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

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

Slow responses of understory plants of maple-dominated forests to white-tailed deer experimental exclusion

We examined the response of understory plants in mature maple-dominated forests of southern Québec, Canada, following about 30 years of high deer densities, using a deer exclosure experiment. An exclosure and a paired control of 625m2 each were established on six sites in 1998. An exclosure and a paired control of 16m2 were added at each of the same sites in 2003 but under a recent canopy gap to determine if light could enhance plant responses. We measured plant richness and abundance, and aboveground biomass of different plant groups for 8 years in the understory plots and for 3 years in the canopy gaps. Four herbaceous species were also monitored individually in the same plots. No significant differences between treatments were found in plots under forest cover, except for lateral obstruction at 0–50cm height which was higher in the exclosures. Under canopy gaps, however, tree seedling and total plant abundance were higher in deer exclosures than in control plots. Trillium erectum recovered partially as individuals were taller, had larger leaves and more frequently produced a flower or a fruit in the absence of deer browsing under forest cover. To a lesser extent, Erythronium americanum and Maianthemum canadense also exhibited signs of recovery but were still at the single-leaf stage after 8 years of recovery. In general, the different plant groups exhibited little recovery following deer exclusion, possibly because of the low light levels that prevailed in the understory of undisturbed maple-dominated forests. The higher latitude of the present study could also contribute to the slow recovery rates of the different groups of plants compared to studies conducted in northeastern USA. Variability among sites and years had an effect on detection of statistically significant differences. Trends are however appearing over time, suggesting that many understory plants are recovering very slowly following deer exclusion. Our results emphasize the importance of studying large herbivore–forest interactions on different groups of plants, but also on specific species, and under different latitudes to be fully understood

L’apprentissage de la langue écrite

Comment les enfants apprennent-ils à lire et à écrire ? D’où proviennent les difficultés observées ? Comment les prévenir ou les enrayer ? Ces questions passionnantes et d’actualité sur le plan de la politique nationale et européenne se sont rapidement muées en sujet de polémiques. Leur mise en avant médiatique a pu laisser penser qu’il existait des ruptures au sein de la communauté scientifique. Un colloque intitulé « Approche cognitive de l’apprentissage de la langue écrite » (Rennes, octobre 2006) avait pourtant permis de montrer une cohésion et une collaboration fécondes entre les nombreux chercheurs français et étrangers qui y participaient. Suite à ce constat, nous souhaitions présenter les avancées récentes de la communauté scientifique internationale dans le domaine de l’apprentissage des procédures de lecture (de l’identification des mots à la compréhension des textes écrits) et de productions des mots écrits (du geste graphique au code orthographique). À travers cette collaboration, le lecteur découvrira que ces avancées s’articulent autour de deux grands axes de recherche qui organisent la structure de l’ouvrage : d’une part, la nature des unités linguistiques prises en compte à l’écrit et d’autre part, les traitements impliqués dans l’installation des procédures de lecture-écriture

A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis.

The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance

A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis.

The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance

Convalescent plasma for hospitalized patients with COVID-19: an open-label, randomized controlled trial

AbstractThe efficacy of convalescent plasma for coronavirus disease 2019 (COVID-19) is unclear. Although most randomized controlled trials have shown negative results, uncontrolled studies have suggested that the antibody content could influence patient outcomes. We conducted an open-label, randomized controlled trial of convalescent plasma for adults with COVID-19 receiving oxygen within 12 d of respiratory symptom onset (NCT04348656). Patients were allocated 2:1 to 500 ml of convalescent plasma or standard of care. The composite primary outcome was intubation or death by 30 d. Exploratory analyses of the effect of convalescent plasma antibodies on the primary outcome was assessed by logistic regression. The trial was terminated at 78% of planned enrollment after meeting stopping criteria for futility. In total, 940 patients were randomized, and 921 patients were included in the intention-to-treat analysis. Intubation or death occurred in 199/614 (32.4%) patients in the convalescent plasma arm and 86/307 (28.0%) patients in the standard of care arm—relative risk (RR) = 1.16 (95% confidence interval (CI) 0.94–1.43,P = 0.18). Patients in the convalescent plasma arm had more serious adverse events (33.4% versus 26.4%; RR = 1.27, 95% CI 1.02–1.57,P = 0.034). The antibody content significantly modulated the therapeutic effect of convalescent plasma. In multivariate analysis, each standardized log increase in neutralization or antibody-dependent cellular cytotoxicity independently reduced the potential harmful effect of plasma (odds ratio (OR) = 0.74, 95% CI 0.57–0.95 and OR = 0.66, 95% CI 0.50–0.87, respectively), whereas IgG against the full transmembrane spike protein increased it (OR = 1.53, 95% CI 1.14–2.05). Convalescent plasma did not reduce the risk of intubation or death at 30 d in hospitalized patients with COVID-19. Transfusion of convalescent plasma with unfavorable antibody profiles could be associated with worse clinical outcomes compared to standard care.</jats:p