BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming

Document Type : Proceedings Paper Conference Date : JUN 23-24, 2011 Conference Location : Portland, ORInternational audienceWe present two related tasks of the BioNLP Shared Tasks 2011: Bacteria Gene Renaming (Rename) and Bacteria Gene Interactions (GI). We detail the objectives, the corpus specification, the evaluation metrics, and we summarize the participants' results. Both issued from PubMed scientific literature abstracts, the Rename task aims at extracting gene name synonyms, and the GI task aims at extracting genic interaction events, mainly about gene transcriptional regulations in bacteria

New treatment options for lupus – a focus on belimumab

Belimumab is the first biologic approved for patients with systemic lupus erythematosus (SLE). Belimumab is the first of a new class of drug targeting B cell-stimulating factors or their receptors to reach the market. Its target, BLyS, also known as BAFF (B cell-activating factor from the tumor necrosis factor family), is a type II transmembrane protein that exists in both membrane-bound and soluble forms. Additionally to a robust rational from murine experiments conducted in lupus prone mice, BLyS circulating levels are increased in SLE patients. After the negative results of a Phase II trial, two Phase III trials met their primary endpoints. Some SLE patients are still refractory to the standard options of care or necessitate prolonged high-dose corticotherapy and/or long-term immunosuppressive regimens. However, some experts still feel that the effect of this biologic might not be clinically relevant and blame the use of the new systemic lupus response index as well as the discrepancies between both trials and the noninclusion of the severe form of the disease as nephritis. In this review, we aim to discuss the characteristics of belimumab, critically evaluate the different steps of its development, and consider its future place in the arsenal against SLE, taking into account the patients’ perspectives

BioNLP Shared Task - The Bacteria Track

Background: We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles. We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions. Results: Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system. Conclusions: The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found commond trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence

First and repeated records of the tropical-temperate crab Asthenognathus atlanticus Monod, 1932 (Decapoda: Brachyura) in the eastern part of the Bay of Seine (eastern English Channel, France)

International audienceAsthenognathus atlanticus Monod, 1932, has been reported for the first time from the eastern part of the bay ofSeine (eastern english Channel). A total of 30 specimens were collected between the years 2008 and 2011, along thenormandy coast from ouistreham to Antifer, mainly on mud and muddy sand habitats, between 10 and 25 m depth. thedistribution range of A. atlanticus has been previously known to cover eastern Atlantic coasts from Angola to the westernenglish Channel, where it reached its northern limits. it is also present in the western part of the Mediterranean Sea. thechanges in the sediment composition of the eastern bay of Seine have probably led to the development of a potentiallyfavorable habitat for this species. However, the data collected have not yet been sufficient to ascertain the origin, and themethod of introduction of the eastern english Channel specimens. in the discussion, we ponder if they might haveoriginated from the western english Channel populations, and was transported as larvae in the eastern english Channel;they could have originated from a more distant population, and have been brought to the eastern english Channel throughhuman activities. each hypothesis is possible in theory

Design, Construction and In Situ Testing of a Muon Camera for Earth Science and Civil Engineering Applications

The MUST2 (MUon Survey Tomography based on Micromegas detectors for Unreachable Sites Technology) camera is based on a thin Time Projection Chamber read by a resistive Micromegas. This innovative combination presents interesting distinctive features compared to existing muon detection technologies. It allows a wide angular acceptance of the detector with a low weight and compact volume, well adapted for confined spaces or underground operation. The current work presents the results obtained during the calibration measurements at the reference site, the Low Background Noise Laboratory (LBNL). Preliminary results from field measurement campaign carried out at the dam overlooking the village of Saint-Saturnin-les-Apt (South-East of France) are presented and discussed

Comparaison des effets sédatif et analgésique de la méthadone et de la morphine par voie intraveineuse chez le chien (étude expérimentale sur 12 chiens lors d'une coelioscopie)

Les effets sédatif et analgésique de la méthadone (0,25 mg/kg) ont été comparés à ceux de la morphine (0,3 mg/kg) chez le chien, par voie intraveineuse lors d une coelioscopie. Une étude randomisée croisée en double aveugle a été réalisée sur des chiens beagles (n=12), répartis aléatoirement en deux groupes parallèles. Un suivi analgésique et cardiorespiratoire a été réalisé jusqu à 24 heures après le réveil. Aucune différence sédative n a été observée. Par contre, une meilleure analgésie per et postopératoire immédiate a été mise en évidence chez les chiens traités méthadone. La fréquence cardiaque per-opératoire est également plus faible dans le groupe méthadone. De plus, la méthadone a permis de réduire le besoin en isoflurane. Par contre, la dose de propofol à l induction à effet n est pas différente significativement. On ne peut pas conclure pour la fréquence respiratoire. Enfin, aucune différence n a été observée pour le score nausée et la température.NANTES-Ecole Nat.Vétérinaire (441092302) / SudocTOULOUSE-EN Vétérinaire (315552301) / SudocSudocFranceF

