Breast cancer and quality of life: medical information extraction from health forums

International audienceInternet health forums are a rich textual resource with content generated through free exchanges among patients and, in certain cases, health professionals. We tackle the problem of retrieving clinically relevant information from such forums, with relevant topics being defined from clinical auto-questionnaires. Texts in forums are largely unstructured and noisy, calling for adapted preprocessing and query methods. We minimize the number of false negatives in queries by using a synonym tool to achieve query expansion of initial topic keywords. To avoid false positives, we propose a new measure based on a statistical comparison of frequent co-occurrences in a large reference corpus (Web) to keep only relevant expansions. Our work is motivated by a study of breast cancer patients' health-related quality of life (QoL). We consider topics defined from a breast-cancer specific QoL-questionnaire. We quantify and structure occurrences in posts of a specialized French forum and outline important future developments

Les sites web de journalisme dit participatif en quête de normes identitaires communes ?

International audienceAre journalistic websites called participative in search of common identical standards ? Since the apparition of the social web, collaborative and participative dimensions have become constituent of news on line. Today, a journalistic website has neither credit nor influence of any sort without a space proper to readers. The expansion of recent news websites qualified as " pure players " such as Agoravox, Rue 89, Mediapart, Owni, Slate or LePost whose editorial lines are quite justly based on this participative aspect brings along the rupture of the journalists' monopole over the production of the media news. These medias are characterized by a similar presentation as a traditional written media on line, whereas they are different as to their functioning and positioning. They are based on news jointly held by passionate net sulfurs, common witnesses of events, experts but equally professional journalists. Moreover, they want themselves to be independent medias, free and transparent and claim therefore to mark themselves out of traditional medias. The on-line papers have recently appeared and seem heading toward the construction of an identity summoning common standards around the participative information. A certain convergence is to be noted about all the journalistic websites called participative, equally in their visuality, their layout, their architecture or their use of social network. The web users seem to share this homogenized feeling. Some users, interviewed concerning a doctoral research, consider themselves unable to make the definition of a journalistic website called participative but know how to recognize them surfing on the web. Let's not forget that these medias have all a national french version, accompanied, in most cases, by a declination of foreign versions (Quebec for Rue 89, Italian and English for Agoravox), local news (Marseillais for Agoravox) or thematic (Eco 89, NatureVox or CareVox). The national version type is rethought for each declination and there are no differences underlined, from one version to the other, as to the layout, suggested activities or the organization of the pages. We therefore suggest in the context of this communication to study standards and values of these socio-technical arrangements. We'll analyze stipulated uses by these journalistic websites called participative : Agoravox, Rue 89 and Mediapart. It is assumed that some actions by these websites are made compulsory, some others impossible or require to be done in a special way. The structure of these websites involves a certain number of constraints guiding users' activities. We aim to analyze the practices stated by these websites following from different operational propositions, their importance and their recurrence. In other words, we're trying to bring to light the affordances of the meanings (Gibson, 1977) of these socio-technical devices we're centering around, on the one hand "€the virtuality of the user€" (Bardini, 1966), which means representations made by the designer in the way of device affordances, on the other hand, "€the virtuality of the designer " (ibid), which means the barriers the user encounters on his way precisely traced out by these affordances, let's say limits and possibilities of the manipulation perceived through the technical object design. We're trying to make the implicit dialogue clear between designers and users detailing this coordination, this adjustment among the virtual members. Besides, we're suggesting to analyze stipulated uses explicitly showed by journalistic websites called participative (stay informed on this site, for example) for instance like those implicitly induced by the website through their operational propositions. The explicit forms of stated uses are clearly apparent ; they can be found in the notice or in the charter published directly on the websites. Nevertheless, how is it possible to collect the stipulated uses taking an implicit form ? We wondered on the proper methods to analyze the data improper to use for a member but to the device. We suggest a quantitative method inspired by the situational semiotic method developed by Alex Mucchielli (2005). This qualitative method allows us to formalize practices stated by these websites still keeping the complexity of the studied phenomena (Morin, 1990) and thus not to lessen the meaning to reductive explanations. In order to limit our interpretations of involved researchers, we're taking support on a grid allowing catching the different meanings arising to the member in situation, dividing the observations on different situational levels at the same time. We're putting forward the analysis of Rue 89, Mediapart and Agoravox to bring to light the standards and values shared by the three newspapers on line making sure to bring out their differences at the same time. We're showing for instance that Agoravox incites the reader among other things, to communicate about the website community whereas Rue 89 suggests its contributors