The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees.

Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential vaccine and drug target, and it has been shown to be a member of a large gene family. To clarify the relationships among the numerous P. falciparum SERAs and to identify orthologs to SERA5 and SERA6 in Plasmodium species affecting rodents, gene trees were inferred from nucleotide and amino acid sequence data for 33 putative SERA homologs in seven different species. (A distance method for nucleotide sequences that is specifically designed to accommodate differing GC content yielded results that were largely compatible with the amino acid tree. Standard-distance and maximum-likelihood methods for nucleotide sequences, on the other hand, yielded gene trees that differed in important respects.) To infer the pattern of duplication, speciation, and gene loss events in the SERA gene family history, the resulting gene trees were then "reconciled" with two competing Plasmodium species tree topologies that have been identified by previous phylogenetic studies. Parsimony of reconciliation was used as a criterion for selecting a gene tree/species tree pair and provided (1) support for one of the two species trees and for the core topology of the amino acid-derived gene tree, (2) a basis for critiquing fine detail in a poorly resolved region of the gene tree, (3) a set of predicted "missing genes" in some species, (4) clarification of the relationship among the P. falciparum SERA, and (5) some information about SERA5 and SERA6 orthologs in the rodent malaria parasites. Parsimony of reconciliation and a second criterion--implied mutational pattern at two key active sites in the SERA proteins-were also seen to be useful supplements to standard "bootstrap" analysis for inferred topologies.

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models.

MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments-namely MNXref-and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

Measurement of parent satisfaction in french-speaking PICUs: a need for translation and cultural adaptation of the empathic questionnaire

Background and aims: Family-centred care is an expected standard in PICU and parent reported outcomes are rarely measured. The Dutch validated EMPATHIC questionnaire provides accurate measures of parental perceptions of family-centred care in PICU. A French version would provide an important resource for quality control and benchmarking with other PICUs. The study aimed to translate and to assess the French cultural adaptation of the EMPATHIC questionnaire. Methods: In September 2012, following approval from the developer, translation and cultural adaptation were performed using a structured method (Wild et al. 2005). This included forward-backward translation and reconciliation by an official translator, harmonization assessed by the research team, and cognitive debriefing with the target users' population. In this last step, a convenience sample of parents with PICU experience assessed the comprehensibility and cultural relevance of the 65-item French EMPATHIC questionnaire. The PICUs in Lausanne, Switzerland and Lille, France participated. Results: Seventeen parents, including 13 French native and 4 French as second language speakers, tested the cognitive equivalence and cultural relevance of the French EMPATHIC questionnaire. The mean agreement for comprehensibility of all 65 items reached 90.2%. Three items fell below the cut-off 80% agreement and were revised for inclusion in the final French version. Conclusions: The translation and the cultural adaptation permitted to highlight a few cultural differences that did not interfere with the main construct of the EMPATHIC questionnaire. Reliability and validity testing with a new sample of parents is needed to strengthen the psychometric properties of the French EMPATHIC questionnaire.

Une européanisation des politiques de conciliation de la vie familiale et professionnelle? : les cas de l'Italie et de la France

Les différents pays membres de l'UE connaissent des politiques dites de « conciliation de la vie professionnelle et familiale » qui correspondent à un ensemble de dispositifs hétéroclites, plus ou moins complexes, mais rarement cohérents. Alliant des objectifs tels que la hausse de la natalité, la protection des mères et des enfants, l'égalité entre femmes et hommes, la lutte contre la pauvreté des enfants et des familles monoparentales et l'activation des femmes, ces politiques sont fortement ancrées dans des traditions nationales de politiques familiales, d'emploi et fiscales. Ces politiques portent en elles l'héritage et les tensions de l'histoire d'un pays. Au moment où un nouvel acteur international, l'Union européenne, intervient de manière de plus en plus explicite dans le débat et dans la définition de ces politiques, la présente étude tend à analyser l'influence exercées par les référentiels européens en matière de politiques de conciliation sur les discours et politiques nationales de l'Italie et de la France. A partir d'une analyse cognitive du processus d'européanisation, nous montrons que les référentiels développés au sein de l'UE, par leur caractère abstrait et flou, n'ont eu jusqu'ici qu'une faible influence sur les discours et politiques en Italie et en France. Croisant une perspective néo-institutionnaliste historique et discursive, notre recherche a été construite autour de deux axes de réflexion. Premièrement, il a été question d'analyser, d'une part, l'évolution du discours tenu par les différentes instances européennes (notamment de la Commission européenne, le Conseil européen et le Fonds Social européen) et, d'autre part, questionner comment un consensus a pu émerger entre des pays et des acteurs qui ont des traditions extrêmement différentes en matière de politique sociale, de politique familiale et de convention de genre. Deuxièmement, il a été question d'analyser si et comment un cadre de référence conçu au niveau communautaire a pu influencer les discours et politiques au niveau national. - The reconciliation of work and family life policies forms, in the EU's member States, a plurality of politics, more or less complex, but rarely coherent. Combining different objectives such as fertility increase, mothers and children protection, equality between men and women, fight against children and lone-parent families poverty and women activation, these policies are part of the national traditions of family, employment and tax policy and bear the heritage and the tensions of the country history. At a moment when a new global player, the European Union, interferes increasingly explicitly in the debate and the definition of reconciling work and family life policies, the question at the heart of this thesis was to define what kind of influence the référentiels of European discourses have on reconciliation policies since the late 1990s, in the Italian and French discourses and policies. Starting from a cognitive analysis of the Europeanization process, we show that the référentiels developed within the EU, by their abstract and vague nature, have had little influence in Italy and France. Crossing an historical and a discursive neo-institutionalist perspective, our research was based on two axes of reasoning. First, we have analysed, on the one hand, the evolution of various European institutions' discoursed (including the European Commission, the European Council and the European Social Fund) and, on the other hand, we have questioned how a consensus has emerged between countries and actors who have very different traditions in social policy, family policy and gender conventions. Secondly, we have observed if and how a framework developed at Community level, as a kind of ideal to strive for, has influenced discourses and policies at the national level.

Rhea-a manually curated resource of biochemical reactions.

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneously occurring reactions. Rhea reactions are described using chemical species from the Chemical Entities of Biological Interest ontology (ChEBI) and are stoichiometrically balanced for mass and charge. They are extensively manually curated with links to source literature and other public resources on metabolism including enzyme and pathway databases. This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models.