Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens

<p>Abstract</p> <p>Background</p> <p>The Enteropathogen Resource Integration Center (ERIC; <url>http://www.ericbrc.org</url>) has a goal of providing bioinformatics support for the scientific community researching enteropathogenic bacteria such as <it>Escherichia coli </it>and <it>Salmonella </it>spp. Rapid and accurate identification of experimental conclusions from the scientific literature is critical to support research in this field. Natural Language Processing (NLP), and in particular Information Extraction (IE) technology, can be a significant aid to this process.</p> <p>Description</p> <p>We have trained a powerful, state-of-the-art IE technology on a corpus of abstracts from the microbial literature in PubMed to automatically identify and categorize biologically relevant entities and predicative relations. These relations include: Genes/Gene Products and their Roles; Gene Mutations and the resulting Phenotypes; and Organisms and their associated Pathogenicity. Evaluations on blind datasets show an F-measure average of greater than 90% for entities (genes, operons, etc.) and over 70% for relations (gene/gene product to role, etc). This IE capability, combined with text indexing and relational database technologies, constitute the core of our recently deployed text mining application.</p> <p>Conclusion</p> <p>Our Text Mining application is available online on the ERIC website <url>http://www.ericbrc.org/portal/eric/articles</url>. The information retrieval interface displays a list of recently published enteropathogen literature abstracts, and also provides a search interface to execute custom queries by keyword, date range, etc. Upon selection, processed abstracts and the entities and relations extracted from them are retrieved from a relational database and marked up to highlight the entities and relations. The abstract also provides links from extracted genes and gene products to the ERIC Annotations database, thus providing access to comprehensive genomic annotations and adding value to both the text-mining and annotations systems.</p

Collins and Sivers asymmetries in muonproduction of pions and kaons off transversely polarised protons

Measurements of the Collins and Sivers asymmetries for charged pions and charged and neutral kaons produced in semi-inclusive deep-inelastic scattering of high energy muons off transversely polarised protons are presented. The results were obtained using all the available COMPASS proton data, which were taken in the years 2007 and 2010. The Collins asymmetries exhibit in the valence region a non-zero signal for pions and there are hints of non-zero signal also for kaons. The Sivers asymmetries are found to be positive for positive pions and kaons and compatible with zero otherwise. © 2015

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

A new parasitoid wasp, Aphaereta vondelparkensis sp. n. (Braconidae, Alysiinae), from a city park in the centre of Amsterdam

Background The parasitic wasp genus Aphaereta Foerster, 1863, belongs to the large subfamily Alysiinae Leach, 1815 (Hymenoptera: Braconidae) and contains solitary or gregarious endoparasitoids of larvae of cyclorrhaphous Diptera living in decaying organic matter. New information A new species, Aphaereta vondelparkensis sp. n. (Braconidae, Alysiinae, Alysiini), from a city park in the centre of Amsterdam (Vondelpark) is described and illustrated. The species was discovered on a so-called taxon expedition, in which experts and citizen scientists collaborate on taxonomic projects. The finding highlights the fact that new animal species can still be discovered today, even in the busiest park of the capital of one of the best studied European countries

FIGURE 2 in Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)

FIGURE 2 Neotype of P. sericatus from Kiev, Ukraine: a, habitus; b, aedeagus, dorsal view (angle of view somewhat more rostral than in fig. 4); c, aedeagus, lateral view; d, genital segment; e, labels.Published as part of Schilthuizen, Menno, van Oostenbrugge, Wesley, Visser, Stefan, van der Meer, Marrit, Delval, Richard, Dias, Claudia, Köster, Heko, Maarschall, Rudie, Peeters, Norbert, Venema, Peter, Zaremba, Ryan, Beltrami, Cristina, Rossato, Marzia, Latella, Leonardo, Nieuwenhuis, Florinda, de Rop, Nicole, Njunjić, Iva, Perreau, Michel & Koene, Joris M., 2021, Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae), pp. 1-20 in Contributions to Zoology 90 (1) on page 9, DOI: 10.1163/18759866-BJA10007, http://zenodo.org/record/834327

Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera:Leiodidae)

Anthropogenic environmental change is leading to changes in distribution for many organisms. While this is frequently discussed for prominent organisms of high conservation value, the same is true for the many cryptic species that rarely figure in debates on the human impact. One such cryptic taxon is the European Ptomaphagus sericatus (Chaudoir, 1845) and related forms. During a citizen science expedition in the Vondelpark, Amsterdam, the Netherlands, we obtained two forms of this species complex. We placed the examination of these specimens in the context of a re-analysis of the species group, and, using DNA barcoding and genital study on material collected thoughout Europe, found that the P. sericatus species complex consists of three distinct, partly sympatric species, one of which was previously undescribed. On the basis of collection data, at least two species, P. medius and P. thebeatles sp. n., show signs of having recently undergone (possibly anthropogenic) range changes, with P. medius even reaching North America. We describe P. thebeatles sp. n.; we raise two subspecies, viz. P. sericatus sericatus (Chaudoir, 1854) and P. sericatus medius (Rey, 1889) to the level of species, and designate a neotype for the former; we identify P. dacicus Jennel, 1934 and P. pyrenaeus Jeannel, 1934 as junior synonyms of P. sericatus, and P. compressitarsus (Rey,1889) as a junior synonym of P. subvillosus Goeze, 1777; we identify P. septentrionalis Jeanne], 1934 and P. miser (Rey, 1889) as junior synonyms of P. medius; we designate lectotypes for P. medius and P. miser