277 research outputs found

    Network-based analysis of eQTL data to prioritize driver mutations

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    In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive phenotype by affecting the same molecular pathways, a phenomenon referred to as parallelism at the molecular pathway level. This implies that successful driver identification depends on interpreting mutated genes in terms of molecular networks. Driver identification and obtaining a network-based understanding of the adaptive phenotype are thus confounded problems that ideally should be solved simultaneously. In this study, a network-based eQTL method is presented that solves both the driver identification and the network-based interpretation problem. As input the method uses coupled genotype-expression phenotype data (eQTL data) of independently evolved lines with similar adaptive phenotypes and an organism-specific genome-wide interaction network. The search for mutational consistency at pathway level is defined as a subnetwork inference problem, which consists of inferring a subnetwork from the genome-wide interaction network that best connects the genes containing mutations to differentially expressed genes. Based on their connectivity with the differentially expressed genes, mutated genes are prioritized as driver genes. Based on semisynthetic data and two publicly available data sets, we illustrate the potential of the network-based eQTL method to prioritize driver genes and to gain insights in the molecular mechanisms underlying an adaptive phenotype. The method is available at http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.htm

    Mining local staircase patterns in noisy data

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    Most traditional biclustering algorithms identify biclusters with no or little overlap. In this paper, we introduce the problem of identifying staircases of biclusters. Such staircases may be indicative for causal relationships between columns and can not easily be identified by existing biclustering algorithms. Our formalization relies on a scoring function based on the Minimum Description Length principle. Furthermore, we propose a first algorithm for identifying staircase biclusters, based on a combination of local search and constraint programming. Experiments show that the approach is promising

    Memristive and tunneling effects in 3D interconnected silver nanowires

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    Due to their memristive properties nanowire networks are very promising for neuromorphic computing applications. Indeed, the resistance of such systems can evolve with the input voltage or current as it confers a synaptic behaviour to the device. Here, we propose a network of silver nanowires (Ag-NWs) which are grown in a nanopourous membrane with interconnected nanopores by electrodeposition. This bottom-up approach fabrication method gives a conducting network with a 3D architecture and a high density of Ag-NWs. The resulting 3D interconnected Ag-NW network exhibits a high initial resistance as well as a memristive behavior. It is expected to arise from the creation and the destruction of conducting silver filaments inside the Ag-NW network. Moreover, after several cycles of measurement, the resistance of the network switches from a high resistance regime, in the GOhm range, with a tunnel conduction to a low resistance regime, in the kOhm range.Comment: 8 pages, 5 figure

    Virus Burden in Lymph Nodes and Blood of Subjects with Primary Human Immunodeficiency Virus Type 1 Infection on Bitherapy

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    At present, it is not known whether undetectable plasma viremia corresponds to an absence of human immunodeficiency virus type 1 (HIV-1) replication in lymphoid tissues. This issue has been explored in 11 subjects with primary HIV-1 infection treated with zidovudine plus didanosine by evaluating virologic markers in blood and lymphoid tissues 9-18 months after initiation of treatment. These markers include plasma viremia, measured with a sensitive assay with a detection limit of 20 HIV-1 RNA copies/mL, infectious virus titers and proviral DNA in lymph node mononuclear cells, and HIV-1 RNA in lymphoid tissue. Five subjects had plasma viremia < 20 copies/mL and showed no evidence of viral replication in lymphoid tissue. Six subjects had both detectable plasma viremia and evidence of HIV-1 RNA in lymphoid tissue. The results indicate that absence of detectable HIV RNA in lymphoid tissue is associated with viremia levels of HIV-1 RNA < 20 copies/m

