MetExploreViz: web component for interactive metabolic network visualization

Summary: MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyse omics data in a biochemical context. Availability and implementation: Documentation and link to GIT code repository (GPL 3.0 license) are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc

Exploration visuelle d'environnement intérieur par détection et modélisation d'objets saillants

Un robot compagnon doit comprendre le lieu de vie de l'homme pour satisfaire une requête telle que "Va chercher un verre dans la cuisine" avec un haut niveau d'autonomie. Pour cela, le robot doit acquérir un ensemble de représentations adaptées aux différentes tâches à effectuer. Dans cette thèse, nous proposons d'apprendre en ligne un modèle d'apparence de structures locales qui pourront être nommées par l'utilisateur. Cela permettra ensuite de caractériser un lieu topologique (ex: la cuisine) par un ensemble de structures locales ou d'objets s'y trouvant (réfrigérateur, cafetière, evier, ...). Pour découvrir ces structures locales, nous proposons une approche cognitive, exploitant des processus visuels pré-attentif et attentif, mis en oeuvre à partir d'un système sensoriel multi-focal. Le processus pré-attentif a pour rôle la détection de zones d'intérêt, supposées contenir des informations visuelles discriminantes: basé sur le modèle de 'saillance' de Itti et Koch, il détecte ces zones dans une carte de saillance, construite à partir d'images acquises avec une caméra large champ; une zone détectée est ensuite suivie sur quelques images afin d'estimer grossièrement la taille et la position 3D de la structure locale de l'environnement qui lui correspond. Le processus attentif se focalise sur la zone d'intérêt: le but est de caractériser chaque structure locale, par un modèle d'apparence sous la forme de mémoires associatives vues-patches-aspects. De chaque image sont extraits des points d'intérêt, caractérisés par un descripteur d'apparence local. Après cette phase d'exploration, l'homme peut annoter le modèle en segmentant les structures locales en objets, en nommant ces objets et en les regroupant dans des zones (cuisine). Ce modèle d'apparence sera ensuite exploité pour la reconnaissance et la localisation grossière des objets et des lieux perçus par le robot. ABSTRACT : A robot companion has to understand a domotic environment in order to execute requests like « Search a glass in the kitchen » with a high level of autonomy. So the robot must acquire several representations adapted to the tasks to be executed. This thesis proposes an on line learning method of an environment model expressed as a set of local structures described by appearance-based characteristics, and possibly named by a tutor. Such descriptions could be used in order to define a topological area (e.g. the kitchen) by a set of local structures or objects that could be found here (e.g. glasses, fridge, pans). For the construction of such a representation, it is proposed a cognitive mehod, based on attentive and preattentive visual processes, acquiring images from a multifocal sensor. The preattentive process aims at detect interest regions, that could contain discriminant visual information ; based on the saliency concept proposed initially bu Itti and Koch, interest regions are extracted from a saliency map, built from images acquired by a short lens or panoramic camera (large view field). Such a region is then tracked on several successive images acquired while the robot is moving, so that the size and the 3D position of the corresponding local structure could be coarsely estimated. Then the attentive process exploits attentionam mechanisms in order to be focused successively on each interest region : it aims to characterize each local structure by an appearance-based model defined by an associative memort views-patches-aspects. Salient scaled patches or SIFT features are extracted from every image. After this exploration step is over, the robot tutor could annotated the model, segmenting local structures in objects, naming objects and grouping them in areas (kitchen). Then, the robot exploits this environment model for the recognition and the coarse localization of objects and areas

1789-1791: triomphe ou échec de la minorité janséniste?

Les jansénistes récusent le nom qui les désigne. Ils ne veulent pas être les partisans de Jansenius, mais les disciples de Saint Augustin, les amis de la vérité, les seuls et vrais catholiques. Tout au long du siècle des Lumières, ils animent une ardente résistance contre l’Église majoritaire, qui est dans l’erreur, et défendent avec une belle énergie les droits du « petit nombre ». Ce combat les conduit à la contestation de la monarchie absolue qui ignore les impératifs de la conscience.L’événement révolutionnaire est pour beaucoup d’entre eux une divine surprise. La constitution civile du clergé semble répondre à la bulle Unigenitus. Comment vont-ils vivre ce bouleversement? Comment vont-ils gérer la tentation majoritaire? A partir des Nouvelles ecclésiastiques, qui existent depuis 1728, mais ne sont plus clandestines, le présent article cherche à comprendre les modalités du ralliement d’une partie des jansénistes à la Révolution.The label “Jansenist” was challenged by the Jansenists themselves. They did not wish to be seen as partisans of Jansenius, but as the disciples of St Augustine, friends of the truth, the only true Catholics. Throughout the Age of the Enlightenment, they maintained their ardent resistance to the majority Church, which was in the wrong, and fervently defended the rights of “the small in number”. This cause led them to contest the absolute monarchy which was oblivious to the calls of conscience. The revolution came for many of them as a divine surprise. The civil constitution of the clergy seemed to come as an answer to the bull Unigenitus. How would they live through such upheaval? How would they face up to the temptation of joining the majority? Taking the Nouvelles ecclésiastiques as its starting point, which had existed since 1728 but was no longer clandestine, this paper seeks to understand the ways in which a section of the Jansenists rallied to the revolutionary cause

Éliane Martin-Haag, Rousseau ou la conscience sociale des Lumières

Éliane Martin-Haag s’est intéressée à Diderot et a déjà publié en 2002 un très remarquable ouvrage : Voltaire du cartésianisme aux Lumières (Vrin). Philosophe, elle traque les ruptures introduites par les Lumières et les interroge à partir de lectures contemporaines. C’est cette double dimension qu’elle applique dans le présent essai à Jean-Jacques Rousseau. Le premier mérite de ce livre est incontestablement de prendre l’œuvre de Rousseau comme un tout. L’auteur refuse en effet de séparer « ..

Le Journal d’un émigré : Robert de Saint-Vincent entre jansénisme et Contre-Révolution

Qui était Robert de Saint-Vincent (1725-1799) ? L’historiographie présente deux images différentes du personnage, d’une part le bouillant opposant à la monarchie absolue, le sévère janséniste qui défend la tolérance civile à l’égard des protestants, et d’autre part l’homme du 25 septembre 1788, celui qui veut fondre 1789 dans le moule de 1614. Les ego-documents redécouverts récemment (ses Mémoires rédigés en émigration et un fragment de correspondance pour les années 1789-1790) permettent de retrouver la cohérence de l’individu et de son système. Robert de Saint-Vincent croit en la monarchie de justice et interprète comme despotisme ministériel toute volonté absolutiste. Pas de roi sans Parlement. Dès lors, on comprend son désarroi, l’impression d’être trahi par les siens et la perception de la Révolution comme le mal absolu, un immense complot jésuite.Who was Robert de Saint-Vincent (1725-1799)? The historiography offers two different images of this personnage: one, the passionate opponent of Absolute Monarchy, a severe jansenist who defended civil tolerance for Protestants; the other, the « the man of 25 September 1788 », who aspired to cast 1789 in the same mould as 1614. The ego-documents recently rediscovered (his mémoires of émigration, and a fragment of his correspondance for the years 1789-1790) endow this individual and his system of thought with a convincing coherency. Robert de Saint-Vincent believed in the monarchy of justice, and regarded as ministerial despotism any form of absolutist power. Not a King without Parlement. From then on, his dissatisfaction is understandable: his impression of being betrayed by his colleagues, and his perception of the Revolution as a total evil, an immense jesuit plot

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

<p>Abstract</p> <p>Background</p> <p>The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.</p> <p>Results</p> <p>We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster.</p> <p>Conclusion</p> <p>The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.</p

A Genomic Reappraisal of Symbiotic Function in the Aphid/Buchnera Symbiosis: Reduced Transporter Sets and Variable Membrane Organisations

Buchnera aphidicola is an obligate symbiotic bacterium that sustains the physiology of aphids by complementing their exclusive phloem sap diet. In this study, we reappraised the transport function of different Buchnera strains, from the aphids Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistaciae and Cinara cedri, using the re-annotation of their transmembrane proteins coupled with an exploration of their metabolic networks. Although metabolic analyses revealed high interdependencies between the host and the bacteria, we demonstrate here that transport in Buchnera is assured by low transporter diversity, when compared to free-living bacteria, being mostly based on a few general transporters, some of which probably have lost their substrate specificity. Moreover, in the four strains studied, an astonishing lack of inner-membrane importers was observed. In Buchnera, the transport function has been shaped by the distinct selective constraints occurring in the Aphididae lineages. Buchnera from A. pisum and S. graminum have a three-membraned system and similar sets of transporters corresponding to most compound classes. Transmission electronic microscopic observations and confocal microscopic analysis of intracellular pH fields revealed that Buchnera does not show any of the typical structures and properties observed in integrated organelles. Buchnera from B. pistaciae seem to possess a unique double membrane system and has, accordingly, lost all of its outer-membrane integral proteins. Lastly, Buchnera from C. cedri revealed an extremely poor repertoire of transporters, with almost no ATP-driven active transport left, despite the clear persistence of the ancestral three-membraned system

MetaNetter 2:A Cytoscape plugin for ab initio network analysis and metabolite feature classification

Metabolomics frequently relies on the use of high resolution mass spectrometry data. Classification and filtering of this data remain a challenging task due to the plethora of complex mass spectral artefacts, chemical noise, adducts and fragmentation that occur during ionisation and analysis. Additionally, the relationships between detected compounds can provide a wealth of information about the nature of the samples and the biochemistry that gave rise to them. We present a biochemical networking tool: MetaNetter 2 that is based on the original MetaNetter, a Cytoscape plugin that creates ab initio networks. The new version supports two major improvements: the generation of adduct networks and the creation of tables that map adduct or transformation patterns across multiple samples, providing a readout of compound relationships. We have applied this tool to the analysis of adduct patterns in the same sample separated under two different chromatographies, allowing inferences to be made about the effect of different buffer conditions on adduct detection, and the application of the chemical transformation analysis to both a single fragmentation analysis and an all-ions fragmentation dataset. Finally, we present an analysis of a dataset derived from anaerobic and aerobic growth of the organism Staphylococcus aureus demonstrating the utility of the tool for biological analysis

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, baumannia cicadellinicola and sulcia muelleri with their insect host, homalodisca coagulata

International audienceEndosymbiotic bacteria from different species can live inside cells of the same eukaryotic organism. Metabolic exchanges occur between host and bacteria but also between different endocytobionts. Since a complete genome annotation is available for both, we built the metabolic network of two endosymbiotic bacteria, Sulcia muelleri and Baumannia cicadellinicola, that live inside specific cells of the sharpshooter Homalodisca coagulata and studied the metabolic exchanges involving transfers of carbon atoms between the three. We automatically determined the set of metabolites potentially exogenously acquired (seeds) for both metabolic networks. We show that the number of seeds needed by both bacteria in the carbon metabolism is extremely reduced. Moreover, only three seeds are common to both metabolic networks, indicating that the complementarity of the two metabolisms is not only manifested in the metabolic capabilities of each bacterium, but also by their different use of the same environment. Furthermore, our results show that the carbon metabolism of S. muelleri may be completely independent of the metabolic network of B. cicadellinicola. On the contrary, the carbon metabolism of the latter appears dependent on the metabolism of S. muelleri, at least for two essential amino acids, threonine and lysine. Next, in order to define which subsets of seeds (precursor sets) are sufficient to produce the metabolites involved in a symbiotic function, we used a graph-based method, PITUFO, that we recently developed. Our results highly refine our knowledge about the complementarity between the metabolisms of the two bacteria and their host. We thus indicate seeds that appear obligatory in the synthesis of metabolites are involved in the symbiotic function. Our results suggest both B. cicadellinicola and S. muelleri may be completely independent of the metabolites provided by the co-resident endocytobiont to produce the carbon backbone of the metabolites provided to the symbiotic system (., thr and lys are only exploited by B. cicadellinicola to produce its proteins)

The languages of peace during the French religious wars

The desirability of peace was a common topos in sixteenth-century political rhetoric, and the duty of the king to uphold the peace for the benefit of his subjects was also a long-established tradition. However, the peculiar circumstances of the French religious wars, and the preferred royal policy of pacification, galvanized impassioned debate among both those who supported and those who opposed confessional coexistence. This article looks at the diverse ways in which peace was viewed during the religious wars through an exploration of language and context. It draws not only on the pronouncements of the crown and its officials, and of poets and jurists, but also on those of local communities and confessional groups. Opinion was not just divided along religious lines; political imperatives, philosophical positions and local conditions all came into play in the arguments deployed. The variegated languages of peace provide a social and cultural dimension for the contested nature of sixteenth-century French politics. However, they could not restore harmony to a war-torn and divided kingdom