Atualmente a cultura da cana de açúcar tem ganhado destaque no cenário mundial devido a seu potencial uso na produção de bioenergia o qual poderia ser beneficiado desenvolvendo-se cultivares com aumento da produtividade de biomassa por unidade de área, o que é por sua vez, determinada pela arquitetura da planta. A brotação lateral é um dos principais fatores que regulam a arquitetura dos vegetais. Recentemente, esta fase do desenvolvimento tem sido estudada intensivamente em plantas consideradas modelo, elucidando em parte as vias genéticas, ambientais e hormonais que regulam este processo. Dentro desta vias, microRNAs, uma classe de pequenos RNAs não codantes que modula pós-transcricionalmente a expressão de genes endógenos, parecem ser importantes reguladores. Em cana de açúcar, a brotação lateral é importante para a arquitetura dos ramos laterais, germinação de gemas e perfilhamento. Entretanto, devido a sua complexidade genética e ausência de mutantes defectivos na brotação lateral, estudos nesta área ao nível molecular são limitados. Neste contexto, este trabalho teve por objetivos estudar em cana de açúcar a via microRNA156/fatores de transcrição do tipo SQUAMOSA promoter-binding-protein (SPL), a qual é associada à regulação do perfilhamento, bem como caracterizar molecularmente o processo de emergência de gemas axilares. Ferramentas computacionais usando o banco publico de ESTs TIGR gene índex permitiram identificar e classificar no genoma de cana de açúcar, diferentes genes associados ao processo de brotação lateral e resposta hormonal. Entres estes, seis genes SPL regulados pelo miR156 foram identificados, sendo um deles (SsSPL1) homólogo a SPLs envolvidas diretamente na regulação do perfilhamento. A expressão da SsSPL1 foi monitorada em diferentes tecidos e órgãos, juntamente com o miR156. Os dados sugerem que a SsPL1, é regulada negativamente pelo miR156, sendo esta via também conservada em cana de açúcar. Foram geradas plantas transgênicas da cultivar RB85486 com o gene endógeno SsmiR156a/b o qual codifica um precursor conservado do miR156 e parece estar associado com a evolução da arquitetura em monocotiledôneas. O acúmulo do miR156 foi avaliado em plantas transformadas via RT-qPCR encontrando variabilidade na sua expressão. Bibliotecas de pequenos RNAs foram geradas em gemas dormentes e em desenvolvimento, permitindo identificar membros de 26 famílias de miRNAs. A expressão de quatro deles, de seus genes-alvo e de outros genes selecionados foi monitorada em gemas dormentes e com 2 e 5 dias após o plantio. Interessantemente, o miR159 foi o mais expresso em gemas axilares de cana e parece ser um fator chave na emergência da gema, já que, segundo os resultados obtidos, esse miRNA parece modular a expressão do seu gene alvo SsGAMyB, o qual é um fator de transcrição implicado na ativação de genes de resposta a giberelina. Durante esta fase inicial do desenvolvimento também foi observado alterações na expressão de genes associados com processos de transdução de sinal associados aos fitohormônios auxina e etileno. Os resultados obtidos indicam que a emergência de gemas laterais é um processo dinâmico em que fitohormônios, fatores de transcrição e microRNAs participam conjuntamente para promover o crescimento e 12 desenvolvimento da nova plântula de cana de açúcar. / Sugarcane is an economically important biofuel crop that recently has become a target for improvement of sustainable biomaterial production due to its high biomass productivity and built-in containment features. Therefore, studies aiming to improve the production of biomass per area are among the most important issues in sugarcane production. Plant biomass is defined, at least in part, by its shoot architecture. Although shoot architecture (branching/tillering) is to some extend influenced by environmental factors, it is determined mainly by the plants genetic program. This includes developmental programs that are regulated by a complex network of genetic pathways that integrate endogenous and environmental cues. Several transcription factors as well as microRNAs are likely part of this network. In this study, we started to investigate the roles of the genetic pathway regulated by the microRNA156 and its targets, the transcription factors SQUAMOSA promoter-binding-protein (SPLs) in sugarcane branching/tillering. We identified six members of the SPL family that were further classified into four subfamilies. In both dicots and monocots, these SPLs are key regulators of the plant shoot architecture. We monitored the expression patterns of SsmiR156 e SsSPL1 in distinct sugarcane tissues/organs. Our observations suggest that miR156 regulates posttranscriptionally SsSPL1 mainly in leaf tissues. We generated transgenic sugarcane plants overexpressing the monocot-specific sugarcane miR156 precursor SsMIR156b/c via biolistic method. This precursor is thought to be important for the evolution of grass shoot architecture. Although we observed higher accumulation of mature SsmiR156b/c in leaf tissues of some transgenic plants as compared with tissues from non-transgenic plants, we could not detect any significant changes in their vegetative architecture. Using deep sequencing approaches, we have generated two small RNA libraries from dormant and outgrown sugarcane lateral buds. Preliminary analyses indicate that a select group of small RNAs are expressed in lateral buds, including over 200 repeat-associated small interfering RNAs (rasiRNAs) and 25 conserved microRNAs (miRNAs). Amongst the miRNAs, miR159 was the most sequenced in the two libraries. We evaluated miR159 accumulation pattern in addition to other selected miRNAs via qRT-PCR in dormant and developing buds. The majority of the evaluated miRNAs accumulate differentially during bud development, though with distinct expression patterns. Interestingly, miR159 accumulates at high levels in dormant buds, but scarcely in developing buds. Conversely, the experimentally confirmed miR159 target, a sugarcane GAMyB-like gene (SsGAMyB), is lowly expressed in dormant buds while its transcripts accumulate at higher levels in developing buds. GAMyB-like genes encode R2R3 MYB domain transcription factors that have been implicated in gibberellin (GA) and abscisic acid (ABA) signaling in germinating seeds. Our data suggest miR159 regulates GAMyB-like genes during sugarcane bud outgrowth. Similarly, SsSPL1 is regulated posttranscriptionally by the miR529, though this gene has sites for both miR529 and miR156. Auxin and ethylene-associated regulatory pathways are affected during sugarcane bud development. Taken together,our data indicate that sugarcane bud outgrowth from rhizomes is a complex developmental process involving hormones, transcription factors as well as microRNAs and other regulatory RNAs.

This paper concerns the creation and evaluation of a branching story written by the author. Branching storylines are unique in that each branch delivers a different experience, wherefore this paper poses and attempts to answer the question, is it possible to offer similar learning experiences regardless of which story path is taken in a branching story structure? As a case study, the story is written for a pervasive game, an application for Android phones. Due to the game’s design and wishing to motivate the players to move around on their own, it was written to be segmented and yet have linear, branching storylines. The case study consisted of creating a game set at a historical site, specifically Karlsborg fort, where the story would give the players an idea of how a day in the life of a sergeant could have looked in 1865. After testing and knowledge-based questionnaires, the data body proved minute, wherefore no significant conclusions are reached; however, it is suggested story nodes are useful for giving each player equal possibility of gleaning specific knowledge from the game, gathering all storylines in event scenes where the specific knowledge is presented.

