Modular analysis of gene expression data with R.

SUMMARY: Large sets of data, such as expression profiles from many samples, require analytic tools to reduce their complexity. The Iterative Signature Algorithm (ISA) is a biclustering algorithm. It was designed to decompose a large set of data into so-called 'modules'. In the context of gene expression data, these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different 'resolutions' of the modular mapping. In this short note, we introduce two BioConductor software packages written in GNU R: The isa2 package includes an optimized implementation of the ISA and the eisa package provides a convenient interface to run the ISA, visualize its output and put the biclusters into biological context. Potential users of these packages are all R and BioConductor users dealing with tabular (e.g. gene expression) data. AVAILABILITY: http://www.unil.ch/cbg/ISA CONTACT: sven.bergmann@unil.ch

Developmental and Anatomical Constraints on Vertebrate Genome Evolution

Pendant ma thèse de doctorat, j'ai utilisé des espèces modèles, comme la souris et le poisson-zèbre, pour étudier les facteurs qui affectent l'évolution des gènes et leur expression. Plus précisément, j'ai montré que l'anatomie et le développement sont des facteurs clés à prendre en compte, car ils influencent la vitesse d'évolution de la séquence des gènes, l'impact sur eux de mutations (i.e. la délétion du gène est-elle létale ?), et leur tendance à se dupliquer. Où et quand il est exprimé impose à un gène certaines contraintes ou au contraire lui donne des opportunités d'évoluer. J'ai pu comparer ces tendances aux modèles classiques d'évolution de la morphologie, que l'on pensait auparavant refléter directement les contraintes s'appliquant sur le génome. Nous avons montré que les contraintes entre ces deux niveaux d'organisation ne peuvent pas être transférées simplement : il n'y a pas de lien direct entre la conservation du génotype et celle de phénotypes comme la morphologie. Ce travail a été possible grâce au développement d'outils bioinformatiques. Notamment, j'ai travaillé sur le développement de la base de données Bgee, qui a pour but de comparer l'expression des gènes entre différentes espèces de manière automatique et à large échelle. Cela implique une formalisation de l'anatomie, du développement et de concepts liés à l'homologie grâce à l'utilisation d'ontologies. Une intégration cohérente de données d'expression hétérogènes (puces à ADN, marqueurs de séquence exprimée, hybridations in situ) a aussi été nécessaire. Cette base de données est mise à jour régulièrement et disponible librement. Elle devrait contribuer à étendre les possibilités de comparaison de l'expression des gènes entre espèces pour des études d'évo-devo (évolution du développement) et de génomique. During my PhD, I used model species of vertebrates, such as mouse and zebrafish, to study factors affecting the evolution of genes and their expression. More precisely I have shown that anatomy and development are key factors to take into account, influencing the rate of gene sequence evolution, the impact of mutations (i.e. is the deletion of a gene lethal?), and the propensity of a gene to duplicate. Where and when genes are expressed imposes constraints, or on the contrary leaves them some opportunity to evolve. We analyzed these patterns in relation to classical models of morphological evolution in vertebrates, which were previously thought to directly reflect constraints on the genomes. We showed that the patterns of evolution at these two levels of organization do not translate smoothly: there is no direct link between the conservation of genotype and phenotypes such as morphology. This work was made possible by the development of bioinformatics tools. Notably, I worked on the development of the database Bgee, which aims at comparing gene expression between different species in an automated and large-scale way. This involves the formalization of anatomy, development, and concepts related to homology, through the use of ontologies. A coherent integration of heterogeneous expression data (microarray, expressed sequence tags, in situ hybridizations) is also required. This database is regularly updated and freely available. It should contribute to extend the possibilities for comparison of gene expression between species in evo-devo and genomics studies.

Space-time within general relativity : a structural realist understanding

ABSTRACT This dissertation investigates the, nature of space-time as described by the theory of general relativity. It mainly argues that space-time can be naturally interpreted as a physical structure in the precise sense of a network of concrete space-time relations among concrete space-time points that do not possess any intrinsic properties and any intrinsic identity. Such an interpretation is fundamentally based on two related key features of general relativity, namely substantive general covariance and background independence, where substantive general covariance is understood as a gauge-theoretic invariance under active diffeomorphisms and background independence is understood in the sense that the metric (or gravitational) field is dynamical and that, strictly speaking, it cannot be uniquely split into a purely gravitational part and a fixed purely inertial part or background. More broadly, a precise notion of (physical) structure is developed within the framework of a moderate version of structural realism understood as a metaphysical claim about what there is in the world. So, the developement of this moderate structural realism pursues two main aims. The first is purely metaphysical, the aim being to develop a coherent metaphysics of structures and of objects (particular attention is paid to the questions of identity and individuality of these latter within this structural realist framework). The second is to argue that moderate structural realism provides a convincing interpretation of the world as described by fundamental physics and in particular of space-time as described by general relativity. This structuralist interpretation of space-time is discussed within the traditional substantivalist-relationalist debate, which is best understood within the broader framework of the question about the relationship between space-time on the one hand and matter on the other. In particular, it is claimed that space-time structuralism does not constitute a 'tertium quid' in the traditional debate. Some new light on the question of the nature of space-time may be shed from the fundamental foundational issue of space-time singularities. Their possible 'non-local' (or global) feature is discussed in some detail and it is argued that a broad structuralist conception of space-time may provide a physically meaningful understanding of space-time singularities, which is not plagued by the conceptual difficulties of the usual atomsitic framework. Indeed, part of these difficulties may come from the standard differential geometric description of space-time, which encodes to some extent this atomistic framework; it raises the question of the importance of the mathematical formalism for the interpretation of space-time.

Climate change impact on biodiversity in Switzerland: a review. Journal for Nature Conservation

A noticeable increase in mean temperature has already been observed in Switzerland and summer temperatures up to 4.8 K warmer are expected by 2090. This article reviews the observed impacts of climate change on biodiversity and consider some perspectives for the future at the national level. The following impacts are already evident for all considered taxonomic groups: elevation shifts of distribution toward mountain summits, spread of thermophilous species, colonisation by new species from warmer areas and phenological shifts. Additionally, in the driest areas, increasing droughts are affecting tree survival and fish species are suffering from warm temperatures in lowland regions. These observations are coherent with model projections, and future changes will probably follow the current trends. These changes will likely cause extinctions for alpine species (competition, loss of habitat) and lowland species (temperature or drought stress). In the very urbanised Swiss landscape, the high fragmentation of the natural ecosystems will hinder the dispersal of many species towards mountains. Moreover, disruptions in species interactions caused by individual migration rates or phenological shifts are likely to have consequences for biodiversity. Conversely, the inertia of the ecosystems (species longevity, restricted dispersal) and the local persistence of populations will probably result in lower extinction rates than expected with some models, at least in 21st century. It is thus very difficult to estimate the impact of climate change in terms of species extinctions. A greater recognition by society of the intrinsic value of biodiversity and of its importance for our existence will be essential to put in place effective mitigation measures and to safeguard a maximum number of native species.

Travailler sur les articulations interprofessionnelles en périnatalité: un objectif obstétrical [Interprofessional collaboration in perinatality: an obstetrical goal]

In the field of perinatality, development of prenatal diagnosis and neonatal management have been impressive. But these were also associated with the emergence of the increasingly important emotional dimension for parents and professionals. Obstetricians dealing with the difficult breaking of bad news, the uncertainties of prenatal diagnosis and the complex somatic, psychological and social follow-up have to work in a multidisciplinary approach. The securing role of a coherent teamwork is recognised by parents as well as health care providers This article discusses interprofessional relationship as an obstetrical goal and give some landmarks in order to improve the management and the collaboration with parents.

Diagnostic value of soluble CD14 subtype (sCD14-ST) presepsin for the postmortem diagnosis of sepsis-related fatalities.

The first aim of this study was to assess the diagnostic performance of presepsin (sCD14-ST) in postmortem serum from femoral blood compared to procalcitonin (PCT) to detect sepsis-related fatalities. The second aim was to compare sCD14-ST levels found in postmortem serum to the values in pericardial fluid to investigate the usefulness of the latter as an alternative biological fluid. Two study groups were formed, a sepsis-related fatalities group and a control group. Radiology (unenhanced CT scans and postmortem angiographies), autopsies, histology, neuropathology, and toxicology as well as other postmortem biochemistry investigations were performed in all cases. Microbiological investigations on right cardiac blood were carried out exclusively in septic cases. The results of this study indicated that postmortem serum PCT and sCD14-ST levels, individually considered, allowed septic cases to be identified. Even though increases in both PCT and sCD14-ST concentrations were observed in the control cases, coherent PCT and sCD14-ST results in cases with suspected sepsis allowed the diagnosis to be confirmed. Conversely, no relevant correlation was identified between postmortem serum and pericardial fluid sCD14-ST levels in either the septic or control groups.

Obesity prevention opinions of school stakeholders: a qualitative study.

BACKGROUND: In general, schools are an important setting to implement current recommendations for obesity prevention in children because the vast majority of children attend school. This study investigated the opinions of different school stakeholders on the feasibility and acceptability of current obesity prevention strategies that could be implemented in Swiss schools. METHODS: Research methods were comprised of a qualitative study which included school directors, physical education teachers, catering staff, school nurses and health educators, parents of young adolescents, and young adolescents interviewed (N = 40) categorized into 6 focus groups. Open-ended questions were used to determine the participants' opinion regarding current obesity prevention recommendations, and healthy eating and physical activity promotion strategies. RESULTS: All participants approved the implementation of nutritional standards for food and drinks sold in schools, but thought that increasing the attractiveness of healthy options was the best strategy to improve eating habits. Enjoying participation in physical activity classes or after-school activities was stressed. Participants suggested offering classes for all students with poor physical condition, independent of weight status. Stakeholders called for governmental support and global coordination of interventions balanced with providing schools with enough autonomy to adapt programs relevant to their individual circumstances. They recommended integrating all school stakeholders in obesity prevention initiatives, with special attention to students and local authorities. CONCLUSIONS: Participants agreed that schools are a crucial setting to implement childhood obesity prevention strategies. They called on school stakeholders to join efforts aiming to encourage healthy behaviors and to support and reinforce parents' efforts by spreading consistent and coherent health messages.

A Bayesian network approach to the database serch problem in criminal proceedings

Background The 'database search problem', that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions. The method's graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication.

A new perspective on the zoogeography of the sibling mouse-eared bat species Myotis myotis and Myotis blythii: Morphological, genetical and ecological evidence

The actual geographic distribution of the two sibling mouse-eared bat species Myotis myotis and Myotis blythii, which occur widely sympatrically in the western Palaearctic region, remains largely controversial. This concerns particularly the specific attribution of marginal populations from the Mediterranean islands and from adjacent areas of North Africa and Asia, which are morphologically intermediate between continental M. myotis and M. blythii from Europe. This study attempts to clarify this question by using four different approaches: cranial morphology, external morphology, genetics and trophic ecology. The three latter methods show unambiguously that North Africa, Malta, Sardinia and Corsica are presently inhabited by monospecific populations of M. myotis. In contrast, cranial morphometrics do not yield conclusive results. These results contradict all recent studies, which attribute North African and Maltese mouse-eared bats to M. blythii and consider that Sardinia and Corsica harbour sympatric populations of the two species. As concerns south-eastern populations, doubts are also expressed about the attribution of the subspecific taxon omari which may actually refer to M. myotis instead of M. blythii. Protein electrophoresis is presently the only absolute method available for determining M. myotis and M. blythii throughout their distribution ranges. However, species identification may be approached by relying on less sophisticated morphometrical methods as presented in this study. Species-specific habitat specializations are probably responsible for the differences observed between the geographic distributions of M. myotis and M. blythii, as they provide a logical groundwork for a coherent model of speciation for these two bat species.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.

The TRANSMED Atlas: geological-geophysical fabric of the Mediterranean region - Final report of the project

Geological research on the Mediterranean region is presently characterized by the transition from disciplinary to multidisciplinary research, as well as from national to international investigations. In order to synthesize and integrate the vast disciplinary and national datasets which are available, it is necessary to implement maximum interaction among geoscientists of different backgrounds. The creation of project-oriented task forces in universities and other research institutions, as well as the development of large international cooperation programs, is instrumental in pursuing such a multidisciplinary and supranational approach. The TRANSMED Atlas, an official publication of the 32nd International Geological Congress (Florence 2004), is the result of an international scientific cooperation program which brought together for over two years sixty-three structural geologists, geophysicists, marine geologists, petrologists, sedimentologists, stratigraphers, paleogeographers, and petroleum geologists coming from eighteen countries, and working for the petroleum industry, academia, and other institutions, both public and private. The TRANSMED Atlas provides an updated, synthetic, and coherent portrayal of the overall geological-geophysical structure of the Mediterranean domain and the surrounding areas. The initial stimulus for the Atlas came from the realization of the extremely heterogeneous nature of the existing geological-geophysical data about such domain. These data have been gathered by universities, oil companies, geological surveys and other institutions in several countries, often using different procedures and standards. In addition, much of these data are written in languages and published in outlets that are not readily accessible to the general international reader. By synthesizing and integrating a wealth of preexisting and new data derived from surficial geology, seismic sections at various scales, and mantle tomographies, the TRANSMED Atlas provides for the first time a coherent geological overview of the Mediterranean region and represents an ideal springboard for future studies.

Validation statistique et structurale du questionnaire analytique de diagnostic de la personnalité (Q.A.P.)

The French Analytical Questionnaire of diagnostic of the Personality (Q.A.P., 1996), who took over from the characterological questionnaire of Berger (1950), is a interesting one for psychologists and characterologists because this test is based on very coherent theoretical corpus. This questionnaire is divided in two parts, the first one consists of three factor or fundamental scales which allow to determine the characterological type of individuals, the second part is made of nine complementary scales allowing to determine more precisely the personality of the subjects. We have done a structural validation of that questionnaire using a large sample (n=865). Several factor analyses were conducted on both part of the test. We also made a reliability analysis of each scale using the alpha of Cronbach and a homogeneity analysis of each question. Thank to these analyses we were able to evalue that instrument and we were able to set up that the factorial structure of the test corresponds to the theoretical one developped by the french school of characterology. The Analytical Questionnaire of diagnostic of the Personnality is globaly reliable in particullary the fist part which is very consistent. The second part is less reliable, and this is partly on due to the correlations between the scales. We have also done a correlational analysis between the first part of the Q.A.P., the questionnaire of Berger and the Rapid Questionnaire of Diagnostic of the Personnality (Q.R.D.P., 1996). The Q.A.P. might be the more reliable one. Finally we have evaluated the impact of gender, age and profession on the factors of the Analytical Questionnaire of diagnostic of the Personnality.

Validation d'une version abrégée du TCI (TCI-56) sur un échantillon de jeunes fumeurs et non-fumeurs

Introduction: The psychobiological seven-factor model proposed by Cloninger et al. (1993) takes into account temperament and character dimensions to describe personality. Four of the dimensions are linked with biological, genetic and neuroanatomic structures, whereas the three other dimensions are related to the degree of individual, social and spiritual development. A study conducted by Wills et al. (1994) with adolescents showed that substance abuse was associated with high scores on Novelty Seeking and low scores on Harm Avoidance and Reward Dependence. The aim of the present study was, firstly, to create a short form of Cloninger's (1993) Temperament and Character Inventory (TCI) and, secondly, to study the impact of nicotine dependence as well as demographic variables on a sample of young adults. Method: We created a short form of the TCI containing 56 items (TCI-56), 8 for each scale. Responses are made on a five-point Likert type scale. A Swiss sample (n=211), of 116 women and 95 men, aged from 15 to 30 years, participated in this study. Our population was divided into a group of 81 smokers and another of 130 non-smokers, according to their scores on the Fagerstörm test for nicotine dependence (1999). Results: The structural validation consisted of two separate factor analysis with varimax rotations, one for the temperamental items, and the other, for the character ones. The first factor analysis conducted on the items of the temperament scales allowed to extract 4 factors explaining 40.7% of the variance. The correlations between factors and scales are the following: r=.71 for Novelty Seeking, r=.69 for Persistence, r=.95 for Harm Avoidance, r=.94 for Reward Dependence. The second factor analysis conducted on the items of the character scales allowed to extract 3 factors explaining 41.5% of the variance. The correlations between factors and scales are the following: r=.94 for Self-Directedness, r=.91 for Cooperativeness and r=.99 for Self-Transcendence. The internal consistencies range from α=.65 to α=.75 for the temperament scales, and from α=.71 to α=.83 for the three character scales. Concerning, the impact of the nicotine dependence, we observed that smokers have significantly higher scores for Novelty seeking, than non-smokers (p=.01). We found no difference for Harm Avoidance and Reward Dependence. Nevertheless, smokers seem to have the tendency to score higher on Transcendence (p=.06). Moreover, people having smoked more than 100 cigarettes in their life have significantly higher scores on this scale (p.04) and the correlation between Transcendence and the Fagerstörm test is significant (r=.19). We also found gender differences: the women (N=116) obtain significantly higher scores for Harm Avoidance (p<.001), for Reward Dependence (p<.001) and for Cooperation (p=.01). We further found a significant correlation between age and Self-Directedness, r=.34. We observed no interaction between gender and smoking or age and smoking on the dimensions of the TCI-56. Discussion: The TCI short form (TCI-56) seems to be a valid and useful inventory to assess personality differences. Confirming the results of others about the relation between addiction and personality, we found that smokers have significantly higher scores for Novelty seeking, than non-smokers. But we were not able to find any significant differences for Harm Avoidance and Reward Dependence. This might be due to our sample that was made of young adults. This study also shows that Transcendence could be an interesting dimension for studies on Tobacco smoking to consider. Concerning the impact of demographic variables, we observed that age and gender have specific and coherent influence on personality.

