Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Hospitals locations, activities and relationships, in Burgundy at the end of the medieval times

L’étude présentée ici est le résultat d’un inventaire des établissements d’assistance présents dans les limites des diocèses d'Autun, d'Auxerre, de Chalon-sur-Saône, de Nevers et du sud du diocèse de Langres, entre les XIIe et XVe siècles, cette aire d'étude correspondant ainsi à un espace d'influence bourguignonne. À partir des données récoltées, un atlas de l'assistance et un répertoire des sources sur les hôpitaux médiévaux de l'espace bourguignon ont été réalisés. Les informations ainsi compilées se sont révélées être très variées, mais aussi particulièrement hétéroclites. Malgré tout, une réflexion a été menée au sujet des caractéristiques de ces hôpitaux et de leurs rapports avec les milieux économiques, religieux, politiques et sociaux qui les environnent. Elle s'articule donc autour de trois parties abordant tour à tour l'influence de facteurs extérieurs sur la création et l'implantation des hôpitaux, puis les interactions entre les structures hospitalières avec les milieux où elles se trouvent ainsi que la façon dont elles peuvent être instrumentalisées, et enfin elle met en parallèle l'évolution des établissements d'assistance avec celle de la société et des rapports de pouvoirs. Il en ressort, entre autres, que les établissements d'assistance sont des points de repère dans la construction du paysage médiéval, qu’ils sont importants pour l'équilibre de la société, mais qu'ils ont également joué un rôle majeur dans les jeux de pouvoirs et dans l'expression de la foi chrétienne médiévale.The study presented here is the conclusion of an inventory about hospitals having existed on the territory of some dioceses (Autun, Auxerre, Chalon-sur-Saône, Nevers and the south of that of Langres diocese) between XIIth and XVth centuries. Based on the data collected, an atlas of assistance and a directory of sources on medieval hospitals of the study area has been made. The compiled informations proved to be very different but also very heterogeneous. Nevertheless, reflexions were conducted about the characteristics of these hospitals and their relationships with their economic, religious, political and social environments. It revolves around three parts dealing by turns the influence of external factors on the creation and implementation of medieval hospitals, interactions between hospitals with the environments where they are and how are they can be manipulated , and it ends with the parallel evolution of institutions with the support of society and power relations. It shows, among other things, that charity hospitals are landmarks in the medieval landscape, they are importants to the balance of society, but they also have a fonction in the power games and in the expression of the medieval Christian faith

Implantations, activités et relations des établissements d'assistance en Bourgogne à la fin du Moyen Age

The study presented here is the conclusion of an inventory about hospitals having existed on the territory of some dioceses (Autun, Auxerre, Chalon-sur-Saône, Nevers and the south of that of Langres diocese) between XIIth and XVth centuries. Based on the data collected, an atlas of assistance and a directory of sources on medieval hospitals of the study area has been made. The compiled informations proved to be very different but also very heterogeneous. Nevertheless, reflexions were conducted about the characteristics of these hospitals and their relationships with their economic, religious, political and social environments. It revolves around three parts dealing by turns the influence of external factors on the creation and implementation of medieval hospitals, interactions between hospitals with the environments where they are and how are they can be manipulated , and it ends with the parallel evolution of institutions with the support of society and power relations. It shows, among other things, that charity hospitals are landmarks in the medieval landscape, they are importants to the balance of society, but they also have a fonction in the power games and in the expression of the medieval Christian faith.L’étude présentée ici est le résultat d’un inventaire des établissements d’assistance présents dans les limites des diocèses d'Autun, d'Auxerre, de Chalon-sur-Saône, de Nevers et du sud du diocèse de Langres, entre les XIIe et XVe siècles, cette aire d'étude correspondant ainsi à un espace d'influence bourguignonne. À partir des données récoltées, un atlas de l'assistance et un répertoire des sources sur les hôpitaux médiévaux de l'espace bourguignon ont été réalisés. Les informations ainsi compilées se sont révélées être très variées, mais aussi particulièrement hétéroclites. Malgré tout, une réflexion a été menée au sujet des caractéristiques de ces hôpitaux et de leurs rapports avec les milieux économiques, religieux, politiques et sociaux qui les environnent. Elle s'articule donc autour de trois parties abordant tour à tour l'influence de facteurs extérieurs sur la création et l'implantation des hôpitaux, puis les interactions entre les structures hospitalières avec les milieux où elles se trouvent ainsi que la façon dont elles peuvent être instrumentalisées, et enfin elle met en parallèle l'évolution des établissements d'assistance avec celle de la société et des rapports de pouvoirs. Il en ressort, entre autres, que les établissements d'assistance sont des points de repère dans la construction du paysage médiéval, qu’ils sont importants pour l'équilibre de la société, mais qu'ils ont également joué un rôle majeur dans les jeux de pouvoirs et dans l'expression de la foi chrétienne médiévale

