218 research outputs found
DĂ©veloppement dâune mĂ©thodologie dâanalyse de la conservation de syntĂ©nie chez les plantes. Du gĂ©nome dâArabidopsis Ă celui du Tournesol
Le tournesol (Helianthus annuus L) est lâune des principales plantes olĂ©agineuses cultivĂ©es. LâĂ©tude des gĂšnes sous tendant les principaux caractĂšres agronomiques est difficile en raison de son grand gĂ©nome pour lequel peu dâinformations existent. Par ailleurs, les moyens financiers et techniques sont loin dâĂȘtre comparables Ă ceux mis en place pour les cĂ©rĂ©ales ou dâautres vĂ©gĂ©taux (carte physique, sĂ©quençage en masse de gĂ©nome, dâARNm, recherche des duplications, des transposons. . .). Pour Ă©tudier lâorganisation du gĂ©nome du tournesol, il a donc Ă©tĂ© envisagĂ© une approche diffĂ©rente basĂ©e sur la conservation de syntĂ©nie avec la plante modĂšle Arabidopsis thaliana. Les informations relatives aux gĂšnes de la plante modĂšle transfĂ©rĂ©es aux sĂ©quences EST et ARNm du tournesol permettent dâoptimiser lâexploitation de ces sĂ©quences. Mon travail de thĂšse a donc consistĂ© Ă mettre au point une mĂ©thode dâanalyse massive du grand nombre de sĂ©quences de tournesol puis de tester expĂ©rimentalement les rĂ©sultats de cette analyse afin dâobtenir de nouvelles informations sur lâorganisation du gĂ©nome du tournesol et dâestimer la conservation de syntĂ©nie avec Arabidopsis. La mise en place de la mĂ©thodologie a abouti Ă la crĂ©ation dâun serveur web appelĂ© Iccare. Cet outil bioinformatique permet la comparaison et lâanalyse dâun grand nombre de sĂ©quences de diffĂ©rents organismes vĂ©gĂ©taux ou animaux avec les sĂ©quences codantes des gĂšnes de lâorganisme modĂšle respectif, Homo sapiens pour les animaux et Arabidopsis thaliana pour les vĂ©gĂ©taux. Les rĂ©sultats sont prĂ©sentĂ©s sous forme graphique en combinant les informations de similitudes aux informations structurales des gĂšnes de lâorganisme modĂšle (introns, rĂ©gions UTR). La combinaison de ces informations permet ainsi dâoptimiser lâexploitation de ces sĂ©quences en utilisant les outils couplĂ©s Ă Iccare (dĂ©finir des amorces ou des sondes). En complĂ©ment de Iccare, Synteny Search (en cours dâachĂšvement) est un site web qui permet de rechercher les relations existantes entre les gĂšnes dâArabidopsis et du riz (conservation de syntĂ©nie) ainsi que les relations de ces gĂšnes au sein dâun mĂȘme gĂ©nome (ils sont uniques, dupliquĂ©s ou appartiennent Ă des familles multigĂ©niques). Cet outil donne des informations complĂ©mentaires sur les gĂšnes sĂ©lectionnĂ©s Ă partir dâIccare afin de vĂ©rifier et dâinterprĂ©ter les rĂ©sultats expĂ©rimentaux (nombre de fragments amplifiĂ©s ou de clones BAC positifs). Iccare a permis de sĂ©lectionner, parmi 60 200 sĂ©quences de tournesol, 20 691 sĂ©quences prĂ©sentant des similitudes avec 3 635 gĂšnes dâArabidopsis. Lâorganisation du gĂ©nome du tournesol et la conservation de syntĂ©nie avec Arabidopsis ont Ă©tĂ© Ă©tudiĂ©es en utilisant des sĂ©quences EST de tournesol qui prĂ©sentaient des similitudes avec 195 gĂšnes localisĂ©s sur le chromosome 5 de la plante modĂšle. Cent cinquante neuf dâentre elles ont servi Ă dĂ©finir des sondes Overgo dans deux rĂ©gions diffĂ©rentes. Le criblage dâune banque de clones BAC avec ces sondes prĂ©sente une efficacitĂ© supĂ©rieure Ă 70%. Des amplifications PCR sur une quarantaine de clones BAC positifs ont permis de confirmer la prĂ©sence des sĂ©quences EST. Ce criblage a aussi dĂ©montrĂ© que la banque utilisĂ©e Ă©tait peu couvrante pour les rĂ©gions Ă©tudiĂ©es ne permettant pas le regroupement en contig des clones BAC de sondes voisines chez la plante modĂšle. Par contre, le regroupement des clones BAC positifs Ă une mĂȘme sonde montre quâil existe plusieurs localisations pour cette sonde, conformĂ©ment aux informations prĂ©alables fournies par Synteny Search. ParallĂšlement aux hybridations, 51 sĂ©quences EST ont servi de matrice Ă la dĂ©finition de couples dâamorces spĂ©cifiques de rĂ©gions conservĂ©es de part et dâautre dâintrons. Lâamplification par PCR sur diffĂ©rents cultivars de tournesol prĂ©sente une efficacitĂ© de 90% et le taux de polymorphisme de taille observĂ© et vĂ©rifiĂ© sur gel dâagarose est de 15%, ce qui a permis dâintĂ©grer 7 nouveaux marqueurs molĂ©culaires Ă une carte gĂ©nĂ©tique issue de lignĂ©es recombinantes (Rachid Al-chaarani et al., 2004). Ces 7 marqueurs ne sont pas liĂ©s entre eux et nâont