Diss.--Paris. / Part of the Cornell Digital Library Math Collection.

Cette recherche se propose de revisiter l'histoire de l'autisme dans ses rapports avec la schizophrénie en interrogeant leur statut respectif dans la psychopathologie et dans la psychanalyse. Outre l'apport de cas de la littérature, j'ai utilisé l'outil clinique de la construction de cas, pour ordonner et commencer à théoriser les rencontres cliniques que j'ai pu faire. Ilhoa,Sacha, Milo et Louis guident les développements théoriques du chapitre axé sur la question du corps, de l'espace de surface à une contenance, de l'objet et de la jouissance pulsionnelle (orale, anale, scopique, invoquante) dans l'autisme de Kanner. Le travail de Jules, David et Lison illustre la difficulté du diagnostic dans la clinique entre schizophrénie autistique et autisme, où parfois seule la question des hallucinations permet de trancher. Je me suis ensuite appuyée sur le travail de Manu et Léon pour rendre compte du rapport au langage, à la pensée, au vivant, aux affects et à l'autre dans l'autisme de haut niveau et le syndrome d'Asperger. Puis sur le récit de Anna, Max et Gaël pour identifier le traitement réel que le schizophrène, qui a une défense mélancolique ou paranoïde, produit de la perte symbolique, de la division subjective. Ces rencontres m'ont appris que la singularité de ces sujets cache une forme spéciale de créativité pour construire un monde plus ordonné. Des modalités de lien à l'autre s'inventent, dans une dépendance n'impliquant pascependant les mêmes modalités de jouissance... Si cela ne voile pas la part intraitable du réel, un travail avec ces sujets est toujours possible, même s'ils ne se manifestent pas et ne parlent pas, même s'ils sont en errance ou dans un entre-deux... Ainsi, l'a-structure de l'autisme n'est pas assimilable au conformisme ou à la dé-structuration qu’entraîne la schizophrénie / This research proposes to revisit the history of autism in its relations with schizophrenia by querying their respective status in the psychopathology and psychoanalysis. In addition to providing case of literature, I used the tool in the construction of clinical cases, to order and begin to theorize the clinical encounters that I have done. Ilhoa, Sacha, Milo and Louis are used as guide for the theoretical developments of the chapter focusing on the question of the body, the space of a surface to capacity, the purpose and enjoyment instinctual (oral, anal, scopic, citing) in 'Kanner autism'. The work of Jules, David and Lison illustrates the difficulty to diagnose between schizophrenia and autism in the clinic, where sometimes only the question of sign and hallucinations enable us to decide. I have then used the work of Manu and Leon to account for the relation to language, to the thought, the living, the affects and the other in the high-functioning autism and Asperger syndrome. Then the story of Anna Max and Gael to identify the actual treatment that the schizophrenic, who has a melancholic or paranoid defence product of the symbolic loss, of the subjective division. These encounters have taught me that in the uniqueness of these individuals lies a special form of creativity to build a more ordered world. Schemes oflinks to the other are invented, which doesn't imply the same terms enjoyment by both parties… If this does not obscure the part of the intractable reality, working with these subjects is always possible, even if they do not come forward and do not speak, even if they are wandering or in an in-between state... Hence, autism astructure is not comparable to the conformism or the deconstruction brought about by schizophrenia

Thermus bacteria are of special interest because of their ability to live in high temperature environments. Their enzymes exhibit higher and stable activity in industry as compared to mesophilic or synthetic counterparts. Thermus bacteria are capable of reducing heavy metals which is essential in eradication of heavy metal pollution and controlling global warming. Genome rearrangements were investigated in Thermus species and the extent to which they affected the distribution of functionally related genes on the chromosome and its implication on the coherence of the metabolic network. The contribution of horizontal gene transfer to genome rearrangements and the shuffling of genes on the chromosome were analysed. Horizontally transferred genes were identified alongside their donors and recipients, their age and relative time of insertion. Metabolic networks were clustered and compared to determine the extent to which they were affected by rearrangements as a measure of evolutionary pressures experienced by organisms. Factors that enhance protein thermostability were analysed by determining dominant substitutions for amino acid residues and their properties. Protein thermostability was measured using the UNAFold algorithm. Amino acid substitutions were compared between less and highly thermophilic orthologous sequences in T. scotoductus SA-01 and T. thermophilus HB27 respectively. Protein structures were modelled for orthologs that met a defined selection criterion. Dominant amino acid substitutions were analysed in the structures to determine their locations. The contribution of dominant substitutions to energy changes in structures was analysed using FoldX program. Results revealed a uniform distribution of functionally related genes among thermophilic and mesophilic organisms. The contribution of horizontal gene transfer to genome rearrangements was found to be insignificant. Metabolic networks for Thermus species were poorly clustered in correlation with their optimum environmental growth temperatures. Non-polar, small and charged amino acids were found to significantly enhance thermostability. Higher occurrence of alanine substituted by serine and threonine; and arginine substituted by glutamine and lysine were observed to influence thermostability. Structural comparison showed that mutations were mostly located on the surfaces and helices of structures. The positions of mutations appeared to influence their energy contribution to the overall structure as measured by FoldX algorithm. / Thesis (PhD)--University of Pretoria, 2013. / gm2014 / Biochemistry / unrestricted

