Improving average ranking precision in user searches for biomedical research datasets

Availability of research datasets is keystone for health and life science study reproducibility and scientific progress. Due to the heterogeneity and complexity of these data, a main challenge to be overcome by research data management systems is to provide users with the best answers for their search queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we investigate a novel ranking pipeline to improve the search of datasets used in biomedical experiments. Our system comprises a query expansion model based on word embeddings, a similarity measure algorithm that takes into consideration the relevance of the query terms, and a dataset categorisation method that boosts the rank of datasets matching query constraints. The system was evaluated using a corpus with 800k datasets and 21 annotated user queries. Our system provides competitive results when compared to the other challenge participants. In the official run, it achieved the highest infAP among the participants, being +22.3% higher than the median infAP of the participant's best submissions. Overall, it is ranked at top 2 if an aggregated metric using the best official measures per participant is considered. The query expansion method showed positive impact on the system's performance increasing our baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively. Our similarity measure algorithm seems to be robust, in particular compared to Divergence From Randomness framework, having smaller performance variations under different training conditions. Finally, the result categorization did not have significant impact on the system's performance. We believe that our solution could be used to enhance biomedical dataset management systems. In particular, the use of data driven query expansion methods could be an alternative to the complexity of biomedical terminologies

Étude comparative sur la propagation de l’endommagement après impact des composites carbone/époxy renforcés par piquage au fil Kevlar et TI-NI

Les matériaux composites stratifiés présentent des propriétés mécaniques enviables dans le plan des couches de fibres, mais ils ont également une faiblesse naturelle dans la direction de l’épaisseur. Cette faiblesse peut donner lieu à l’apparition de zones délaminées invisibles à l’oeil nu, particulièrement lors d’un impact à faible vitesse. Par conséquent, beaucoup de travaux de recherche ont été dédiés à l’étude de méthodes de renfort interlaminaire pour les stratifiés, dont notamment l’insertion de coutures transversales. Ce projet de recherche propose donc d’utiliser la technique de couture avec un fil métallique en alliage TiNi présentant un comportement superélastique. La combinaison de ces deux éléments devrait permettre l’amélioration de la résistance à la propagation du délaminage lors d’un chargement en flexion. En premier lieu, un modèle numérique a été développé pour servir d’outil d’analyse des structures composites. Le modèle 3-D a été construit dans l’environnement ANSYS à partir d’éléments solides à 20 noeuds et d’éléments shell à 8 noeuds. La technique d’endommagement progressif a été implémentée, permettant ainsi de prédire la propagation du délaminage dans une plaque stratifiée soumise à différents chargements. Le modèle a d’abord été validé en traction quasi-statique avant d’être utilisé pour simuler des essais de flexion trois-points. Par la suite, des plaques de composite carbone/époxy ont été fabriquées, chaque plaque comprenant des échantillons renforcés de couture et d’autres non renforcés. Deux types de renforts ont été utilisés : des fils TiNi superélastiques et des fils de Kevlar, à titre de référence. Les plaques renforcées ont été découpées pour permettre l’observation des coutures internes au microscope optique. Des essais standardisés d’impact à faible vitesse et de compression résiduelle après impact ont été menés (ASTM D7136 et D7137) sur les échantillons renforcés et non renforcés. Les renforts de Kevlar se sont montrés les plus performants pour réduire la zone endommagée après impact, ainsi que pour améliorer la résistance résiduelle en compression. Les renforts de TiNi ont tout de même présenté une amélioration encourageante pour ce qui est de la performance lors de l’impact, alors que la différence lors de l’essai de compression s’est avérée très faible par rapport aux échantillons non renforcés. En troisième lieu, la performance en flexion trois-points des échantillons a été quantifiée expérimentalement en calculant l’énergie nécessaire pour créer un volume unitaire de matériau endommagé (Gv, J/mm3). Ce paramètre s’apparente au taux de restitution de l’énergie de déformation (Strain Energy Release Rate) communément rencontré dans les travaux sur le délaminage. Les résultats ont montré que bien que les renforts de Kevlar permettaient d’améliorer la ténacité à l’endommagement lors de l’impact, cette performance n’était pas entièrement reportée sur la ténacité à l’endommagement durant l’essai de flexion. Ainsi, en relativisant l’énergie de déformation dégagée lors de la propagation du délaminage par rapport au volume de délaminage engendré, on constate que les renforts de TiNi augmentent la valeur de cette résistance à l’endommagement. Finalement, l’étude numérique du comportement des renforts a permis d’identifier des différences qui étaient imperceptibles sur les courbes Force-Déplacement. Les deux types de renforts semblent favoriser la propagation interlaminaire du délaminage lors de la flexion, bien que ce comportement soit moins prononcé dans le cas du TiNi. Cependant, les fils de Kevlar semblent plus efficaces pour freiner la propagation latérale du délaminage entre les lignes de couture

