Outils de visualisation de données de cartes à puce pour une société de transport collectif

RÉSUMÉ : De plus en plus de sociétés de transport en commun font le choix de systèmes automatisés de perception des titres de transport par carte à puce et réalisent que ces données recueillies au jour le jour, depuis déjà 2008 pour la grande région de Montréal, constituent un potentiel immense à exploiter pour la planification de leur offre de transport. Dans ce contexte, cette maîtrise recherche s’inscrit dans un projet global mené depuis trois ans en collaboration avec divers partenaires. Elle fait suite aux précédents travaux de recherche menés sur l’enrichissement des transactions des cartes à puce en leur associant les origines et les destinations des trajets. Pour les fins de ce projet, le Réseau de Transport de Longueuil (RTL) a mis à disposition les 3,1 millions de transactions de bus et de métro du mois de mars 2013. La société Thales a rendu disponible son portail « Analytics For Transportation » développé par le département CeNTAI (Centre de Traitement et d’Analyse de l’Information). L’objectif principal de cette maîtrise recherche est de concevoir des interfaces permettant de visualiser et d’analyser les transactions de cartes à puce, enrichies de leurs destinations, répondant ainsi aux besoins d’un exploitant de transport en commun. Les sous-objectifs, correspondant aux étapes de la recherche, sont les suivants : - Rendre opérationnel l’algorithme de détermination des destinations - Conceptualiser la structure des données la plus adéquate pour permettre leur visualisation - Créer des interfaces de visualisation répondant aux besoins d’un exploitant de transport en commun. Ce mémoire commence par une revue de littérature présentant d’une part les projets des années précédentes sur l’estimation de l’origine puis de la destination des déplacements et d’autre part d’autres projets liés à la visualisation de ce type de données. Les raisonnements employés pour répondre aux trois sous-objectifs précités sont exposés dans une section méthodologie. La dernière section présente les résultats et analyses obtenus à partir de ces données enrichies. Les contributions apportées par ce mémoire sont : - L’optimisation et la refonte de l’algorithme d’estimation des destinations et son adaptation à un réseau défini selon le format GTFS (General Transit Feed Specification)- La présentation d’aperçus rapides et ergonomiques obtenus grâce à l’utilisation d’outils libres (Elasticsearch et Kibana) analysant ces données enrichies de carte à puce - La conception d’une nouvelle interface web personnalisée et développée pour alimenter un tableau de bord présentant des indicateurs clés pour une société de transport en commun à partir des données transmises par le RTL. En conclusion, ce projet de recherche propose une solution opérationnelle qui, pour un jeu de données de transactions de cartes à puce, permet, en une étape, d’estimer la destination des trajets de chaque transaction des usagers, de préparer des statistiques supplémentaires (distance et temps de trajet, séquences de tronçons …) et de les exporter vers un fichier texte et vers une base de données (Elasticsearch). Le tout est réalisé en un temps relativement court : 20 minutes pour 3 millions de transactions, temps d’exportation compris. Les données sont alors directement disponibles et exploitables dans des portails web configurés ou développés pour l’occasion prenant en compte les besoins des clients. Parmi les 3,1 millions de transactions disponibles, 20% sont des transactions de métro. Ces dernières permettent d’aider l’algorithme dans l’estimation des destinations. Lorsqu’elles sont prises en compte, elles n’améliorent que de 1% le nombre total de destinations des trajets de bus portant à 79% le nombre de trajets OD en bus recomposés pour notre jeu de données de mars 2013. Les séquences de tronçons ou déplacements ont été recomposées au cours de l’algorithme. Il en ressort par exemple que 66% des déplacements de bus, ou séquences de tronçons, effectués par les usagers sont des trajets directs sans correspondance. La part d’usagers effectuant des déplacements d’une seule correspondance est respectivement 12% du bus vers le bus et 20% du bus vers le métro. En définitive, ce projet de recherche permet de montrer que l’analyse de gros volumes de données en un temps limité est possible et une solution opérationnelle est présentée. En effet, il faudrait un temps de traitement de seulement 32 heures pour enrichir les transactions des 8 dernières années du RTL, à raison de 3 millions de données par mois. Ces données de type OD seraient alors disponibles pour alimenter les analyses des différents départements d’une société de transport en commun tels que la gestion des opérations du réseau, la planification et même le marketing et la finance. Les outils de visualisation développés permettraient alors d’aider le RTL dans la rédaction d’un cahier des charges auprès d’une entreprise offrant des solutions BI (Business Intelligence) pour visualiser leurs données métier.----------ABSTRACT : Public transit authorities are choosing more and more smart card automated fare collection systems and realize that those daily recovered data, since 2008 for the greater Montreal region, have a great potential for their planning and operations. In this context, this research master is part of a global project held for three-year period in collaboration with various partners. It follows previous research works on data enrichment of smart card transactions by combining their trip origin and destination. For the purpose of this project, the transit authority RTL (Réseau de Transport de Longueuil) provided one month (March 2013) of bus and metro smart card transactions (3.1 million). As far as Thales is concerned, they made available their “Analytics For Transportation” portal developed by its CeNTAI Department (Centre de Traitement et d’Analyse de l’Information). The main objective of this master research is to design interfaces for viewing and analyzing smart card transactions, enriched of their destination, while meeting the needs of a transit operator. The sub-objectives, corresponding to the steps of this research, are: - Make operational the algorithm determining trip destinations - Conceptualize the most adequate data structure enabling their visualization - Design visualization interfaces meeting the needs of a transit operator This thesis starts with a literature review with, on the one hand, the previous works on the estimation of the trips origin and destination, and, on the other hand, other projects on data visualization. The steps followed to meet the above three sub-objectives are described in the methodology section. The final section presents the results and analysis obtained from these enriched data. The main achievements of this project are: - The optimization and redesign of the algorithm estimating trip destinations and its adaptation to a network defined with the GTFS format (General Transit Feed Specification) - The presentation of ergonomic insights, obtained thanks to the use open source tools (Elasticsearch, Kibana), enabling those enriched smart card data to be quickly analyzed The design of a new customized web interface developed to present other key indicators used by a public transport company. In conclusion, this research project presents an operational solution, which for a set of smart card transaction data offers, in one step, to estimate the destination of each smart card transaction trip, to prepare additional statistics (distance and travel time, trip-leg sequences …) and to export those enriched transactions to a text file or a data base (Elasticsearch). The whole process is made within a relatively short time: 20 minutes for 3 million transactions, export time included. The data is then directly available and usable in web portals configured or developed for the occasion and which take into account the needs of the customers. Of the 3.1 million available transactions, 20% are metro transactions. These transactions help the algorithm in the estimation of a trip destination. These metro transactions only help to find 1 more percent of destinations, resulting in 79% of trip destinations recovered for our March 2013 dataset. Trip-legs have also been reconstructed by the algorithm. It shows for example that 66% of bus travels are made without a transfer. The share of users making only one transfer represents respectively 12% from bus to bus and represents 20% from bus to metro. In the end, this research shows that the analysis of large volume of data within a limited period of time is possible and an operational solution is presented. Indeed, it would require a processing time of 32 hours to enhance the RTL smart card transactions of the last 8 years, with 3 million transactions per month. These OD type of data would then be available to power the analysis of the various departments of a public transit authority such as operations, planning and even marketing and finance. The developed visualization prototypes would then help the RTL in drafting the specifications of a new tool sold and designed by a company selling BI (Business Intelligence) solutions to visualize their business data

