OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

<p>Abstract</p> <p>Background</p> <p>Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required.</p> <p>Results</p> <p>Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes <url>http://ibi.imim.es/osirisform.html</url>. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, <url>http://ibi.imim.es/OSIRISv1.2.html</url>) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented.</p> <p>Conclusion</p> <p>OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.</p

Changes in leisure-time physical activity among Brazilian pregnant women: comparison between two birth cohort studies (2004 – 2015)

Abstract Background Low levels of leisure-time physical activity (LTPA) during pregnancy have been shown in studies conducted worldwide. Surveillance is extremely important to monitor the progress of physical activity patterns over time and set goals for effective interventions to decrease inactivity among pregnant women. The aim of this study was to evaluate time changes in LTPA among Brazilian pregnant women in an 11-year period (2004–2015) by comparing data from two birth cohort studies. Methods Two population-based birth cohort studies were carried out in the city of Pelotas, southern Brazil, in 2004 and 2015. A total of 4244 and 4271 mothers were interviewed after delivery. Weekly frequency and duration of each session of LTPA in a typical week were reported for the pre-pregnancy period and for each trimester of pregnancy. Trends in both recommended LTPA (≥150 min/week) and any LTPA (regardless of weekly amount) were analysed overtime. Changes were also calculated separately for subgroups of maternal age, schooling, family income, parity, pre-pregnancy body mass index and pre-pregnancy LTPA. Results The proportion of women engaged in recommended levels of LTPA pre-pregnancy increased from 11.2% (95%CI 10.0–12.2) in 2004 to 15.8% (95%CI 14.6–16.9) in 2015. During pregnancy, no changes were observed over the period for the first (10.6 to 10.9%) and second (8.7 to 7.9%) trimesters, whereas there was a decrease from 3.4% (95%CI 2.9–4.0) to 2.4% (95%CI 1.9–2.8) in the last trimester. Major decreases in LTPA in the last trimester were observed among women who were younger, with intermediate to high income, high schooling, primiparous, pre-pregnancy obese and, engaged in LTPA before pregnancy. Changes in any LTPA practice followed the same patterns described for recommended LTPA. Conclusions Despite the increase in the proportion of women engaged in LTPA before pregnancy between 2004–2015, LTPA levels remained stable during the first and second trimesters of pregnancy and declined during the third gestational trimester over the period. Interventions to encourage the maintenance of LTPA practice throughout pregnancy are urgently needed

Plasma endothelin-1 as screening marker for cerebral vasospasm after subarachnoid hemorrhage

Cerebral vasospasm complicating subarachnoid hemorrhage causes ischemic stroke and worsens the neurological outcome. The potential role of endothelin-1 in vasospasm pathogenesis may provide therapeutic opportunities. A recent meta-analysis however, did not support the use of endothelin antagonists. Apart from clinical assessment, transcranial Doppler and interval angiography, there are no sensitive screening markers for evolving vasospasm. We investigate the ability of serial measurement of endothelin-1 to predict the development of vasospasm following subarachnoid hemorrhage