The BioGRID Interaction Database: 2011 update

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions

Concept for Predicting Vibrations in Machine Tools Using Machine Learning

Vibrations have a significant influence on quality and costs in metal cutting processes. Existing methods for predicting vibrations in machine tools enable an informed choice of process settings, however they rely on costly equipment and specialised staff. Therefore, this contribution proposes to reduce the modelling effort required by using machine learning based on data gathered during production. The approach relies on two sub-models, representing the machine structure and machining process respectively. A method is proposed for initialising and updating the models in production

Gut-derived short-chain fatty acids modulate skin barrier integrity by promoting keratinocyte metabolism and differentiation

Barrier integrity is central to the maintenance of healthy immunological homeostasis. Impaired skin barrier function is linked with enhanced allergen sensitization and the development of diseases such as atopic dermatitis (AD), which can precede the development of other allergic disorders, for example, food allergies and asthma. Epidemiological evidence indicates that children suffering from allergies have lower levels of dietary fibre-derived short-chain fatty acids (SCFA). Using an experimental model of AD-like skin inflammation, we report that a fermentable fibre-rich diet alleviates systemic allergen sensitization and disease severity. The gut-skin axis underpins this phenomenon through SCFA production, particularly butyrate, which strengthens skin barrier function by altering mitochondrial metabolism of epidermal keratinocytes and the production of key structural components. Our results demonstrate that dietary fibre and SCFA improve epidermal barrier integrity, ultimately limiting early allergen sensitization and disease development. The Graphical Abstract was designed using Servier Medical Art images (https://smart.servier.com). [Image: see text

Does oral sodium bicarbonate therapy improve function and quality of life in older patients with chronic kidney disease and low-grade acidosis (the BiCARB trial)? Study protocol for a randomized controlled trial

Date of acceptance: 01/07/2015 © 2015 Witham et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Acknowledgements UK NIHR HTA grant 10/71/01. We acknowledge the financial support of NHS Research Scotland in conducting this trial.Peer reviewedPublisher PD

Yersinia pseudotuberculosis serotype O : 1 infection in a captive Seba's short tailed-fruit bat (Carollia perspicillata) colony in Switzerland

BackgroundBetween February and April 2016, a slight increase in mortality was observed in a colony consisting of 400 captive Seba's short-tailed bats (Carollia perspicillata). These animals cohabited with other nocturnal animal species in a dome of a private zoo in Switzerland.ResultsGross and histological analysis of two (14.3%) out of the 13 animals submitted for necropsy within this period revealed a necrosuppurative pneumonia, hepatitis, splenitis, enterocolitis, and endometritis, with abundant intralesional colonies of Gram-negative rods. Yersinia (Y.) pseudotuberculosis serotype O:1 and biotype 1 belonging to the sequence type ST90 was isolated from the affected organs in both animals. Following this diagnosis, 1/4 of the colony (99 animals) was culled and submitted for gross and histopathological analysis, and a bacterial culture selective for Yersinia spp. of lung, liver, and spleen was performed. From these 99 animals, one gravid female was tested and found to be positive for Y. pseudotuberculosis in the absence of clinical symptoms and histopathological lesions. PCR analysis of altogether three bacterial isolates for virulence factors revealed the presence of the ail gene, and one isolate was also positive for the virF and yadA plasmid genes.ConclusionsThese findings suggest that Carollia perspicillata are susceptible to lethal yersiniosis but do not represent a regular reservoir for Y. pseudotuberculosis. Culling of 1/4 of the population was sufficient to limit the spread of this infection among the colony. Moreover, no infections were detected in cohabitant nocturnal animals and caretakers, indicating that the zoonotic risk in this case was low.Peer reviewe