Dans cette thèse, nous nous intéressons à l’amélioration du schéma de Yee pour traiter demanière plus efficace et pertinente les problèmes industriels auxquels nous sommes confrontés à l’heureactuelle. Pour cela, nous cherchons avant tout à diminuer les erreurs numériques de dispersion et àaméliorer les modélisations des géométries courbes ainsi que des réseaux de câbles. Pour répondre àces besoins, une solution basée sur un schéma Galerkin discontinu pourrait être envisagée. Toutefois,l’utilisation d’une telle technique sur la totalité du volume de calcul est relativement coûteuse. De plus,la prise en compte de structures filaires sur un tel schéma n’est pas encore opérationnelle. C’est pourquoi,dans l’optique d’avoir un outil industriel, et après une étude bibliographique, nous nous sommes plutôtorientés sur l’étude d’un schéma éléments finis (FEM) sur maillage cartésien qui possède toutes lesbonnes propriétés du schéma de Yee. Notamment, à l’ordre d’approximation spatiale égal à 0 ce schémaFEM est exactement le schéma de Yee, et, pour des ordres supérieurs, il permet de réduire fortementl’erreur de dispersion numérique de ce dernier. Dans le travail de cette thèse, pour ce schéma, nous avons notamment donné un critère de stabilité théorique, étudié sa convergence théorique et fait une analyse de l’erreur de dispersion. Pour tenircompte des possibilités d’ordre d’approximation spatiale variable par direction, nous avons mis en placeune stratégie d’affectation des ordres suivant le maillage donné. Ceci nous a permis d’obtenir un pas detemps optimal pour une précision souhaitée tout en réduisant les coûts de calcul. Après avoir porté ceschéma sur des machines de production, différents problèmes de CEM, antennes, IEM ou foudre ont ététraités afin de montrer les avantages et le potentiel de celui-ci. En conclusion de ces expérimentationsnumériques, il s’avère que la méthode est limitée par le manque de précision pour prendre en comptedes géométries courbes. Afin d’améliorer cela, nous avons proposé une hybridation entre ce schéma et leschéma GD que l’on peut étendre aux autres schémas comme les méthodes différences finies (FDTD) etvolumes finis (FVTD). Nous avons montré que la technique d’hybridation proposée conserve l’énergie etest stable sous une condition que nous avons évaluée de manière théorique. Des exemples de validationont ensuite été montrés. Enfin, pour tenir compte des réseaux de câbles, un modèle de fils minces d’ordred’approximation spatiale élevé a été proposé. Malheureusement, celui-ci ne peut pas couvrir l’ensembledes cas industriels et pour remédier à cela, nous avons proposé une hybridation de notre approche avecune équation de ligne de transmission. L’intérêt de cette hybridation a été montré sur un certain nombred’exemples, que nous n’aurions pas pu traiter par un modèle de structure filaire simple. / In this thesis, we study the improvement of the Yee’s scheme to treat efficiently and in arelevant way the industrial issues we are facing nowadays. For that, we first of all try to reduce thenumerical errors of dispersion and then to improve the modeling of the curved surfaces and of theharness networks. To answer these needs, a solution based on a Galerkin Discontinuous (GD) methodhas been first considered. However, the use of such method on the entire modeling volume is quite costly ;moreover the wires are not taken into account in this method. That is the reason why, with the objectiveof an industrial tool and after a large bibliographic research, we headed for the study of finite elementsscheme (FEM) on a Cartesian mesh which has all the good properties of the Yee’s scheme. Especially,this scheme is exactly the Yee’s scheme when the spatial order of approximation is set to zero. Forthe higher orders, this new scheme allows to greatly reduce the numerical error of dispersion. In theframe of this thesis and for this scheme, we give a theoretical criterion of stability, study its theoreticalconvergence and we perform an analysis of the error of dispersion. To take into account the possibilityof the variable spatial orders of approximation in each direction, we put in place a strategy of orderaffectation according to the given mesh. This strategy allows to obtain an optimal time step for a givenselected precision while reducing the cost of the calculations. Once this new scheme has been adaptedto large industrial computing means, different EMC, antennas, NEMP or lightning problems are treatedto demonstrate the advantages and the potential of this scheme. As a conclusion of these numericalsimulations we demonstrate that this method is limited by a lack of precision when taking into accountcurved geometries. To improve the treatment of the curved surfaces, we propose an hybridization between this scheme andthe GD scheme. This hybridization can also be applied to other methods such as Finite Differences(FDTD) or Finite Volumes (FVTD). We demonstrate that the technique of hybridization proposed,allows to conserve the energy and is stable under a condition that we study theoretically. Some examplesare presented for validation. Finally and to take into account the cables, a thin wire model with a highorder of spatial approximation is proposed. Unfortunately, this model does not allow to cover all theindustrial cases. To solve this issue we propose an hybridization with a transmission line method. Theadvantage of this hybridization is demonstrated thanks to different cases which would not have beenfeasible with a more simple thin wire method.

