Characterisation of InlA truncation in Listeria monocytogenes isolates from farm animals and human cases in the province of Quebec

The introduction of Listeria monocytogenes into the food production chain is a concern, with numerous grouped cases of listeriosis associated with milk-derived or pork-derived products have been documented. Management of this zoonotic pathogen considers all strains as an equal risk. Recently, a new perspective for characterisation of strain virulence was introduced with the discovery of the unaltered sequence of InlA as a determinant of strain virulence; this has also been reported as an infrequent finding among so-called environmental strains, that is, strains isolated from food or from surfaces in food industries. The aim of this study was to differentiate L monocytogenes strains isolated from animal cases versus those from human cases and to differentiate clinical strains from environmental ones using a Caenorhabditis elegans virulence testing model. In Quebec in 2013/2014, the surveillance of L monocytogenes clinical isolates registered a total of 20 strains of animal origin and 16 pulsed-field gel electrophoresis types isolated from human cases. The mixed PCR multiplex agglutination protocol used for geno-serotyping clearly discriminated genogroup IVB strains from bovine and human origins. The presence of a premature stop codon single nucleotide polymorphism in the inlA gene sequence in clinical strains and the identical behaviour of particular strains in the C elegans model are discussed in this paper from the perspective of industrial management of L monocytogenes risk

New techniques for myocardial fonction détermination and tissue characterization

As cardiac diseases still remain one of the main causes of death (1), developing new techniques for the détection and follow-up of these diseases is of major importance. Several imaging means exist, and are regularly used for diagnostic and follow-up purposes. Among those, magnetic resonance imaging (MRI) is a great choice as it is non-invasive, non-ionizing, and can provide images of diagnostic quality for ail the organs. Thanks to these advantages, many studies have been done using MRI, and techniques are still being developed and improved every day. A part which is always important is the quantitative description of the tissues of interest: qualitative imaging is important when looking at the anatomy of the body, but when it is about differentiating two types of tissue within the same organ, in longitudinal studies where the patient serves as his/her own control, and to guide and monitor therapy, it is critically important to have an accurate, précisé and quantitative approach to characterizing différent tissues. During this thesis, several techniques have been developed for the quantification of lésions and their impact on the left ventricle of the heart. This project has been split in two: the topic of the first part is the quantification of the régional left ventricular movement, i.e. the rotation and contraction of the left ventricle (LV) during the cardiac cycle. The second part will be focusing on measuring a magnetic property of the myocardium, called T2, in order to detect any injury in the tissue of the heart, and to characterize changes after treatment of the injury. The first chapter will provide a général introduction to the topic, as well as a description of the main concerns for the use of the techniques discussed. The second chapter will focus on the first project, the movement of the heart. A new technique for the accurate quantification of the left ventricular contraction and rotation patterns will be described. This technique allows to remove adverse effects related to through plane motion during the acquisition, and to capture the actual motion of the heart. In a translational effort, the 3rd chapter shows a practical application of the technique developed in the preceding chapter: the technique has been used in heart transplanted patients, in order to test the hypothesis that there is a link between graft rejection and altered motion patterns of the left ventricle. While these above chapters focused on the quantification of régional function of the heart the ensuing and final 4th chapter will describe the second project of this thesis: T2 quantification is a most useful approach to detecting altérations in the water content of the tissue - which typically happens in response to an insuit which may include ischemia, inflammation, etc. An improvement of the T2 quantification technique will be presented, as well as a validation of the proposed technique in healthy volunteers and patients. The final chapter will then discuss the results presented in this thesis and is followed by an outlook. -- Les maladies cardiovasculaires sont encore une des causes majeures de décès dans les pays développés (1). Il est donc toujours plus important de développer de nouvelles techniques pour la détection et le suivi de ces maladies. Plusieurs options d'imagerie existent à l'heure actuelle, et elles sont utilisées chaque jour pour le diagnostic et le suivi des patients. Parmi celles-ci, l'imagerie par résonance magnétique, ou IRM, est un choix intéressant, car elle est non- invasive, non ionisante, et permet d'obtenir des images de tous les organes de qualité suffisante pour effectuer un diagnostic. De par ces avantages, l'IRM est une technique de choix, et de nombreuses études ont été menées De par ces avantages, de nombreuses études ont été menées avec cette technique, et de nouvelles améliorations sont développées chaque jour. Il est toujours important de pouvoir obtenir une description quantitative de l'objet d'intérêt: en effet, bien que l'imagerie qualitative permette d'observer l'anatomie du corps, elle ne permet pas de différencier deux types de tissu dans le même organe. Ainsi, lors d'études longitudinales, où les patients seront leur propre contrôle, de même que pour la gestion du traitement, il est particulièrement important d'avoir des méthodes précises, efficaces et quantitatives pour différencier les tissus. Au cours de cette thèse, plusieurs techniques ont été développées pour quantifier les lésions présentes ainsi que leur impact sur le ventricule gauche (VG) du cœur. Ce projet a été séparé en deux parties : la première discute de la quantification du mouvement local du ventricule gauche, c'est à dire les mouvements de rotation et contraction du ventricule gauche durant le cycle cardiaque. La deuxième partie porte sur la mesure d'une propriété magnétique, appelée T2, dans le but de détecter toute lésion présente dans le myocarde, et de caractériser les changements après le traitement. Le premier chapitre donnera une introduction générale du sujet, ainsi qu'une description des principaux défis lors de l'utilisation de techniques décrites. Le second chapitre portera sur le premier projet, la caractérisation du mouvement du cœur. Une nouvelle technique pour la quantification précise de la contraction et rotation ventriculaires sera décrite. Cette méthode permet notamment de s'affranchir des effets négatifs des mouvements perpendiculaires au plan d'image, et d'obtenir ainsi une image du vrai mouvement du cœur. Le 3ème chapitre, étant le résultat d'un effort pour la translation des techniques du stade expérimental au stade clinique, démontre l'application pratique de la technique développée dans le chapitre précédent. Elle a été utilisée chez des patients transplantés cardiaques, afin de tester l'hypothèse qu'il existe un lien entre le rejet du greffon et des altérations du mouvement du ventricule gauche. Bien que le sujet des chapitres précédents aie été la quantification de la fonction ventriculaire locale, le 4ème chapitre décrira le deuxième projet de cette thèse, la quantification T2 : elle est particulièrement utile dans la détection des altérations du contenu en eau d'un tissu, ce qui arrive généralement en réponse à une agression, telle qu'une ischémie, une inflammation, etc. Une amélioration de la technique de cartographie T2 sera présentée, ainsi qu'une validation dans des volontaires sains et des patients. Enfin, le chapitre final discutera des résultats présentés dans cette thèse et se terminera par une présentation des futures améliorations

