Short communication. SNP analyses of the 5HT1R and STAT genes in Pacific white shrimp, Litopenaeus vannamei

La industria de la producción de camarón es una de las industrias acuícolas que se encuentra en más crecimiento en la actualidad. Los estudios para encontrar marcadores genéticos son muy efectivos para la mejora de sus propiedades y de gran interés para los productores de camarón. En este trabajo se utilizaron seis individuos de una población de Litopenaeus vannamei, donde se encontraron cuatro polimorfismos de nucleótido único (SNPs) en el gen 5HT1R (5-hidroxitriptamina receptor1) y un SNP en el gen STAT (transductor de señal y activador de la transcripción). Sin embargo, el polimorfismo en el gen STAT resultó ser homocigoto en una población diferente utilizada para análisis de asociación. Los presentes análisis revelaron que el alelo C, en dos polimorfismos SNP (C109T y C395G) del gen 5HT1R, tiende a estar asociado con el aumento del peso corporal. Consideramos que hay necesidad de hacer nuevos estudios utilizando una muestra más amplia y diversa de la población en cuestión.

Administrations publiques et autorités cantonales : analyses sur la base des résultats de l'enquête BADAC sur les administrations cantonales 2004

Les administrations publiques et les autorités politiques sont méconnues sur le plan suisse, notamment au niveau cantonal. Les thèmes traités dans cette étude couvrent les structures administratives, le personnel de la fonction publique ainsi que les autorités politiques cantonales (gouvernements et parlements). L'étude dresse le portrait des acteurs du secteur public en tenant compte de l'âge, du sexe, de l'expérience et du statut d'emploi. Elle présente également la force des partis dans les parlements et les gouvernements sous forme de graphiques, de cartes et de tableaux. L'étude s'inscrit dans le cadre des travaux d'analyses de la BADAC (Base de données des cantons et des villes suisses). Elle présente les résultats de la dernière enquête sur les administrations cantonales (ESAC04), complétés par des données de l'Office fédéral de la statistique. Les résultats sont ventilés par canton mais aussi selon la langue majoritaire dans le canton. La plupart des données peuvent être téléchargées depuis le site de la BADAC (www.badac.ch ). Les indicateurs retenus possèdent des codes d'identification avec un système de renvoi aux sources et aux méthodes de calculs.

Identification and mutational analyses of phosphorylation sites of the calcineurin-binding protein CbpA and the identification of domains required for calcineurin binding in Aspergillus fumigatus.

Calcineurin is a key protein phosphatase required for hyphal growth and virulence in Aspergillus fumigatus, making it an attractive antifungal target. However, currently available calcineurin inhibitors, FK506 and cyclosporine A, are immunosuppressive, limiting usage in the treatment of patients with invasive aspergillosis. Therefore, the identification of endogenous inhibitors of calcineurin belonging to the calcipressin family is an important parallel strategy. We previously identified the gene cbpA as the A. fumigatus calcipressin member and showed its involvement in hyphal growth and calcium homeostasis. However, the mechanism of its activation/inhibition through phosphorylation and its interaction with calcineurin remains unknown. Here we show that A. fumigatus CbpA is phosphorylated at three distinct domains, including the conserved SP repeat motif (phosphorylated domain-I; PD-I), a filamentous fungal-specific domain (PD-II), and the C-terminal CIC motif (Calcipressin Inhibitor of Calcineurin; PD-III). While mutation of three phosphorylated residues (Ser208, Ser217, Ser223) in the PD-II did not affect CbpA function in vivo, mutation of the two phosphorylated serines (Ser156, Ser160) in the SP repeat motif caused reduced hyphal growth and sensitivity to oxidative stress. Mutational analysis in the key domains in calcineurin A (CnaA) and proteomic interaction studies confirmed the requirement of PxIxIT motif-binding residues (352-NIR-354) and the calcineurin B (CnaB)-binding helix residue (V371) for the binding of CbpA to CnaA. Additionally, while the calmodulin-binding residues (442-RVF-444) did not affect CbpA binding to CnaA, three mutations (T359P, H361L, and L365S) clustered between the CnaA catalytic and the CnaB-binding helix were also required for CbpA binding. This is the first study to analyze the phosphorylation status of calcipressin in filamentous fungi and identify the domains required for binding to calcineurin.

Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multiobjective global optimization and pareto filters

Optimization models in metabolic engineering and systems biology focus typically on optimizing a unique criterion, usually the synthesis rate of a metabolite of interest or the rate of growth. Connectivity and non-linear regulatory effects, however, make it necessary to consider multiple objectives in order to identify useful strategies that balance out different metabolic issues. This is a fundamental aspect, as optimization of maximum yield in a given condition may involve unrealistic values in other key processes. Due to the difficulties associated with detailed non-linear models, analysis using stoichiometric descriptions and linear optimization methods have become rather popular in systems biology. However, despite being useful, these approaches fail in capturing the intrinsic nonlinear nature of the underlying metabolic systems and the regulatory signals involved. Targeting more complex biological systems requires the application of global optimization methods to non-linear representations. In this work we address the multi-objective global optimization of metabolic networks that are described by a special class of models based on the power-law formalism: the generalized mass action (GMA) representation. Our goal is to develop global optimization methods capable of efficiently dealing with several biological criteria simultaneously. In order to overcome the numerical difficulties of dealing with multiple criteria in the optimization, we propose a heuristic approach based on the epsilon constraint method that reduces the computational burden of generating a set of Pareto optimal alternatives, each achieving a unique combination of objectives values. To facilitate the post-optimal analysis of these solutions and narrow down their number prior to being tested in the laboratory, we explore the use of Pareto filters that identify the preferred subset of enzymatic profiles. We demonstrate the usefulness of our approach by means of a case study that optimizes the ethanol production in the fermentation of Saccharomyces cerevisiae.

Data triangulation in the context of opioids monitoring via wastewater analyses.

BACKGROUND: The need to contextualise wastewater-based figures about illicit drug consumption by comparing them with other indicators has been stressed by numerous studies. The objective of the present study was to further investigate the possibility of combining wastewater data to conventional statistics to assess the reliability of the former method and obtain a more balanced picture of illicit drug consumption in the investigated area. METHODS: Wastewater samples were collected between October 2013 and July 2014 in the metropolitan area of Lausanne (226,000 inhabitants), Switzerland. Methadone, its metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP), the exclusive metabolite of heroin, 6-monoacetylmorphine (6-MAM), and morphine loads were used to estimate the amounts of methadone and heroin consumed. RESULTS: Methadone consumption estimated from EDDP was in agreement with the expectations. Heroin estimates based on 6-MAM loads were inconsistent. Estimates obtained from morphine loads, combined to prescription/sales data, were in agreement with figures derived from syringe distribution data and general population surveys. CONCLUSIONS: The results obtained for methadone allowed assessing the reliability of the selected sampling strategy, supporting its ability to capture the consumption of a small cohort (i.e., 743 patients). Using morphine as marker, in combination with prescription/sales data, estimates in accordance with other indicators about heroin use were obtained. Combining different sources of data allowed strengthening the results and suggested that the different indicators (i.e., administration route, average dosage and number of consumers) contribute to depict a realistic representation of the phenomenon in the investigated area. Heroin consumption was estimated to approximately 13gday(-1) (118gday(-1) at street level).

Lake-level and salinity reconstruction from diatom analyses in Quillagua Formation (Late Neogene, Central Andean Forearc, Northern Chile)

A sedimentary and micropaleontological study of the Quillagua Formation provides a detailed paleohydrological reconstruction of the lacustrine system which occupied the present-day hyperarid Quillagua-Llamara fore-arc Basin (Northern Chile) from lattermost Miocene to Early Pliocene times.

Méta-analyses d'essais randomisés sur données individuelles dans le traitement des cancers ORL non métastatiques : principes, résultats, perspectives [Individual patient data meta-analyses of randomized trials for the treatment of non-metastatic head and neck squamous cell carcinomas: Principles, results and perspectives].

Meta-analyses are considered as an important pillar of evidence-based medicine. The aim of this review is to describe the main principles of a meta-analysis and to use examples of head and neck oncology to demonstrate their clinical impact and methodological interest. The major role of individual patient data is outlined, as well as the superiority of individual patient data over meta-analyses based on published summary data. The major clinical breakthrough of head and neck meta-analyses are summarized, regarding concomitant chemotherapy, altered fractionated chemotherapy, new regimens of induction chemotherapy or the use of radioprotectants. Recent methodological developments are described, including network meta-analyses, the validation of surrogate markers. Lastly, the future of meta-analyses is discussed in the context of personalized medicine.

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses.

