OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents

Motivation: Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. Results: We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. Availability: The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. Contact: [email protected]

Charge carrier transfer in the gas electron multiplier at low gas gains

Connected to the Linear Collider project TESLA at DESY, studies on the readout of TPCs based on the GEM-technology are ongoing. For particle identication via dE/dx - measurement, a good energy resolution is indispensable, and therefore losses of primary electrons have to be avoided. It turned out, that in the GEM transverse diffusion inside or close to the holes is a not negligible reason for these losses. For Ar-CH4 90:10 and TPC-like field configurations it was found, that when operated in normal amplification mode, the Standard Geometry GEM should not lose primaries, whereas for low gains, also when operated in magnetic fields up to 5T, a GEM with larger pitch and hole diameter would be necessary

Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer

Contains fulltext : 234196.pdf (Publisher’s version ) (Open Access

Prognostic impact of mRNA levels of osteopontin splice variants in soft tissue sarcoma patients

<p>Abstract</p> <p>Background</p> <p>It is well known that osteopontin (OPN) plays an important role in tumor progression and that a high OPN expression level in several tumor entities correlates with poor prognosis in cancer patients. However, little is known about the prognostic relevance of the OPN mRNA splice variants.</p> <p>Methods</p> <p>We analyzed the mRNA expression levels of different OPN splice variants in tumor tissue of 124 soft tissue sarcoma (STS) patients. Quantitative real-time PCR (qRT-PCR) was used to analyze the mRNA expression level of three OPN splice variants (OPN-a, -b and -c).</p> <p>Results</p> <p>The multivariate Cox's proportional hazard regression model revealed that high mRNA expression levels of OPN splice variants are significantly associated with poor prognosis in STS patients (n = 124). Women (n = 68) with high mRNA expression levels of OPN-a and OPN-b have an especially elevated risk of tumor-related death (OPN-a: RR = 3.0, P = 0.01, CI = 1.3-6.8; OPN-b: RR = 3.4, P = 0.01, CI = 1.4-8.2). In particular, we found that high mRNA expression levels of OPN-b and OPN-c correlated with a high risk of tumor-related death in STS patients that received radiotherapy (n = 52; OPN-b: RR = 10.3, P < 0.01, CI = 2.0-53.7; OPN-c: RR = 11.4, P < 0.01, CI = 2.2-59.3).</p> <p>Conclusion</p> <p>Our study shows that elevated mRNA expression levels of OPN splice variants are negative prognostic and predictive markers for STS patients. Further studies are needed to clarify the impact of the OPN splice variants on prognosis.</p

Iron mineral dissolution releases iron and associated organic carbon during permafrost thaw

It has been shown that reactive soil minerals, specifically iron(III) (oxyhydr)oxides, can trap organic carbon in soils overlying intact permafrost, and may limit carbon mobilization and degradation as it is observed in other environments. However, the use of iron(III)-bearing minerals as terminal electron acceptors in permafrost environments and thus their stability and capacity to prevent carbon mobilization during permafrost thaw is poorly understood. We have followed the dynamic interactions between iron and carbon, using a space for time-approach, across a thaw gradient in Abisko (Sweden), where wetlands are expanding rapidly due to permafrost thaw. We show through bulk (selective extractions, EXAFS) and nanoscale analysis (correlative SEM and nanoSIMS) that organic carbon is bound to reactive Fe primarily in the transition between organic and mineral horizons in palsa underlain by intact permafrost (41.8 ± 10.8 mg carbon per g soil, 9.9 to 14.8% of total soil organic carbon). During permafrost thaw, water-logging and O2 limitation lead to reducing conditions and an increase in abundance of Fe(III)-reducing bacteria which favor mineral dissolution and drive mobilization of both iron and carbon along the thaw gradient. By providing a terminal electron acceptor, this rusty carbon sink is effectively destroyed along the thaw gradient and cannot prevent carbon release with thaw

A novel splice variant of the stem cell marker LGR5/GPR49 is correlated with the risk of tumor-related death in soft-tissue sarcoma patients

