Evolution of the Helvetic shelf (Switzerland) during the Barremian-early Aptian : paleoenvironmental, paleogeographic and paleoceanographic controlling factors

The Early Cretaceous has experienced the development of large shallow-water carbonate platform in tropical and subtropical regions, favoured by exceptionally warm climatic conditions, optimal trophic conditions and a suitable tectonic and paleogeographic context. This period was also characterized by shorter intervals, in which the widespread deposition of marine sediments enriched in organic matter occurred ("oceanic anoxic episodes": OAE). This study focuses on the Barremian- Aptian interval, during which the Urgonian platform developed throughout the northern Tethyan passive margin. Due to the Alpine orogeny, sediments belonging to this platform - named locally Schrattenkalk Formation, are presently outcropping in the Helvetic Alps. This study aims to reconstruct the paleogeographic evolution of the Helvetic platform, and to define the environmental and oceanographic factors, which influenced its development. Several key episodes in the life of this platform have been identified: - The installation of the platform, covering hemipelagic sediments of the Drusberg Member, near the limit between the early and late Barremian. - The temporary change of carbonate production type during the basal Aptian, with the deposition of the Rawil Member. - And finally the definitive interruption of photozoan carbonate platform sedimentation in the study area, during the early Aptian. The sedimentological, biostratigraphical and chemostratigraphic (8I3C) data lead to the sequential subdivision of eleven sections and one core, located throughout the different Helvetic nappes of Switzerland. The sequence stratigraphie framework, initially defined for the Urgonian carbonate platform of the Vercors area (SE France), is confirmed in the Helvetic nappes, where the same number of sequences was observed. Many similarities between these two areas are put forward in this work. The sequence stratigraphie framework helped to highlight the installation of a bioclastic body, included in the Schrattenkalk Formation, since the middle Early Barremian (sequence B2). The age of the installation of the rudist-rich limestone, which corresponds to the Urgonian facies sensu stricto, is attributed to the late Barremian (maximum flooding surface of the sequence B3). This age coincides with the one determined in other northern Tethyan areas for the installation of the Urgonian platform. The results of this study show a strong tectonic control of the platform architecture, with the presence of syn-sedimentary faults in a perpendicular position to the progradation direction of the platform. The presence of these faults was highlighted by the study of the evolution of the microfacies distribution and by thickness variations in different areas. Sea level fluctuations also played an important role in the various life phases of the platform. Three major falls in sea level have been identified. A significant emersion of the proximal domain has been observed, involving an important drop of the relative sea level, leading to the exposure of the Drusberg Member hemipelagic series. A second major drop in sea level is identified near the Barremian-Aptian boundary, and a third is registered on the top of the Upper Schrattenkalk Member on the whole platform; it is associated with a karst affecting the underlying limestones to a depth of over 20 meters. This observation sheds new light on the conditions linked to the demise of Urgonian platform, which was strongly influenced by this phase of emersion.

The evolution and distribution of second-hand house prices in Barcelona

The aim of this study is to collect and analyze variables that could have a relationship with the second-hand house prices in Barcelona, as much disaggregated as possible from 2008 to 2011 and make a statistical analysis. The study consists of two parts. The first part is the preliminary study of the data and the second part is the econometric analysis of the data to see if there is any relationship between the second-hand house prices and the variables chosen. Finally, we looked at if there was any atypical observation and if the model presented multicollinarity. With all this information, we extract some conclusions and then, we analyzed more deeply the information.