to favor the visibility of sharing paying activities. This communication aims eventually to enlighten the reader about the normative processes engaged in the construction of a mutual culture and identity among all the journalistic webs called participative.Depuis l'émergence du web social, les dimensions collaboratives et participatives sont devenues constitutives de l'actualité en ligne. À l'heure actuelle, un site web de journalisme ne semble plus pouvoir être crédible ni influent sans l'ouverture d'un espace réservé aux lecteurs. Cette rupture du monopole des journalistes sur la production de l'information médiatique s'accompagne de l'essor de nouveaux sites web d'informations qualifiés de " pure players ", tels qu'Agoravox, Rue89, Mediapart, Owni ou encore Slate ou LePost qui fondent justement leur ligne éditoriale sur cet aspect participatif. Ces médias se caractérisent par une présentation similaire à celle d'un journal de presse écrite traditionnelle en ligne, mais sont finalement différents par leur fonctionnement et leur positionnement. Ils reposent sur la co-production d'informations entre des internautes passionnés d'actualité, des citoyens témoins d'évènements, des experts mais aussi des journalistes professionnels. Par ailleurs, ils se définissent comme des médias indépendants, libres et transparents et prétendent ainsi se distinguer des médias traditionnels. L'apparition de ces journaux en ligne est récente et ces derniers semblent en phase de construction d'une identité en convoquant des normes communes autour de la culture de l'information participative. Nous notons d'ailleurs une certaine convergence entre tous les sites web de journalisme dit participatif tout autant dans leur visuel, leur mise en page, leur architecture ou encore leur utilisation des réseaux sociaux. Ce sentiment d'homogénéité semble partagé par les internautes. Certains usagers, interviewés dans le cadre d'une recherche doctorale, affirment être incapables de définir les caractéristiques d'un site web de journalisme dit participatif mais savent par contre les reconnaitre au détour de leur navigation sur le web. Notons également que ces journaux disposent tous d'une version nationale française, accompagnée pour une grande partie par une déclinaison de versions étrangères (québécoise pour Rue89, italienne et anglaise pour Agoravox), locales (marseillaise pour Agoravox) ou encore thématiques (Eco89, NaturaVox ou CareVox). Le modèle de la version nationale est reproduit pour chaque déclinaison et nous constatons que la mise en page, les activités proposées ou encore l'organisation des pages ne différent pas d'une version à l'autre. La standardisation visuelle, organisationnelle et communicationnelle de ces sites web semble s'accompagner d'une harmonisation culturelle. Nous proposons donc dans le cadre de cette communication d'étudier les normes et valeurs de ces dispositifs socio-techniques. Nous analyserons les usages prescrits par trois sites web de journalisme dit participatif : Agoravox, Rue89 et Mediapart. Nous partons du principe que ces sites web rendent certaines actions obligatoires, d'autres impossibles ou imposent de les faire d'une certaine manière. La structure de ces sites web incorpore un certain nombre de contraintes qui guident les activités des usagers. L'objectif est d'analyser les pratiques prescrites par ces sites web qui découlent des différentes propositions d'actions, leur importance et leur récurrence. En d'autres termes, nous cherchons à mettre en évidence les affordances de sens (Gibson, 1977) de ces dispositifs sociotechniques. Nous articulons, d'un côté, la " virtualité de l'usager " (Bardini, 1996), c'est à dire les représentations que le concepteur se fait de l'usager potentiel et qu'il traduit en affordances dans le dispositif et de l'autre côté " la virtualité du concepteur " (ibid), c'est à dire les frontières que l'usager rencontre dans son usage et qui sont tracées précisément par ces affordances, soit les limites et possibilités de maniement perçues à travers le design de l'objet technique. Nous cherchons à comprendre ce dialogue implicite entre concepteurs et usagers en détaillant cette coordination, cet ajustement entre les acteurs virtuels. Par ailleurs, nous proposons d'analyser les usages prescrits affichés explicitement par les sites web de journalisme dit participatif (" ce site vous permet de vous informer " par exemple) comme ceux qui sont induits implicitement par le site web au travers de ses propositions d'action. Les formes explicites d'usages prescrits sont nettement apparentes ; elles figurent dans le mode d'emploi ou dans les chartes publiées directement sur les sites web. Cependant, comment recueillir les usages prescrits qui prennent une forme implicite ? Nous nous sommes alors interrogées sur les méthodes adéquates pour analyser des données qui ne sont pas propres à l'usage d'un acteur mais qui sont propres au dispositif. Nous proposons une méthode qualitative inspirée de la méthode sémiotique situationnelle développée par Alex Mucchielli (2005). Cette méthode qualitative nous permet de formaliser les pratiques prescrites par les trois sites web tout en conservant la complexité des phénomènes étudiés (Morin, 1990) et ainsi de ne pas réduire le sens à des explications trop réductrices. Pour limiter les interprétations liées à notre statut de chercheures impliquées, nous prenons appui sur une grille permettant de saisir les différentes significations qui surgissent pour l'acteur en situation, tout en découpant l'observation sur différents niveaux situationnels. Nous présenterons les analyses de Rue89, Mediapart et Agoravox pour enfin mettre en évidence les normes et valeurs partagées par les trois journaux en ligne, en veillant également à identifier leurs différences. Nous montrerons par exemple qu'Agoravox incite entre autre le lecteur à communiquer sur la communauté du site web, alors que Rue89 propose à ses contributeurs de disposer de visibilité en participant à certaines activités payantes. Cette communication vise finalement à éclairer le lecteur sur les processus normatifs engagés dans la construction d'une culture et d'une identité communes à tous les sites web de journalisme dit participatif

