L‘adaptation des bactéries à leur environnement résulte de régulations de l’expression génique pour optimiser leur physiologie aux conditions de culture. Le contrôle de la concentration des ARNm constitue l’une de ces régulations. Il dépend à la fois des variations de transcription et de dégradation des messagers. Si ces deux mécanismes sont bien étudiés à l’échelle moléculaire chez E. coli, leurs poids respectifs sur la régulation du niveau des transcrits à l’échelle du génome restent inconnus en raison de l’absence de données omiques relatives à la dégradation des ARNm lors de changements environnementaux. D’autre part, les paramètres déterminant la stabilité des messagers sont mal identifiés et n’ont jamais été hiérarchisés.Au cours de cette thèse, la stabilité de chacun des ARNm d’E. coli a été mesurée par la détermination du stabilome. Plus précisément, le temps de demi-vie de près de 70 % de tous les messagers a pu être déterminé de façon fiable pour quatre taux de croissance différents obtenus dans les mêmes conditions de culture à l’aide de chémostats. Pour la première fois, cette étude démontre qu’une croissance bactérienne plus rapide entraîne une augmentation globale de la dégradation des transcrits. L’intégration de ces données avec les données transcriptomiques montre que même si la transcription est le mécanisme principal de régulation du niveau des messagers, la dégradation exerce un effet inverse dans la plupart des cas. De plus, le rôle de la dégradation dans le contrôle de la concentration des ARNm s’accentue de façon significative avec l’augmentation du taux de croissance et affecte particulièrement les gènes impliqués dans le métabolisme carboné central. À partir des données de stabilité générées à différents taux de croissance, des approches de biologie intégrative ont permis d’identifier et de hiérarchiser les déterminants de la dégradation des ARNm. Ainsi, la concentration des messagers qui est le principal paramètre, mais aussi le biais de codon, la longueur de la séquence codante et la présence de certains motifs de séquence déterminent la stabilité d’un ARNm. Toutefois, si la hiérarchie des déterminants identifiés reste identique avec la variation du taux de croissance, la stabilité des ARNm de certaines catégories fonctionnelles en est dépendante. Cependant, d’autres déterminants du temps de demi-vie des messagers, en particulier à fort taux de croissance, restent encore à être identifiés. La protéine CsrA, appartenant au système Csr, est un exemple de régulateur post-transcriptionnel qui contrôle positivement ou négativement l’expression d’ARNm par divers mécanismes qui peuvent modifier leur stabilité. Toutefois, l’étendue de l’action de CsrA sur la stabilité des ARNm à l’échelle omique n’a jamais été étudiée. En comparant les stabilomes et transcriptomes d’une souche sauvage et d’une souche où l’activité de CsrA est diminuée, les effets indirects transcriptionnels de CsrA ont été mesurés et de nouveaux ARNm cibles de CsrA dont la stabilité est régulée par la protéine (en majorité stabilisés) ont été identifiés. De plus, la protéine CsrD, régulateur de la stabilité des ARN non codants CsrB/C, n’est pas impliquée dans la régulation de la stabilité des ARNm, mais agit sur la transcription de nombreux gènes indépendamment de son rôle au sein du système Csr. En conclusion, ces travaux ont permis de mieux appréhender les régulations de la stabilité des ARNm, en identifiant leurs déterminants et en caractérisant leur rôle et portée dans le contrôle de la concentration des messagers. Ils soulignent en particulier l’importance de ces régulations dans le processus d’adaptation bactérien / Bacterial adaptation to environment results from regulations of gene expression to optimize cell physiology to growth conditions. Control of mRNA concentration is one of those regulations. It depends on both variations of transcription and transcript degradation. Although these two mechanisms are well defined at the molecular level in E. coli, their respective impact on mRNA level regulation is still unknown at the genome scale because of a lack of omic data on mRNA stability during changing environment. Moreover, parameters determining messenger stability are not yet clearly identified and have never been ranked.During this PhD, the stability of each of the E. coli mRNAs was measured through stabilome determination. More precisely, the half-life of around 70 % of all messengers was reliably determined at four different growth rates obtained in the same growth conditions in chemostats. For the first time, this study demonstrated that increase of growth rate led to global increase of transcript degradation. Integration of these data with transcriptomic data showed that although transcription was the main mechanism which regulated mRNA level, messenger degradation exerted an opposite effect in most of the cases. The role of messenger degradation in the control of mRNA concentration was significantly accentuated with increasing