Stochastic models and numerical algorithms for a class of regulatory gene networks

Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many regulatory gene networks, and study the steady state distributions of the associated Gillespie algorithm by providing efficient numerical algorithms. We also study a regulatory gene network of interest in synthetic biology and in gene therapy, using mean-field models with time delays. Convergence of the related time-nonhomogeneous Markov chain is established for a class of linear catalytic networks with feedback loop

Détection de contradiction dans les commentaires

L'analyse des avis (commentaires) générés par les utilisateurs devient de plus en plus exploitable par une variété d'applications. Elle permet de suivre l'évolution des avis ou d'effectuer des enquêtes sur des produits. La détection d'avis contradictoires autour d'une ressource Web (ex. cours, film, produit, etc.) est une tâche importante pour évaluer cette dernière. Dans cet article, nous nous concentrons sur le problème de détection des contradictions et de la mesure de leur intensité en se basant sur l'analyse du sentiment autour des aspects spécifiques à une ressource (document). Premièrement, nous identifions certains aspects, selon les distributions des termes émotionnels au voisinage des noms les plus fréquents dans l'ensemble des commentaires. Deuxièmement, nous estimons la polarité de chaque segment de commentaire contenant un aspect. Ensuite, nous prenons uniquement les ressources contenant ces aspects avec des polarités opposées (positive, négative). Troisièmement, nous introduisons une mesure de l'intensité de la contradiction basée sur la dispersion conjointe de la polarité et du rating des commentaires contenant les aspects au sein de chaque ressource. Nous évaluons l'efficacité de notre approche sur une collection de MOOC (Massive Open Online Courses) contenant 2244 cours et leurs 73873 commentaires, collectés à partir de Coursera. Nos résultats montrent l'efficacité de l'approche proposée pour capturer les contradictions de manière significative

Visualisation of Physical Lung Simulation: an Interactive Application to Assist Physicians

International audienceRadiation therapy of cancer necessitates accurate tumour targeting. Unfortunately, during the treatment the tumour and the related organs can undergo large displacement and deformation. Physicians need an estimation of these movements, for an adapted therapy. In this paper, we propose a methodology to provide physicians with reconstructed 4D (3D+time) CT scans, considered as essential data. Moreover we propose an interactive visualisation tool, permitting the exploration of reconstructed 4D CT scans as well as the generation of new CT scan sections in any direction of the 3D space

The Fe XXII I(11.92 A)/I(11.77 A) Density Diagnostic Applied to the Chandra High Energy Transmission Grating Spectrum of EX Hydrae

Using the Livermore X-ray Spectral Synthesizer, which calculates spectral models of highly charged ions based primarily on HULLAC atomic data, we investigate the temperature, density, and photoexcitation dependence of the I(11.92 A)/I(11.77 A) line ratio of Fe XXII. We find that this line ratio has a critical density n_c \approx 5x10^13 cm^-3, is approximately 0.3 at low densities and 1.5 at high densities, and is very insensitive to temperature and photoexcitation, so is a useful density diagnostic for sources like magnetic cataclysmic variables in which the plasma densities are high and the efficacy of the He-like ion density diagnostic is compromised by the presence of a bright ultraviolet continuum. Applying this diagnostic to the Chandra High Energy Transmission Grating spectrum of the intermediate polar EX Hya, we find that the electron density of its T_e \approx 12 MK plasma is n_e = 1.0^{+2.0}_{-0.5} x 10^14 cm^-3, orders of magnitude greater than that typically observed in the Sun or other late-type stars.Comment: 11 pages including 3 encapsulated postscript figures; LaTeX format, uses aastex.cls; accepted on 2003 April 3 for publication in The Astrophysical Journa

Steady-state expression of self-regulated genes

Motivation: Regulatory gene networks contain generic modules such as feedback loops that are essential for the regulation of many biological functions. The study of the stochastic mechanisms of gene regulation is instrumental for the understanding of how cells maintain their expression at levels commensurate with their biological role, as well as to engineer gene expression switches of appropriate behavior. The lack of precise knowledge on the steady-state distribution of gene expression requires the use of Gillespie algorithms and Monte-Carlo approximations. Methodology: In this study, we provide new exact formulas and efficient numerical algorithms for computing/modeling the steady-state of a class of self-regulated genes, and we use it to model/compute the stochastic expression of a gene of interest in an engineered network introduced in mammalian cells. The behavior of the genetic network is then analyzed experimentally in living cells. Results: Stochastic models often reveal counter-intuitive experimental behaviors, and we find that this genetic architecture displays a unimodal behavior in mammalian cells, which was unexpected given its known bimodal response in unicellular organisms. We provide a molecular rationale for this behavior, and we implement it in the mathematical picture to explain the experimental results obtained from this network. Contact: [email protected], [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Stochastic Models and Numerical Algorithms for a Class ofRegulatory Gene Networks

Regulatory gene networks contain generic modules, like those involving feedback loops, which are essential for the regulation of many biological functions (Guido etal. in Nature 439:856-860, 2006). We consider a class of self-regulated genes which are the building blocks of many regulatory gene networks, and study the steady-state distribution of the associated Gillespie algorithm by providing efficient numerical algorithms. We also study a regulatory gene network of interest in gene therapy, using mean-field models with time delays. Convergence of the related time-nonhomogeneous Markov chain is established for a class of linear catalytic networks with feedback loop

De l’agglomération antique de la Croix de la Pierre à la paroisse de Saint-Martin-de-Claix (Beaulieu, Charbonnier-les-Mines - Puy-de-Dôme) : nouvelles données sur la topographie urbaine durant l’Antiquité et sur l’évolution du territoire à l’époque médiévale

L’article a pour objet de publier les données acquises au cours des cinq dernières années sur le site antique de la Croix de la Pierre (Beaulieu, Charbonnier-les-Mines – 63). Les résultats de plusieurs opérations archéologiques (un diagnostic, des prospections pédestres et aériennes) sont présentés, permettant d’avoir une vision plus précise de cette agglomération, récemment découverte, et de son organisation spatiale. Grâce aux sources textuelles, l’histoire de ce site antique – délaissé vraisemblablement à la fin du Haut-Empire – peut être suivie au cours du Moyen Âge : elle est caractérisée par la christianisation des lieux et par de profondes modifications dans l’organisation spatiale.The article aims to publish the data acquired during the last five years on the ancient terrain of la Croix de la Pierre (Beaulieu, Charbonnier-les-Mines – Puy-de-Dôme). The results of several archaeological operations (diagnosis, pedestrian surveys and aerial photography) are presented and analyzed. It is now possible to have a clearer view of this town, recently discovered, and its spatial organization. Thanks to textual data, the history of this ancient terrain - abandoned probably at the end of the Early Roman Empire- can be followed during the Middle Ages: it is characterized by the Christianization of area and profound changes in the spatial organization

De l’agglomération antique de la Croix de la Pierre à la paroisse de Saint-Martin-de-Claix (Beaulieu, Charbonnier-les-Mines - Puy-de-Dôme) : nouvelles données sur la topographie urbaine durant l’Antiquité et sur l’évolution du territoire à l’époque médiévale

L’article a pour objet de publier les données acquises au cours des cinq dernières années sur le site antique de la Croix de la Pierre (Beaulieu, Charbonnier-les-Mines – 63). Les résultats de plusieurs opérations archéologiques (un diagnostic, des prospections pédestres et aériennes) sont présentés, permettant d’avoir une vision plus précise de cette agglomération, récemment découverte, et de son organisation spatiale. Grâce aux sources textuelles, l’histoire de ce site antique – délaissé vraisemblablement à la fin du Haut-Empire – peut être suivie au cours du Moyen Âge : elle est caractérisée par la christianisation des lieux et par de profondes modifications dans l’organisation spatiale.The article aims to publish the data acquired during the last five years on the ancient terrain of la Croix de la Pierre (Beaulieu, Charbonnier-les-Mines – Puy-de-Dôme). The results of several archaeological operations (diagnosis, pedestrian surveys and aerial photography) are presented and analyzed. It is now possible to have a clearer view of this town, recently discovered, and its spatial organization. Thanks to textual data, the history of this ancient terrain - abandoned probably at the end of the Early Roman Empire- can be followed during the Middle Ages: it is characterized by the Christianization of area and profound changes in the spatial organization

Les habitudes technologiques au cégep : résultats d'une enquête effectuée auprès de 30 724 étudiants

Texte en anglais.Bibliographie : pages 55-56

Fast Non-Linear Projections using Graphics Hardware

http://artis.imag.fr/Publications/2008/GHFP08/International audienceLinear perspective projections are used extensively in graphics. They provide a non-distorted view, with simple computations that map easily to hardware. Non-linear projections, such as the view given by a fish-eye lens are also used, either for artistic reasons or in order to provide a larger field of view, e.g. to approximate environment reflections or omnidirectional shadow maps. As the computations related to non-linear projections are more involved, they are harder to implement, especially in hardware, and have found little use so far in practical applications. In this paper, we apply existing methods for non-linear projections [Lloyd et al. 2006; Hou et al. 2006; Fournier 2005] to a specific class: non-linear projections with a single center of projection, radial symmetry and convexity. This class includes, but is not limited to, paraboloid projections, hemispherical projections and fish-eye lenses. We show that, for this class, the projection of a 3D triangle is a single curved triangle, and we give a mathematical analysis of the curved edges of the triangle; this analysis allows us to reduce the computations involved, and to provide a faster implementation. The overhead for non-linearity is bearable and can be balanced with the fact that a single nonlinear projection can replaces as many as five linear projections (in a hemicube), with less discontinuities and a smaller memory cost, thus making non-linear projections a practical alternative. More at http://artis.imag.fr/Publications/2008/GHFP0