Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods

Whole genome sequencing (WGS) enables complete characterization of bacterial pathogenic isolates at single nucleotide resolution, making it the ultimate tool for routine surveillance and outbreak investigation. The lack of standardization, and the variation regarding bioinformatics workflows and parameters, however, complicates interoperability among (inter)national laboratories. We present a validation strategy applied to a bioinformatics workflow for Illumina data that performs complete characterization of Shiga toxin-producing Escherichia coli (STEC) isolates including antimicrobial resistance prediction, virulence gene detection, serotype prediction, plasmid replicon detection and sequence typing. The workflow supports three commonly used bioinformatics approaches for the detection of genes and alleles: alignment with blast+, kmer-based read mapping with KMA, and direct read mapping with SRST2. A collection of 131 STEC isolates collected from food and human sources, extensively characterized with conventional molecular methods, was used as a validation dataset. Using a validation strategy specifically adopted to WGS, we demonstrated high performance with repeatability, reproducibility, accuracy, precision, sensitivity and specificity above 95 % for the majority of all assays. The WGS workflow is publicly available as a ‘push-button’ pipeline at https://galaxy.sciensano.be. Our validation strategy and accompanying reference dataset consisting of both conventional and WGS data can be used for characterizing the performance of various bioinformatics workflows and assays, facilitating interoperability between laboratories with different WGS and bioinformatics set-ups

Modélisation multiphasique d'écoulements et de phénomènes de dispersion issus d'explosion

Ce travail porte sur la modélisation de la formation et la dispersion d'un nuage de gouttes, par déconfinement d'un liquide: agression extérieure ou situation accidentelle. Le but est la construction d'un modèle apte à reproduire simultanément les conditions génératrices de la formation du nuage et l'évolution de ce nuage dans le temps (dispersion). La principale difficulté réside en la différence des modèles adaptés à la description d'écoulements caractérisant chaque étape du phénomène global : modèle d'écoulement multiphasique à phases compressibles (milieux continus) initialement, puis fragmentation et formation du nuage de gouttes dispersées dans une phase porteuse (modèle d'écoulements dilués). En l'absence de modèle analytique unique apte à décrire l'ensemble de ces processus, on propose une approche originale pour réaliser un couplage effectif entre ces deux modèles. La problématique de formation et de dispersion de liquide implique la prise en compte de plusieurs phénomènes physiques: fragmentation, transferts de chaleur et de masse ainsi que la traînée entre les phases. Ces différents phénomènes sont introduits dans le modèle global via des termes d'interactions présents dans les systèmes d'équations. La construction de ce modèle complet à permis la réalisation de calculs décrivant la formation et la dispersion d'un nuage de gouttes pouvant intervenir lors de situations accidentelles sur des sites industriels par exemple.This work focuses on modeling the formation and the dispersion of a cloud of droplets, induced by ejection of a liquid, resulting from an external aggression or an accidental situation. The goal is to build a model able to reproduce simultaneously the conditions which generate the cloud formation and the cloud evolution in time (dispersion). The main difficulty lies in the differences between the already existing models adapted to the description of flows which are able to characterize each stage of the global phenomenon: initially a multiphase flow model with compressible phases (Continuum), then the atomization and the formation of a cloud of droplets dispersed in a carrier phase (dilute flow model). We propose a new approach to achieve an effective coupling between these two models. The problem of the formation and the dispersion of the liquid requires to take into account several physical phenomena: atomization, heat and mass transfers and drag between phases. These phenomena are included in the global model through interaction terms involved in the systems of equations. The construction of this model has permited the realization of calculations describing the formation and dispersion of a cloud of droplets which may occur during, for axample, in accidental situations at industrial sites

Modélisation multiphasique d'écoulements et de phénomènes de dispersion issus d'explosion

