hundred questionnaires were completed. In bivariate analyses, experiencing more ergonomic problems, perceiving risks for the future, a higher impact of work on life, and lower levels of trust and of perceived quality of meetings were associated with poorer outcomes. Multivariate analysis showed that (a) ergonomic problems and impact of work on life predicted higher levels of both Compassion Fatigue and Burnout; (b) impact of life on work was associated with Compassion Fatigue and lower levels of trust and perceiving more risks for the future with Burnout only; (c) perceived quality of meetings, need of training, and perceiving no risks for the future predicted higher levels of Compassion Satisfaction. CONCLUSIONS: In order to provide adequate mental health services, service providers need to give their employees adequate ergonomic conditions, giving special attention to time pressures. Building trustful relationships with management and within the teams is also crucial. Training and meetings are other important targets for potential improvement. Additionally, insecurity about the future should be addressed as it can affect both Burnout and Compassion Satisfaction. Finally, strategies to reduce possible work-life conflicts need to be considered

Do serum biomarkers really measure breast cancer?

Background Because screening mammography for breast cancer is less effective for premenopausal women, we investigated the feasibility of a diagnostic blood test using serum proteins. Methods This study used a set of 98 serum proteins and chose diagnostically relevant subsets via various feature-selection techniques. Because of significant noise in the data set, we applied iterated Bayesian model averaging to account for model selection uncertainty and to improve generalization performance. We assessed generalization performance using leave-one-out cross-validation (LOOCV) and receiver operating characteristic (ROC) curve analysis. Results The classifiers were able to distinguish normal tissue from breast cancer with a classification performance of AUC = 0.82 ± 0.04 with the proteins MIF, MMP-9, and MPO. The classifiers distinguished normal tissue from benign lesions similarly at AUC = 0.80 ± 0.05. However, the serum proteins of benign and malignant lesions were indistinguishable (AUC = 0.55 ± 0.06). The classification tasks of normal vs. cancer and normal vs. benign selected the same top feature: MIF, which suggests that the biomarkers indicated inflammatory response rather than cancer. Conclusion Overall, the selected serum proteins showed moderate ability for detecting lesions. However, they are probably more indicative of secondary effects such as inflammation rather than specific for malignancy.United States. Dept. of Defense. Breast Cancer Research Program (Grant No. W81XWH-05-1-0292)National Institutes of Health (U.S.) (R01 CA-112437-01)National Institutes of Health (U.S.) (NIH CA 84955