Les travaux portent sur l’étude de la formation de motifs sédimentaires à l’aval d’un cylindre vertical soumis à un courant. Le cylindre simule une fondation monopieu d’éolienne en mer, ou une pile de pont. Une modélisation théorique est développée. Les résultats obtenus sont en bon accord avec les résultats expérimentaux acquis au cours de la thèse. Une étude préliminaire expérimentale et théorique sur le tri sédimentaire au voisinage du cylindre est également effectuée. / This work concerns the study of sediment patterns formation downstream a vertical cylinder under a steady current. The cylinder simulates an offshore monopile foundation, or a bridge pile. A theoretical modeling is developed. The results are in good agreement with the experimental results obtained in the framework of this PhD. An experimental and theoretical preliminary study on sediment segregation in the vicinity of the cylinder is also performed.

La matérialisation de vues est une technique efficace d'optimisation de requêtes. Dans cette thèse, nous proposons une nouvelle vision "orientée utilisateur" de solutions pour le problème de sélection de vues à matérialiser dans les entrepôt de données : l'utilisateur fixe le temps de réponse maximal. Dans cette vision nous proposons des algorithmes qui s'avèrent compétitifs avec les algorithmes de type "orienté système", dans lesquels les ressources, comme la mémoire, sont considérées comme la contrainte forte. L'approche "orientée utilisateur" est étudiée avec un contexte dynamique de système d'optimisation de requêtes. Nous analysons la stabilité de ce système par rapport à la dynamique de la charge de requêtes et des données qui sont insérées ou supprimées. Le concept clé de nos algorithmes de sélection de vues à matérialiser est la bordure. Ce concept a été très étudié en fouille de données dans le cadre du calcul des fréquents maximaux. Plusieurs algorithmes séquentiels ont été proposés pour résoudre ce problème. Nous proposons un nouvel algorithme séquentiel MineWithRounds, facilement parallélisable, qui se distingue des autres propositions par une garantie théorique d'accélération dans le cas de machines à plusieurs unités de calcul et à mémoire partagée. / The materialization of views is an effective technique for optimizing queries. In this thesis, we propose a new vision, we qualify it as "user oriented", of the solutions to the problem of selecting views to materialize in data warehouses : the user fixes the maximum response time. In this vision, we propose algorithms that are competitive with the algorithms "oriented system" type, where resources such as memory, are considered as the major constraint. The "user oriented" approach is studied under a dynamic context. We analyze the stability of this system with respect to the dynamic query workload dynamic as well as data dynamic (insertions and deletions). The key concept of our algorithms for selecting views to materialize is the border. This concept has been widely studied in the data mining community under the maximal frequent itemset extration setting. Many sequential algorithms have been proposed. We propose a new sequential algorithm MineWithRounds, easily parallelizable, which differs from the others in that it guarantees a theoretical speed up in the case of multiprocessors shared memory case.

Magister Scientiae - MSc / In summary there currently exist techniques to discover miRNA however both require many calculations to be performed during the identification limiting their use at a genomic level. Machine learning techniques are currently providing the best results by combining a number of calculated and statistically derived features to identify miRNA candidates, however almost all of these still include computationally intensive secondary-structure calculations. It is the aim of this project to produce a miRNA identification process that minimises and simplifies the number of computational elements required during the identification process. / South Africa