RNA Locally Optimal Secondary Structures

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Prosper: image and robot-guided prostate brachytherapy

Brachytherapy for localized prostate cancer consists in destroying cancer by introducing iodine radioactive seeds into the gland through hollow needles. The planning of the position of the seeds and their introduction into the prostate is based on intra-operative ultrasound (US) imaging. We propose to optimize the global quality of the procedure by: i) using 3D US; ii) enhancing US data with MRI registration; iii) using a specially designed needle-insertion robot, connected to the imaging data. The imaging methods have been successfully tested on patient data while the robot accuracy has been evaluated on a realistic deformable phantom

Medical image computing and computer-aided medical interventions applied to soft tissues. Work in progress in urology

Until recently, Computer-Aided Medical Interventions (CAMI) and Medical Robotics have focused on rigid and non deformable anatomical structures. Nowadays, special attention is paid to soft tissues, raising complex issues due to their mobility and deformation. Mini-invasive digestive surgery was probably one of the first fields where soft tissues were handled through the development of simulators, tracking of anatomical structures and specific assistance robots. However, other clinical domains, for instance urology, are concerned. Indeed, laparoscopic surgery, new tumour destruction techniques (e.g. HIFU, radiofrequency, or cryoablation), increasingly early detection of cancer, and use of interventional and diagnostic imaging modalities, recently opened new challenges to the urologist and scientists involved in CAMI. This resulted in the last five years in a very significant increase of research and developments of computer-aided urology systems. In this paper, we propose a description of the main problems related to computer-aided diagnostic and therapy of soft tissues and give a survey of the different types of assistance offered to the urologist: robotization, image fusion, surgical navigation. Both research projects and operational industrial systems are discussed

