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Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing
No full textInternational audienceBackgroundThe B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia.Methods and ResultsVidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications
A Temporal QoS Ontology for ERTMS/ETCS
No full textInternational Conference on Knowledge Engineering and Ontological Engineering, Londres, ROYAUME-UNI, 18-/01/2016 - 19/01/2016Ontologies offer a means for representing and sharing information in many domains, particularly in complex domains. For example, it can be used for representing and sharing information of System Requirement Specification (SRS) of complex systems like the SRS of ERTMS/ETCS written in natural language. Since this system is a real-time and critical system, generic ontologies, such as OWL and generic ERTMS ontologies provide minimal support for modeling temporal information omnipresent in these SRS documents. To support the modeling of temporal information, one of the challenges is to enable representation of dynamic features evolving in time within a generic ontology with a minimal redesign of it. The separation of temporal information from other information can help to predict system runtime operation and to properly design and implement them. In addition, it is helpful to provide a reasoning and querying techniques to reason and query temporal information represented in the ontology in order to detect potential temporal inconsistencies. Indeed, a user operation, such as adding a new constraint on existing planning constraints can cause temporal inconsistencies, which can lead to system failures. To address this challenge, we propose a lightweight 3-layer temporal Quality of Service (QoS) ontology for representing, reasoning and querying over temporal and non-temporal information in a complex domain ontology. Representing QoS entities in separated layers can clarify the distinction between the non QoS entities and the QoS entities in an ontology. The upper generic layer of the proposed ontology provides an intuitive knowledge of domain components, specially ERTMS/ETCS components. The separation of the intermediate QoS layer from the lower QoS layer allows us to focus on specific QoS Characteristics, such as temporal or integrity characteristics. In this paper, we focus on temporal information that can be used to predict system runtime operation. To evaluate our approach, an example of the proposed domain ontology for handover operation, as well as a reasoning rule over temporal relations in this domain-specific ontology, are given
Vocabulary skills are well developed in university students with dyslexia: Evidence from multiple case studies
No full textInternational audienceMost studies in adults with developmental dyslexia have focused on identifying the deficits responsible for their persistent reading difficulties, but little is known on how these readers manage the intensive exposure to written language required to obtain a university degree. The main objective of this study was to identify certain skills, and specifically vocabulary skills, that French university students with dyslexia have developed and that may contribute to their literacy skills. We tested 20 university students with dyslexia and 20 normal readers (matched on chronological age, gender, nonverbal IQ, and level of education) in reading, phonological, vocabulary breadth (number of known words), and vocabulary depth (accuracy and precision) tasks. In comparing vocabulary measures, we used both Rasch model and single case study methodologies. Results on reading and phonological tasks confirmed the persistence of deficits in written word recognition and phonological skills. However, using the Rasch model we found that the two groups performed at the same level in the vocabulary breadth task, whereas dyslexics systematically outperformed their chronological age controls in the vocabulary depth task. These results are supplemented by multiple case studies. The vocabulary skills of French university students with dyslexia are well developed. Possible interpretations of these results are discussed
Dissertations as Data
No full textInternational audienceProblem/goalThe paper provides an overview and empirical evidence on the usability of electronic theses and dissertations (ETDs) and related research data for text and data mining (TDM) techniques.Research method/procedureThe first part of the paper is a review of recent publications and projects on the potential and usefulness of ETDs for TDM, followed by a description of our own research projects in the field.Anticipated resultsUsually, research studies on dissertations and data address the handling and potential exploitation of dissertations as a “data vehicle”, where data are published together with the dissertation (e.g. as a kind of data appendix), or as a “gateway to data”, where the data are not published together with the text but are available on a distant server. Yet, often the data are not available; or data, methodology, tools, primary sources are mingled, not indexed, badly described, and unrelated with the text, unconnected with other files.Our paper will describe a different approach that may be helpful to cope with this problem, in particular (but not only) when it is impossible to distinguish between data