donc pas permis de dĂ©finir de conservation de syntĂ©nie entre tournesol et Arabidopsis. En conclusion, Iccare permet de facilement et rapidement traiter un grand nombre de donnĂ©es, de transfĂ©rer les informations structurelles des gĂšnes pour faciliter et optimiser la dĂ©finition dâamorces et de sondes et dâinterprĂ©ter les rĂ©sultats expĂ©rimentaux Ă lâaide de Synteny Search. En revanche, lâorganisation du gĂ©nome du tournesol et la syntĂ©nie existant avec Arabidopsis nâont pas pu ĂȘtre Ă©valuĂ©es clairement. Les donnĂ©es prĂ©liminaires obtenues laissent Ă penser que lâespace entre les gĂšnes du tournesol semble proportionnel Ă la diffĂ©rence de taille observĂ©e avec le gĂ©nome dâArabidopsis, expliquant ainsi la difficultĂ© Ă regrouper les clones BAC en contig. Un mode dâĂ©volution du gĂ©nome du tournesol possible est donc lâaugmentation de distance intergĂ©nique pouvant ĂȘtre due Ă des transposons et rĂ©trotransposons. ABSTRACT : The sunflower (Helianthus annuus L) is one of most cultivated oil-seed plant. His great genome size makes difficult the study of gene of interest (agronomic traits) especially that few information about it are available. Others plants or crops have more technical an financial means than for sunflower (physical map, massive genome and mRNA sequencing, duplication search, transposons. . .). In order to study the sunflower genome organization, we have developped a new method based ont synteny conservation with the model plant Arabidopsis thaliana. The transfert of gene information to the EST ou mRNA sequences of the sunflower permits to optimize the sequence exploitation. My thesis works consist in developping a new methology of massive analysis of sunflower sequences then test experimentally the results in order to get new information about the genome organization of the sunflower and to estimate the degree of synteny with the Arabidopsis genome. The methodology leads to the creation of a web server called Iccare. This bioinformatic tool permits to compare and analyse a high number of sequences from differents plants or animals organisms with the coding sequences of gene from the model organism which is respectively Homo sapiens for the animals and Arabidopsis thaliana for the plants. The results are displayed according to the location of the genes on the chromosomes of the reference organism. Genes structure information and sequence similarities are combined in a graphical representation in order to optimize the sequence exploitation by designing primers or probes. The Synteny Search web site (not finished yet) complete the Iccare web server, it permits to search the relation existing between the Arabidopsis genes and those of the rice (synteny conservation) and the relation between the genes within a genome (lonely genes, duplicated genes or genes belonging to multigenic family). This tool allows the access the information about the selected genes on Iccare in order to verify and interpret the experimental results (amplified fragment number or hybrided BAC clones). The Iccare web server had permit to select among 60,200 sunflower sequences, 20,691 sequences presenting similarities with 3,635 Arabidopsis genes. The genome organization of the sunflower and the synteny conservation with Arabidopsis had been studied by using EST sequences of the sunflower wich present some similarities to 195 genes located on the chromosome 5 of the model plant. One hundred and fifty nine EST sequences had been used to design Overgo probes in two differents regions of the fifth chromosome. These probes have been screened on a BAC clones library and over 70% were efficient. PCR amplification on forty BAC clones had confirmed the screening. The screening had also shown that the BAC clones library is less covering than expected in the studied regions. Some BAC clones had been fingerprinted and contig had been made showing different location for some Overgo probes according to the Synteny Search web site results. In addition to the screening, fifty one EST sequences had been used to design primer couple on conserved exons regions on both sides of an intron. PCR amplification on different sunflower cultivar with the primer couples presents 90% of efficiency and the size polymorphism rate on agarose is about 15%. Seven primer couples are used as molecular marker and are assigned on a genetic map (Recombinant Inbreed Lines). These