Association of Rideshare Use With Alcohol-Associated Motor Vehicle Crash Trauma.

Importance: Motor vehicle crashes (MVCs) are an important public health concern. Recent trends suggest that introducing rideshare services has decreased the incidence of MVCs. However, detailed analyses linking rideshare volume, convictions for impaired driving, and nonfatal MVC traumas remain inconclusive.

CX, DPX, and PCW: Web Servers for the Visualization of Interior and Protruding Regions of Protein Structures in 3D and 1D.

The CX and DPX web-based servers at http://pongor.itk.ppke.

A Network-Based Target Overlap Score for Characterizing Drug Combinations: High Correlation with Cancer Clinical Trial Results.

Drug combinations are highly efficient in systemic treatment of complex multigene diseases such as cancer, diabetes, arthritis and hypertension. Most currently used combinations were found in empirical ways, which limits the speed of discovery for new and more effective combinations. Therefore, there is a substantial need for efficient and fast computational methods.

Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.

[Therapeutic strategies to increase the effectiveness of cough].

Cough is a natural reflex that protects respiratory airways against infections or mucus retention. Cough maintains an adequate cleaning of the airways and is a mainstay of respiratory therapy. It can be triggered voluntarily by the patient or by a specific cough device.

ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes.

The comQXPA locus of Bacillus subtilis encodes a quorum sensing (QS) system typical of Gram positive bacteria. It encodes four proteins, the ComQ isoprenyl transferase, the ComX pre-peptide signal, the ComP histidine kinase, and the ComA response regulator. These are encoded by four adjacent genes all situated on the same chromosome strand.

PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra.

Motivation: Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Algorithmic searches for PTMs from tandem mass spectrum data (MS/MS) tend to be hampered by noisy data as well as by a combinatorial explosion of search space. This leads to high uncertainty and long search-execution times.

JBioWH: an open-source Java framework for bioinformatics data integration.

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.

A parallel systematic-Monte Carlo algorithm for exploring conformational space.

Computational algorithms to explore the conformational space of small molecules are complex and computer demand field in chemoinformatics. In this paper a hybrid algorithm to explore the conformational space of organic molecules is presented. This hybrid algorithm is based in a systematic search approach combined with a Monte Carlo based method in order to obtain an ensemble of low-energy conformations simulating the flexibility of small chemical compounds.

In silico analysis of accurate proteomics, complemented by selective isolation of peptides.

Protein identification by mass spectrometry is mainly based on MS/MS spectra and the accuracy of molecular mass determination. However, the high complexity and dynamic ranges for any species of proteomic samples, surpass the separation capacity and detection power of the most advanced multidimensional liquid chromatographs and mass spectrometers. Only a tiny portion of signals is selected for MS/MS experiments and a still considerable number of them do not provide reliable peptide identification.

Impact of socioethnic factors on outcomes following traumatic brain injury.

Background: Ethnic minorities and low income families tend to be in poorer health and have worse outcomes for a spectrum of diseases. Health care provider bias has been reported to potentially affect the distribution of care away from poorer communities, minorities, and patients with a history of substance abuse. Trauma is perceived as a disease of the poor and medically underserved.

Evaluation of phenylthiocarbamoyl-derivatized peptides by electrospray ionization mass spectrometry: selective isolation and analysis of modified multiply charged peptides for liquid chromatography-tandem mass spectrometry experiments.

Edman degradation in the gas phase has been observed by collision activated dissociation of N-terminal phenylthiocarbamoyl (PTC) protonated peptide to yield abundant complementary b₁ and y(n-1) ion pairs. Here, we demonstrated the relation between the observed losses of aniline and/or the entire PTC derivatizing group with the availability of mobile protons using electrospray ionization mass spectrometry. In order to select the peptides with more efficient fragmentation, while simplifying the mixture of peptides, we extend the phenylisotiocyanate (PITC) derivatization of amino groups to the selective isolation of multiply charged peptides (those having the number of arginines and histidines residues higher than one) using a procedure previously developed in our group.