L’évolution de la microélectronique suit plusieurs axes notamment la miniaturisation des éléments actifs (réduction de taille des transistors), et l’augmentation de la densité d’interconnexion qui se traduisent par la loi de Gordon Moore qui prédit que la densité d'intégration sur silicium doublerait tous les deux ans. Ces évolutions ont pour conséquence la réduction des prix et du poids des composants. L’hybridation ou flip chip est une technologie qui s’inscrit dans cette évolution, elle consiste en l’assemblage de matériaux hétérogènes. Dans cette étude il s‘agit d’un circuit de lecture Silicium et d’un circuit de détection InP ou GaAs assemblés par l’intermédiaire d’une matrice de billes d’indium. La connexion flip chip est basée sur l’utilisation d’une jonction par plots métalliques de faibles dimensions qui permet de diminuer les pertes électriques (faible inductance et faible bruit), une meilleure dissipation thermique, une bonne tenue mécanique. Enfin elle favorise la miniaturisation avec l’augmentation de la compacité et de la densité d’interconnexion.Les travaux de thèse se concentrent sur deux axes principaux. Le premier concerne l’hybridation par brasure avec la technologie des billes d’indium par refusion, et le second concerne l’hybridation par pression à température ambiante (nano-scratch) par l’intermédiaire des nanostructures (Nano-fils d’or, Nano-fils ZnO). Ces travaux ont permis la réalisation d’un détecteur InGaAs avec extension visible de format TV 640*512 pixels au pas de 15 µm. Ces travaux ont également permis la validation mécanique de l’assemblage d’un composant de format double TV 1280*1024 pixels au pas de 10 µm par cette même méthode de reflow. Pour l’axe hybridation à froid, nos travaux ont permis la validation d’une méthode de croissance de nano-fils ZnO par une voix hydrothermique à basse température (<90°C). / Evolution of microelectronics follows several major roads, in particular the size decrease of active elements (reduction of size of transistors), better electrical performances, high I/O density and smaller size. This revolution has been predicted by Gordon Moore who suggested that integrated circuits would double in complexity every 24 months. As a consequence, this evolution induces both the reduction of prices and the weight of components.The term flip chip describes the method of electrically connecting the die to the package substrate. Flip chip microelectronic assembly is the direct electrical connection of face-down (or flipped) integrated circuit (IC) chips onto substrates, circuit boards, or carriers, using conductive bumps on the chip bond pads. Flip chip offers the highest speed electrical performance, reduces the delaying inductance and capacitance of the connection, Smallest Size Greatest I/O Flexibility, Most Rugged, high I/O density and Lowest Cost.This thesis work study concentrates on two main directions. The first one concerns hybridization by means of the technology of Indium bumps associated to a reflow process and the second one is about pressure induced hybridization at low temperature using nanostructures (Nano-scratch). In this work, we have developed a complete process to assemble a focal plane array format of 640 x 512 pixels with a pitch of 15 µm. These studies also allowed the mechanical validation of hybridization of a focal plane arrays 1280*1024 pixels with a pitch of 10 µm. Concerning alternative technologies to flip chip reflow, we introduced and demonstrate the relevance of a method of growth of ZnO nanorods using low temperature wet chemical growth and further hybridization at ambient temperature.

INTRODUÇÃO: A deleção do cromossomo 9p tem sido encontrada em 14 a 36% dos pacientes com carcinoma renal tipo células claras (CRCC) e está associado a tumores de alto grau, estágio avançado, presença de metástases linfonodais e sistêmicas. OBJETIVOS: Avaliar se a deleção do cromossomo 9p é fator preditor independente de pior sobrevida livre de recorrência e câncer-específica em pacientes com CRCC localizado. MÉTODOS: Neste estudo de coorte retrospectivo, amostras tumorais de 94 pacientes com CRCC NX-0 M0, submetidos à nefrectomia radical ou cirurgia renal conservadora, foram analisadas através das técnicas de microarranjo tecidual e hibridização in situ com fluorescência. RESULTADOS: O tempo de seguimento médio foi de 11,6 anos e a deleção do 9p foi encontrada em cerca de 15% dos casos. A sobrevida câncer específica estimada em 5 e 10 anos foi respectivamente de 99% e 96% nos pacientes sem a referida perda cromossômica e de 71% e 57% naqueles com perda do 9p (p < 0,001). A deleção do cromossomo 9p foi fator prognóstico independente na análise multivariada, aumentando o risco de morte pela doença em 28x (IC 95% 5-155, p < 0,001). Tal deleção foi o preditor mais importante de mortalidade câncer específica, superior a qualquer fator patológico analisado, inclusive ao tamanho tumoral. Em pacientes com baixo risco de progressão, isto é, baixo escore SSIGN (0-2), baixo risco segundo a UISS e baixo risco segundo a Tríade Patológica da USP, tumores deletados do 9p estão significativamente associados com pior sobrevida câncer-específica em 10 anos: respectivamente 70%, 67% e 67% versus 98%, 97% e 98% naqueles sem a perda do 9p. CONCLUSÃO: A deleção do cromossomo 9p estabelece independentemente um pior prognóstico para pacientes com CRCC localizado, fornece informação clínica relevante adicional e pode aperfeiçoar a habilidade preditora dos principais sistemas prognósticos atuais / INTRODUCTION: Deletion of chromosome 9p has been found in 14-36% of patients with clear cell renal cell carcinoma (ccRCC) and is associated with high grade tumors, advanced tumor stage, presence of lymph node involvement and metastases. OBJECTIVES: To assess whether deletion of chromosome 9p is an independent predictor of worse recurrence-free and cancer-specific survival in patients with localized ccRCC. METHODS: In this retrospective cohort study, tumor samples of 94 patients with NX-0 M0 ccRCC undergoing radical nephrectomy or renal conservative surgery, were analyzed using tissue microarray and fluorescence in situ hybridization. RESULTS: Mean follow-up was 11.6 years and 9p deletion was found in near 15% of cases. Estimated cancer-specific survival at 5 and 10 years was, respectively, 99% and 96% in patients without such chromosomal loss and 71% and 57% in those with 9p loss (p < 0.001). Deletion of chromosome 9p is an independent prognostic factor in multivariate analysis, increasing the risk of disease-specific death in 28x (95% CI 5-155, p < 0.001). This deletion was the strongest predictor of cancer-specific mortality, superior to any analysed pathological factor, including tumor size. In patients at low risk of progression, namely low score (0-2) SSIGN, low risk UISS and low risk USP Pathological Triad, 9p-deleted tumors were associated with worse 10 years cancer-specific survival: respectively 70%, 67% and 67% versus 98%, 97% and 98% in those with no 9p loss. CONCLUSIONS: Deletion of chromosome 9p independently establishes a worse prognosis for patients with localized ccRCC, provides relevant additional clinical information and can improve the predictive ability of the main current prognostic models

O feijão é importante fonte carboidratos, vitaminas, minerais e fibras. No Brasil, a produtividade desta leguminosa é baixa e um dos fatores é a ocorrência de doenças como a antracnose causada pelo Colletothrichum lindemuthianum, que gera perdas de até 100% da produção. Plantas possuem diversos mecanismos de defesa contra patógenos e relatos apontam que o silício é capaz não só de promover mudanças morfológicas nas folhas, mas também de ativar os genes de resistência. O presente trabalho foi dividido em três estudos que tinham como objetivo: (1) entender a resposta de três cultivares de feijoeiro ao silício disponível na solução nutritiva; (2) identificar a contribuição do Si na expressão de genes relacionados à infecção pelo fungo através da construção de duas bibliotecas subtrativas por supressão (SSH), visando selecionar genes diferencialmente representados durante a infecção da planta com a raça 65 de C. lindemuthianum (a) e durante a infeção da planta na presença de uma maior dose silicato de potássio (75 ppm) no substrato (b); (3) identificar a resposta de dez transcritos selecionados no Estudo 2 para tentar entender a resposta dos mesmos em diferentes períodos (0; 6; 42; 72 h) após a inoculação, com ou sem suplemento de Si. Como resultados, foi observado que para as três cultivares avaliadas o Si começa a ser absorvido 14 dias após o transplante. Também foi identificado por de microscopia de varredura (MEV) que não há diferença significativa entre o número de tricomas e cada cultivar, mas que para o número de estômatos a cultivar IAC-Harmonia destacou-se das demais. Além disso, quando as três cultivares foram suplementadas com Si, houve a formação de uma cera epicuticular descrita como mecanismo de defesa da planta contra fungos; e que através de EDX (Energy-dispersive X-ray spectroscopy) foi possível constatar que plantas tratadas com Si apresentam maior teor deste elemento nas folhas. Através de inoculações com a raça 65 do patógeno verificou-se o efeito do mineral na redução da severidade da doença nas cultivares IAC-Harmonia e Pérola. No segundo estudo, duas bibliotecas de hibridização subtrativa por supressão (SSH), foram construídas visando selecionar os genes diferencialmente expressos entre plantas inoculadas e não-inoculadas (A) e entre plantas inoculadas e tratadas ou não com 75 ppm de Si (B). Foram geradas 991 sequências únicas, anotadas através do GeneOntolgy. Quinze genes de cada biblioteca foram selecionados para os experimentos de validação por RT-qPCR. Para a Biblioteca A, 11/15 genes foram positivamente regulados, e em B, 14/15. No terceiro estudo ficou evidenciado que a inoculação com o patógeno alterou positivamente a expressão de sete genes, enquanto que o tratamento com 75 ppm de Si alterou a expressão de oito genes, em pelo menos um dos tempos avaliados / Beans are an important source of carbohydrates, vitamins, minerals and fibers. In Brazil, this legume still has low productivity and one of the factors involved is the occurrence of diseases such as anthracnose, caused by the fungus Colletothrichum lindemuthianum, which causes losses in production of up to 100%. Plants present several defense mechanisms against pathogens and the reports indicate that silicon does not only promote morphological changes in leaves, but also activates resistance genes. This work was divided into three studies aiming: (1) to understand the response of three bean cultivars to a silicon source in a nutrient solution, (2) to identify the contribution of Si in the expression of genes related to the infection by the fungus by constructing two subtractive suppression libraries (SSH), to select genes differentially represented during infection of the plant with race 65 of C. lindemuthianum (a) and during infection of the plant in the presence of higher dose of potassium silicate (75 ppm) in the substrate (b), (3) to identify the response of ten selected transcripts in Study 2 in various periods (0, 6, 42, 72 h) after inoculation, with or without supplemental Si. As a result, it was observed that for all three cultivars Si begins to be absorbed 14 days after transplantation. Was also identified by microscopy (SEM) that there is no significant difference between the number of trichomes among cultivars, but that the number of stomata for the IAC-Harmonia stood out from the rest. Moreover, when the three cultivars were supplemented with Si, thus forming an epicuticular wax described as a defense mechanism against plant fungi, and that by EDX (Energy-dispersive X-ray spectroscopy) it was found that plants treated with Si have higher content of this element in leaves. Through inoculations with race 65 of the pathogen it was verified the effect of the mineral in reducing disease severity in IAC-Pérola and IAC - Harmonia. In the second study, two libraries from suppression subtractive hybridization (SSH) were constructed in order to select the differentially expressed genes between inoculated and non-inoculated (A) and between plants inoculated and treated or not with 75 ppm of Si (B). In total, 991 unique sequences were generated, those recorded by GeneOntolgy. Fifteen genes from each library were selected for the validation experiments by RT-qPCR. For library A, 11/15 genes were positively regulated, and in B, 14/15. In the third study it is showed that inoculation with the pathogen positively altered expression of seven genes, whereas treatment with 75 ppm of Si changed the expression of eight genes, in at least one of the times analyzed

Les biocapteurs sont des outils de détection et d'analyse puissants qui ont été largement utilisés dans les domaines de la santé, de la recherche biomédicale et de l’environnement. Cependant, différents biocapteurs utilisent différents transducteurs qui varient par la nature des substrats utilisés et par la chimie de surface. Tous ces paramètres peuvent avoir un effet sur les réactions biomoléculaires aux interfaces et conduire à des variations de la mesure de la constante de dissociation Kd. Dans ce contexte, ce travail de thèse visait à comparer trois techniques différentes : biopuce avec une détection par fluorescence, biocapteur à fluorescence par champ évanescent et biocapteur par résonance de plasmon de surface (SPR). Ces trois techniques ont été comparées pour la détermination de la constant de dissociation de l'hybridation de l'ADN. Pour la biopuce à fluorescence classique, le substrat est une lame de verre et la mesure est effectuée à la fin de l'expérience. Dans le cas du biocapteur à fluorescence à champ évanescent, le polystyrène est le substrat et une détection en temps réel est réalisée. La SPR est réalisée sur un film d'or mince. C'est une technique en temps réel et sans marquage. Les deux techniques basées sur la fluorescence nécessitent de marquer les cibles avec un fluorophore avant la mesure. Un facteur important déterminant la performance de l'analyse est la chimie de surface du capteur. Ici, nous avons optimisé la chimie de la surface de l'or pour le greffage d'ADN modifié thiol. Nous avons étudié deux méthodes de nettoyage: la solution de piranha et le plasma d'oxygène, dans le but d'obtenir une surface d'or propre sans oxydation de l'or. Ensuite, nous avons optimisé les paramètres lors de la mesure SPR comme par exemple la structure interfaciale du capteur, la force ionique .... Enfin, ces trois techniques ont été utilisées pour mesurer la constante de formation du duplex ADN/ADN. Les résultats ont montré que les Kd sont du même ordre de grandeur pour les trois techniques. De plus, pour les trois techniques, une augmentation de la densité de sonde de surface a entraîné une baisse d’affinité telle que mesurée. / Biosensors are powerful detection and analysis tools that have been widely applied in pharmaceuticals, healthcare, biomedical research, and environmental monitoring. However different biosensors use different transducers and therefore different substrates and surface chemistries. All of these parameters may have an effect on the biomolecular reactions at the interface and lead to a deviation in dissociation constant Kd measurements. In this context, this PhD work aimed at comparing three different techniques: fluorescent microarray, evanescent field fluorescence biosensor and surface plasmon resonance (SPR) biosensor, to determine DNA hybridization Kd. For the classical fluorescence microarray, the substrate is a glass slide and the detection is performed at the end of the experiment. In the case of evanescent field fluorescence biosensor, polystyrene is the substrate and it permits a real-time detection. SPR is performed on thin gold film. It is a real-time and a label-free technique. The two fluorescent based techniques require to label the targets with fluorescent dyes prior to the measurements. One important factor determining the performance of the analysis is the surface chemistry of the sensor chip. Herein, we have optimized gold surface chemistry for thiol modified DNA grafting. We studied two cleaning methods: piranha solution and oxygen plasma, aiming at obtaining a clean gold surface without oxidation of the gold. Then, we optimized SPR assay parameters such as interfacial structure of sensor chip, ionic strength... After, these three techniques were used to measure the DNA hybridization Kd. The results showed that the Kds measured are similar for the three techniques. In addition, increasing surface probe density resulted in an increase of Kd of DNA hybridization.

Os genes homeobox atuam na morfogênese e na diferenciação celular e vêm sendo relacionados a cânceres em humanos. O projeto “Genoma Câncer de Cabeça e Pescoço" encontrou aproximadamente 20 desses genes possivelmente envolvidos com esse tipo de neoplasia e o PITX1 foi um dos genes encontrados. Sabe-se que o gene PITX1 está relacionado ao desenvolvimento das estruturas anteriores do embrião, porém sua participação em neoplasias não está bem estabelecida até o momento. Nesse estudo nos propusemos a verificar a presença de transcritos do gene PITX1 em carcinomas epidermóides de boca e tecidos não tumorais adjacentes, analisando sua possível relação com a morfologia das células neoplásicas. Para tanto, os transcritos do gene foram amplificados por RT-PCR e sua localização celular determinada por hibridização in situ com sondas de mRNA específicas. Os resultados mostraram que o transcrito sofreu amplificação em 86,2% dos casos, sendo que 28% foram somente nos tumores, 16% somente nos tecidos não tumorais e 56% em ambos os tecidos. A análise estatística através do Z-test (teste de diferença de proporção entre duas populações) mostrou que não houve diferença significativa entre a amplificação e o tipo de tecido analisado. Reações de hibridização in situ mostraram marcação predominante no componente epitelial de maneira heterogênea ora intensa ora branda em populações celulares diversas tanto nos tecidos tumorais quantos nos tecidos não tumorais adjacentes à lesão, sem relação aparente com a morfologia celular. De maneira geral, o sinal foi mais intenso no epitélio do tecido não tumoral quando comparado ao neoplásico. Frente aos resultados obtidos sugere-se que o gene PITX1 pode estar envolvido na carcinogênese de boca, sendo que a sua expressão está reduzida na maioria das células do carcinoma epidermóide de boca. / Homeobox genes have functions on morphogenesis and cell differentiation and have been related with cancer in humans. PITX1 was one of the genes found in the Head and Neck Cancer Genome Project. It is known that PITX1 gene is related with anterior structures of the developing embryo, although its relation with neoplasm is not we ll established. In this study we proposed to verify the presence of PITX1 gene transcripts in oral squamous cell carcinoma and adjacent non-tumoral tissues, analyzing its possible relation with the morphology of neoplastic cells. For such study, gene transcripts were amplified by RT -PCR and its cellular localization determined by in situ hybridization with specific riboprobes. Results showed that the transcript was amplified in 86,2% of the cases; 28% were only in the tumors, 16% non-tumoral tissues and 56% were amplified in both tissues. Statistics analysis by Z-test showed there was no significant difference between amplification and the type of tissue analyzed. In situ hybridization reactions showed transcripts mostly expressed in the epithelium component in a heterogenic manner sometimes intense and others discrete in several cells populations in both tumoral and non-tumoral adjacent tissues, with no apparent relationship to cell morphology. In general, signal was more intense in the non-tumoral epithelium when compared to the neoplasia. These results suggest that PITX1 gene can be involved with oral carcinogenesis and that its expression is reduced in most of the oral squamous cell carcinoma.