Unsupervised clustering analysis of data from an online community to identify lupus patient profiles with regards to treatment preferences

International audienceObjective: Lupus is a chronic complex autoimmune disease. Non-adherence to treatment can affect patient outcomes. Considering patients' preferences into medical decisions may increase acceptance to their medication. The PREFERLUP study used unsupervised clustering analysis to identify profiles of patients with similar treatment preferences in an online community of French lupus patients. Methods: An online survey was conducted in adult lupus patients from the Carenity community between August 2018 and April 2019. Multiple Correspondence Analysis (MCA) was used with three unsupervised clustering methods (hierarchical, kmeans and partitioning around medoids). Several indicators (measure of connectivity, Dunn index and Silhouette width) were used to select the best clustering algorithm and choose the number of clusters. Results: The 268 participants were mostly female (96%), with a mean age of 44.3 years 83% fulfilled the American College of Rheumatology (ACR) self-reported diagnostic criteria for systemic lupus erythematosus. Overall, the preferred route of administration was oral (62%) and the most important feature of an ideal drug was a low risk of side-effects (32%). Hierarchical clustering identified three clusters. Cluster 1 (59%) comprised patients with few comorbidities and a poor ability to identify oncoming flares; 84% of these patients desired oral treatments with limited side-effects. Cluster 2 (13%) comprised younger patients, who had already participated in a clinical trial, were willing to use implants and valued the compatibility of treatments with pregnancy. Cluster 3 (28%) comprised patients with a longer lupus duration, poorer control of the disease and more comorbidities; these patients mainly valued implants and injections and expected a reduction of corticosteroid intake. Conclusions: Different profiles of lupus patients were identified according to their drug preferences. These clusters could help physicians tailor their therapeutic proposals to take into account individual patient preferences, which could have a positive impact on treatment acceptance and then adherence. The study highlights the value of data acquired directly from patient communities

BioAlvis II, NLP-based semantic mining of literature on molecular biology of bacteria

International audienc

Comparison of medetomidine-morphine and medetomidine-methadone for sedation, isoflurane requirement and postoperative analgesia in dogs undergoing laparoscopy.

OBJECTIVE To compare the effects of intravenous (IV) medetomidine-morphine and medetomidine-methadone on preoperative sedation, isoflurane requirements and postoperative analgesia in dogs undergoing laparoscopic surgery. STUDY DESIGN Randomized, crossover trial. ANIMALS Twelve adult Beagle dogs weighing 15.1 ± 4.1 kg. METHODS Dogs were administered medetomidine (2.5 μg kg(-1) ) IV 5 minutes before either methadone (MET) or morphine (MOR) (0.3 mg kg(-1) ) IV. Anaesthesia was induced with propofol, maintained with isoflurane in oxygen, and depth was clinically assessed and adjusted by an anaesthetist blinded to the treatment. Animals underwent laparoscopic abdominal biopsies. Sedation and nausea scores, pulse rate (PR), respiratory rate (fR ), noninvasive systolic arterial blood pressure (SAP), rectal temperature (RT) and pain scores were recorded before drug administration, 5 minutes after medetomidine injection and 10 minutes after opioid administration. Propofol dose, PR, fR , SAP, oesophageal temperature (TOES ), end-tidal carbon dioxide and end-tidal isoflurane concentration (Fe'Iso) were recorded intraoperatively. Pain scores, PR, fR , SAP and RT were recorded 10 minutes after extubation, every hour for 6 hours, then at 8, 18 and 24 hours. The experiment was repeated with the other drug 1 month later. RESULTS Nine dogs completed the study. After opioid administration and intraoperatively, PR, but not SAP, was significantly lower in MET. Fe'Iso was significantly lower in MET. Temperature decreased in both treatments. Pain scores were significantly higher in MOR at 3 hours after extubation, but not at other time points. Two dogs required rescue analgesia; one with both treatments and one in MOR. CONCLUSION AND CLINICAL RELEVANCE At the dose used, sedation produced by both drugs when combined with medetomidine was equivalent, while volatile anaesthetic requirements and PR perioperatively were lower with methadone. Postoperative analgesia was deemed to be adequate for laparoscopy with either protocol, although methadone provided better analgesia 3 hours after surgery