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

Réorganisation fonctionnelle et structurale des cortex auditifs, visuels et associatifs chez les sourds profonds congénitaux ou prélinguaux

En raison de l’utilisation d’un mode de communication totalement différent de celui des entendants, le langage des signes, et de l’absence quasi-totale d’afférences en provenance du système auditif, il y a de fortes chances que d’importantes modifications fonctionnelles et structurales s’effectuent dans le cerveau des individus sourds profonds. Les études antérieures suggèrent que cette réorganisation risque d’avoir des répercussions plus importantes sur les structures corticales situées le long de la voie visuelle dorsale qu’à l’intérieur de celles situées à l’intérieur de la voie ventrale. L’hypothèse proposée par Ungerleider et Mishkin (1982) quant à la présence de deux voies visuelles dans les régions occipitales, même si elle demeure largement acceptée dans la communauté scientifique, s’en trouve aussi relativement contestée. Une voie se projetant du cortex strié vers les régions pariétales postérieures, est impliquée dans la vision spatiale, et l’autre se projetant vers les régions du cortex temporal inférieur, est responsable de la reconnaissance de la forme. Goodale et Milner (1992) ont par la suite proposé que la voie dorsale, en plus de son implication dans le traitement de l’information visuo-spatiale, joue un rôle dans les ajustements sensori-moteurs nécessaires afin de guider les actions. Dans ce contexte, il est tout à fait plausible de considérer qu’un groupe de personne utilisant un langage sensori-moteur comme le langage des signes dans la vie de tous les jours, s’expose à une réorganisation cérébrale ciblant effectivement la voie dorsale. L’objectif de la première étude est d’explorer ces deux voies visuelles et plus particulièrement, la voie dorsale, chez des individus entendants par l’utilisation de deux stimuli de mouvement dont les caractéristiques physiques sont très similaires, mais qui évoquent un traitement relativement différent dans les régions corticales visuelles. Pour ce faire, un stimulus de forme définie par le mouvement et un stimulus de mouvement global ont été utilisés. Nos résultats indiquent que les voies dorsale et ventrale procèdent au traitement d’une forme définie par le mouvement, tandis que seule la voie dorsale est activée lors d’une tâche de mouvement global dont les caractéristiques psychophysiques sont relativement semblables. Nous avons utilisé, subséquemment, ces mêmes stimulations activant les voies dorsales et ventrales afin de vérifier quels pourraient être les différences fonctionnelles dans les régions visuelles et auditives chez des individus sourds profonds. Plusieurs études présentent la réorganisation corticale dans les régions visuelles et auditives en réponse à l’absence d’une modalité sensorielle. Cependant, l’implication spécifique des voies visuelles dorsale et ventrale demeure peu étudiée à ce jour, malgré plusieurs résultats proposant une implication plus importante de la voie dorsale dans la réorganisation visuelle chez les sourds. Suite à l’utilisation de l’imagerie cérébrale fonctionnelle pour investiguer ces questions, nos résultats ont été à l’encontre de cette hypothèse suggérant une réorganisation ciblant particulièrement la voie dorsale. Nos résultats indiquent plutôt une réorganisation non-spécifique au type de stimulation utilisé. En effet, le gyrus temporal supérieur est activé chez les sourds suite à la présentation de toutes nos stimulations visuelles, peu importe leur degré de complexité. Le groupe de participants sourds montre aussi une activation du cortex associatif postérieur, possiblement recruté pour traiter l’information visuelle en raison de l’absence de compétition en provenance des régions temporales auditives. Ces résultats ajoutent aux données déjà recueillies sur les modifications fonctionnelles qui peuvent survenir dans tout le cerveau des personnes sourdes, cependant les corrélats anatomiques de la surdité demeurent méconnus chez cette population. Une troisième étude se propose donc d’examiner les modifications structurales pouvant survenir dans le cerveau des personnes sourdes profondes congénitales ou prélinguales. Nos résultats montrent que plusieurs régions cérébrales semblent être différentes entre le groupe de participants sourds et celui des entendants. Nos analyses ont montré des augmentations de volume, allant jusqu’à 20%, dans les lobes frontaux, incluant l’aire de