PORGY: Interactive and Visual Reasoning with Graph Rewriting Systems

International audienceGraph rewriting systems have long been around in theoretical computer science, and are used as a computing model in discrete mathematics, algebra, mathematical logic or even linguistics. Graph rewriting systems operate on graphs by substituting local patterns. Starting from an initial graph, the system iterates transformation rules in a non necessarily deterministic way. The combination of rule applications turn the study of such a system into an involved task requiring high level expertise. The inherent complexity of graph rewriting systems motivated the use of graphical diagrams, even by experts, to convey ideas and theoretical concepts. In these situations, users are not experts in theoretical computer science but rather focus on how a graph rewriting system behaves as a model of the problem they study. Questions emerging from the target application nevertheless translate into questions about the rewriting system. The goal of this work is to allow users to experiment with a graph rewriting system, and reason about the system or the model it supports based on graphical representations of all its components. Visually reasoning about the system, domain experts are able to abstract and refine models, use simulation and deduction to compute or check postulated properties and make testable predictions about possible outcomes. PORGY possesses genuine features and appears to be the first system to offer multiple coordinated views, allowing users to visualize and manipulate the system at both a global and local scale

Porgy : une plate-forme visuelle et interactive pour la réécriture de graphes : présentation lors de la journée Visu 2012

Voir http://visu2012.imag.fr/ pour plus d'informationsGraph rewriting systems (GRSs) operate on graphs by substituting local patterns according to a set of rewriting rules. The apparent simplicity of GRSs hides an incredible complexity and turns the study of these systems into an involved task requiring high-level expertise. We designed PORGY, an interactive visual environment to fully support GRSs related tasks, exploiting a long historical tradition of GRSs with node-link representations of graphs. PORGY enables rule-based modeling and simulation steering through graphical representations and direct manipulation of all GRSs components. This talk presents PORGY and some case studies mainly based on bioinformatics data

The nonstructural NS1 protein of influenza viruses modulates TP53 splicing through host factor CPSF4

International audienceInfluenza A viruses (IAV) are known to modulate and "hijack" several cellular host mechanisms, including gene splicing and RNA maturation machineries. These modulations alter host cellular responses and enable an optimal expression of viral products throughout infection. The interplay between the host protein p53 and IAV, in particular through the viral nonstructural protein NS1, has been shown to be supportive for IAV replication. However, it remains unknown whether alternatively spliced isoforms of p53, known to modulate p53 transcriptional activity, are affected by IAV infection and contribute to IAV replication. Using a TP53 minigene, which mimics intron 9 alternative splicing, we have shown here that the NS1 protein of IAV changes the expression pattern of p53 isoforms. Our results demonstrate that CPSF4 (cellular protein cleavage and polyadenylation specificity factor 4) independently and the interaction between NS1 and CPSF4 modulate the alternative splicing of TP53 transcripts, which may result in the differential activation of p53-responsive genes. Finally, we report that CPSF4 and most likely beta and gamma spliced p53 isoforms affect both viral replication and IAV-associated type I interferon secretion. All together, our data show that cellular p53 and CPSF4 factors, both interacting with viral NS1, have a crucial role during IAV replication that allows IAV to interact with and alter the expression of alternatively spliced p53 isoforms in order to regulate the cellular innate response, especially via type I interferon secretion, and perform efficient viral replication

Randomized clinical trial of multimodal physiotherapy treatment compared to overnight lidocaine ointment in women with provoked vestibulodynia: Design and methods

Provoked vestibulodynia (PVD) is a highly prevalent and debilitating condition yet its management relies mainly on non-empirically validated interventions. Among the many causes of PVD, there is growing evidence that pelvic floor muscle (PFM) dysfunctions play an important role in its pathophysiology. Multimodal physiotherapy, which addresses these dysfunctions, is judged by experts to be highly effective and is recommended as a firstline treatment. However, the effectiveness of this promising intervention has been evaluated through only two small uncontrolled trials. The proposed bi-center, single-blind, parallel group, randomized controlled trial (RCT) aims to evaluate the efficacy of multimodal physiotherapy and compare it to a frequently used first-line treatment, topical overnight application of lidocaine, in women with PVD. A total of 212 women diagnosed with PVD according to a standardized protocol were eligible for the study and were randomly assigned to either multimodal physiotherapy or lidocaine treatment for 10weeks. The primary outcome measure is pain during intercourse (assessed with a numerical rating scale). Secondary measures include sexual function, pain quality, psychological factors (including pain catastrophizing, anxiety, depression and fear of pain), PFM morphology and function, and patients' global impression of change. Assessments are made at baseline, post-treatment and at the 6-month follow-up. This manuscript presents and discusses the rationale, design and methodology of the first RCT investigating physiotherapy in comparison to a commonly prescribed first-line treatment, overnight topical lidocaine, for women with PVD

