A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. This is the first polynomial-delay algorithm for this problem and we show that in practice, it is faster than previous approaches. This enables us to deal with larger instances and therefore to discover novel alternative splicing events, especially long ones, that were previously overseen using existing methods.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Navigating in a sea of repeats in RNA-seq without drowning

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one of the main examples. Most transcriptome assemblers are based on de Bruijn graphs and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are twofold. First, we introduce a formal model for repre- senting high copy number repeats in RNA-seq data and exploit its properties for inferring a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying in a de Bruijn graph a subgraph with this charac- teristic is NP-complete. In a second step, we show that in the specific case of a local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs. In particular, we designed and implemented an algorithm to efficiently identify AS events that are not included in repeated regions. Finally, we validate our results using synthetic data. We also give an indication of the usefulness of our method on real data

Localized approach to galvanic coupling in an aluminum–magnesium system

The corrosion behavior of a pure aluminum/pure magnesium couple in a weakly conductive sodium sulfate solution was investigated. Potential and current distributions on the surface of the model couple at the beginning of immersion were obtained by solving the Laplace equation using a finite element method algorithm. Magnesium acted as the anode of the system while oxygen and water were reduced on aluminum. Calculations predicted a large current peak at the Al/Mg interface related to a local increase in both Mg dissolution and oxygen and water reduction on aluminum, leading to a local pH increase. Optical and scanning electron microscope observations confirmed the strong dissolution of magnesium concomitantly with depassivation of aluminum at the Al/Mg interface. Local electrochemical impedance spectroscopy showed the detrimental effects of the galvanic coupling both on aluminum and magnesium

Simulating the galvanic coupling between S-Al2CuMg phase particles and the matrix of 2024 aerospace aluminium alloy

Study of the corrosion behaviour of a magnetron sputtered Al–Cu/Al–Cu–Mg model alloy couple in sulphate solutions has been undertaken to gain insight into the galvanic coupling between the matrix and SAl2CuMg particles in the 2024 aluminium alloy (AA2024). Polarisation curves and local electrochemical impedance spectroscopy measurements (LEIS) were performed on the individual alloys and on the model alloy couple. SEM enabled correlation of electrochemical phenomena to the observed damage. The corrosion behaviour of the sputtered alloys was shown to be representative of the AA2024, with the Al–Cu–Mg alloy part undergoing localised corrosion and the Al–Cu alloy part remaining passive

Assessing the Exceptionality of Coloured Motifs in Networks

Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model the notion of a functional/evolutionary building block. However, algorithms that enumerate all the motifs of a network may produce a very large output, and methods to decide which motifs should be selected for downstream analysis are needed. A widely used method is to assess if the motif is exceptional, that is, over- or under-represented with respect to a null hypothesis. Much effort has been put in the last thirty years to derive P-values for the frequencies of topological motifs, that is, fixed subgraphs. They rely either on (compound) Poisson and Gaussian approximations for the motif count distribution in Erdös-Rényi random graphs or on simulations in other models. We focus on a different definition of graph motifs that corresponds to coloured motifs. A coloured motif is a connected subgraph with fixed vertex colours but unspecified topology. Our work is the first analytical attempt to assess the exceptionality of coloured motifs in networks without any simulation. We first establish analytical formulae for the mean and the variance of the count of a coloured motif in an Erdös-Rényi random graph model. Using simulations under this model, we further show that a Pólya-Aeppli distribution bette

Gravitational action for a massive Majorana fermion in 2d quantum gravity

We compute the gravitational action of a free massive Majorana fermion coupled to two-dimensional gravity on compact Riemann surfaces of arbitrary genus. The structure is similar to the case of the massive scalar. The small-mass expansion of the gravitational yields the Liouville action at zeroth order, and we can identify the Mabuchi action at first order. While the massive Majorana action is a conformal deformation of the massless Majorana CFT, we find an action different from the one given by the David-Distler-Kawai (DDK) ansatz.Comment: 40 page

Short and long-term genome stability analysis of prokaryotic genomes.

