L’évolution d’une coopération bibliothéconomique dans le secteur de la santé: le consortium des ressources électroniques du RUIS de l’UdeM

Sous l’impulsion de la Loi 83, loi modifiant la Loi sur les services de santé et les services sociaux et d’autres dispositions législatives, sanctionnée en 2005, et fort d’une expérience issue d’une coopération de plus de 30 ans entre les bibliothèques des sciences de la santé de l’Université de Montréal et les bibliothèques de ses hôpitaux affiliés, un consortium est né ayant pour but de regrouper les efforts et augmenter l’offre documentaire pour mieux desservir ses clientèles. Après avoir décrit quelques consortiums canadiens dans le domaine de la santé, les auteurs présentent le nouveau consortium des ressources électroniques du Réseau universitaire intégré de santé de l’Université de Montréal (RUISUM)qui s’est vu confié le mandat de procurer des ressources informationnelles en sciences de la santé ainsi que des services afin de mieux soutenir l’enseignement, la recherche, la formation professionnelle continue et le soutien à la démarche clinique dans les établissements membres. Le territoire desservi par le RUIS de l’Université couvre un bassin de population de 3 millions d’habitants, représente 40% des soins de la santé de la province et s’adresse à plus de 25 000 professionnels de la santé. Dans le respect des stratégies de chaque établissement membre, le consortium du RUISUM a redéfinit le couple produit marché pour se positionner dans le segment des bibliothèques virtuelles. Il met l’accent sur la formation aux compétences informationnelles, sur l’interaction avec le personnel de la bibliothèque et utilise le web comme outil

Integrating information literacy in health sciences curricula: a case study from Québec

Objective: To portray an information literacy programme demonstrating a high level of integration in health sciences curricula and a teaching orientation aiming towards the development of lifelong learning skills. The setting is a French-speaking North American university. Methods: The offering includes standard workshops such as MEDLINE searching and specialised sessions such as pharmaceutical patents searching. A contribution to an international teaching collaboration in Haiti where workshops had to be thoroughly adapted to the clientele is also presented. Online guides addressing information literacy topics complement the programme. Results and evaluation: A small team of librarians and technicians taught 276 hours of library instruction during the 2011-2012 academic year. Methods used for evaluating information skills include scoring features of literature searches and user satisfaction surveys. Discussion: Privileged contacts between librarians and faculty resulting from embedded library instruction as well as from active participation in library committees result in a growing reputation of library services across academic departments and bring forth collaboration opportunities. Sustainability and evolution of the library instruction programme is warranted by frequent communication with partners in the clinical field, active involvement in academic networks and health library associations, and reflective professional strategies

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod

Toll-Like Receptor 3 (TLR3) Plays a Major Role in the Formation of Rabies Virus Negri Bodies

Human neurons express the innate immune response receptor, Toll-like receptor 3 (TLR3). TLR3 levels are increased in pathological conditions such as brain virus infection. Here, we further investigated the production, cellular localisation, and function of neuronal TLR3 during neuronotropic rabies virus (RABV) infection in human neuronal cells. Following RABV infection, TLR3 is not only present in endosomes, as observed in the absence of infection, but also in detergent-resistant perinuclear inclusion bodies. As well as TLR3, these inclusion bodies contain the viral genome and viral proteins (N and P, but not G). The size and composition of inclusion bodies and the absence of a surrounding membrane, as shown by electron microscopy, suggest they correspond to the previously described Negri Bodies (NBs). NBs are not formed in the absence of TLR3, and TLR3−/− mice—in which brain tissue was less severely infected—had a better survival rate than WT mice. These observations demonstrate that TLR3 is a major molecule involved in the spatial arrangement of RABV–induced NBs and viral replication. This study shows how viruses can exploit cellular proteins and compartmentalisation for their own benefit

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.

This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.3448Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.We thank all participants of all the studies included for enabling this research by their participation in these studies. Computer resources for this project have been provided by the high-performance computing centers of the University of Michigan and the University of Regensburg. Group-specific acknowledgments can be found in the Supplementary Note. The Center for Inherited Diseases Research (CIDR) Program contract number is HHSN268201200008I. This and the main consortium work were predominantly funded by 1X01HG006934-01 to G.R.A. and R01 EY022310 to J.L.H

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

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

Contamination and Biomarkers in the Great Blue Heron, an Indicator

breeding colonies of the great blue heron on the St. Lawrence River and its 12 estuary (Que´bec, Canada) were investigated in the framework of a biomonitoring program. Fledglings from 13 colonies in freshwater were more contaminated with mercury, PCBs and many organic contaminants than 14 those from estuarine colonies. The level of contamination in the St. Lawrence River is generally below the 15 levels of toxicological effects for the great blue heron. The molar ratio of retinol: retinyl palmitate in heron 16 eggs was correlated with total PCBs (r=0.79) and mirex (r=0.90). In plasma, all biochemical parameters 17 were significantly different between freshwater and marine colonies. Plasma retinol concentrations at the 18 Dickerson and He´ron colonies were significantly lower compared with those at Grande Ile (p&lt;0.05) and 19 Steamboat (p&lt;0.001). Based on retinoid and b-carotene concentrations in eggs, low plasma retinol was not 20 associated with possible dietary deficiency. Plasma retinol was negatively correlated with many PCB 21 congeners, total PCBs (r=)0.78), p,p¢-DDE, trans-nonachlor and a-HCH. Similarly, the hormone T3 was 22 correlated with many PCB congeners, total PCBs (r=)0.69) and the same organochlorine chemicals. 23 Plasma LDH concentrations were different among freshwater colonies, Grande Ile and He´ron colonies 24 having LDH values significantly greater than those of Steamboat (respectively, p&lt;0.05 and p&lt;0.01). 25 Globally, the health status of the St. Lawrence great blue heron population was judged to be acceptable, 26 however, several biomarkers indicated positive responses to contaminants