growth rate and affected particularly genes involved in central carbon metabolism. Using mRNA stability data produced at different growth rates, integrative biology approaches allowed identification and ranking of the determinants of messenger stability. mRNA concentration which was the main parameter, but also codon bias, length of the coding sequence, sequence motifs contributed to transcript stability. However, although the hierarchy of determinants remained identical with variations of growth rate, the stability of mRNAs belonging to specific functional categories differed with the growth rate. Nevertheless, other determinants of messenger half-life, in particular at high growth rates still remain to be discovered. The CsrA protein, which belongs to the Csr system, is one example of a post-transcriptional regulator. CsrA positively or negatively controls expression of several mRNAs by mechanisms able to modify transcript stability. Nevertheless, the extent of CsrA effect on mRNA stability at the omic level has never been studied. By comparing stabilomes and transcriptomes of the wild type strain with a strain with reduced CsrA activity, the indirect transcriptional effects of CsrA were measured and new mRNAs whose stability was targeted by CsrA (mostly stabilized), were identified. Moreover, the CsrD protein, a regulator of CsrB/C small RNA stability, was not involved in mRNA stability regulation, but played a role in transcriptional regulation of many genes independently of its role in the Csr system. To conclude, this work provides a better understanding of the regulation of the mRNA stability. It identifies mRNA stability determinants and characterizes the role and extent of mRNA stability regulation in the control of messenger concentration. The study underlines the importance of this regulation in the process of bacterial adaptation

Communication over a wireless channel is a challenging task because of the inherent fading effects. Any wireless communication system employs some form of diversity improving techniques in order to improve the reliability of the channel. This thesis deals with efficient code design for two different spatial diversity techniques, viz, diversity by employing multiple antennas at the transmitter and/or the receiver, and diversity through cooperative commu- nication between users. In other words, this thesis deals with efficient code design for (1) multiple-input multiple-output (MIMO) channels, and (2) wireless relay channels. Codes for the MIMO channel are termed space-time (ST) codes and those for the relay channels are called distributed ST codes. The first part of the thesis focuses on ST code construction for MIMO fading channel with perfect channel state information (CSI) at the receiver, and no CSI at the transmitter. As a measure of performance we use the rate-diversity tradeoff and the Diversity-Multiplexing Gain (D-MG) Tradeoff, which are two different tradeoffs characterizing the tradeoff between the rate and the reliability achievable by any ST code. We provide two types of code constructions that are optimal with respect to the rate-diversity tradeoff; one is based on the rank-distance codes which are traditionally applied as codes for storage devices, and the second construction is based on a matrix representation of a cayley algebra. The second contribution in ST code constructions is related to codes with a certain nonvanishing determinant (NVD) property. Motivation for these constructions is a recent result on the necessary and sufficient conditions for an ST code to achieve the D-MG tradeoff. Explicit code constructions satisfying these conditions are provided for certain number of transmit antennas. The second part of the thesis focuses on distributed ST code construction for wireless relay channel. The transmission protocol follows a two-hop model wherein the source broadcasts a vector in the first hop and in the second hop the relays transmit a vector that is a transformation of the received vector by a relay-specific unitary transformation. While the source and relays do not have CSI, at the destination we assume two different scenarios (a) destina- tion with complete CSI (b) destination with only the relay-destination CSI. For both these scenarios, we derive a Chernoff bound on the pair-wise error probability and propose code design criteria. For the first case, we provide explicit construction of distributed ST codes with lower decoding complexity compared to codes based on some earlier system models. For the latter case, we propose a novel differential encoding and differential decoding technique and also provide explicit code constructions. At the heart of all these constructions is the cyclic division algebra (CDA) and its matrix representations. We translate the problem of code construction in each of the above scenarios to the problem of constructing CDAs satisfying certain properties. Explicit examples are provided to illustrate each of these constructions.

