La donnée de séquences nucléotidiques permet d'inférer des arbres phylogénétiques, ou phylogénies, qui décrivent leur lien de parenté au cours de l'évolution. Associer à ces séquences leur date de prélèvement ou leur pays de collecte, permet d'inférer la localisation temporelle ou spatiale de leurs ancêtres communs. Ces données et procédures sont très utilisées pour les séquences de virus et, notamment, celles du virus de l'immunodéficience humaine (VIH), afin d'en retracer l'histoire épidémique à la surface du globe et au cours du temps. L'utilisation de séquences échantillonnées à des moments différents (ou hétérochrones) sert aussi à estimer leur taux de substitution, qui caractérise la vitesse à laquelle elles évoluent.Les méthodes les plus couramment utilisées pour ces différentes tâches sont précises, mais lourdes en temps de calcul car basées sur des modèles complexes, et ne peuvent traiter que quelques centaines de séquences. Devant le nombre croissant de séquences disponibles dans les bases de données, souvent plusieurs milliers pour une étude donnée, le développement de méthodes rapides et efficaces devient indispensable. Nous présentons une méthode de distances, Ultrametric Least Squares, basée sur le principe des moindres carrés, souvent utilisé en phylogénie, qui permet d'estimer le taux de substitution d'un ensemble de séquences hétérochrones, dont on déduit ensuite facilement les dates des spéciations ancestrales. Nous montrons que le critère à optimiser est parabolique par morceaux et proposons un algorithme efficace pour trouver l'optimum global.L'utilisation de séquences échantillonnées en des lieux différents permet aussi de retracer les chaînes de transmission d'une épidémie. Dans ce cadre, nous utilisons la totalité des séquences disponibles (~3 500) du sous-type C du VIH-1 (VIH de type 1), responsable de près de 50% des infections mondiales au VIH-1, pour estimer ses principaux flux migratoires à l'échelle mondiale, ainsi que son origine géographique. Des outils novateurs, basés sur le principe de parcimonie combiné avec différents critères statistiques, sont utilisés afin de synthétiser et interpréter l'information contenue dans une grande phylogénie représentant l'ensemble des séquences étudiées. Enfin, l'origine géographique et temporelle de ce variant (VIH-1 C) au Sénégal est précisément explorée lors d'une seconde étude, portant notamment sur les hommes ayant des rapports sexuels avec des hommes. / Nucleotide sequences data enable the inference of phylogenetic trees, or phylogenies, describing their evolutionary re-lationships during evolution. Combining these sequences with their sampling date or country of origin, allows inferring the temporal or spatial localization of their common ancestors. These data and methods are widely used with viral sequences, and particularly with human immunodeficiency virus (HIV), to trace the viral epidemic history over time and throughout the globe. Using sequences sampled at different points in time (or heterochronous) is also a mean to estimate their substitution rate, which characterizes the speed of evolution. The most commonly used methods to achieve these tasks are accurate, but are computationally heavy since they are based on complex models, and can only handle few hundreds of sequences. With an increasing number of sequences avail-able in the databases, often several thousand for a given study, the development of fast and accurate methods becomes essential. Here, we present a new distance-based method, named Ultrametric Least Squares, which is based on the princi-ple of least squares (very popular in phylogenetics) to estimate the substitution rate of a set of heterochronous sequences and the dates of their most recent common ancestors. We demonstrate that the criterion to be optimized is piecewise parabolic, and provide an efficient algorithm to find the global minimum.Using sequences sampled at different locations also helps to trace transmission chains of an epidemic. In this respect, we used all available sequences (~3,500) of HIV-1 subtype C, responsible for nearly 50% of global HIV-1 infections, to estimate its major migratory flows on a worldwide scale and its geographic origin. Innovative tools, based on the principle of parsimony, combined with several statistical criteria were used to synthesize and interpret information in a large phylogeny representing all the studied sequences. Finally, the temporal and geographical origins of the HIV-1 subtype C in Senegal were further explored and more specifically for men who have sex with men.

