To address the shortcomings in existing Markov model implementations in handling large amount of metagenomic data with comparable or better accuracy in classification, we developed a new algorithm based on pseudo-count supplemented standard Markov model (SMM), which leverages the power of higher order models to more robustly classify reads at different taxonomic levels. Assessment on simulated metagenomic datasets demonstrated that overall SMM was more accurate in classifying reads to their respective taxa at all ranks compared to the interpolated methods. Higher order SMMs (9th order or greater) also outperformed BLAST alignments in assigning taxonomic labels to metagenomic reads at different taxonomic ranks (genus and higher) on tests that masked the read originating species (genome models) in the database. Similar results were obtained by masking at other taxonomic ranks in order to simulate the plausible scenarios of non-representation of the source of a read at different taxonomic levels in the genome database. The performance gap became more pronounced with higher taxonomic levels. To eliminate contaminations in datasets and to further improve our alignment-free approach, we developed a new framework based on a genome segmentation and clustering algorithm. This framework allowed removal of adapter sequences and contaminant DNA, as well as generation of clusters of similar segments, which were then used to sample representative read fragments to constitute training datasets. The parameters of a logistic regression model were learnt from these training datasets using a Bayesian optimization procedure. This allowed us to establish thresholds for classifying metagenomic reads by SMM. This led to the development of a Python-based frontend that combines our SMM algorithm with the logistic regression optimization, named POSMM (Python Optimized Standard Markov Model). POSMM provides a much-needed alternative to metagenome profiling programs. Our algorithm that builds the genome models on the fly, and thus obviates the need to build a database, complements alignment-based classification and can thus be used in concert with alignment-based classifiers to raise the bar in metagenome profiling.

Policy conflict plays an important role in shaping public policy—both as a process and as a product. The policy conflict framework—a theoretical framework, developed by Christopher Weible and Tanya Heikkila in 2017—considers position divergence among policymakers a key characteristic of policy conflict, which can be affected several factors including organizational and network affiliation of policymakers. This dissertation analyzes position divergence among local and regional officials over community sustainability policy, with a focus on affordable housing, which is a major concern of community sustainability. This research examines if, and how, local government officials' engagement with regional governance can play a role in shaping their policy positions. Understanding what influences officials' policy positions is essential in managing conflicts that arise in the making of sustainability policies in general and affordable housing policies, in particular. This study argues that local government officials' engagement with regional governance can lower policy position divergence among them by influencing their policy core beliefs and policy relevant knowledge. This analysis includes testing several hypotheses using data from a state-wide survey of local and regional policymakers. Employing cross-tabulation, multivariate regression, and ordered logit analysis, this study finds that (a) policymakers share a wide range of policy positions on community sustainability policies and (b) for local government officials engaged with regional governance, position divergence on community sustainability is lower than that among those who are not engaged with regional governance. Although position divergence on affordable housing among those engaged with regional governance is generally lower than those who are not engaged with regional governance, this finding is not robust. In some regions and localities, the relationship between position divergence and engagement with regional governance does not hold. Furthermore, this study finds that local government officials' engagement with regional governance is associated with higher levels of policy relevant knowledge, which can influence the policymakers' policy positions. The relationship, if any, between policymakers' core beliefs and their engagement with regional governance is weak and statistically insignificant. This cross-sectional analysis based on limited data suggests that local government officials' policy core beliefs are not related to their engagement with regional governance. However, future studies with better data may yield different results. / Doctor of Philosophy / Policy conflicts can impede the policymaking process; they usually influence and shape policy goals. Metropolitan governance is rife with policy conflicts. Especially in substantive policy areas such as community sustainability and affordable housing, policy conflicts are quite common. Policy conflicts emerge because of policy actors' divergent views, beliefs, priorities, preferences, and aspirations. To ensure a smoother policymaking process, mechanisms to handle conflicts are imperative. Regional governance can offer one such mechanism to handle policy conflicts that arise due to divergent policy positions of local government officials. This dissertation examines policy conflicts focusing on community sustainability policies. Analyzing survey data from Maryland, this study finds that (a) local government officials share a wide range of policy positions on community sustainability policies, (b) local government officials engaged with regional governance take policy positions that are more homogeneous compared to those who are not engaged with regional governance, and (c) officials engaged regional governance tend to have better policy relevant knowledge than others.