molecular markers are not linked and any syntenic blocks can be defined between the sunflower genome and the Arabidopsis genome. In conlusion, the Iccare web server permits to facilitate and accelerate the traitement of high number data, to transfert structural information of genes in order to optimize the primer design and the probe design and to interpret experimental results aided by the Synteny Search web site. In spite of these new tools, the genome organization of the sunflower and the synteny conservation with the Arabidopsis genome are not elucidated. The preliminary data leave with thoughts that space between the sunflower genes seems proportional to the differente genome size between the sunflower genome and the Arabidopsis genome. These data can explain the difficulty to contig BAC clones. One evolution of the sunflower genome possibility is the increase of intergenic length due to transposons and retrotransposons
The TopModL Initiative
International audienceWe believe that there is a very strong need for an environment to support research and experiments on model-driven engineering. Therefore we have started the TopModL project, an open-source initiative, with the goal of building a development community to provide: (1) an executable environment for quick and easy experimentation, (2) a set of source files and a compilation tool chain, (3) a web portal to share artefacts developed by the community. The aim of TopModL is to help the model-engineering research community by providing the quickest path between a research idea and a running prototype. In addition, we also want to identify all the possible contributions, understand how to make it easy to integrate existing components, while maintaining architectural integrity. At the time of writing we have almost completed the bootstrap phase (known as Blackhole), which means that we can model TopModL and generate TopModL with TopModL. Beyond this first phase, it is now of paramount importance to gather the best possible description of the requirements of the community involved in model-driven engineering to further develop TopModL, and also to make sure that we are able to reuse or federate existing efforts or goodwill. This paper is more intended to set up a basis for a constructive discussion than to offer definitive answers and closed solutions
Improving Prediction Accuracy of Memory Interferences for Multicore Platforms
International audienceMemory interferences may introduce important slowdowns in applications running on COTS multi-core processors. They are caused by concurrent accesses to shared hardware resources of the memory system. The induced delays are difficult to predict, making memory interferences a major obstacle to the adoption of COTS multi-core processors in real-time systems. In this article, we propose an experimental characterization of ap-plications' memory consumption to determine their sensitivity to memory interferences. Thanks to a new set of microbenchmarks, we show the lack of precision of a purely quantitative characterization. To improve accuracy, we define new metrics quantifying qualitative aspects of memory consumption and implement a profiling tool using the VALGRIND framework. In addition, our profiling tool produces high resolution profiles allowing us to clearly distinguish the various phases in applications' behavior. Using our microbenchmarks and our new characterization, we train a state-of-the-art regressor. The validation on applications from the MIBENCH and the PARSEC suites indicates significant gain in prediction accuracy compared to a purely quantitative characterization
Maximizing Parallelism without Exploding Deadlines in a Mixed Criticality Embedded System
International audienceComplex embedded systems today commonly involve a mix of real-time and best-effort applications. The recent emergence of low-cost multicore processors raises the possibility of running both kinds of applications on a single machine, with virtualization ensuring isolation. Nevertheless, memory contention can introduce other sources of delay, that can lead to missed deadlines. In this paper, we present a combined offline/online memory bandwidth monitoring approach. Our approach estimates and limits the impact of the memory contention incurred by the best-effort applications on the execution time of the real-time application. We show that our