Thesis submitted in fulfilment of the requirements for the degree Master of Technology Chemistry in the Faculty of (Science) Supervisor: Professor T.N. van der Walt Bellville campus Date submitted: October 2011 / It is important to quantify polymeric components in a coating because they greatly influence the performance of a coating. The difficulty associated with analysis of polymers by Fourier transform infrared (FTIR) analysis’s is that colinearities arise from similar or overlapping spectral features. A quantitative FTIR method with attenuated total reflectance coupled to multivariate/ chemometric analysis is presented. It allows for simultaneous quantification of 3 polymeric components; a rheology modifier, organic opacifier and styrene acrylic binder, with no prior extraction or separation from the paint. The factor based methods partial least squares (PLS) and principle component regression (PCR) permit colinearities by decomposing the spectral data into smaller matrices with principle scores and loading vectors. For model building spectral information from calibrators and validation samples at different analysis regions were incorporated. PCR and PLS were used to inspect the variation within the sample set. The PLS algorithms were found to predict the polymeric components the best. The concentrations of the polymeric components in a coating were predicted with the calibration model. Three PLS models each with different analysis regions yielded a coefficient of correlation R2 close to 1 for each of the components. The root mean square error of calibration (RMSEC) and root mean square error of prediction (RMSEP) was less than 5%. The best out-put was obtained where spectral features of water was included (Trial 3). The prediction residual values for the three models ranged from 2 to -2 and 10 to -10. The method allows paint samples to be analysed in pure form and opens many opportunities for other coating components to be analysed in the same way.

Este trabalho aborda o problema de controle ótimo por modos deslizantes via função penalidade para sistemas de tempo discreto. Para resolver este problema será desenvolvido uma estrutura matricial alternativa baseada no problema de mínimos quadrados ponderados e funções penalidade. A partir desta nova formulação é possível obter a lei de controle ótimo por modos deslizantes, as equações de Riccati e a matriz do ganho de realimentação através desta estrutura matricial alternativa. A motivação para propormos essa nova abordagem é mostrar que é possível obter uma solução alternativa para o problema clássico de controle ótimo por modos deslizantes. / This work introduces a penalty function approach to deal with the optimal sliding mode control problem for discrete-time systems. To solve this problem an alternative array structure based on the problem of weighted least squares penalty function will be developed. Using this alternative matrix structure, the optimal sliding mode control law of, the matrix Riccati equations and feedback gain were obtained. The motivation of this new approach is to show that it is possible to obtain an alternative solution to the classic problem of optimal sliding mode control.

Análise cinética diferencial explora diferenças em taxas reacionais entre os analitos e um sistema reacional comum; etapas de separação prévia dos analitos podem então ser prescindidas. Sistemas de análise por injeção em fluxo (FIA) se afiguram como uma ferramenta importante para métodos envolvendo essa estratégia, pois permitem um controle preciso da dispersão de reagentes / amostras e da temporização. O objetivo deste trabalho foi então explorar estes dois aspectos favoráveis visando a determinação simultânea de cobre e de níquel, a partir de suas reações com o reagente cromogênico 5-Br-PADAP. Três alíquotas de amostra eram simultaneamente inseridas, por meio de um injetor proporcional, no fluxo transportador reagente (5-Br-PADAP 75 mg L-1 + sistema tampão 0,5 mol L-1 em ácido acético / acetato, pH 4,7) de um sistema FIA em linha única. Durante o transporte em direção ao detector, as zonas estabelecidas se coalesciam, originando uma zona complexa que era monitorada a 562 nm. Os valores locais máximos e mínimos da função concentração / tempo obtida eram considerados para calibração multivariada utilizando a ferramenta quimiométrica PLS-2 (partial least squares - 2). A concentração do reagente, a capacidade tampão, a temperatura, a vazão, os comprimentos do percurso analítico e das alças de amostragem, bem como a distância inicial entre as zonas de amostra estabelecidas foram avaliados para construção dos modelos matemáticos. Estes foram criados a partir de 24 soluções-padrão mistas de Cu2+ e Ni2+ (0,00-1,60 mg L-1 em HNO3 a 0,1% v/v). Duas variáveis latentes foram suficientes para capturar > 98 % das variâncias inerentes ao conjunto de dados e erros médios das previsões (RMSEP) foram estimados em 0,025 e 0,071 mg L-1 para Cu e Ni, salientando a boa precisão do modelo de calibração. O sistema proposto apresenta boas figuras de mérito: fisicamente estável, quando mantido em operação por quatro horas ininterruptas, consumo de 314 \'mü\'g 5-Br-PADAP por amostra, frequência analítica de 33 amostras por hora (165 dados, 66 determinações) e erros nas leituras em sinais de absorbância tipicamente < 5%. Entretanto, verificou-se a inexatidão das previsões efetuadas pelo modelo proposto, quando comparadas aos resultados