Evolution et ampleur de la violence parmi les jeunes : résultats d'une étude comparative entre les cantons de Vaud et de Zurich : rapport dans le cadre du programme nationale Jeunes et violence

La violence parmi les jeunes est un thème récurrent dans les médias qui suscite de nombreuses inquiétudes dans la population. Les enquêtes standardisées répétées auprès des jeunes sur la violence qu'ils ont expérimentée, en tant qu'auteurs ou victimes, constituent une source précieuse de données pour étudier l'évolution de ce phénomène ainsi que d'autres formes de délinquance et de comportements à risque. Elles permettent également de décrire et de mieux comprendre les contextes dans lesquels les incidents violent se produisent et quelles sont les causes potentielles du passage à l'acte. Ces enquêtes sont un moyen efficace de dresser un état des lieux qui va bien au-delà de ce que peuvent montrer les statistiques officielles de la police et de la justice. En vue des enquêtes de 2014, les méthodologies des deux études cantonales ont été harmonisées de manière à augmenter les possibilités de comparaison. Ce processus d'harmonisation ainsi que la présente étude comparative ont été financés par l'Office fédéral des assurances sociales (OFAS). Par ailleurs, les habitudes des jeunes ayant évolué au cours des dix dernières années, un certain nombre de comportements ont été intégrés dans les questionnaires vaudois et zurichois de 2014, comme le cyber-harcèlement et la violence au sein des jeunes couples. La présente étude cherche à répondre à deux questions fondamentales : 1. Comment la violence parmi les jeunes ainsi que ses contextes et facteurs de risque ont-ils évolué ces dernières années ? 2. Quelles similarités et différences trouvons-nous entre les cantons de Vaud et de Zurich en 2014 ? Par conséquent, l'étude est divisée en deux parties : la première traite de l'évolution de la violence et d'autres problèmes comportementaux entre 1999 (Zurich) respectivement 2004 (Lausanne) et 2014 chez les jeunes habitants la ville de Lausanne ou de Zurich ; la seconde partie dresse le portrait de la situation en 2014 dans les cantons de Vaud et de Zurich. Pour des raisons d'échantillonnage les analyses dans le temps sont limitées à des comparaisons inter-villes plutôt qu'inter-cantonales.

Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.

Tipping the scales: Evolution of the allometric slope independent of average trait size.

The scaling of body parts is central to the expression of morphology across body sizes and to the generation of morphological diversity within and among species. Although patterns of scaling-relationship evolution have been well documented for over one hundred years, little is known regarding how selection acts to generate these patterns. In part, this is because it is unclear the extent to which the elements of log-linear scaling relationships-the intercept or mean trait size and the slope-can evolve independently. Here, using the wing-body size scaling relationship in Drosophila melanogaster as an empirical model, we use artificial selection to demonstrate that the slope of a morphological scaling relationship between an organ (the wing) and body size can evolve independently of mean organ or body size. We discuss our findings in the context of how selection likely operates on morphological scaling relationships in nature, the developmental basis for evolved changes in scaling, and the general approach of using individual-based selection experiments to study the expression and evolution of morphological scaling.

The life history of retrocopies illuminates the evolution of new mammalian genes.

New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88-280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the "life history" of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.

Evolution of cameral accounting

Abstract

Evolution: the end of an ancient asexual scandal.

Bdelloid rotifers were believed to have persisted and diversified in the absence of sex. Two papers now show they exchange genes with each other, via horizontal gene transfers as known in bacteria and/or via other forms of non-canonical sex.

Evolution à long term du syndrom de Widal après chirurgie endoscopique endonasale

Ce travail de recherche a été effectué dans le cadre d'une formation post-graduée à l'Hôpital de La Chaux-de-Fonds, dans lequel le service ORL bénéficie d'un recrutement significatif pour les pathologies naso-sinusiennes, en particulier les polyposes. Ces pathologies sont grevées d'un handicap fonctionnel considérable, de par l'obstruction nasale, la limitation des efforts physiques et les troubles olfactifs comme principales répercussions. J'ai ainsi répertorié 303 interventions endonasales pour ablation de polypes et drainage des cavités sinusales. effectuées entre 1987 et 2006. L'étude s'est focalisée sur les 33 patients atteints d'une polypose nasale mais également d'un asthme et d'une intolérance à l'aspirine, réalisant la triade de Widal. La prévalence en Europe pour la polypose nasale est de 1 à 2 %, dont 10 à 20 % de syndromes de Widal. Cette entité est grevée d'une morbidité plus sévère en raison des mécanismes métaboliques induisant des récidives de polypes précoces, rendant la maladie plus difficile à contrôler. Ces patients ont été évalués d'une part subjectivement par une échelle visuelle analogique pour les symptômes rhinologiques et généraux, et d'autre part via une analyse objective du status endonasal de la polypose à la fin du suivi. Pour chaque patient, les troubles fonctionnels résiduels (obstruction nasale, rhinorrhée, troubles olfactifs, céphalées, éternuements, larmoiement) ainsi que le status endonasal à la fin du suivi ont été analysés pour détecter d'éventuelles associations significatives avec les caractéristiques pré-opératoires (âge, sexe, allergies, antécédants de chirurgie endonasale, données scanographiques, status endonasal). Deux groupes ont été identifiés selon la sévérité de l'atteinte fonctionnelle résiduelle. La valeur moyenne de la gêne à la fin du suivi pour l'ensemble du collectif est de 3.9/10 sur l'échelle visuelle analogique (0= absence de gêne, 10= gêne maximale). Les facteurs de mauvais pronostic qui ont été identifiés sont le sexe féminin et la présence de polyallergies, mais sans relation statistiquement significative. La seule différence statistiquement significative est le stade avancé de polypose nasale à la fin du suivi dans le groupe présentant l'atteinte fonctionnelle la plus importante (groupe 2). Malgré la combinaison des traitements chirurgicaux et médicamenteux par corticoïdes et anti-leucotriènes, la maladie de Widal est grevée d'une gêne fonctionnelle résiduelle non négligeable dans notre suivi moyen de 11,6 ans. Ceci relativise les résultats parfois trop optimistes des études avec un suivi plus court, sachant que les délais avant une deuxième intervention chirurgicale dans notre série ont été de 6,5 ans. L'évolution des traitements immuno-modulateurs topiques et systémiques combinés aux interventions chirurgicales ponctuelles renforce l'arsenal thérapeutique dans la prise en charge des patients atteints de la maladie de Widal. Cette étude pourra être élargie au collectif entier des ethmoïdectomies répertoriées (n=303) dans le service ORL et actualisées, afin de rechercher et mettre en évidence d'autres associations en comparant le groupe des polyposes simples au groupe des triades de Widal.

Evolution of mammographic image quality in the state of Rio de Janeiro

Objective:To evaluate the evolution of mammographic image quality in the state of Rio de Janeiro on the basis of parameters measured and analyzed during health surveillance inspections in the period from 2006 to 2011.Materials and Methods:Descriptive study analyzing parameters connected with imaging quality of 52 mammography apparatuses inspected at least twice with a one-year interval.Results:Amongst the 16 analyzed parameters, 7 presented more than 70% of conformity, namely: compression paddle pressure intensity (85.1%), films development (72.7%), film response (72.7%), low contrast fine detail (92.2%), tumor mass visualization (76.5%), absence of image artifacts (94.1%), mammography-specific developers availability (88.2%). On the other hand, relevant parameters were below 50% conformity, namely: monthly image quality control testing (28.8%) and high contrast details with respect to microcalcifications visualization (47.1%).Conclusion:The analysis revealed critical situations in terms of compliance with the health surveillance standards. Priority should be given to those mammography apparatuses that remained non-compliant at the second inspection performed within the one-year interval.

GENETIC ARCHITECTURE, EVOLUTION AND MAINTENANCE OF A COLOR CLINE AT A CONTINENTAL SCALE

On a geological time scale the conditions on earth are very variable and biological patterns (for example the distributions of species) are very dynamic. Understanding large scale patterns of variation observed today thus requires a deep understanding of the historical factors that drove their evolution. In this thesis, we reevaluated the evolution and maintenance of a continental color cline observed in the European barn owl (Tyto alba) using population genetic tools. The colour cline spans from south-est Europe where most individual have pure white underparts to north and east Europe where most individuals have rufous-brown underparts. Our results globally showed that the old scenario, stipulating that the color cline evolved by secondary contact of two color morphs (white and rufous) that evolved in allopatry during the last ice age has to be revised. We collected samples of about 700 barn owls from the Western Palearctic to establish the first population genetic data set for this species. Individuals were genotyped at 22 microsatellites markers, at one mitochondrial gene, and at a candidate color gene. The color of each individuals was assessed and their sex determined by molecular methods. We first showed that the genetic variation in Western Europe is very limited compared to the heritable color variation. We found no evidences of different glacial lineages, and showed that selection must be involved in the maintenance of the color cline (chapter 1). Using computer simulations, we demonstrated that the post-glacial colonization of Europe occurred from the Iberian Peninsula and that the color cline could not have evolved by neutral demographic processes during this colonization (chapter 2). Finally we reevaluated the whole history of the establishment of the Western Palearctic variation of the barn owl (chapter 3): This study showed that all Western European barn owls descend from white barn owls phenotypes from the Middle East that colonized the Iberian Peninsula via North-Africa. Following the end of the last ice age (20'000 years ago), these white barn owls colonized Western Europe and under selection a novel rufous phenotype evolved (during or after the colonization). An important part of the color variation could be explained by a single mutation in the melanocortin-1-receptor (MC1R) gene that appeared during or after the colonization. The colonization of Europe reached until Greece, where the rufous birds encountered white ones (which reached Greece from the Middle East over the Bosporus) in a secondary contact zone. Our analyses show that white and rufous barn owls in Greece interbreed only to a limited extent. This suggests that barn owls are at the verge of becoming two species in Greece and demonstrates that European barn owls represent an incipient ring species around the Mediterranean. The revisited history of the establishment of the European barn owl color cline makes this model system remarkable for several aspects. It is a very clear example of strong local adaptation that can be achieved despite high gene flow (strong color and MC1R differentiation despite almost no neutral genetic differentiation). It also offers a wonderful model system to study the interactions between colonization processes and selection processes which have, for now, been remarkably understudied despite their potentially ubiquitous importance. Finally it represents a very interesting case in the speciation continuum and appeals for further studying the amount of gene flow that occurs between the color morphs in Greece. -- Sur l'échelle des temps géologiques, les conditions sur terre sont très variables et les patrons biologiques (telle que la distribution des espèces) sont très dynamiques. Si l'on veut comprendre des patrons que l'on peut observer à large échelle aujourd'hui, il est nécessaire de d'abord comprendre les facteurs historiques qui ont gouverné leur établissement. Dans cette thèse, nous allons réévaluer, grâce à des outils modernes de génétique des populations, l'évolution et la maintenance d'un cline de couleur continental observé chez l'effraie des clochers européenne (Tyto alba). Globalement, nos résultats montrent que le scenario accepté jusqu'à maintenant, qui stipule que le cline de couleur a évolué à partir du contact secondaire de deux morphes de couleur (blanches et rousses) ayant évolué en allopatrie durant les dernières glaciations, est à revoir. Afin de constituer le premier jeu de données de génétique des populations pour cette espèce, nous avons récolté des échantillons d'environ 700 effraies de l'ouest Paléarctique. Nous avons génotypé tous les individus à 22 loci microsatellites, sur un gène mitochondrial et sur un autre gène participant au déterminisme de la couleur. Nous avons aussi mesuré la couleur de tous les individus et déterminé leur sexe génétiquement. Nous avons tout d'abord pu montrer que la variation génétique neutre est négligeable en comparaison avec la variation héritable de couleur, qu'il n'existe qu'une seule lignée européenne et que de la sélection doit être impliquée dans le maintien du cline de couleur (chapitre 1). Grâce à des simulations informatiques, nous avons démontré que l'ensemble de l'Europe de l'ouest a été recolonisé depuis la Péninsule Ibérique après les dernières glaciations et que le cline de couleur ne peut pas avoir évolué par des processus neutre durant cette colonisation (chapitre 2). Finalement, nous avons réévalué l'ensemble de l'histoire postglaciaire de l'espèce dans l'ouest Paléarctique (chapitre 3): l'ensemble des effraies du Paléarctique descendent d'effraie claire du Moyen-Orient qui ont colonisé la péninsule ibérique en passant par l'Afrique du nord. Après la fin de la dernière glaciation (il y a 20'000 ans), ces effraies claires ont colonisé l'Europe de l'ouest et ont évolués par sélection le phénotype roux (durant ou après la colonisation). Une part importante de la variation de couleur peut être expliquée par une mutation sur le gène MC1R qui est apparue durant ou juste après la colonisation. Cette vague de colonisation s'est poursuivie jusqu'en Grèce où ces effraies rousses ont rencontré dans une zone de contact secondaire des effraies claires (qui sont remontées en Grèce depuis le Moyen-Orient via le Bosphore). Nos analyses montrent que le flux de gènes entre effraies blanches et rousses est limité en Grèce, ce qui suggère qu'elles sont en passe de former deux espèces et ce qui montre que les effraies constituent un exemple naissant de spéciation en anneaux autour de la Méditerranée. L'histoire revisitée des effraies des clochers de l'ouest Paléarctique en fait un système modèle remarquable pour plusieurs aspects. C'est un exemple très claire de forte adaptation locale maintenue malgré un fort flux de gènes (différenciation forte de couleur et sur le gène MC1R malgré presque aucune structure neutre). Il offre également un très bon système pour étudier l'interaction entre colonisation et sélection, un thème ayant été remarquablement peu étudié malgré son importance. Et il offre finalement un cas très intéressant dans le « continuum de spéciation » et il serait très intéressant d'étudier plus en détail l'importance du flux de gènes entre les morphes de couleur en Grèce.

Mixed subtype of congenital mesoblastic nephroma with poor evolution: a case report and literature review

Abstract A male child born at 27 weeks, weighting 1305 g and presenting with a right-sided abdominal tumor. Computed tomography scan demonstrated the presence of a solid mass compressing the right kidney. Puncture biopsy revealed congenital mesoblastic nephroma. The patient underwent total right nephroureterectomy, and died on the second day after surgery.

Importance of amoebae as a tool to isolate amoeba-resisting microorganisms and for their ecology and evolution: the Chlamydia paradigm.

Free-living amoebae are distributed worldwide and are frequently in contact with humans and animals. As cysts, they can survive in very harsh conditions and resist biocides and most disinfection procedures. Several microorganisms, called amoeba-resisting microorganisms (ARMs), have evolved to survive and multiply within these protozoa. Among them are many important pathogens, such as Legionella and Mycobacteria, and also several newly discovered Chlamydia-related bacteria, such as Parachlamydia acanthamoebae, Estrella lausannensis, Simkania negevensis or Waddlia chondrophila whose pathogenic role towards human or animal is strongly suspected. Amoebae represent an evolutionary crib for their resistant microorganisms since they can exchange genetic material with other ARMs and develop virulence traits that will be further used to infect other professional phagocytes. Moreover, amoebae constitute an ideal tool to isolate strict intracellular microorganisms from complex microbiota, since they will feed on other fast-growing bacteria, such as coliforms potentially present in the investigated samples. The paradigm that ARMs are likely resistant to macrophages, another phagocytic cell, and that they are likely virulent towards humans and animals is only partially true. Indeed, we provide examples of the Chlamydiales order that challenge this assumption and suggest that the ability to multiply in protozoa does not strictly correlate with pathogenicity and that we should rather use the ability to replicate in multiple and diverse eukaryotic cells as an indirect marker of virulence towards mammals. Thus, cell-culture-based microbial culturomics should be used in the future to try to discover new pathogenic bacterial species.