The study of gene families critically depends on the correct reconstruction of gene genealogies, as for instance in the case of transcription factor genes like Hox genes and Dlx gene families. Proteins belonging to the same family are likely to share some of the same protein interaction partners and may thus face a similar selective environment. This common selective environment can induce co-evolutionary pressures and thus can give rise to correlated rates and patterns of evolution among members of a gene family. In this study, we simulate the evolution of a family of sequences which share a set of interaction partners. Depending on the amount of sequence dedicated to protein–protein interaction and the relative rate parameters of sequence evolution three outcomes are possible: if the fraction of the sequence dedicated to interaction with common co-factors is low and the time since divergence is small, the trees based on sequence information tend to be correct. If the time since gene duplication is long two possible outcomes are observed in our simulations. If the rate of evolution of the interaction partner is small compared to the rate of evolution of the focal protein family, the reconstructed trees tend towards star phylogenies. As the rate of evolution of the interaction partner approaches that of the focal protein family the reconstructed phylogenies tend to be incorrectly resolved. We conclude that the genealogies of gene families can be hard to estimate, in particular if the proteins interact with a conserved set of binding partners, as is likely the case for transcription factors.

On sait que la matrice d'incidence associée à une substitution ne suffit pas pour déterminer complètement le système dynamique associé, même dans des cas très simples, il existe plusieurs substitutions associées à une même matrice car il existe de nombreux mots ayant le même abélianisé. Dans cette thèse, on étudie les points communs de deux lignes brisées associées à deux substitutions $sigma_1$ et $sigma_2$ irréductibles unimodulaires de type Pisot qui ont la même matrice d'incidence. On identifie les points communs de ces deux lignes brisées à partir d'un algorithme. On montre ainsi que l'intersection de ces deux lignes brisées est aussi une ligne brisée associée au point fixe d'une nouvelle substitution. On montre plus précisément que si $sigma_1$ vérifie la conjecture Pisot et $0$ est un point intérieur à son fractal de Rauzy alors ces points communs peuvent être engendrés par une substitution définie sur un alphabet appelé alphabet des paires équilibrées. Cette substitution est obtenue à partir d'un algorithme, l'algorithme des paires équilibrées. On obtient ainsi l'intersection des intérieurs des deux fractals de Rauzy. En prenant la clôture de cet ensemble on obtient un ensemble substitutif. La condition que $0$ est un point intérieur au fractal de Rauzy associé à la substitution $sigma_1$ nous permet de montrer que l'intersection des deux fractals de Rauzy est de mesure positive. Dans une deuxième partie du travail on s'intéresse à l'étude de la frontière du fractal de Rauzy. Le fractal de Rauzy est dit fractal mais c'est en fait sa frontière qui est fractale. / The matrix of a substitution is not sufficient to completely determine the dynamics associated with it, even in the simplest cases since there are many words with the same abelianization. In this paper we study the common points of the canonical broken lines associated with two different irreducible Pisot unimodular substitutions σ1 and σ2 having the same incidence matrix. We prove that if σ1 verifies the Pisot conjecture and 0 is an inner point to the Rauzy fractal associated with the substitution σ1 then these common points can be generated with a substitution on an alphabet of so-called balanced pairs, and we obtain in this way the intersection of the interior of two Rauzy fractals.

Orientador: Ali Messaoudi / Banca: Salvador Addas Zanata / Banca: Claudio Aguinaldo Buzzi / Resumo: Uma substituicão é uma aplicação de um conjunto nito A (alfabeto) ao conjunto das palavras nitas sobre A. Neste trabalho, estudaremos propriedades topológicas e métricas dos sistemas din^amicos associados a substituicões. Em particular, mostraremos que, para uma classe de substituicões, o sistema dinâmico associado é minimal e ergódico. / Abstract: A substitution is a map from a nite set A (alphabet) to the set of nite words whose letters belong to A. In this work, we study some topological and metrical properties of the dynamical system associated to a substitution. In particular, we prove that for a class of substitutions, the associated dynamical system is minimal and ergodic. / Mestre

Recent years have witnessed the integration of theoretical advances in population genetics with large-scale analyses of complete genomes. As a result, a growing number of studies suggest the frequent occurrence of deleterious as well as adaptive mutations. Given the evidence for the widespread occurrence of selection, the finite sizes of natural populations, and the limited recombination in every genome, mutations under selection are expected to alter the fate of genetically linked mutations. The consequences of this non-independent behavior of mutations can be described by the Hill-Robertson effect in terms of the reduction in the effective population size (Ne). Reduction in the effective population size has two effects: 1) a reduction in levels of genetic variation and 2) a reduction in the effectiveness of selection that is manifested in an increased probability of fixation of deleterious mutations and a reduced probability of fixation of advantageous mutations. Changes in Ne that have previously been frequently associated with changes in recombination rate can also occur locally, in association with changes in the number of sites under selection even when the recombination rate remains uniform. The main objective of the work presented in this thesis is to investigate these local effects of the non-independent behavior of mutations on patterns of polymorphism and divergence in Drosophila using computer simulation and experimental approaches. A computer simulation approach is developed to investigate the local consequences of linked selection on estimates of selection and the proportion of adaptive substitutions using the McDonald-Kreitman framework. The results suggest that even a high level of recombination is unlikely to remove all the effects of linked selection. Ignoring these local linkage effects leads to misleading estimates of the intensity of selection and the proportion of adaptive substitutions. Two predictions of the Hill-Robertson effect were tested empirically by examining patterns of polymorphism and divergence combined with codon bias estimates in genes with and without introns: 1) the effectiveness of selection and polymorphism levels are expected to be reduced in the center of the long coding sequence of genes without introns (the intragenic Hill-Robertson effect), and 2) introns are expected to function as modifiers of recombination thereby increasing the effectiveness of selection in the central region of the coding sequence of genes containing centrally located introns. The evidence from divergence and codon bias patterns in genes with a long coding sequence supports the presence of the intragenic Hill-Robertson effect. However, polymorphism levels do not show the expected decrease in the center of the coding sequence. With regard to the second prediction, results indicate that intron presence does not increase the effectiveness of selection at synonymous sites in the set of investigated genes. Rather, intron presence is associated with increased levels of adaptation at nonsynonymous sites. Further investigations are necessary to clarify the role of introns in mediating the increase in adaptation.

No / We investigated the brightness (i.e., perceived luminance) of isolated L- and M-cone pulses to seek a perceptual correlate of our previous reports that M-on electroretinograms resemble L-off responses, implying the operation of post-receptoral opponent processing. Using triple silent substitutions, cone increments were generated in a 4-primary ganzfeld, masked by random positive or negative luminance bias. The results show that M-cone increments decrease in brightness, while L-cone increments increase. These differences became smaller as field size reduced; this was not eccentricity or area dependent. We speculate about early retinal input into brightness perception.