    Esquis’sons ! Outils d’aide à la conception d’environnements sonores durables

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    The present project explores in 6 sustainable neighbourhoods in Europe (Germany, Spain, France andSweden) the sound qualities of intermediate spaces located on the building facades like balconies, loggias,terraces and circulations. A cross analysis of the physical dimensions of the built space, of the soundenvironment and of the user’s perceptions allows to describe the minimum conditions of existence of theseremarkable sound situations. All of this work is compiled in a directory that is the first tool for sound design ofsuch type of spaces. This directory is available in paper format in the Appendix of this report and online onthe portal Esquis'Sons (esquissons.fr). Thanks to this application (free download on the website), it ispossible to make a 3D virtual environment sounds and to hear the impact of architectural choices made bydesigners. The auralization module is informed by the geometric characteristics of the spatial pattern andvice versa. In other words, this application lets you sketch a space by listening.Ce prĂ©sent projet Ă©tudie dans 6 quartiers durables en Europe (Allemagne, Espagne, France et SuĂšde) lesqualitĂ©s sonores des espaces intermĂ©diaires situĂ©s en façade de bĂątiments que sont les balcons, les loggias,les terrasses et les circulations. Une analyse croisĂ©e de la forme physique, de l’environnement sonore et duressenti des usagers permet de faire Ă©merger les conditions minimales d’existence de situations sonoresremarquables. L’ensemble de ce travail est compilĂ© dans un rĂ©pertoire qui est le premier outil d’aide Ă  laconception sonore de ce type d’espace pour les architectes. Ce rĂ©pertoire est consultable en format papieren annexe de ce rapport et en ligne sur le portail Esquis’Sons (esquissons.fr). La recherche articule Ă  cetteanalyse un outil d’esquisse sonore qui intĂšgre les principaux rĂ©sultats de la phase de terrain dans uneinterface paramĂ©trique utilisant les logiciels Rhinoceros, Max MSP et le plug-in Grasshopper. Grace Ă  cetteapplication (en libre tĂ©lĂ©chargement sur le site), il est possible de « sonoriser » un environnement virtuel 3Det d’entendre les consĂ©quences de choix architecturaux. Le module d’auralisation est informĂ© par lescaractĂ©ristiques gĂ©omĂ©triques du modĂšle spatial et inversement. Autrement dit, cette application permetd’esquisser un espace en l’écoutant

    Deciphering hybrid larch reaction norms using random regression

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    The link between phenotypic plasticity and heterosis is a broad fundamental question, with stakes in breeding. We report a case-study evaluating temporal series of wood ring traits of hybrid larch (Larix decidua × L. kaempferi and reciprocal) in relation to soil water availability. Growth rings record the tree plastic responses to past environmental conditions, and we used random regressions to estimate the reaction norms of ring width and wood density with respect to water availability. We investigated the role of phenotypic plasticity on the construction of hybrid larch heterosis and on the expression of its quantitative genetic parameters. The data came from an intra-/interspecific diallel mating design between both parental species. Progenies were grown in two environmentally contrasted sites, in France. Ring width plasticity with respect to water availability was confirmed, as all three taxa produced narrower rings under the lowest water availability. Hybrid larch appeared to be the most plastic taxon as its superiority over its parental species increased with increasing water availability. Despite the low heritabilities of the investigated traits, we found that the expression of a reliable negative correlation between them was conditional to the water availability environment. Finally, by means of a complementary simulation, we demonstrated that random regression can be applied to model the reaction norms of non-repeated records of phenotypic plasticity bound by a family structure. Random regression is a powerful tool for the modeling of reaction norms in various contexts, especially perennial species

    Emulsification en continu avec un microsystĂšme en vue de l'encapsulation d'antioxydants