The hierarchical structures of the NEO-PI-R and the 16PF5

The present study compares the higher-level dimensions and the hierarchical structures of the fifth edition of the 16 PF with those of the NEO PI-R. Both inventories measure personality according to five higher-level dimensions. These inventories were however constructed according to different methods (bottom-up vs. top-down). 386 participants filled out both questionnaires. Correlations, regressions and canonical correlations made it possible to compare the inventories. As expected they roughly measure the same aspects of personality. There is a coherent association among four of the five dimensions measured in the tests. However Agreeableness, the remaining dimension in the NEO PI-R, is not represented in the 16 PF 5. Our analyses confirmed the hierarchical structures of both instruments, but this confirmation was more complete in the case of the NEO PI-R. Indeed, a parallel analysis indicated that a four-factor solution should be considered in the case of the 16 PF 5. On the other hand, the NEO PI-R's five-factor solution was confirmed. The top-down construction of this instrument seems to make for a more legible structure. Of the two five-dimension constructs, the NEO PI-R thus seems the more reliable. This confirms the relevance of the Five Factor Model of personality.

La construction de l'identité de soi dans la famille.

Cet article présente une réflexion sur le développement de l'identité de soi chez l'enfant. Nous étudions pour cela le développement de l'autobiographie, la façon dont l'enfant apprend à raconter qui « il » est. Les narrations autobiographiques apparaissent tôt dans le développement dans une forme linguistique même rudimentaire, et sont produites notamment lorsque l'enfant a vécu une expérience émotionnellement chargée. La narration autobiographique permet d'intégrer le divers de l'expérience en un tout cohérent, selon la perspective du narrateur, et de donner sens aux événements vécus en les organisant en fonction d'un agent, d'une action, d'un temps et d'un lieu. La sélection des événements à raconter et la valeur à leur donner résultent d'un apprentissage social, réalisé en premier lieu dans la famille, qui va à long terme modéliser la façon dont l'enfant se raconte. Des exemples d'interactions narratives mère-enfant illustrant cet apprentissage sont présentés. A contrario, le conflit familial peut menacer cette intégration ; différentes formes de conflit et leurs conséquences possibles sur le développement de l'autobiographie sont évoquées. This paper presents a reflection about the development of the self in children, through the study of autobiographical narratives - i.e. the way the child tells who "she/he" is. Children produce narratives early in the development, even in a simple linguistic form. Narratives are first triggered when the child has lived an emotional event. The function of narratives is to integrate the various aspects of the lived event in a coherent whole. It organizes the events according to an agent, an action, a time and a place. The child learns in the interaction with significant others what events are to be told and which is the value to give to them. This social learning will in the long run shape the way the child tells who she/he is. We illustrate this process through examples of narrative interactions between mothers and children. Finally, the way conflicts in the family might disturb this learning process is discussed, as well as the consequences they might have on the development of the self.