Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinfor- maticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this `up-to- dateness' came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities.We show that the performance of Biblio- MetReS in identifying gene co-occurrence is as least as good as that of other com- parable applications (STRING and iHOP). In addition, we also show that the iden- tification of GO processes is on par to that reported in the latest BioCreAtIvE chal- lenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from docu- ments that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains `up-to-dateness' of the results.RA was partially supported by the Ministerio de Ciencia e Innovación (MICINN, Spain through grant BFU2010-17704). FS was partially funded by the MICINN, with grants TIN2011-28689-C02-02. The authors are members of the research groups 2009SGR809 and 2009SGR145, funded by the “Generalitat de Catalunya”. AU is funded by a Generalitat de Catalunya (AGAUR) PhD fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Biblio-MetReS: A bibliometric network reconstruction application and server

<p>Abstract</p> <p>Background</p> <p>Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow <b>expert </b>users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no <b>user friendly </b>tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available.</p> <p>Results</p> <p>This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document.</p> <p>Conclusions</p> <p>Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio-MetReS is an application that can be downloaded from <url>http://metres.udl.cat/</url>. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.</p

Nivelación hidrostática entre dos mareógrafos situados en el Puerto de Barcelona

Este estudio pretende relacionar los registros (marzo de 2013 a febrero de 2014) de dos mareógrafos situados en el Puerto de Barcelona y que se han denominado BCN2 y BCN3. El mareógrafo BCN2 pertenece a la RED de MAReógrafos de Puertos del Estado (REDMAR) y refiere los datos al NMMA1995 mientras que BCN3, propiedad de la Autoridad Portuaria de Barcelona, los refiere a la Red Topográfica del Puerto de Barcelona observada mediante técnicas GNSS. Ambos mareógrafos están separados unos 3Km. en línea recta y unos 8Km. por tierra. El objetivo ha sido determinar la diferencia existente entre los ceros de referencia de los dos mareógrafos. El nivel de mar observado por los mareógrafos, sin tener en cuenta la acción del oleaje, está afectado por la marea astronómica y la marea meteorológica. La marea meteorológica es de tipo aleatorio, por el contrario la marea astronómica es de carácter determinista y se puede resolver realizando el análisis de armónicos. Para ello, una vez realizado el control de calidad de los datos brutos, se utilizó la aplicación T_TIDE en MATLAB obteniendo como resultado para cada mareógrafo tres gráficas y dos ficheros. Las gráficas representan respectivamente el nivel del mar observado, la marea astronómica y la meteorológica o residuo y de los dos ficheros, uno corresponde al cálculo de los componentes armónicos, del que nos interesa la componente Z0 (nivel medio del mar) y el segundo contiene la componente meteorológica. Se puede concluir en que el cero de referencia de BCN3 está situado 0,096 metros por encima del NMMA 1995.Peer ReviewedPostprint (published version

Allopurinol blocks aortic aneurysm in a mouse model of Marfan syndrome via reducing aortic oxidative stress

Background Increasing evidence indicates that redox stress participates in MFS aortopathy, though its mechanistic contribution is little known. We reported elevated reactive oxygen species (ROS) formation and NADPH oxidase NOX4 upregulation in MFS patients and mouse aortae. Here we address the contribution of xanthine oxidoreductase (XOR), which catabolizes purines into uric acid and ROS in MFS aortopathy. Methods and results In aortic samples from MFS patients, XOR protein expression, revealed by immunohistochemistry, increased in both the tunicae intima and media of the dilated zone. In MFS mice (Fbn1C1041G/+), aortic XOR mRNA transcripts and enzymatic activity of the oxidase form (XO) were augmented in the aorta of 3-month-old mice but not in older animals. The administration of the XOR inhibitor allopurinol (ALO) halted the progression of aortic root aneurysm in MFS mice. ALO administrated before the onset of the aneurysm prevented its subsequent development. ALO also inhibited MFS-associated endothelial dysfunction as well as elastic fiber fragmentation, nuclear translocation of pNRF2 and increased 3′-nitrotyrosine levels, and collagen maturation remodeling, all occurring in the tunica media. ALO reduced the MFS-associated large aortic production of H2O2, and NOX4 and MMP2 transcriptional overexpression. Conclusions Allopurinol interferes in aortic aneurysm progression acting as a potent antioxidant. This study strengthens the concept that redox stress is an important determinant of aortic aneurysm formation and progression in MFS and warrants the evaluation of ALO therapy in MFS patients

Characterization of the CPAP-treated patient population in Catalonia

There are different phenotypes of obstructive sleep apnoea (OSA), many of which have not been characterised. Identification of these different phenotypes is important in defining prognosis and guiding the therapeutic strategy. The aim of this study was to characterise the entire population of continuous positive airway pressure (CPAP)-treated patients in Catalonia and identify specific patient profiles using cluster analysis. A total of 72,217 CPAP-treated patients who contacted the Catalan Health System (CatSalut) during the years 2012 and 2013 were included. Six clusters were identified, classified as “Neoplastic patients” (Cluster 1, 10.4%), “Metabolic syndrome patients” (Cluster 2, 27.7%), “Asthmatic patients” (Cluster 3, 5.8%), “Musculoskeletal and joint disorder patients” (Cluster 4, 10.3%), “Patients with few comorbidities” (Cluster 5, 35.6%) and “Oldest and cardiac disease patients” (Cluster 6, 10.2%). Healthcare facility use and mortality were highest in patients from Cluster 1 and 6. Conversely, patients in Clusters 2 and 4 had low morbidity, mortality and healthcare resource use. Our findings highlight the heterogeneity of CPAP-treated patients, and suggest that OSA is associated with a different prognosis in the clusters identified. These results suggest the need for a comprehensive and individualised approach to CPAP treatment of OSA.This study was supported by the Spanish Respiratory Society (SEPAR), Associació Lleidatana de Respiratori (ALLER) and ResMed, a company that provides diagnostic services and treatment for sleep apnoea