and dissertations and thus to process the data appropriately (data repository etc.). Our approach is to consider the dissertation as a whole (text, metadata, data, numbers, facts, figures etc.), as “material” potentially exploitable by TDM tools (including natural language processing) designed for unstructured information, i.e. lacking a pre-defined data model or not organized in a pre-defined manner.These tools and techniques may be helpful to find patterns or other useful information but usually involve some kind of structuring the documents, e.g. through manual tagging with metadata. A quite different condition is the legal feasibility. While in some countries TDM for scientific purpose does not require copyright clearance because copyright exceptions recognize that it is legal to extract content for data analytics, in other countries like in France copyright-based legal barriers to TDM are still waiting for removal.Our paper will address these issues, in a general way but also with regards to recent research on content mining of UK dissertations in law and chemistry, to automatic processing of PhD metadata for innovation search and identification of scientific skills and to our own research projects on TDM of unstructured information in the fields of cultural and industrial heritage, geographical data and academic publishing. In particular, we will draw on preliminary results of our interdisciplinary research project TERRE-ISTEX (2016-2018) that will retrieve, organize and make accessible knowledge related to geographical territories from heterogeneous digital academic resources available on the ISTEX platform and in dissertations.Also, we will address the issue of retro-digitisation of older print dissertations and related material in order to make them usable for automatic content mining and to valorise these often hidden treasures of academic heritage.Practical implications/originalityThe paper will provide an up-date on an emerging and promising field of research and development. Our results will be useful for academic libraries and repositories, for the conception and creation of added value services for their ETDs
Marqueurs physiologiques pour le contrôle de BCI actives/réactives
No full textNational audienceLa connaissance encore imprécise des corrélations entre l'activité mentale d'un individu et les signaux qu'on utilise pour l'analyser d'une part, et le faible rapport signal à bruit de ces derniers d'autre part, font qu'il est n'est pas possible d identifier dans ces signaux des indices pertinents pour établir un canal de communication sans imposer a priori un paradigme très précis. Dans les interfaces actives, les tâches mentales que l'utilisateur réalise sont ainsi censées entraîner des variations temporelles de potentiels, d'amplitudes et/ou de fréquence de rythmes cérébraux dont les corrélations avec l'état mental sont parfaitement connues. Dans les interfaces réactives, les perceptions de stimuli audio, visuels, ou tactiles, et les réactions cognitives qu'elles induisent chez l'individu, entraînent des modifications des activités d'aires cérébrales qui peuvent aisément être mises en évidence. Ce chapitre est dédié à la description des marqueurs physiologiques dont la détection, au travers d'une analyse des variations de signaux, constitue le premier maillon de la chaîne de communication qu'établit une interface cerveau-machine
Bounds for Learning from Evolutionary-Related Data in the Realizable Case
No full textInternational audienceThis paper deals with the generalization ability of classifiers trained from non-iid evolutionary-related data in which all training and testing examples correspond to leaves of a phylogenetic tree. For the re-alizable case, we prove PAC-type upper and lower bounds based on symmetries and matchings in such trees
La libre recherche de la vérité. La Nouvelle Académie à la lumière de la digression du Théétète
No full textInternational audienceOn examine comment le "scepticisme" de la Nouvelle Académie (Arcésilas, Carnéade) peut s'être réclamé de la description du philosophe proposée par Platon dans la digression du Théétète, et en particulier de la définition de celui-ci par sa liberté
Impacts of Immigration on an Ageing Welfare State: An Applied General Equilibrium Model for France
No full textInternational audienceImmigration is often seen as an instrument of adaptation for ageing countries. In this paper, we evaluate, using a dynamic general equilibrium model, the contribution of migration policy in reducing the tax burden associated with the ageing population in France. Four alternative scenarios, compared with a baseline scenario based on official projections, are simulated with the aim of quantifying the effects of immigration on French social protection finances. We show that the age and, to a lesser extent, the skill structure of immigrants are the key features that mainly determine the effects on social protection finances. Overall, these effects are all the more positive in the short to medium term if the migration policy is selective (in favour of more skilled workers). In the long term, the beneficial effects of a selective policy may disappear. But whatever the degree of selectivity of the migration policy, the financial gains from higher consequent migration flows are relatively moderate compared with the demographic changes implied by ageing