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    National audienceRESUME Cette Ă©tude porte sur une problĂ©matique qui intĂ©resse le secteur des complĂ©ments alimentaires et celui de la santĂ©. Des chercheurs ont rĂ©cemment dĂ©veloppĂ© un protocole [1] permettant une extraction et une « encapsulation » par Ă©mulsification d'antioxydants naturels (astaxanthine, ïą carotĂšnes ou lycopĂšnes), pour la plupart issus de microalgues, basĂ©es sur l'emploi de molĂ©cules plus respectueuses de l'environnement et peu couteuses. Ce protocole est Ă  ce stade rĂ©alisĂ© manuellement, en rĂ©acteur batch et met en jeu des petits volumes. Il serait intĂ©ressant de le transposer vers un procĂ©dĂ© fonctionnant en continu permettant de traiter des volumes plus importants, de maniĂšre plus reproductible et en limitant le contact de la phase lipidique avec l'oxygĂšne. L'idĂ©e proposĂ©e ici est de mettre en oeuvre un micromĂ©langeur [2] dĂ©veloppĂ© par les laboratoires GEPEA et LTeN afin d'Ă©tudier son potentiel vis-Ă -vis de ce type d'application. Ce type de micromĂ©langeur (Figure 1), basĂ© sur un mĂ©lange intime des fluides dans un volume trĂšs rĂ©duit (< 1mL) et avec un temps de sĂ©jour trĂšs faible (de l'ordre de la milliseconde), peut ĂȘtre une solution intĂ©ressante au regard des contraintes liĂ©es Ă  cette application. Les dĂ©bits maximaux atteints par ce dispositif sont de l'ordre de 600 mL/min ce qui est compatible avec une production Ă  pteite ou moyenne Ă©chelle. D'autre part, s'agissant de la perspective de l' « usine du futur », la mise en oeuvre de systĂšmes intensifiĂ©s s'inscrit dans une dynamique de dĂ©veloppement de procĂ©dĂ©s miniaturisĂ©s et globalement plus Ă©conomes en Ă©nergie. Cette Ă©tude se concentre dans un premier temps sur des tests de formulation et d'Ă©musification Ă  l'Ă©chelle paillasse avec un systĂšme fonctionnant en batch, de type rotor-stator, en faisant varier divers paramĂštres tels que la vitesse et le temps de rotation du rotor, les proportions des deux phases et la composition de celles-ci. Cette premiĂšre phase de l'Ă©tude permet d'affiner le choix de formulations d'Ă©mulsions de type huile dans eau offrant une bonne stabilitĂ©. Des essais sont ensuite menĂ©s avec le micromĂ©langeur sur les formulations les plus intĂ©ressantes vis-Ă -vis de l'application visĂ©e. Les Ă©mulsions ainsi obtenues avec les deux systĂšmes sont alors comparĂ©es en termes de distribution granulomĂ©trique et de stabilitĂ© au cours du temps. Dans un dernier temps, l'Ă©tude s'intĂ©resse Ă  l'incorporation de ïą carotĂšnes dans la formulation avec en particulier l'Ă©valuation de l'efficacitĂ© de rĂ©tention des ïą carotĂšnes dans la phase lipidique et l'Ă©tude de la stabilitĂ© chimique des Ă©mulsions obtenues. MOTS-CLES DU THEME ProcĂ©dĂ©s Ă©mergents, MicroprocĂ©dĂ©s, Microfluidique. MOTS-CLES LIBRES Emulsion, Fractionnement, procĂ©dĂ© continu, antioxydan

    PheNetic : network-based interpretation of molecular profiling data

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    Molecular profiling experiments have become standard in current wet-lab practices. Classically, enrichment analysis has been used to identify biological functions related to these experimental results. Combining molecular profiling results with the wealth of currently available interactomics data, however, offers the opportunity to identify the molecular mechanism behind an observed molecular phenotype. In this paper, we therefore introduce 'PheNetic', a userfriendly web server for inferring a sub-network based on probabilistic logical querying. PheNetic extracts from an interactome, the sub-network that best explains genes prioritized through a molecular profiling experiment. Depending on its run mode, PheNetic searches either for a regulatorymechanism that gave explains to the observed molecular phenotype or for the pathways (in) activated in the molecular phenotype. The web server provides access to a large number of interactomes, making sub-network inference readily applicable to a wide variety of organisms. The inferred sub-networks can be interactively visualized in the browser. PheNetic's method and use are illustrated using an example analysis of differential expression results of ampicillin treated Escherichia coli cells. The PheNetic web service is available at http://bioinformatics.intec.ugent.be/phenetic/

    Medical image computing and computer-aided medical interventions applied to soft tissues. Work in progress in urology

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    Until recently, Computer-Aided Medical Interventions (CAMI) and Medical Robotics have focused on rigid and non deformable anatomical structures. Nowadays, special attention is paid to soft tissues, raising complex issues due to their mobility and deformation. Mini-invasive digestive surgery was probably one of the first fields where soft tissues were handled through the development of simulators, tracking of anatomical structures and specific assistance robots. However, other clinical domains, for instance urology, are concerned. Indeed, laparoscopic surgery, new tumour destruction techniques (e.g. HIFU, radiofrequency, or cryoablation), increasingly early detection of cancer, and use of interventional and diagnostic imaging modalities, recently opened new challenges to the urologist and scientists involved in CAMI. This resulted in the last five years in a very significant increase of research and developments of computer-aided urology systems. In this paper, we propose a description of the main problems related to computer-aided diagnostic and therapy of soft tissues and give a survey of the different types of assistance offered to the urologist: robotization, image fusion, surgical navigation. Both research projects and operational industrial systems are discussed