Earlier ecological studies on the relation between H. pylori infection and stomach cancer have considered that the relation between these two variables, as estimated by the exposure coefficient, is constant. However, there is evidence to suggest that this relation changes geographically due to differences in strains of H. pylori. Since the prevalence of H. pylori varies with socio-economic status, the association between the latter and stomach cancer mortality may also vary geographically. This thesis studies stomach cancer by taking into account the geographical variability of the exposure coefficients. The study proposes the use of regression mixtures, clustering models and spatially varying regressions for the study of varying exposure coefficients. The effect of transformations of variables in these models appears to have been little considered. We provide new necessary conditions for invariance under transformations of variables for mixed effect models in general, and for the proposed models in particular. In addition, we show that varying exposure coefficients may induce a varying baseline risk. The regression mixtures and the clustering model are applied to a data set on stomach cancer incidence and H. pylori prevalence in 57 countries worldwide. We extend the clustering model to reflect any distance measure between the geographical units, including the Euclidean distance, in the formation of clusters. We also show that the clustering model performs better than the regression mixture model when the aim is to identify connected clusters and the observations present large variance. The results obtained with the clustering model supported the existence of three clusters where the interaction between the human and H. pylori populations have similar characteristics. Spatially varying regressions are applied to a data set of areal death counts of stomach cancer and spending power in 275 counties in continental Portugal. We provide an original strategy for implementing multivectorial intrinsic autoregressions as the distribution for the random effects. The results obtained with the application of this methodology were consistent with a varying exposure coefficient of spending power.

Three separate studies of the effect of plant pathogen on population biology of its host are presented in the thesis. Two are using field data about a widespread system of plant Falcaria vulgaris and its systemic rust fungus Puccinia sii-falcariae. The first study shows, that the disease prevalences in 40 populations of the plant were correlated with the moisture, the soil reaction and the cover of the herb layer at the localities. This was probably a result of the interaction of the life history of the plant and different effect the disease has at various localities. Similar pattern was found in the second study that aimed to determine long-term effect of the disease at the population level at four chosen localities over 4-5 years. Population growth rates were only rarely predicted to be higher for the healthy part of the population when compared with the whole population. Other analyses have however found big differences among years and localities. The locality type (slope vs. field populations) was important factor influencing population stage composition and importance of life cycle transitions for the growth of the population. Finally, the last study explores the possibility that systemic infection in clonal plants might be able to select against clonality. The result of the modelling showed that more...

<p>This dissertation investigates the influence of spatially explicit animal behavior active subsidy distribution patterns. Active subsidies are animal-transported consumption and resources transfers from donor to recipient ecosystems. Active subsidies influence ecosystem structure, function and services in recipient ecosystems. Even though active subsidies affect ecosystem dynamics, most ecosystem models consider the influence of spatially-explicit animal behavior on active subsidy distributions, limiting the ability to predict corresponding spatial impacts across ecosystems. Spatial subsidy research documents the need for systematic models and analyses frameworks to provide generally insights into the relationship between animal space use behavior and active subsidy patterns, and advance knowledge of corresponding ecosystem impacts for a variety of taxa and ecological scenarios.</p> <p> </p> <p>To advance spatial subsidy research, this dissertation employs a combined individual-based and movement ecology approach in abstract modeling frameworks to systematically investigate the influence of 1) animal movement behavior given mortality (chapter 2), 2) animal sociality (chapter 3) and 3) landscape heterogeneity (chapter 4) on active subsidy distribution. This dissertation shows that animal movement behavior, sociality and landscape heterogeneity influence the extent and intensity of active distribution and impacts in recipient ecosystems. Insights from this dissertation demonstrate that accounting for these factors in the development of ecosystem models will consequentially enhance their utility for predicting active subsidy spatial patterns and impacts. This dissertation advances spatial subsidy research by providing a road map for developing a comprehensive, unifying framework of the relationship between animal behavior and active subsidy distributions.</p>