Watson-Crick paired B-form DNA is the genetic material in most of the biological systems. Integrity of DNA is of utmost importance for the normal functioning of any organism. Various environmental factors, chemicals and endogenous agents constantly challenge integrity of the genome resulting in mutagenesis. Over the past few decades multiple reports suggest that DNA can adopt alternative conformations other than the right handed double helix. Such structures occur within the context of B-DNA as sequence dependent structural variations and are facilitated by free energy derived from negative supercoiling, which may be generated during physiological processes like transcription, replication, etc. or binding of proteins. Multiple groups have shown that these structures render fragility to the genome owing to single-strandedness (presence of unpaired bases). This conformational polymorphism of the DNA is due to the presence of several repetitive elements across the genome. Some of the common non-B DNA structures include Z-DNA, H-DNA (triplex DNA), cruciform DNA, G-quadruplexes and RNA: DNA hybrid (R-loops). Over the past few decades G-quadruplex structures have gained tremendous importance owing to its role in physiology and pathology. Recently it has been shown that novel sequence motifs, called GNG or bulges can fold into G-quadruplexes, thus increasing the propensity of such structures genome-wide. Neurological diseases, psychiatric diseases and genomic disorders (due to deletions, translocations, duplications and inversions) are some of the consequences of non-B DNA structures in the human genome. Inadvertent genomic rearrangements in human can lead to different diseases including cancer. Immediate consequence of genomic rearrangement includes structural alteration of genome through joining of distant sequences. t(8;14) translocation is the hallmark of Burkitt’s lymphoma, which results in deregulation of c-MYC gene that may contribute to oncogenic transformation. In the present study, we delineate the causes of fragility within the c-MYC gene. In order to do this, breakpoints at the c-MYC locus from Burkitt’s lymphoma patient sequences reported in database were plotted and analysed. Interestingly, unlike many other translocations, breakpoints at c-MYC locus were widespread, except for a cluster of breakpoints downstream to promoter 2 (P2). Previous studies indicate that the translocation breakpoint clusters often correlate with formation of non-B DNA structures. The entire breakpoint cluster downstream of P2 was divided into Region 1, Region 2 and Region 3. Interestingly, in silico analysis of the breakpoint clusters revealed no evidence for predictive classic non-B DNA motifs in Region 2; whereas Region 1 harboured a G-quadruplex motif on the template strand and Region 3 had two short inverted repeats. Intriguingly, as the nontemplate strand of Region 2 was G skewed with a good number of AID binding motifs, we tested the MYC breakpoint Region 2 for its potential to form R-loop due to binding of nascent RNA to template DNA. Our results showed that MYC Region 2 can form RNA-DNA hybrid in a transcription dependent manner in physiological orientation. Observed structure was sensitive to RNase H. We showed Region 2 hindered action of Dpn I upon transcription confirming formation of R-loop structure. Owing to single strandedness, Region 2 R-loop was shown to be sensitive to P1 nuclease as opposed to the untranscribed control. The single strandedness of the Region 2 R-loop was characterized at a single molecule level through bisulfite modification assay. The assay corroborated formation of R-loop along with providing snapshots of various length R-loops formed upon Region 2 transcription. Besides, various biophysical and biochemical assays showed the complementary region (template strand) to be single-stranded in stretches, upon transcription. Length of RNA within the R-loop was within a range of 75 to 250 nt. To delineate the mechanism of R-loop formation we tested the sensitivity of R-loop formation to RNase A during and post transcription; and found that R-loop formation was abrogated in presence of RNase A during transcription suggesting that R-loop formation followed a “thread back model”. Intriguingly we observed that two short regions of the template strand exhibited high degree of single strandedness. To investigate the reason for such unusual single strandedness, oligonucleotides spanning the region was designed and subjected for CD and EMSA studies. EMSA showed robust intramolecular G-quadruplex structure formation in presence of KCl, whereas CD confirmed that both regions formed parallel G-quadruplexes. We also showed the precise involvement of guanines in structure formation through DMS protection assay. Further, the region of interest was cloned into appropriate vectors and primer extension assays were performed in presence of G-quadruplex stabilizing agents like TMPyP4 and KCl. Increasing concentration of these stabilizing agents enhanced the formation of G-quadruplexes in a double stranded context, which hindered polymerase progression. Since these G-quadruplex structures utilized sequences which are deviant to the consensus of G-quadruplex motifs, non-B DNA predicting tools were unable to score them. On closer analysis of the sequences we found that, these G-quadruplexes involve duplex hairpin and GNG motifs during structure formation. Besides, both the G-quadruplexes were highly thermostable and were able to fold back upon renaturation. Till recently, it has been believed that G-quadruplex structures are formed using a minimum of four, 3 guanine tracts, with connecting loops ranging from one to seven. Recent studies have reported deviation from this general convention. One such deviation is the involvement of bulges in the guanine tracts. In the present study, guanines along with GNG motifs have been extensively studied using recently reported HOX11 breakpoint fragile region I as a model template. By strategic mutagenesis approach we show that the core elements of a G-quadruplex are not equally important in structure formation when flanked by GNG motifs. Importantly, the positioning and number of GNG/GNGNG can dictate the formation of G-quadruplexes. In addition to HOX11 fragile region, GNG motifs of HIF1-alpha can fold into intramolecular G-quartet. However, GNG motifs in mutant VEGF sequence could not participate in structure formation, suggesting that the usage of GNG is context dependent. Importantly, we show that when two stretches of guanines are flanked by two independent GNG motifs in a naturally occurring sequence (SHOX), it can fold into an intramolecular G-quadruplex. Interestingly, intra molecular GNG G-quadruplexes were able to fold back after complete denaturation of the oligonucleotides. Besides one of the intra molecular GNG G-quadruplexes was purified and confirmed for parallel conformation. Finally, we show the specific binding of G-quadruplex binding protein, Nucleolin and G-quadruplex antibody BG4 to SHOX G-quadruplex through EMSA studies. Thus, the study provides novel insights into the role of GNG motifs in G-quadruplex structure formation, which may have both physiological and pathological implications. In conclusion, we show formation of transcription dependent R-loop and G-quadruplex structures at the c-MYC gene locus in a mutually exclusive manner. The data presented here, in conjunction with studies from other laboratories suggests that these structures could impart fragility within the c-MYC gene locus during t(8;14) translocation. Besides, we characterised unusual G-quadruplexes harbouring GNG motifs. We find that positioning and number of GNG can dictate the formation of G-quadruplexes and is context dependent.