approach is compatible with the hardware counters provided by current small commodity multicore processors. Using our approach, the system designer can limit the overhead on the real-time application to under 5% of its expected execution time, while still enabling progress of the best-effort applications. I. INTRODUCTION In many embedded system domains, such as the automotive industry, it is necessary to run applications with different levels of criticality [13]. Some applications may have nearly hard real-time constraints, while others may need only best-effort access to the CPU and memory resources. A typical example is the car dashboard, which may display both critical real-time information, such as an alarm, and non critical information, such as travel maps and suggestions on how to outsmart traffic. Traditionally, multiple applications are integrated in a vehicle using a federated architecture: Every major function is implemented in a dedicated Electronic Control Unit (ECU) [28] that ensures fault isolation and error containment. This solution, however, multiplies the hardware cost, and, in an industry where every cent matters, is increasingly unacceptable. Recently, efforts have been made to develop an integrated architecture, in which multiple functions share a single ECU. AUTOSAR [16] is a consortium of actors from the automotive industry that defines a software architecture to exploit the benefits of integrated architectures by facilitating the reuse of applications. The AUTOSAR standard targets applications that control vehicle electrical systems and that are scheduled on a real-time operating system that is compliant with the AUTOSAR OS standard. Infotainment applications, however, typically target a Unix-like operating system, and thus still require the use of a federated architecture. Recent experimental small uniform memory access commodity multicore systems provide a potential path towards a complete low-cost integrated architecture. Systems such as the Freescale SABRE Lite [1] offer sufficient CPU power to run multiple applications on a single low-cost ECU. Using Virtualized architectures [8], [18], [34], multiple operatin
Understanding the Memory Consumption of the MiBench Embedded Benchmark
International audienceComplex embedded systems today commonly involve a mix of real-time and best-effort applications. The recent emergence of small low-cost commodity multi-core processors raises the possibility of running both kinds of applications on a single machine, with virtualization ensuring that the best-effort applications cannot steal CPU cycles from the real-time applications. Nevertheless, memory contention can introduce other sources of delay, that can lead to missed deadlines. In this paper, we analyze the sources of memory consumption for the real-time applications found in the MiBench embedded benchmark suite
DĂ©veloppement dâun procĂ©dĂ© de revĂȘtement zinc-Nickel rĂ©pondant aux exigences du secteur aĂ©ronautique
La sociĂ©tĂ© MECAPROTEC Industries en collaboration avec les laboratoires CIRIMAT et ELECTRODEP, dĂ©veloppe un procĂ©dĂ© de dĂ©pĂŽt ZnNi rĂ©pondant aux exigences du secteur aĂ©ronautique, en vue de la substitution du cadmiage Ă©lectrolytique. Ces exigences, diffĂ©rentes de celles du secteur automobile, imposent de nouveaux critĂšres de choix qui viennent sâajouter Ă celui du comportement en corrosion. Ainsi, pour des piĂšces en aciers Ă haute rĂ©sistance mĂ©canique, les procĂ©dĂ©s Ă©lectrolytiques peuvent ĂȘtre Ă lâorigine dâune fragilisation des piĂšces par occlusion dâhydrogĂšne. Il est donc indispensable pour le dĂ©veloppement de ce nouveau procĂ©dĂ© et son application Ă des ensembles aĂ©ronautiques, dâĂ©valuer ce risque Ă partir dâessais normalisĂ©s et dây remĂ©dier. De plus, dans le cas d'applications sur des assemblages vissĂ©s, les caractĂ©ristiques tribologiques des alliages ZnNi devront ĂȘtre adaptĂ©es afin dâĂ©viter les risques de grippage. Du point de vue anticorrosion, un post-traitement de finition par chromatation est souvent utilisĂ© pour accroĂźtre les performances des revĂȘtements cadmiĂ©s. Dans le cas des revĂȘtements ZnNi, il conviendra bien sĂ»r dâatteindre des performances identiques en utilisant un traitement de finition sans chromate. Câest ce que nous tentons de faire en dĂ©veloppant un procĂ©dĂ© de finition par voie sol-gel. Pour rendre compatible le procĂ©dĂ© ZnNi avec toutes ou partie de ces contraintes, des recherches amonts sont rĂ©alisĂ©es en parallĂšle des nvestigations industrielles. Le but est de tendre vers une maĂźtrise complĂšte du procĂ©dĂ© et pour cela, de rechercher quels sont les paramĂštres opĂ©ratoires qui conditionnent les aractĂ©ristiques des dĂ©pĂŽts afin dâadapter celles-ci, Ă celles imposĂ©es par les exigences aĂ©ronautiques
