Activity of 9-acridanone-hydrazone drugs detected at the pre-postural phase, in the experimental schistosomiasis mansoni

The compound Ro-15.5458/000, derivative in the class of 9-acridanone-hydrazones, was found to be effective against Schistosoma mansoni in mice, killing almost all the skin schistosomules (24 hr after infection), when administered at the dose of 100 mg/kg. In experiments carried out with Cebus monkeys, the drug was shown to be fully effective at 25 mg/kg, 7 days after infection. These data, associated with the good results obtained earlier at the post-postural phase of schistosomiasis, allow the inference that this promising compound may be important in the set of antischistosomal drugs, depending on further toxicological and clinical tests.

Scientific Evidence in Europe : Admissibility, Evaluation and Equality of Arms

This study was commissioned by the European Committee on Crime Problems at the Council of Europe to describe and discuss the standards used to asses the admissibility and appraisal of scientific evidence in various member countries. After documenting cases in which faulty forensic evidence seems to have played a critical role, the authors describe the legal foundations of the issues of admissibility and assessment of the probative value in the field of scientific evidence, contrasting criminal justice systems of accusatorial and inquisitorial tradition and the various risks that they pose in terms of equality of arms. Special attention is given to communication issues between lawyers and scientific experts. The authors eventually investigate possible ways of improving the system. Among these mechanisms, emphasis is put on the adoption of a common terminology for expressing the weight of evidence. It is also proposed to adopt an harmonized interpretation framework among forensic experts rooted in good practices of logical inference.

Transmission disequilibrium of small CNVs in simplex autism.

We searched for disruptive, genic rare copy-number variants (CNVs) among 411 families affected by sporadic autism spectrum disorder (ASD) from the Simons Simplex Collection by using available exome sequence data and CoNIFER (Copy Number Inference from Exome Reads). Compared to high-density SNP microarrays, our approach yielded ∼2× more smaller genic rare CNVs. We found that affected probands inherited more CNVs than did their siblings (453 versus 394, p = 0.004; odds ratio [OR] = 1.19) and that the probands' CNVs affected more genes (921 versus 726, p = 0.02; OR = 1.30). These smaller CNVs (median size 18 kb) were transmitted preferentially from the mother (136 maternal versus 100 paternal, p = 0.02), although this bias occurred irrespective of affected status. The excess burden of inherited CNVs among probands was driven primarily by sibling pairs with discordant social-behavior phenotypes (p < 0.0002, measured by Social Responsiveness Scale [SRS] score), which contrasts with families where the phenotypes were more closely matched or less extreme (p > 0.5). Finally, we found enrichment of brain-expressed genes unique to probands, especially in the SRS-discordant group (p = 0.0035). In a combined model, our inherited CNVs, de novo CNVs, and de novo single-nucleotide variants all independently contributed to the risk of autism (p < 0.05). Taken together, these results suggest that small transmitted rare CNVs play a role in the etiology of simplex autism. Importantly, the small size of these variants aids in the identification of specific genes as additional risk factors associated with ASD.

Big data and other challenges in the quest for orthologs.

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org. CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.

Extended truncated Tweedie-Poisson model

It has been argued that by truncating the sample space of the negative binomial and of the inverse Gaussian-Poisson mixture models at zero, one is allowed to extend the parameter space of the model. Here that is proved to be the case for the more general three parameter Tweedie-Poisson mixture model. It is also proved that the distributions in the extended part of the parameter space are not the zero truncation of mixed poisson distributions and that, other than for the negative binomial, they are not mixtures of zero truncated Poisson distributions either. By extending the parameter space one can improve the fit when the frequency of one is larger and the right tail is heavier than is allowed by the unextended model. Considering the extended model also allows one to use the basic maximum likelihood based inference tools when parameter estimates fall in the extended part of the parameter space, and hence when the m.l.e. does not exist under the unextended model. This extended truncated Tweedie-Poisson model is proved to be useful in the analysis of words and species frequency count data.

On the use of IRMS in forensic science: proposals for a methodological approach.

The flourishing number of publications on the use of isotope ratio mass spectrometry (IRMS) in forensicscience denotes the enthusiasm and the attraction generated by this technology. IRMS has demonstratedits potential to distinguish chemically identical compounds coming from different sources. Despite thenumerous applications of IRMS to a wide range of forensic materials, its implementation in a forensicframework is less straightforward than it appears. In addition, each laboratory has developed its ownstrategy of analysis on calibration, sequence design, standards utilisation and data treatment without aclear consensus.Through the experience acquired from research undertaken in different forensic fields, we propose amethodological framework of the whole process using IRMS methods. We emphasize the importance ofconsidering isotopic results as part of a whole approach, when applying this technology to a particularforensic issue. The process is divided into six different steps, which should be considered for a thoughtfuland relevant application. The dissection of this process into fundamental steps, further detailed, enablesa better understanding of the essential, though not exhaustive, factors that have to be considered in orderto obtain results of quality and sufficiently robust to proceed to retrospective analyses or interlaboratorycomparisons.

What do we gain from simplicity versus complexity in species distribution models?

Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species' occurrence-environment relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g. generalized linear/additive models, tree-based models, maximum entropy, etc.), and the variety of ways that such models can be implemented, permits substantial flexibility in SDM complexity. Building models with an appropriate amount of complexity for the study objectives is critical for robust inference. We characterize complexity as the shape of the inferred occurrence-environment relationships and the number of parameters used to describe them, and search for insights into whether additional complexity is informative or superfluous. By building 'under fit' models, having insufficient flexibility to describe observed occurrence-environment relationships, we risk misunderstanding the factors shaping species distributions. By building 'over fit' models, with excessive flexibility, we risk inadvertently ascribing pattern to noise or building opaque models. However, model selection can be challenging, especially when comparing models constructed under different modeling approaches. Here we argue for a more pragmatic approach: researchers should constrain the complexity of their models based on study objective, attributes of the data, and an understanding of how these interact with the underlying biological processes. We discuss guidelines for balancing under fitting with over fitting and consequently how complexity affects decisions made during model building. Although some generalities are possible, our discussion reflects differences in opinions that favor simpler versus more complex models. We conclude that combining insights from both simple and complex SDM building approaches best advances our knowledge of current and future species ranges.

Evolution of decision-making and learning under fluctuating social environments

The capacity to learn to associate sensory perceptions with appropriate motor actions underlies the success of many animal species, from insects to humans. The evolutionary significance of learning has long been a subject of interest for evolutionary biologists who emphasize the bene¬fit yielded by learning under changing environmental conditions, where it is required to flexibly switch from one behavior to another. However, two unsolved questions are particularly impor¬tant for improving our knowledge of the evolutionary advantages provided by learning, and are addressed in the present work. First, because it is possible to learn the wrong behavior when a task is too complex, the learning rules and their underlying psychological characteristics that generate truly adaptive behavior must be identified with greater precision, and must be linked to the specific ecological problems faced by each species. A framework for predicting behavior from the definition of a learning rule is developed here. Learning rules capture cognitive features such as the tendency to explore, or the ability to infer rewards associated to unchosen actions. It is shown that these features interact in a non-intuitive way to generate adaptive behavior in social interactions where individuals affect each other's fitness. Such behavioral predictions are used in an evolutionary model to demonstrate that, surprisingly, simple trial-and-error learn¬ing is not always outcompeted by more computationally demanding inference-based learning, when population members interact in pairwise social interactions. A second question in the evolution of learning is its link with and relative advantage compared to other simpler forms of phenotypic plasticity. After providing a conceptual clarification on the distinction between genetically determined vs. learned responses to environmental stimuli, a new factor in the evo¬lution of learning is proposed: environmental complexity. A simple mathematical model shows that a measure of environmental complexity, the number of possible stimuli in one's environ¬ment, is critical for the evolution of learning. In conclusion, this work opens roads for modeling interactions between evolving species and their environment in order to predict how natural se¬lection shapes animals' cognitive abilities. - La capacité d'apprendre à associer des sensations perceptives à des actions motrices appropriées est sous-jacente au succès évolutif de nombreuses espèces, depuis les insectes jusqu'aux êtres hu¬mains. L'importance évolutive de l'apprentissage est depuis longtemps un sujet d'intérêt pour les biologistes de l'évolution, et ces derniers mettent l'accent sur le bénéfice de l'apprentissage lorsque les conditions environnementales sont changeantes, car dans ce cas il est nécessaire de passer de manière flexible d'un comportement à l'autre. Cependant, deux questions non résolues sont importantes afin d'améliorer notre savoir quant aux avantages évolutifs procurés par l'apprentissage. Premièrement, puisqu'il est possible d'apprendre un comportement incorrect quand une tâche est trop complexe, les règles d'apprentissage qui permettent d'atteindre un com¬portement réellement adaptatif doivent être identifiées avec une plus grande précision, et doivent être mises en relation avec les problèmes écologiques spécifiques rencontrés par chaque espèce. Un cadre théorique ayant pour but de prédire le comportement à partir de la définition d'une règle d'apprentissage est développé ici. Il est démontré que les caractéristiques cognitives, telles que la tendance à explorer ou la capacité d'inférer les récompenses liées à des actions non ex¬périmentées, interagissent de manière non-intuitive dans les interactions sociales pour produire des comportements adaptatifs. Ces prédictions comportementales sont utilisées dans un modèle évolutif afin de démontrer que, de manière surprenante, l'apprentissage simple par essai-et-erreur n'est pas toujours battu par l'apprentissage basé sur l'inférence qui est pourtant plus exigeant en puissance de calcul, lorsque les membres d'une population interagissent socialement par pair. Une deuxième question quant à l'évolution de l'apprentissage concerne son lien et son avantage relatif vis-à-vis d'autres formes plus simples de plasticité phénotypique. Après avoir clarifié la distinction entre réponses aux stimuli génétiquement déterminées ou apprises, un nouveau fac¬teur favorisant l'évolution de l'apprentissage est proposé : la complexité environnementale. Un modèle mathématique permet de montrer qu'une mesure de la complexité environnementale - le nombre de stimuli rencontrés dans l'environnement - a un rôle fondamental pour l'évolution de l'apprentissage. En conclusion, ce travail ouvre de nombreuses perspectives quant à la mo¬délisation des interactions entre les espèces en évolution et leur environnement, dans le but de comprendre comment la sélection naturelle façonne les capacités cognitives des animaux.

Des hommes en mouvement : vers une reconfiguration des modèles masculins? L'exemple de la Suisse

This project is a study of the men's movement in Switzerland, especially regarding organizations seeking to redefine male identity. So far, this topic has been understudied, in Switzerland. The few studies available on the subject mostly adopt a (pro)feminist perspective. Their main purpose is to criticize men's movement participants. What is more, scarce researches on this problem mostly conducted by members of the Swiss men's movement themselves are mainly descriptive and methodologically problematic. In this context, I initiated the first national and sociological study of the men's movement in Switzerland. My main goals are: firstly, to propose a typology of organizations forming the men's movement in Switzerland. Secondly, I develop a sociological analysis of this phenomenon, taking into account in this process especially the characteristics of the Swiss context. Consequently, I adopted a mixed method approach, which included two main research steps: Firstly, I defined a representative sample of men's movement organizations in Switzerland. Based on a content analysis of men's organizations' websites, I was able to distinguish three ideal-types: Radical Criticism of Masculinity, Criticism of Hegemonic Masculinity, Defense of Men and Traditional Masculinity. Based on these three concepts, I subsequently analyzed the discourse on masculinity amongst men's movement organizations. Secondly, I conducted a survey of men's movement participants. This survey was based on the results of the content analysis. In this particular stage, I mainly used factor analysis. My results show that it would be all too simplistic to characterize the men's movement, in Switzerland, as a criticism of women's emancipation. On the contrary, my analysis reveals a more complex picture: The two main factors, which influence the men's movement, in Switzerland, are the contemporary sociological context and the Swiss society's particular features. I find that male roles, on the one hand, depend very much on today's cultural shift from materialistic to self-expression values. On the other hand, male role models reflect a social adaptation process. Moreover, as a reaction to deep changes in contemporary family structures, I observe an individualization process, characterized by separation between parental and conjugal functions that greatly shapes male role models. - Cette thèse analyse le phénomène des hommes en mouvement, dans le contexte de la Suisse. Cet ensemble est formé d'organisations regroupant des hommes impliqués consciemment dans un processus d'actions et de réflexions sur l'identité masculine. La revue de la littérature révèle qu'en Suisse, le sujet des hommes en mouvement est très peu étudié. Jusqu'ici, les rares recherches s'y intéressant adoptent généralement une approche (pro)féministe, dont l'objectif est de dénoncer ce phénomène. En outre, de rares recherches, issues des acteurs mêmes de ce mouvement, proposent une vue descriptive de l'ensemble, mais souffrant de faiblesses méthodologiques. Par notre recherche, nous souhaitons contribuer à l'étude de ce sujet, en initiant la première étude d'envergure nationale portant sur les hommes en mouvement. L'objectif final est de déboucher sur une typologie des organisations réunissant les hommes en mouvement, puis sur une analyse de la spécificité de cet ensemble, dans le contexte suisse. Pour remplir ces objectifs, nous avons mis en place un dispositif de méthodes mixtes, en deux phases. Lors d'une première étape, nous avons sélectionné un échantillon représentatif de la diversité des organisations masculines. Par une analyse de contenu effectuée sur la documentation récoltée sur les sites Internet de ces dernières, nous avons pu, en utilisant une démarche inductive et qualitative, faire émerger trois idéaux-types : Critique radicale de la masculinité, Critique de la masculinité hégémonique, Défense des hommes et de la masculinité traditionnelle. Ces concepts permettent de rendre compte, de manière schématique, des trois types de discours contemporains sur l'identité masculine diffusés par les hommes en mouvement. Lors d'une seconde étape, nous avons réalisé une enquête auprès des membres des organisations masculines. Pour y parvenir, nous avons créé un questionnaire incluant des propositions élaborées à partir des résultats de l'étape précédente. Lors de cette phase, nous avons réalisé une analyse factorielle. Les résultats montrent que le phénomène du mouvement des hommes ne saurait se réduire, en Suisse, à un mouvement de ressac visant à attaquer les droits des femmes. Au contraire, il s'agit d'un phénomène complexe, fortement dépendant du contexte sociologique contemporain et des caractéristiques de la société helvétique. Nous affirmons, entre autres, que les modèles masculins observables dans cet ensemble sont façonnés, d'une part, par une transition culturelle, caractérisée par le passage des valeurs matérialistes aux valeurs d'expression de soi. D'autre part, les modèles masculins prônés par les hommes en mouvement reflètent un processus d'adaptation sociale. En effet, en réaction au contexte de reconfiguration des formes familiales, on assiste à une individualisation des rapports de filiation et au détachement de la fonction parentale et conjugale, qui imprègnent fortement les modèles masculins défendus par ces hommes.

'Next generation' biogeography: towards understanding the drivers of species diversification and persistence

The drivers of species diversification and persistence are of great interest to current biogeography, especially in those global biodiversity hotspots' harbouring most of Earth's animal and plant life. Classical multispecies biogeographical work has yielded fascinating insights into broad-scale patterns of diversification, and DNA-based intraspecific phylogeographical studies have started to complement this picture at much finer temporal and spatial scales. The advent of novel next-generation sequencing (NGS) technologies provides the opportunity to greatly scale up the numbers of individuals, populations and species sampled, potentially merging intraspecific and interspecific approaches to biogeographical inference. Here, we outline these prospects and issues by using the example of an undisputed hotspot, the Cape of southern Africa. We outline the current state of knowledge on the biogeography of species diversification within the Cape, review the literature for phylogeographical evidence of its likely drivers and mechanisms, and suggest possible ways forward based on NGS approaches. We demonstrate the potential of these methods and current bioinformatic issues with the help of restriction-site-associated DNA (RAD) sequencing data for three highly divergent species of the Restionaceae, an important plant radiation in the Cape. A thorough understanding of the mechanisms that facilitate species diversification and persistence in spatially structured, species-rich environments will require the adoption of novel genomic and bioinformatic tools in biogeographical studies.

Usefulness of microsatellite typing in population genetic studies of Trypanosoma cruzi

Through microsatellite analysis of 53 monoclonal populations of Trypanosoma cruzi, we found a remarkable degree of genetic polymorphism with no single multilocus genotype being observed more than once. The microsatellite profile proved to be stable during 70 generations of the CL Brener clone in culture. The microsatellite profiling presented also high diagnostic sensitivity since DNA amplifications could be achieved with less than 100 fg DNA, corresponding to half parasite total DNA content. Based on these technical attributes the microsatellite assay turns out to be an important tool for direct typing T. cruzi in biological samples. By using this approach we were able to type T. cruzi in feces of artificially infected bugs and in single cells sorted by FACS. The microsatellites have shown to be excellent markers for T. cruzi phylogenetic reconstruction. We used maximum parsimony based on the minimum number of mutational steps to build an unrooted Wagner network, which confirms previous conclusions based on the analysis of the D7 domain of the LSU rDNA gene that T. cruzi is composed by two major groups. We also obtained evidence that strains belonging to rRNA group 2 are subdivided into two genetically distant clusters, and that one of these clusters is more related to rRNA group 1/2. These results suggest different origins for these strains.

Hierarchical conditional random fields for parts based models matching

A parts based model is a parametrization of an object class using a collection of landmarks following the object structure. The matching of parts based models is one of the problems where pairwise Conditional Random Fields have been successfully applied. The main reason of their effectiveness is tractable inference and learning due to the simplicity of involved graphs, usually trees. However, these models do not consider possible patterns of statistics among sets of landmarks, and thus they sufffer from using too myopic information. To overcome this limitation, we propoese a novel structure based on a hierarchical Conditional Random Fields, which we explain in the first part of this memory. We build a hierarchy of combinations of landmarks, where matching is performed taking into account the whole hierarchy. To preserve tractable inference we effectively sample the label set. We test our method on facial feature selection and human pose estimation on two challenging datasets: Buffy and MultiPIE. In the second part of this memory, we present a novel approach to multiple kernel combination that relies on stacked classification. This method can be used to evaluate the landmarks of the parts-based model approach. Our method is based on combining responses of a set of independent classifiers for each individual kernel. Unlike earlier approaches that linearly combine kernel responses, our approach uses them as inputs to another set of classifiers. We will show that we outperform state-of-the-art methods on most of the standard benchmark datasets.

Creació d'una eina en Java que a partir d'OWL i JESS generi SCORM

Aquest projecte consisteix en generar un programa escrit en llenguatge Java, que utilitzant un motor d'inferència a través d'una llibreria anomenada JESS, pugui llegir un document en format OWL que és una representació de l'ontologia (representació del coneixement) sobre una assignatura, transformant-lo al format de triples que és capaç d'interpretar JESS.