L’étude de l’adsorption et de la mobilité des ions dans les argiles est importante pour mieux appréhender de nombreux processus géochimiques et environnementaux, de même que pour prédire le comportement des radionucléides dans les conditions du stockage géologique. A cause de leurs tailles très petites (< 2μm), il n’est pas toujours évident d’étudier les argiles à l’aide des méthodes et techniques expérimentales existantes. L’une des alternatives à ce problème consiste alors à utiliser la modélisation moléculaire pour les étudier. En plus de leurs tailles fines, les argiles présentent également des structures complexes, qui peuvent survenir en raison de la multiplicité de possibilités de distributions et d’arrangements des substitutions isomorphiques dans leurs couches. Il a été clairement démontré qu’il existe une corrélation entre la distribution des substitutions dans les couches des argiles et les propriétés de ces dernières. En revanche, ceci reste à démontrer en ce qui concerne l’arrangement de ces substitutions dans les couches de l’argile. Dans ce travail, la modélisation moléculaire est utilisée pour déterminer et comparer les propriétés d’hydratation, ainsi que la structure et la mobilité des ions (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺, Ni²⁺, UO₂²⁺) et de l’eau dans l’espace interfoliaire de trois modèles de montmorillonite, différents entre eux par l’arrangement des substitutions isomorphiques dans les couches de l’argile.L’adsorption et la diffusion des cations cités plus haut et de l’eau sont également étudiées à la surface de la montmorillonite et les résultats sont comparés à ceux obtenus dans l’espace interfoliaire à 298 K et à 363 K. Les résultats obtenus dans ce travail s’accordent bien avec les observations expérimentales, et font ressortir une corrélation plus ou moins importante entre le modèle d’argile utilisé et le type de propriété calculée. Cette corrélation dépend également de la nature du cation présent dans la structure de la montmorillonite et de sa teneur en eau. / The study of adsorption and ion mobility in clay minerals is important for a better understanding of many geochemical and environmental processes, as well as to predict the behavior of radionuclides in geological storage conditions. Because of their very small size (<2μm), it is not always easy to study clays by using the existing experimental methods and techniques. One alternative to this issue is to use computational molecular modeling to carry out clay studies. In addition to their tiny size, clays minerals also have complex structures, which can appear due to various possibilities in the distribution and arrangement of isomorphic substitutions in their layers. It has been clearly demonstrated that there is a strong correlation between the distribution of substitutions in the clay layers and their properties. However, this remains to be shown regarding the arrangement of the substitutions in the layers of the clay. In this work, computational molecular modeling techniques are used to determine and compare the hydration properties, as well as the structure and mobility of ions (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺, Ni²⁺,UO₂²⁺) and water in the interlayer space of the three models of montmorillonite, that differ from each other by the arrangement of isomorphic substitutions in the clay layers.The adsorption and diffusion of the previously listed cations and water are also studied on the surface of montmorillonite clay and the results are compared to those obtained in the interlayer space both at 298 K and at 363 K. The data generated in this work agree well with experimental observations, and show a more or less significant correlation between the clay model used and the type of property calculated.

Nous étudions dans ce mémoire les propriétés des ensembles de pavages engendrés par des jeux de tuiles de Wang exhibant une ou plusieurs directions de déterminisme local, en accordant une importance toute particulière aux jeux déterministes dans les quatre directions diagonales simultanément, dits 4-way déterministes. Après avoir proposé une construction alternative d’un jeu de tuiles apériodique 4-way déterministe, nous étudions plusieurs problèmes de décision sur ces objets et complétons en particulier le résultat d’indécidabilité du problème du pavage dans le cadre 4-way déterministe établi par Lukkarila en montrant l’indécidabilité du problème du pavage périodique 4-way déterministe. Nous montrons également que des familles complexes de coloriages du plan telles que celles engendrées par les substitutions restent sofiques dans un cadre 4-way déterministe. Nous proposons une bi-déterminisation des constructions de jeux de tuiles point-fixe de Durand, Romashchenko et Shen et en tirons quelques premières applications. Enfin, nous considérons l’opportunité d’élargir le rayon de la règle locale de déterminisme afin de limiter les directions d’expansivité et ainsi de permettre la construction localement déterministe de systèmes de particules et collisions non triviaux. Nous introduisons un nouveau modèle syntaxique commode afin de travailler à rayon deux et revisitons des problématiques de Lukkarila dans ce cadre. / In this thesis, we study some properties of the sets of tilings generated by Wang tilesets that exhibit one or more directions of local determinism, focusing in particular on tilesets that are simultaneously deterministic in the four diagonal directions, referred to as 4-way deterministic. After having exposed an alternative construction of a 4-way deterministic aperiodic tileset, we study several decision problems on these objects and complete in particular Lukkarila’s result of undecidability of the Domino Problem in the 4-way deterministic setting proving the undecidability of the 4-way deterministic periodic Domino Problem. We also prove that some complex families of colorings of the plane such that those generated by substitutions remain sofic in the 4-way deterministic setting. We propose a bi-determinization of the constructions by Durand, Romashchenko and Shen of fixed-point tilesets and give some first applications. Finally, we investigate the idea of extending the radius of the local rule of determinism in order to reduce the set of directions of expansiveness and thus allow the local realization of non-trivial particles and collisions systems. We introduce a new and convenient syntactic model to deal with radius two and revisit some of Lukkarila’s problems in this setting.