Le problème de placement sur deux dimensions consiste à décider s’il existe un rangement d’objets rectangulaires dans une boîte donnée. C’est un problème combinatoire difficile (à la complexité du respect des capacités s’ajoute celle du positionnement des objets).Dans cette thèse, nous considérons les variantes sans rotation des objets et avec ou sansoptimisation de la valeur des objects placés.Nous menons une étude exploratoire des méthodologies qui peuvent être développéesà l’interface de la programmation mathématique, de l’optimisation combinatoire et de lathéorie des graphes. Notre objectif est aussi de développer des approches non basées surune discrétisation de la boîte, les plus performantes à l’heure actuelle.Dans ce mémoire, nous effectuons d’abord une étude théorique des qualités de bornesqui peuvent être obtenues avec les différentes formulations classiques. Au cours de cetteétude, nous renforçons certaines de ces formulations et en proposons de nouvelles formulations. Une étude qualitative des bornes issues de la relaxation linéaire des formulationstestés sur des jeux d’instances classiques de la littérature confirme l’étude théorique. Cetteétude permet de se rendre compte des facteurs déterminant la qualité des bornes et desenjeux à relever par la programmation mathématique.Par la suite, nous avons développé et testé deux approches de résolution innovantes.L’une est basée sur la décomposition de Dantzig-Wolfe associée à un branchement surles contraintes disjonctives de non recouvrement des objets. Cette approche a permis uneamélioration des résultats obtenus par la programmation mathématique.L’autre approche constitue en une approche combinatoire basée sur diverses caractérisations des graphes d’intervalles (modélisant le chevauchement des objets selon leurprojection sur chaque axe). Un premier algorithme est basé sur l’énumération de matricesde uns-consécutifs. Un autre utilise des arbres étiquetés pour éliminer plus efficacement lescas de symétries entre placements. Ces approches ont l’avantage de ne pas dépendre d’unediscrétisation du conteneur / The two dimensional orthogonal packing problem consists in deciding whether thereexists a packing of rectangular items in a given bin. This is a hard combinatorial problem(in addition to capacity constraints, one has to face the complexity of item positionning).In this thesis, we consider the case without item rotation and with or without packingvalue optimization.We explore methodologies at the interface of mathematical programming, combinatorial optimization and graph theory. Our aim is also to develop approaches not based on abin discretization (i.e. an alternative to such methods that are currently the most effective).In this work, we perform a theorical study of the quality of bounds of differents classicalformulations. We tighten some formulations and we propose new formulations. We perform a numerical study to test bound quality on classical instances. This study permits toidentify the determinant factor in the quality of mathematical programming formulations.We develop and test two resolution approaches. The first is based on Dantzig-Wolfedecomposition associated with a branching on no-overlapping disjunctive constraints. Thisapproach permits to improve results obtained by mathematical programming.The second approach establish a combinatorial approach based on multiple intervalgraph caracterization (modelling the item no-overlapping according to their projection oneach axis). The first algorithm is based on consecutive ones matrices enumeration. An otheruse labelled tree to eliminate more efficiently symmetry in packing. These approaches haveto advantage of being independent from bin discretization

The high latitude thickets of Acropora cervicornis off Broward County flourish despite the presence of natural and anthropogenic impacts. These populations provided a unique study area in contrast to disease-stricken populations of the Florida Keys. This study used time-sequenced photographs to examine how A. cervicornis was affected by tissue loss attributed to white-band disease during 2007–2008. Variables monitored included healthy colony skeletal extension rates, diseased colony skeletal extension rates, and tissue loss. The transmissibility of the three white-band syndromes found in the Scooter and Oakland thickets was examined through tissue grafting experiments. Skeletal extension rates of healthy and diseased colonies were generally not significantly different. Mean skeletal extension for A. cervicornis colonies in Broward County was observed to be 9.6 cm/y (SD=3.95, Range: 1.02–19.9). Mean linear tissue loss from disease signs was 2.6 mm/d (SD=4.3, Range: 0.023–16.8). Although the majority of active disease lesions caused severe tissue loss upon contact with healthy branches, in 25% of the cases there was no tissue loss. Disease signs were also observed in 10% of the control grafting trials. A. cervicornis thickets in Broward County were growing at rates similar to those observed in this species elsewhere in Florida, but faster than other areas of the Western Atlantic. Tissue loss rate from disease lesions was lower than reported elsewhere. White-band disease and/or other tissue loss syndromes are always present in Broward County, but the low prevalence of affected colonies, inconsistent transmission of a presumptive agent that causes the disease signs, and optimum branch skeletal extension seems to limit effects on the thickets. Results of this research are significant as the current protected status of acroporid corals no longer allows manipulative research such as coral grafting for transmissibility of potential disease pathogens.

