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International audience; Background and objectives The fact that metabolism and immune function are regulated by an endogenous molecular clock that generates circadian rhythms suggests that the magnitude of ischemia reperfusion, and subsequent inflammation on kidney transplantation, could be affected by the time of the day. Design, setting, participants, & measurements We evaluated 5026 individuals who received their first kidney transplant from deceased heart-beating donors. In a cause-specific multivariable analysis, we compared delayed graft function and graft survival according to the time of kidney clamping and declamping. Participants were divided into those clamped between midnight and noon ( ante meridiem [ am ] clamping group; 65%) or clamped between noon and midnight ( post meridiem [ pm ] clamping group; 35%), and, similarly, those who underwent am declamping (25%) or pm declamping (75%). Results Delayed graft function occurred among 550 participants (27%) with am clamping and 339 (34%) with pm clamping (adjusted odds ratio, 0.81; 95% confidence interval, 0.67 to 0.98; P =0.03). No significant association was observed between clamping time and overall death-censored graft survival (hazard ratio, 0.92; 95% confidence interval, 0.77 to 1.10; P =0.37). No significant association of declamping time with delayed graft function or graft survival was observed. Conclusions Clamping between midnight and noon was associated with a lower incidence of delayed graft function, whereas declamping time was not associated with kidney graft outcomes.

Levamisole was initially prescribed for the treatment of intestinal worms. Because of immunomodulatory properties, levamisole has been used in inflammatory pathologies and in cancers in association with 5-fluorouracil. Levamisole is misused as a cocaine adulterant. Post-marketing reports have implicated levamisole in the occurrence of adverse drug reactions (ADRs) and its use is now limited in Europe and North America. In contrast, all other parts of the World continue to use single-dose levamisole as an anthelmintic. The aim of this study was to identify ADRs reported after levamisole exposure in VigiBase, the World Health Organisation's pharmacovigilance database, and analyse their frequency compared to other drugs and according to levamisole type of use.All levamisole-related ADRs were extracted from VigiBase. Disproportionality analyses were conducted to investigate psychiatric, hepatobiliary, renal, vascular, nervous, blood, skin, cardiac, musculoskeletal and general ADRs associated with levamisole and other drugs exposure. In secondary analyses, we compared the frequency of ADRs between levamisole and mebendazole and between levamisole type of use.Among the 1763 levamisole-related ADRs identified, psychiatric disorders (reporting odds ratio with 95% confidence intervals: 1.4 [1.2-2.6]), hepatobiliary disorders (2.4 [1.9-4.3]), vasculitis (6.5 [4.1-10.6]), encephalopathy (22.5 [17.4-39.9]), neuropathy (4.3 [2.9-7.1]), haematological disorders, mild rashes and musculoskeletal disorders were more frequently reported with levamisole than with other drug. The majority of levamisole-related ADRs occurred when the drug was administrated for a non-anti-infectious indication.The great majority of the levamisole-related ADRs concerned its immunomodulatory indication and multiple-dose regimen. Our results suggest that single-dose treatments for anthelmintic action have a good safety profile.

International audience; Background: Stuttering is a speech disorder characterized by poor fluency of speech despite the speech production organs being normal. Numerous factors contribute to stuttering, and it may also be an iatrogenic effect of certain drugs. The aim of this study was to investigate the association between stuttering and drug exposure.Research design and methods: We investigated the association between drugs and stuttering. We analyzed reports in the World Health Organization global individual case safety reports database (Vigibase) up to 31 May 2020 with the MedDRA lower level terms 'stutter' and 'stuttering.' The association between a drug and the occurrence of the adverse drug reaction was estimated by disproportionality analysis. Reporting odds ratios (ROR) were calculated with 95% confidence intervals.Results: In total, 724 notifications were identified using the MedDRA terms selected. The main drugs implicated were methylphenidate (ROR = 19.58; 95% CI: 13.3-28.8), topiramate (ROR = 12.5; 95% CI: 7.1-22.1), olanzapine (ROR = 12; 95% CI: 8-17.9) and golimumab (ROR = 10.2; 95% CI: 5.5-19.1).Conclusions: When stuttering occurs in a patient treated by drugs affecting neurotransmission, a drug-induced origin of the stutter should be considered.

Mass media plays an important role in the construction and circulation of risk perception associated with animals. Widely feared groups such as spiders frequently end up in the spotlight of traditional and social media. We compiled an expert-curated global database on the online newspaper coverage of human-spider encounters over the past ten years (2010–2020). This database includes information about the location of each human-spider encounter reported in the news article and a quantitative characterisation of the content—location, presence of photographs of spiders and bites, number and type of errors, consultation of experts, and a subjective assessment of sensationalism. In total, we collected 5348 unique news articles from 81 countries in 40 languages. The database refers to 211 identified and unidentified spider species and 2644 unique human-spider encounters (1121 bites and 147 as deadly bites). To facilitate data reuse, we explain the main caveats that need to be made when analysing this database and discuss research ideas and questions that can be explored with it. Finnish Museum of Natural History (LUOMUS; University of Helsinki, Helsinki, Finland). info:eu-repo/semantics/publishedVersion

International audience; The Open Microscopy Environment Remote Objects (OMERO) is an open source image manager used by many biologists to store, organize, view and share microscopy images, while the open source software ImageJ/Fiji is a very popular program used to analyse them. However, there is a lack of an easy-to-use generic tool to run a workflow on a batch of images without having to download them to local computers; and to automatically organize the results in OMERO. To offer this functionality, we have built three tools in Java language: “Simple OMERO Client”, a library to communicate with an OMERO database from Java softwares ; an ImageJ/Fiji plugin to run a macro-program on a batch of images from OMERO and “OMERO Macro extensions“, a dedicated vocabulary to interact with OMERO in macro-programming. The latter is intended for developers, with additional possibilities using tag criteria, while the “Batch OMERO plugin” is more geared towards non-IT scientists and has a very easy to use interface. Both tools are illustrated with a use case.

The inherent risk of agranulocytosis associated with clozapine requires the realization of weekly white blood cell monitoring (WBCM) during the 18 first weeks of treatment. The aim of this study was to assess the compliance with WBCM during clozapine initiation for schizophrenia and Parkinson's disease (PD) subjects.The analysis was conducted using SNDS data on a cohort of new users of clozapine in 2018. We analyzed all reimbursements for WBCM from 2 weeks before the index date to 18 weeks after (optimal monitoring during hospitalization was assumed). The primary outcome was the proportion of good realization of WBCM according to different thresholds of completion (70%; 80%; 90%). Descriptive and comparative analyses with chi-squared test or Student's t-test were performed.Two hundred and ninety-six subjects were included. Rates of patients with WBCM realization over 70%, 80%, and 90% of WBCM expected were, respectively, 78.1%, 70.0%, and 56.9% for subjects with schizophrenia and 71.3%, 63.2%, and 47.8% for PD subjects. Only hospitalization during the follow-up period for schizophrenia subjects was significantly associated with good WBCM realization.We observed rather good results for compliance with clozapine initial monitoring. Other studies are needed to confirm our results.

International audience; The heterogeneity of electronic health records model is a major problem: it is necessary to gather data from various models for clinical research, but also for clinical decision support. The Observational Medical Outcomes Partnership – Common Data Model (OMOP-CDM) has emerged as a standard model for structuring health records populated from various other sources. This model is proposed as a relational database schema. However, in the field of decision support, formal ontologies are commonly used. In this paper, we propose a translation of OMOP-CDM into an ontology, and we explore the utility of the semantic web for structuring EHR in a clinical decision support perspective, and the use of the SPARQL language for querying health records. The resulting ontology is available online.