Die Organisation von Handelsstrukturen bringt seit je her weitreichende soziale, politische sowie ökonomische Implikationen mit sich. Da die zugrundeliegenden Dynamiken von Handelssystemen a priori unbekannt sind bieten Konzepte aus der Theorie komplexer Systeme nützliche Werkzeuge, um neue Muster zu entdecken, sowie neue Hypothesen zu den Vorgängen innerhalb der Handelssysteme zu entwickeln. Einen nützlichen Ansatz stellen dabei komplexe Netzwerke dar, da Handelsströme zwischen ökonomischen Einheiten sinnvoll als Knoten und Verbindungen im Netzwerk darstellbar sind. In dieser Arbeit erweitern wir spezielle Methoden auf komplexen Netzwerken, um die Netzwerk-Topologie des Handels auf globaler und auf nationaler Ebene zu untersuchen. Auf dem Level einzelner Industriesektoren erhalten wir neue Einblicke in die topologische Struktur des internationalen Handelsnetzwerks. Dazu führen wir neue Netzwerkmaße ein, welche die Funktion von Knoten in Subgraphen unter dem Blickwinkel, dass das Gesamtsystem durch ein Netzwerk aus mehreren Subnetzwerken dargestellt wird, beschreiben. Im Zuge der Globalisierung gewinnen bilaterale Handelsabkommen bei Entscheidungsträgern an Aufmerksamkeit und werden in zunehmender Zahl verhandelt. Wir entwickeln in dieser Arbeit einen neuen Ansatz, um die Auswirkungen dieser Abkommen auf die beteiligten Ökonomien zu analysieren und zu quantifizieren. Weiterhin behandeln wir die Fragestellung, in welchem Maß Handel als ein Übermittler von Nachfrage- und Angebotsveränderungen auf andere Industrien angesehen werden kann. Schließlich betrachten wir Handelsnetzwerke auf der Ebene von einzelnen Firmen und beschreiben die Funktion von einzelnen Knoten, insbesondere deren Rolle innerhalb von 3er-Motiven. Obwohl alle Methoden und Maße, die wir im Zuge dieser Arbeit einführen, aus Fragen im Kontext des Handels motiviert sind, sind die methodischen Konzepte auf komplexe Netzwerke in anderen Forschungsrichtungen anwendbar. / The organization of trade and its patterns and structures have always had far reaching implications among social, political and economic dimensions. The underlying dynamics of trade systems are often a priori unknown and concepts from complex system theory provide useful tools to discover new patterns and to develop new hypotheses on the mechanisms of the system. Complex networks offer a particularly useful approach to trade systems, as trade flows between economic entities can be intuitively and meaningfully represented as nodes and links in a network. In this thesis, we extend specific methods of complex networks with a focus on the relations between different subnetworks to investigate the network topology of trade on both the global and national scale. On an aggregation level considering individual industries as nodes, we obtain new insights about the topological structure of the international trade network by introducing new network measures that characterize the roles of nodes in subnetworks from a network of networks perspective. During the process of globalization bilateral trade agreements have received rising attention among policy makers and have been negotiated at an increasing pace. Here, we develop a framework to analyze and quantify impacts of these agreements on the involved economies. A further question that we address is to what extent trade can be regarded as a mediator of demand and supply spillovers to other industries. Finally, we look into trade networks at the scale of individual business firms and describe the role of nodes with a focus on 3-node motifs. Although all new methods and measures introduced in this thesis are motivated by questions in the context of trade, the methodological concepts are widely applicable to complex networks of other research disciplines.