<p>Abstract</p> <p>Background</p> <p>The human leucine-rich, repeat-containing G protein-coupled receptor (LGR) 5, also called GPR49, is a marker of stem cells in adult intestinal epithelium, stomach and hair follicles. LGR5/GPR49 is overexpressed in tumors of the colon, ovary and liver and in basal cell carcinomas. Moreover, an expression in skeletal muscle tissues was also detected. However, there has been no investigation regarding the expression and function of LGR5/GPR49 in soft-tissue sarcomas (STS) yet.</p> <p>Methods</p> <p>Seventy-seven frozen tumor samples from adult STS patients were studied using quantitative real-time TaqMan™ PCR analysis. The mRNA levels of wild type <it>LGR5/GPR49 </it>and a newly identified splice variant of <it>LGR5/GPR49 </it>lacking exon 5 (that we called <it>GPR49Δ5</it>) were quantified.</p> <p>Results</p> <p>A low mRNA expression level of <it>GPR49Δ5</it>, but not wild type <it>LGR5/GPR49</it>, was significantly correlated with a poor prognosis for the disease-associated survival of STS patients (RR = 2.6; P = 0.026; multivariate Cox's regression hazard analysis). Furthermore, a low mRNA expression level of <it>GPR49Δ5 </it>was associated with a shorter recurrence-free survival (P = 0.043). However, tumor onset in patients with a lower expression level of <it>GPR49Δ5 </it>mRNA occurred 7.5 years later (P = 0.04) than in patients with a higher tumor level of <it>GPR49Δ5 </it>mRNA.</p> <p>Conclusion</p> <p>An attenuated mRNA level of the newly identified transcript variant <it>GPR49Δ5 </it>is a negative prognostic marker for disease-associated and recurrence-free survival in STS patients. Additionally, a lower <it>GPR49Δ5 </it>mRNA level is associated with a later age of tumor onset. A putative role of <it>GPR49Δ5 </it>expression in tumorigenesis and tumor progression of soft tissue sarcomas is suggested.</p

Computerbasierte Erfassung von Fremdsprachenkompetenzen im Unterricht der Primarstufe: Bericht zum Projekt „Erfassung von Entwicklungsprofilen im frühen schulischen Fremdsprachenlernen“

Le projet « Recensement des profils de développement dans le cadre de l’apprentissage précoce des langues étrangères à l’école » fait partie du programme de recherche 2012-2015 du Centre scientifique de compétence sur le plurilinguisme (CSP). Son objectif était de contribuer à créer, dans le cadre de l’enseignement des langues étrangères à l’école primaire (de la troisième à la sixième), une culture d’évaluation à la fois informatisée et orientée sur l’apprentissage grâce au développement d’instruments adaptés à la vérification des compétences. Les travaux de développement se sont inspirés du concept de la progression des apprentissages (learning progressions), surtout appliqué en didactique des sciences naturelles, où il constitue souvent la base des programmes, de l’enseignement et de l’évaluation.The project “Mapping developmental profiles in early language learning at school” is part of the research programme 2012-2015 of the Research Centre on Multilingualism. The overall objective of the project was to develop adequate instruments to assess language competence and thus contribute to a learning- oriented and computer-assisted assessment culture in foreign language instruction at primary schools (third to sixth class). To develop these instruments, the general work processes were guided by the notion of learning progressions, which are frequently used as the basis for developing curricula, teaching and conducting assessments in (most commonly) the natural sciences.Das Projekt „Erfassung von Entwicklungsprofilen im frühen schulischen Fremdsprachenlernen“ ist Teil des Forschungsprogramms 2012-2015 des Wissenschaftlichen Kompetenzzentrums für Mehrsprachigkeit (KFM). Das Ziel bestand darin, durch die Entwicklung von geeigneten Instrumenten zur Kompetenzerfassung einen Beitrag zu einer lernorientierten und gleichzeitig computerunterstützten Beurteilungskultur im Fremdsprachenunterricht an Primarschulen (dritte bis sechste Klasse) zu leisten. Die Entwicklungsarbeiten orientierten sich an der Idee von Lernprogressionen (learning progressions), mit der vor allem in der Didaktik der Naturwissenschaften als Grundlage für Curricula, Unterricht und Beurteilung gearbeitet wird.Il progetto sui ”profili di sviluppo nell’apprendimento delle lingue straniere nella scuola elementare” rientra nel programma di ricerca 2012-2015 del Centro scientifico di competenza per il plurilinguismo. Attraverso l’elaborazione di strumenti idonei al rilevamento di competenze si è voluto fornire, nell’ambito dell’insegnamento delle lingue straniere nella scuola elementare (dal terzo al sesto anno), un contributo a una cultura della valutazione che sia orientata all’apprendimento e che si affidi al contempo all’ausilio di mezzi informatici. Il lavoro di elaborazione era incentrato sulle progressioni di apprendimento (learning progressions), un concetto sovente applicato ai programmi, alle lezioni e alle valutazioni nella didattica delle scienze naturali