International audience; The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change).To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)—a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting.SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language).The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.

Background Ivermectin is known to cause severe encephalopathies in subjects infected with loiasis, an endemic parasite in Sub-Saharan Africa (SSA). In addition, case reports have described ivermectin-related serious adverse drug reactions (sADRs) such as toxidermias, hepatic and renal disorders. The aim of this study was to identify suspected sADRs reported after ivermectin administration in VigiBase, the World Health Organization’s global individual case safety reports database and analyze their frequency relative to the frequency of these events after other antinematodal drugs reported in SSA and other areas of the world (ROW). Methods All antinematodal-related sADRs were extracted from VigiBase. Disproportionality analyses were conducted to investigate nervous, cutaneous, psychiatric, respiratory, renal, hepatic and cardiac suspected sADRs reported after ivermectin and benzimidazole drug administration across the world, in SSA and RoW. Principal findings 2041 post-ivermectin or post-benzimidazole suspected sADRs were identified including 667 after ivermectin exposure (208 in SSA and 459 in the RoW). We found an increased reporting for toxidermias, encephalopathies, confusional disorders after ivermectin compared to benzimidazole drug administration. Encephalopathies were not only reported from SSA but also from the RoW (adjusted reporting odds ratios [aROR] 6.30, 95% confidence interval: 2.68–14.8), highlighting the fact these types of sADR occur outside loiasis endemic regions. Conclusion We described for the first time suspected sADRs associated with ivermectin exposure according to geographical origin. While our results do not put in question ivermectin’s excellent safety profile, they show that as for all drugs, appropriate pharmacovigilance for adverse reactions is indicated., Author summary Ivermectin is a drug used worldwide for various indications: onchocerciasis, lymphatic filariasis, strongyloidiasis, human sarcoptic scabies, acarodermatitis and rosacea. In the early 1990s, it was discovered that ivermectin could induce severe encephalopathies in some patients with high parasite loads of Loa loa, a filarial nematode. This objective of this pharmacovigilance study is to summarize serious neurological and non-neurological post-ivermectin adverse drug reactions reported in the World Health Organization database called VigiBase. This study shows that reported serious adverse drug reactions associated with ivermectin are fairly consistent with those mentioned in the official product information of ivermectin but also provides some new signals. Serious post-ivermectin encephalopathies can also occur outside of Loa loa endemic regions but the understanding of the mechanism by which it occurs requires further studies. A new signal concerning two serious toxidermias (DRESS syndrome and acute generalized exanthematous pustulosis) is also described. A lack of reporting of adverse drug reactions is noticeable in some Sub-Saharan African countries, and actions are needed to increase the reporting rates of these adverse effects in these countries.

Background Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources. The diversity of information used to describe life-scientific digital resources presents an obstacle to their utilization. Although several standardization efforts are emerging, no information schema has been sufficiently detailed to enable uniform semantic and syntactic description—and cataloguing—of bioinformatics resources. Findings Here we describe biotoolsSchema, a formalized information model that balances the needs of conciseness for rapid adoption against the provision of rich technical information and scientific context. biotoolsSchema results from a series of community-driven workshops and is deployed in the bio.tools registry, providing the scientific community with >17,000 machine-readable and human-understandable descriptions of software and other digital life-science resources. We compare our approach to related initiatives and provide alignments to foster interoperability and reusability. Conclusions biotoolsSchema supports the formalized, rigorous, and consistent specification of the syntax and semantics of bioinformatics resources, and enables cataloguing efforts such as bio.tools that help scientists to find, comprehend, and compare resources. The use of biotoolsSchema in bio.tools promotes the FAIRness of research software, a key element of open and reproducible developments for data-intensive sciences.

International audience; Benchmarking is a common and effective method for measuring and analyzing ICU performance. With the existence of national registries, objective information can now be obtained to allow benchmarking of ICU care within and between countries. The present manuscript briefly describes the current status of benchmarking in healthcare and critical care and presents the LOGIC project, an initiative to promote international benchmarking for intensive care units. Currently 13 registries have joined LOGIC. We showed large differences in the utilization of ICU as well as resources and in outcomes. Despite the need for careful interpretation of differences due to variation in definitions and limited risk adjustment, LOGIC is a growing worldwide initiative that allows access to insightful epidemiologic data from ICUs in multiple databases and registries.

ObjectiveTo determine the observed and expected incidence rates of paraneoplastic neurologic syndromes (PNSs) and autoimmune encephalitides (AEs) diagnosed in France between 2016 and 2018, we conducted a population-based epidemiologic study.MethodsObserved incidence rates were stratified by sex, age groups, region of care, year of diagnosis, and disease subgroups. National expected incidence rates were calculated based on rates obtained in the area directly adjacent to the Reference Center using a mixed Poisson model and compared with observed incidence rates.ResultsSix hundred thirty-two patients with definite PNS or AE met the inclusion criteria. The observed incidence rate of definite PNS and AE in France was 3.2 per million person-years (CI95%: 2.9–3.4) compared with an expected incidence rate of 7.1 per million person-years (CI95%: 3.9–11.4). The national observed incidence rate for the antibody-positive AE subgroup increased from 1.4 per million person-years (CI95%: 1.2–1.7) in 2016 to 2.1 per million person-years (CI95%: 1.7–2.4) in 2018, thus surpassing the incidence rate of classical PNS (1.2 per million person-years [CI95%: 1.0–1.5]) of 2018.ConclusionsThere was a significant widespread year-to-year increase in the incidence of diagnoses registered with the Reference Center for all subgroups of PNS and AE studied. The national observed incidence rate is likely underestimated due to underdiagnosis and underreporting.

International audience; Information relevant to pharmacogenomics studies is available in several open databases, which makes it difficult to synthetize the available data. Within the PractikPharma project, several databases were integrated to PGxLOD, a resource dedicated to the generation and verification of pharmacogenomic influence on drug responses. The Comparative Toxicogenomic Database (CTD) describes the toxic effects of many chemicals on living species based on the literature. Since drugs are peculiar chemicals and side effects are peculiar toxic effects, we aimed at extracting information from CTD that matches drug side effects in the human specie.

International audience; Purpose: Despite the benefits of adjuvant endocrine therapy (AET) for reducing recurrence and mortality risks after hormone-sensitive breast cancer, AET adherence is sub-optimal for a high proportion of women. However, little is known about long-term patterns of AET adherence over the minimally recommended 5 years. Our objectives were to: (1) identify 5-year AET adherence trajectory groups; (2) describe trajectory groups according to adherence measures traditionally used (i.e., Proportion of Days Covered); and (3) explore factors associated with trajectories.Methods: We conducted a 5-year cohort study using data from a French national study that included AET dispensing data. Women diagnosed with first non-metastatic breast cancer and having at least 1 AET dispensing in the 12 months after diagnosis were included. Group-based trajectory modeling was used to identify adherence trajectory groups by clustering similar patterns of monthly AET dispensing. Multinomial logistic regressions were used to identify factors associated with trajectories.Results: Among 674 women, five AET adherence trajectory groups were identified: (1) quick decline and stop (5.2% of women); (2) moderate decline and stop (6.4%); (3) slow decline (17.2%); (4) high adherence (30.0%); and (5) maintenance of very high adherence (41.2%). Mean 5-year Proportion of Days Covered varied from 10 to 97% according to trajectories. Women who did not receive chemotherapy or a personalized care plan were more likely to belong to trajectories where AET adherence declined and stopped.Conclusion: Our results provide information on the diversity of longitudinal AET adherence patterns, the timing of decline and discontinuation and associated factors that could inform healthcare professionals.