In many fields of science, engineering, and economics large amounts of data are stored and there is a need to analyze these data in order to extract information for various purposes. Data mining is a general concept involving different tools for performing this kind of analysis. The development of mathematical models and efficient algorithms is of key importance. In this thesis we discuss algorithms for the reduced rank regression problem and algorithms for the computation of the best multilinear rank approximation of tensors. The first two papers deal with the reduced rank regression problem, which is encountered in the field of state-space subspace system identification. More specifically the problem is \[ \min_{\rank(X) = k} \det (B - X A)(B - X A)\tp, \] where $A$ and $B$ are given matrices and we want to find $X$ under a certain rank condition that minimizes the determinant. This problem is not properly stated since it involves implicit assumptions on $A$ and $B$ so that $(B - X A)(B - X A)\tp$ is never singular. This deficiency of the determinant criterion is fixed by generalizing the minimization criterion to rank reduction and volume minimization of the objective matrix. The volume of a matrix is defined as the product of its nonzero singular values. We give an algorithm that solves the generalized problem and identify properties of the input and output signals causing a singular objective matrix. Classification problems occur in many applications. The task is to determine the label or class of an unknown object. The third paper concerns with classification of handwritten digits in the context of tensors or multidimensional data arrays. Tensor and multilinear algebra is an area that attracts more and more attention because of the multidimensional structure of the collected data in various applications. Two classification algorithms are given based on the higher order singular value decomposition (HOSVD). The main algorithm makes a data reduction using HOSVD of 98--99 \% prior the construction of the class models. The models are computed as a set of orthonormal bases spanning the dominant subspaces for the different classes. An unknown digit is expressed as a linear combination of the basis vectors. The resulting algorithm achieves 5\% in classification error with fairly low amount of computations. The remaining two papers discuss computational methods for the best multilinear rank approximation problem \[ \min_{\cB} \| \cA - \cB\| \] where $\cA$ is a given tensor and we seek the best low multilinear rank approximation tensor $\cB$. This is a generalization of the best low rank matrix approximation problem. It is well known that for matrices the solution is given by truncating the singular values in the singular value decomposition (SVD) of the matrix. But for tensors in general the truncated HOSVD does not give an optimal approximation. For example, a third order tensor $\cB \in \RR^{I \x J \x K}$ with rank$(\cB) = (r_1,r_2,r_3)$ can be written as the product \[ \cB = \tml{X,Y,Z}{\cC}, \qquad b_{ijk}=\sum_{\lambda,\mu,\nu} x_{i\lambda} y_{j\mu} z_{k\nu} c_{\lambda\mu\nu}, \] where $\cC \in \RR^{r_1 \x r_2 \x r_3}$ and $X \in \RR^{I \times r_1}$, $Y \in \RR^{J \times r_2}$, and $Z \in \RR^{K \times r_3}$ are matrices of full column rank. Since it is no restriction to assume that $X$, $Y$, and $Z$ have orthonormal columns and due to these constraints, the approximation problem can be considered as a nonlinear optimization problem defined on a product of Grassmann manifolds. We introduce novel techniques for multilinear algebraic manipulations enabling means for theoretical analysis and algorithmic implementation. These techniques are used to solve the approximation problem using Newton and Quasi-Newton methods specifically adapted to operate on products of Grassmann manifolds. The presented algorithms are suited for small, large and sparse problems and, when applied on difficult problems, they clearly outperform alternating least squares methods, which are standard in the field.

