Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori.

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes.

La chute comme événement du parcours de vie : signification, conséquences, adaptation et prévention

La chute chez les personnes âgées est considérée comme un problème de santé publique en raison de sa fréquence, de ses conséquences ainsi que de l'efficacité de certain programmes de prévention. La chute est pourtant très souvent non signalée par les personnes ou par les professionnels. Je postule que la chute est un événement traumatisant ; j'examine d'une part son impact sur les trajectoires de personnes à partir de 50 ans et d'autre part l'adaptation à cet événement. Mobilisant différents types de données existantes, ce travail met en évidence les nombreux impacts de la chute au-delà de la santé, et notamment sur les dimensions sociales et sur la qualité de vie ; en comparaison à d'autres événements de santé, la chute présente un effet sur plusieurs indicateurs qui s'exprime tant à court qu'à long terme. J'identifie des facteurs de vulnérabilité à la chute : le moment de survenue de l'événement est un critère déterminant, l'adaptation étant plus difficile quand la chute survient chez des moins de 65 ans ; la gravité de l'événement entrave également la probabilité de s'y adapter. Par contre, les ressources institutionnelles sont sous-utilisées par les personnes concernées et les effets d'un programme généraliste de prévention des chutes fondé sur de l'activité physique et de l'éducation pour la santé sont modestes et ne se maintiennent pas au-delà de l'intervention. Au final, cette thèse apporte une contribution originale à l'étude psychosociale de la chute envisagée au moyen du modèle de la vulnérabilité : ses conclusions permettent d'ajuster des interventions qui devraient prioritairement viser à renforcer les ressources et stratégies individuelles et ensuite à gérer les conséquences identitaires et émotionnelles liées à la chute.

On the Adoption of Partial Least Squares in Psychological Research: Caveat Emptor

The partial least squares technique (PLS) has been touted as a viable alternative to latent variable structural equation modeling (SEM) for evaluating theoretical models in the differential psychology domain. We bring some balance to the discussion by reviewing the broader methodological literature to highlight: (1) the misleading characterization of PLS as an SEM method; (2) limitations of PLS for global model testing; (3) problems in testing the significance of path coefficients; (4) extremely high false positive rates when using empirical confidence intervals in conjunction with a new "sign change correction" for path coefficients; (5) misconceptions surrounding the supposedly superior ability of PLS to handle small sample sizes and non-normality; and (6) conceptual and statistical problems with formative measurement and the application of PLS to such models. Additionally, we also reanalyze the dataset provided by Willaby et al. (2015; doi:10.1016/j.paid.2014.09.008) to highlight the limitations of PLS. Our broader review and analysis of the available evidence makes it clear that PLS is not useful for statistical estimation and testing.

Associations between fruit and vegetable consumption and psychological distress: results from a population-based study.

BACKGROUND: Several studies observed associations of various aspects of diet with mental health, but little is known about the relationship between following the 5-a-day recommendation for fruit and vegetables consumption and mental health. Thus, we examined the associations of the Swiss daily recommended fruit and vegetable intake with psychological distress. METHODS: Data from 20,220 individuals aged 15+ years from the 2012 Swiss Health Survey were analyzed. The recommended portions of fruit and vegetables per day were defined as 5-a-day (at least 2 portions of fruit and 3 of vegetables). The outcome was perceived psychological distress over the previous 4 weeks (measured by the 5-item mental health index [MHI-5]). High distress (MHI-5 score ≤ 52), moderate distress (MHI-5 > 52 and ≤ 72) and low distress (MHI-5 > 72 and ≤ 100) were differentiated and multinomial logistic regression analyses adjusted for known confounding factors were performed. RESULTS: The 5-a-day recommendation was met by 11.6 % of the participants with low distress, 9.3 % of those with moderate distress, and 6.2 % of those with high distress. Consumers fulfilling the 5-a-day recommendation had lower odds of being highly or moderately distressed than individuals consuming less fruit and vegetables (moderate vs. low distress: OR = 0.82, 95 % confidence interval [CI] 0.69-0.97; high vs. low distress: OR = 0.55, 95 % CI 0.41-0.75). CONCLUSIONS: Daily intake of 5 servings of fruit and vegetable was associated with lower psychological distress. Longitudinal studies are needed to further determine the causal nature of this relationship.

Gut physiology mediates a trade-off between adaptation to malnutrition and susceptibility to food-borne pathogens.

The animal gut plays a central role in tackling two common ecological challenges, nutrient shortage and food-borne parasites, the former by efficient digestion and nutrient absorption, the latter by acting as an immune organ and a barrier. It remains unknown whether these functions can be independently optimised by evolution, or whether they interfere with each other. We report that Drosophila melanogaster populations adapted during 160 generations of experimental evolution to chronic larval malnutrition became more susceptible to intestinal infection with the opportunistic bacterial pathogen Pseudomonas entomophila. However, they do not show suppressed immune response or higher bacterial loads. Rather, their increased susceptibility to P. entomophila is largely mediated by an elevated predisposition to loss of intestinal barrier integrity upon infection. These results may reflect a trade-off between the efficiency of nutrient extraction from poor food and the protective function of the gut, in particular its tolerance to pathogen-induced damage.

Measuring individuals' response quality in self-administered psychological tests : an introduction to Gendre's functional method

The functional method is a new test theory using a new scoring method that assumes complexity in test structure, and thus takes into account every correlation between factors and items. The main specificity of the functional method is to model test scores by multiple regression instead of estimating them by using simplistic sums of points. In order to proceed, the functional method requires the creation of hyperspherical measurement space, in which item responses are expressed by their correlation with orthogonal factors. This method has three main qualities. First, measures are expressed in the absolute metric of correlations; therefore, items, scales and persons are expressed in the same measurement space using the same single metric. Second, factors are systematically orthogonal and without errors, which is optimal in order to predict other outcomes. Such predictions can be performed to estimate how one would answer to other tests, or even to model one's response strategy if it was perfectly coherent. Third, the functional method provides measures of individuals' response validity (i.e., control indices). Herein, we propose a standard procedure in order to identify whether test results are interpretable and to exclude invalid results caused by various response biases based on control indices.

Testing Local Adaptation in a Natural Great Tit-Malaria System: An Experimental Approach.

Finding out whether Plasmodium spp. are coevolving with their vertebrate hosts is of both theoretical and applied interest and can influence our understanding of the effects and dynamics of malaria infection. In this study, we tested for local adaptation as a signature of coevolution between malaria blood parasites, Plasmodium spp. and its host, the great tit, Parus major. We conducted a reciprocal transplant experiment of birds in the field, where we exposed birds from two populations to Plasmodium parasites. This experimental set-up also provided a unique opportunity to study the natural history of malaria infection in the wild and to assess the effects of primary malaria infection on juvenile birds. We present three main findings: i) there was no support for local adaptation; ii) there was a male-biased infection rate; iii) infection occurred towards the end of the summer and differed between sites. There were also site-specific effects of malaria infection on the hosts. Taken together, we present one of the few experimental studies of parasite-host local adaptation in a natural malaria system, and our results shed light on the effects of avian malaria infection in the wild.

Guideline adaptation: a methodology to enhance efficiency in guideline development and improve utilization.

BACKGROUND: Developing and updating high-quality guidelines requires substantial time and resources. To reduce duplication of effort and enhance efficiency, we developed a process for guideline adaptation and assessed initial perceptions of its feasibility and usefulness. METHODS: Based on preliminary developments and empirical studies, a series of meetings with guideline experts were organised to define a process for guideline adaptation (ADAPTE) and to develop a manual and a toolkit made available on a website (http://www.adapte.org). Potential users, guideline developers and implementers, were invited to register and to complete a questionnaire evaluating their perception about the proposed process.