Soient $X$ et $Y$ des variétés au dessus d’un corps $F$. Dans de nombreuses situations, il s’avère important de savoir si un cycle algébrique modulo équivalence rationnelle y sur Y, défini au dessus du corps des fonctions $F(X)$ de $X$, est en fait déjà défini au niveau du corps de base $F$. Dans cet essai, on traite de cette question, en faisant varier la variété $X$ parmi des variétés telles que des quadriques, des variétés projectives homogènes ou des espaces principaux homogènes. Dans chaque situation, on utilise des outils appropriés tels que les opérations de Steenrod, des résultats de décomposition motivique, ou certains invariants cohomologiques de groupes algébriques. / Let $X$ and $Y$ be some varieties over a field $F$. In many situations, it is important to know if an algebraic cycle modulo rational equivalence $y$ on $Y$ defined over the function field $F(X)$ of $X$ is actually defined over the base field $F$. In this dissertation, we study that matter, making the variety $X$ vary among varieties such as quadrics, projective homogeneous varieties or principal homogeneous spaces. In each situation, we use appropriate tools, such as Steenrod operations, motivic decomposition results or cohomological invariants of algebraic groups.

Cette thèse est consacrée à définir et étudier des invariants motiviques associés aux ensembles semi-algébriques dans les corps valués. Ceux-ci sont les combinaisons booléennes d'ensembles définis par des inégalités valuatives. L'outil principal que nous utilisons est l'intégration motivique, une forme de théorie de la mesure à valeurs dans le groupe de Grothendieck des variétés définies sur le corps résiduel. Dans une première partie, on définit la notion de densité locale motivique. C'est un analogue valuatif du nombre de Lelong complexe, de la densité réelle de Kurdyka-Raby et de la densité p-adique de Cluckers-Comte-Loeser. C'est un invariant métrique à valeurs dans un localisé du groupe de Grothendieck des variétés. Notre résultat principal est que cet invariant se calcule sur le cône tangent muni de multiplicités motiviques. On établit un analogue de la formule de Cauchy-Crofton locale. On montre enfin que dans le cas d'une courbe plane, la densité motivique est égale à la somme des inverses des multiplicités des branches. L'objet de la seconde partie est de définir un morphisme d'anneau du groupe de Grothendieck des ensembles semi-algébriques sur un corps valué K vers le groupe de Grothendieck de la catégorie d'Ayoub des motifs rigides analytiques sur K. On montre qu'il étend le morphisme qui envoie la classe d'une variété algébrique sur la classe de son motif cohomologique à support compact. Cela fournit donc une notion virtuelle de motif cohomologique à support compact pour les variétés rigides analytiques. On montre également un théorème de dualité permettant de comparer le motif cohomologique de la fibre de Milnor analytique avec la fibre de Milnor motivique. / This thesis is devoted to define and study some motivic invariants associated to semialgebraic sets in valued fields. They are boolean combinations of sets defined by valuative inequalities. Our main tool is the theory of motivic integration, which is a kind of measure theory with values in the Grothendieck group of varieties defined over the residue field. In the first part, we define the notion of motivic local density. It is a valuative analog of complex Lelong number, Kurdyka-Raby real density and p-adic density of Cluckers- Comte-Loeser. It is a metric invariant with values in a localization of the Grothendieck group of varieties. Our main result is that it can be computed on the tangent cone with motivic multiplicities. We also establish an analog of the local Cauchy-Crofton formula. We finally show that the density of a germ of plane curve defined over the residue field is equal to the sum of the inverses of the multiplicities of the formal branches of the curve. The goal of the second part is to define a ring morphism from the Grothendieck group of semi-algebraic sets defined over a valued field K to the Grothendieck group of Ayoub’s categoryof rigid analytic motives over K. We show that it extends the morphism sending the class of an algebraic variety to the class of its cohomological motive with compact support. This gives a notion of virtual cohomological motive with compact support for rigid analytic varieties. We also show a duality theorem allowing us to compare the cohomological motive of the analytic Milnor fiber with the motivic Milnor fiber.