Analysis of hepatitis C virus RNA dimerization and core–RNA interactions

The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3′-untranslated region (3′-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3′-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus

De quoi parlent les patients dans les forums de santé : classification non-supervisée par LDA

National audienceNowadays, social media is increasingly used by patients and health professionals. This is a rich text resource, generated by many exchanges between patients and in some cases health professionals. In this paper, we use unsupervised learning model known as LDA (Latent Dirichlet Allocation) to detect the different topics on health forums and social networks discussed by patients. Our main objective is to detect the different themes by patients during their accounts in social media and compare them with predefined themes existing in the questionnaires used in clinical trials. We also show pretreatments to be performed on these data for such tasks.De nos jours, les médias sociaux sont de plus en plus utilisés par les patients et les professionnels de santé. Il s'agit d'une ressource textuelle riche, générée par les très nombreux échanges entre patients et, dans certains cas, professionnels de santé. Dans cet article, nous utilisons le modèle d'apprentissage non supervisé connu sous le nom de LDA (Allocation de Dirichlet Latente) afin de détecter les différents thèmes abordés sur les forums de santé et les réseaux sociaux par les patients. Notre objectif est de repérer les nouveaux thèmes directement issus des préoccupations des patientes atteintes de cancer du sein et de les comparer aux thèmes existant dans les auto-questionnaires proposés dans les essais cliniques en oncologie. Mots

Molecular analysis of two local falciparum malaria outbreaks on the French Guiana coast confirms the msp1 B-K1/varD genotype association with severe malaria

BACKGROUND: Plasmodium falciparum outbreaks can occur in the coastal area of French Guiana, where the population is essentially non-immune. Two sporadic outbreaks were observed, including one with severe malaria cases. To characterize these outbreaks and verify previous observations of specific genotype characteristics in severe malaria in this area, all cases from each outbreak were studied. METHODS: P. falciparum genotypes for six genetic loci were determined by PCR amplification from peripheral blood parasites. The msp1/block2 and msp2 genotypes were determined by DNA sequencing. Microsatellite and varD genotyping was based on size polymorphism and locus-specific amplification. RESULTS: The outbreak including severe malaria cases was associated with a single genotype. The other mild malaria outbreak was due to at least five distinct genotypes. CONCLUSION: Two distinct types of outbreak occured despite systematic and sustained deployement of malaria control measures, indicating a need for reinforced vigilance. The varD/B-K1 msp1 linkage and its association with severe malaria in this area was confirmed

Negative cell cycle regulation by Calcineurin is necessary for proper beta cell regeneration in zebrafish

peer reviewedStimulation of pancreatic beta cell regeneration could be a therapeutic lead to treat diabetes. Unlike humans, the zebrafish can efficiently regenerate beta cells, notably from ductal pancreatic progenitors. To gain insight into the molecular pathways involved in this process, we established the transcriptomic profile of the ductal cells after beta cell ablation in the adult zebrafish. These data highlighted the protein phosphatase calcineurin as a new potential modulator of beta cell regeneration. We showed that calcineurin overexpression abolished the regenerative response, leading to glycemia dysregulation. On the opposite, calcineurin inhibition increased ductal cell proliferation and subsequent beta cell regeneration. Interestingly, the enhanced proliferation of the progenitors was paradoxically coupled with their exhaustion. This suggests that the proliferating progenitors are next entering in differentiation. Calcineurin appears as a guardian which prevents an excessive progenitor proliferation to preserve the pool of progenitors. Altogether, our findings reveal calcineurin as a key player in the balance between proliferation and differentiation to enable a proper beta cell regeneration

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning—possibly mediated by intrinsically disordered protein segments—is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication

Bioavailability of Macro and Micronutrients Across Global Topsoils: Main Drivers and Global Change Impacts

Understanding the chemical composition of our planet\u27s crust was one of the biggest questions of the 20th century. More than 100 years later, we are still far from understanding the global patterns in the bioavailability and spatial coupling of elements in topsoils worldwide, despite their importance for the productivity and functioning of terrestrial ecosystems. Here, we measured the bioavailability and coupling of thirteen macro- and micronutrients and phytotoxic elements in topsoils (3–8 cm) from a range of terrestrial ecosystems across all continents (∼10,000 observations) and in response to global change manipulations (∼5,000 observations). For this, we incubated between 1 and 4 pairs of anionic and cationic exchange membranes per site for a mean period of 53 days. The most bioavailable elements (Ca, Mg, and K) were also amongst the most abundant in the crust. Patterns of bioavailability were biome-dependent and controlled by soil properties such as pH, organic matter content and texture, plant cover, and climate. However, global change simulations resulted in important alterations in the bioavailability of elements. Elements were highly coupled, and coupling was predictable by the atomic properties of elements, particularly mass, mass to charge ratio, and second ionization energy. Deviations from the predictable coupling-atomic mass relationship were attributed to global change and agriculture. Our work illustrates the tight links between the bioavailability and coupling of topsoil elements and environmental context, human activities, and atomic properties of elements, thus deeply enhancing our integrated understanding of the biogeochemical connections that underlie the productivity and functioning of terrestrial ecosystems in a changing world

Figeac et sa région (Lot). Prospection pédestre

Dans le cadre d’une maîtrise d’archéologie médiévale sur le thème de l’extraction du grès aux époques médiévale et moderne dans la région de Figeac (Lot), le territoire de quinze communes a été prospecté afin de repérer des vestiges de carrières de pierre de taille. Les sites mis au jour sont essentiellement des fronts de taille de faible étendue, ne dépassant guère 0,50 m de hauteur. Hormis la grande carrière de Lagrave (commune de Faycelles) qui fait l’objet d’une étude depuis 1999, plusieu..

Utilisation des MOFs (metal organic frameworks) comme nouveaux précurseurs pour les matériaux de batterie Li-ion