Le champ d’application de la Convention de Vienne de 1980 sur la vente internationale de marchandises constitue une question très délicate. En effet, le caractère abstrait et supplétif de ladite Convention a donné naissance à une jurisprudence fort divergente et à une doctrine rarement en accord. Les difficultés d’application de la Convention démontrent clairement les limites de cette dernière à s’adapter aux nouveaux contrats de vente internationale. Ces difficultés sont-elles dues à une mauvaise interprétation des termes de la convention ? Serait-il juste de compléter les lacunes de la Convention de Vienne par d’autres Conventions telles que les règles d’UNIDROIT ou les principes de droit européen des contrats ? Faut-il aller «au-delà» de la Convention de Vienne ? Toutes ces questions doivent être gardées en tête pour bien analyser le champ d’application de ladite Convention. / The scope of application of the 1980 Vienna Convention on Contracts for the International Sale of Goods is a very delicate issue. Indeed, its abstract and supplementary nature has given rise to markedly divergent judgements and rarely agreeing doctrine. The difficulties arising from the application of the CISG clearly exemplfy its limited ability to adap to novel international sale of goods contracts. Are these difficulties attributable to faulty interpretations of the provisions of the CISG? Would it be opportune to compensate for the CISG's shortcomings by resorting to other instruments, such as the UNIDROIT rules or the principles of European contract law? Is it necessary to look beyond the Vienna Convention? All these questions must be considered in order to properly analyse the scope of application of the CISG.

Tout modèle cinématique appliqué à la propagation du rift sud kenyan (RSK) et à sa divergence vers l’ouest au nord de la Tanzanie (DNT) doit nécessairement intégrer la vallée axiale Magadi-Natron (études antérieures), mais aussi le bloc soulevé Oldoinyo Ogol (OOB) à l’ouest (ce travail). Notre étude, basée pour l'essentiel sur l'interprétation d'imagerie satellitale SRTM 30 m, nous permet (1) de préciser l'organisation morphostructurale de l'ensemble du RSK, (2) d'identifier 2 systèmes successifs de failles bordières, (3) d'affirmer le rôle majeur de celle d'Oldoinyo Ogol, (4) d'élaborer un modèle de rifting en 2 étapes (7-3 Ma et <3 Ma) et (5) d'attribuer le « shift » latéral du domaine rifté (OOB), puis sa divergence le long de la branche d'Eyasi (DNT) à la présence d'une discontinuité transverse protérozoïque, à laquelle on rapporte aussi le développement précoce et 'hors axe' du segment magmatique des « Crater Highlands », démontrant ainsi l'importance de l'héritage structural sur la cinématique du rifting. L’analyse quantitative des populations de failles démontre le caractère « restricted » des failles intrarift et aboutit aussi à préciser l'évolution, dans l'espace et le temps, du taux d'extension, depuis un stade précoce à déformation localisée jusqu'à un stade récent à déformation diffuse (<3 Ma). L’analyse des réseaux de drainage identifiés sur le compartiment de socle bordant à l'ouest le dispositif RSK-NTD démontre (1) leur contrôle étroit par le dispositif lithologique et tectonique du socle, (2) la nature polyphasée du soulèvement lié aux failles bordières, et (3) le caractère déséquilibré du réseau actuel en cours de soulèvement. / Any kinematic model applied to the southerly-propagating and diverging South Kenya rift (SKR) should necessarily integrate the structure of the Magadi-Natron axial trough (previous studies), but also those of the Oldoinyo Ogol (OOB) offset block to the west. Our work is chiefly based on SRTM 30 m satellite imagery analysis, and allows us (1) to precise the morphostructural arrangement of the entire SKR,(2) to identify 2 successive border faults systems, (3) to emphasize the role of the Ol Doinyo Ogol master fault, (4) to elaborate a 2-stage rift model (7-3 Ma et <3 Ma), and (5) to attribute a key-role to a transverse Proterozoic discontinuity on the lateral shift of the OOB, as well as on the split of the rift into the Eyasi rift arm and on the off-axis location of the early Crater Highlands magmatic segment, hence demonstrating the importance of basement structural inheritance on rift kinematics.The quantitative analysis of fault populations shows the restricted nature of most intra-rift faults, and leads us to precise the spatiotemporal evolution of extension from a stage of localized strain (border faults) to a stage of diffuse extension (<3 Ma).From the analysis of the river drainage extracted from the basement uplifted block bounding the rift system to the west, it is assumed that (1) lithological and tectonic basement features exerted a strong control on the river network, (2) fault-related basement uplift is polyphased, and (3) the unsteady nature of the present-day river drainage is due to still active rift-flank uplift in the southern portion of the rift system.

Les travaux de cette thèse portent sur la détection et le diagnostic des défauts naissants dans les systèmes d’ingénierie et industriels, par des approches statistiques non-paramétriques. Un défaut naissant est censé provoquer comme tout défaut un changement anormal dans les mesures des variables du système. Ce changement est imperceptible mais aussi imprévisible dû à l’important rapport signal-sur défaut, et le faible rapport défaut-sur-bruit caractérisant le défaut naissant. La détection et l’identification d’un changement général nécessite une approche globale qui prend en compte la totalité de la signature des défauts. Dans ce cadre, la divergence de Kullback-Leibler est proposée comme indicateur général de défauts, sensible aux petites variations anormales cachées dans les variations du bruit. Une approche d’analyse spectrale globale est également proposée pour le diagnostic de défauts ayant une signature fréquentielle. L’application de l’approche statistique globale est illustrée sur deux études différentes. La première concerne la détection et la caractérisation, par courants de Foucault, des fissures dans les structures conductrices. La deuxième application concerne le diagnostic des défauts de roulements dans les machines électriques tournantes. En outre, ce travail traite le problème d’estimation de l’amplitude des défauts naissants. Une analyse théorique menée dans le cadre d’une modélisation par analyse en composantes principales, conduit à un modèle analytique de la divergence ne dépendant que des paramètres du défaut. / This phD dissertation deals with the detection and diagnosis of incipient faults in engineering and industrial systems by non-parametric statistical approaches. An incipient fault is supposed to provoke an abnormal change in the measurements of the system variables. However, this change is imperceptible and also unpredictable due to the large signal-to-fault ratio and the low fault-to-noise ratio characterizing the incipient fault. The detection and identification of a global change require a ’global’ approach that takes into account the total faults signature. In this context, the Kullback-Leibler divergence is considered to be a ’global’ fault indicator, which is recommended sensitive to abnormal small variations hidden in noise. A ’global’ spectral analysis approach is also proposed for the diagnosis of faults with a frequency signature. The ’global’ statistical approach is proved on two application studies. The first one concerns the detection and characterization of minor cracks in conductive structures. The second application concerns the diagnosis of bearing faults in electrical rotating machines. In addition, the fault estimation problem is addressed in this work. A theoretical study is conducted to obtain an analytical model of the KL divergence, from which an estimate of the amplitude of the incipient fault is derived.

The objective of this work was to understand microbial population density and diversity, both spatially and temporally, in wetland mesocosms to gain a better fundamental understanding for use in the optimization and design of constructed wetlands (CWs). A standardized community level physiological profiling (CLPP) data analysis protocol was adapted and utilized for CW mesocosms. A new one-dimensional metric was developed to track community divergence using BIOLOGTM ECO plate data. The method proved easy to use, did not require a background in multivariate statistics, and accurately described community divergence in mesocosm systems. To study mesocosm biofilm-bound bacterial communities an appropriate detachment protocol was required. Various shaking protocols were evaluated for their effectiveness in the detachment of bacteria from mesocosm pea gravel, with a focus on detachment of viable and representative bacterial communities. A protocol based on mechanical shaking with buffer and enzymes was identified as an optimal approach and used further in this study. The bacterial communities associated with the interstitial water, pea gravel media, and rhizospheric regions from both planted and unplanted CW mesocosms were profiled using the CLPP method and compared. Vertical community stratification was observed for all mesocosm systems. Rhizospheric communities were found to be significantly more active than their gravel-associated counterparts, suggesting that although rhizospheric bacteria were less abundant in the mesocosms they may play a more significant role in the removal and fate of water born contaminants. The start-up dynamics of CW mesocosms was investigated using the CLPP and standard CW characterization methods over an eight month period. All mesocosms showed a steep increase in interstitial community divergence until day 75-100, at which point a steady-state was reached. The interstitial communities were also characterized in terms of similarity based on experimental design treatments (planted/unplanted and origin of seeding inoculum). Four stages were identified during the start-up consisting of an initial stage where mesocosm communities were differentiated based on origin of the inoculum, a period where adjustments and shifts occurred in all mesocosm, a time where all mesocosm communities were quite similar, and a final state where community differentiations were made based plant presence in the mesocosms.

The objective of this work was to understand microbial population density and diversity, both spatially and temporally, in wetland mesocosms to gain a better fundamental understanding for use in the optimization and design of constructed wetlands (CWs). A standardized community level physiological profiling (CLPP) data analysis protocol was adapted and utilized for CW mesocosms. A new one-dimensional metric was developed to track community divergence using BIOLOGTM ECO plate data. The method proved easy to use, did not require a background in multivariate statistics, and accurately described community divergence in mesocosm systems. To study mesocosm biofilm-bound bacterial communities an appropriate detachment protocol was required. Various shaking protocols were evaluated for their effectiveness in the detachment of bacteria from mesocosm pea gravel, with a focus on detachment of viable and representative bacterial communities. A protocol based on mechanical shaking with buffer and enzymes was identified as an optimal approach and used further in this study. The bacterial communities associated with the interstitial water, pea gravel media, and rhizospheric regions from both planted and unplanted CW mesocosms were profiled using the CLPP method and compared. Vertical community stratification was observed for all mesocosm systems. Rhizospheric communities were found to be significantly more active than their gravel-associated counterparts, suggesting that although rhizospheric bacteria were less abundant in the mesocosms they may play a more significant role in the removal and fate of water born contaminants. The start-up dynamics of CW mesocosms was investigated using the CLPP and standard CW characterization methods over an eight month period. All mesocosms showed a steep increase in interstitial community divergence until day 75-100, at which point a steady-state was reached. The interstitial communities were also characterized in terms of similarity based on experimental design treatments (planted/unplanted and origin of seeding inoculum). Four stages were identified during the start-up consisting of an initial stage where mesocosm communities were differentiated based on origin of the inoculum, a period where adjustments and shifts occurred in all mesocosm, a time where all mesocosm communities were quite similar, and a final state where community differentiations were made based plant presence in the mesocosms.