Combining niche modelling and landscape genetics to study local adaptation: A novel approach illustrated using alpine plants

Understanding the factors that shape adaptive genetic variation across species niches has become of paramount importance in evolutionary ecology, especially to understand how adaptation to changing climate affects the geographic range of species. The distribution of adaptive alleles in the ecological niche is determined by the emergence of novel mutations, their fitness consequences and gene flow that connects populations across species niches. Striking demographical differences and source sink dynamics of populations between the centre and the margin of the niche can play a major role in the emergence and spread of adaptive alleles. Although some theoretical predictions have long been proposed, the origin and distribution of adaptive alleles within species niches remain untested. In this paper, we propose and discuss a novel empirical approach that combines landscape genetics with species niche modelling, to test whether alleles that confer local adaptation are more likely to occur in either marginal or central populations of species niches. We illustrate this new approach by using a published data set of 21 alpine plant species genotyped with a total of 2483 amplified fragment length polymorphisms (AFLP), distributed over more than 1733 sampling sites across the Alps. Based on the assumption that alleles that were statistically associated with environmental variables were adaptive, we found that adaptive alleles in the margin of a species niche were also present in the niche centre, which suggests that adaptation originates in the niche centre. These findings corroborate models of species range evolution, in which the centre of the niche contributes to the emergence of novel adaptive alleles, which diffuse towards niche margins and facilitate niche and range expansion through subsequent local adaptation. Although these results need to be confirmed via fitness measurements in natural populations and functionally characterised genetic sequences, this study provides a first step towards understanding how adaptive genetic variation emerges and shapes species niches and geographic ranges along environmental gradients.

Les critères STOPP/START.v2 : adaptation en langue française. [STOPP/START.v2 criteria: Adaptation into French language]

Objectif STOPP/START est un outil de détection de la prescription médicamenteuse potentiellement inappropriée chez la personne de 65 ans ou plus. La version initiale de 2008 vient d'être mise à jour et améliorée par ses auteurs. Nous en présentons l'adaptation et la validation en langue française. Méthodes L'adaptation en français de l'outil STOPP/START.v2 a été réalisée par deux experts, confirmée par la méthode de traduction-inverse, et finalisée d'après les commentaires de neufs évaluateurs francophones, gériatres, pharmaciens cliniciens, et médecin généraliste de quatre pays (France, Belgique, Suisse, Canada). La validation a été complétée par une analyse de concordance inter-juge (CCI) des critères STOPP/START.v2 appliqués à dix vignettes cliniques standardisées. Résultats Les 115 critères de STOPP/START.v2 en français sont, par rapport à la version originale anglaise, identiques par leur classification mais adaptés en termes de présentation (critères START.v2 commençant par la condition clinique, et accompagnés par une justification du caractère inapproprié de l'omission) voire de formulation de certains critères. Cette adaptation en français est validée par (i) la traduction-inverse montrant le respect du sens clinique de la version originale, (ii) l'identification semblable des critères lorsque appliqués à dix vignettes cliniques par les neuf évaluateurs, et (iii) le haut niveau de concordance de ces neuf évaluations tant pour STOPP.v2 (CCI 0,849) que pour START.v2 (CCI 0,921). Conclusion L'adaptation en langue française des critères STOPP/START.v2 fournit aux cliniciens un outil de détection de la prescription médicamenteuse potentiellement inappropriée chez les personnes de 65 ans et plus qui est logique, fiable et facile à utiliser. Objective STOPP/START is a screening tool to detect potentially inappropriate prescribing in persons aged 65 or older. Its Irish authors recently updated and improved the initially published version of 2008. We present the adaptation and validation into French language of this updated tool. Methods STOPP/START.v2 was adapted into French by two experts, then confirmed by a translation-back translation method and finalised according to the comments of nine French-speaking assessors - geriatricians, pharmacologists and a general physician - from four countries (France, Belgium, Switzerland, and Canada). The validation was completed by an inter-rater reliability (IRR) analysis of the STOPP/START.v2 criteria applied to 10 standardized clinical vignettes. Results In comparison to the original English version, the 115 STOPP/START.v2 criteria in French language classify in identical manner, but the presentation has been adjusted (START.v2 first specifies the clinical condition followed by an explanation of the inappropriateness of the prescription or omission). This adaptation into French language was validated by means of (i) the translation/back-translation, which showed that the French version complied with the clinical meaning of the original criteria; (ii) the similar screening results when applied by the nine specialists to the 10 cases; and (iii) the high level of inter-rater reliability of these 9 evaluations, for both STOPP (IRR 0.849) and START.v2 (IRR 0.921). Conclusion The adaptation into French of the STOPP/START.v2 criteria provides clinicians with a screening tool to detect potentially inappropriate prescribing in patients aged 65 and older that is more logical, more reliable and easier to use.