L’histoire de l’ostréiculture française met en évidence la fragilité de cette production face à la surexploitation des stocks et l’apparition de maladies. En particulier, la production d’huître plate, Ostrea edulis, a fortement diminué suite à l’apparition de deux maladies parasitaires dont la bonamiose. Les moyens de lutte contre la bonamiose sont relativement restreints. Ils sont essentiellement basés sur la surveillance de la santé des huîtres afin de limiter la dissémination et la propagation de la maladie. Cependant l’utilisation de modèles prédictifs de l’évolution de la maladie en zone infectée permettrait d’optimiser la gestion des stocks et minimiser l’impact des agents pathogènes. De plus, le développement d’animaux résistants à l’infection pourrait permettre de relancer cette production. Ces différentes approches nécessitent des outils diagnostiques adaptés, une bonne connaissance du cycle de vie de l’agent pathogène, et, plus particulièrement des interactions du parasite avec son hôte. Dans ce contexte, l’objectif principal du travail de thèse proposé est de comprendre les interactions entre l’huître plate Ostrea edulis et son parasite Bonamia ostreae, et, plus particulièrement les bases moléculaires de la résistance au parasite. Dans un premier temps, la réalisation d’une banque soustractive d’ADNc a permis d’identifier des ESTs différentiellement exprimées chez des hémocytes en réponse au parasite. L’expression de certains gènes dont une galectine a été mesurée en PCR en temps réel dans le contexte d’infections in vitro. En complément, la réponse cellulaire a été étudiée par cytométrie en flux et l’infection contrôlée en microscopie. Ces expériences ont montré une multiplication parasitaire dans les hémocytes au cours du temps associée à une diminution de la production d’EOR et d’estérases. Dans un second temps, il a été entrepris une étude comparative entre une population d’huîtres plates résistantes à la bonamiose et une population naturelle. Les résultats obtenus tendent à montrer qu’une modulation de l’apoptose et une diminution de la phagocytose seraient impliquées dans les mécanismes liés à la résistance à la bonamiose. Ce travail est le premier à étudier la réponse des hémocytes d’huîtres plates à une infection par le parasite Bonamia ostreae au niveau cellulaire et moléculaire. / The history of the French oyster production highlights the fragility of this production against overexploitation and disease outbreaks. In particular, the production of flat oyster, Ostrea edulis, has decreased following the emergence of two parasitic diseases including bonamiosis. The means to fight against bonamiosis are relatively limited. They are mainly based on oyster health surveillance to limit the spread of the disease. However, the use of predictive models of disease progression in infected area would help to improve stock management and minimize the impact pathogens. Moreover the development of resistant animals could help to revive this production. These different approaches require appropriate diagnostic tools, a good knowledge of the life cycle of the pathogen, and the interactions between the parasite and its host. In this context, the main objective of the phD work is to understand the interactions between the flat oyster Ostrea edulis and the parasite Bonamia ostreae, and particularly the molecular basis of the resistance to the parasite. In a first step, a subtractive cDNA bank allowed the identification of ESTs differentially expressed in haemocytes in response to the parasite. Expression of some genes, among which a galectin, was measured by Real Time PCR in the context of in vitro infections. In addition, the cellular response was investigated by flow cytometry and the infection was checked by microscopy. These experiments showed a multiplication of the parasite inside haemocytes associated with a decreased of esterases and of the production of ROS. In a second step, a comparative approach was carried out between a population of oysters resistant to bonamiosis and a natural population. Results suggest that modulation of apopotosis and decrease of phagocytosis could be involved in mechanisms related to resistance to bonamiosis. This work is the first study on the response of haemocytes of flat oysters to an infection with the parasite Bonamia ostreae at the cellular and molecular levels.

Dans ce mémoire, nous présentons une stratégie basée sur une approche hybridedans le domaine temporel, couplant une méthode de résolution des équations de Maxwelldans le domaine 3D (FDTD) avec une méthode de résolution des équations de ligne detransmission, afin de pouvoir simuler des problèmes électromagnétiques de grande échelle. Lemémoire donne les éléments d’hybridation pour deux cadres d’utilisation de cette approche :une approche multi-domaine et une approche multi-résolution ou d’échelle.L’approche multi-domaine est une extension de la méthode FDTD 3D à plusieurs sousdomainesreliés par des structures filaires sur lesquelles on résout une équation de lignes detransmission par un formalisme FDTD 1D. La difficulté est d’abord d’avoir une définitionimplicite du champ électromagnétique dans la théorie des lignes de transmission, et d’autrepart de prendre en compte les effets du sol sur les courants induits au niveau des lignes etsur les champs électromagnétiques.L’approche multi-résolution ou d’échelle est conçue pour étendre les capacités de la méthodeFDTD au traitement du routage de câbles complexes ayant une section plus petite quela taille de la cellule. Ce mémoire présente différentes techniques pour évaluer les paramètresde la ligne, basées sur la résolution d’un problème de Laplace 2D, ainsi qu’une méthode decouplage champs/câbles basée sur le courant de mode commun.L’ensemble de ce travail nous a permis de proposer une méthode numérique efficace pourcalculer les effets électromagnétiques induits par une source (type onde plane ou dipolaire)sur des sites de grande dimension, composés de plusieurs bâtiments reliés entre eux par unréseau de câbles. Dans ce cadre une application à la foudre a été réalisée. / In this thesis, we present a strategy based on a hybrid approach in the timedomain, by coupling 3D method (FDTD) with a multi-conductors transmission line (MTL)method, in order to simulate complex large scale electromagnetic problems. This reportgives the theoretical and numerical elements for coupling these approaches for two kindof problems, which are the multi domains approach and the multi scale approach. Themultiple domains approach is an extension of the classical FDTD method taking into accountseveral 3D subdomains, interconnected by a wire network, on which a 1D transmission lineformalism is used. The main issues are, on one hand to have an implicit expression ofthe electromagnetic field in the transmission line approach, and on the other hand to beable to take into account the ground effects on the induced currents, on the transmissionline parameters and on the electromagnetic field. The multi scale approach is developed toextend the capabilities of FDTD to deal with complex cables routing. We assume that thecross section of the cables are smallest than the cell size, and in these problems, the 1Dtransmission line problem is physically included in the 3D global computational domain.The work done in this thesis leaded to a new field to transmission line coupling based onthe common mode current, and an evaluation of the transmission. line parameters basedon a Laplace equation resolution in 2D. In this work, we have elaborated and proposedefficient numerical strategies for the computation of electromagnetic induced effects on largeand complex sites, composed of several interconnected distant buildings. An application tolightning problems have been done.

O Sarcoma Sinovial revela consistentemente t(X;18) resultando em SS18- SSX1, SS18-SSX2 e raramente SS18-SSX4. Dos 328 casos incluídos neste estudo, Sarcoma Sinovial foi considerado a primeira possibilidade diagnóstica ou um importante diagnóstico diferencial em 134 casos: destes, cDNA de qualidade foi obtido em 131. A fusão SS18-SSX foi identificada em 126 (96%) casos (74 SS18-SSX1, 52 SS18-SSX2) através de qRT-PCR e 120 (92%) por RT-PCR convencional. 101 casos no array de tecidos, analisados por FISH, revelaram que 87 (86%) mostraram rearranjo do SS18. Quatro casos positivos por RT-PCR mostraram perda de um sinal spectrum green e 15 casos revelaram cópias múltiplas de SS18: ambos os achados são potencialmente problemáticos na interpretação de resultados. Um dos 3 casos não analisados por RT-PCR por não ter gerado cDNA de qualidade, foi positivo por FISH. A fusão SS18-SSX1 foi demonstrada em 56 SS monofásicos e 18 SS bifásicos. SS18-SSX2 foi detectada em 41 monofásicos e 11 bifásicos. Áreas pouco diferenciadas foram identificadas em 44 casos (31%). Não houve correlação estatisticamente significante entre os subtipos bifásico, monofásico e o tipo de fusão. Cinco casos foram negativos através dos três métodos utilizados, três de localização pleural. Após correlação clínica, o diagnóstico de mesotelioma foi favorecido em um caso, tumor fibroso solitário em outro e o diagnóstico de sarcoma sem outras especificações no terceiro. A possibilidade do diagnóstico de TMBNP não pode ser excluída nos outros dois casos. Nós concluímos que os métodos moleculares são ferramentas auxiliares importantes para o diagnóstico de SS com 95% de sensibilidade e 100% de especificidade, mas os resultados devem ser interpretados à luz de características clínicas e dados imunohistoquímicos. / Synovial Sarcoma