Ce travail porte sur la modélisation de la formation et la dispersion d'un nuage de gouttes, par déconfinement d'un liquide: agression extérieure ou situation accidentelle. Le but est la construction d'un modèle apte à reproduire simultanément les conditions génératrices de la formation du nuage et l'évolution de ce nuage dans le temps (dispersion). La principale difficulté réside en la différence des modèles adaptés à la description d'écoulements caractérisant chaque étape du phénomène global: modèle d'écoulement multiphasique à phases compressibles (milieux continus) initialement, puis fragmentation et formation du nuage de gouttes dispersées dans une phase porteuse (modèle d'écoulements dilués). En l'absence de modèle analytique unique apte à décrire l'ensemble de ces processus, on propose une approche originale pour réaliser un couplage effectif entre ces deux modèles. La problématique de formation et de dispersion de liquide implique la prise en compte de plusieurs phénomènes physiques: fragmentation, transferts de chaleur et de masse ainsi que la traînée entre les phases. Ces différents phénomènes sont introduits dans le modèle global via des termes d'interactions présents dans les systèmes d'équations. La construction de ce modèle complet à permis la réalisation de calculs décrivant la formation et la dispersion d'un nuage de gouttes pouvant intervenir lors de situations accidentelles sur des sites industriels par exemple.This work focuses on modeling the formation and the dispersion of a cloud of droplets, induced by ejection of a liquid, resulting from an external aggression or an accidental situation. The goal is to build a model able to reproduce simultaneously the conditions which generate the cloud formation and the cloud evolution in time (dispersion). The main difficulty lies in the differences between the already existing models adapted to the description of flows which are able to characterize each stage of the global phenomenon: initially a multiphase flow model with compressible phases (Continuum), then the atomization and the formation of a cloud of droplets dispersed in a carrier phase (dilute flow model). We propose a new approach to achieve an effective coupling between these two models. The problem of the formation and the dispersion of the liquid requires to take into account several physical phenomena: atomization, heat and mass transfers and drag between phases. These phenomena are included in the global model through interaction terms involved in the systems of equations. The construction of this model has permited the realization of calculations describing the formation and dispersion of a cloud of droplets which may occur during, for axample, in accidental situations at industrial sites.AIX-MARSEILLE1-Bib.electronique (130559902) / SudocSudocFranceF

Finding Innovative Technical Solutions in Patents Through Improved Evolution Trends

Abstract Patents represent a reservoir richly endowed with exploitable technical information, where a structured exploration of inventions can unveil essential knowledge for solving industrial problems. Several authors exploit patents using the evolution laws of the TRIZ theory to anticipate technological leaps, categorize patents in a TRIZ perspective, forecast technology, etc. TRIZ laws can be completed with Polovinkin’s rules, design rules, better known as “design heuristics,” and the rules of the art of engineering (engineering best practices). In this chapter, we propose evolution trends composed of all these elements and presented in the form of cards to assist users. After selecting pertinent patents, they can be classified into discovery matrices and analyzed in a timeline classification structured according to their technological branches. The evolution trends enable us to decipher the evolution in inventions being followed or to be followed by each technological branch. An in-depth analysis of several technological branches linked to the technical problem in question allows us to inspire users with original ideas, identify opportunities for innovation, and propose hybrid solutions. To illustrate our approach, we look for possible evolutions of current, deep offshore biphasic separation systems

Ecological data

Genetic sampling of trees in the forests of Nékoro, Tiéa, Pindai, Mepouiri and Nassirah was completed with a phyto-sociological survey of all the neighboring botanical species of Ixora margaretae. Around each sampled tree, and over a distance of 4 meters, all the species were identified. These data were used to characterize the floral composition of the dry forests of Nékoro and Tiéa, and the main ecological traits of Ixora margaretae. The same protocol was used for the dry forests of Mepouiri and Pindai and the mesic forest of Nassirah, but because of the low number of Ixora margaretae, it was difficult to interpret the results for these patches of forests

SSRData

SSRDat