L'intensification et l'homogénéisation des paysages agricoles a rendu les agrosystèmes plus sensibles aux bioagresseurs. Pour limiter les impacts de ces bioagresseurs sans recourir de manière intensive aux pesticides, une solution efficace est l'utilisation de variétés résistantes. La durabilité de ces résistances peut être faible, en lien avec l'adaptation des populations pathogènes. Il est donc nécessaire de concevoir des systèmes de culture permettant le contrôle des bioagresseurs et la préservation des ressources variétales. Ces stratégies de gestion peuvent reposer sur la combinaison de pratiques agricoles et d'organisation spatiale de ces pratiques, pour des pathosystèmes dont les agents sont dispersés par le vent. D'une part, la conception de ces stratégies peut bénéficier d'une approche participative, prenant en compte les conditions de culture et l'organisation des acteurs locaux. D'autre part, l'évaluation de ces stratégies, dont l'expérimentation est délicate du fait des échelles spatiale et temporelle requises, peut bénéficier d'une approche modélisatrice. Dans ce cadre, ce travail de thèse a mis au point et testé, sur deux régions d'étude, une méthode participative de construction de scénarios d'organisation spatiale des systèmes de culture, évalués vis-à-vis du contrôle du phoma du colza et de la gestion des résistances. Les scénarios co-construits explorent les futurs agricoles possibles en identifiant les tendances possibles d'évolution du contexte (économique, politique, règlementaire, épidémique), de manière prédictive ou plus exploratoire. Ils ont ensuite été évalués numériquement à l'aide d'un modèle préexistant, vis-à-vis de trois critères pertinents pour les acteurs : les pertes de rendement, la taille de la population pathogène et sa structure. Ces scénarios ont ensuite été évalués à l'aide de régressions linéaires, de manière à identifier les pratiques agricoles les plus influentes sur les trois critères d'évaluation considérés. Cette analyse a été réalisée à deux échelles spatiales complémentaires : l'échelle d'une petite région agricole et l'échelle locale, considérant plusieurs centaines de mètres autour des parcelles de colza pouvant être infectées. Ces analyses ont permis de mettre en évidence la prépondérance des rotations, des variétés et de la gestion des résidus de colza dans l'évolution de la maladie et sur la durabilité des résistances. Elles ont également montré la nécessité de prendre en compte plusieurs échelles pour la gestion de la maladie : si la taille de la population pathogène et les pertes de rendement peuvent être déterminées à partir de la composition en termes de systèmes de culture à l'échelle du paysage, une échelle plus locale est nécessaire pour évaluer l'évolution de la structure génétique de la population. Cet indicateur est en effet très lié aux variétés et aux pratiques présentes dans les 500 mètres autour des parcelles porteuses de la résistance considérée. Finalement, l'exploration de règles spatiales (isolement) et temporelles (maximisation des surfaces un an sur deux) des parcelles de colza ou des types variétaux a mis en exergue le fort potentiel de stratégies basées sur ces règles pour la gestion des résistances. La mise en place de ces stratégies nécessiterait une coordination entre les différents acteurs, à l'échelle du territoire agricole, qui pourrait s'avérer nécessaire en cas d'épidémie importante de phoma. La méthode mise en place pourrait être utilisée pour explorer la gestion d'autres thématiques à composante spatiale, comme par exemple l'érosion ou la gestion d'autres bioagresseurs. Ceci pourrait permettre une évaluation multicritère, prenant par exemple en compte les bioagresseurs de différentes cultures composant une même rotation, identifiant ainsi les pratiques les plus à mêmes de gérer simultanément les différentes thématiques locales. / The intensification and the homogenization of agricultural systems led to agrosystèmes that are more sensible to pests and diseases. To limit the impacts of these pests and diseases without increasing pesticides use, an efficient solution is the use of resistant cultivars. Sustainability of these resistances can be low, in link with the adaptation of pathogen populations. It is thus necessary to design cropping systems allowing both the control of pests and diseases and preservation of cultivar resistances. Such management strategies can combine cropping practices and their spatial organization, for pathosystems whose agents are wind-dispersed. The design of these strategies can benefit from participatory approaches, taking into account the local cropping systems and stakeholders' organizations. The evaluation of these strategies, hardly testable in reality due to the spatial and temporal scales involved, can benefit from a modeling approach. Within this scope, this PhD thesis designed and tested, in two study regions, a participatory method of scenarios design, aiming at building with local stakeholders scenarios of spatial organization of cropping systems and to assess them with regards to their performances on phoma stem canker of winter oilseed rape and resistance durability management. Participatory designed scenarios explore agricultural futures that may happen by identifying the possible evolutions of the context (economic, political, regulatory or epidemic), in a predictive or more exploratory way. Scenarios are then evaluated numerically with a pre-existing model, for three criteria relevant for the stakeholders: yield losses, structure and size of the pathogen population. This analysis has been performed at two complementary spatial scales: the regional and the local scale, considering hundreds of meters around fields cropped with sensitive cultivars. These analyses showed the importance of crop rotations, cultivars and tillage for the evolution of the disease and resistance sustainability. These analyses also showed the necessity of taking into account different scales for disease management. Indeed, size of the pathogen population and yield losses are well related to the landscape composition in terms of cropping practices, but a more local scale is necessary for the assessment of the genetic structure of the pathogen population. This indicator is thus significantly linked with the cultivars and cropping practices in the 500 meters around fields cropped with the considered resistance. Finally, we explored spatial (isolation) and temporal rules for rapeseed spatial and temporal allocations that could be used to manage resistance. For these strategies to be applied, coordination between stakeholders at the agricultural territory would be necessary, which could be necessary in case of strong phoma stem canker epidemics. The method we applied could be used to explore other thematic with a spatial component, as for instance pests or erosion. This could allow a multi-criteria analysis, for instance taking into account pathogens of different crops included in a rotation, thus identifying the cropping practices that could promote management of these local problems.