consistently harbors t(X;18) resulting in SS18-SSX1, SS18-SSX2 and rarely SS18-SSX4 fusion transcripts. Of 328 cases included in our study, synovial sarcoma was either the primary diagnosis or was very high in the differential diagnosis in 134 cases: of these, amplifiable cDNA was obtained from 131. SS18-SSX fusion products were found in 126 (96%) cases, (74 SS18-SSX1, 52 SS18-SSX2), using quantitative and 120 by conventional RT-PCR. 101 cases in a tissue microarray, analyzed by FISH, revealed that 87 (86%) showed SS18 rearrangement: 4 reverse transcriptase polymerase chain reaction positive cases, reported as negative for FISH, showed loss of one spectrum green signal, and 15 cases had multiple copies of the SS18 gene: both findings are potentially problematic when interpreting results. One of 3 cases, not analyzed by RT PCR due to poor quality RNA, was positive by FISH. SS18-SSX1 was present in 56 monophasic and 18 biphasic synovial sarcoma: SS18-SSX2 was detected in 41 monophasic and 11 biphasic synovial sarcoma. Poorly differentiated areas were identified in 44 cases (31%). There was no statistically significant association between biphasic, monophasic and fusion type. Five cases were negative for SS18 rearrangement by all methods, 3 of which were pleural-sited neoplasms. Following clinical input, a diagnosis of mesothelioma was favored in one case, a sarcoma, not-otherwise specified in another and a solitary fibrous tumor in the third case. The possibility of a malignant peripheral nerve sheath tumor could not be excluded in the other 2 cases. We concluded that the employment of a combination of molecular approaches is a powerful aid to diagnosing synovial sarcoma giving at least 96% sensitivity and 100% specificity but results must be interpreted in the light of other modalities such as clinical findings and immunohistochemical data.

Os genes homeobox atuam na morfogênese e na diferenciação celular e vêm sendo relacionados a cânceres em humanos. O projeto “Genoma Câncer de Cabeça e Pescoço” encontrou aproximadamente 20 desses genes possivelmente envolvidos com esse tipo de neoplasia e o PITX1 foi um dos genes encontrados. Sabe-se que o gene PITX1 está relacionado ao desenvolvimento das estruturas anteriores do embrião, porém sua participação em neoplasias não está bem estabelecida até o momento. Nesse estudo nos propusemos a verificar a presença de transcritos do gene PITX1 em carcinomas epidermóides de boca e tecidos não tumorais adjacentes, analisando sua possível relação com a morfologia das células neoplásicas. Para tanto, os transcritos do gene foram amplificados por RT-PCR e sua localização celular determinada por hibridização in situ com sondas de mRNA específicas. Os resultados mostraram que o transcrito sofreu amplificação em 86,2% dos casos, sendo que 28% foram somente nos tumores, 16% somente nos tecidos não tumorais e 56% em ambos os tecidos. A análise estatística através do Z-test (teste de diferença de proporção entre duas populações) mostrou que não houve diferença significativa entre a amplificação e o tipo de tecido analisado. Reações de hibridização in situ mostraram marcação predominante no componente epitelial de maneira heterogênea ora intensa ora branda em populações celulares diversas tanto nos tecidos tumorais quantos nos tecidos não tumorais adjacentes à lesão, sem relação aparente com a morfologia celular. De maneira geral, o sinal foi mais intenso no epitélio do tecido não tumoral quando comparado ao neoplásico. Frente aos resultados obtidos sugere-se que o gene PITX1 pode estar envolvido na carcinogênese de boca, sendo que a sua expressão está reduzida na maioria das células do carcinoma epidermóide de boca. / Homeobox genes have functions on morphogenesis and cell differentiation and have been related with cancer in humans. PITX1 was one of the genes found in the Head and Neck Cancer Genome Project. It is known that PITX1 gene is related with anterior structures of the developing embryo, although its relation with neoplasm is not we ll established. In this study we proposed to verify the presence of PITX1 gene transcripts in oral squamous cell carcinoma and adjacent non-tumoral tissues, analyzing its possible relation with the morphology of neoplastic cells. For such study, gene transcripts were amplified by RT -PCR and its cellular localization determined by in situ hybridization with specific riboprobes. Results showed that the transcript was amplified in 86,2% of the cases; 28% were only in the tumors, 16% non-tumoral tissues and 56% were amplified in both tissues. Statistics analysis by Z-test showed there was no significant difference between amplification and the type of tissue analyzed. In situ hybridization reactions showed transcripts mostly expressed in the epithelium component in a heterogenic manner sometimes intense and others discrete in several cells populations in both tumoral and non-tumoral adjacent tissues, with no apparent relationship to cell morphology. In general, signal was more intense in the non-tumoral epithelium when compared to the neoplasia. These results suggest that PITX1 gene can be involved with oral carcinogenesis and that its expression is reduced in most of the oral squamous cell carcinoma.