How to Use Biomechanical Job Exposure Matrices with Job History to Access Work Exposure for Musculoskeletal Disorders? Application of Mathematical Modeling in Severe Knee Pain in the Constances Cohort.

INTRODUCTION: Musculoskeletal disorders related to work might be caused by the cumulative effect of occupational exposures during working life. We aimed to develop a new model which allows to compare the accuracy of duration of work and intensity/frequency associations in application to severe knee pain. METHODS: From the CONSTANCES cohort, 62,620 subjects who were working at inclusion and coded were included in the study. The biomechanical job exposure matrix "JEM Constances" was used to assess the intensity/frequency of heavy lifting and kneeling/squatting at work together with work history to characterize the association between occupational exposure and severe knee pain. An innovative model G was developed and evaluated, allowing to compare the accuracy of duration of work and intensity/frequency associations. RESULTS: The mean age was 49 years at inception with 46 percent of women. The G model developed was slightly better than regular models. Among the men subgroup, odds ratios of the highest quartile for the duration and low intensity were not significant for both exposures, whereas intensity/duration were for every duration. Results in women were less interpretable. CONCLUSIONS: Though higher duration increased strength of association with severe knee pain, intensity/frequency were important predictors among men. Exposure estimation along working history should have emphasis on such parameters, though other outcomes should be studied and have a focus on women.

ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra.

MOTIVATION: In metabolomics, the detection of new biomarkers from Nuclear Magnetic Resonance (NMR) spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses, in a reproducible way. RESULTS: We present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments. It contains an automatic approach to identify and quantify metabolites in a complex mixture spectrum and uses the results of the quantification in untargeted and targeted statistical analyses. ASICS was shown to improve the precision of quantification in comparison to existing methods on two independent datasets. In addition, ASICS successfully recovered most metabolites that were found important to explain a two level condition describing the samples by a manual and expert analysis based on bucketing. It also found new relevant metabolites involved in metabolic pathways related to risk factors associated with the condition. AVAILABILITY AND IMPLEMENTATION: ASICS is distributed as an R package, available on Bioconductor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics.

Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows.