On a temporal model for the chikungunya Disease: modeling, theory and numerics

International audienceReunion Island faced two episodes of Chikungunya, a vector-borne disease, in 2005 and in 2006. The latter was of unprecedented magnitude: one third of the population was infected. Until the severe episode of 2006, our knowledge of Chikungunya was very limited. The principal aim of our study is to propose a model, including human and mosquito compartments, that is associated to the time course of the first epidemic of Chikungunya. By computing the basic reproduction number R0, we show there exists a disease-free equilibrium that is locally asymptotically stable if the basic reproduction number is less than 1. Moreover, we give a necessary condition for global asymptotic stability of the disease-free equilibrium. Then, we propose a numerical scheme that is qualitatively stable and present several simulations as well as numerical estimates of the basic reproduction number for some cities of Reunion Island. For the episode of 2005, R0 was less than one, which partly explains why no outbreak appeared. Using recent entomological results, we investigate links between the episode of 2005 and the outbreak of 2006. Finally, our work shows that R0 varied from place to place on the island, indicating that quick and focused interventions, like the destruction of breeding sites, may be effective for controlling the disease

Effectiveness and Safety of an Intracameral Injection of Cefuroxime for the Prevention of Endophthalmitis After Cataract Surgery With or Without Perioperative Capsular Rupture

International audienceIMPORTANCE:Postoperative endophthalmitis (POE) often results in severe visual impairment. In clinical studies, an intracameral cefuroxime injection at the end of surgery was found to be effective at reducing the incidence of POE. Two important issues are the retinal safety of cefuroxime and its use for patients with perioperative capsular rupture where the risk of POE is dramatically increased.OBJECTIVE:To assess the effectiveness and retinal safety of an intracameral injection of cefuroxime sodium for the prevention of POE and its possible use in cases of a perioperative capsular rupture of the lens.DESIGN, SETTING, AND PARTICIPANTS:Population-based cohort study of patients 40 years of age or older who underwent cataract surgery at 1 of 1546 French health care facilities, public or private, and whose medical records were obtained from the national administrative database. Data analyses were performed between March and November 2015.MAIN OUTCOMES AND MEASURES:The effectiveness and safety of the prophylactic injection of cefuroxime as measured by the incidence of POE and cystoid macular edema.RESULTS:From January 2010 to October 2014, a total of 3 351 401 eyes of 2 434 008 patients 40 years of age or older (58.9% were women, and the mean [SD] age was 73.9 [9.5] years) underwent cataract surgery; 1941 patients (0.08%) developed POE during the 6 weeks after cataract surgery. The incidence of POE after cataract surgery decreased over the course of the study (0.11%, 0.09%, 0.08%, 0.06%, and 0.05% in 2010, 2011, 2012, 2013, and 2014, respectively [P = .001 for trend]) as the use of cefuroxime prophylactic injections increased (11.1%, 14.4%, 32.8%, 64.8%, and 79.1% in 2010, 2011, 2012, 2013, and 2014, respectively [P = .001 for trend]). After multivariate adjustment, the risk of POE was reduced with the use of cefuroxime (odds ratio, 0.61 [95% CI, 0.56-0.68]). The retinal safety of an injection of cefuroxime, which was assessed by multiadjusted odds of retinal cystoid macular edema, was not increased for patients receiving cefuroxime injections (odds ratio, 0.86 [95% CI, 0.71-1.05]). For patients with a perioperative capsular rupture of the lens (the major risk factor for POE), the incidence of POE was lower for those who received an injection of cefuroxime than for those who did not (0.37% vs 0.51%, respectively [P = .001]), whereas an increased risk of cystoid macular edema was not identified for those who received or did not receive an injection of cefuroxime (5.6% vs 7.3%, respectively [P = .12]).CONCLUSIONS AND RELEVANCE:These data suggest that, in routine practice, the intracameral injection of cefuroxime at the conclusion of cataract surgery is associated with a lower risk of POE and is safe for patients with or without a perioperative capsular rupture. While these data might be used to support the consideration of its routine use to prevent POE, in the absence of a randomized clinical trial, they cannot prove a direct cause-and-effect relationship between the injection of cefuroxime and POE