Objectives The aim of this study was to develop a risk score integrating cytochrome P450 2C19 loss-of-function genotypes with clinical risk factors influencing clopidogrel response that would allow the identification with more precision of subjects at risk for high platelet reactivity (HPR) and adverse clinical outcomes. Background Clopidogrel is the most broadly used platelet P2Y12 inhibitor. However, a considerable number of patients achieve inadequate platelet inhibition, with persistent HPR, an established marker of increased thrombotic risk, underscoring the need for tools to help identify these subjects. Although carriers of loss-of-function alleles of the cytochrome P450 2C19 enzyme have reduced clopidogrel metabolism leading to increased rates of HPR and thrombotic complications, this explains only a fraction of the pharmacodynamic response to clopidogrel, and a number of clinical factors have also been shown to have contributing roles. Methods Three prospective and independent studies were used to: 1) develop a risk score integrating genetic and clinical factors to identify patients with HPR while on clopidogrel; 2) investigate the external validity of the risk score; and 3) define clinical outcomes associated with the risk score in a cohort of patients with myocardial infarction treated with clopidogrel. Results A risk score ABCD-GENE (Age, Body Mass Index, Chronic Kidney Disease, Diabetes Mellitus, and Genotyping) was developed incorporating 5 independent predictors of HPR: 4 clinical (age >75 years, body mass index >30 kg/m2, chronic kidney disease [glomerular filtration rate Conclusions The ABCD-GENE score is a simple tool to identify patients with HPR on clopidogrel and who are at increased risk for adverse ischemic events, including mortality, following an acute myocardial infarction. In patients with a high ABCD-GENE score, long-term oral P2Y12 inhibitors other than clopidogrel should be considered.

BACKGROUND: Treatment management and outcomes of unruptured nonsaccular aneurysms are different compared with their saccular counterparts. PURPOSE: Our aim was to analyze the outcomes after flow diversion among nonsaccular unruptured lesions. DATA SOURCES: A systematic search of 3 data bases (2005–2019) was performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. STUDY SELECTION: We included studies reporting flow diversion for nonsaccular unruptured aneurysms of the posterior and distal anterior circulations. Anterior circulation lesions were included if located distal to the petrocavernous and supraclinoid ICA (MCA, A1, anterior communicating artery, A2). Giant dolichoectatic holobasilar lesions were excluded because of their poor treatment outcomes. DATA ANALYSIS: Aneurysm occlusion and complication rates were calculated (random effects meta-analysis). DATA SYNTHESIS: We included 15 studies (213 aneurysms). The long-term adequate occlusion rate was 85.3% (137/168; 95% CI, 78.2%–92.4%; I(2) = 42.3%). Treatment-related complications were 17.4% (41/213; 95% CI, 12.45%–22.4%; I(2) = 0%). Overall, 15% (37/213; 95% CI, 10%–20%; I(2) = 0%) were ischemic events. Procedure-related morbidity was 8% (20/213; 95% CI, 5%–12%; I(2) = 0%). Fusiform or dissecting types had comparable adequate occlusion (116/146 = 83%; 95% CI, 74%–92%; I(2) = 48% versus 33/36 = 89%; 95% CI, 80%–98%; I(2) = 0%; P = .31) and complication rates (35/162 = 17%; 95% CI, 10%–25%; I(2) = 24% versus 11/51 = 19%; 95% CI, 10%–31%; I(2) = 0%; P = .72). Aneurysm size (>10 versus ≤10 mm) was independently associated with a higher rate of complications (OR = 6.6; 95% CI, 1.3–15; P = .02). The rate of ischemic events after discontinuation of the antiplatelet therapy was 5% (5/93; 95% CI, 2%–9%; I(2) = 0%). LIMITATIONS: Small and retrospective studies were available for this meta-analysis. CONCLUSIONS: Unruptured nonsaccular aneurysms located in the posterior and distal anterior circulations can be effectively treated with flow diversion. Nevertheless, treatment-related complications are not negligible, with about 15% ischemic events and 8% morbidity. Larger size (>10 mm) significantly increases the risk of procedure-related adverse events.

International audience; Multiple drug hypersensitivity syndrome (MDHS) is defined as confirmed drug hypersensitivity (DH) to at least 2 chemically and pharmacologically unrelated drugs. Reports of MDHS are scarce and poorly specified, and studies that diagnose MDHS on the basis of positive allergy test results are lacking.Objective: To evaluate retrospectively the frequency and characteristics of patients with MDHS in a large database.Methods: We included all patients who consulted and were tested in our Allergy Unit between September 1996 and February 2018 for a suspicion of DH. Clinical history and allergy workup results compiled in our Drug Allergy and Hypersensitivity Database were reviewed, and data of patients with a diagnosis of MDHS were retrieved and analyzed.Results: During this period a total of 9250 patients were explored and 1819 tested positive for at least 1 drug. Forty-five cases, 30 female and 15 male patients cumulating 92 DHs, were confirmed as having MDHS. An immunologic mechanism, as demonstrated by positive skin testing, accounted for 59 DHs. Drug provocation tests were performed to confirm the diagnosis for the remaining 33 DHs. Of the 92 DHs in this series, 38 were classified as type IV and 21 as type I allergies; 33 remained of undetermined mechanism. Drug class occurrences seem to differ from those in monoallergic patients.Conclusions: Our data support the concept of MDHS as a distinct and rare subgroup of DH. The prevalence in our database was 2.5% in the total DH alleged patient population and 0.5% of the demonstrated DHs. Skin testing and drug provocation tests are mandatory for confirming the diagnosis.

Objective.To identify baseline variables that predict remission according to different criteria in rheumatoid arthritis (RA) in a comprehensive French ESPOIR early arthritis database.Methods.Individual variables and indices at baseline were analyzed in 664 patients for capacity to predict remission either 6 or 12 months later according to 4 criteria that require a formal joint count: the American College of Rheumatology/European League Against Rheumatism Boolean criteria, the Simplified Disease Activity Index, the Clinical Disease Activity Index, and the 28-joint Disease Activity Score; and 2 remission criteria that do not require a formal joint count: the Routine Assessment of Patient Index Data 3 (RAPID3) and the RAPID3 ≤ 3 + swollen joint, using univariate and multivariate logistic regressions.Results.Remission was predicted significantly 6 and/or 12 months later in 26.8%–51.4% of patients, according to all 6 criteria by younger age, low index scores, and better status for the 6/7 clinical RA core dataset measures: tender joint count, swollen joint count (SJC), physician’s global estimate, patient self-report Health Assessment Questionnaire (HAQ) physical function, pain, and patient’s global estimate. Remission was not predicted by the absence of “poor prognosis RA” indicators, rheumatoid factor (RF), anticitrullinated protein antibodies (ACPA), or radiographic erosions. In multivariate regressions that included only 3 variables, low HAQ function predicted remission by all criteria as effectively as SJC, erythrocyte sedimentation rate, or C-reactive protein.Conclusion.Younger age and 6 core dataset clinical measures, but not the absence of traditional “poor prognosis RA” indicators, RF, ACPA, or radiographic erosions, predicted remission according to 6 criteria, including 2 without a formal joint count.

Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary. To address this need, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. It is designed for memory and computational efficiency and works across multiple platforms. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is used in multiple modeling and visualization tools, and we also provide reference Application Programming Interfaces and model examples to catalyze further adoption. SONATA format is free and open for the community to use and build upon with the goal of enabling efficient model building, sharing, and reproducibility., Author summary Neuroscience is experiencing a rapid growth of data streams characterizing composition, connectivity, and activity of brain networks in ever increasing details. Data-driven modeling will be essential to integrate these multimodal and complex data into predictive simulations to advance our understanding of brain function and mechanisms. To enable efficient development and sharing of such large-scale models utilizing diverse data types, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is already supported by several popular tools for model building, simulations, and visualization. It is free and open for everyone to use and build upon and will enable increased efficiency, reproducibility, and scientific exchange in the community.

International audience; More than two decades of functional magnetic resonance imaging (fMRI) of the human brain have succeeded to identify, with a growing level of precision, the neural basis of multiple cognitive skills within various domains (perception, sensorimotor processes, language, emotion and social cognition …). Progress has been made in the comprehension of the functional organization of localized brain areas. However, the long time required for fMRI acquisition limits the number of experimental conditions performed in a single individual. As a consequence, distinct brain localizations have mostly been studied in separate groups of participants, and their functional relationships at the individual level remain poorly understood. To address this issue, we report here preliminary results on a database of fMRI data acquired on 78 individuals who each performed a total of 29 experimental conditions, grouped in 4 cross-domains functional localizers. This protocol has been designed to efficiently isolate, in a single session, the brain activity associated with language, numerical representation, social perception and reasoning, premotor and visuomotor representations. Analyses are reported at the group and at the individual level, to establish the ability of our protocol to selectively capture distinct regions of interest in a very short time. Test-retest reliability was assessed in a subset of participants. The activity evoked by the different contrasts of the protocol is located in distinct brain networks that, individually, largely replicate previous findings and, taken together, cover a large proportion of the cortical surface. We provide detailed analyses of a subset of regions of relevance: the left frontal, left temporal and middle frontal cortices. These preliminary analyses highlight how combining such a large set of functional contrasts may contribute to establish a finer-grained brain atlas of cognitive functions, especially in regions of high functional overlap. Detailed structural images (structural connectivity, micro-structures, axonal diameter) acquired in the same individuals in the context of the ARCHI database provide a promising situation to explore functional/structural interdependence. Additionally, this protocol might also be used as a way to establish individual neurofunctional signatures in large cohorts.

International audience; Background:Patients with autism have been often reported to have a smaller corpus callosum (CC) than control subjects.; Methods:We conducted a meta-analysis of the literature, analyzed the CC in 694 subjects of the Autism Brain Imaging Data Exchange project, and performed computer simulations to study the effect of different analysis strategies.; Results:Our meta-analysis suggested a group difference in CC size; however, the studies were heavily underpowered (20% power to detect Cohen's d = .3). In contrast, we did not observe significant differences in the Autism Brain Imaging Data Exchange cohort, despite having achieved 99% power. However, we observed that CC scaled nonlinearly with brain volume (BV): large brains had a proportionally smaller CC. Our simulations showed that because of this nonlinearity, CC normalization could not control for eventual BV differences, but using BV as a covariate in a linear model would. We also observed a weaker correlation of IQ and BV in cases compared with control subjects. Our simulations showed that matching populations by IQ could then induce artifactual BV differences.; Conclusions:The lack of statistical power in the previous literature prevents us from establishing the reality of the claims of a smaller CC in autism, and our own analyses did not find any. However, the nonlinear relationship between CC and BV and the different correlation between BV and IQ in cases and control subjects may induce artifactual differences. Overall, our results highlight the necessity for open data sharing to provide a more solid ground for the discovery of neuroimaging biomarkers within the context of the wide human neuroanatomical diversity.

Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania . However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani , L. guyanensis , and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers.

This publication hasn't any creative commons license associated. This deposit is composed by the main article plus the supplementary materials of the publication. This deposit is composed by a publication in which the IGC's authors have had the role of collaboration (it's a collaboration publication). This type of deposit in ARCA is in restrictedAccess (it can't be in open access to the public), and can only be accessed by two ways: either by requesting a legal copy from the author (the email contact present in this deposit) or by visiting the following link: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005715#sec022 Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge "Introduction to Bioinformatics" course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery-mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online "question and discussion" forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. National Human Genome Research Institute; Office of the Director; National Institutes of Health grant: (U41HG006941). info:eu-repo/semantics/publishedVersion

International audience; Many decision systems are based on a hierarchical approach, enriching the known context used to finally choose the right potential action. Designing the scheme for browsing the clinical guidelines is a task devoted to expert in infectious diseases. Designing the data model is a task devoted to the expert in data modeling. As a consequence, browsing scheme and data model generally differ in terms of abstraction levels. While the browsing scheme proposes to navigate into depth, the data model stays flat. We propose here a novel method to design in parallel the browsing scheme and the data model so that both of them reflect the different abstraction levels in decision process.

Motivation: Spontaneous adverse event reports have a high potential for detecting adverse drug reactions. However, due to their dimension, exploring such databases requires statistical methods. In this context, disproportionality measures are used. However, by projecting the data onto contingency tables, these methods become sensitive to the problem of co-prescriptions and masking effects. Recently, logistic regressions have been used with a Lasso type penalty to perform the detection of associations between drugs and adverse events. However, the choice of the penalty value is open to criticism while it strongly influences the results. Results: In this paper, we propose to use a logistic regression whose sparsity is viewed as a model selection challenge. Since the model space is huge, a Metropolis-Hastings algorithm carries out the model selection by maximizing the BIC criterion. Thus, we avoid the calibration of penalty or threshold. During our application on the French pharmacovigilance database, the proposed method is compared to well established approaches on a reference data set, and obtains better rates of positive and negative controls. However, many signals are not detected by the proposed method. So, we conclude that this method should be used in parallel to existing measures in pharmacovigilance., Comment: 7 pages, 3 figures, submitted to Biometrical Journal

International audience; Pentameric ligand gated ion channels (pLGICs) mediate signal transduction. The binding of an extracellular ligand is coupled to the transmembrane channel opening. So far, all known agonists bind at the interface between subunits in a topologically conserved "orthosteric site" whose amino acid composition defines the pharmacological specificity of pLGIC subtypes. A striking exception is the bacterial proton-activated GLIC protein, exhibiting an uncommon orthosteric binding site in terms of sequence and local architecture. Among a library of Gloeobacter violaceus metabolites, we identified a series of cinnamic acid derivatives, which antagonize the GLIC proton-elicited response. Structure-activity analysis shows a key contribution of the carboxylate moiety to GLIC inhibition. Molecular docking coupled to site-directed mutagenesis support that the binding pocket is located below the classical orthosteric site. These antagonists provide new tools to modulate conformation of GLIC, currently used as a prototypic pLGIC, and opens new avenues to study the signal transduction mechanism.