Patients’ perception of their involvement in shared treatment decision making : key factors in the treatment of inflammatory bowel disease

Objectives This study aims to characterize the relationships between the quality of the information given by the physician, the involvement of the patient in shared decision making (SDM), and outcomes in terms of satisfaction and anxiety pertaining to the treatment of inflammatory bowel disease (IBD). Methods A Web survey was conducted among 200 Canadian patients affected with IBD. The theoretical model of SDM was adjusted using path analysis. SAS software was used for all statistical analyses. Results The quality of the knowledge transfer between the physician and the patient is significantly associated with the components of SDM: information comprehension, patient involvement and decision certainty about the chosen treatment. In return, patient involvement in SDM is significantly associated with higher satisfaction and, as a result, lower anxiety as regards treatment selection. Conclusions This study demonstrates the importance of involving patients in shared treatment decision making in the context of IBD. Practice implications Understanding shared decision making may motivate patients to be more active in understanding the relevant information for treatment selection, as it is related to their level of satisfaction, anxiety and adherence to treatment. This relationship should encourage physicians to promote shared decision making

Exploring the use of a participative design in the early development of a predictive test : the importance of physician involvement

In this study, we contribute to the personalized medicine and health care management literature by developing and testing a new participative design approach. We propose that involving gastroenterologists in the development of a predictive test to assist them in their clinical decision-making process for the treatment of inflammatory bowel diseases will increase the likelihood of their acceptance of the innovation. Based on data obtained from 6 focus groups across Canada from a total of 28 physicians, analyses reveal that current tools do not enable discriminating between treatment options to find the best fit for each patient. Physicians expect a new predictive tool to have the capability of showing clear reliability and significant benefits for the patient, while being accessible in a timely manner that facilitates clinical decisions. Physicians also insist on their key role in the implementation process, hence confirming the relevance and importance of participative designs in personalized medicine

Effects of Asm-024, A Modulator of Acetylcholine Receptor Function, On Airway Responsiveness and Allergen-Induced Responses in Patients with Mild Asthma

OBJECTIVES: To evaluate the safety, tolerability and clinical activity of ASM-024, a new cholinergic compound with dual nicotinic and muscarinic activity, in mild allergic asthma

Development and aetiology of body dissatisfaction in adolescent boys and girls

This longitudinal study aims to describe the development of body dissatisfaction (BD), measured with the Contour Drawing Rating Scale, between the ages of 14 and 18, and to identify factors associated with BD at age 18, among 413 adolescents. Between the ages of 14 and 18, the proportion of girls wanting to be thinner increased, although it remained unchanged among boys. A ratio of 1:2 girls and 1:5 boys reported having seriously tried to lose weight. Factors associated with BD in girls at age 18 were (1) wanting to be thinner, (2) body mass index (BMI), (3) weight control behaviours and (4) negative comments about weight. Factors associated with BD in boys at age 18 were (1) wanting to be thinner or bigger, (2) BMI, (3) having experienced sexual intercourse and (4) negative comments about weight. The high prevalence of BD and weight-related concerns suggest a need for early interventions

Le FORUM, Vol. 39 No. 2

https://digitalcommons.library.umaine.edu/francoamericain_forum/1045/thumbnail.jp

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements