E-Biothon: an experimental platform for BioInformatics

International audienceThe E-Biothon platform is an experimental Cloud platform to help speed up and advance research in biology, health and environment. It is based on a Blue Gene/P system and a web portal that allow members of the bioinformatics community to easily launch their scientific applications. We describe in this paper the technical capacities of the platform, the different applications supported and finally a set of user experiences on the platform

Experiencing transitions in life of mothers of young children

V magistrskem delu smo raziskovali doživljanje življenjskih prehodov mater majhnih otrok. Teoretični del je bil namenjen pregledu literature s področja blagostanja, življenjskih prehodov in materinstva. Za raziskovanje doživljanja življenjskih prehodov je bil uporabljen psihološko fenomenološki pristop. V skladu s tem smo pridobili vpogled v doživljanje šestih udeleženk, hkrati pa vnaprej nismo predvidevali rezultatov ali postavljali hipotez. Cilj psihološko fenomenološke metode je bil oblikovati splošni opis bistvenih značilnosti doživljanja oziroma osnovne strukture, ki določa raziskovano doživljanje. Na podlagi intervjujev smo oblikovali splošno strukturo doživljanja življenjskih prehodov pri materah majhnih otrok. Ugotovili smo, da je za polovico udeleženk materinstvo najpomembnejši prehod v življenju, za ostale tri pa je na drugem mestu. Bistvene spremembe prehoda v materinstvo je mogoče razdeliti na dva dela: povzamejo občutenje, ki se dotika drugih in okolice ter občutenje, ki jih ima ženska do same sebe. Prav tako materinstvo pomembno zaznamuje doživljanje na področju telesnega, relacijskega, čustvenega in duhovnega blagostanja. Vpogled v doživljanje življenjskih prehodov pri materah majhnih otrok, ki ga daje ta raziskava, je lahko uporabna in v pomoč ljudem, ki profesionalno delujejo na področju psihologije, psihoterapije ali na katerem drugem profesionalnem področju, ki vključuje delo z ljudmi, še posebej z ženskami. Kot tako, bo lahko omogočilo pripravo strokovnih smernic programov za ženske, priprave na starševstvo ali podporne skupine za ženske. Verjamemo pa, da bo delo v pomoč tudi tistim, ki si želijo pridobiti vedenje in znanje o tej tematiki, saj lahko služi kot pomoč pri razumevanju doživljanja žensk, ko se te soočajo z življenjskimi prehodi, predvsem s prehodom v materinstvo.This Masters thesis researches how mothers with young children dealt with and experienced their life transition to the role of being a mother. The theoretical part of the thesis focuses on the literature review from the fields of welfare, life transitions and motherhood. A psychological-phenomenological approach has been used to research the life transitions. Based on this an insight into the transition experience of six women has been received, whereas there were no predictions on the outcome or setting hypothesis. The goal of the psychological-phenomenological method is to form a general description of key characteristics or the basic structure, which describe the researched transition. Based on performed interviews a general structure of experiencing the life transitions with mothers with young children has been made. The results show that for half of women experiencing motherhood is the most important transition in life, whereas the other three placed it to the second position in importance of life transitions. Key changes in the transition to the motherhood can be divided to feelings referring to the surrounding and others and secondly, feelings which a woman experiences with regard to herself. Motherhood also significantly affects woman’s relations to physical, relational, emotional and spiritual well-being. Insight to experiencing the life transitions with mothers with young children which this research offers, is useful and of help to anyone who is professionally involved in the fields of psychology, psychotherapy or any other related field which involves working with people, especially women. As such the thesis can enable preparation of professional guidelines and programs for women, parenthood preparations or support groups for women. We believe, that thesis will also assist to those, that would like to develop knowledge on this topic as it can serve as outreach at understanding of experiencing of women, when these are deal with different life transitions, particulary transition to the motherhood

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors

Class A G-protein-coupled receptors (GPCRs) constitute the largest family of transmembrane receptors in the human genome. Understanding the mechanisms which drove the evolution of such a large family would help understand the specificity of each GPCR sub-family with applications to drug design. To gain evolutionary information on class A GPCRs, we explored their sequence space by metric multidimensional scaling analysis (MDS). Three-dimensional mapping of human sequences shows a non-uniform distribution of GPCRs, organized in clusters that lay along four privileged directions. To interpret these directions, we projected supplementary sequences from different species onto the human space used as a reference. With this technique, we can easily monitor the evolutionary drift of several GPCR sub-families from cnidarians to humans. Results support a model of radiative evolution of class A GPCRs from a central node formed by peptide receptors. The privileged directions obtained from the MDS analysis are interpretable in terms of three main evolutionary pathways related to specific sequence determinants. The first pathway was initiated by a deletion in transmembrane helix 2 (TM2) and led to three sub-families by divergent evolution. The second pathway corresponds to the differentiation of the amine receptors. The third pathway corresponds to parallel evolution of several sub-families in relation with a covarion process involving proline residues in TM2 and TM5. As exemplified with GPCRs, the MDS projection technique is an important tool to compare orthologous sequence sets and to help decipher the mutational events that drove the evolution of protein families

The Modern City as an Oeuvre: Theory and Practice of The Production of Space in Henri Lefebvre’s “Intellectual Activism” and European Street Art

Throughout the second half of the twentieth century, capitalism – in particular its latest evolution, which the French theorist Henri Lefebvre calls “neocapitalism” – imposed its dominance over the space of modern cities (Production  8). This article aims to elucidate the way in which two modes of opposition to the neocapitalist domination of space, namely Western European street art and Henri Lefebvre’s theory, affect citizens’ experience of space. Throughout this article, it will become clear that Lefebvre and Western European street art share similar strategies of spatial resistance, based on the reconfiguration of what Lefebvre describes as the individual’s experience of the “perceived” and “conceived space” (38). However, what I call the paradox of visibility faced by these two figures of contestation casts doubt upon their ability to allow for a re-appropriation of the city space by its citizens. This will precipitate a questioning of their efficiency as strategies of spatial resistance

The Modern City as an Oeuvre: Theory and Practice of The Production of Space in Henri Lefebvre’s “Intellectual Activism” and European Street Art

Throughout the second half of the twentieth century, capitalism – in particular its latest evolution, which the French theorist Henri Lefebvre calls “neocapitalism” – imposed its dominance over the space of modern cities (Production  8). This article aims to elucidate the way in which two modes of opposition to the neocapitalist domination of space, namely Western European street art and Henri Lefebvre’s theory, affect citizens’ experience of space. Throughout this article, it will become clear that Lefebvre and Western European street art share similar strategies of spatial resistance, based on the reconfiguration of what Lefebvre describes as the individual’s experience of the “perceived” and “conceived space” (38). However, what I call the paradox of visibility faced by these two figures of contestation casts doubt upon their ability to allow for a re-appropriation of the city space by its citizens. This will precipitate a questioning of their efficiency as strategies of spatial resistance

Intérêt du scanner multicoupe dans le bilan des cardiopathies congénitales (étude rétrospective)

L'objectif de ce travail est d'évaluer l'intérêt du scanner multicoupe dans la prise en charge des cardiopathies congénitales. Cette étude rétrospective portant sur 170 cas a analysé l'indication et l'interprétation de chaque examen tomodensitométrique. Dans 90% des cas le scanner apportait une réponse aux interrogations des cliniciens. Il représente une avancée réelle dans l'étude morphologique tridimensionnelle des cardiopathies congénitales et peut se substituer à l'angiographie conventionnelle dans de nombreuses indications. Il permet d'orienter la prise en charge thérapeutique de cardiopathies complexes comme la tétralogie de Fallot et l'atrésie pulmonaire à septum ouvert et joue un rôle important dans la surveillance post opératoire de nombreuses malformations. Mais, ce n'est qu'au terme d'une analyse échographique que le scanner peut être justifié à titre complémentaire. Son indication doit être argumentée de questions précises afin d'adopter le protocole d'exploration approprié. La synchronisation cardiaque est préférable pour l'analyse des artères coronaires, y compris chez le nouveau né. La limitation de dose délivrée doit rester un objectif prioritaire, en particulier chez les enfants, plus radiosensibles.TOULOUSE3-BU Santé-Centrale (315552105) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

License GPL Repository CRAN

Description Bios2mds is primarily dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results

L'occitan à l'école. Éveil aux parlers régionaux

Fabre Sylvette, Chabbert Marie-Henriette, Gros Georges. L'occitan à l'école. Éveil aux parlers régionaux. In: Repères pour la rénovation de l'enseignement du français à l'école élémentaire, n°53, 1979. Pour une pédagogie de l'oral. Faire pratiquer et observer l'oral tel qu'il est. L'occitan à l'école. pp. 28-87

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

International audienceBACKGROUND: The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to protein families, MDS provides information complementary to the information derived from tree-based methods. Moreover, MDS gives a unique opportunity to compare orthologous sequence sets because it can add supplementary elements to a reference space. RESULTS: The R package bios2mds (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. Bios2mds starts with a sequence alignment, builds a matrix of distances between the aligned sequences, and represents this matrix by MDS to visualize a sequence space. This package also offers the possibility of performing K-means clustering in the MDS derived sequence space. Most importantly, bios2mds includes a function that projects supplementary elements (a.k.a. "out of sample" elements) onto the space defined by reference or "active" elements. Orthologous sequence sets can thus be compared in a straightforward way. The data analysis and visualization tools have been specifically designed for an easy monitoring of the evolutionary drift of protein sub-families. CONCLUSIONS: The bios2mds package provides the tools for a complete integrated pipeline aimed at the MDS analysis of multiple sets of orthologous sequences in the R statistical environment. In addition, as the analysis can be carried out from user provided matrices, the projection function can be widely used on any kind of data.</p

Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins

International audienceAbstract Summary Both dynamic correlations in protein sidechain motions during molecular dynamics (MD) simulations and evolutionary correlations in multiple sequence alignments (MSAs) of homologous proteins may reveal functionally important residues. We developed the R package Bios2cor that provides a unique framework to investigate and, possibly, integrate both analyses. Bios2cor starts with an MSA or an MD trajectory and computes correlation/covariation scores between positions in the MSA or between sidechain dihedral angles or rotamers in the MD trajectory. In addition, Bios2cor provides a variety of tools for the analysis, the visualization and the interpretation of the data. Availability and implementation The R package Bios2cor is available from the Comprehensive R Archive Network, at https://CRAN.R-project.org/package=Bios2cor