The experimental works and modelling DFT approaches conducted in this thesis aim at understanding the selectivity mechanism toward cobalt of a ligand from the imidazole family from a multi metallic nickel, manganese and cobalt (Ni2+, Mn2+, Co2+) solution, mimicking a leached battery solution. The as synthetized ZIF material (Zeolitic-Imidazolate Framework) can then be used in a closed loop process as precursor for cathode components. Experimental work using 2-methylimidazole (2-MeIm) ligand has been led, to study the Co2+ selectivity through ZIF-67 synthesis from Ni2+, Mn2+,Co2+ solution. This work has then been extended to other ligands from the same family (imidazole, 4-methylimidazole, benzimidazole), in order to use this concept for the synthesis of other ZIFs.Nickel-based co-products can crystallized when reacting with 2-MeIm, leading to Nix2-MeImy(MeOH)z complexes of unresolved stoichiometry. Those complexes are soluble in the solvent used for the synthesis, and can be washed away. Those complexes are not soluble when the synthesis temperature is superior to 70°C. Nickel can also react with the ligand by precipitating as an amorphous component, of which the kinetic of precipitation are lower than the one of the ZIF-67. DFT modelling has elucidated the coordination of the Ni centers as square planar, which is most likely found in this amorphous component. In a multi-metallic media of Ni2+ and Co2+, 2-MeIm ligands coordinates preferentially with Co2+, inhibiting the precipitation of Nix2-MeImy(MeOH)z in the favor of ZIF-67 synthesis. Manganese does not react with Imi ligands, but its oxidation followed by its precipitation as oxides is triggered by high-pKa ligands. Ligand modelling helped to calculate their pKa and their values follows this trend pKa2-MeIm>pKaImi>pKa4-MeIm>pKaBzIm. 2-MeIm ligand appears to be enhancing Mn2+ oxidation, when BzIm is the ligand achieving the best selectivity (inhibiting Mn2+ oxidation). This approach is to be used to evaluate the best ligand to be used to enhance the selectivity of the process, which is in part determined by its ability to not trigger Mn2+ oxydation. For now, the yield of the selectivity process with BzIm is of 70 %mol.Les travaux expérimentaux et de modélisation par DFT menés dans le cadre de cette thèse ont pour objectif l’élucidation des mécanismes de sélectivité envers le cobalt d’un ligand de la famille des imidazoles au sein d’une solution multi métallique de nickel, manganèse et cobalt (Ni2+, Mn2+, Co2+) simulant une solution de batteries dissoutes. Le matériau ZIF (Zeolitic Imidazolate Framework) ainsi synthétisé peut être utilisé en boucle fermée en tant que précurseur de matériaux de cathode. Les études expérimentales ont été menées en utilisant le ligand 2 methylimidazole (2-MeIm) pour étudier sa sélectivité lors de la synthèse du ZIF-67 à partir d’une solution de Ni2+, Mn2+ et Co2+. Par la suite, ces études ont été étendues à d’autres ligands de la même famille (imidazole (Im), 4 méthylimidazole (4 MeIm) et benzimidazole (BzIm)), pour valider l’application de ce concept à la synthèse de plusieurs ZIFs.Les co-produits à base de nickel issus de la cristallisation des complexes de stoechiométrie inconnue de type Nix2-MeImy(MeOH)z sont solubles dans le medium de synthèse et peuvent donc être lavés. Ces complexes sont insolubles quand la température de synthèse est supérieure à 70°C. Le nickel réagit également avec les ligands en formant un matériau amorphe dont la cinétique de précipitation est inférieure à celle des ZIFs. L’approche par modélisation a mis en avant la coordination préférentielle en plan-carré des complexes de Ni2+, certainement adoptée au sein de ce matériau amorphe. Dans un milieu composé de nickel et de cobalt, les ligands 2-MeIm se lient préférentiellement au Co2+, inhibant la précipitation des complexes Nix2-MeImy(MeOH)z et favorisant la synthèse du ZIF-67. Le manganèse ne réagit pas avec les ligands de la solution, mais son oxydation suivie de sa précipitation sous forme d’oxyde sont favorisées par les ligands de haut pKa. La modélisation des ligands a permis de calculer leur pKa. La tendance de ces valeurs calculées est pKa2-MeIm>pKaImi>pKa4-MeIm>pKaBzIm. L’utilisation du ligand 2-MeIm favorise la précipitation de l’oxyde de Mn, quand le BzIm est le ligand ne favorisant pas la précipitation de Mn. Cette approche qui permet d’anticiper la tendance à l’oxydation de Mn2+ est à utiliser choisir le ligand selon contraintes de pureté du produit. Actuellement, le rendement de ce procédé de précipitation sélective du cobalt en utilisant le BzIm est de l’ordre de 70 %mol