Submitted by Ana Valéria de Jesus Moura (anavaleria_131@hotmail.com) on 2018-05-30T15:33:16Z No. of bitstreams: 1 ANA CONCEIÇÃO BARBUDA SANCHES GUIMARÃES FERREIRA.pdf: 6225011 bytes, checksum: 14a0290c3aeb54a346421970e5a467ee (MD5) / Approved for entry into archive by Ana Valéria de Jesus Moura (anavaleria_131@hotmail.com) on 2018-05-30T15:34:13Z (GMT) No. of bitstreams: 1 ANA CONCEIÇÃO BARBUDA SANCHES GUIMARÃES FERREIRA.pdf: 6225011 bytes, checksum: 14a0290c3aeb54a346421970e5a467ee (MD5) / Made available in DSpace on 2018-05-30T15:34:13Z (GMT). No. of bitstreams: 1 ANA CONCEIÇÃO BARBUDA SANCHES GUIMARÃES FERREIRA.pdf: 6225011 bytes, checksum: 14a0290c3aeb54a346421970e5a467ee (MD5) / Com esta pesquisa, pretendeu-se demonstrar para o sistema de justiça brasileiro a importância de se adotar a Teoria da Transcendência dos Motivos Determinantes nas decisões proferidas pelo Supremo Tribunal Federal, no controle concentrado de Constitucionalidade. Isso se faz a partir da articulação com o Direito dos Animais e da análise de julgados da Magna Corte de Justiça sobre o tema da tutela de proteção aos animais não-humanos. As decisões definitivas de mérito proferidas pelo Supremo Tribunal Federal, nas ações diretas de inconstitucionalidade, produzem efeitos erga omnes e vinculante, retirando do ordenamento jurídico o ato normativo ou lei incompatível com a Constituição (art. 102, §2º da CF). Contudo, tais efeitos abrangem somente o dispositivo da sentença. O STF declarou a inconstitucionalidade da estadual Lei nº 15.299/2013 que regulamentava a atividade da “vaquejada” como prática desportiva e cultura, mas os limites objetivos desta declaração somente vincularam tão somente ao Estado do Ceará, uma vez que não são reconhecidos os efeitos transcendentais desta decisão. No caso em tela, o Direito Fundamental de Proteção ao Meio Ambiente (artigo 225 da Constituição Federal) sobrepõe-se aos valores culturais da atividade desportiva, diante da crueldade intrínseca aplicada aos animais na vaquejada. Este fundamento foi o motivo determinante para o deslinde de mérito da causa. Contudo, o STF não vem reconhecendo a extensão do efeito vinculante de que são dotadas suas decisões em controle concentrado de constitucionalidade. Argumenta-se sobre a fragilidade da configuração do STF como corte constitucional em razão especialmente das matérias variadas de sua competência e forma de constituição. Ao lado destes impasses, outro se insurge, relativamente a Emenda Constitucional 96/2017, que acresceu novo inciso ao art. 225, §1º, da Constituição Federal, no ensejo de não serem considerados cruéis as práticas desportivas que utilizem animais, desde que sejam manifestações culturais. Demonstra-se que a superação legislativa ofende direito fundamental, apresentando-se como inconstitucional, em razão da prescrição contida no artigo 60, § 4º, da CF. Examina-se, ainda, a importância da consolidação do microssistema de precedentes judiciais gestado pelo novo Código de Processo Civil, que oportuniza um diálogo entre as fontes contidas no Civil Law, Common Law, Stare Decisis, sinalizando que a aplicação pelo STF da Teoria da Transcendência dos motivos determinantes pode contribuir e promover a consolidação dos princípios da segurança e coerência jurídica, primados dos Direitos Fundamentais, no qual se insere o Brasil. / The present research demonstrates the importance for the Brazilian justice system in adopting the Theory of Transcendence of Determining Motives in the decisions handed down by the Federal Supreme Court, in the concentrated control of Constitutionality and it happens from the articulation with the Law of the Animals and the analysis of Judged by the Magna Court on the protection of non-human animals. The final decisions of merit rendered by the Federal Supreme Court in the direct actions of unconstitutionality produce erga omnes and binding effects, removing from the legal system the normative act or law incompatible with the Constitution (article 102, § 2 of the CF). However, such effects cover only the sentence device. The STF declared the unconstitutionality of state law number. 