Live Genomics for Pathogen Monitoring in Public Health

Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in a short lapse of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the “local” level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a “streaming approach” (pipeline). Such pipeline would include NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted “comprehensible” results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences

Prediction of suspended sediment concentrations in river flows

Studying the suspended sediments concentration (SSC) is of critical interest for water management. However, acquiring information on suspended sediment concentration (SSC) through direct in situ measurements has always been a challenging task due to technical difficulties especially in flows where the character of suspended materials changes frequently. Ideally, researchers would like to be able to measure the suspended-sediment concentration at all points in a given river. Regarding the cost in terms of material and labor time, they simplify the task to the measurement at all points in a cross section, the measurement along one vertical or even the measurement at one point. Each time the procedure includes a smaller portion of the river, spatial error becomes grater. Regarding all these difficulties, numerical modeling is used instead of or coupled with in situ measurement to optimize the cost of studying suspended sediments concentration. Various numerical and analytical formulas of different order of complexity are used to represent SSC, and knowing the complexity of transport in rivers, it is still impossible to have a universal profile. In this context, we are interested into establishing an innovative model to predict SSC in river flows. The model suggested in the present study is obtained by combining the properties of the sediment diffusivity coefficients of the parabolic constant model and of the model presented by Itakura and Kishi (1980). The model established is validated with a range of experimental data

Modélisation mathématique du transport des sédiments en suspension dans les écoulements de surface (de l'empirique au numérique)

La distribution verticale de la concentration des sédiments en suspension joue un rôle majeur dans l étude du taux et la capacité de transport d une rivière. Il existe, dans la bibliographie, plusieurs modèles de distribution des vitesses et des concentrations dont les conditions d utilisation sont souvent ambigües. Vue la difficulté des mesures sur terrain, il est nécessaire d utiliser et de savoir choisir un profil numérique.Le but de cette thèse est de concevoir de nouveaux outils pour étudier la distribution verticale des vitesses et des concentrations. Dans ce contexte, nous présentons deux nouveaux coefficients de diffusivités obtenus par l introduction d opérateurs de corrections au profil parabolique. Ces deux modèles donnent en utilisant l équation de convection diffusion et le principe de Boussinesq deux profils analytiques de concentration et de vitesse. Aussi nous mettons au point une méthode qui permet de faire le choix entre les différents modèles mathématiques représentants le même phénomène physique et deux méthodes pour l intersection des profils et pour l extension des profils dans les cas où le modèle applicable n est pas unique ou n existe pas. Ensuite, nous appliquons cette méthode à l étude des profils verticaux de vitesse et des distributions de la concentration des sédiments en suspension en régime stationnaire et uniforme, et nous développons le code expert pour la distribution verticale des concentrations, code_ERESA.Dans une annexe, nous testons l utilisation du code de volumes finies code_Saturne pour l étude de la distribution verticale des vitesses et des concentrations des sédiments en suspension dans les écoulements de surface.The vertical distribution of suspended sediment concentration and velocity plays a major role in the study of the transport rate and the transport capacities of a river. Many suspended sediments concentration and velocity profiles exist in the literature, having ambiguous conditions of application. In addition, it is not easy to conduct in situ measurements. This reveals, not only the utility of using numerical profiles, but also the responsibility of choosing an optimal one.The present thesis aims to conceive new tools for studying the vertical velocity and concentration distribution. In this context, we present two new sediment diffusivity coefficients obtained by the introduction of correction operator on the parabolic diffusivity coefficient. These models are implemented in the convection diffusion equation to generate two analytical concentration profiles and using the Boussinesq assumption, they lead to two analytical velocity profiles. Also, we conceive a method for choosing between different mathematical representation of a same physical phenomenon, and two methods for the intersection between these representations when more than one is applicable and for the extension of the representations to the cases where no model is applicable. We apply this method on the study of the vertical velocity profile and the sediment distribution in steady and uniform sediment laden open channel flows, and we develop the expert system for the vertical sediment concentration distribution code_ERESA.In an appendix, we test the use of the finite volume code_Saturne for the study of the vertical velocity distribution and suspended sediment concentration in open channel flows.STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF