There are two main parts in this thesis. The first one concerns valvometry, which is here the study of the distance between both parts of the shell of an oyster, over time. The health status of oysters can be characterized using valvometry in order to obtain insights about the quality of their environment. We consider that a renewal process with four states underlies the behaviour of the studied oysters. Such a hidden process can be retrieved from a valvometric signal by assuming that some probability density function linked with this signal, is bimodal. We then compare several estimators which take this assumption into account, including kernel density estimators.In another chapter, we compare several regression approaches, aiming at analysing transcriptomic data. To understand which explanatory variables have an effect on gene expressions, we apply a multiple testing procedure on these data, through the linear model FAMT. The SIR method may find nonlinear relations in such a context. It is however more commonly used when the response variable is univariate. A multivariate version of SIR was then developed. Procedures to measure gene expressions can be expensive. The sample size n of the corresponding datasets is then often small. That is why we also studied SIR when n is less than the number of explanatory variables p.

As bacteriocinas são peptídeos antimicrobianos produzidos por algumas bactérias, que atuam como bio-conservantes e têm grande potencial de aplicação em produtos cárneos. Estudos mostram que as bacteriocinas de bactérias lácticas (BAL) a serem utilizadas em um determinado alimento são mais eficientes quando produzidas por bactérias lácticas isoladas do mesmo tipo de alimento. Este estudo objetivou obter novas BAL produtoras de bacteriocinas a partir de mortadela fatiada, caracterizar as bacteriocinas produzidas, obter a bacteriocina semi-purificada e verificar seu potencial de aplicação in vitro e in situ no controle de Listeria monocytogenes e na vida de prateleira (VDP) de mortadela fatiada. Foram obtidos 19 isolados de BAL comprovadamente produtoras de bacteriocinas, que foram avaliadas quanto ao espectro de ação frente a uma grande variedade de bactérias Gram positivas e Gram negativas, e estabilidade em diferentes pH. As que apresentaram melhor estabilidade e inibiram maior número de bactérias foram avaliadas quanto a estabilidade térmica e resistência a diferentes agentes químicos e concentrações de NaCl. As que apresentaram maior resistência foram submetidas a testes de otimização da produção da bacteriocina em diferentes combinações de tempo/temperatura. Com base nestes resultados, selecionou-se um isolado que identificado como Lactobacillus curvatus pelo sequenciamento do gene 16S e confirmado por reações de PCR com primers específicos. A bacteriocina produzida por este isolado foi submetida a uma purificação por extração ácida e aplicada em fatias de mortadela experimentalmente contaminadas com um pool de cepas de Listeria monocytogenes, observando-se as contagens deste patógeno durante o armazenamento em refrigeração (7°C) por 40 dias em embalagem à vácuo. Paralelamente, foi realizada contagem de bactérias láticas para avaliar o efeito da bacteriocina nesta população, responsável pela VDP deste produto. A bacteriocina parcialmente purificada foi capaz de reduzir em 1 ciclo logarítmico a população inicial de Listeria monocytogenes na mortadela fatiada, que foi mantida durante os 40 dias de análise. Durante toda a VDP, a contagem de L. monocytogenes permaneceu constante, sem multiplicação nas condições de armazenamento do produto tanto nas amostras testes quanto controle. A bacteriocina semi-purificada não teve ação inibitória contra as bactérias lácticas presentes no produto e portanto não teve impacto na VDP do produto. Os resultados indicaram que a bacteriocina produzida pelo isolado L. curvatus RJC 1 apresenta potencial de aplicação em produtos cárneos fatiados como bioconservante. / Bacteriocins are peptides with antimicrobial properties produced by some bacteria, that act as bio-preservatives with great potential of application in meat products. Several studies show that bacteriocins from lactic acid bacteria (LAB) to be used in a specific food product have a better performance when produced by LAB isolated from the same kind of product. This study aimed to obtain new bacteriocinogenic LAB from sliced Bologna, to characterize the bacteriocins produced, to obtain a semi-purified bacteriocin, and to verify its potential of application in vitro and in situ in the control of Listeria monocytogenes and in the shelf-life of sliced bologna. 