BACKGROUND: Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction factors, we performed genome-wide scans for human genes sharing molecular and evolutionary signatures of known restriction factors and tested the anti-HIV-1 activity of the most promising candidates. RESULTS: Our analyses identified 30 human genes that share characteristics of known restriction factors. Functional analyses of 27 of these candidates showed that over-expression of a strikingly high proportion of them significantly inhibited HIV-1 without causing cytotoxic effects. Five factors (APOL1, APOL6, CD164, TNFRSF10A, TNFRSF10D) suppressed infectious HIV-1 production in transfected 293T cells by >90% and six additional candidates (FCGR3A, CD3E, OAS1, GBP5, SPN, IFI16) achieved this when the virus was lacking intact accessory vpr, vpu and nef genes. Unexpectedly, over-expression of two factors (IL1A, SP110) significantly increased infectious HIV-1 production. Mechanistic studies suggest that the newly identified potential restriction factors act at different steps of the viral replication cycle, including proviral transcription and production of viral proteins. Finally, we confirmed that mRNA expression of most of these candidate restriction factors in primary CD4+ T cells is significantly increased by type I interferons. CONCLUSIONS: A limited number of human genes share multiple characteristics of genes encoding for known restriction factors. Most of them display anti-retroviral activity in transient transfection assays and are expressed in primary CD4+ T cells.

Les codes de l'obligations : méta-analyses pragmatologiques de l'application de méthodes en sciences sociales

Cette thèse rassemble une série de méta-analyses, c'est-à-dire d'analyses ayant pour objet des analyses produites par des sociologues (notamment celles résultant de l'application de méthodes de traitement des entretiens). Il s'agit d'une démarche réflexive visant les pratiques concrètes des sociologues. Celles-ci sont envisagées comme des activités gouvernées par des règles. Une part importante de cette thèse sera donc consacrée au développement d'un outil d'analyse « pragmatologique » (E. Durkheim), c'est-à-dire permettant l'étude des pratiques et des règles en rapport avec elles. Pour aborder les règles, la philosophie analytique d'inspiration wittgensteinienne apporte plusieurs propositions importantes. Les règles sont ainsi considérées comme des concepts d'air de famille : il n'y a pas de définitions communes recouvrant l'ensemble des règles. Pour étudier les règles, il convient alors de faire des distinctions à partir de leurs usages. Une de ces distinctions concerne la différence entre règles constitutives et règles régulatives : une règle constitutive crée une pratique (e.g. le mariage), alors qu'une règle régulative s'applique à des activités qui peuvent exister sans elle (e.g. les règles du savoir-vivre). L'activité méthodologique des sociologues repose et est contrainte par ces types de règles, qui sont pour l'essentiel implicites. Cette thèse vise donc à rendre compte, par la description et la codification des règles, du caractère normatif des méthodes dans les pratiques d'analyse de la sociologie. Elle insiste en particulier sur les limites logiques qu'instituent les règles constitutives, celles-ci rendant impossibles (et non pas interdites) certaines actions des sociologues. This thesis brings together a series of meta-analyzes, that is, analyzes that tackle analyzes produced by sociologists (notably those resulting from the application of methods in treating interviews). The approach is reflexive and aimed at the concrete practices of sociologists, considered as activities governed by rules. An important part of this thesis is therefore devoted to the development of a "pragmatological" analytical tool (Durkheim) to conduct a study of such practices and of the rules that govern them. To approach these rules, Wittgenstein-inspired analytic philosophy offers several important proposals. The rules are, at first, seen as concepts of family resemblance, assuming that there is no common definition accounting for all rules. In order to conduct the study of such rules, it is therefore necessary to discern how they are respectively used. One of these distinctions concerns the difference between constitutive rules and regulative rules: a constitutive rule creates a practice (for example marriage), while a regulative rule applies to activities that can exist outside of the rule (for example, the rules of etiquette). The methodological activity of sociologists relies on, and is constrained by these types of rules, which are essentially implicit. Through the description and codification of rules, this thesis aims to account for the normative character of methods governing analytical practices in sociology. Particular emphasis is on the logical limits established by constitutive rules, limits that render several of the sociologist's actions impossible (rather than forbidden).

Materiaalimallin määrityksestä kylmämuovattujen putkipalkkien K-liitosten FE-analyysissä

Työssä on tutkittu kylmämuovattujen nelikulmaisten putkipalkkien K-liitosten mallinnusta epälineaarisella elementtimenetelmällä. Työn tärkeimpänä tavoitteena on ollut kehittää putkipalkin osien materiaalimalleja siten, että liitosten kestävyyttä voidaan tutkia laboratoriokokeiden ohella luotettavasti myös elementtimenetelmällä. Toisena tavoitteena on ollut tutkia, voidaanko putkipalkkien liitosten mitoitusohjeita turvallisesti soveltaa kylmämuovatuille putkipalkeille, joissa valmistusprosessi aiheuttaa muutoksia materiaaliominaisuuksiin, erityisesti muodonmuutoskykyyn. Työssä tehtyjen laboratoriokokeiden ja elementtianalyysien perusteella elementti-menetelmä on käyttökelpoinen työkalu putkipalkkiliitosten staattista kestävyyttä määritettäessä, kun materiaalimallit on määritetty oikein. Erityisesti liitoksen käyttö-rajatilan mukaisen kestävyyden laskennassa elementtimenetelmällä saadaan hyvin laboratoriokokeita vastaavia tuloksia. Tehdyt laboratoriokokeet osoittavat myös, että Eurocode 3:n mukaisia putkipalkkien liitosten mitoitusohjeita voi turvallisesti käyttää kylmämuovatuille putkipalkeille.

