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Sinorhizobium meliloti is a model bacterium for the study of symbiotic nitrogen fixation (SNF). It infects the roots of alfalfa as well as some other legumes and differentiates into N2-fixing bacteroids within the plant cells of specialized nodule organs. To understand genes essential for SNF and, in the longer term, to facilitate the manipulation of this SNF process for agricultural purposes, it is highly desirable to construct the minimal genome for SNF in this organism. S. meliloti harbors two replicons required for SNF, a 1.7-Mb chromid (pSymB) and a 1.4-Mb megaplasmid (pSymA). A previous deletion analysis revealed that only four gene regions, accounting for <12% of the total sequences of pSymA and pSymB that, were essential for SNF. In the first part of the thesis, I report the cloning of these two pSymA SNF-essential regions on a plasmid (pTH3255) in Escherichia coli, and the integration of this plasmid into the genome of a ∆pSymA S. meliloti derivative strain (the strain was named as RmP4291 after integration). Plant root dry weight and nitrogenase-catalyzed acetylene reduction assays were carried out on RmP4291 with four host plants, including Medicago sativa, Medicago truncatula, Melilotus alba and Melilotus officinalis. Nodule kinetic assays were also performed on RmP4291 and RmP110(wt). The results showed that the SNF-essential regions from pSymA were sufficient to restore the symbiotic capabilities to the ∆pSymA derivative strain with all the host plants tested, except a significant reduction (~40%) in SNF by RmP4291 was noticed on M. officinalis compared to that by wildtype S. meliloti. A higher alfalfa nodulation efficiency of RmP4291 compared to that of wildtype RmP110 was also discovered. In the second part of the thesis, a histochemical staining method for S. meliloti nodules was developed by integrating the marker genes gusA (β-glucuronidase) and celB (β-glucosidase) into the S. meliloti genome. This staining method was found to be useful in the study of nodule competitiveness. A nodule competition assay was carried out between RmP4291 and RmP110 using the new staining method. RmP4291 was found to be significantly reduced in nodulation competitiveness compared to wildtype S. meliloti. The development of the histochemical staining method for S. meliloti nodules will accelerate the identification of genes required for nodule competitiveness in the organism, which will be of crucial importance to the construction of the minimal genome strains with high SNF efficiency. / Thesis / Master of Science (MSc) / Nitrogen is one of the critical elements for life. Biological nitrogen fixation plays a crucial role in providing fixed nitrogen for the ecosystem on Earth. Our Laboratory has endeavored to establish a minimal symbiotic genome in Sinorhizobium meliloti, a model nitrogen fixing bacterium which forms symbiosis with certain kinds of legumes. Building this minimal symbiotic genome will improve our understanding of the symbiotic nitrogen fixation process in S. meliloti at gene level. It may also help in eventually introducing a nitrogen fixation system into other organisms. In this study, the minimal symbiotic genome of the pSymA replicon in S. meliloti was constructed. In addition, a staining method to detect specific S. meliloti strains in nodules was established. This method is potentially useful in finding genes related to nodule competitiveness, and these are potentially important for augmenting the genes that constitute the minimal symbiotic genome.

Background: Canine hypothyroidism is thought to cause abnormalities in glucose homeostasis, but the effect on glucose tolerance and insulin sensitivity has not been determined to date. Hypothesis/Objectives: The purpose of the study was to investigate whether hypothyroidism has an effect on glucose tolerance and insulin sensitivity in dogs. We hypothesized that hypothyroidism causes insulin resistance. Animals: Sixteen euthyroid bitches were randomly selected and allocated into two groups. In 8 dogs, hypothyroidism was induced by administration of 1 mCi/kg I-131. Experiments were performed on non-anesthetized, fasted dogs in anestrous approximately 12 months after hypothyroidism was induced. Methods: The insulin-modified frequently sampled intravenous glucose tolerance test (FSIGT) and minimal model analysis were used to determine basal insulin and glucose concentrations, acute insulin response to glucose (AIRg), insulin sensitivity (SI), glucose effectiveness (SG) and the disposition index (DI). Results: In the hypothyroid group, basal glucose concentrations were mildly decreased (P = 0.0079), whereas basal insulin was increased (P = 0.019). Insulin sensitivity was reduced in the hypothyroid group (P<0.001), whereas AIRg was higher (P=0.01). Other parameters were not different between groups. Conclusions/Clinical Importance: Hypothyroidism negatively affects glucose homeostasis by inducing insulin resistance. In hypothyroid dogs, the disposition index (insulin sensitivity x insulin secretion) remained unchanged due to a compensatory increase in insulin secretion, thereby maintaining glucose tolerance. In cases with impaired insulin secretion, such as canine diabetes mellitus, concurrent hypothyroidism can have important clinical implications in the successful management of the disease. / Master of Science

