No description available.

Rapidly rising levels of atmospheric greenhouse gases including carbon dioxide and methane since the industrial revolution have drawn scientific attention to the importance of the global carbon cycle to the climate (Cubasch et al., 2013). Tropical peatlands, the majority of which are located in the Indonesian region, are a major source of uncertainty in the carbon cycle as the relationships between carbon accumulation and hydrological changes remain poorly understood (Hergoualc’h & Verchot, 2011, Page et al., 2011). An important driver of carbon emissions in tropical peatlands is fire, which in the Indonesian region is strongly influenced on interannual timescales by the El Niño/Southern Oscillation (ENSO). However, it is not clear how ENSO and fire have varied at decadal to centennial scales over the past two millennia. This thesis explores long term tropical hydrological variability and ENSO-like climate change from palaeorecords and their interactions with fire. Using a wide range of instrumental, proxy and model datasets and a novel reconstruction method, two separate reconstructions of long-term ENSO-like climate change are produced based on precipitation and temperature data. These show no evidence of a difference between the ENSO-like behaviour of precipitation and temperature. There is limited evidence for a difference in long-term ENSO-like state between the Medieval Climate Anomaly and the Little Ice Age. Reconstructions of hydrological variability and biomass burning in the Indonesian region suggest that precipitation and fire have been positively correlated over the past 2,000 years, which is contrary to the modern-day relationship on ENSO timescales. This throws up questions of long-term versus short-term interactions and feedbacks between fire, climate and vegetation. It is likely that anthropogenic activity in the Indonesian region has significantly altered the stability of the fire regime. Further research combining proxy data, climate and fire models, and using more robust statistical analysis is necessary to untangle the natural and anthropogenic driving factors at different time resolutions.

No description available.

No description available.

No description available.

La radiation adaptative des Equoidea est encore mal comprise en raison notamment de la méconnaissance de la phylogénie de cette super-famille. La principale irrésolution de ces relations de parenté porte sur les pachynolophes, Equoidea européens rapprochés des Equidae ou des Palaeotheriidae. Pendant une grande part de l'Éocène, l'Europe est isolée et subit à la fin de cette période de profonds changements climatiques. Lors de la Grande Coupure son isolement s'achève, tandis que l'aridité du climat s'installe, et des faunes migrantes provoquent l'extinction de nombreux groupes endémiques. Un Equoidea européen basal, richement représenté par un matériel bien préservé permet d'appuyer une des hypothèses phylogénétiques les plus récentes. Cependant, les caractères couramment utilisés pour débattre de cette question n'apportent pas de réponse claire et définitive. Aussi, cette étude se propose de mener des investigations sur des régions encore peu explorées de ces animaux comme le neurocrâne, grâce à la microtomographie (CT scan), qui permet un accès non destructif aux structures (encéphale, pétreux, labyrinthe osseux, sinus). Outre l'intérêt phylogénétique, ces organes peuvent, de par leurs fonctions, receler un intérêt paléoécologique. Jusqu'à présent, peu d'études à large échelle ont porté sur ces structures chez les Perissodactyla, s'agissant pour la plupart de mentions anecdotiques. Comme préalable indispensable, une étude modèle a été réalisée sur un Equidae sauvage actuel afin de mieux appréhender la variabilité de ces structures méconnues. Pour la première fois, un large échantillon d'Equoidea européens a été scanné et leurs structures neurocrâniennes reconstruites en trois dimensions virtuelles. Ce sont au total 20 espèces qui ont été échantillonnées, couvrant l'évolution de ces animaux de leur origine à leur extinction, pendant plus de 20 millions d'années. Leurs crânes ont été scannés, leurs structures internes reconstruites, comparées et analysées au moyen de la cladistique. Une nouvelle hypothèse phylogénétique propose des relations de parenté intra-Equoidea et montre la pertinence des caractères neurocrâniens, tout en conduisant à envisager une étude plus vaste. Les Palaeotheriidae apparaissent comme un groupe très diversifié, notamment au regard des Equidae éocènes d'Amérique du Nord, et caractérisé par une évolution en mosaïque. Ils connaissent une évolution cérébrale précoce par rapport aux faunes contemporaines (Equidae, Cetartiodactyla, Carnivora), ce qui, via le développement de nouvelles stratégies adaptatives, pourrait expliquer partiellement cette grande diversification familiale. Un parallèle est envisagé avec l'évolution endémique des Notoungulata, qui semblent eux aussi montrer une complexification cérébrale précoce. Cependant, face à un environnement biotique et abiotique bouleversé (fin de l'Éocène et lors de la Grande Coupure), ces structures complexes impliquant un coût métabolique important et une trop grande spécialisation, avec en conséquence, moins de potentiel adaptatif, auraient pu les désavantager et les conduire à l'extinction. / The Equoidea adaptive radiation still remains badly known, especially due to the ignorance of their phylogeny. The main indecision of these relationships concerns the pachynolophs, European Equoidea either approached to the Equidae or to the Palaeotheriidae. During a great part of the Eocene times, Europe was isolated, and, at the end of this period, has undergone strong climatic changes. That isolation ended at the « Grande Coupure » event, whereas an arid climate moved, and migrant faunas caused the extinction of many endemic groups. A basal European Equoidea, richly represented by well-preserved material, can support one of the latest phylogenetic hypotheses. However, commonly used characters to discuss this issue do not provide a clear and definitive answer.Therefore, this study aims to investigate on unexplored regions of these animals as the neurocranium through microtomography (CT), which allows access to non-destructive structures (brain, petrosal, bony labyrinth, and sinus).Furthermore phylogenetic interest these bodies may, through their functions, harbor paleoecological interest. Until now, few large-scale studies have focused on those structures in the Perissodactyla, with regard to most were anecdotal reports. As a prerequisite, a model study was performed on a wild current Equidae to better understand the variability of these unknown structures. For the first time, a large sample of European Equoidea has been scanned and their neurocranium structures virtually reconstructed in three-dimensions. A total of 20 species were sampled, covering the evolution of these animals from their origin to their extinction, for over 20 million years. Their skulls were scanned; their internal structures reconstructed compared and analyzed using cladistics. A new phylogenetic hypothesis provides intra Equoidea relationships and shows the relevance of neurocranium characters, while driving to consider a larger study. The Palaeotheriidae appears as a highly diverse group, particularly with regard to Eocene Equidae in North America, and characterized by a mosaic evolution. Their brain evolved earlier than that of contemporary faunas (Equidae, Cetartiodactyla, Carnivora); which may partially explain the strong diversification of that family, through the development of new adaptive strategies.

Depuis sa formation, la Terre subit un refroidissement lent. La chaleur provenant du noyau et de la désintégration des éléments radioactifs présents dans le manteau est évacuée vers la surface par convection. L’évolution des structures thermiques ainsi créées contrôle de nombreux phénomènes de surface tels que le mouvement des continents et le niveau marin. L’étude présentée ici s’attache à déterminer quelles structures convectives terrestres peuvent être reconstruites, sur quelle période de temps et avec quelle précision. La chaoticité de la convection implique que les incertitudes initialement présentes sur le champ de température croissent exponentiellement au cours du temps et peuvent créer des structures convectives artificielles dans les modèles. A l’aide de la méthode des expériences jumelles initialement développée par Lorenz [1965] en météorologie, le temps de Lyapunov et l’horizon de prédiction sont calculés pour la première fois en géodynamique mantellique. Différentes rhéologies sont étudiées. La valeur du temps de Lyapunov pour notre modèle le plus proche de la Terre suggère qu’une erreur de 5% sur les conditions initiales limite l’horizon de prédiction à 95 millions d’années. D’autre part, la qualité de la prédiction des structures thermiques dépend de notre capacité à décrire de façon réaliste les propriétés rhéologiques du manteau. L’utilisation d’une rhéologie pseudo-plastique dans les modélisations de convection en 3D sphérique, permet aujourd’hui de générer une tectonique de plaques compatible au premier ordre avec les caractéristiques cinématiques de la surface terrestre. Une stratégie cohérente de reconstruction peut alors être élaborée. L’état thermique actuel du manteau est reconstruit en imposant les vitesses de surface de ces 200 derniers millions d’années [Seton et al., 2012; Shephard et al., 2013] sur un modèle de convection généré par le code StagYY [Tackley, 2008]. La morphologie et la position des slabs reconstruits varient considérablement avec le contraste de viscosité et la pseudo-plasticité. L’erreur introduite par l’utilisation de rhéologies différentes lors des reconstructions est ainsi plus importante que les erreurs liées aux incertitudes sur les conditions initiales et les vitesses de surface. Ces résultats montrent l’importance du choix la rhéologie sur la qualité des prédictions réalisées. Ils mettent également en évidence rôle clé du contraste de viscosité et de la pseudo-plasticité pour reconstruire des slabs cohérents et des subductions plates, structures propres à la convection terrestre. / Since its formation, the Earth is slowly cooling. The heat produced by the core and the radioactive decay in the mantle is evacuated toward the surface by convection. The evolving convective structures thereby created control a diversity of surface phenomena such as vertical motion of continents or sea level variation. The study presented here attempts to determine which convective structures can be predicted, to what extent and over what timescale. Because of the chaotic nature of convection in the Earth’s mantle, uncertainties in initial conditions grow exponentially with time and limit forecasting and hindcasting abilities. Following the twin experiments method initially developed by Lorenz [1965] in weather forecast, we estimate for the first time the Lyapunov time and the limit of predictability of Earth’s mantle convection. Our numerical solutions for 3D spherical convection in the fully chaotic regime, with diverse rheologies, suggest that a 5% error on initial conditions limits the prediction of Earth’s mantle convection to 95 million years. The quality of the forecast of convective structures also depends on our ability to describe the mantle properties in a realistic way. In 3D numerical convection experiments, pseudo plastic rheology can generate self-consistent plate tectonics compatible at first order with Earth surface behavior [Tackley, 2008]. We assessed the role of the temperature dependence of viscosity and the pseudo plasticity on reconstructing slab evolution, studying a variety of mantle thermal states obtained by imposing 200 million years of surface velocities extracted form tectonic reconstructions [Seton et al., 2012; Shephard et al., 2013]. The morphology and position of the reconstructed slabs largely vary when the viscosity contrast increases and when pseudo plasticity is introduced. The errors introduced by the choices in the rheological description of the mantle are even larger than the errors created by the uncertainties in initial conditions and surface velocities. This work shows the significant role of initial conditions and rheology on the quality of predicted convective structures, and identifies pseudo plasticity and large viscosity contrast as key ingredients to produce coherent and flat slabs, notable features of Earth’s mantle convection.