Broca et d’autres régions adjacentes impliqués dans le contrôle moteur et la production du langage. Les lobes temporaux semblent aussi présenter des différences morphométriques même si ces dernières ne sont pas significatives. Enfin, des différences de volume sont également recensées dans les parties du corps calleux contenant les axones permettant la communication entre les régions temporales et occipitales des deux hémisphères.Due to the use of a mode of communication completely different from hearing people, Due to [the use of] a communication mode completely different from hearing people, the sign language and the absence of afferences from the auditory system, it is likely that significant functional and structural changes take place in the brains of profoundly deaf individuals. Previous studies suggest this reorganization may have greater impact on cortical structures located along the dorsal visual pathway than within the regions located inside the ventral pathway. The hypothesis, widely accepted by the scientific community, proposed by Ungerleider and Mishkin (1982) for the presence of two visual pathways in the occipital regions is also fairly contested. According to this hypothesis, one stream projecting from the striate cortex to the posterior parietal regions is involved in spatial vision and a second stream projecting to regions of the inferior temporal cortex underlying form recognition. Goodale and Milner (1992) subsequently proposed that the dorsal pathway, in addition to its involvement in the processing of visuospatial information, takes part in the necessary sensorymotor adjustments to guide actions. In this context, it is plausible to consider that a group of people using sensorimotor language (e.g., sign language) in their everyday life, the cerebral reorganization is more suited to target the dorsal pathway. The first objective of the study is to explore both visual pathways, especially the dorsal pathway, in hearing subjects by the use of two similar motion stimuli that evoke different types of processing. This was done with a form-from-motion stimuli and a global motion stimuli. Our results indicate that both dorsal and ventral pathways process forms defined by motion, while only the dorsal pathway is activated during a task of global motion whose psychophysical characteristics are relatively similar. Subsequently, we used these stimuli to activate the dorsal and ventral stream to investigate functional differences in the visual and auditory brain regions in profoundly deaf individuals. Several studies show cortical reorganization in the visual and auditory areas in response to the absence of a sensory modality. However, few studies have explored the specific involvement of dorsal and ventral visual streams, despite several results suggesting greater involvement of the dorsal pathway in visual reorganization with the deaf population. Following the use of functional brain imaging to investigate these issues, our results differed from the hypothesis suggesting a reorganization specifically targeting the dorsal pathway. Rather, our results indicate a non-specific reorganization to the different types of stimulations used. Indeed, the superior temporal gyrus was activated with the deaf following the presentation of our visual stimuli, regardless of their complexity. The group of deaf participants also showed activation of the posterior association cortex, possibly recruited to process visual information in the absence of competition from the temporal auditory regions. These results add to data already collected on the functional changes that may occur throughout the brains of deaf people, however, the anatomical correlates of deafness remains unknown in this population. A third study aimed to explore the structural changes occurring in the brains of prelingual and congenital profoundly deaf. Our results show that several brain regions appear to be different between the groups of participants composed of the deaf and hearing. Our analysis showed volume increases of up to 20% in the frontal lobe, including Broca's area and adjacent regions involved in motor control and language production. The temporal lobes also presented some morphometric differences even if they are not significant. Though not significant, the temporal lobes also presented some morphometric differences. Finally, differences in volume were also found in parts of the corpus callosum considered to carry fibers connecting the temporal and occipital lobes of both hemispheres

Examining the ethical and social issues of health technology design through the public appraisal of prospective scenarios : a study protocol describing a multimedia-based deliberative method

Background: The design of health technologies relies on assumptions that affect how they will be implemented, such as intended use, complexity, impact on user autonomy, and appropriateness. Those who design and implement technologies make several ethical and social assumptions on behalf of users and society more broadly, but there are very few tools to examine prospectively whether such assumptions are warranted and how the public define and appraise the desirability of health innovations. This study protocol describes a three-year study that relies on a multimedia-based prospective method to support public deliberations that will enable a critical examination of the social and ethical issues of health technology design. Methods: The first two steps of our mixed-method study were completed: relying on a literature review and the support of our multidisciplinary expert committee, we developed scenarios depicting social and technical changes that could unfold in three thematic areas within a 25-year timeframe; and for each thematic area, we created video clips to illustrate prospective technologies and short stories to describe their associated dilemmas. Using this multimedia material, we will: conduct four face-to-face deliberative workshops with members of the public (n = 40) who will later join additional participants (n = 25) through an asynchronous online forum; and analyze and integrate three data sources: observation, group deliberations, and a self-administered participant survey. Discussion: This study protocol will be of interest to those who design and assess public involvement initiatives and to those who examine the implementation of health innovations. Our premise is that using user-friendly tools in a deliberative context that foster participants’ creativity and reflexivity in pondering potential technoscientific futures will enable our team to analyze a range of normative claims, including some that may prove problematic and others that may shed light over potentially more valuable design options. This research will help fill an important knowledge gap; intervening earlier in technological development could help reduce undesirable effects and inform the design and implementation of more appropriate innovations

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

Measurement of the Hadronic Photon Structure Function F_2^gamma at LEP2

The hadronic structure function of the photon F_2^gamma is measured as a function of Bjorken x and of the factorisation scale Q^2 using data taken by the OPAL detector at LEP. Previous OPAL measurements of the x dependence of F_2^gamma are extended to an average Q^2 of 767 GeV^2. The Q^2 evolution of F_2^gamma is studied for average Q^2 between 11.9 and 1051 GeV^2. As predicted by QCD, the data show positive scaling violations in F_2^gamma. Several parameterisations of F_2^gamma are in agreement with the measurements whereas the quark-parton model prediction fails to describe the data.Comment: 4 pages, 2 figures, to appear in the proceedings of Photon 2001, Ascona, Switzerlan

Search for the Standard Model Higgs Boson with the OPAL Detector at LEP

This paper summarises the search for the Standard Model Higgs boson in e+e- collisions at centre-of-mass energies up to 209 GeV performed by the OPAL Collaboration at LEP. The consistency of the data with the background hypothesis and various Higgs boson mass hypotheses is examined. No indication of a signal is found in the data and a lower bound of 112.7GeV/C^2 is obtained on the mass of the Standard Model Higgs boson at the 95% CL.Comment: 51 pages, 21 figure

Measurement of the B0 Lifetime and Oscillation Frequency using B0->D*+l-v decays

The lifetime and oscillation frequency of the B0 meson has been measured using B0->D*+l-v decays recorded on the Z0 peak with the OPAL detector at LEP. The D*+ -> D0pi+ decays were reconstructed using an inclusive technique and the production flavour of the B0 mesons was determined using a combination of tags from the rest of the event. The results t_B0 = 1.541 +- 0.028 +- 0.023 ps, Dm_d = 0.497 +- 0.024 +- 0.025 ps-1 were obtained, where in each case the first error is statistical and the second systematic.Comment: 17 pages, 4 figures, submitted to Phys. Lett.

Search for Yukawa Production of a Light Neutral Higgs Boson at LEP

Within a Two-Higgs-Doublet Model (2HDM) a search for a light Higgs boson in the mass range of 4-12 GeV has been performed in the Yukawa process e+e- -> b bbar A/h -> b bbar tau+tau-, using the data collected by the OPAL detector at LEP between 1992 and 1995 in e+e- collisions at about 91 GeV centre-of-mass energy. A likelihood selection is applied to separate background and signal. The number of observed events is in good agreement with the expected background. Within a CP-conserving 2HDM type II model the cross-section for Yukawa production depends on xiAd = |tan beta| and xihd = |sin alpha/cos beta| for the production of the CP-odd A and the CP-even h, respectively, where tan beta is the ratio of the vacuum expectation values of the Higgs doublets and alpha is the mixing angle between the neutral CP-even Higgs bosons. From our data 95% C.L. upper limits are derived for xiAd within the range of 8.5 to 13.6 and for xihd between 8.2 to 13.7, depending on the mass of the Higgs boson, assuming a branching fraction into tau+tau- of 100%. An interpretation of the limits within a 2HDM type II model with Standard Model particle content is given. These results impose constraints on several models that have been proposed to explain the recent BNL measurement of the muon anomalous magnetic moment.Comment: 24 pages, 9 figures, Submitted to Euro. Phys. J.