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

ETUDE DES EFFETS HEMODYNAMIQUES ET ANTIFIBROSANTS DE L'ADMINISTRATION CHRONIQUE D'UN DONNEUR DE MONOXYDE D'AZOTE (NO) SPECIFIQUE DU FOIE DANS UN MODELE DE FIBROSE HEPATIQUE CHEZ LE RAT (DES PHARMACIE SPECIALISEE)

ANGERS-BU Médecine-Pharmacie (490072105) / SudocSudocFranceF

“Ndongobacter massiliensis” gen. nov., sp. nov., a new bacterial genus isolated from human urine sample after de novo kidney transplantation

International audienceno abstrac

“Ndongobacter massiliensis” gen. nov., sp. nov., a new bacterial genus isolated from human urine sample after de novo kidney transplantation

International audienceno abstrac

Pneumocystis jirovecii pneumonia in HIV-negative patients: A prospective study with focus on immunosuppressive drugs and markers of immune impairment

International audienc

NATURAL KILLER CELL ACTIVATION IS A POTENT CYTOTOXIC MECHANISM SUSTAINING ADVERSE CYTOTOXIC EFFECTS OF DONOR-SPECIFIC ANTIBODIES IN SOLID ORGAN TRANSPLANTATION

International audienceno abstrac

NATURAL KILLER CELL ACTIVATION IS A POTENT CYTOTOXIC MECHANISM ă SUSTAINING ADVERSE CYTOTOXIC EFFECTS OF DONOR-SPECIFIC ANTIBODIES IN ă SOLID ORGAN TRANSPLANTATION

International audienceno abstrac

In vivo transcriptomic profiling using cell encapsulation identifies effector pathways of systemic aging

Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here, we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence, and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.We thank Phoukham Phothirath and Oliver Rizzo of the preclinical investigations group of Nestlé Research for expert advice and support with in vivo experiments. OM, JNF, and CFB are supported by the Fondation Suisse de Recherche sur les Maladies Musculaires (FSRMM). CFB is supported by the Canadian Institutes of Health Research (CIHR, PJT-162442), the Natural Sciences and Engineering Research Council of Canada (NSERC, RGPIN-2017-05490), the Fonds de Recherche du Québec – Santé (FRQS, Dossiers 296357, 34813, and 36789), the ThéCell Network (supported by the FRQS), the Canadian Stem Cell Network, and a research chair of the Centre de Recherche Médicale de l’Université de Sherbrooke (CRMUS). PMC is supported by ERC-2016-AdG-741966, La Caixa-HEALTH-HR17-00040, MDA, AFM, MWRF, UPGRADE-H2020-825825, RTI2018-096068-B-I00, a María de Maeztu Unit of Excellence award to UPF (MDM-2014-0370), and a Severo Ochoa Center of Excellence award to the CNIC (SEV-2015-0505). XH is recipient of a Severo Ochoa FPI (SEV-2015-0505-17-1) predoctoral fellowship