Les instabilités aéroélastiques de bandes d’acier constituent aujourd’hui l’un des problèmes majeurs dans les sections de refroidissement par jets impactants des lignes de recuit continues.En effet, le traitement thermique des nouveaux aciers nécessite de très fortes pentes de température impliquant constamment des augmentations de vitesse de soufflage susceptibles de mettre en jeu des instabilités aéroélastiques. Des flottements ainsi que des divergences de bande ont déjà été constatées et identifiées. Ces deux instabilités impliquent dans la plupart des cas des chocs entre la bande et les buses de soufflage ce qui engendre des défauts de surface sur la bande.Un banc d’essai a été conçu et fabriqué dans le but d’analyser ces instabilités et d’anticiper leur apparition. A partir d’observations, la dynamique structurelle de la bande a été simplifiée à un mode de rotation rigide. Le banc comporte une plaque oscillante en mouvement forcé.Celle-ci est impactée par un dispositif de plusieurs jets axisymétriques turbulents ayant une disposition identique à celle des tours industrielles. Les efforts aérodynamiques stationnaires et instationnaires agissant sur la plaque sont mesurés au moyen de capteurs de pression.L’impact de plusieurs jets en interaction crée de très importants gradients de pression sur la plaque il est donc nécessaire que la grille de prises de pression soit très fine pour que l’estimation des efforts aérodynamiques soit correcte. La plaque est donc instrumentée de 91capteurs de pression sur une surface de 18 cm². Elle peut également être translatée dans les ois directions de l’espace, ce qui permet d’obtenir la distribution des efforts instationnaires ainsi que des coefficients aéroélastiques sur une grande surface de plaque et à différentes distances d’impact.Les mesures de pression stationnaires ont permis d’établir les courbes d’évolution des efforts d’impact des jets sur la plaque en fonction de la distance jet-plaque ainsi que de la géométrie des buses. Les résultats ont permis de déterminer la stabilité statique de la plaque en mouvement de pompage. Les mesures de vitesses des jets libres ont été effectuées paranémométrie à fil chaud et ont permis de déterminer leurs propriétés statistiques.Les mesures de coefficients aéroélastiques sur la plaque en rotation ont été effectuées surune seule géométrie de soufflage, pour différentes vitesses réduites. Les résultats mettent en évidence l’importance des effets de bords sur la stabilité de plaque. Des méthodes de post traitements ont proposées afin d’extrapoler les résultats à différentes largeurs de bande. Ils sont confrontés aux travaux de Regardin et al. (réf. [1]) et mettent en évidence des désaccords avec le cas réel. Des suggestions sont apportées afin d’améliorer la représentativité du banc vis-à-vis des bandes industrielles. / Aeroelastic instabilities of steel strips impinged by arrays of cooling gas jets have becomeone of the main issues in cooling sections of continuous annealing lines. Indeed, the new steeltreatments require very high temperature variation rates which involve increases in jetvelocities that are likely to onset some aeroelastic instabilities. Strip flutter and divergencehave already been observed and identified. These two aeroelastic instabilities imply a strongrisk of contact with the blowing boxes, which can seriously blemish the strip.An experimental test rig was designed and built in order to analyze and predict of theseinstabilities. From observations, the strip’s structural dynamics was simulated by a rigidrotation mode. The rig included a forced oscillating plate which is impinged by an array ofaxisymmetric jets having the exact industrial geometry. The plate was instrumented withpressure sensors to measure the steady and unsteady surface pressures. The impingement ofinteracting jets creates very large pressure gradients on the plate and therefore a tight mesh ofpressure taps (91 over an 18cm² jet impingement surface) was necessary to allow a goodestimation of the aerodynamic loads The plate could also be moved in the three coordinatedirections as to obtain surface mappings of the unsteady jet forces and aeroelastic coefficientscan be obtained over a wide area and different jet-to-plate distances.The variation of the impinging aerodynamic forces was established as a function of the jetto-plate distance for different nozzle geometries. These results were used to determine the jetstatic stability in plunging motion. Velocity and turbulence measurements in free jets werecarried out using hot wire anemometry in order to determine their statistical properties.Aeroelastic coefficient measurements were carried out on the oscillating plate with onlyone nozzle geometry and different reduced velocities. Results show that the plate’s stability ismainly dependent on the boundary effects. Post processing methods are suggested in order toapply the results to larger plates. Results are compared to the data of Regardin et al. (réf. [1])and emphasize some discrepancies with respect to the real case. Finally some improvementsto the test-rig are suggested for it to be more representative of the industrial situation.