Ten simple rules for developing visualization tools in genomics
Our following 10 simple rules are dedicated to biologists and bioinformaticians who, while already being at the crossroads of many fields, want to venture further into the land of Data Visualization (âdatavisâ or âdatavizâ for short). They combine tips and advice that we would have wanted when we first started our own journeys, gathered from our experiences in building genomic and/or datavis tools, and the time spent with related communities. Additionally, they address current challenges in computational biology and the needs of the community
Electronic Sensors for Assessing Interactions between Healthcare Workers and Patients under Airborne Precautions
International audienceBackground: Direct observation has been widely used to assess interactions between healthcare workers (HCWs) and patients but is time-consuming and feasible only over short periods. We used a Radio Frequency Identification Device (RFID) system to automatically measure HCW-patient interactions. Methods: We equipped 50 patient rooms with fixed sensors and 111 HCW volunteers with mobile sensors in two clinical wards of two hospitals. For 3 months, we recorded all interactions between HCWs and 54 patients under airborne precautions for suspected (n=40) or confirmed (n=14) tuberculosis. Number and duration of HCW entries into patient rooms were collected daily. Concomitantly, we directly observed room entries and interviewed HCWs to evaluate their self- perception of the number and duration of contacts with tuberculosis patients. Results: After signal reconstruction, 5490 interactions were recorded between 82 HCWs and 54 tuberculosis patients during 404 days of airborne isolation. Median (interquartile range) interaction duration was 2.1 (0.8-4.4) min overall, 2.3 (0.8-5.0) in the mornings, 1.8 (0.8-3.7) in the afternoons, and 2.0 (0.7-4.3) at night (P,1024). Number of interactions/day/HCW was 3.0 (1.0-6.0) and total daily duration was 7.6 (2.4-22.5) min. Durations estimated from 28 direct observations and 26 interviews were not significantly different from those recorded by the network. Conclusions: The RFID was well accepted by HCWs. This original technique holds promise for accurately and continuously measuring interactions between HCWs and patients, as a less resource-consuming substitute for direct observation. The results could be used to model the transmission of significant pathogens. HCW perceptions of interactions with patients accurately reflected reality
Developing an acoustic-phonetic characterization of dysarthric speech in French
- ISBN: 2-9517408-6-7 - Domaines: Phonetic Databases, Phonology, Person IdentificationInternational audienceThis paper presents the rationale, objectives and advances of an on-going project (the DesPho-APaDy project funded by the French National Agency of Research) which aims to provide a systematic and quantified description of French dysarthric speech, over a large population of patients and three dysarthria types (related to the parkinson's disease, the Amyotrophic Lateral Sclerosis disease, and a pure cerebellar alteration). The two French corpora of dysarthric patients, from which the speech data have been selected for analysis purposes, are firstly described. Secondly, this paper discusses and outlines the requirement of a structured and organized computerized platform in order to store, organize and make accessible (for selected and protected usage) dysarthric speech corpora and associated patients' clinical information (mostly disseminated in different locations: labs, hospitals, ...). The design of both a computer database and a multi-field query interface is proposed for the clinical context. Finally, advances of the project related to the selection of the population used for the dysarthria analysis, the preprocessing of the speech files, their orthographic transcription and their automatic alignment are also presented
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