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The dissertation introduces Sphere Support Vector Machines (SphereSVM) and Minimal Norm Support Vector Machines (MNSVM) as the new fast classification algorithms that use geometrical properties of the underlying classification problems to efficiently obtain models describing training data. SphereSVM is based on combining minimal enclosing ball approach, state of the art nearest point problem solvers and probabilistic techniques. The blending of the three speeds up the training phase of SVMs significantly and reaches similar (i.e., practically the same) accuracy as the other classification models over several big and large real data sets within the strict validation frame of a double (nested) cross-validation (CV). MNSVM is further simplification of SphereSVM algorithm. Here, relatively complex classification task was converted into one of the simplest geometrical problems -- minimal norm problem. This resulted in additional speedup compared to SphereSVM. The results shown are promoting both SphereSVM and MNSVM as outstanding alternatives for handling large and ultra-large datasets in a reasonable time without switching to various parallelization schemes for SVMs algorithms proposed recently. The variants of both algorithms, which work without explicit bias term, are also presented. In addition, other techniques aiming to improve the time efficiency are discussed (such as over-relaxation and improved support vector selection scheme). Finally, the accuracy and performance of all these modifications are carefully analyzed and results based on nested cross-validation procedure are shown.

O objetivo do trabalho é apresentar alguns resultados acerca de anéis de grupos e aplicações, segundo o que foi estudado em livros e artigos sobre o assunto. Inicialmente, apresentaremos alguns fatos básicos sobre anéis de grupos, que podem ser encontrados em [5], e em seguida, apresentaremos os resultados principais, mais recentes, que foram estudados em dois artigos diferentes. No primeiro artigo [4], apresentou-se uma forma de calcular o número de componentes simples de certas álgebras de grupos abelianos finitos, bem como também foi apresentada uma forma de calcular geradores idempotentes de códigos abelianos minimais, suas dimensões e seus pesos. No segundo artigo [2], encontra-se uma descrição feita dos idempotentes centrais primitivos da álgebra de grupo racional de grupos nilpotentes finitos. / Our goal in this project is to present some results about group rings and its applications, as presented in books and articles about this subject. First of all we are going to establish some basic fact about group rings, which can be found mainly in [5], and then we will present the main results, which are more recent, and have been studied in two different articles. In [4], the authors presented a way of evaluating the number of simple components of some finite group algebras, as well presented a way of evaluating idempotent generators of some minimal abelian codes, their dimension and their weights. In [2] there is a complete description of all the primitive central idempotents of the rational group algebra of finite nilpotent groups.

Cette thèse se concentre sur la commande optimale des systèmes de complémentarité linéaire (notés LCS). Les LCS sont des systèmes dynamiques définis par des équations différentielles algébriques (ÉDA), où une des variables est définie par un problème de complémentarité linéaire.Ces systèmes se retrouvent dans la modélisation de nombreux phénomènes, tels que les équilibres dynamiques de Nash, les systèmes dynamiques hybrides ou encore la modélisation de circuits électriques. Les propriétés des solutions à ces ÉDA dépendent essentiellement de propriétés que doit vérifier la matrice D présente dans la complémentarité.Ces contraintes de complémentarité posent des problèmes à deux niveaux. Premièrement, l’analyse de ces systèmes dynamiques font souvent appel à des outils pointus, et leurs études laissent encore des questions non résolues. Deuxièmement, la commande optimale pour ces systèmes pose des soucis à cause d’une part de présence éventuelle de l’état dans les contraintes, et d’autre part une violation assurée des qualifications des contraintes qui sont une hypothèse récurrente des problèmes d’optimisation.La recherche de ce manuscrit se concentre sur la commande optimale de ces systèmes. On s’intéresse principalement à la commande quadratique (minimisation d’une fonctionnelle quadratique en l’état et la commande), et à la commande temps minimal. Les résultats se concentrent sur deux pans: d’un côté, on opère une approche analytique du problème afin de trouver des conditions nécessaires d’optimalité (si possible, on démontre qu’elles sont suffisantes) ; dans un deuxième temps, une approche numérique est effectuée, avec le soucis d’obtenir des résultats numériques précis de manière rapide. / This thesis focuses on the optimal control of Linear Complementarity Systems (LCS). LCS are dynamical systems defined through Differential Algebraic Equations (DAE), where one of the variable is defined by a Linear Complementarity Problem.These systems can be found in the modeling of various phenomena, as Nash equilibria, hybrid dynamical systems or modeling of electrical circuits. Properties of the solution to these DAE essentially depend on properties that the matrix D in the complementarity must meet. These complementarity constraints induce two different challenges. First, the analysis of these dynamical systems often use state of the art tools, and their study still has some unansweredquestions. Second, the optimal control of these systems causes troubles due to on one hand the presence of the state in the constraints, on the other hand the violation of Constraint Qualifications, that are a recurring hypothesis for optimisation problems.The research presented in this manuscript focuses on the optimal control of these systems. We mainly focus on the quadratic optimal control problem (minimisation of a quadratic functional involving the state and the control), and the minimal time control. The results present two different aspects: first, we start with an analytical approach in order to find necessary conditions of optimality (if possible, these conditions are proved to be sufficient); secondly, a numerical approach is tackled, with the aim of getting precise results with a reduced computational time.

O objetivo do trabalho é apresentar alguns resultados acerca de anéis de grupos e aplicações, segundo o que foi estudado em livros e artigos sobre o assunto. Inicialmente, apresentaremos alguns fatos básicos sobre anéis de grupos, que podem ser encontrados em [5], e em seguida, apresentaremos os resultados principais, mais recentes, que foram estudados em dois artigos diferentes. No primeiro artigo [4], apresentou-se uma forma de calcular o número de componentes simples de certas álgebras de grupos abelianos finitos, bem como também foi apresentada uma forma de calcular geradores idempotentes de códigos abelianos minimais, suas dimensões e seus pesos. No segundo artigo [2], encontra-se uma descrição feita dos idempotentes centrais primitivos da álgebra de grupo racional de grupos nilpotentes finitos. / Our goal in this project is to present some results about group rings and its applications, as presented in books and articles about this subject. First of all we are going to establish some basic fact about group rings, which can be found mainly in [5], and then we will present the main results, which are more recent, and have been studied in two different articles. In [4], the authors presented a way of evaluating the number of simple components of some finite group algebras, as well presented a way of evaluating idempotent generators of some minimal abelian codes, their dimension and their weights. In [2] there is a complete description of all the primitive central idempotents of the rational group algebra of finite nilpotent groups.

The aim of this dissertation lies in establishing an o-minimal de Rham cohomology theory for smooth abstract-definable manifolds in an o-minimal expansion of the real field which admits smooth cell decomposition and defines the exponential function, by following the classical de Rham cohomology. We can specify the o-minimal cohomology groups and attain some properties as the existence of Mayer-Vietoris sequence and the invariance under smooth abstract-definable diffeomorphisms. However, in order to obtain the invariance of our o-minimal cohomology under abstract-definable homotopy we must, working in a tame context that defines sufficiently many primitives, assume the validity of a statement related to Bröcker\'s problem. / O objetivo desta tese reside em estabelecer uma cohomologia de De Rham o-minimal para variedades definíveis abstratas lisas em uma expansão o-minimal do corpo ordenado dos reais, a qual admite decomposição celular lisa e define a função exponencial, seguindo a cohomologia de De Rham clássica. Além de especificarmos os grupos da cohomologia de Rham o-minimal, obtemos algumas propriedades, como a existência da sequência de Mayer-Vietoris e a invariância sob difeomorfismos definíveis abstratos lisos. Todavia, a fim de lograrmos a invariância de nossa cohomologia o-minimal sob homotopia definível abstrata devemos, além de trabalhar num contexto moderado no qual muitas primitivas são definidas, assumir a validade de uma asserção relacionada ao problema de Bröcker.