Le champ d’application de la Convention de Vienne de 1980 sur la vente internationale de marchandises constitue une question très délicate. En effet, le caractère abstrait et supplétif de ladite Convention a donné naissance à une jurisprudence fort divergente et à une doctrine rarement en accord. Les difficultés d’application de la Convention démontrent clairement les limites de cette dernière à s’adapter aux nouveaux contrats de vente internationale. Ces difficultés sont-elles dues à une mauvaise interprétation des termes de la convention ? Serait-il juste de compléter les lacunes de la Convention de Vienne par d’autres Conventions telles que les règles d’UNIDROIT ou les principes de droit européen des contrats ? Faut-il aller «au-delà» de la Convention de Vienne ? Toutes ces questions doivent être gardées en tête pour bien analyser le champ d’application de ladite Convention. / The scope of application of the 1980 Vienna Convention on Contracts for the International Sale of Goods is a very delicate issue. Indeed, its abstract and supplementary nature has given rise to markedly divergent judgements and rarely agreeing doctrine. The difficulties arising from the application of the CISG clearly exemplfy its limited ability to adap to novel international sale of goods contracts. Are these difficulties attributable to faulty interpretations of the provisions of the CISG? Would it be opportune to compensate for the CISG's shortcomings by resorting to other instruments, such as the UNIDROIT rules or the principles of European contract law? Is it necessary to look beyond the Vienna Convention? All these questions must be considered in order to properly analyse the scope of application of the CISG.

Multiple Sequenzalignments (MSAs) von homologen Proteinen sind nützliche Werkzeuge, um kompensatorische Mutationen zwischen nicht-konservierten Residuen zu charakterisieren. Die Identifizierung dieser Residuen in MSAs ist eine wichtige Aufgabe um die strukturellen Grundlagen und molekularen Mechanismen von Proteinfunktionen besser zu verstehen. Trotz der vielen Anzahl an Literatur über kompensatorische Mutationen sowie über die Sequenzkonservierungsanalyse für die Erkennung von wichtigen Residuen, haben vorherige Methoden meistens die biochemischen Eigenschaften von Aminosäuren nicht mit in Betracht gezogen, welche allerdings entscheidend für die Erkennung von kompensatorischen Mutationssignalen sein können. Jedoch werden kompensatorische Mutationssignale in MSAs oft durch das Rauschen verfälscht. Aus diesem Grund besteht ein weiteres Problem der Bioinformatik in der Trennung signifikanter Signale vom phylogenetischen Rauschen und beziehungslosen Paarsignalen. Das Ziel dieser Arbeit besteht darin Methoden zu entwickeln, welche biochemische Eigenschaften wie Ähnlichkeiten und Unähnlichkeiten von Aminosäuren in der Identifizierung von kompensatorischen Mutationen integriert und sich mit dem Rauschen auseinandersetzt. Deshalb entwickeln wir unterschiedliche Methoden basierend auf klassischer- und quantum Informationstheorie sowie multiple Testverfahren. Unsere erste Methode basiert auf der klassischen Informationstheorie. Diese Methode betrachtet hauptsächlich BLOSUM62-unähnliche Paare von Aminosäuren als ein Modell von kompensatorischen Mutationen und integriert sie in die Identifizierung von wichtigen Residuen. Um diese Methode zu ergänzen, entwickeln wir unsere zweite Methode unter Verwendung der Grundlagen von quantum Informationstheorie. Diese neue Methode unterscheidet sich von der ersten Methode durch gleichzeitige Modellierung ähnlicher und unähnlicher Signale in der kompensatorischen Mutationsanalyse. Des Weiteren, um signifikante Signale vom Rauschen zu trennen, entwickeln wir ein MSA-spezifisch statistisches Modell in Bezug auf multiple Testverfahren. Wir wenden unsere Methode für zwei menschliche Proteine an, nämlich epidermal growth factor receptor (EGFR) und glucokinase (GCK). Die Ergebnisse zeigen, dass das MSA-spezifisch statistische Modell die signifikanten Signale vom phylogenetischen Rauschen und von beziehungslosen Paarsignalen trennen kann. Nur unter Berücksichtigung BLOSUM62-unähnlicher Paare von Aminosäuren identifiziert die erste Methode erfolgreich die krankheits-assoziierten wichtigen Residuen der beiden Proteine. Im Gegensatz dazu, durch die gleichzeitige Modellierung ähnlicher und unähnlicher Signale von Aminosäurepaare ist die zweite Methode sensibler für die Identifizierung von katalytischen und allosterischen Residuen.