International audience; Personality is thought to affect obesity risk but before such information can be incorporated into prevention and intervention plans, robust and converging evidence concerning the most relevant personality traits is needed. We performed a meta-analysis based on individual-participant data from nine cohort studies to examine whether broad-level personality traits predict the development and persistence of obesity (n = 78,931 men and women; mean age 50 years). Personality was assessed using inventories of the Five-Factor Model (extraversion, neuroticism, agreeableness, conscientiousness and openness to experience). High conscientiousness - reflecting high self-control, orderliness and adherence to social norms - was associated with lower obesity risk across studies (pooled odds ratio [OR] = 0.84; 95% confidence interval [CI] = 0.80-0.88 per 1 standard deviation increment in conscientiousness). Over a mean follow-up of 5.4 years, conscientiousness predicted lower obesity risk in initially non-obese individuals (OR = 0.88, 95% CI = 0.85-0.92; n = 33,981) and was associated with greater likelihood of reversion to non-obese among initially obese individuals (OR = 1.08, 95% CI = 1.01-1.14; n = 9,657). Other personality traits were not associated with obesity in the pooled analysis, and there was substantial heterogeneity in the associations between studies. The findings indicate that conscientiousness may be the only broad-level personality trait of the Five-Factor Model that is consistently associated with obesity across populations.

International audience; Studying gene-environment (G × E) interactions is important, as they extend our knowledge of the genetic architecture of complex traits and may help to identify novel variants not detected via analysis of main effects alone. The main statistical framework for studying G × E interactions uses a single regression model that includes both the genetic main and G × E interaction effects (the "joint" framework). The alternative "stratified" framework combines results from genetic main-effect analyses carried out separately within the exposed and unexposed groups. Although there have been several investigations using theory and simulation, an empirical comparison of the two frameworks is lacking. Here, we compare the two frameworks using results from genome-wide association studies of systolic blood pressure for 3.2 million low frequency and 6.5 million common variants across 20 cohorts of European ancestry, comprising 79,731 individuals. Our cohorts have sample sizes ranging from 456 to 22,983 and include both family-based and population-based samples. In cohort-specific analyses, the two frameworks provided similar inference for population-based cohorts. The agreement was reduced for family-based cohorts. In meta-analyses, agreement between the two frameworks was less than that observed in cohort-specific analyses, despite the increased sample size. In meta-analyses, agreement depended on (1) the minor allele frequency, (2) inclusion of family-based cohorts in meta-analysis, and (3) filtering scheme. The stratified framework appears to approximate the joint framework well only for common variants in population-based cohorts. We conclude that the joint framework is the preferred approach and should be used to control false positives when dealing with low-frequency variants and/or family-based cohorts.

Objectives In November 2015, a plasmid-mediated colistin resistance, MCR-1, was described in animals, food and humans in China, and it was considered as a potential emerging threat to public health. Therefore, we screened for the mcr-1 gene a European collection of colistin-resistant Escherichia coli ( n =218) and Salmonella spp. ( n =74) isolated from diseased food-producing animals between 2004 and 2014 and characterized the mcr-1 -positive clones. Methods Screening for mcr-1 gene was performed by PCR on isolates for which inhibition diameter was E. coli isolates were then characterized by phylogrouping, multilocus sequence typing and pulsed-field gel electrophoresis typing. Antibiotic susceptibility was determined by disk diffusion testing or by broth microdilution. Results Among the collection, 42 E. coli and three Salmonella spp. were positive for mcr-1, with continuous detection since 2004 mainly from bovine and swine digestive infections. Most of the mcr-1 -positive strains were resistant to amoxicillin and cotrimoxazole but remained susceptible to cephalosporins, carbapenems and piperacillin/tazobactam. All but one isolate were resistant to colistin, with a minimum inhibitory concentration of >2 mg/L. Most of the mcr-1 -positive E. coli belonged to the phylogroup A with two prevalent clonal complexes, CC10 and CC165, in which sequence type 10 and sequence type 100 were overrepresented and pulsed-field gel electrophoresis typing revealed a high diversity of pulsotypes. Conclusions MCR-1 was detected yearly in European food-producing animal since 2004 with a high diversity of pulsotypes supporting the dissemination of mcr-1 via plasmids.

International audience; We report on a database, named BIL&GIN, designed for investigating the cognitive, behavioral, genetic, and brain morphological/functional correlates of hemispheric specialization. The database contains records from a sample of 453 adult participants enriched in left-handers (45%, N=205) as compared to the general population. For each subject, socio-demographic data, hand and eye laterality, family handedness, and cognitive abilities in the language, motor, visuo-spatial, and numerical domains have been recorded. T1-MRI and DTI data were also acquired, as well as resting-state functional MRI. Task-evoked functional MRI was performed in a sub-sample of 303 subjects (157 left-handers) using a customized functional battery of 16 cognitive tasks exploring the same three cognitive domains. Performances at the tasks executed in the magnet as well as post-acquisition debriefing were recorded. A saliva sample was obtained from the subjects of this sub-sample from which DNA was extracted. The BIL&GIN contains results of imaging data processing for each subject, namely maps of tissue (GM, WM, CSF) probability, cortical thickness, cortical surface, and diffusion parameters as well as regional values of these phenotypes for regions of both AAL and FreeSurfer parcellations. For the subjects who underwent FMRI, individual SPM contrast maps for each of the 8 runs were also calculated and included in the database, as well as corresponding BOLD variations in ROIs of the AAL and AICHA atlases, and Wilke's hemispheric functional lateralization index. The BIL&GIN data sharing is based on a collaborative model.

International audience; Environmental genomics can describe all forms of organisms--cellular and viral--present in a community. The analysis of such eco-systems biology data relies heavily on reference databases, e.g., taxonomy or gene function databases. Reference databases of symbiosis sensu lato, although essential for the analysis of organism interaction networks, are lacking. By mining existing databases and literature, we here provide a comprehensive and manually curated database of taxonomic links between viruses and their cellular hosts.

International audience; The Mediterranean basin has been the theater of migration crossroads followed by settlement of several societies and cultures in prehistoric and historical times, with important consequences on genetic and genomic determinisms. Here, we present the Mediterranean Founder Mutation Database (MFMD), established to offer web-based access to founder mutation information in the Mediterranean population. Mutation data were collected from the literature and other online resources and systematically reviewed and assembled into this database. The information provided for each founder mutation includes DNA change, amino-acid change, mutation type and mutation effect, as well as mutation frequency and coalescence time when available. Currently, the database contains 383 founder mutations found in 210 genes related to 219 diseases. We believe that MFMD will help scientists and physicians to design more rapid and less expensive genetic diagnostic tests. Moreover, the coalescence time of founder mutations gives an overview about the migration history of the Mediterranean population. MFMD can be publicly accessed from http://mfmd.pasteur.ma.

International audience; OBJECTIVES: We evaluated the respective influence of the causative pathogen and infection site on hospital mortality from severe sepsis related to community-, hospital-, and intensive care unit-acquired infections. DESIGN: We used a prospective observational cohort 10-yr database. We built a subdistribution hazards model with corrections for competing risks and adjustment for potential confounders including early appropriate antimicrobial therapy. SETTING: Twelve intensive care units. PATIENTS: We included 4,006 first episodes of acquisition-site-specific severe sepsis in 3,588 patients. INTEVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We included 1562 community-acquired, 1432 hospital-acquired, and 1012 intensive care unit-acquired episodes of severe sepsis. After adjustment, we found no independent associations of the causative organism, multidrug resistance of the causative organism, infection site, or presence of bacteremia with mortality. Early appropriate antimicrobial therapy was consistently associated with better survival in the community-acquired (0.64 [0.51-0.8], p = .0001), hospital-acquired (0.72 [0.58-0.88], p = .0011), and intensive care unit-acquired (0.79 [0.64-0.97], p = .0272) groups. CONCLUSION: The infectious process may not exert as strong a prognostic effect when severity, organ dysfunction and, above all, appropriateness of early antimicrobials are taken into account. Our findings emphasize the importance of developing valid recommendations for early antimicrobial therapy.