obtidos por ICP OES. A partir deste fato, tornam-se necessários maiores estudos referentes a este tipo de matriz, bem como de técnicas de mascaramento dos possíveis interferentes presentes / Differential kinetic analysis exploits the differences in reaction rates between the analytes and a common reactant system; prior steps of analyte separation can then be waived. Flow-injection systems (FIA) are considered as an important tool for methods involving such a strategy because they allow precise control of sample / reagent dispersion and timing. The aim of this work was then to exploit these two favorable aspects for the simultaneous determination of copper and nickel using the 5-Br-PADAP chromogenic reagent. Three sample aliquots were simultaneously inserted by means of a proportional injector into reagent carrier stream (75 mg L-1 5-Br-PADAP + 0.5 mol L-1 acetic acid / acetate, pH 4.7) of a single-line FIA system. During transport towards detection, the established zones coalesce themselves, resulting in a complex zone that was monitored at 562 nm. The local maximum and minimum values of the concentration / time obtained function were considered for multivariate calibration using the PLS-2 (partial least squares - 2) chemometric tool. The reagent concentration, buffering capacity, temperature, flow rate and lengths of the analytical path, sampling loops and initial distance between plugs were established and evaluated for the construction of mathematical models. To this end, 24 Cu2+ and Ni2+ (0.00 - 1.60 mg L-1, also 0.1% v/v HNO3) mixed standard solutions were used. Two latent variables were enough to capture > 98% of the variance inherent in the data set and average prediction errors (RMSEP) were estimated as 0.025 and 0.071 mg L-1 for Cu and Ni, emphasizing the good precision the calibration model. The proposed system presents good figures of merit: physical stability when kept in operation for four uninterrupted hours, consumption of 314 \'mü\'g 5-Br-PADAP per sample, sample throughput of 33 h-1 (165 data, 66 determinations) and error readings in absorbance signals typically <5%. However, inaccuracy of the predictions made by the proposed model when compared to results obtained by ICP OES was noted. Thus, further studies involving this type of matrix, as well as masking techniques of potential interferences present, are recommended

Esta tese apresenta novos algoritmos que resolvem problemas de estimativas filtrada, suavizadora e preditora para sistemas singulares no tempo discreto usando apenas argumentos determinísticos. Cada capítulo aborda inicialmente as estimativas para o sistema nominal e em seguida, as versões robustas para o sistema com incertezas limitadas. Os resultados encontrados podem ser aplicados tanto em sistemas invariantes como variantes no tempo discreto, utilizando a mesma estrutura do filtro de Kalman. Nos últimos anos, uma quantidade significativa de trabalhos envolvendo estimativas singulares foi publicada enfocando apenas a estimativa filtrada sob a justificativa de que a estimativa preditora era de significativa complexidade quando modelada pelo método dos mínimos quadrados. Por este motivo, poucos trabalhos, como NIKOUKHAH et al. (1992) e ZHANG et al. (1998), deduziram a estimativa preditora. Este último artigo apresentou também um algoritmo para a estimativa suavizadora, mas usando o modelo de inovação ARMA. No entanto, até onde foi possível identificar, nenhum trabalho até agora resolveu o problema de estimativa robusta, considerando incertezas nos parâmetros, para sistemas singulares. Para a dedução das estimativas singulares robustas, esta tese tomou como base SAYED (2001), que deduz o filtro de Kalman robusto com incertezas limitadas utilizando uma abordagem determinística, o chamado filtro BDU. Os filtros robustos para sistemas singulares apresentados nesta tese, são mais abrangentes que os apresentados em SAYED (2001). Quando particularizados para o espaço de estados sem incertezas, todos os filtros se assemelham ao filtro de Kalman. / New algorithms to optimal recursive filtering, smoothed and prediction for general time-invariant or time-variant descriptor systems are proposed in this thesis. The estimation problem is addressed as an optimal deterministic trajectory fitting. This problem is solved using exclusively deterministic arguments for systems with or without uncertainties. Kalman type recursive algorithms for robust filtered, predicted and smoothed estimations are derived. In the last years, many papers have paid attention to the estimation problems of linear singular systems. Unfortunately, all those works were concentrated only on the study of filtering problems, for nominal systems. The predicted and smoothed filters are more involved and were considered only by few works : NIKOUKHAH et al. (1992) and ZHANG et al. (1998) had proposed a unified approach for filtering, prediction and smoothing problems which were derived by using the projection formula and were calculated based on the ARMA innovation model, but they had not considered the uncertainties. In this thesis its applied for descriptor systems a robust procedure for usual state space systems developed by SAYED (2001), called BDU filter. It is obtained a robust descriptor Kalman type recursions for filtered, predicted and smoothed estimates. Considering the nominal state space, all descriptor filters developed in this work collapse to the Kalman filter.

