A raiva é uma zoonose viral que afeta o Sistema Nervoso Central (SNC) causando encefalite e meningoencefalite, de evolução aguda e fatal, que acomete mamíferos carnívoros e morcegos, e periodicamente se manifesta sob a forma de epizootias ou surtos epidêmicos em populações humanas. Neste estudo foram analisadas 16.190 amostras de bovinos, equídeos e morcegos, e menos frequentemente de outros mamíferos durante o período de 1981 a 2012, provenientes do Estado do Paraná. Desse total, 2.766 amostras foram positivas para raiva; 81,74% foram de bovinos, 10,34% de equídeos, 4,05% de morcegos, 2,31% em animais de produção não bovinos, 1,52% em caninos e 0,04%em outros animais. Ao longo da série histórica, há, para os bovinos, uma tendência de aumento das notificações e não foram observadas variação sazonal e cíclica. Na análise espaço-temporal foi detectado um aglomerado mais provável de notificações de raiva em bovinos, envolvendo 20 municípios da região litorânea e metropolitana de Curitiba entre 1981 e 1987. Além dele, foram detectados seis aglomerados secundários sugerindo uma migração da raiva ao longo do tempo no Estado do Paraná. Ao longo da série histórica dos equídeos há uma tendência de diminuição das notificações e não foram observadas variação sazonal e cíclica. Os clusters encontrados na análise espaço-temporal da raiva nos equídeos corroboram com aqueles encontrados na análise dos bovinos localizados nas mesmas regiões durante no mesmo período, sugerindo a migração do vírus da raiva no mesmo sentido da observada na análise dos bovinos. Durante o período de 1981 a 1997, os casos de raiva em morcegos acompanham o trajeto da migração dos aglomerados dos bovinos e dos equídeos, o que demonstra que a raiva ocorre endemicamente no território do Estado do Paraná em herbívoros e morcegos. / Rabies is a viral zoonosis that affects the central nervous system (CNS) causing encephalitis and meningoencephalitis, acute and fatal outcome, which affects mammalian carnivores and bats, and periodically manifests itself in the form of epidemics or outbreaks in human populations. In this study 16,190 samples of cattle, horses and bats, and less frequently other mammals were analyzed during the period 1981 to 2012, from the State of Paraná. Of this total, 2,766 samples were positive for rabies; 81.74 % were bovine, equine 10.34 %, 4.05 % of bats, 2.31 % in livestock no bovine, 1.52 % in canine, and 0.04% in other animals. Throughout the time series, there is, for cattle, a trend of increased reporting and no seasonal or cyclical variations were observed. In spatio-temporal analysis, more likely to notifications of rabies in cattle, a cluster involving 20 municipalities in coastal and metropolitan Curitiba between 1981 and 1987 was detected. Besides this, six sub clusters were detected suggesting a migration of anger over time in the state of Paraná. Throughout the historical series of equine there is a downward trend in notifications and no seasonal and cyclical variations were observed. Clusters found in the spatio-temporal analysis of rabies in horses corroborate those found in the analysis of cattle located in the same regions during the same period, suggesting the migration of rabies virus in the same direction as that observed in the cattle analysis. During the period from 1981 to 1997, cases of rabies in bats follow the migration path of clusters of bovine and equine. This shows that rabies is endemic in the state of Paraná in herbivores and bats.

Facial expressions convey a wealth of information about our feelings, personality and mental state. In this thesis we seek efficient ways of representing and analysing facial expressions of varying intensities. Firstly, we analyse state-of-the-art systems by decomposing them into their fundamental components, in an effort to understand what are the useful practices common to successful systems. Secondly, we address the problem of sequence registration, which emerged as an open issue in our analysis. The encoding of the (non-rigid) motions generated by facial expressions is facilitated when the rigid motions caused by irrelevant factors, such as camera movement, are eliminated. We propose a sequence registration framework that is based on pre-trained regressors of Gabor motion energy. Comprehensive experiments show that the proposed method achieves very high registration accuracy even under difficult illumination variations. Finally, we propose an unsupervised representation learning framework for encoding the spatio-temporal evolution of facial expressions. The proposed framework is inspired by the Facial Action Coding System (FACS), which predates computer-based analysis. FACS encodes an expression in terms of localised facial movements and assigns an intensity score for each movement. The framework we propose mimics those two properties of FACS. Specifically, we propose to learn from data a linear transformation that approximates the facial expression variation in a sequence as a weighted sum of localised basis functions, where the weight of each basis function relates to movement intensity. We show that the proposed framework provides a plausible description of facial expressions, and leads to state-of-the-art performance in recognising expressions across intensities; from fully blown expressions to micro-expressions.

Les structures extensives d'âge Mésozoïque tardif (Crétacé) sont très répandues en Eurasie orientale, depuis la Transbaïkalie en Russie jusqu'à l'intérieur de la Chine du Sud. Elles constituent la plus grande province de distension crustale dans le monde. Cette thèse a sélectionné des structures développées dans trois endroits différents du bloc de Chine du sud en utilisant les méthodes de la géologie structurale, de l'anisotropie de la susceptibilité magnétique et de la géochronologie (U-Pb sur zircon et titanite, U-Th-Pb sur monazite et Ar-Ar sur micas et amphiboles). L'expression des structures extensives diffère selon les endroits étudiés: (1) la ceinture orogénique de HP/UHP Tongbai-Dabie, le long de la bordure nord du bloc de Chine du sud a été remaniée par au Crétacé par la formation d'un antiforme ou d'un dôme métamorphique extensif. Contemporaine de la migmatisation et du magmatisme syntectonique, le régime extensif a commencé à environ 145 Ma et s'est approché de son point culminant vers 130 Ma. Ce qui a été interprété comme le résultat de la suppression de la racine orogénique. Localement, un nouvel épisode de distension vers 110-90 Ma a également été enregistré; (2) le batholite de Dayunshan-Mufushan intrudif dans l'orogène Neoproterozoic Jiangnan se compose de deux phases d'intrusions granitiques d'âge Jurassique (ca. 150 Ma) et Crétacé inférieur (ca. 132 Ma). Le pluton le plus récent s'est mis en place dans un contexte d'extension NW-SE correspondant au processus amincissement crustal du Crétacé inférieur, avec une faille de détachement développée le long de sa bordure ouest; (3) l'anticlinal de Huangling dans le craton du Yangtze est un pli asymétrique d'axe N-S formé entre le Jurassique et le Crétacé inférieur. Sur les deux flancs, la couverture sédimentaire a participé à une série de plis d'effondrement de vergence opposée et de glissements banc-sur-banc des couches. Les exemples étudiés ci-dessus représentent une série de structures d'extension d'âge Crétacé développées dans différents niveaux structuraux: exhumation de croûte inférieure et moyenne de accommodée par un fort étirement, mise en place syntectonique de plutons granitiques avec étirement limité, déformation de la couverture sédimentaire sous une faible extension. Ils indiquent que la Chine du Sud a également participé au régime extensif bien connu en Chine du Nord. Ces résultats apportent des données nouvelles de première main permettant de discuter le cadre tectonique et géodynamiques spatio-temporel du régime extensif du Crétacé sur la marge orientale de l'Eurasie. / Late Mesozoic extensional structures are widespread in eastern Eurasia (from Transbaikalia region in Russia to inland South China). They constitute the largest crustal extensional province in the world. This thesis selected extensional structures developed in three different tectonic settings in the South China block. Detailed studies including structural geology, anisotropy of magnetic susceptibility and geochronology (zircon and titanite U-Pb, monazite U-Th-Pb, and mica Ar-Ar) were conducted. The expression of these extensional structures is not the same for each area: (1) the Tongbai-Dabie HP/UHP orogenic belt along the northern edge of the South China block was reworked by Cretaceous extensional antiform or metamorphic core complex. Coeval with migmatization and syntectonic magmatism, the extensional regime started at ca. 145 Ma, and approached its climax at ca. 130 Ma that was signaled by removal of the orogenic root. Locally, a late (110-90 Ma) extensional event was also recorded; (2) the Dayunshan-Mufushan batholith intruding the Neoproterozoic Jiangnan orogen is composed of two phases of granitic intrusions with Late Jurassic (ca. 150 Ma) and Early Cretaceous (ca. 132 Ma) ages, respectively. The late pluton emplaced under a NW-SE extensional setting corresponding to the Early Cretaceous crustal thinning process, with a detachment fault developed along its western margin; (3) the Huangling anticline within the Yangtze craton is a nearly N-S striking asymmetric dome formed between the Late Jurassic and Early Cretaceous. The sedimentary cover on the two flanks was involved in a series of oppositely-directed collapse folding and layer-parallel slipping. These examples of Cretaceous extensional structures in different tectonic levels (exhumation of middle-lower crust by strong stretching, syn-tectonic emplacement of granitic pluton with limited stretching, deformation of sedimentary cover under a weak extension) indicates that South China also was involved into the regional extensional regime coeval with the destruction of the North China craton. These results provide first-hand new structural evidence for further discussing the temporal-spatial framework and geodynamic setting of the Cretaceous extensional tectonics on the eastern margin of Eurasia.

For centuries, river catchments and their constituent habitats have been altered and modified through various human activities to maximise provision of tangible benefits like food and water, while impacting on their capacity to provide other less obvious but equally important benefits for human survival. However, in the last few decades, perceptions on the role of catchments as mere providers of tangible benefits have been changing, as recognition has been given to other human beneficial services like regulation of floods. This recognition has drawn increased interest in both science and policy, towards understanding human-nature relations and how approaches like the ecosystem services concept can inform sustainable management of catchments. Although, the multiple and differently weighted relationships existing between habitats and ecosystem services have been acknowledged, the relationship between spatio-temporal change in habitats and spatio-temporal change in ecosystem services delivery, has not received as much attention in the research literature. In this thesis, it is argued that this is an important omission as spatio-temporal habitat change could have broader consequences for ecosystem services provided by a catchment. On this basis, this study maps and assesses the influence of habitat changes across space and time on ecosystem services delivery at a local catchment scale. Approaches to assessing ecosystem service delivery across landscapes and catchments draw on habitat mapping data for those landscapes or catchments. Such data are in turn used as proxies for estimating different ecosystem services delivered by the landscape or catchment based on their integration with other spatial or non-spatial data. To date this approach has been applied to assess contemporary delivery of different ecosystem services. The basis of the approach taken in this study involved comparing a pre-existing contemporary ecosystem service assessment of two chosen sub catchments of the Tweed catchment in Scotland, with a similar assessment based on a set of older “historic” habitat maps for the mid-20th century period. Derivation of the digital map base for the latter was a major focus of the present study. Aerial photography taken during the Royal Air Force surveys in the 1940s archived in the Royal Commission on Ancient and Historical Monuments of Scotland were obtained and first scanned digitally, arranged into a mosaic of adjacent images and ortho-rectified to remove camera distortion. These photo mosaics were then visually interpreted and, aided with ancillary data, the current (2009) habitat maps were edited and backdated to derive the historic habitat maps for the study catchments. The Spatial Evidence for Natural Capital Evaluation (SENCE) ecosystem services mapping approach was then used to translate generated habitat maps into ecosystem service supply maps. Findings show that the study catchments changed from multifunctional to intensively managed landscapes by 2009, with a higher capacity for supplying provisioning ecosystem services, while their capacity to supply regulating and supporting ecosystem services was reduced. Findings also show that a change in one habitat type results in changes in multiple ecosystem services, while changes in the spatial configuration of habitats reduces areas with high supply capacity for regulating and supporting ecosystem services. This study concludes that ecosystem service delivery is not only affected by changes in gross area of constituent habitats but also by spatial changes in the configuration and distribution of these habitats. In this regard, it is argued that recognising and understanding changes in ecosystem services adds an important strand in catchment management. It is therefore suggested that planning for future ecosystem services in catchment management needs to be informed by historic baselines.

L’objectif de cette thèse est de d’écrire l’évolution du produit dans les trois dimensions (spatiale, temporelle et spatio-temporelle). Dans le contexte industriel actuel, les modèles produit sont considérés uniquement du point de vue spatial pendant la phase de conception et du point de vue temporel pendant la phase d’assemblage. Le manque de lien entre le produit et le process mène à des incompréhensions de définition de produit et entraine de mauvaises interprétations en conception. Cependant, le produit ´évolue à travers le temps et subit des changements tout au long des phases de conception et d’assemblage. L’aspect dynamique des activités de conception nécessite de lier ces deux dimensions afin de pouvoir représenter l’évolution du produit et avoir une cohérence des informations. Par conséquent, la dimension spatio-temporelle (i.e. permettant de lier l’espace et le temps) a besoin d’être ajoutée et les relations entre la modélisation du produit et sa séquence d’assemblage ont besoin d’être particulièrement étudiées. Cette thèse en mécanique et conception s’est inspirée de divers domaines comme la gestion des connaissances, les systèmes d’information géographique et la philosophie. Ici le produit est considéré d’un point de vue perdurantiste. Le perdurantisme considère l’objet comme étant compose de tranches temporelles et gardant toujours la même identité quelque soit le changement subi. D’après les précédentes déclarations, cette thèse introduit une nouvelle description du couple produit-process afin d’assurer la compréhension des intentions de conception aux acteurs projet. Dans le but d’atteindre cet objectif, une théorie mereotopologique, permettant de d´écrire le produit comme perçu dans la réalité, et de développée et implémentée dans un modèle ontologique pour être formalisée. La théorie JANUS d´écrit qualitativement l’évolution du produit à travers le temps dans un contexte de conception orientée assemblage, permettant l’intégration de la séquence d’assemblage d`es le début du processus de conception. La théorie permet la description formelle des relations liant les informations et connaissances du couple produit-process. Ces efforts ont pour but d’apporter une base concrète pour la description des changements d’entités spatiales (telles que les composants) et leurs relations `a travers l’espace et le temps. Cette théorie basée sur les régions lie les dimensions spatiale, temporelle et spatio-temporelle et apporte donc une vision perdurantiste en conception de produit. Ensuite, PRONOIA2 – une ontologie formelle basée sur la précédente théorie –développée. De ce fait, les informations liées à l’assemblage sont rendues accessibles et exploitables par des systèmes de gestion d’information et les outils de XAO afin de supporter les activités de l’architecte produit et du concepteur. En effet, les informations et connaissances liées à la conception de produit, ainsi que la séquence d’assemblage associée, ont besoin d’une fondation sémantique et logique afin d’être gérées de manière cohérente et proactive. Suite au développement de la théorie JANUS et de l’ontologie PRONOIA2, l’approche proposée permet d’associer les informations spatiales (gérées par le PDM) et les informations temporelles (gérées par le MPM) à travers des relations mereotopologiques spatio-temporelles. Par conséquent, de nouvelles entités doivent être gérées dans le PLM, en utilisant notamment l’ontologie et un système hub, afin d’assurer un maintien des principes d’ingénierie proactives et améliorer la compréhension de l’architecte produit et du concepteur concernant l’ évolution du produit. / The major goal of this research is to describe product evolution in the three dimensions (i.e. spatial, temporal andspatiotemporal). In the current industrial context, product models are only considered from a purely spatial point ofview during the design stage and from a purely temporal point of view during the assembly stage. The lack of linkbetween product and process leads to misunderstanding in engineering definition and causes wrong designinterpretation. However, the product undergoes changes throughout the design and assembly phases. The dynamicaspect of design activities requires linking both dimensions in order to be able to represent product evolution andhave consistent information. As such, spatiotemporal dimension (i.e. linking space and time) needs to be added andrelationships between product modelling and assembly sequences need to be particularly studied.This PhD thesis in mechanical design draws inspiration from several domains such as mathematics, geographicinformation systems and philosophy. Here the product is considered from a perdurantist point of view. Perdurantismregards the object as being composed of temporal slices and always keeping the same identity whatever changesundergone. Based on this statement, this PhD thesis introduces a novel product-process description so as to ensureproduct architect's and designer's understanding of design intents at the early design stages. In order to achieve thisobjective, a mereotopological theory, enabling the product description as it is perceived in the real world, has beendeveloped and implemented in an ontology model to be formalized.The JANUS theory qualitatively describes product evolution over time in the context of AOD, integrating assemblysequence planning in the early product design stages. The theory enables the formal relationships description ofproduct-process design information and knowledge. The proposed efforts aim at providing a concrete basis fordescribing changes of spatial entities (i.e. product parts) and their relationships over time and space. This regionbasedtheory links together spatial, temporal and spatiotemporal dimensions, therefore leading to a perdurantistphilosophy in product design.Then, PRONOIA2 - a formal ontology based on the previous mereotopological theory - is developed. Assemblyinformation is accessible and exploitable by information management systems and computer-aided X tools in orderto support product architects and designer's activities. Indeed product design information and knowledge as well asthe related assembly sequence require a semantic and logical foundation in order to be managed consistently andprocessed proactively.Based on JANUS theory and PRONOIA2 ontology, the MERCURY approach enables associating spatial information(managed by PDM) and temporal information (managed by MPM) through spatiotemporal mereotopologicalrelationships. Therefore, new entities are managed through PLM, using ontology and hub system, so as to ensureproactive engineering and improve product architects' and designers' understanding of product evolution.

Traumatic injuries lead to articular cartilage lesion formation and result in the development of osteoarthritis. Recent research suggests that the early stage of mechanical injuries involve cell death (apoptosis and necrosis) and inflammation. In this thesis, we focus on building mathematical models to investigate the biological mechanism involving chondrocyte death and inflammatory responses in the process of cartilage degeneration. Chapter 1 describes the structure of articular cartilage, the process of carti- lage degeneration, and reviews of existing mathematical models. Chapter 2 presents a delay-diffusion-reaction model of cartilage lesion formation under cyclic loading. Computational methods were used to simulate the impact of varying loading stresses and erythropoietin levels. The model is parameterized with experimental results, and is therefore clinically relevant. Due to numerical limitations using delay differential equations, a new model is presented using tools for population dynamics. Chapter 3 presents an age and space-structured model of articular cartilage lesion formation un- der a single blunt impact. Age structure is introduced to represent the time delay in cytokine synthesis and cell transition. Numerical simulations produce similar tempo- ral and spatial patterns to our experimental data. In chapter 4, we extend our model under the cyclic loading setting. Chapter 5 builds a spatio-temporal model adapted from the former models, and investigates the distribution of model parameters using experimental data and statistical methods. Chapter 6 concludes.

The increased concentration of greenhouse gases is associated with the global warming in the lower troposphere. For over twenty years, the space physics community has studied a hypothesis of global cooling in the thermosphere, attributable to greenhouse gases. While the global temperature increase in the lower troposphere has been relatively well established, the existence of global changes in the thermosphere is still under investigation. A central difficulty in reaching definite conclusions is the absence of data with sufficiently long temporal and sufficiently broad spatial coverage. Time series of data that cover several decades exist only in a few separated regions. The space physics community has struggled to combine the information contained in these data, and often contradictory conclusions have been reported based on the analyses relying on one or a few locations. To detect global changes in the ionosphere, we present a novel statistical methodology that uses all data, even those with incomplete temporal coverage. It is based on a new functional regression approach that can handle unevenly spaced, partially observed curves. While this research makes a solid contribution to the space physics community, our statistical methodology is very flexible and can be useful in other applied problems.

Exposure to fine particulate matter (PM2.5) in the ambient air is associated with various health effects. There is increasing evidence which implicates the central role played by specific chemical components such as heavy metals of PM2.5. Given the fact that humans are exposed to complex mixtures of environmental pollutants such as PM2.5, research efforts are intensifying to study the mixtures composition and the emission sources of ambient PM, and the exposure-related health effects. Factor analysis as well source apportionment models are statistical tools potentially useful for characterizing mixtures in PM2.5. However, classic factor analysis is designed to analyze samples of independent data. To handle (spatio-)temporally correlated PM2.5 data, a Bayesian approach is developed and using source apportionment, a latent factor is converted to a mixture by utilizing loadings to compute mixture coefficients. Additionally there have been intensified efforts in studying the metal composition and variation in ambient PM as well as its association with health outcomes. We use non parametric smoothing methods to study the spatio-temporal patterns and variation of common PM metals and their mixtures. Lastly the risk of low birth weight following exposure to metal mixtures during pregnancy is being investigated.

Ces dernières années ont vu une croissance phénoménale dans la production et la diffusion des données spatiales de sources aussi variées qu'hétérogènes. Cela a généré des besoins d'intégration dans des entrepôts de données et des perspectives d'analyse exploratoire et de fouille de données spatiales et spatiotemporelles. Nos travaux se placent dans ce contexte visant l'analyse et l'extraction des connaissances depuis les bases de données spatiotemporelles. Ils traitent différents aspects allant de la modélisation avancée des données spatiales, à la fouille de ces données en passant par leur intégration dans un entrepôt, l'optimisation des requêtes et l'analyse en ligne. Ainsi, nous décrivons nos approches pour la modélisation 3D, puis pour la modélisation spatiotemporelle d'objets mobiles. Ensuite, l'intégration de données spatiales est traitées selon deux aspects : l'intégration de formats et l'intégration de données par l'appariement géométrique. Une architecture d'entrepôt de données spatiales basée sur les standards XML et GML est proposée, puis dotée d'une technique d'optimisation de requêtes spatiales basée sur un cache sémantique. L'exploration des données spatiotemporelles a donné lieu à des solutions originales extension de l'OLAP. Enfin, différentes approches sont proposées pour la fouille de données spatiales. Nous avons ouvert le spectre de nos recherches à la fouille d'autres données complexes, telles que les données séquentielles et textuelles. Ces travaux ainsi que les développements futurs sont exposés dans ce mémoire.

Cette thèse a pour cadre général la modélisation et l'étude des systèmes dynamiques étendus. Nous nous sommes plus particulièrement intéressés aux systèmes possédant une longueur naturelle de discrétisation. Les modèles ainsi obtenus offrent la possibilité de tenir compte de processus trop coûteux numériquement dans des modèles continus. Nous avons considéré deux applications : les nuages moléculaires opaques et la transition vers la turbulence par intermittence spatio-temporelle. Les modèles détaillés de nuages moléculaires ont montré que dans ces régions il n'y a pas de processus dominant. Une description réaliste doit inclure une chimie comprenant une centaine d'espèces au sein d'un fluide turbulent dont le bilan thermique local nécessite la résolution des équations du transfert radiatif. Nous avons développé un modèle minimal, de type ``réseau d'itérations couplées'', en nous plaçant à un niveau phénoménologique. L'étude de ce modèle a montré qu'il est indispensable de prendre en compte ces trois aspects pour décrire les processus contrôlant globalement l'évolution de ces systèmes. En 1986, Y. Pomeau prédit l'existence d'un scénario spécifique et ``universel'' de transition vers la turbulence par intermittence spatio-temporelle. Nous avons étudié le rôle des structures propagatives couramment observées dans les simulations numériques et les expériences, qui peuvent a priori limiter la validité de l'équivalence entre systèmes stochastiques et déterministes. Nous avons montré à partir d'un modèle minimal d'intermittence spatio-temporelle, que ces structures propagatives jouent en effet un rôle actif dans l'apparition du régime turbulent spécifique.