R|S Atlas: Identifying existing cohort study data resources to accelerate epidemiological research on the influence of religion and spirituality on human health.

Objective: Many studies have documented significant associations between religion and spirituality (R/S) and health, but relatively few prospective analyses exist that can support causal inferences. To date, there has been no systematic analysis of R/S survey items collected in US cohort studies. We conducted a systematic content analysis of all surveys ever fielded in 20 diverse US cohort studies funded by the National Institutes of Health (NIH) to identify all R/S-related items collected from each cohort's baseline survey through 2014.

Measuring health-care delays among privately insured patients with tuberculosis in the USA: an observational cohort study.

Background: A high index of suspicion is needed to initiate appropriate testing for tuberculosis due to its protean symptoms, yet health-care providers in low-incidence settings are becoming less familiar with the disease as rates decline. We aimed to estimate delays in tuberculosis diagnosis and treatment at the US national level between 2008 and 2016.

Methods: In this retrospective observational cohort study, we repurposed private insurance claims data provided by Aetna (Connecticut, USA), to measure health-care delays in tuberculosis diagnosis in the USA in 2008-16.

A Semi-Automated Approach for Multilingual Terminology Matching: Mapping the French Version of the ICD-10 to the ICD-10 CM.

The aim of this study was to develop a simple method to map the French International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) with the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10 CM). We sought to map these terminologies forward (ICD-10 to ICD-10 CM) and backward (ICD-10 CM to ICD-10) and to assess the accuracy of these two mappings. We used several terminology resources such as the Unified Medical Language System (UMLS) Metathesaurus, Bioportal, the latest version available of the French ICD-10 and several official mapping files between different versions of the ICD-10.

Combining clinical and genomics queries using i2b2 - Three methods.

We are fortunate to be living in an era of twin biomedical data surges: a burgeoning representation of human phenotypes in the medical records of our healthcare systems, and high-throughput sequencing making rapid technological advances. The difficulty representing genomic data and its annotations has almost by itself led to the recognition of a biomedical "Big Data" challenge, and the complexity of healthcare data only compounds the problem to the point that coherent representation of both systems on the same platform seems insuperably difficult. We investigated the capability for complex, integrative genomic and clinical queries to be supported in the Informatics for Integrating Biology and the Bedside (i2b2) translational software package.

A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey.

The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly available in hundreds of files. This Data Descriptor describes a single unified and universally accessible data file, merging across 255 separate files and stitching data across 4 surveys, encompassing 41,474 individuals and 1,191 variables. The variables consist of phenotype and environmental exposure information on each individual, specifically (1) demographic information, physical exam results (e.

PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

Background: Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted.

tranSMART: An Open Source Knowledge Management and High Content Data Analytics Platform.

The tranSMART knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. tranSMART bridges the prolific world of basic science and clinical practice data at the point of care by merging multiple types of data from disparate sources into a common environment.

A web server for inferring the human N-acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype.

Unlabelled: N-acetyltransferase-2 (NAT2) is an important enzyme that catalyzes the acetylation of aromatic and heterocyclic amine carcinogens. Individuals in human populations are divided into three NAT2 acetylator phenotypes: slow, rapid and intermediate. NAT2PRED is a web server that implements a supervised pattern recognition method to infer NAT2 phenotype from SNPs found in NAT2 gene positions 282, 341, 481, 590, 803 and 857.

FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins.

Unlabelled: Conformational switches observed in the protein backbone play a key role in a variety of fundamental biological activities. This paper describes a web-server that implements a pattern recognition algorithm trained on the examples from the Database of Macromolecular Movements to predict residue positions involved in conformational switches. Prediction can be performed at an adjustable false positive rate using a user-supplied protein sequence in FASTA format or a structure in a Protein Data Bank (PDB) file.