International audience; OBJECTIVE: To estimate breast cancer incidence in the general population using a method that corrects for lack of sensitivity and specificity in the identification of incident breast cancer in inpatient claims data. STUDY DESIGN AND SETTINGS: Two-phase study: phase 1 to identify incident cases in claims data, and phase 2 to estimate sensitivity and specificity in a subset of the population. Two algorithms (1: principal diagnosis; 2: principal diagnosis+specific surgery procedures) were used to identify incident cases in claims of women aged 20 years or older, living in a French district covered by a cancer registry. Sensitivity and specificity were estimated in one district and used to correct incident cases identified. RESULTS: The sensitivity and specificity for algorithms 1 and 2 were 69.0% and 99.89%, and 64.4% and 99.93%, respectively. In contrast to specificity, the sensitivity for both algorithms was lower for women younger than 40 years and older than 65 years. Cases reported by cancer registries were closer to cases identified with algorithm 2 (-3.2% to +20.1%) and to corrected numbers with algorithm 1 (-1% to +15%). CONCLUSION: To obtain reliable estimates of breast cancer incidence in the general population, sensitivity and specificity, which reflect medical and coding practice variations, are necessary.

International audience; OBJECTIVE: To examine the association between predefined adverse events (AE) (including nosocomial infections) and intensive care unit (ICU) mortality, controlling for multiple adverse events in the same patient and confounding variables. DESIGN: Prospective observational cohort study of the French OUTCOMEREA multicenter database. SETTING: Twelve medical or surgical ICUs. PATIENTS: Unselected patients hospitalized for > or = 48 hrs enrolled between 1997 and 2003. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Of the 3,611 patients included, 1415 (39.2%) experienced one or more AEs and 821 (22.7%) had two or more AEs. Mean number of AEs per patient was 2.8 (range, 1-26). Six AEs were associated with death: primary or catheter-related bloodstream infection (BSI) (odds ratio [OR], 2.92; 95% confidence interval [CI], 1.6-5.32), BSI from other sources (OR, 5.7; 95% CI, 2.66-12.05), nonbacteremic pneumonia (OR, 1.69; 95% CI, 1.17-2.44), deep and organ/space surgical site infection without BSI (OR, 3; 95% CI, 1.3-6.8), pneumothorax (OR, 3.1; 95% CI, 1.5-6.3), and gastrointestinal bleeding (OR, 2.6; 95% CI, 1.4-4.9). The results were not changed when the analysis was confined to patients with mechanical ventilation on day 1, intermediate severity of illness (Simplified Acute Physiology Score II between 35 and 55), no treatment-limitation decisions, or no cardiac arrest in the ICU. CONCLUSIONS: AEs were common and often occurred in combination in individual patients. Several AEs independently contributed to death. Creating a safe ICU environment is a challenging task that deserves careful attention from ICU physicians.

CggR belongs to the SorC family of bacterial transcriptional regulators which control the expression of genes and operons involved in carbohydrate catabolism. CggR was first identified in Bacillus subtilis where it represses the gapA operon encoding the five enzymes that catalyze the central part of glycolysis. Here we present a structure/function study demonstrating that the C-terminal region of CggR regulates the DNA binding activity of this repressor in response to binding of a phosphorylated sugar. Molecular modeling of CggR revealed a winged-helix DNA-binding motif followed by a C-terminal domain presenting weak but significant homology with glucosamine-6-phosphate deaminases from the NagB family. In silico ligand screening suggested that the CggR C-terminal domain would bind preferentially bi-phosphorylated compounds, in agreement with previous studies that proposed fructuose-1,6-biphosphate (FBP) as the inducer metabolite. In vitro, FBP was the only sugar compound capable of interfering with CggR cooperative binding to DNA. FBP was also found to protect CggR against trypsin degradation at two arginine residues predicted to reside in a mobile loop forming the active site lid of the NagB enzymes. Replacement of residues predicted to interact with FBP led to mutant CggR with altered repressor activity in vivo but retaining their structural integrity and DNA binding activity in vitro. Interestingly, some of the mutant repressors responded with different specificity towards mono- and di-phospho-fructosides. Based on these results, we propose that the activity of the CggR-like repressors is controlled by a phospho-sugar binding (PSB) domain presenting structural and functional homology with NagB enzymes.

International audience; BACKGROUND: Previous studies reported that statin use was associated with a decreased risk of venous thromboembolism (VTE), whereas no association was found between fibrate use and VTE. This report aims to test the hypothesis that part of these contrasting associations is related to total homocysteine level (tHcy). MATERIALS AND METHODS: This report from a case-control study included 677 cases hospitalised with confirmed VTE and no major acquired risk factor of VTE and their 677 controls. Statin and fibrate exposure was defined as a current use of drugs at admission. Fasting serum tHcy was measured in all patients. RESULTS: The estimated odds ratio for VTE related to statin use was 0.53 (CI 95% 0.37-0.78), whereas it was 1.88 (CI 95% 1.29-2.74) for fibrate use. No difference was found for tHcy levels between patients who were current users of statin compared to non users (17.7 micromol/L+/-7.3 in users vs 18.4 micromol/L+/-8.4 in non users, p=0.50). In contrast, fibrate users had a significant higher mean level of tHcy than non users (23.2 micromol/L+/-8.7 in users vs 18.4 micromol/L+/-8.4 in non users, p

International audience; ESPOIR is a French multicenter cohort of patients with undifferentiated arthritis enrolled within six months of symptom onset, naive to disease-modifying antirheumatic drugs and corticosteroid therapy, and either having rheumatoid arthritis (RA) or being at risk for progression to RA. The cohort is sponsored by the French Society for Rheumatology (Société française de rhumatologie [SFR]). Between December 2002 and March 2005, 813 patients were enrolled at 14 regional university hospitals, with the participation of a network of community-based rheumatologists. The objective was to establish a database on recent-onset inflammatory joint disease and, more specifically, on RA to serve for scientific research in the clinical, epidemiological, pathophysiological, and healthcare-cost fields. Ten years after enrolment were started, the cohort still has about 500 patients. The scientific committee has approved 104 clinical research projects, of which many are ongoing, and 54 original articles written by numerous French and international groups have been published. These projects cover a vast spectrum of topics including environmental factors, diagnosis, outcomes, prognosis, disease evaluation, imaging, genetics, biomarkers, costs, and RA management strategies.

Rationale : The meta-Analysis of Cell-based CaRdiac study is the first prospectively declared collaborative multinational database, including individual data of patients with ischemic heart disease treated with cell therapy. Objective : We analyzed the safety and efficacy of intracoronary cell therapy after acute myocardial infarction (AMI), including individual patient data from 12 randomized trials (ASTAMI, Aalst, BOOST, BONAMI, CADUCEUS, FINCELL, REGENT, REPAIR-AMI, SCAMI, SWISS-AMI, TIME, LATE-TIME; n=1252). Methods and Results : The primary end point was freedom from combined major adverse cardiac and cerebrovascular events (including all-cause death, AMI recurrance, stroke, and target vessel revascularization). The secondary end point was freedom from hard clinical end points (death, AMI recurrence, or stroke), assessed with random-effects meta-analyses and Cox regressions for interactions. Secondary efficacy end points included changes in end-diastolic volume, end-systolic volume, and ejection fraction, analyzed with random-effects meta-analyses and ANCOVA. We reported weighted mean differences between cell therapy and control groups. No effect of cell therapy on major adverse cardiac and cerebrovascular events (14.0% versus 16.3%; hazard ratio, 0.86; 95% confidence interval, 0.63–1.18) or death (1.4% versus 2.1%) or death/AMI recurrence/stroke (2.9% versus 4.7%) was identified in comparison with controls. No changes in ejection fraction (mean difference: 0.96%; 95% confidence interval, −0.2 to 2.1), end-diastolic volume, or systolic volume were observed compared with controls. These results were not influenced by anterior AMI location, reduced baseline ejection fraction, or the use of MRI for assessing left ventricular parameters. Conclusions : This meta-analysis of individual patient data from randomized trials in patients with recent AMI revealed that intracoronary cell therapy provided no benefit, in terms of clinical events or changes in left ventricular function. Clinical Trial Registration: URL: http://www.clinicaltrials.gov. Unique identifier: NCT01098591.

Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the family Partitiviridae, the provenance of their CP remained obscure. Here we show that the CP of amalgaviruses is homologous to the nucleocapsid proteins of negative-strand RNA viruses of the genera Phlebovirus (Bunyaviridae) and Tenuivirus. The chimeric genomes of amalgaviruses are a testament to the effectively limitless gene exchange between viruses that shaped the evolution of the virosphere. Reviewers: This article was reviewed by Lakshminarayan M. Iyer and Nick V. Grishin. For complete reviews, see the Reviewers’ Reports section. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0047-8) contains supplementary material, which is available to authorized users.

International audience; Up-to-date evidence on levels and trends for age-sex-specific all-cause and cause-specific mortality is essential for the formation of global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013) we estimated yearly deaths for 188 countries between 1990, and 2013. We used the results to assess whether there is epidemiological convergence across countries. We estimated age-sex-specific all-cause mortality using the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data. We generally estimated cause of death as in the GBD 2010. Key improvements included the addition of more recent vital registration data for 72 countries, an updated verbal autopsy literature review, two new and detailed data systems for China, and more detail for Mexico, UK, Turkey, and Russia. We improved statistical models for garbage code redistribution. We used six different modelling strategies across the 240 causes; cause of death ensemble modelling (CODEm) was the dominant strategy for causes with sufficient information. Trends for Alzheimer's disease and other dementias were informed by meta-regression of prevalence studies. For pathogen-specific causes of diarrhoea and lower respiratory infections we used a counterfactual approach. We computed two measures of convergence (inequality) across countries: the average relative difference across all pairs of countries (Gini coefficient) and the average absolute difference across countries. To summarise broad findings, we used multiple decrement life-tables to decompose probabilities of death from birth to exact age 15 years, from exact age 15 years to exact age 50 years, and from exact age 50 years to exact age 75 years, and life expectancy at birth into major causes. For all quantities reported, we computed 95% uncertainty intervals (UIs). We constrained cause-specific fractions within each age-sex-country-year group to sum to all-cause mortality based on draws from the uncertainty distributions. Global life expectancy for both sexes increased from 65.3 years (UI 65.0-65.6) in 1990, to 71.5 years (UI 71.0-71.9) in 2013, while the number of deaths increased from 47.5 million (UI 46.8-48.2) to 54.9 million (UI 53.6-56.3) over the same interval. Global progress masked variation by age and sex: for children, average absolute differences between countries decreased but relative differences increased. For women aged 25-39 years and older than 75 years and for men aged 20-49 years and 65 years and older, both absolute and relative differences increased. Decomposition of global and regional life expectancy showed the prominent role of reductions in age-standardised death rates for cardiovascular diseases and cancers in high-income regions, and reductions in child deaths from diarrhoea, lower respiratory infections, and neonatal causes in low-income regions. HIV/AIDS reduced life expectancy in southern sub-Saharan Africa. For most communicable causes of death both numbers of deaths and age-standardised death rates fell whereas for most non-communicable causes, demographic shifts have increased numbers of deaths but decreased age-standardised death rates. Global deaths from injury increased by 10.7%, from 4.3 million deaths in 1990 to 4.8 million in 2013; but age-standardised rates declined over the same period by 21%. For some causes of more than 100,000 deaths per year in 2013, age-standardised death rates increased between 1990 and 2013, including HIV/AIDS, pancreatic cancer, atrial fibrillation and flutter, drug use disorders, diabetes, chronic kidney disease, and sickle-cell anaemias. Diarrhoeal diseases, lower respiratory infections, neonatal causes, and malaria are still in the top five causes of death in children younger than 5 years. The most important pathogens are rotavirus for diarrhoea and pneumococcus for lower respiratory infections. Country-specific probabilities of death over three phases of life were substantially varied between and within regions. For most countries, the general pattern of reductions in age-sex specific mortality has been associated with a progressive shift towards a larger share of the remaining deaths caused by non-communicable disease and injuries. Assessing epidemiological convergence across countries depends on whether an absolute or relative measure of inequality is used. Nevertheless, age-standardised death rates for seven substantial causes are increasing, suggesting the potential for reversals in some countries. Important gaps exist in the empirical data for cause of death estimates for some countries; for example, no national data for India are available for the past decade. Bill & Melinda Gates Foundation.

Background The nonhuman primate (NHP)-related injuries in rabies-enzootic countries is a public health problem of increasing importance. The aims of this work are to collect data concerning rabies transmission from NHPs to humans; to collate medical practices regarding rabies postexposure prophylaxis (PEP) in different countries, and to provide an evidence base to support the decision to apply rabies PEP in this context. Methodology To retrieve information, we conducted a literature search from 1960 to January 2013. All reports of rabies in NHPs and rabies transmission to humans by infected NHPs were included. Also included were studies of travelers seeking care for rabies PEP in various settings. Data collected by the French National Reference Centre for Rabies concerning NHPs submitted for rabies diagnosis in France and human rabies exposure to NHPs in travelers returning to France were analyzed for the periods 1999–2012 and 1994–2011, respectively. Principal findings A total of 159 reports of rabies in NHPs have been retrieved from various sources in South America, Africa, and Asia, including 13 cases in animals imported to Europe and the US. 134 were laboratory confirmed cases. 25 cases of human rabies following NHP-related injuries were reported, including 20 from Brazil. Among more than 2000 international travelers from various settings, the proportion of injuries related to NHP exposures was about 31%. NHPs rank second, following dogs in most studies and first in studies conducted in travelers returning from Southeast Asia. In France, 15.6% of 1606 travelers seeking PEP for exposure to any animal were injured by monkeys. Conclusions/significance Although less frequently reported in published literature than human rabies, confirmed rabies cases in NHPs occur. The occurrence of documented transmission of rabies from NHPs to human suggests that rabies PEP is indicated in patients injured by NHPs in rabies-enzootic countries., Author Summary No international consensus or even a consensus among existing national recommendations about rabies postexposure prophylaxis (PEP) following a nonhuman primate (NHP)-related injury currently exists. Epidemiologic studies and reports collated in this review indicate that the number of rabies case reported in NHPs are rare compared with humans. This finding might be because of a lower contact rate of NHPs with rabid reservoir but also very likely because of underreporting. Nevertheless, documented cases and subsequent transmission to humans have been reported from various sources in South America, Africa, and Asia. Further, international travelers often report NHP-related injuries and NHPs can be close to humans. Little is currently known of the pathobiology of rabies virus shedding in primates, which implies that rabies PEP and administration of rabies immunoglobulin should be considered in patients with a possible exposure.

International audience; Occupational exposures make important contributions to asthma morbidity. The role of low/moderate level irritant exposures remains unclear. We aimed to determine which occupational exposures are associated with asthma in an eastern European country with low asthma prevalence. The Estonian Genome Center of University of Tartu collected data from 50 077 adults in 2002-2011. Asthma was assessed through a questionnaire regarding diagnosed diseases, current health status and medication. Exposures to 22 agents during the current and longest held jobs were estimated using an asthma-specific job-exposure matrix. Analyses included 34 015 subjects (aged 18-65 years, 67.0% females), of which 1209 (3.6%) reported asthma (608 with physician-confirmed diagnosis). After adjusting for age, sex and smoking habits, lifetime occupational exposure to known asthmagens (20.4%) was significantly associated with physician-diagnosed asthma (OR 1.28, 95% CI 1.03-1.59), especially high molecular weight agents (flour: OR 2.36, 95% CI 1.31-4.27; animals: OR 1.62, 95% CI 1.00-2.60). Exposure to low/moderate levels of irritants (17.4%) was associated with physician-diagnosed asthma (OR 1.88, 95% CI 1.48-2.37). More pronounced associations were observed in subjects reporting current treated asthma. Beyond confirming the effect of known asthmagens (which are well-known, mostly from observations in western countries), the results provide evidence for a role of low/moderate exposure to irritants. This finding, observed in a country with a low prevalence of asthma and atopy, provides new insight into the understanding of asthma heterogeneity.

International audience; ESPOIR (Etude et Suivi des POlyarthrites Indifférenciées Récentes) is a multicentre national cohort sponsored by the French Society for Rheumatology. The patients had early arthritis (

International audience; A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate approximately 96%) unambiguously assigned into one of the target classes. The application of PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED-CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED-CLASS.

The human genome is thought to contain about 80,000 genes and presently only 3,000 are known to be implicated in genetic diseases. In the near future, the entire sequence of the human genome will be available and the development of new methods for point mutation detection will lead to a huge increase in the identification of genes and their mutations associated with genetic diseases as well as cancers, which is growing in frequency in industrial states. The collection of these mutations will be critical for researchers and clinicians to establish genotype/phenotype correlations. Other fields such as molecular epidemiology will also be developed using these new data. Consequently, the future lies not in simple repositories of locus-specific mutations but in dynamic databases linked to various computerized tools for their analysis and that can be directly queried on-line. To meet this goal, we devised a generic software called UMD (Universal Mutation Database). It was developed as a generic software to create locus-specific databases (LSDBs) with the 4(th) Dimension(R) package from ACI. This software includes an optimized structure to assist and secure data entry and to allow the input of various clinical data. Thanks to the flexible structure of the UMD software, it has been successfully adapted to nine genes either involved in cancer (APC, P53, RB1, MEN1, SUR1, VHL, and WT1) or in genetic diseases (FBN1 and LDLR). Four new LSDBs are under construction (VLCAD, MCAD, KIR6, and COL4A5). Finally, the data can be transferred to core databases.

International audience; AIM: To evaluate the performance of a query on international classification of diseases 10(th) version (ICD10) codes in the database of the programme for the medicalisation of information systems (programme de médicalisation des systèmes d'information, PMSI) to identify serious adverse drug reactions (ADR). METHODS: The query concerned hospital stays of patients discharged from the French University Hospital of Rennes in 2009. All the hospitalization summaries including a selected ICD10 code were analysed to validate ADR. RESULTS: Out of 383 cases, 142 cases were validated (37.1%). Performance of some ICD10 codes was particularly interesting, above 40% (T88.6, L27.0, J70.4, G62.0 and N14.1) and 79.5% of the ADR were detected by these five codes. During the study period, 98 ADR of the same type were spontaneously reported by physicians, 22 of which were common with the ICD10 query. CONCLUSIONS: The use of PMSI can be a tool for signal detection of serious ADR, in addition to spontaneous reporting.

International audience; OBJECTIVES: Since 2007, a number of transplantation centers have been routinely using an expert system for tacrolimus (TAC) dose adjustment in kidney allograft recipients, based on PK modeling and Bayesian estimation for area-under-the-curve (AUC) determination. This has allowed the setting up of a large database of TAC pharmacokinetic profiles and AUC values, a part of which was analyzed here. METHODS: We retrospectively studied 2030 requests posted by 21 different centers for routine TAC dose adjustment in 1000 different adult renal transplant patients (not enrolled in any kind of concentration-controlled clinical trial). For each request, the following information was obtained: time elapsed since transplantation, TAC daily dose, calculated AUC, and trough concentration (C0). RESULTS: The dose-standardized exposure to TAC significantly and progressively increased in the months after transplantation: from month (M) 1 to M9 C0/dose increased from 2.33 to 3.44 mcg*L(1)*mg(1) and AUC/dose from 43.1 to 64.2 mcg*h(1)*L(1)*mg(1), respectively. On the contrary, in patients beyond the first year whose C0 or AUC was in the target range, the odds of remaining in this range were high for a long time period, suggesting a low intrapatient variability in the stable phase. Regression analyses showed that the correlation between C0 and AUC was better in the first 3-month period (r(2) = 0.76) than later on (r(2) ≤ 0.67). Using the regression equations obtained, AUC ranges corresponding to different applicable C0 targets were calculated. CONCLUSIONS: From a large number of kidney graft recipients, we have estimated the relationships between C0 and AUC, modeled the evolution of TAC exposure with time and defined AUC targets that could be useful to lead further controlled-concentration trials and improve routine TAC therapeutic drug monitoring.

International audience; UNLABELLED: The aim of this study was the description of breast carcinoma over a 10-year period according to pathology data. METHOD: Descriptive epidemiological study based on data collection of pathological code ADICAP (injury, organ, and applied technical), histological, hormonal, node and administrative data. From January 1st 2000 to December 31st 2009, 6186 women living in Finistère have had a diagnosis of invasive breast carcinoma. The incidence rate involved from 125 per 100,000 women to 136 in 2009. Average age to the first diagnosis was 61.4 ± 13.6; class of age with the more important incidence rate was for the 50-74 years old. The different histological subtypes varied over the period (P

International audience; This study proposes a method to facilitate the remote follow up of patients suffering from cardiac pathologies and treated with an implantable device, by synthesizing a 12-lead surface ECG from the intracardiac electrograms (EGM) recorded by the device. Two methods (direct and indirect), based on dynamic time-delay artificial neural networks (TDNNs) are proposed and compared with classical linear approaches. The direct method aims to estimate 12 different transfer functions between the EGM and each surface ECG signal. The indirect method is based on a preliminary orthogonalization phase of the available EGM and ECG signals, and the application of the TDNN between these orthogonalized signals, using only three transfer functions. These methods are evaluated on a dataset issued from 15 patients. Correlation coefficients calculated between the synthesized and the real ECG show that the proposed TDNN methods represent an efficient way to synthesize 12-lead ECG, from two or four EGM and perform better than the linear ones. We also evaluate the results as a function of the EGM configuration. Results are also supported by the comparison of extracted features and a qualitative analysis performed by a cardiologist.