Les problèmes environnementaux liés à l’excès d’azote d’origine agricole restent une préoccupation majeure en France malgré une réglementation contraignante. Pour concilier maintien de la production agricole et limitation de cet excès, des stratégies novatrices d’atténuation des flux d’azote ont été identifiées, puis leurs effets ont été simulés à l’échelle de paysages agricoles à l’aide de modèles agro-hydrologiques spatialisés. Pour cela, la méthodologie mise en oeuvre a consisté, à partir d’enquêtes de fermes dans deux contextes contrastés (Bretagne et Gascogne),à simuler des scénarios : i) d’optimisation des pratiques agricoles en accord avec le 5ème programme d’actions de la directive Nitrate et ii) d’aménagements paysagers du territoire et en particulier des zones environnementales (prairies fauchées non-fertilisées), en variant l’emprise et la localisation. Les résultats montrent l’intérêt de placer ces zones en position d’interception (i.e. en zone riparienne humide), plutôt qu’en tête de thalweg, notamment sur le site breton où circulations d’eau sub-superficielles dominent. Cette solution limiterait les pertes nitriques sans augmenter les autres émissions d’azote. / Environmental issues related to the excess of reactive nitrogen of agricultural origin activity, are still a major concern in France despite restrictive regulations. To reconcile sustained agricultural production and reduced nitrogen emissions, we identified innovative mitigation strategies and simulated their effects were simulated using distributed agro-hydrological models. The approach consisted in farm surveys in two contrasted situations (NW and SW of France) a basis to simulate the following scenarios :i) optimisation of agricultural practices according to the 5th action programme of the Nitrate Directive ii) conversion of agricultural land into environmental zones (unmanaged grasslands), with varying extension and in different landscape positons. Results show the interest of locating them in an interception position (i.e. in humid zones around the stream network) rather than in headwater position, especially in the NW catchment were subsurface flow is the dominant pathway. This solution would reduce nitrate losses without increasing other nitrogen emissions.