Effectiveness of 0.05% oxymetazoline (Vicks Sinex Micromist) nasal spray in the treatment of objective nasal congestion demonstrated to 12h post-administration by magnetic resonance imaging

Introduction: This study aimed to assess the qualitative and quantitative utility of MRI imaging to illustrate the magnitude and duration of the effect of a standard 100 μg dose of oxymetazoline in a commercially available formulation that also contains aromatic oils. Methods: This was a randomized, open label, single dose, parallel group study in 21 adult male and female subjects who reported moderate to severe nasal congestion due to acute upper respiratory tract infection or hay fever. MRI scans were acquired using a 3T Philips Achieva scanner with a 16 channel head receive coil. High resolution MRI scans of the nasal turbinates were obtained immediately prior to dosing (baseline) and at approximately 1, 8, 10, 11, and 12 hours after dosing. The efficacy variables of primary interest were inferior turbinate total volume at 8 and 12 hours post-dosing. The secondary efficacy variables analysed were inferior turbinate total volume at 1, 10, and 11 hours post-dosing, middle turbinate total volume at 1, 8, 10, 11, and 12 hours post-dosing. Results: Changes from baseline volumes measured for the inferior and middle turbinates of subjects receiving the oxymetazoline formulation showed significant (P<0.05) decreases at all times up to and including 12 hours post-administration. No significant decreases from baseline were detected in subjects receiving a sham ‘spray’ (untreated control - spray bottles with no spray solution). Statistical ANCOVA results of inferior and middle turbinate volume indicated significant differences (P<0.05) at all measurement points up to and including 12 hours post-administration between the oxymetazoline treatment group and the untreated control with the only exception the middle turbinate volume at 10 hours (P=0.0896). The significant changes were likely to be clinically relevant though this was not measured in the study. No AEs were reported during this study and no other safety evaluations were made. Conclusions: This study showed that MRI assessment of nasal congestion in human volunteers is a robust, repeatable and viable measurement technique. The application of a 100 µg Vicks Sinex Micromist® nasal decongestant (0.05% oxymetazoline solution) delivered a highly significant reduction in inferior and middle turbinate volumes compared with the application of a control, measurable by the MRI method up to and including a 12 hour post-dose scan

Categorizing diffuse parenchymal lung disease in children

Background Aim of this study was to verify a systematic and practical categorization system that allows dynamic classification of pediatric DPLD irrespective of completeness of patient data. Methods The study was based on 2322 children submitted to the kids-lung-register between 1997 and 2012. Of these children 791 were assigned to 12 DPLD categories, more than 2/3 belonged to categories manifesting primarily in infancy. The work-flow of the pediatric DPLD categorization system included (i) the generation of a final working diagnosis, decision on the presence or absence of (ii) DPLD and (iii) a systemic or lung only condition, and (iv) the allocation to a category and subcategory. The validity and inter-observer dependency of this workflow was re-tested using a systematic sample of 100 cases. Results Two blinded raters allocated more than 80 % of the re-categorized cases identically. Non-identical allocation was due to lack of appreciation of all available details, insufficient knowledge of the classification rules by the raters, incomplete patient data, and shortcomings of the classification system itself. Conclusions This study provides a suitable workflow and hand-on rules for the categorization of pediatric DPLD. Potential pitfalls were identified and a foundation was laid for the development of consensus-based, international categorization guidelines