"Fluid-structure interaction arises in a wide array of technological applications including naval and marine hydrodynamics, civil and wind engineering and flight vehicle aerodynamics. When a fluid flows over a bluff body such as a circular cylinder, the periodic vortex shedding in the wake causes fluctuating lift and drag forces on the body. This phenomenon can lead to fatigue damage of the structure due to large amplitude vibration. It is widely believed that the wake structures behind the structure determine the hydrodynamic forces acting on the structure and control of wake structures can lead to vibration control of the structure. Modeling this complex non-linear interaction requires coupling of the dynamics of the fluid and the structure. In this thesis, however, the vibration of the flexible cylinder is prescribed, and the focus is on modeling the fluid dynamics in its wake. Low-dimensional iterative circle maps have been found to predict the universal dynamics of a two-oscillator system such as the rigid cylinder wake. Coupled map lattice (CML)models that combine a series of low-dimensional circle maps with a diffusion model have previously predicted qualitative features of wake patterns behind freely vibrating cables at low Reynolds number. However, the simple nature of the CML models implies that there will always be unmodelled wake dynamics if a detailed, quantitative comparison is made with laboratory or simulated wake flows. Motivated by a desire to develop an improved CML model, we incorporate self-learning features into a new CML that is trained to precisely estimate wake patterns from target numerical simulations and experimental wake flows. The eventual goal is to have the CML learn from a laboratory flow in real time. A real-time self-learning CML capable of estimating experimental wake patterns could serve as a wake model in a future anticipated feedback control system designed to produce desired wake patterns. A new convective-diffusive map that includes additional wake dynamics is developed. Two different self-learning CML models, each capable of precisely estimating complex wake patterns, have been developed by considering additional dynamics from the convective-diffusive map. The new self-learning CML models use adaptive estimation schemes which seek to precisely estimate target wake patterns from numerical simulations and experiments. In the first self-learning CML, the estimator scheme uses a multi-variable least-squares algorithm to adaptively vary the spanwise velocity distribution in order to minimize the state error (difference between modeled and target wake patterns). The second self-learning model uses radial basis function neural networks as online approximators of the unmodelled dynamics. Additional unmodelled dynamics not present in the first self-learning CML model are considered here. The estimator model uses a combination of a multi-variable normalized least squares scheme and a projection algorithm to adaptively vary the neural network weights. Studies of this approach are conducted using wake patterns from spectral element based NEKTAR simulations of freely vibrating cable wakes at low Reynolds numbers on the order of 100. It is shown that the self-learning models accurately and efficiently estimate the simulated wake patterns within several shedding cycles. Next, experimental wake patterns behind different configurations of rigid cylinders were obtained. The self-learning CML models were then used for off-line estimation of the stored wake patterns. With the eventual goal of incorporating low-order CML models into a wake pattern control system in mind, in a related study control terms were added to the simple CML model in order to drive the wake to the desired target pattern of shedding. Proportional, adaptive proportional and non-linear control techniques were developed and their control efficiencies compared."

En Analyse Sensorielle, les préférences des consommateurs sont généralement modélisées en fonction de données sensorielles par les méthodes de cartographie des préférences. L'objectif de cette thèse est de modéliser les préférences des consommateurs en intégrant, en plus des données sensorielles, de nouvelles variables relatives à leur perception des produits. Nous appellerons ces variables les dimensions subjectives. Elles recouvrent des dimensions pragmatiques liées à l'utilisation du produit et des dimensions plus symboliques telles que l'esthétisme, la modernité, l'originalité…Les problématiques relatives aux dimensions subjectives ont d'abord été étudiées lors d'une étude exploratoire sur des tasses à café. L'ensemble du travail a ensuite été réalisé sur 11 sièges de voitures. Dans un premier temps, des entretiens qualitatifs ont été réalisés auprès de 16 consommateurs d'une part et de 2 designers d'autre part. Ces entretiens ont permis d'identifier les dimensions subjectives caractéristiques des sièges. Une évaluation quantitative des dimensions subjectives et des préférences a ensuite été réalisée par 110 consommateurs. Enfin, les sièges ont été caractérisés sensoriellement par des experts. Les préférences des consommateurs ont été modélisées en fonction des données sensorielles et des dimensions subjectives par des modèles d'équations structurelles à variables latentes, plus précisément par Partial Least Square Path Modeling. Quatre modèles, fondés sur les groupes de préférences, ont été mis en place. Selon le groupe étudié, la contribution des deux jeux de données diffère et quatre profils de clients sont identifiés. D'un point de vue méthodologique, ce travail fournit des éléments de réponse sur l'intérêt des dimensions subjectives pour la modélisation des préférences. L'ensemble de la démarche est en cours d'application sur un produit alimentaire : le chocolat. / In Sensory Science, preference mapping is used to explain consumers' preferences with sensory data. This PhD aims to integrate not only sensory data but also new variables that are related to consumers' perception of the product in the modelling of consumers' preferences. These variables are labelled as subjective dimensions. They address the pragmatic dimensions that cover the context of use of the products and more symbolic dimensions, such as aesthetics, modernity, originality…An exploratory study based on coffee cups was a first mean to approach the issues related to subjective dimensions. Then, all the work was done on a study of 11 car seats. The first step consisted in qualitative interviews of 16 consumers and of 2 designers. These interviews allowed identifying the subjective dimensions that characterize car seats. 110 consumers then performed a quantitative evaluation of their preferences and subjective dimensions. Finally, the seats were characterized by experts with sensory descriptors. The consumers' preferences were modelled according to both sensory data and subjective dimensions, using structural equations: the Partial Least Square Path Modeling. Four models based on preferences clustering were established. The contribution of two kinds of data differed according to the considered cluster, which led to the identification of four customer profiles. From a methodological point of view, this work provides first elements about the benefit of subjective dimensions in preference modelling. The methodology is being implemented on a food product: chocolate.

Orientador: Douglas Domingues Bueno / Resumo: Os fenômenos associados aos sistemas aeroelásticos definem uma importante classe de problemas envolvida no projeto de aeronaves. Algumas análises podem ser realizadas utilizando a formulação no domínio da frequência, porém, para alguns problemas específicos a análise no domínio do tempo mostra-se mais conveniente, especialmente para projeto de controladores e inclusão de não linearidades. Em particular, forças aerodinâmicas não estacionárias são tipicamente obtidas no domínio da frequência reduzida. Tais formulações não permitem de maneira direta, através de uma transformada inversa, obter modelos matemáticos no domínio do tempo e, portanto, é necessário o uso de um método de aproximação, como o de Roger-Abel. No entanto, uso deste método de aproximação apresenta algumas lacunas com relação ao significado físico e escolha dos parâmetros de atraso. Desta forma, o presente texto explora a influência dos estados de atraso demonstrando que é responsável pela correção da fase entre o movimento e as forças aerodinâmicas resultantes e, também, propõe uma forma de avaliação da qualidade da aproximação obtida. A partir da aproximação das cargas aerodinâmicas se obtém o modelo matemático do sistema aeroelástico, e através de simulações numéricas computacionais, tem-se a resposta do sistema aeroelástico no domínio do tempo devido à cargas de rajada $1-cosseno$. A partir da análise da resposta à rajada é possível avaliar condições em que a rajada se apresenta de maneira mais crítica para... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The phenomena associated with the aeroelastic systems define an important class of problems involved in aircraft design. Some analyzes may be performed in the frequency domain, however, for some specific problems time domain analysis is more convenient, especially for controller design and the inclusion of nonlinearities. In particular, non-stationary aerodynamic forces are typically obtained in the reduced frequency domain. Such formulations do not allow, by means of an inverse transform, to obtain mathematical models in the time domain, and therefore it is necessary to use an approximation method, such as that of Roger-Abel. However, the use of this approximation method presents some gaps with respect to the physical meaning and choice of lag parameters. In this way, the present text explores the influence of the lag states demonstrating that it is responsible for the correction of the phase between the movement and the resulting aerodynamic forces and also proposes a method to evaluate the quality of the approximation achieved. From the approximation of the aerodynamic loads the mathematical model of the aeroelastic system is obtained, and through computational numerical simulations, has the response of the aeroelastic system in the time domain due to the 1-cosine gust load. From the analysis of the response to the gust, it is possible to evaluate conditions in which the gust is presented in a more critical way for the study system. / Mestre

Les processus autorégressifs à bifurcation (BAR) ont été au centre de nombreux travaux de recherche ces dernières années. Ces processus, qui sont l'adaptation à un arbre binaire des processus autorégressifs, sont en effet d'intérêt en biologie puisque la structure de l'arbre binaire permet une analogie aisée avec la division cellulaire. L'objectif de cette thèse est l'estimation les paramètres de variantes de ces processus autorégressifs à bifurcation, à savoir les processus BAR à valeurs entières et les processus BAR à coefficients aléatoires. Dans un premier temps, nous nous intéressons aux processus BAR à valeurs entières. Nous établissons, via une approche martingale, la convergence presque sûre des estimateurs des moindres carrés pondérés considérés, ainsi qu'une vitesse de convergence de ces estimateurs, une loi forte quadratique et leur comportement asymptotiquement normal. Dans un second temps, on étudie les processus BAR à coefficients aléatoires. Cette étude permet d'étendre le concept de processus autorégressifs à bifurcation en généralisant le côté aléatoire de l'évolution. Nous établissons les mêmes résultats asymptotiques que pour la première étude. Enfin, nous concluons cette thèse par une autre approche des processus BAR à coefficients aléatoires où l'on ne pondère plus nos estimateurs des moindres carrés en tirant parti du théorème de Rademacher-Menchov. / Bifurcating autoregressive (BAR) processes have been widely investigated this past few years. Those processes, which are an adjustment of autoregressive processes to a binary tree structure, are indeed of interest concerning biology since the binary tree structure allows an easy analogy with cell division. The aim of this thesis is to estimate the parameters of some variations of those BAR processes, namely the integer-valued BAR processes and the random coefficients BAR processes. First, we will have a look to integer-valued BAR processes. We establish, via a martingale approach, the almost sure convergence of the weighted least squares estimators of interest, together with a rate of convergence, a quadratic strong law and their asymptotic normality. Secondly, we study the random coefficients BAR processes. The study allows to extend the principle of bifurcating autoregressive processes by enlarging the randomness of the evolution. We establish the same asymptotic results as for the first study. Finally, we conclude this thesis with an other approach of random coefficient BAR processes where we do not weight our least squares estimators any more by making good use of the Rademacher-Menchov theorem.

The goal of the work is to provide monetary valuation of changes in visual aspects of the landscape as a result of construction of an additional wind turbine in the village Maletín. For a suitable method for achieving the goal is being selected the contingent valuation method. A key element of this method is being considered the carefully compiled questionnaire, on which basis is made the quantification and evaluation of collected data. The representative sample consists of 112 households and the selected payment method is the increase of the monthly bill for electricity. The questionnaire reports that 54.3% of households consider the impact of wind turbines on the landscape Maletín to be positive. With the construction of additional wind turbine agree less than 74.3% of households and the most common reason is to obtain grants for the village and to produce cleaner energy from wind turbines. With the construction of new wind turbine while increasing monthly bill agrees 28.6% of all households living in the village Maletín. Estimation of changes in a welfare, thus improving the quality of the environment, is based on estimated central values, that has been calculated from selected characteristics and nonparametric estimation. The average household's willingness to pay for construction of wind turbine is estimated to be between 77 CZK - 200 CZK per month.