Social trust : a public good?

Combining theories on social trust and social capital with sociopsychological approaches and applying contextual analyses to Swiss and European survey data, this thesis examines under what circumstances generalised trust, often understood as public good, may not benefit everyone, but instead amplify inequality. The empirical investigation focuses on the Swiss context, but considers different scales of analysis. Two broader questions are addressed. First, might generalised trust imply more or less narrow visions of community and solidarity in different contexts? Applying nonlinear principal component analysis to aggregate indicators, Study 1 explores inclusive and exclusive types of social capital in Europe, measured as regional configurations of generalised trust, civic participation and attitudes towards diversity. Study 2 employs multilevel models to examine how generalised trust, as an individual predisposition and an aggregate climate at the level of Swiss cantons, is linked to equality- directed collective action intention versus radical right support. Second, might high-trust climates impact negatively on disadvantaged members of society, precisely because they reflect a normative discourse of social harmony that impedes recognition of inequality? Study 3 compares how climates of generalised trust at the level of Swiss micro-regions and subjective perceptions of neighbourhood cohesion moderate the negative relationship between socio-economic disadvantage and mental health. Overall, demonstrating beneficial, as well as counterintuitive effects of social trust, this thesis proposes a critical and contextualised approach to the sources and dynamics of social cohesion in democratic societies. -- Cette thèse combine des théories sur le capital social et la confiance sociale avec des approches psychosociales et s'appuie sur des analyses contextuelles de données d'enquêtes suisses et européennes, afin d'étudier dans quelles circonstances la confiance généralisée, souvent présentée comme un bien public, pourrait ne pas bénéficier à tout le monde, mais amplifier les inégalités. Les études empiriques, centrées sur le contexte suisse, intègrent différentes échelles d'analyse et investiguent deux questions principales. Premièrement, la confiance généralisée implique-t-elle des visions plus ou moins restrictives de la communauté et de la solidarité selon le contexte? Dans l'étude 1, une analyse à composantes principales non-linéaire sur des indicateurs agrégés permet d'explorer des types de capital social inclusif et exclusif en Europe, mesurés par des configurations régionales de confiance généralisée, de participation civique, et d'attitudes envers la diversité. L'étude 2 utilise des modèles multiniveaux afin d'analyser comment la confiance généralisée, en tant que prédisposition individuelle et climat agrégé au niveau des cantons suisses, est associée à l'intention de participer à des actions collectives en faveur de l'égalité ou, au contraire, à l'intention de voter pour la droite radicale. Deuxièmement, des climats de haute confiance peuvent-ils avoir un impact négatif sur des membres désavantagés de la société, précisément parce qu'ils reflètent un discours normatif d'harmonie sociale qui empêche la reconnaissance des inégalités? L'étude 3 analyse comment des climats de confiance au niveau des micro-régions suisses et la perception subjective de faire partie d'un environnement cohésif modèrent la relation négative entre le désavantage socio-économique et la santé mentale. En démontrant des effets bénéfiques mais aussi contre-intuitifs de la confiance sociale, cette thèse propose une approche critique et contextualisée des sources et dynamiques de la cohésion sociale dans les sociétés démocratiques.

Nonlinear prediction based on score function

The linear prediction coding of speech is based in the assumption that the generation model is autoregresive. In this paper we propose a structure to cope with the nonlinear effects presents in the generation of the speech signal. This structure will consist of two stages, the first one will be a classical linear prediction filter, and the second one will model the residual signal by means of two nonlinearities between a linear filter. The coefficients of this filter are computed by means of a gradient search on the score function. This is done in order to deal with the fact that the probability distribution of the residual signal still is not gaussian. This fact is taken into account when the coefficients are computed by a ML estimate. The algorithm based on the minimization of a high-order statistics criterion, uses on-line estimation of the residue statistics and is based on blind deconvolution of Wiener systems [1]. Improvements in the experimental results with speech signals emphasize on the interest of this approach.