Obtaining accurate estimates of animal abundance is made difficult by the fact that most animal species are detected imperfectly. Early attempts at building likelihood models that account for unknown detection probability impose a simplifying assumption unrealistic for many populations, however: no births, deaths, migration or emigration can occur in the population throughout the study (i.e., population closure). In this dissertation, I develop likelihood models that account for unknown detection and do not require assuming population closure. In fact, the proposed models yield a statistical test for population closure. The basic idea utilizes a procedure in three steps: (1) condition the probability of the observed data on the (unobserved) period- specific abundances; (2) multiply this conditional probability by the (prior) likelihood for the period abundances; and (3) remove (via summation) the period- specific abundances from the joint likelihood, leaving the marginal likelihood of the observed data. The utility of this procedure is two-fold: step (1) allows detection probability to be more accurately estimated, and step (2) allows population dynamics such as entering migration rate and survival probability to be modeled. The main difficulty of this procedure arises in the summation in step (3), although it is greatly simplified by assuming abundances in one period depend only the most previous period (i.e., abundances have the Markov property). I apply this procedure to form abundance and site occupancy rate estimators for both the setting where observed point counts are available and the setting where only the presence or absence of an animal species is ob- served. Although the two settings yield very different likelihood models and estimators, the basic procedure forming these estimators is constant in both. / Graduation date: 2012

<p>Soft matter systems exhibiting spatially modulated patterns on a mesoscale are characterized by many long-lived metastable phases for which relaxation to equilibrium is difficult and a satisfactory thermodynamic description is missing. Current dynamical theories suffer as well, because they mostly rely on an understanding of the underlying equilibrium behavior. This thesis relates the study of two canonical examples of modulated systems: microphase and cluster crystal formers. Microphases are the counterpart to gas-liquid phase separation in systems with competing short-range attractive and long-range repulsive interactions. Periodic lamellae, cylinders, clusters, etc., are thus observed in a wide variety of physical and chemical systems, such as multiblock copolymers, oil-water surfactant mixtures, charged colloidal suspensions, and magnetic materials. Cluster crystals in which each lattice site is occupied by multiple particles are formed in systems with steep soft-core repulsive interactions. Dendrimers have been proposed as a potential experimental realization. In order to access and understand the equilibrium properties of modulated systems, we here develop novel Monte Carlo simulation methods. A thermodynamic integration scheme allows us to calculate the free energy of specific modulated phases, while a [N]pT ensemble simulation approach, in which both particle number and lattice spacing fluctuate, allows us to explore their phase space more efficiently. With these two methods, we solve the equilibrium phase behavior of five schematic modulated-phase-forming spin and particle models, including the axial next-nearest-neighbor Ising (ANNNI) model, the Ising-Coulomb (IC) model, the square-well linear (SWL) model, the generalized exponential model of index 4 (GEM-4) and the penetrable sphere model (PSM). Interesting new physics ensues. In the ANNNI layered regime, simple phases are not found to play a particularly significant role in the devil's flowers and interfacial roughening plays at most a small role. With the help of generalized order parameters, the paramagnetic-modulated critical transition of the ANNNI model is also studied. We confirm the XY universality of the paramagnetic-modulated transition and its isotropic nature. With our development of novel free energy minimization schemes, the determination of a first phase diagram of a particle-based microphase former SWL is possible. We identify the low temperature GEM-4 phase diagram to be hybrid between the Gaussian core model (GCM) and the PSM. The system additionally exhibits S-shaped doubly reentrant phase sequences as well as critical isostructural transitions between face-centered cubic (FCC) cluster solids of different integer occupancy. The fluid-solid coexistence in the PSM phase diagram presents a crossover behavior around T~0.1, below which the system approaches the hard sphere limit. Studying this regime allows us to correct and reconcile prior DFT and cell theory work around this transition.</p> / Dissertation