Les systèmes d'alarmes jouent un rôle critique dans la bonne exploitation des installations industrielles modernes. Cependant, dans la plupart de ces systèmes, les alarmes ne sont pas toujours traitées correctement par les opérateurs car il y a régulièrement beaucoup trop d’alarmes à gérer, notamment lors des avalanches d’alarmes. Pour réduire le flux d'alarmes, notre approche consiste à détecter des redondances entre alarmes qui pourraient être supprimées. Pour atteindre cet objectif, nous recherchons dans un premier temps les adjacences fréquentes entre les alarmes contenues dans un historique. Ceci est réalisé en adaptant l’algorithme de recherche de motifs fréquents AprioriAll. Nous explorons également une seconde méthode consistant à trouver des précédences systématiques. Pour les découvrir, nous identifions les relations de domination et de mutuelle dépendance contenues dans l’historique des alarmes. Pour faciliter l’analyse experte, les relations découvertes sont traduites sous la forme d’un réseau de Pétri.Ces deux méthodes sont ensuite confrontées à un historique d’alarmes industriel fourni par General Electric. Les résultats obtenus montrent que nos deux méthodes permettent une réduction globale du flux d'alarmes qui est plus importante durant les avalanches. / Alarm systems play an important role for the safe and efficient operation of modern industrial plants. However, in most of industrial alarm systems, alarm flows cannot always be correctly managed by the operators as they often turn into alarm floods, sequences of numerous alarms occurring in a short period of time. To reduce the alarm flows, this report focuses on detection of redundant alarms that could be removed. This objective is met by, first, looking for frequent adjacency in the alarm log. To identify them, the frequent pattern mining algorithm AprioriAll is adapted. Another way to find potentially redundant alarms is to look for systematic predecessors. To discover them, dominations and mutual dependencies contained in the alarm log are identified. To ease this analysis, the discovered relations are depicted in the form of Petri nets.Both those methods are then tested against an industrial alarm log made available by General Electric. The results show that both methods allow a reduction of the alarm flow, with the biggest reduction being during alarm floods.

Cette thèse s'inscrit dans le cadre de la biologie des systèmes et porte plus particulièrement sur un problème relatif aux réseaux biologiques hétérogènes. Elle se concentre sur les relations entre le métabolisme et le contexte génomique, en utilisant une approche de fouille de graphes.Il est communément admis que des étapes enzymatiques successives impliquant des produits de gènes situés à proximité sur le chromosome traduisent un avantage évolutif du maintien de cette relation de voisinage au niveau métabolique ainsi que génomique. En conséquence, nous choisissons de nous concentrer sur la détection de réactions voisines catalysées par des produits de gènes voisins, où la notion de voisinage peut être modulée en autorisant que certaines réactions et/ou gènes soient omis. Plus spécifiquement, les motifs recherchés sont des trails de réactions (c'est-à-dire des séquences de réactions pouvant répéter des réactions, mais pas les liens entre elles) catalysées par des produits de gènes voisins. De tels motifs de voisinage sont appelés des motifs métaboliques et génomiques.De plus, on s'intéresse aux motifs de voisinage métabolique et génomique conservés, c'est-à-dire à des motifs similaires pour plusieurs espèces. Parmi les variations considérées pour un motif conservé, on considère l'absence/présence de réactions et/ou de gènes, ou leur ordre différent.Dans un premier temps, nous proposons des algorithmes et des méthodes afin d'identifier des motifs de voisinage métabolique et génomique conservés. Ces méthodes sont implémentées dans le pipeline libre CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods). À l'aide de CoMetGeNe, on analyse une sélection de 50 espèces bactériennes, en utilisant des données issues de la base de connaissances KEGG.Dans un second temps, un développement de la détection de motifs conservés est exploré en prenant en compte la similarité chimique entre réactions. Il permet de mettre en évidence une classe de modules métaboliques conservés, caractérisée par le voisinage des gènes intervenants. / This thesis fits within the field of systems biology and addresses a problem related to heterogeneous biological networks. It focuses on the relationship between metabolism and genomic context through a graph mining approach.It is well-known that succeeding enzymatic steps involving products of genes in close proximity on the chromosome translate an evolutionary advantage in maintaining this neighborhood relationship at both the metabolic and genomic levels. We therefore choose to focus on the detection of neighboring reactions being catalyzed by products of neighboring genes, where the notion of neighborhood may be modulated by allowing the omission of several reactions and/or genes. More specifically, the sought motifs are trails of reactions (meaning reaction sequences in which reactions may be repeated, but not the links between them). Such neighborhood motifs are referred to as metabolic and genomic patterns.In addition, we are also interested in detecting conserved metabolic and genomic patterns, meaning similar patterns across multiple species. Among the possible variations for a conserved pattern, the presence/absence of reactions and/or genes may be considered, or the different order of reactions and/or genes.A first development proposes algorithms and methods for the identification of conserved metabolic and genomic patterns. These methods are implemented in an open-source pipeline called CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods). By means of this pipeline, we analyze a data set of 50 bacterial species, using data extracted from the KEGG knowledge base.A second development explores the detection of conserved patterns by taking into account the chemical similarity between reactions. This allows for the detection of a class of conserved metabolic modules in which neighboring genes are involved.

No description available.