BACKGROUND: Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. RESULTS: We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. CONCLUSION: In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were able to explore genome organization stability at different time-scales and to find significant differences for pathogen and non-pathogen species. The output of our framework also allows to identify the conserved gene clusters and/or partial occurrences thereof, making possible to explore how gene clusters assembled during evolution.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

La fonctionnalisation du récit au coeur des relations publiques : l'art de jumeler faits et effets

Ce mémoire sur l'étude des relations publiques vise à déceler les fils qui se tissent dans l'ombre des coulisses et qui forment une histoire reprise publiquement dans les médias. Nous investiguerons deux concepts clés soit le pouvoir et la communication, afin de faire converger notre réflexion vers le concept de la communication fonctionnalisée, prémisse de départ de notre questionnement. Nous présenterons aussi les assises théoriques propres au tournant narratif illustré par de nombreux auteurs sous la forme du Storytelling et qui, suivant la logique de la communication fonctionnalisée, introduit cette fois le concept du récit fonctionnalisé. Nous explorerons par la suite les diverses tendances journalistiques fondées sur la personnalisation et l'actualisation des faits en nous appuyant sur la présentation de divers auteurs traitant des enjeux des médias d'aujourd'hui. Par la suite, nous juxtaposerons à notre présentation des organisations médiatiques l'évolution de la pratique des relations publiques en questionnant le pouvoir propre à cette pratique et les enjeux organisationnels qui s'y rattachent. En regard de ces enjeux, nous chercherons à mieux saisir leurs places dans la sphère médiatique. Il sera ainsi possible de questionner leur rôle en analysant leur participation dans l'identification et la présentation de témoignages, d'histoires, mettant de l'avant divers intervenants qui prendront la parole dans la sphère publique afin de partager leurs récits. Nous en viendrons ainsi à questionner la fonctionnalisation du récit au cœur des relations publiques, interrogeant le rôle de ces professionnels qui de plus en plus insufflent aux faits l'effet nécessaire pour favoriser l'incorporation d'intérêts privés dans le paysage médiatique québécois. \ud ______________________________________________________________________________ \ud MOTS-CLÉS DE L’AUTEUR : relations publiques, communication, récit fonctionnalisé, communication fonctionnalisée, journalistes, médias, storytelling, culture industrielle, pouvoir, porte-parol

Influence of Post-Welding Heat Treatment on the Corrosion Behavior of a 2050-T3 Aluminum-Copper-Lithium Alloy Friction Stir Welding Joint

The corrosion behavior of a Friction Stir Welding joint in 2050-T3 Al-Cu-Li alloy was studied in 1 M NaCl solution and the influence of T8 post-welding heat treatment on its corrosion susceptibility was analyzed. After exposure to 1 M NaCl solution, the heat affected zone (HAZ) of the weld without post-welding heat treatment was found to be the most extensively corroded zone with extended intergranular corrosion damage while, following T8 post-welding heat treatment, no intergranular corrosion was observed in the HAZ and the global corrosion behavior of the weld was significantly improved. The corrosion damage observed on the welded joints after immersion in 1 M NaCl solution was compared to that obtained after 750 h Mastmaasis Wet Bottom tests. The same corrosion damage was observed. Various stationary electrochemical tests were carried out on the global welded joint and/or each of the metallurgical zones of the welded joint to understand the corrosion damage observed. TEM observations helped in bringing meaningful elements to analyze the intrinsic electrochemical behavior of the different zones of the weld related to their microstructure. However, galvanic coupling tests showed that galvanic coupling effects between the different zones of the weld were at least partially responsible for its corrosion behavior

Procédé de fabrication de Gaz Naturel de Synthèse par couplage d'une méthanation avec une électrolyse de vapeur d'eau à haute température

National audienceLe procédé présenté ici est un procédé de type Power-to-Gas dont l'objectif est de produire un gaz de synthèse injectable sur les réseaux de gaz naturel, en couplant une électrolyse de vapeur d'eau à haute température à cellule à oxyde solide (Solid Oxide Electrolysis Cell) et une hydrogénation de CO2 afin de produire du méthane, composant majeur du gaz naturel de synthèse. La simulation de ce procédé est réalisée avec le logiciel de simulation ProSim Plus 3® et des modèles spécifiquement développés pour l'électrolyseur à haute température d'une part et pour le réacteur de méthanation d'autre part ont été mis en place. Ces modèles permettent également l'évaluation économique puisque le calcul d'un paramètre de dimensionnement de ces réacteurs est intégré. La simulation, lors de la génération du gaz de synthèse, montre un rendement énergétique élevé (79,2%), supérieur au rendement des filières à basse température. Le procédé développé pour le stockage est également utilisable pour régénérer de l'électricité par réaction électrochimique à partir de gaz naturel