Reconstruction of the 3-D fields with a depth-averaged model for open-channel flows in the smooth turbulent case

International audienceA two-dimensional depth-averaged model is derived for open-channel flows in the smooth turbulent case. The derivation is consistently obtained with a method of matched asymptotic expansions in the outer and inner layers using a mixing length model of turbulence including the free-surface reduction of the eddy viscosity. The shear effects are taken into account by an extra tensor variable of the model called the enstrophy tensor. The friction coefficient is an explicit expression of the water depth. The three-dimensional velocity field and the friction velocity can be reconstructed from the values of the depth-averaged quantities. Numerical simulations show that the enstrophy can be used to evaluate the development of the turbulent boundary layer. In the case of subcritical unsteady flows, the reconstructed velocity can be described with a logarithmic law modified by Coles’ wake function with apparent von Kármán constant, integration constant and wake-strength parameter, which differ from their values in steady flows. In the viscous sublayer the steady-state relation between the velocity and the vertical coordinate, in the inner scaling, is not valid for unsteady flows. Large errors on the calculation of the von Kármán constant can be made if the validity of the steady-state relation is assumed for unsteady flows. The comparisons of the reconstructed velocity profiles in the case of one-dimensional unsteady open-channel flows and two-dimensional wide trapezoidal channels show a good agreement with experiments

MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

International audienceMotivation: Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution. Results: We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments

TnSeek : analysing Tn-seq data for multiple conditions and multiple species

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HoSAGE: Sarcopenia in Older Patients before and after Treatment with Androgen Deprivation Therapy and Radiotherapy for Prostate Cancer

International audienceBackground: Sarcopenia is a muscle disease defined by a loss of muscle strength associated to a decrease in skeletal muscle mass. In addition to aging, many factors may contribute to sarcopenia as cancer and/or androgen deprivation therapy (ADT).Objectives: The aims of this study are to describe the prevalence of sarcopenia in older prostate cancer patients before initiation of treatment with ADT and radiotherapy, and to evaluate the impact of ADT on the occurrence or aggravation of sarcopenia in this population.Design: Longitudinal study.Participants and setting: Sarcopenia was prospectively evaluated in 31 consecutive patients aged 70 to 88 years, referred in one hospital unit of south eastern France, for a comprehensive geriatric assessment (CGA) before cancer treatment initiation.Measurements and results: CGA, measures of muscle strength and physical performances were performed at baseline (T0) and at the end of cancer treatment (T1). Appendicular skeletal muscle mass was measured by Dual-energy X-ray absorptiometry (DXA) at the end of treatment. At T0, 8 patients (among 31) had a probable sarcopenia according to European consensus, and 18 had altered physical performance. At T1, 15 patients (among 19) had abnormal one leg balance test. Finally, only one patient had a sarcopenia confirmed by DXA.Conclusion: This preliminary study showed a high prevalence of muscle disorders before initiation of ADT in a population of elderly cancer prostate patients with intermediate frailty status, and an increased risk of falls at the end of ADT. This highlighted the importance of screening for sarcopenia before treatment initiation, to prevent the occurrence or aggravation of sarcopenia by possible adjustment of treatment, and implementation of appropriate exercise and nutrition interventions

Développement d'un modèle dispersif hyperbolique pour les vagues côtières et implémentation dans Tolosa.

International audienceIn this study, we propose a new hyperbolic model with the same dispersive properties as the classical Serre-Green-Naghdi model capable to capture the wave breaking phenomenon. The hyperbolisation of the equations is based on taking into account the finite character of the sound speed and thus the compressibility of the sea water. The method therefore involves introducing acoustic energy into the system. In the case of coastal waves, the effects of static compressibility are negligible. The resulting model is then a hyperbolic approximation of the Serre-Green-Naghdi equations. The modelling of breakingwaves is obtained by adapting to this pseudo-compressible approach the depth-averaging method of Large-Eddy Simulations (LES) where the small scale turbulence is modelled by a turbulent viscosity, whereas the large scales are taken into account in the model by an anisotropic tensor variable called enstrophy.Dans cette étude, nous proposons un nouveau modèle hyperbolique avec les mêmes propriétés dispersives que le modèle classique de Serre-Green-Naghdi capable de capturer le phénomène de déferlement des vagues. L'hyperbolisation des équations est basée sur la prise en compte du caractère fini de la vitesse du son et donc de la compressibilité de l'eau de mer. La méthode implique donc d'introduire une énergie acoustique dans le système. Dans le cas des vagues côtières, les effets de compressibilité statique sont négligeables. Le modèle obtenu est alors une approximation hyperbolique des équations de Serre-Green-Naghdi. La modélisation du déferlement est obtenue par l'adaptation à cette approche pseudo-compressible de la méthode de moyenne sur la profondeur des équations de la simulation des grandes échelles de la turbulence (SGS) où les petites échelles de la turbulence sont modélisées par une viscosité turbulente, en revanche les grandes échelles sont prises en compte dans le modèle par une variable tensorielle anisotrope appelée enstrophie

Développement d'un modèle dispersif hyperbolique pour les vagues côtières et implémentation dans Tolosa.

International audienceIn this study, we propose a new hyperbolic model with the same dispersive properties as the classical Serre-Green-Naghdi model capable to capture the wave breaking phenomenon. The hyperbolisation of the equations is based on taking into account the finite character of the sound speed and thus the compressibility of the sea water. The method therefore involves introducing acoustic energy into the system. In the case of coastal waves, the effects of static compressibility are negligible. The resulting model is then a hyperbolic approximation of the Serre-Green-Naghdi equations. The modelling of breakingwaves is obtained by adapting to this pseudo-compressible approach the depth-averaging method of Large-Eddy Simulations (LES) where the small scale turbulence is modelled by a turbulent viscosity, whereas the large scales are taken into account in the model by an anisotropic tensor variable called enstrophy.Dans cette étude, nous proposons un nouveau modèle hyperbolique avec les mêmes propriétés dispersives que le modèle classique de Serre-Green-Naghdi capable de capturer le phénomène de déferlement des vagues. L'hyperbolisation des équations est basée sur la prise en compte du caractère fini de la vitesse du son et donc de la compressibilité de l'eau de mer. La méthode implique donc d'introduire une énergie acoustique dans le système. Dans le cas des vagues côtières, les effets de compressibilité statique sont négligeables. Le modèle obtenu est alors une approximation hyperbolique des équations de Serre-Green-Naghdi. La modélisation du déferlement est obtenue par l'adaptation à cette approche pseudo-compressible de la méthode de moyenne sur la profondeur des équations de la simulation des grandes échelles de la turbulence (SGS) où les petites échelles de la turbulence sont modélisées par une viscosité turbulente, en revanche les grandes échelles sont prises en compte dans le modèle par une variable tensorielle anisotrope appelée enstrophie