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While pleiotropic adaptive mutations are thought to be central for evolution, little is known on the downstream molecular effects allowing adaptation to complex ecologically relevant environments. Here we show that Escherichia coli MG1655 adapts rapidly to the intestine of germ-free mice by single point mutations in EnvZ/OmpR two-component signal transduction system, which controls more than 100 genes. The selective advantage conferred by the mutations that modulate EnvZ/OmpR activities was the result of their independent and additive effects on flagellin expression and permeability. These results obtained in vivo thus suggest that global regulators may have evolved to coordinate activities that need to be fine-tuned simultaneously during adaptation to complex environments and that mutations in such regulators permit adjustment of the boundaries of physiological adaptation when switching between two very distinct environments

A defective Krab-domain zinc-finger transcription factor contributes to altered myogenesis in myotonic dystrophy type 1

Myotonic dystrophy type 1 (DM1) is an RNA-mediated disorder caused by a non-coding CTG repeat expansion that, in particular, provokes functional alteration of CUG-binding proteins. As a consequence, several genes with misregulated alternative splicing have been linked to clinical symptoms. In our search for additional molecular mechanisms that would trigger functional defects in DM1, we took advantage of mutant gene-carrying human embryonic stem cell lines to identify differentially expressed genes. Among the different genes found to be misregulated by DM1 mutation, one strongly downregulated gene encodes a transcription factor, ZNF37A. In this paper, we show that this defect in expression, which derives from a loss of RNA stability, is controlled by the RNA-binding protein, CUGBP1, and is associated with impaired myogenesis—a functional defect reminiscent of that observed in DM1. Loss of the ZNF37A protein results in changes in the expression of the subunit α1 of the receptor for the interleukin 13. This suggests that the pathological molecular mechanisms linking ZNF37A and myogenesis may involve the signaling pathway that is known to promote myoblast recruitment during development and regeneratio

Distinct B cell subsets in Peyer's patches convey probiotic effects by Limosilactobacillus reuteri

Background: Intestinal Peyer's patches (PPs) form unique niches for bacteria-immune cell interactions that direct host immunity and shape the microbiome. Here we investigate how peroral administration of probiotic bacterium Limosilactobacillus reuteri R2LC affects B lymphocytes and IgA induction in the PPs, as well as the downstream consequences on intestinal microbiota and susceptibility to inflammation.Results: The B cells of PPs were separated by size to circumvent activation-dependent cell identification biases due to dynamic expression of markers, which resulted in two phenotypically, transcriptionally, and spatially distinct subsets: small IgD(+)/GL7(-)/S1PR1(+)/Bcl6, CCR6-expressing pre-germinal center (GC)-like B cells with innate-like functions located subepithelially, and large GL7(+)/S1PR1(-)/Ki67(+)/Bcl6, CD69-expressing B cells with strong metabolic activity found in the GC. Peroral L. reuteri administration expanded both B cell subsets and enhanced the innate-like properties of pre-GC-like B cells while retaining them in the sub-epithelial compartment by increased sphingosine-1-phosphate/S1PR1 signaling. Furthermore, L. reuteri promoted GC-like B cell differentiation, which involved expansion of the GC area and autocrine TGF beta-1 activation. Consequently, PD-1-T follicular helper cell-dependent IgA induction and production was increased by L. reuteri, which shifted the intestinal microbiome and protected against dextran-sulfate-sodium induced colitis and dysbiosis.Conclusions: The Peyer's patches sense, enhance and transmit probiotic signals by increasing the numbers and effector functions of distinct B cell subsets, resulting in increased IgA production, altered intestinal microbiota, and protection against inflammation

Structural constraints for the Crh protein from solid-state NMR experiments

We demonstrate that short, medium and long-range constraints can be extracted from proton mediated, rare-spin detected correlation solid-state NMR experiments for the microcrystalline 10.4 × 2 kDa dimeric model protein Crh. Magnetization build-up curves from cross signals in NHHC and CHHC spectra deliver detailed information on side chain conformers and secondary structure for interactions between spin pairs. A large number of medium and long-range correlations can be observed in the spectra, and an analysis of the resolved signals reveals that the constraints cover the entire sequence, also including inter-monomer contacts between the two molecules forming the domain-swapped Crh dimer. Dynamic behavior is shown to have an impact on cross signals intensities, as indicated for mobile residues or regions by contacts predicted from the crystal structure, but absent in the spectra. Our work validates strategies involving proton distance measurements for large and complex proteins as the Crh dimer, and confirms the magnetization transfer properties previously described for small molecules in solid protein samples