FastFlood: a fast and simple 2D hydrodynamic or hydrostatic numerical solution to river flow in landscape evolution models

International audienceModelling river hydrodynamics in an efficient approach remains a technical challenge which limits our ability to assess river flood hazard or to use process-based erosion laws at a high-resolution in landscape evolution models. Here we present a fast iterative method, entitled FastFlood, to compute river depth and velocity in 2D on a digital elevation model (DEM). This new method solves for the 2D shallow water equation, without the inertia terms, by iteratively building the river water depth using classical flow routing algorithms based on directed acyclic graphs, including the classical single or multi-flow, applied to the water surface. At each iteration, the water depth of each cell of the DEM increases by an increment that is a function of water discharge, computed using a flow accumulation operation, and decreases based on a flow resistance equation, in a manner similar to the Floodos model (Davy et al., 2017). In the hydrostatic mode, this operation is repeated until reaching a near constant water depth over the entire DEM, which occurs after a few tens or hundreds of iterations. FastFlood can also solve for the dynamic propagation of a flood in the hydrodynamic mode. In this case, the water depth increment is only a function of the water discharge exiting the direct upstream neighbors and the iterations are replaced by a time evolution of the water depth. Water depths obtained with the hydrostatic solution were validated against an analytical solution in the case of a rectangular channel and with the Floodos model for natural DEMs. Compared to previous hydrodynamic models, the main benefits of FastFlood are its simplicity of implementation, which mainly requires a classical flow routing algorithm, and its efficiency. Indeed, for a DEM of 106 cells, the algorithm takes about 2 minutes on a laptop to find the hydrostatic solution, about 10 times faster than using the Floodos model (Davy et al., 2017) that was already significantly faster than other hydrodynamic models. Moreover, the computational time scales a little more than linearly with the number of cells, which makes FastFlood a suitable solution even for DEMs larger than 106 – 107 cells. In the future, we expect to make progress on the numerical method by adapting graph-based solutions to the issue of flow water routing. Following Davy et al. (2017), we will also include FastFlood in a landscape evolution model to couple it to process-based laws for erosion, transport and deposition of sediments

FastFlood: a fast and simple 2D hydrodynamic or hydrostatic numerical solution to river flow in landscape evolution models

International audienceModelling river hydrodynamics in an efficient approach remains a technical challenge which limits our ability to assess river flood hazard or to use process-based erosion laws at a high-resolution in landscape evolution models. Here we present a fast iterative method, entitled FastFlood, to compute river depth and velocity in 2D on a digital elevation model (DEM). This new method solves for the 2D shallow water equation, without the inertia terms, by iteratively building the river water depth using classical flow routing algorithms based on directed acyclic graphs, including the classical single or multi-flow, applied to the water surface. At each iteration, the water depth of each cell of the DEM increases by an increment that is a function of water discharge, computed using a flow accumulation operation, and decreases based on a flow resistance equation, in a manner similar to the Floodos model (Davy et al., 2017). In the hydrostatic mode, this operation is repeated until reaching a near constant water depth over the entire DEM, which occurs after a few tens or hundreds of iterations. FastFlood can also solve for the dynamic propagation of a flood in the hydrodynamic mode. In this case, the water depth increment is only a function of the water discharge exiting the direct upstream neighbors and the iterations are replaced by a time evolution of the water depth. Water depths obtained with the hydrostatic solution were validated against an analytical solution in the case of a rectangular channel and with the Floodos model for natural DEMs. Compared to previous hydrodynamic models, the main benefits of FastFlood are its simplicity of implementation, which mainly requires a classical flow routing algorithm, and its efficiency. Indeed, for a DEM of 106 cells, the algorithm takes about 2 minutes on a laptop to find the hydrostatic solution, about 10 times faster than using the Floodos model (Davy et al., 2017) that was already significantly faster than other hydrodynamic models. Moreover, the computational time scales a little more than linearly with the number of cells, which makes FastFlood a suitable solution even for DEMs larger than 106 – 107 cells. In the future, we expect to make progress on the numerical method by adapting graph-based solutions to the issue of flow water routing. Following Davy et al. (2017), we will also include FastFlood in a landscape evolution model to couple it to process-based laws for erosion, transport and deposition of sediments