This thesis focus on the epitaxial growth and optical characterization of diluted InAs/InP(001) quantum dots for the realisation of new nanophotonic devices emitting at 1.55 [micro]m. The structural and optical properties of the quantum islands are correlated to different growth parameters of a solid source molecular beam epitaxy system. Our results highlight the influence of InAs surface reconstructions on the island shape. Dots rather than elongated dashes usually observed can be directly formed by adequate growth conditions. Dash to dot shape transition is also demonstrated by post-growth treatments. Low dot densities are obtained for small InAs deposited thickness. Their emission wavelength is easily tuned to 1.55 [micro]m using the"double cap" procedure for the growth of the InP capping layer. Optical properties of such single InAs/InP quantum dots are then evaluated. Micro-photoluminescence studies reveal sharp and well separated emission lines near 1.55 [micro]m from single dots confirming their atom-like properties. Last, we propose for the first time a high spatial resolution method to study the carrier transport in the vicinity of a single quantum dot using a low-voltage cathodoluminescence technique. A direct measurement of the carrier diffusion length before capture into one dot has been obtained. These results open the way to the integration of these single dots into optical micro-cavities for the realisation of quantum light sources at 1.55 [micro]m.

Metabolites consumed and produced by microorganisms for mass and energy conservation may cause changes in a microorganism’s environment. The microorganisms are unable to tolerate a particular environment for a long period. They may leave their old existence to find a new environment to sustain life. Essentially, organisms need to maintain their metabolic processes to survive in the new environment. Limitations of experimental studies to explore cell functions and regulations in detail result in insufficient information to explain processes of metabolic expressions under environments of organisms. Consequently, mathematical modeling and computer simulations have been conducted to combine all possible cellular metabolic fluxes into single or multiple connected networks. Metabolic modeling based on linear programming (LP) subjected to constraints with an optimization approach is often applied metabolic reconstruction. The LP objective function is maximized to obtain an optimal value of biomass flux. Optimal solutions in LP problems can be used to explain how metabolites function in metabolic reactions. As an LP problem may have many optimal solutions, this study proposes a method for enumerating all alternate optimal solutions to evaluate important reactions of metabolic pathways in microorganisms. The algorithm for generating alternate optimal solutions is implemented in MetModelGUI, a Java-based software for creating and analyzing metabolic reconstructions. The algorithm is applied to models of five microorganisms: Trypanosoma cruzi, Thermobifida fusca, Helicobacter pylori, Cryptococcus neoformans and Clostridium thermocellum. The results are analyzed using principal component analysis, and insight into the essential and non-essential pathways for each organism is derived

Midshaft is the most commonly used site for behavioral and robusticity inferences in cross-sectional studies of the femur. This work tries to revive an alternative location because the midshaft, as much as it is easy to locate, does not necessarily reflect the same adaptive remodeling in every individual. Femoral waist which is defined as the shaft’s mechanically weakest point is reintroduced as an alternative. The aim of this work is to describe waist’s general patterns of distribution along the shaft, to test which morphological characteristics influence its position, to compare its inferential potential with the midshaft, and to evaluate applicability of the concept under the mechanical predictions about stress and strain distribution along the femur. A total of 251 individuals representing four temporal samples spanning the Eneolithics to 19th century were analyzed using CT-derived cross-sectional properties. The results showed that the femoral waist tends to center around the midshaft but with a rather large amount of variation and that the samples do not seem to differ in this respect. General levels of mechanical loading and robusticity may influence its distribution as evidenced from the Early Middle Ages males who were the most robust group (in body size adjusted parameters) and had their waists positioned more proximally. Variables that influence waist’s location are primarily related to strain distribution but not its magnitude. Thus, neck-shaft angle, anteversion angle, femoral inclination, crural index, and femoral curvature proved to be significant predictors (their importance varies between sexes), while body size measures were insignificant. Behavioral and robusticity inferences made from the femoral waist and midshaft are rather incompatible. In closely related populations, results from the two locations would probably lead to different interpretations while in rather distant units (species or genera), this would not be as problematic. Whenever possible, true cross-sectional properties should be used to locate the femoral waist. External methods using subperiosteal contour are more acceptable than methods estimating cross-sectional properties only from external dimensions. Lastly, the femoral waist position can potentially be used for taxonomic purposes in earlier hominins as well as for the reconstruction of other femoral characteristics (e.g., femoral length). / acase@tulane.edu