Persistent headaches one year after bacterial meningitis: prevalence, determinants and impact on quality of life

International audienceBackground: Little is known on headaches long-term persistence after bacterial meningitis and on their impact on patients' quality of life.Methods: In an ancillary study of the French national prospective cohort of community-acquired bacterial meningitis in adults (COMBAT) conducted between February 2013 and July 2015, we collected self-reported headaches before, at onset, and 12 months (M12) after meningitis. Determinants of persistent headache (PH) at M12, their association with M12 quality of life (SF 12), depression (Center for Epidemiologic Studies Depression Scale) and neuro-functional disability were analysed.Results: Among the 277 alive patients at M12 87/274 (31.8%), 213/271 (78.6%) and 86/277 (31.0%) reported headaches before, at the onset, and at M12, respectively. In multivariate analysis, female sex (OR: 2.75 [1.54-4.90]; p < 0.001), pre-existing headaches before meningitis (OR: 2.38 [1.32-4.30]; p < 0.01), higher neutrophilic polynuclei percentage in the CSF of the initial lumbar puncture (OR: 1.02 [1.00-1.04]; p < 0.05), and brain abscess during the initial hospitalisation (OR: 8.32 [1.97-35.16]; p < 0.01) were associated with M12 persistent headaches. Neither the responsible microorganism, nor the corticoids use were associated with M12 persistent headaches. M12 neuro-functional disability (altered Glasgow Outcome Scale; p < 0.01), M12 physical handicap (altered modified Rankin score; p < 0.001), M12 depressive symptoms (p < 0.0001), and M12 altered physical (p < 0.05) and mental (p < 0.0001) qualities of life were associated with M12 headaches.Conclusion: Persistent headaches are frequent one year after meningitis and are associated with quality of life alteration

One-Year Sequelae and Quality of Life in Adults with Meningococcal Meningitis: Lessons from the COMBAT Multicentre Prospective Study

Trial registration: ClinicalTrial.Gov identification number NCT01730690.International audienceIntroduction: COMBAT is a prospective, multicentre cohort study that enrolled consecutive adults with community-acquired bacterial meningitis (CABM) in 69 participating centres in France between February 2013 and July 2015 and followed them for 1 year.Methods: Patients aged at least 18 years old, hospitalised with CABM were followed during their hospitalisation and then contacted by phone 12 months after enrolment. Here we present the prevalence of sequelae at 12 months in a subgroup of patients with meningococcal meningitis.Results: Five of the 111 patients with meningococcal meningitis died during initial hospitalisation and two died between discharge and 12 months, leaving 104 patients alive 1 year after enrolment, 71 of whom provided 12-month follow-up data. The median age was 30.0 years and 54.1% of the patients had no identified risk factor for meningitis. More than 30% reported persistent headache, more than 40% were not satisfied with their sleep and 10% had concentration difficulties. Hearing loss was present in about 15% of the patients and more than 30% had depressive symptoms. About 13% of the patients with a previous professional activity had not resumed work. On the SF-12 Health Survey, almost 50% and 30% had physical component or mental component scores lower than the 25th percentile of the score distribution in the French general population. There was a non-significant improvement in the patients' disability scores from hospital discharge to 12 months (p = 0.16), but about 10% of the patients had residual disability.Conclusions: Although most patients in our cohort survive meningococcal meningitis, the long-term burden is substantial and therefore it is important to ensure a prolonged follow-up of survivors and to promote preventive strategies, including vaccination

Relationship between serotypes, disease characteristics and 30-day mortality in adults with invasive pneumococcal disease

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Impact on disease mortality of clinical, biological, and virological characteristics at hospital admission and overtime in COVID‐19 patients

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