Isolement et caractérisation des saponosides de trois plantes de la famille des araliaceae et dracaenaceae et évaluation de leurs activités cytotoxiques sur cellules tumorales

L intérêt des substances d origine naturelle, potentiellement anti-tumorales nous a amené à nous intéresser aux saponines triterpéniques et stéroïdiques de plantes issues de la biodiversité africaine de la famille des Araliaceae et des Dracaenaceae. En effet, des études antérieures menées sur quelques plantes de ces deux familles ont conduit à l obtention de molécules complexes et originales possédant d excellentes propriétés cytotoxiques, immuno-modulatrices, anti-inflammatoires. Au vu de ces résultats nous avons entrepris des investigations pharmaco-chimiques sur Cussonia arborea (Araliaceae), Dracaena deisteliana et Dracaena arborea (Dracaenaceae), plantes médicinales couramment utilisées en pharmacopée traditionnelle africaine pour traiter différentes maladies. Les travaux menés ont conduit à l isolement de 31 composés purs en utilisant les différentes techniques analytiques du laboratoire notamment les diverses techniques de chromatographie liquide successive à pression atmosphérique, moyenne pression et flash chromatographie sur silice en phase normale et en phase inverse. Les structures ont été déterminées par les méthodes de spectrométrie de masse en source FAB et de spectroscopie de RMN 1D et 2D (COSY, TOCSY, NOESY, HMBC et HSQC). Parmi les 07 composés purs obtenus des écorces de Cussonia arborea, 5 sont des nouvelles saponines triterpéniques dont un dérivé de l acide ursolique, un dérivé de l hédéragénine et trois dérivés de l acide oléanolique, tous disubstitués en position 3 et 28 par des chaînes oligosaccharidiques. 13 composés purs sont obtenus à partir des feuilles de Cussonia arborea, dont 7 nouvelles saponines triterpéniques dérivés de l acide ursolique, de l acide 23-hydroxyursolique, de l hédéragénine et de l acide oléanolique dont 04 d entre elles sont obtenues sous forme de mélanges inséparables d isomères acide oléanolique/acide ursolique et hédéragénine/acide 23-hydroxyursolique. A partir des écorces de Dracaena arborea et des tiges de Dracaena deisteliana, nous avons isolé et caractérisé 10 saponines stéroïdiques dont 4 nouvelles et une sapogénine. Les activités de certains de ces produits purs ont été évaluées sur deux lignées de cellules cancéreuses coliques humaines HCT 116 et HT-29.The interest of the substances from natural origin, potentially antitumor led us to interest in triterpenoid and steroidal saponins of plants from the African biodiversity belonging to the Araliaceae and Dracaenaceae families of plants. Indeed, of the former studies undertaken on some plants of these two families led to obtaining complex and original molecules having excellent cytotoxic, immuno-modulating, anti-inflammatory properties. Within sight of these results we undertook pharmaco-chemical investigations on Cussonia arborea (Araliaceae), Dracaena deisteliana, and Dracaena arborea (Dracaenaceae), medicinal plants usually used in african traditional pharmacopeia to treat various diseases. The work led to the isolation of 31 pure compounds by using the various analytical techniques in particular the various chromatography techniques (CC, MPLC, TLC, flash) on silica gel, normal and reversed phases. The structures were determined by the methods of mass spectrometry (FAB, ESI, IE) and 1D (1H and 13C) and 2D (COSY, TOCSY, NOESY, HMBC and HSQC) NMR spectroscopy. Among the 07 pure compounds obtained of the barks of Cussonia arborea, 5 are new triterpenoid saponins derivatives of ursolic acid, hederagenin and three derived from the acid oleanolic, all disubstituted in position 3 and 28 by oligosaccharidic chains. 13 pure compounds were obtained from leaves of Cussonia arborea, seven of which are new triterpenoid saponins derivatives of oleanolic acid, ursolic acid, hederagenin and 23-hydroxyursolic acid of which four were obtained as mixtures of isomers oleanolic acid/ursolic acid and hederagenin/23-hydroxyursolic acid. From the bark of Dracaena arborea and stem of Dracaena deisteliana, we isolated and characterized ten steroidal saponins including 4 new and sapogenin. The activities of some of these pure products were evaluated on two cancerous lines human colic cells HCT 116 and HT-29.DIJON-BU Doc.électronique (212319901) / SudocSudocFranceF