15,299 / 2013, which regulated the activity of the "vaquejada" as sports practice and culture, but the objective limits of this statement were only binding on the State of Ceará, because the transcendental effects of this decision are not recognized. In the present case, the Fundamental Right to protect the environment (Article 225 of the Federal Constitution) overlaps with the cultural values of sporting activity, given the intrinsic cruelty applied to animals in the “vaquejada”. This plea was the determining factor for the merits of the case, but the Supreme Court has not been acknowledging the extent of the binding effect of its decisions on concentrated constitutionality control. It argues about the fragility of the configuration of the STF as a constitutional court due in particular to the varied matters of its competence and form of constitution. Beside these impasses, another problem appears, regarding Constitutional Amendment 96/2017, which added a new subsection to art. 225, paragraph 1, of the Federal Constitution, in the event that sporting practices that use animals are not considered cruel, provided that they are cultural manifestations. It demonstrated that the overcoming of legislation offends fundamental right, presenting itself as unconstitutional, due to the prescription contained in article 60, § 4, of the CF. It also examines the importance of consolidating of the judicial precedents micro-system established by the new Code of Civil Procedure, which provides a dialogue between the sources contained in the Civil Law, Common Law, Stare Decisis, indicating that the STF’ s application of Transcendence of the determinant motives can contribute and promote the consolidation of the principles of security and legal coherence, primacy of Fundamental Rights, in which Brazil is inserted.

Submitted by Gabriel Campos Pérgola (gabrielpergola@gmail.com) on 2013-02-04T12:56:43Z No. of bitstreams: 1 DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) / Rejected by Suzinei Teles Garcia Garcia (suzinei.garcia@fgv.br), reason: Prezado Gabriel, Não recebemos os arquivo em PDF. Att. Suzi 3799-7876 on 2013-02-05T18:53:00Z (GMT) / Submitted by Gabriel Campos Pérgola (gabrielpergola@gmail.com) on 2013-02-05T19:00:17Z No. of bitstreams: 2 DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) / Approved for entry into archive by Suzinei Teles Garcia Garcia (suzinei.garcia@fgv.br) on 2013-02-05T19:07:12Z (GMT) No. of bitstreams: 2 DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) / Made available in DSpace on 2013-02-05T19:09:04Z (GMT). No. of bitstreams: 2 DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) DissertationGabrielPergola2013.pdf: 521205 bytes, checksum: 85369078a82b0d5cc02f8248961e9214 (MD5) Previous issue date: 23-01-13 / Portfolio insurance allows a manager to limit downside risk while allowing participation in upside markets. The purpose of this dissertation is to introduce a framework to portfolio insurance optimization from a hybrid frequentist-Bayesian approach. We obtain the joint distribution of regular returns from a frequentist statistical method, once the outliers have been identified and removed from the data sample. The joint distribution of extreme returns, in its turn, is modelled by a Bayesian network, whose topology reflects the events that can significantly impact the portfolio performance. Once we link the regular and extreme distributions of returns, we simulate future scenarios for the portfolio value. The insurance subportfolio is then optimized by the Differential Evolution algorithm. We show the framework in a step by step example for a long portfolio including stocks participating in the Bovespa Index (Ibovespa), using market data from 2008 to 2012. / Seguros de carteiras proporcionam aos gestores limitar o risco de downside sem renunciar a movimentos de upside. Nesta dissertação, propomos um arcabouço de otimização de seguro de carteira a partir de um modelo híbrido frequentista-Bayesiano com uso de derivativos. Obtemos a distribuição conjunta de retornos regulares através de uma abordagem estatística frequentista, uma vez removidos os outliers da amostra. A distribuição conjunta dos retornos extremos, por sua vez, é modelada através de Redes Bayesianas, cuja topologia contempla os eventos que o gestor considera crítico ao desempenho da carteira. Unindo as distribuições de retornos regulares e extremos, simulamos cenários futuros para a carteira. O seguro é, então, otimizado através do algoritmo Evolução Diferencial. Mostramos uma aplicação passo a passo para uma carteira comprada em ações do Ibovespa, utilizando dados de mercado entre 2008 e 2012.