Using ontologies for R functions management

International audienceThe research work of biologists often requires the development of a lot of scripts or functions to manipulate and analyse experimental data. In the laboratory LEPSE specialized on the analysis and modelling of plant responses and adaptation to variable environmental stresses, dozens of R functions are produced every year, concerning various fields such as genetic analyses, high throughput data phenotyping or environmental interactions and involving several databases. As a result, there is an important turn-over of function authors and users which generates different problems like re-using, sharing or understanding of these functions. In this context, in the framework of the DESIR project1, we have initiated a knowledge management action aiming to capitalize, organize, share and valorize these functions through the development of a knowledgebased repository of these functions. Given the great diversity of the functions produced, their associated documentation is heterogeneous and it is not pertinent to organise them into packages. We decided instead to index them with some formalized knowledge describing them, in order to retrieve them by formal reasoning. For this purpose, we developed an ontology providing a controlled and structured vocabulary that captures the concepts and properties necessary to describe R functions. This ontology comprises concepts and properties to describe functions – like ”Author”, ”Intention”, ”Argument”, ”Value” – as well as the relations between functions – like ”hasForRCoreCall”, ”canBeUsedAfter”, ”isAdaptedFrom”, ”looksLike”. As a result functions can be retrieved according to a wide range of criterii: thier author and/or the graphics produced, their intention(s) (e.g. perform multidimensional exploration), the function(s) they call (e.g. the ”lm” R core function or a specific function of the repository) –more generally, it is relevant to generate the call graph of one function to understand it–, the functions from which they are adapted –this makes easier the maintenance of the repository–, the functions after or before which they should be used –this helps to construct chainings of treatments–, their similarity with other functions, etc. To formalize both the ontology and the annotations of R functions, we adopted the SemanticWeb models : The annotations are represented into the Resource Description Framework2 (RDF) and the ontology in the Ontology Web Language3 (OWL). As a result we are able to semantically retrieve R functions by expressing queries in the SPARQL language4. We developed a semantic web application for the repository and search of annotated R functions. It relies upon the semantic engine Corese (Corby et al. 2004) dedicated to ontological query answering on the Semantic Web: Corese enables to interpret and process SPARQL queries on RDF annotations and OWL ontologies. Our application provides an environment for (1) storage and annotation : a prototype of Web user interface allows authors to upload R functions (one function per file) and to describe them in a few minutes; and (2) powerful search: users can find and get R functions with a global and accurate understanding and receive suggestions to support their search. To conclude, we have built a semantic repository of annotated R functions to centralize and share R functions for biologists. It capitalizes expert know-hows that would otherwise oftenly be lost or become nonusable because of a lack of documentation and description. We are convinced that this kind of repository developed for the LEPSE could benefit a much wider community of R function authors and users and be adapted to handle other programming languages

Using ontologies of software : example of R functions management

International audienceIn a scientific context, making available scientific resources like computer programs is a real challenge for multidisciplinary research teams. In this paper, we propose an ontology-based approach to manage, share, reuse and promote software programs in a research community. Specifically, we were interested in the capitalization of R functions, R being a language for statistics and graphics. We designed an ontology to annotate R functions. We adopted the Semantic Web models: annotations are represented into the Resource Description Framework and the ontology in the Ontology Web Language. In the so-built semantic repository, R functions can be retrieved by expressing semantic queries in the SPARQL language. As a result, we have developed a new kind of software repository with semantic inferences. It is based upon the Corese semantic search engine and accessible through a Web Service. It has been adopted by a multidisciplinary team in life sciences

Using annotations for R function management, MOQA : Méta-données et Ontologies pour la Qualité des Annotations

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Using ontologies of software : example of R functions management

International audienceIn a scientific context, making available scientific resources like computer programs is a real challenge for multidisciplinary research teams. In this paper, we propose an ontology-based approach to manage, share, reuse and promote software programs in a research community. Specifically, we were interested in the capitalization of R functions, R being a language for statistics and graphics. We designed an ontology to annotate R functions. We adopted the Semantic Web models: annotations are represented into the Resource Description Framework and the ontology in the Ontology Web Language. In the so-built semantic repository, R functions can be retrieved by expressing semantic queries in the SPARQL language. As a result, we have developed a new kind of software repository with semantic inferences. It is based upon the Corese semantic search engine and accessible through a Web Service. It has been adopted by a multidisciplinary team in life sciences

A Pharmacoepidemiological study of intravitreal drug consumption in the first 12 months of treatment. The EPIdemiology and SAFEty collaboration

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