19 bacteriocin producer LAB, were evaluated as to spectrum of action against a great variety of Gram positives and Gram negatives bacteria and pH stability. The ones with better stability and that inhibited a larger number of bacteria were evaluated according to its thermal stability and resistance against different chemical agents and NaCl concentrations. The ones that showed better resistance were submitted to tests to optimize the bacteriocin production in different combinations of time and temperature. Based on these results, one was selected, identified as Lactobacillus curvatus by gene 16S sequencing and confirmed by PCR reactions with specific primers. The bacteriocin produced by this strain was submitted to partial purification by acid extraction and was applied in mortadella slices experimentally contaminated with a pool of L. monocytogenes strains, observing the counts of this pathogen along refrigerated (7ºC) storage fo r 40 days in vacuum package. Parallel, it was done LAB counts to evaluate the effect of the bacteriocin on this population, responsible for limiting the shelf life of this product. The semi-purified bacteriocin was able to reduce 1 log cicle of the initial population of L. monocytogenes in the sliced mortadella, which was maintained during the 40 days of analysis. Along the whole shelf-life, the counts of L. monocytogenes remained constant, without multiplication in the storage conditions in the test samples as well as in the control samples. The semi-purified bacteriocin did not act against de LAB naturally present at the product, having no impact in the shelf life of the product. The results indicated that the bacteriocin produced by the isolated L. curvatus RJC 1 presents potential of application in sliced deli products as a bio-preservative.

As bacteriocinas são peptídeos antimicrobianos produzidos por algumas bactérias, que atuam como bio-conservantes e têm grande potencial de aplicação em produtos cárneos. Estudos mostram que as bacteriocinas de bactérias lácticas (BAL) a serem utilizadas em um determinado alimento são mais eficientes quando produzidas por bactérias lácticas isoladas do mesmo tipo de alimento. Este estudo objetivou obter novas BAL produtoras de bacteriocinas a partir de mortadela fatiada, caracterizar as bacteriocinas produzidas, obter a bacteriocina semi-purificada e verificar seu potencial de aplicação in vitro e in situ no controle de Listeria monocytogenes e na vida de prateleira (VDP) de mortadela fatiada. Foram obtidos 19 isolados de BAL comprovadamente produtoras de bacteriocinas, que foram avaliadas quanto ao espectro de ação frente a uma grande variedade de bactérias Gram positivas e Gram negativas, e estabilidade em diferentes pH. As que apresentaram melhor estabilidade e inibiram maior número de bactérias foram avaliadas quanto a estabilidade térmica e resistência a diferentes agentes químicos e concentrações de NaCl. As que apresentaram maior resistência foram submetidas a testes de otimização da produção da bacteriocina em diferentes combinações de tempo/temperatura. Com base nestes resultados, selecionou-se um isolado que identificado como Lactobacillus curvatus pelo sequenciamento do gene 16S e confirmado por reações de PCR com primers específicos. A bacteriocina produzida por este isolado foi submetida a uma purificação por extração ácida e aplicada em fatias de mortadela experimentalmente contaminadas com um pool de cepas de Listeria monocytogenes, observando-se as contagens deste patógeno durante o armazenamento em refrigeração (7°C) por 40 dias em embalagem à vácuo. Paralelamente, foi realizada contagem de bactérias láticas para avaliar o efeito da bacteriocina nesta população, responsável pela VDP deste produto. A bacteriocina parcialmente purificada foi capaz de reduzir em 1 ciclo logarítmico a população inicial de Listeria monocytogenes na mortadela fatiada, que foi mantida durante os 40 dias de análise. Durante toda a VDP, a contagem de L. monocytogenes permaneceu constante, sem multiplicação nas condições de armazenamento do produto tanto nas amostras testes quanto controle. A bacteriocina semi-purificada não teve ação inibitória contra as bactérias lácticas presentes no produto e portanto não teve impacto na VDP do produto. Os resultados indicaram que a bacteriocina produzida pelo isolado L. curvatus RJC 1 apresenta potencial de aplicação em produtos cárneos fatiados como bioconservante. / Bacteriocins are peptides with antimicrobial properties produced by some bacteria, that act as bio-preservatives with great potential of application in meat products. Several studies show that bacteriocins from lactic acid bacteria (LAB) to be used in a specific food product have a better performance when produced by LAB isolated from the same kind of product. This study aimed to obtain new bacteriocinogenic LAB from sliced Bologna, to characterize the bacteriocins produced, to obtain a semi-purified bacteriocin, and to verify its potential of application in vitro and in situ in the control of Listeria monocytogenes and in the shelf-life of sliced bologna. 19 bacteriocin producer LAB, were evaluated as to spectrum of action against a great variety of Gram positives and Gram negatives bacteria and pH stability. The ones with better stability and that inhibited a larger number of bacteria were evaluated according to its thermal stability and resistance against different chemical agents and NaCl concentrations. The ones that showed better resistance were submitted to tests to optimize the bacteriocin production in different combinations of time and temperature. Based on these results, one was selected, identified as Lactobacillus curvatus by gene 16S sequencing and confirmed by PCR reactions with specific primers. The bacteriocin produced by this strain was submitted to partial purification by acid extraction and was applied in mortadella slices experimentally contaminated with a pool of L. monocytogenes strains, observing the counts of this pathogen along refrigerated (7ºC) storage fo r 40 days in vacuum package. Parallel, it was done LAB counts to evaluate the effect of the bacteriocin on this population, responsible for limiting the shelf life of this product. The semi-purified bacteriocin was able to reduce 1 log cicle of the initial population of L. monocytogenes in the sliced mortadella, which was maintained during the 40 days of analysis. Along the whole shelf-life, the counts of L. monocytogenes remained constant, without multiplication in the storage conditions in the test samples as well as in the control samples. The semi-purified bacteriocin did not act against de LAB naturally present at the product, having no impact in the shelf life of the product. The results indicated that the bacteriocin produced by the isolated L. curvatus RJC 1 presents potential of application in sliced deli products as a bio-preservative.

Deux parties principales composent cette thèse. La première d'entre elles est consacrée à la valvométrie, c'est-à-dire ici l'étude de la distance entre les deux parties de la coquille d'une huître au cours du temps. La valvométrie est utilisée afin de déterminer si de tels animaux sont en bonne santé, pour éventuellement tirer des conclusions sur la qualité de leur environnement. Nous considérons qu'un processus de renouvellement à quatre états sous-tend le comportement des huîtres étudiées. Afin de retrouver ce processus caché dans le signal valvométrique, nous supposons qu'une densité de probabilité reliée à ce signal est bimodale. Nous comparons donc plusieurs estimateurs qui prennent en compte ce type d'hypothèse, dont des estimateurs à noyau.Dans un second temps, nous comparons plusieurs méthodes de régression, dans le but d'analyser des données transcriptomiques. Pour comprendre quelles variables explicatives influent sur l'expression de gènes, nous avons réalisé des tests multiples grâce au modèle linéaire FAMT. La méthode SIR peut être envisagée pour trouver des relations non-linéaires. Toutefois, elle est principalement employée lorsque la variable à expliquer est univariée. Une version multivariée de cette approche a donc été développée. Le coût d'acquisition des données transcriptomiques pouvant être élevé, la taille n des échantillons correspondants est souvent faible. C'est pourquoi, nous avons également étudié la méthode SIR lorsque n est inférieur au nombre de variables explicatives p. / There are two main parts in this thesis. The first one concerns valvometry, which is here the study of the distance between both parts of the shell of an oyster, over time. The health status of oysters can be characterized using valvometry in order to obtain insights about the quality of their environment. We consider that a renewal process with four states underlies the behaviour of the studied oysters. Such a hidden process can be retrieved from a valvometric signal by assuming that some probability density function linked with this signal, is bimodal. We then compare several estimators which take this assumption into account, including kernel density estimators.In another chapter, we compare several regression approaches, aiming at analysing transcriptomic data. To understand which explanatory variables have an effect on gene expressions, we apply a multiple testing procedure on these data, through the linear model FAMT. The SIR method may find nonlinear relations in such a context. It is however more commonly used when the response variable is univariate. A multivariate version of SIR was then developed. Procedures to measure gene expressions can be expensive. The sample size n of the corresponding datasets is then often small. That is why we also studied SIR when n is less than the number of explanatory variables p.

Cette thèse est consacrée au problème de la réduction de dimension. Cette thématique centrale en Statistique vise à rechercher des sous-espaces de faibles dimensions tout en minimisant la perte d'information contenue dans les données. Tout d'abord, nous nous intéressons à des méthodes de statistique multidimensionnelle dans le cas de variables qualitatives. Nous abordons la question de la rotation en Analyse des Correspondances Multiples (ACM). Nous définissons l'expression analytique de l'angle de rotation planaire optimal pour le critère de rotation choisi. Lorsque le nombre de composantes principales retenues est supérieur à deux, nous utilisons un algorithme de rotations planaires successives de paires de facteurs. Nous proposons également différents algorithmes de classification de variables qualitatives qui visent à optimiser un critère de partitionnement basé sur la notion de rapports de corrélation. Un jeu de données réelles illustre les intérêts pratiques de la rotation en ACM et permet de comparer empiriquement les différents algorithmes de classification de variables qualitatives proposés. Puis nous considérons un modèle de régression semiparamétrique, plus précisément nous nous intéressons à la méthode de régression inverse par tranchage (SIR pour Sliced Inverse Regression). Nous développons une approche basée sur un partitionnement de l'espace des covariables, qui est utilisable lorsque la condition fondamentale de linéarité de la variable explicative est violée. Une seconde adaptation, utilisant le bootstrap, est proposée afin d'améliorer l'estimation de la base du sous-espace de réduction de dimension. Des résultats asymptotiques sont donnés et une étude sur des données simulées démontre la supériorité des approches proposées. Enfin les différentes applications et collaborations interdisciplinaires réalisées durant la thèse sont décrites. / This thesis concentrates on dimension reduction approaches, that seek for lower dimensional subspaces minimizing the lost of statistical information. First we focus on multivariate analysis for categorical data. The rotation problem in Multiple Correspondence Analysis (MCA) is treated. We give the analytic expression of the optimal angle of planar rotation for the chosen criterion. If more than two principal components are to be retained, this planar solution is used in a practical algorithm applying successive pairwise planar rotations. Different algorithms for the clustering of categorical variables are also proposed to maximize a given partitioning criterion based on correlation ratios. A real data application highlights the benefits of using rotation in MCA and provides an empirical comparison of the proposed algorithms for categorical variable clustering. Then we study the semiparametric regression method SIR (Sliced Inverse Regression). We propose an extension based on the partitioning of the predictor space that can be used when the crucial linearity condition of the predictor is not verified. We also introduce bagging versions of SIR to improve the estimation of the basis of the dimension reduction subspace. Asymptotic properties of the estimators are obtained and a simulation study shows the good numerical behaviour of the proposed methods. Finally applied multivariate data analysis on various areas is described.

This thesis presents a numerical exploration of the dynamics governing rotating flow driven by a surface stress in the " sliced cylinder " model of Pedlosky & Greenspan (1967) and Beardsley (1969), and its close relative, the " sliced cone " model introduced by Griffiths & Veronis (1997). The sliced cylinder model simulates the barotropic wind-driven circulation in a circular basin with vertical sidewalls, using a depth gradient to mimic the effects of a gradient in Coriolis parameter. In the sliced cone the vertical sidewalls are replaced by an azimuthally uniform slope around the perimeter of the basin to simulate a continental slope. Since these models can be implemented in the laboratory, their dynamics can be explored by a complementary interplay of analysis and numerical and laboratory experiments. ¶ In this thesis a derivation is presented of a generalised quasigeostrophic formulation which is valid for linear and moderately nonlinear barotropic flows over large-amplitude topography on an f-plane, yet retains the simplicity and conservation properties of the standard quasigeostrophic vorticity equation (which is valid only for small depth variations). This formulation is implemented in a numerical model based on a code developed by Page (1982) and Becker & Page (1990). ¶ The accuracy of the formulation and its implementation are confirmed by detailed comparisons with the laboratory sliced cylinder and sliced cone results of Griffiths (Griffiths & Kiss, 1999) and Griffiths & Veronis (1997), respectively. The numerical model is then used to provide insight into the dynamics responsible for the observed laboratory flows. In the linear limit the numerical model reveals shortcomings in the sliced cone analysis by Griffiths & Veronis (1998) in the region where the slope and interior join, and shows that the potential vorticity is dissipated in an extended region at the bottom of the slope rather than a localised region at the east as suggested by Griffiths & Veronis (1997, 1998). Welander's thermal analogy (Welander, 1968) is used to explain the linear circulation pattern, and demonstrates that the broadly distributed potential vorticity dissipation is due to the closure of geostrophic contours in this geometry. ¶ The numerical results also provide insight into features of the flow at finite Rossby number. It is demonstrated that separation of the western boundary current in the sliced cylinder is closely associated with a " crisis " due to excessive potential vorticity dissipation in the viscous sublayer, rather than insufficient dissipation in the outer western boundary current as suggested by Holland & Lin (1975) and Pedlosky (1987). The stability boundaries in both models are refined using the numerical results, clarifying in particular the way in which the western boundary current instability in the sliced cone disappears at large Rossby and/or Ekman number. A flow regime is also revealed in the sliced cylinder in which the boundary current separates without reversed flow, consistent with the potential vorticity " crisis " mechanism. In addition the location of the stability boundary is determined as a function of the aspect ratio of the sliced cylinder, which demonstrates that the flow is stabilised in narrow basins such as those used by Beardsley (1969, 1972, 1973) and Becker & Page (1990) relative to the much wider basin used by Griffiths & Kiss (1999). ¶ Laboratory studies of the sliced cone by Griffiths & Veronis (1997) showed that the flow became unstable only under anticyclonic forcing. It is shown in this thesis that the contrast between flow under cyclonic and anticyclonic forcing is due to the combined effects of the relative vorticity and topography in determining the shape of the potential vorticity contours. The vorticity at the bottom of the sidewall smooths out the potential vorticity contours under cyclonic forcing, but distorts them into highly contorted shapes under anticyclonic forcing. In addition, the flow is dominated by inertial boundary layers under cyclonic forcing and by standing Rossby waves under anticyclonic forcing due to the differing flow direction relative to the direction of Rossby wave phase propagation. The changes to the potential vorticity structure under strong cyclonic forcing reduce the potential vorticity changes experienced by fluid columns, and the flow approaches a steady free inertial circulation. In contrast, the complexity of the flow structure under anticyclonic forcing results in strong potential vorticity changes and also leads to barotropic instability under strong forcing. ¶ The numerical results indicate that the instabilities in both models arise through supercritical Hopf bifurcations. The two types of instability observed by Griffiths & Veronis (1997) in the sliced cone are shown to be related to the western boundary current instability and " interior instability " identified by Meacham & Berloff (1997). The western boundary current instability is trapped at the western side of the interior because its northward phase speed exceeds that of the fastest interior Rossby wave with the same meridional wavenumber, as discussed by Ierley & Young (1991). ¶ Numerical experiments with different lateral boundary conditions are also undertaken. These show that the flow in the sliced cylinder is dramatically altered when the free-slip boundary condition is used instead of the no-slip condition, as expected from the work of Blandford (1971). There is no separated jet, because the flow cannot experience a potential vorticity " crisis " with this boundary condition, so the western boundary current overshoots and enters the interior from the east. In contrast, the flow in the sliced cone is identical whether no-slip, free-slip or super-slip boundary conditions are applied to the horizontal flow at the top of the sloping sidewall, except in the immediate vicinity of this region. This insensitivity results from the extremely strong topographic steering near the edge of the basin due to the vanishing depth, which demands a balance between wind forcing and Ekman pumping on the upper slope, regardless of the lateral boundary condition. The sensitivity to the lateral boundary condition is related to the importance of lateral friction in the global vorticity balance. The integrated vorticity must vanish under the no-slip condition, so in the sliced cylinder the overall vorticity budget is dominated by lateral viscosity and Ekman friction is negligible. Under the free-slip condition the Ekman friction assumes a dominant role in the dissipation, leading to a dramatic change in the flow structure. In contrast, the much larger depth variation in the sliced cone leads to a global vorticity balance in which Ekman friction is always dominant, regardless of the boundary condition.