Earthquake is undoubtedly one of the greatest natural disasters that can induce serious structural damage and huge losses of properties and lives. The resulting destructive consequences not only have made structural seismic analysis and design much more important but have impelled the necessity of more realistic representation of ground motions, such as inclusion of ground motion spatial variations in earthquake modelling and seismic analysis and design of structures. Recorded seismic ground motions exhibit spatial variations in their amplitudes and phases, and the spatial variabilities have an important effect on the responses of structures extended in space, such as long span bridges. Because of the multi-parametric nature and the complexity of the problems, the development of specific design provisions on spatial variabilities of ground motions in modern seismic codes has been impeded. Eurocode 8 is currently the only seismic standard worldwide that gives a set of detailed guidelines to explicitly tackle spatial variabilities of ground motions in bridge design, providing both a simplified design scheme and an analytical approach. However, there is gap between the code-specified provisions in Eurocode 8 and the realistic representation of spatially varying ground motions (SVGM) and the corresponding stochastic vibration analysis (SVA) approaches. This study is devoted to bridge this gap on modelling of SVGM and development of SVA approaches for structures extended in space under SVGM. A complete and realistic SVGM representation approach is developed by accounting for the incoherence effect, wave-passage effect, site-response effect, ground motion nonstationarity, tridirectionality, and spectra-compatibility. This effort brings together various aspects regarding rational seismic scenarios determination, comprehensive methods of accounting for varying site effects, conditional modelling of SVGM nonstationarity, and code-specified ground motion spectra-compatibility. A comprehensive, systematic, and efficient SVA methodology is derived for long span structures under tridirectional nonstationary SVGM. An absolute-response-oriented scheme of pseudo-excitation method and an improved high precision direct integration method are proposed to reduce the enormous computational effort of conventional nonstationary SVA. A scheme accounting for tridirectional varying site-response effect is incorporated in the nonstationary SVA scheme systematically. The proposed highly efficient and accurate SVA approach is implemented and verified in a general finite element analysis platform to make it readily applicable in SVA of complex structures. Based on the proposed SVA approach, parametric studies of two practical long span bridges under SVGM are conducted. To account for spatial randomness and variability of soil properties in soil-structure interaction analysis of structures under SVGM, a meshfree-Galerkin approach is proposed within the Karhunen-Loeve expansion scheme for representation of spatial soil properties modelled as a random field. The meshfree shape functions are proposed as a set of basis functions in the Galerkin scheme to solve integral equation of Karhunen-Loeve expansion, with a proposed optimization scheme in treating the compatibility between the target and analytical covariance models. The accuracy and validity of the meshfree-Galerkin scheme are assessed and demonstrated by representation of covariance models for various homogeneous and nonhomogeneous spatial fields. The developed modelling approaches of SVGM and the derived analytical SVA approaches can be applied to provide more refined solutions for quantitatively assessing code-specified design provisions and developing new design provisions. The proposed meshfree-Galerkin approach can be used to account for spatial randomness and variability of soil properties in soil-structure interaction analysis.

The affect on leaf area index (LAI) and net ecosystem production (NEP) of the mountain pine beetle (Dendroctonus ponderosae) (MPB) outbreak in British Columbia affecting lodgepole pine (Pinus contorta var. latifolia) forests was examined from 1999 to 2008. The process-based carbon (C) cycle model – Boreal Ecosystem Productivity Simulator (BEPS) with remotely sensed LAI inputs was used to produce annual NEP maps, which were validated using field measurements. The annual NEP ranged from 2.43 to -8.03 MtC between 1999 and 2008, with sink to source conversion in 2000. The inter-annual variability for both LAI and NEP displayed initial decreases followed by a steadily increasing trend from 2006 to 2008 with NEP returning to near C neutrality in 2008 (-1.84 MtC). The resistance of LAI and NEP to MPB attack was attributed to ecosystem resilience in the form of secondary overstory growth and increased production of non-attacked host trees.

The affect on leaf area index (LAI) and net ecosystem production (NEP) of the mountain pine beetle (Dendroctonus ponderosae) (MPB) outbreak in British Columbia affecting lodgepole pine (Pinus contorta var. latifolia) forests was examined from 1999 to 2008. The process-based carbon (C) cycle model – Boreal Ecosystem Productivity Simulator (BEPS) with remotely sensed LAI inputs was used to produce annual NEP maps, which were validated using field measurements. The annual NEP ranged from 2.43 to -8.03 MtC between 1999 and 2008, with sink to source conversion in 2000. The inter-annual variability for both LAI and NEP displayed initial decreases followed by a steadily increasing trend from 2006 to 2008 with NEP returning to near C neutrality in 2008 (-1.84 MtC). The resistance of LAI and NEP to MPB attack was attributed to ecosystem resilience in the form of secondary overstory growth and increased production of non-attacked host trees.