La Fièvre de la Vallée du Rift (VFVR) est une arbovirose zoonotique affectant principalement les ruminants et les humains. Son éco-épidémiologie complexe implique de nombreuses espèces de vecteurs, d'hôtes et de voies de transmission. Ainsi, différents mécanismes de transmission et d'émergence sont impliqués dans la circulation du virus de la FVR (VFVR) et ceux-ci dans des écosystèmes contrastés d'Afrique, de la Péninsule Arabique et des îles du sud-ouest de l'Océan Indien, dont l'île de Madagascar.Par sa superficie, sa grande diversité éco-climatique et sa faune et flore endémique, Madagascar est considérée comme une île continent. On y retrouve, en effet, des écosystèmes variés plus ou moins favorables aux moustiques : semi-arides dans le sud-ouest, humides et froids sur les hautes terres centrales, per-humide dans l'est et humides et chaud dans le nord-ouest. Madagascar a été affectée par deux épidémies de FVR en 1990-91 puis 2008-09. Une étude menée lors de la dernière épidémie a montré que le virus avait largement diffusé dans l'île de façon hétérogène.Compte tenu de la complexité des mécanismes de transmission de la FVR et de la diversité des écosystèmes de Madagascar, nous avons supposé que cette hétérogénéité spatiale était due à des mécanismes de transmission et d'émergence qui variaient en fonction des écosystèmes de l'île. Ainsi, le premier objectif de ce travail de thèse étaient de déterminer les mécanismes et les dynamiques de transmission de la FVR inhérents aux différents écosystèmes de Madagascar. Le second objectif a été d'identifier les mécanismes d'émergence de la FVR à Madagascar et de déterminer s'il sera possible, et nécessaire, de prédire cette émergence à l'échelle des écosystèmes.Dans le cadre de ce travail de thèse deux enquêtes sérologiques nationales, l'une bovine (2008) et l'autre humaine (2011-13) ont, premièrement, été analysées par un modèle linéaire mixte généralisé afin d'identifier les facteurs environnementaux et comportementaux favorables à la circulation du virus chez les bovins et les humains. Deuxièmement, deux enquêtes sérologiques bovines, l'une réalisée en 2008 et l'autre en 2014, ont été analysées pour reconstruire la dynamique de transmission de la FVR dans les différents écosystèmes de l'île. Cette reconstruction a été réalisée à partir de données de séroprévalence et d'âge inclues dans un modèle Bayésien hiérarchique pour estimer la force d'infection annuelle de 1992 à 2014. Enfin, afin de faire le lien biologique avec les résultats des travaux menés à une échelle nationale et de décrire les mécanismes de transmission à une échelle fine, des enquêtes longitudinales entomologiques et sérologiques ont été réalisées entre 2015 et 2016 dans un écosystème à risque. Et ceci, afin de décrire la transmission saisonnière du VFVR chez les ruminants associée à la dynamique de transmission des vecteurs potentiels.Nos résultats ont montré que la région du nord-ouest de l'île est une région à risque de transmission. D'une part, elle est constituée d'environnements associant une forte densité de bovins à des zones humides, inondables et irriguées, favorables aux espèces d'Anopheles et Culex. D'autre part, le VFVR semble avoir circulé de façon relativement intense lors de la période inter-épizootique de 1992 à 2007, puis sa transmission a soudainement augmenté en 2007-2008, ce qui est concomitant avec l'apparition des foyers de FVR en 2008. Pour finir, 6 ans après l'épidémie de FVR à Madagascar, le virus semble toujours circuler à bas bruit dans la région. Cette circulation étant probablement due à une transmission vectorielle favorisée par l'abondance de vecteurs potentiels dans la région.Les résultats de ces différents travaux nous ont permis de présenter des hypothèses de transmission dans les différents écosystèmes de l'île et ainsi de proposer des stratégies de surveillance, de prévention et de lutte contre la FVR adaptées au contexte de Madagascar. / Rift Valley fever (RVF) is a zoonotic vector-borne disease affecting ruminants and humans. Its complex eco-epidemiology involves several species of vectors, hosts and transmission routes. These particularities allowed the circulation of RVF virus (RVFV) in a variety of ecosystems involving different transmission and emergence mechanisms. Indeed, the RVFV has affected contrasted eco-regions in Africa, Arabian Peninsula and South-West Indian Ocean islands, including Madagascar.Madagascar is considered as a continent island due to its ecological diversity and its endemicity level of the flora and the fauna. In particular, the variation of the Malagasy ecosystems (semi-arid in the south, humid and cold in the highlands, humid and warm in the north-west and per-humid in the east) has an impact in their presence and /or the relative abundance of some mosquito species. Madagascar was heavily affected by RVF in 1990-91 and 2008-2009, with evidence of a large and heterogeneous spread of the disease.Thus considering the diversity of RVF eco-epidemiological cycles and the variety of Malagasy ecosystems, we hypothesized that, in Madagascar, the mechanisms of transmission would be different according to these ecosystems. Therefore, the first objective of this thesis was to understand the mechanisms and the dynamics of transmission of RVFV in the different ecosystems. The second objective was to determine the mechanisms of emergence of RVFV and if it would be necessary and possible to predict the emergence of RVFV outbreaks according to the ecosystems.Firstly, we analyzed both cattle and human serological data performed at the national level using generalized linear mixed models to identify the environmental and behavioral factors associated with RVF transmission in both cattle and human. Secondly, we reconstructed the dynamic of transmission of RVF in the different Malagasy ecosystems. Seroprevalence data of cattle of known age were fitted using Bayesian hierarchical models to estimate the annual force of infection from 1992 to 2014. Thirdly, to understand the biological process link to the mechanisms of transmission at the national scale, we investigated the fine scale mechanisms of transmission of RVFV in pilot area of an at-risk region. We, thus, performed both longitudinal entomological and serological surveys between 2015 and 2016, in order to describe the seasonal transmission of RVFV among ruminants and its association with the dynamics of RVFV potential vectors.Our results showed that the northwestern part of Madagascar is an at-risk region for RVFV transmission. On one hand, it is characterized by high cattle densities associated with humid, floodplain and irrigated areas suitable for RVFV potential vector like Anopheles and Culex species. On the other hand, RVFV had probably circulated intensively in the region during the 1992-2007 inter-epizootic period and its transmission increased suddenly in 2007-08, almost concomitantly with the first outbreaks recorded in 2008. Finally, RVFV was still circulated in the northwestern region at low level, 6 years after the last epidemic. This circulation is likely due to vectorial transmission favoring by the abundance of several potential vectors of RVFV in this pilot region.Finally, our better understanding of the mechanisms of transmission of RVFV throughout Madagascar allowed us to propose hypothesis of transmission in different ecosystems of Madagascar and consequently refine strategies for RVF surveillance and prevention.

Les systèmes carbonatés lacustres salins présentent un fort potentiel d’enregistrement des changements paléogéographiques et paléoclimatiques. Ce manuscrit présente une méthode d’analyse pluridisciplinaire (sédimentologie, écologie, stratigraphie, paléontologie, géochimie et paléomagnétisme) et multi-échelle (µm au km) appliquée au bassin lacustre d’Alès et des régions limitrophes au cours du Priabonien (–38 à –33,5Ma). Cette approche a permis d’apporter de nouveaux éléments dans les reconstitutions paléoenvironnementales, paléogéographiques et paléoclimatiques du sud–est de la France au Priabonien. De nouveaux concepts sédimentologiques et stratigraphiques transposables à d’autres systèmes lacustres sont mis en avant. Enfin, les observations permettent de reconstituer, dans un cadre temporel bien contraint, l’histoire de la détérioration climatique précédant la limite Eocène–Oligocène qui correspond à la plus grande crise climatique de ces 50 derniers millions d’années. / Lacustrine carbonate systems are of great interest to record the paleogeographic and paleoclimatic changes. This manuscript provides a multi-disciplinary (sedimentology, ecology, stratigraphy, paleontology, geochemistry and paleomagnetism) and a multi-scale (from µm to km) analysis dedicated to the Alès Basin and the neighboring areas during the Priabonian (–38 to –33.5Ma). Such joint approach has already allowed us to bring new elements regarding the paleoecological, paleoenvironmental and paleoclimatic interpretations. New sedimentological ideas and stratigraphic concepts emerge and could be transposed to such saline lacustrine systems as analogues. Finally, the well-defined chronostratigraphic framework can be used to decipher the climatic deterioration recording prior to the Terminal Eocene Event at the Eocene–Oligocene boundary (the most profound climatic change of the past 50 million years.

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Les données sismiques et les forages des marges continentales distales permettent de comprendre l'architecture et l'évolution de ces domaines, dont l’évolution thermique est peu connue, même si on connaît que les systèmes hydrothermaux jouent un rôle clé dans la distribution des flux de chaleur. Cette thèse vise à étudier les produits diagénétiques dans les sédiments de pré- à post-rift, qui enregistrent l'évolution des interactions roche-fluide. Deux analogues fossiles ont été étudiés: la marge distale adriatique et le système hyper-étiré pyrénéen. Les études de terrain, pétrographiques et géochimiques révèlent une forte hétérogénéité dans la composition des fluides. Dans les premières phases de rifting, dominées par des failles normales à fort pendage, les fluides sont riches en carbonate,tandis que dans les dernières phases, caractérisées par des failles de détachement à faible pendage qui exhument les roches de la croûte continentale et du manteau, les fluides résultent riches en silice. Cette thèse a donc démontré que l'évolution tectonique des marges de rifting comporte aussi des changements spécifiques dans la chimie des fluides hydrothermaux. / Seismic and drill hole data from deep-water distal rifted margins allow to understand the architecture and evolution of these yet little investigated domain. Nonetheless, the thermal evolution is poorly constrained even if hydrothermal systems play a key role in determining the heat fluxes. This Thesis aims to investigate breccias, cements, veins and replacement minerals within the pre- to post-rift sediments that could testify the space-time evolution of rock-fluid interactions. Two fossil analogues are studied: the Adriatic distal margin and the Pyrenean hyper-extended system. Field, petrography and geochemical analyses reveal a strong heterogeneity in the composition of the fluids as well as their hydrothermal features. Two main types of fluids occur: carbonate-rich fluids refer to early rifting phases dominated by high-angle normal faults; silica-rich fluids are related to the last rifting stages characterized by low-angle detachment faults exhuming upper crust and mantle-related rocks. The results of this Thesis highlight how specific changes in the chemistry of the fluid system are intimate lylinked to the tectonic evolution of rifted margins.

La fièvre de la Vallée du Rift (FVR) est une zoonose due à un virus transmissible par une large variété de vecteurs. Au cours des quinze dernières années, elle a rendu malades des dizaines de milliers de personnes, entrainé des centaines de décès humains et provoqué la mort de plus de 100 000 ruminants domestiques en Afrique et dans la péninsule arabique. Suite à la découverte de la présence du virus à Mayotte, les autorités sanitaires, le Cirad (Centre de coopération internationale en recherche agronomique pour le développement) et les éleveurs ont créé en 2009 un système de surveillance en santé animale, le SESAM. L‘objectif de cette thèse était de faire un état des lieux de la situation épidémiologique de la FVR chez les ruminants à Mayotte en 2012-2013, d’évaluer les perspectives de persistance de la maladie et d’étudier les perceptions et les priorités des éleveurs vis-à-vis de cette maladie. En 2012, le fonctionnement du dispositif de surveillance de la FVR a été révisé avec un renouvellement partiel du groupe d’éleveurs sentinelles et un renforcement de la surveillance événementielle basée sur la recherche systématique de la FVR en cas d’avortement ou de mortalité anormale. Une baisse continue de la séroprévalence de 2010 à 2013 a été observée. En 2012-2013, le taux d’incidence est resté stable avec environ deux séroconversions pour 100 animaux-ans. Ce taux est très inférieur au taux d’incidence de 18% observé en 2011. Le virus de la FVR n’a été détecté dans aucun des prélèvements réalisés dans le cadre de la déclaration officielle des avortements chez les ruminants (n=41). Des critères d’évaluation de la performance du dispositif de surveillance ont été proposés et ont mis en évidence une amélioration de la qualité des données entre 2010 et 2013. Un modèle dynamique de type SIR a permis d’estimer le niveau de transmission hôte-vecteur attendu qui expliquerait au mieux la séroprévalence observée de 2008 à 2013 à Mayotte. La probabilité de transmission hôte-vecteur estimée par ce modèle est cinq fois plus faible qu’attendue. Dans ces conditions, la probabilité de persistance de la FVR, en l’absence de nouvelle introduction d’animaux virémiques reste inférieure à 10%, cinq ans après l’arrivée du virus. Enfin, la priorisation des problèmes sanitaires à Mayotte par une démarche d’épidémiologie participative et des réunions d’éleveurs a mis en évidence que les cinq problèmes spontanément rapportés comme les plus importants chez les bovins sont dans l’ordre le charbon symptomatique, les tiques, le syndrome « bavite-fièvre-grippe», le syndrome « dermatophilose-boutons » et la diarrhée. La FVR est absente de ce classement mais les avortements arrivent en 9ème position et à la première selon le critère de « risque ». La surveillance, et les approches interdisciplinaires de modélisation et de sciences humaines doivent être poursuivies pour évaluer plus précisément le risque de réémergence de la FVR à Mayotte et anticiper les réponses à y apporter. La surveillance doit aussi s’adapter aux attentes des éleveurs et développer l’approche syndromique ainsi que s’intégrer pleinement aux dispositifs régionaux et nationaux. / Rift Valley fever (RVF) is a vector-borne zoonosis, with a wide variety of potential competent vectors. During the last fifteen years, RVF caused tens of thousands of human cases, hundreds of human deaths and more than 100,000 domestic ruminant deaths in Africa and in the Arabic peninsula. After the first detection of RVF in Mayotte, an animal health surveillance network has been created in 2009, namely the SESAM. The aim of this PhD was to assess the epidemiological situation of Mayotte toward RVF in 2012-2013, to assess the persistence probability of RVF in the territory and to document farmers’ perceptions and health priorities. In 2012, RVF surveillance has been revised in order to partially renew the pool of the sentinel herds. The passive surveillance with systematic RVF detection assay on abortion and abnormal mortality was enforced. A continuous decrease in the seroprevalence was observed based on 2010-2013 data. During 2012-2013, a steady incidence rate of about 2 seroconversions per 100 animal-year was observed. This rate is much lower than the previous assessment of 18% during 2011. RVF virus was not detected in any of the 41 declared abortion cases. Surveillance performance criteria were discussed and assessed showing mainly an increase in data quality between 2010 and 2013. A SIR dynamic model was built based on vector knowledge and observed seroprevalence in Mayotte from 2008 to 2013. Estimated host-vector transmission rate was fivefold lower than expected according to current literature. Persistence probability, without reintroduction of viremic animals, was predicted to be 10% five years after virus introduction. Finally, health problem prioritization in Mayotte was studied through focus groups, gathering 164 farmers. The five main issues stated were: blackleg, ticks, a respiratory « fever/flu-like» syndrome, a dermatologic syndrome and diarrhoea. RVF was absent from the priority problems list in which abortions were ranked 9th. However abortions came first when « risk » criteria was taken into account, raising issues of cultural risk perceptions. Further surveillance and research using transdisciplinary approaches that mix mathematical modelling and the humanities should be continued with the view to assess more precisely reemergence probability in Mayotte and anticipate mitigating measures. Surveillance and research should also align with farmers’ expectations. The development of syndromic surveillance (abortion, death, etc.) requires strengthening surveillance network and identification data quality. Mayotte surveillance components should also be fully integrated within the regional and national schemes.

As coquinas de bivalves do Grupo Lagoa Feia (Eoaptiano) ocorrem na área sudoeste da Bacia de Campos e constituem reservatórios de hidrocarbonetos. Foram descritos 1030 metros de testemunhos e 368 lâminas delgadas para definir os controles estratigráficos dos eventos e produtos diagenéticos observados e propor um método de predição da paragênese diagenética. Inicialmente foram definidas 34 fácies sedimentares posteriormente agrupadas em 7 associações de fácies nas quais foram reconhecidos os conjuntos de processos geneticamente relacionados, que levaram à interpretação do paleosistema deposicional. Sete produtos eodiagenéticos foram observados na seção informalmente denominada Coquina Inferior e desses, quatro alteram bastante as características permoporosas primárias das rochas, sendo eles: cimentação por calcita blocosa em mosaico, cimentação por sílica microcristalina (quartzo), cimentação por calcedônia e dissolução. Interpreta-se um forte controle do(s) tipo(s) de produto(s) diagenético(s) com a variação do nível base do lago, conforme as seguintes premissas: o cimento de sílica microcristalina ocorre preferencialmente quando o nível base está alto e as rochas sob condições lacustre freáticas, pois, devido ao grande escoamento superficial, o lago neste momento encontra-se enriquecido em Si (proveniente do intemperismo e lixiviação das seções de rochas anteriores), porém ainda diluído (com um volume de água muito amplo), favorecendo a precipitação do quartzo e não da calcedônia. A partir do momento em que o nível do lago cai relativamente, a concentração de Si aumenta e a calcedônia passa a ser o cimento principal. Neste momento, as rochas estão sob condições de ambiente de zona de mistura, pois o nível do lago estaria mais baixo, porém ainda não totalmente em condições de domínio meteórico. A seguir, com nível do lago mais baixo ainda, as rochas passam para o ambiente meteórico e ocorre a precipitação de calcita blocosa (provavelmente necessitando de um tempo de residência baixo, pois o mineral ocorre em todo o intervalo da Coquina Inferior) no meteórico freático, e dissolução no meteórico vadoso. Quando o nível do lago volta a subir, as condições favorecem novamente a precipitação de calcedônia, e, em um nível posterior, mais alto ainda, de sílica microcristalina, iniciando assim um novo ciclo de alterações diagenéticas. A correlação entre a paleobatimetria deposicional da associação de fácies sedimentar e o nível base requerido para determinado(s) tipo(s) de produto(s) diagenético(s) encontrado(s) levou à criação de uma curva de \"velocidade relativa de variação do nível base\", que pôde também ser construída sinteticamente a partir das fácies sedimentares e dos perfis de raios gama e sônico. Tendo em mãos essa curva sintética, foi possível fazer o \"caminho inverso\" e criar um modelo preditivo (ou seja, sem descrição da diagênese em lâminas delgadas) da paragênese diagenética a partir da associação de fácies sedimentar e da \"velocidade relativa de variação do nível base\" em escala de poço (1D) e também em um grid geocelular (3D). A seção Coquina Inferior dos reservatórios da Bacia de Campos apresenta elevado grau de heterogeneidade vertical, gerada pela ciclicidade estratigráfica e pela intensa modificação eodiagenética. O entendimento dos fatores controladores da diagênese levou à criação de um método preditivo da paragênese diagenética em escala de poço (1D) e também em um grid geocelular (3D) que poderá ser usado para a caracterização e gerenciamento de outros campos petrolíferos em carbonatos. / The bivalve coquina from Lagoa Feia Group (Eoaptian), occurs in southwestern part of Campos Basin and consists petroleum reservoirs. 1030 meters of core and 368 thin sections were described to define the stratigraphic controls of the diagenetic events and then create a diagenetic paragenesis predictive method. Firstly, 34 sedimentary facies were defined and then grouped in seven facies associations. These associations have the same genetically depositional process relationship and they were used to define the depositional paleosystem. Seven eodiagenetic products were observed in the informally called Lower Coquina section and four from these products cause an important primary rock permeability and porosity alteration: block calcite cementation, microcrystaline silica (quartz) cementation, chalcedony cementation and dissolution. There is a strong control of the diagentic(s) product(s) type(s) and the base level variation. Microcrystaline silica occurs when the base level is high and the conditions are under lacustrine phreatic environment. Under these conditions, the lake has a Si enrichment due to run off great rates but still diluted, because the huge volume of water. This situation favors the precipitation of quartz instead of chalcedony. When the lake level falls, Si concentration rises, and chalcedony becomes the main cement phase. At this time, the conditions are mostly under mixing zone. When the lake falls again, meteoric environment becomes predominant. At the meteoric phreatic environment blocky calcite occurs as cement and at the meteoric vadose zone environment dissolution is the main process. When the lake level raises again, the conditions favor the precipitation of chalcedony and, in the next level, (higher base level than previous) the conditions are good to microcrystaline silica precipitation. At this moment, a new diagenetic cycle is started. The correlation between depositional paleobathymetry of sedimentary facies association and the lake level required for different types of diagenetic paragenesis led to the creation of a curve called \"relative velocity of base level variation\". This curve may also be calculated synthetically from sedimentary facies, gamma ray and velocity logs. With this synthetic curve it was possible to do a \"reverse path\" procedure and generated a diagenetic paragenesis predictive method. The coquina reservoir has a high level of heterogeneity due to stratigraphic cyclicality and due to eodiagenetic transformations. The understanding of diagenetic controls led to a diagenetic predictive method creation on 1D (well) and 3D (geocell grid). This knowledge can be used for the characterization and management of others carbonates associated oil fields.

Análises de proveniência sedimentar são tradicionalmente utilizadas com o objetivo de reconstruir a relação entre depósitos sedimentares e suas respectivas áreas fonte, de forma a permitir a composição do contexto tectônico regional. Uma aplicação menos explorada dos métodos de análise de proveniência sedimentar é a avaliação detalhada das variações de áreas fonte ao longo da história de preenchimento de uma bacia sedimentar e das variações locais de proveniência em intervalos estratigráficos específicos. Tais estudos podem trazer importantes inferências sobre a configuração dos alto estruturais vizinhos à bacia sedimentar, assim como informações a respeito de eventos tectônicos capazes de mudar o padrão das drenagens que alimentam a bacia sedimentar. Na Bacia Camaquã (Ediacarano-Cambriano, RS) o Grupo Santa Bárbara e o Grupo Guaritas registram eventos de atividade de altos estruturais durante a sedimentação, responsáveis pela segmentação da bacia em sub-bacias. O Grupo Santa Bárbara compreende sucessões siliciclásticas distribuídas em três sub-bacias separadas pelos altos de Caçapava do Sul e da Serra das Encantadas. Na sub-bacia ocidental esse grupo apresenta depósitos de arenitos e conglomerados aluviais, depósitos siltoarenosos de ambientes fluviais distais e lacustres e depósitos conglomeráticos de leques aluviais, que compõem um ciclo retrogradacional inicial, seguido por dois ciclos progradacionais separados por uma superfície brusca. O Grupo Santa Bárbara na sub-bacia central, por sua vez, apresenta uma sucessão siltoarenosa com base conglomerática, que se estende até a porção média da sucessão sedimentar, quando dá lugar a depósitos conglomeráticos de leques aluviais que são depois sucedidos por nova sucessão siltoarenosa no topo da unidade. O Grupo Guaritas apresenta depósitos de rios entrelaçados na base e no topo da unidade, com interdigitação de sistemas deposicionais eólicos, de rios entrelaçados e de leques aluviais na porção intermediária da sucessão. Os depósitos do Grupo Santa Bárbara na sub-bacia ocidental foram investigados em detalhe por meio de levantamentos sistemáticos de dados de proveniência em escala de afloramento, em lâmina delgada e por meio de análises isotópicas em zircões detríticos. Os resultados mostram áreas fonte distintas entre os depósitos aluviais da base e do topo da unidade, sendo que em ambos a proveniência é local. Os depósitos da base têm áreas fonte a oeste e sudoeste da bacia, enquanto os depósitos do topo da unidade têm áreas fonte a leste da bacia, no alto de Caçapava da Sul, sugerindo uma mudança na configuração das áreas fonte que teria início correspondente ao primeiro nível conglomerático da sucessão aluvial intermediária da unidade. Adicionalmente os dados de proveniência indicam ausência de deslocamento entre áreas fonte e depósitos sedimentares indicando que o rejeito das falhas de borda é normal, como esperado para bacias do tipo rift. As sucessões sedimentares do Grupo Santa Bárbara na sub-bacia central foram investigadas de maneira preliminar por meio de análise de proveniência macroscópica. Os dados indicam pouca variação de áreas fonte na história da bacia, com áreas fonte predominantemente no Alto da Serra das Encantadas, que estaria então soerguido. Nos depósitos conglomeráticos superiores há uma contribuição de litoclastos atribuídos ao Alto de Caçapava do Sul. O Grupo Guaritas teve depósitos sedimentares do topo de sua sucessão estudados por meio de análise de proveniência macroscópica em depósitos de leques aluviais e em depósitos fluviais, que cobrem os anteriores em contato erosivo. Os dados apontam para proveniência estritamente local, do Alto da Serra das Encantadas nos depósitos de leques aluviais, enquanto que os depósitos fluviais contam com áreas fonte mais distantes, sugerindo que o Alto da Serra das Encantadas sofreu subsidência e foi recoberto nesse intervalo de tempo. Os dados indicam que o soerguimento do Alto de Caçapava do Sul, que se deu durante a deposição do Grupo Santa Bárbara e individualizou a sub-bacia ocidental, teria provocado uma progradação instantânea dos depósitos sedimentares, ao contrário do previsto em modelos tectônicos disponíveis, em consequência do aumento do aporte sedimentar pela erosão de sedimentos pouco litificados depositados sobre o Alto de Caçapava do Sul e de uma queda na taxa de subsidência das bacias provocado por um amplo domeamento antes da nucleação da falha de borda. Tal progradação está registrada nas sucessões aluviais intermediárias do Grupo Santa Bárbara nas sub-bacias ocidental e central. Após o estabelecimento da falha normal na borda leste do alto estrutural há uma passagem brusca para depósitos mais distais, na sub-bacia ocidental seguida de progradação de cunhas clásticas no topo da unidade, enquanto que na sub-bacia central há uma retrogradação sugerindo que o soerguimento do Alto de Caçapava do Sul tenha resultado na captura de um sistema de drenagem que alimentava toda a bacia para o graben da bacia ocidental, diminuindo assim o aporte sedimentar na sub-bacia central. O Grupo Guaritas indica, por sua vez, uma situação inversa, com mudança nos sistemas deposicionais provocada pela subsidência do Alto da Serra das Encantadas, que teria permitido a captura de sistemas de drenagem para dentro da bacia, promovendo o aumento do aporte sedimentar e a substituição dos sistemas eólicos e de leques aluviais por sistemas fluviais entrelaçados. / Sedimentary provenance is generally used aiming the reconstruction of the relations between sedimentary deposits and their source areas, in order to interpret the regional tectonic setting. An application that is less frequent in sedimentary provenance analysis is the detailed assessment of the changes in the source areas during the infilling history of a sedimentary basin and of the local variation of the provenance data in specific stratigraphic intervals. Such studies can result in important inferences concerning the configuration of adjacent structural highs, as well as information about tectonic events that are capable of changing the drainage network feeding the sedimentary basin. In the Camaquã Basin (RS) the Santa Bárbara and Guaritas groups register events of syn-sedimentary movement of structural highs, which caused the segmentation of the basin into sub-basins. The Santa Bárbara Group comprises siliciclastic successions distributed in three sub-basins separated by the Caçapava do Sul and Serra das Encantadas structural highs. The western sub-basin contains alluvial sandstones and conglomerates, siltstones and sandstones of fluvial and lacustrine environments, and alluvial fan conglomerates, disposed in a initial retrogradatinoal cycle, and two overlying progradational cycles, which are separated by a abrupt flooding surface. In the central sub-basin, the Santa Bárbara Group comprises a siltstone and sandstone succession with conglomerates at its base, followed by alluvial fan conglomeratic deposits in the middle part of the sedimentary succession, which in turn is succeeded by another succession of siltstones and sandstones at the top of the group. The Guaritas Group shows braided river deposits both at the base and the top of the unit, with interfingering of eolian, braided river and alluvial fan systems in the intermediate part of the succession. The deposits of the Santa Bárbara Group in the western sub-basin were investigated in detail through systematic studies of provenance both at the outcrop scale and in thin sections and by detrital zircon isotope analysis. The results show distinct source areas for the alluvial deposits of the base and the top of the unit, with a local sources for both of them. The lower deposits had source areas to the west and southwest of the basin, while the upper ones had source areas to the east of the basin, on the Caçapava do Sul High, suggesting a change in the configuration of the source areas, with its onset corresponding to the first conglomeratic level of the intermediate alluvial succession of the Santa Bárbara Group. The provenance data also shows that there is no significant lateral displacement deposits relative to their source areas, suggesting that the main displacement of the border faults was normal, as expected for rift basins. The sedimentary successions of the Santa Bárbara Group in the central sub-basin were preliminarily investigated through macroscopic provenance analysis. The data implies only in small changes of the source areas through the history of the basin, with source areas in the Serra das Encantadas High, which was then uplifted. In the upper conglomeratic deposits there is some contribution of lithoclasts from the Caçapava do Sul High. The sedimentary deposits of the top of the Guaritas Group were studied through macroscopic provenance analysis in alluvial fan and fluvial deposits, the latter covering the alluvial fans in erosive contact. The data points to strictly local provenance, from the Serra das Encantadas High in the alluvial fan deposits, while the fluvial deposits had also more distant source areas. This suggests that the Serra das Encantadas High subsided during this period, and was covered by the younger fluvial deposits. The collected data suggests that the Caçapava do Sul High uplift, which took place during the deposition of the Santa Bárbara Group and individualized the western sub-basin, triggered a progradation of the sedimentary deposits. This is not in accordance with the existing models, and could be explained as a result of both of an increase in the sedimentary input by erosion of unlithified sediments deposited on the Caçapava do Sul High and of the fall in the subsidence rates of the sedimentary basins due to a wide doming before the nucleation of the main border fault. Such progradation is registered in the alluvial successions of the Santa Bárbara Group in the western and central sub-basins. After the definition of the normal faulting in the eastern border of the structural high, an abrupt passage to distal facies took place in the occidental sub-basin, which was in turn was followed by progradation of clastic wedges on the top of the unit, while in the central sub-basin there is a retrogradation, suggesting that the uplift of the Caçapava do Sul High would have resulted in the capture of a main drainage system, that fed the entire basin, to the western basin graben, and so decreasing the sedimentary input to the central sub-basin. The Guaritas Group in its turn indicates a change in the depositional systems caused by the subsidence of the Serra das Encantadas High, which allowed the capture of drainage systems to the basin, thus increasing the sedimentary input and the substitution of the eolian and alluvial fan systems by braided fluvial systems.

This report studies impostor rendering for use with the virtual reality head mounted display Oculus Rift. The technique is replacing 3D models with 2D versions to speed up rendering, in a 3D engine. It documents the process of developing a prototype in C++ and DirectX11 and the required research needed to complete the assignment. Included in this report are also the steps involved in getting Oculus Rift support to work in a custom 3D engine and measuring the impact of impostor rendering when rendering to two screens of the head mounted display. The goal was to find the maximum models the engine could draw, while keeping the frame rate locked at 60 frames per second. 2 testers at Nordicstation came to the conclusion that 40-50 meters was the optimal distance for impostor rendering. Any closer and the flatness was noticeable. The results showed a clear improvement in frame rate when rendering a graphically intensive scene. The end result showed that the goal could be achieved at a maximum of 3000 trees with 1000 leaves. Impostor rendering was deemed effective when drawing beyond 500 trees at a time. Less than that and the technique was not needed to achieve 60 frames per second. / Denna rapport undersöker renderingstekniken impostors när den används i en simpel 3D motor tillsammans med virtuella verklighetshjälmen Oculus Rift. Impostors betyder på engelska bedragare och tekniken går ut på att den byter ut avancerade 3D modeller mot simpla 2D versioner när de är ett visst avstånd ifrån användarens virtuella kamera. Om den är korrekt implementerad ska användaren inte märka att vissa modeller är platta och tekniken sparar på resurser då grafikmotorn inte behöver rita ut alla modeller. Rapporten går igenom vad som undersöktes i förundersökningen för att kunna utveckla en prototyp med utvecklingspråket C++ och DirectX 11. I rapporten står även hur prototypen utvecklades och hur stöd för Oculus Rift lades till. De slutliga resultaten visade att impostors hade en stor påverkan på uppdateringshastigheten när antalet 3D modeller som skulle ritas var många, annars hade tekniken ingen påverkan för att nå 60 bilder per sekund. 2 testare från Nordicstation kom fram till att ett avstånd på 40-50 meter från spelarens kamera till utritning av impostors var lämplig, för att dölja att de endast är platta versioner av 3d modeller. Testet visade att motorn kunde rita ut 3000 träd, med 1000 löv på varje, och hålla 60 bilder per sekund, vilket var målet. Detta på ett avstånd av 40m på impostors. Impostorrendering var effektiv när man ritade ut fler än 500 träd åt gången. Mindre antal gav ingen märkbar effekt på testdatorn som användes för testet.

Thesis (Ph.D. (Biochemistry)) -- University of Limpopo, 2021 / Introduction: Rift Valley fever virus (RVFV) is an arthropod-born RNA zoonotic virus causing Rift Valley fever (RVF) disease. RVFV is prevalent across sub-Saharan Africa and the Arabian Peninsula with no existing effective and approved antiviral remedies for humans or animals. RVFV has developed mechanisms to hide from immune recognition and induce anti-apoptosis processes to keep the infected host cells viable in an attempt to advance their viral progeny. RVFV is a single-stranded enveloped RNA genome virus composed of 3 segments; the L, M and S segments. The S segment is known to encode a non-structural protein (NSs) identified to be the main virulence factor promoting viral replication through immune suppression. RVFV elicits a set of diverse symptoms ranging from a febrile illness to more severe symptoms that usually culminate in life-threatening haemorrhagic fever with high fatality rates. Thus, this study was designed to investigate the efficacy of lithium as a potential drug for reduction of RVFV load and amelioration of imbalanced and dysregulated inflammatory responses observed in Huvec and Raw 264.7 macrophages infected with this virus. Methods and results: The MTT and Cyquant viability assays were used to demonstrate that lithium exerts no cytotoxic effects on non-infected Raw 264.7 macrophage cells but rather promotes cell growth and proliferation. Conversely, lithium was shown to significantly induce cell death in RVFV-infected Raw 264.7 macrophages. The Annexin-V/PI apoptosis assay was employed to demonstrate that RVFV induces apoptosis as a mode of cell death on Raw 264.7 cells. RVFV-induced apoptosis was accompanied by antagonistic Bax/Bcl-2 protein expression ratios. RVFV-infected cells treated with lithium resulted in higher levels of apoptosis signals compared to untreated RVFV-infected cells. Analysis of apoptosis stages using the real-time cell analyser (RTCA) also revealed that lithium induced early forms of apoptosis in RVFV-infected cells. Interestingly, induction of early apoptosis in these cells corresponds with lower viral load, probably as a result of early inhibition of viral progeny replication, as determined using viral titration assay. Immune response profiles elicited in Raw 264.7 macrophages infected with RVFV and treated with lithium were monitored. An ELISA assay was used to determine the effect of lithium on cytokines and chemokine production in this cell model. The results obtained showed that lithium significantly stimulated production of IFN-γ as RVFV-infected lithium-treated cells produced high levels of IFN-γ compared to lithium-free RVFV-infected control cells. Furthermore, in the same setting, the secondary pro-inflammatory cytokine, IL-6, and chemokine, RANTES, were stimulated by lithium 12 hrs post-infection (pi). Lithium was shown to significantly stimulate TNF-α production as early as 3 hrs pi. In addition to TNF-α expression, the expression of the regulatory cytokine, IL-10, was significantly stimulated by lithium with the highest expression peak at 12 hrs pi. As determined using the H2DCF-DA and DAF-2 DA florigenic assays, reduced production of the ROS and RNS was observed in RVFV-infected lithium-treated cells as opposed to untreated RVFV-infected controls. This was further supported by the Western blot assay results that showed low expression of the iNOS while upregulating expression of heme oxygenase and IκB in RVFV-infected lithium-treated cells. Results from immunocytochemistry and Western blot assays revealed that lithium inhibits NF-κB nuclear translocation in RVFV-infected cells compared to lithium-free RVFV-infected cells and 5 mg/ml LPS controls. This study hypothesises persistent and deregulated inflammation as the central phenomenon responsible for endothelial damage and haemorrhagic fever in RVFV pathogenesis. Supernatants were collected from RVFV-infected macrophage cells treated with lithium and their effects on the integrity of endothelial cells were evaluated. The xcelligence real-time cell analyser system (RTCA) and transwell assay that measure endothelial monolayer integrity were used to demonstrate that lithium protects endothelial cells from RVFV-induced cellular damage. Moreover, lithium was shown to upregulate expression of cytoplasmic molecules such as α and β-catenins involved in attaching the cadherin molecules to the actin cytoskeleton on the endothelial cell. Expression of α-catenins, talins, zyxins and vinculins that attach integrins to the extracellular matrix and to other cells were observed to be upregulated by supernatants from RVFV-infected Raw 264.7 macrophage cells treated with lithium. Endothelial cell monolayer exposed to supernatants from RVFV-infected lithium-treated Raw 264.7 cells displayed upregulated expression of transmembrane molecules such as E-cadherins and N-cadherins. However, expression of VE-cadherins was observed to be lower compared to those treated with supernatants from lithium-free RVFV-infected Raw 264.7 control cells. Conclusion: These findings propose that lithium limits viral replication and viral load in macrophages by inducing early apoptosis in RVFV-infected cells. Since lithium was shown to promote Raw 264.7 macrophage proliferation, it is thus suggested that the use of lithium as an RVFV antiviral drug is less likely to elicit leukocytopenia. Lithium seems to regulate excessive inflammation in RVFV-infected Raw 264.7 macrophages by modulating the NF-kB signalling pathway. The endothelial integrity observed in the permeability assays has been supported by the expression of the molecules involved in keeping the cell to cell adhesion intact. This study links endothelial integrity patterns exerted by lithium with lowered production of inflammatory mediators such as ROS and RNS as these molecules are involved in destabilisation of cell junctions. Results from this study point towards the use of lithium as a potential treatment for RVFV infections by limiting viral replication, restricting viral spread and restoring the inflammation-regulating machinery. Key words. Lithium, Rift Valley fever virus, NF-kB, endothelial integrity, inflammation and apoptosis / Poliomyelitis Research foundation and National Research Foundation

La stratigraphie synrift du bloc de faille est divisée en trois groupes stratigraphiques, représentant une épaisseur de 1624 m. Le Groupe inférieur est composé de sédiments fluvio-lacustres, le Groupe moyen comporte les Gilbert-deltas géants et leurs faciès fins associés, le Groupe supérieur est formé de Gilbert-deltas récents à actuels ainsi que de formations superficielles. La discordance basale de l’Unité du prérift présente une paléotopographie. La phase d'extension précoce (Groupe inférieur) est caractérisée par une très faible subsidence assurée par l’activité précoce de la faille de Pirgaki et des failles mineures. La transition avec la phase d'extension principale (Groupe moyen) est marquée par un approfondissement du bassin ainsi que par une augmentation du taux de subsidence. La phase d'abandon et de soulèvement du bloc (Groupe supérieur) est caractérisée par des évènements de creusement-comblement. Le Gilbert-delta géant de Kerinitis se serait déposé dans la période Pléistocène inférieur-Pléistocène moyen, en milieu marin. L’étude de la sédimentologie de faciès a permis de mettre en évidence quatre associations de faciès : topset, foreset, bottomset, prodelta. L’architecture stratigraphique est composée de onze Unités Stratigraphiques (SU) séparées par onze Surfaces Stratigraphiques (KSS). Dans un contexte de création continue d’espace d’accommodation, les SU se déposent pendant les maxima et les périodes de chute du niveau marin. Les KSS se mettent en place pendant des périodes d’augmentation du niveau marin. Les quatres étapes de construction du Gilbert-delta de Kerinitis ont enregistré le début, le maximum et l’arrêt de l’activité du système de failles / Synrift stratigraphy on a normal fault block is subdivided into three groups. The Lower group is composed of continental sediments (fluvio-lacustrine). The Middle group contains the giant Gilbert-type fan deltas and their associated fine-grained facies. The Upper group is composed of the recent to present day Gilbert-deltas and superficial deposits. The Lower group is marked by a low subsidence rate on the young Pirgaki fault and some secondary faults. A marked increase in subsidence rate mark the transition to the Middle group. It is proposed that the increase in subsidence rate is due to the connexion between two major faults. The Upper group was deposited during uplift of the study area in the footwall of the Helike fault. It is suggested that the giant Kerinitis Gilbert-type fan delta was deposited during the Early to early Middle Pleistocene, under marine conditions. Facies characterizing a range of depositional processes are assigned to four facies associations: topset, foreset, bottomset and prodelta. The stratal architecture is composed of eleven Key Stratal Surfaces (KSS) separating eleven Stratal Units (SU). In this subsidence-dominated system, each SU records a highstand period and principally a period of decreasing eustatic sea level. The KSS, record transgressions that took place in periods of rapid sea level rise. The eustatic signal, controlling the deposition of the SU is of higher frequency than the tectonic signal, which controlled four stages of delta growth. The four delta growth stages are linked with the initiation, maximum growth and the abrupt death of the Pirgaki-Kerinitis fault system