Cette thèse est une contribution au document intitulé "Detector Baseline Document (DBD)" décrivant le conceptde détecteur ILD envisagé auprès du collisionneur linéaire international électron-positon ILC (acronyme del'anglais International Linear Collider).Les objectifs de physique de l'ILD nécessitent un détecteur de vertex (VXD) particulièrement léger, rapide et trèsgranulaire permettant d'atteindre une résolution sans précédent sur le paramètre d'impact des trajectoiresreconstruites des particules produites dans les interactions étudiées. Le principal objectif de cette thèse est demontrer comment optimiser les paramètres du VXD dans le cas ou il est composé de Capteurs à Pixels Actifsfabriqués en technologie industrielle CMOS (CAPS). Ce travail a été réalisé en étudiant la sensibilité desperformances d'étiquetage des saveurs lourdes et de la précision sur les rapports d'embranchement hadroniquedu boson de Higgs aux différents paramètres du VXD.Le cahier des charges du VXD, particulièrement ambitieux, a nécessité le développement d'une nouvelletechnologie de capteurs de pixels de silicium, les CAPS, dont le groupe PICSEL de l'IPHC est à l'origine. Lavitesse de lecture et l'influence des paramètres qui régissent la fabrication des capteurs en fonderie ont étéétudiées dans cette thèse, et des prototypesde CAPS ont été caractérisés sur faisceau de particules. Enfin, les performances de trajectométrie d'un VXDcomposé de CAPS a été évalué avec des études de simulation. / This thesis is a contribution to the " Detector Baseline Document ", describing the ILD detector which is intendedfor the International Linear Collider (ILC).The physics goals of the ILD call for a vertex detector (VXD) particularly light, rapid and very granular allowing toreach an unprecedented resolution on the impact parameter of the tracks that reconstruct the particles producedin the studied interactions. The principle goal of this thesis is to show how to optimise the parameters of the VXDin the case that is composed of Active Pixel Sensors manufactured in industrial CMOS technology (CAPS). Thiswork has been realised by studying the sensitivity of the performance of the heavy flavour tagging and theprecision on the hadronic branching fractions of the Higgs boson as a function of different sets of VXDparameters.The specifications of the VXD, particularly ambitious, call for the development of a novel silicon pixel sensorstechnology, the CAPS, which was pioneered by the PICSEL group of IPHC. The readout speed and the influenceof the fabrication parameters have been studied in this thesis, and CAPS prototypes have been characterised intest beams. Finally, the tracking performance of a CAPS based VXD has been evaluated with simulation studies.

Cette thèse étudie certaines propriétés fractales et trajectorielles de processus de branchement en temps et espace continus. De façon informelle, ce type de processus est obtenu en considérant l'évolution d'une population où les individus se reproduisent et meurent au cours du temps, et ce de manière aléatoire. Le premier chapitre concerne la classe des processus de branchement avec immigration. On donne une formule semi-explicite pour la transformée de Laplace des temps d'atteinte ainsi qu'une condition nécessaire et suffisante de récurrence-transience. Ces deux résultats illustrent la compétition branchement/immigration. Le second chapitre considère l'arbre Brownien et ses mesures de temps local, dites mesures de niveau. On montre que celles-ci s'obtiennent comme restriction, à une constante près explicitée, d'une certaine mesure de Hausdorff sur l'arbre. Le résultat est montré simultanément pour tous niveaux. Le troisième chapitre étudie le Super-mouvement Brownien associé à un mécanisme de branchement général. Sa mesure d'occupation totale est obtenue comme restriction d'une certaine mesure de packing dans l'espace euclidien. Le résultat est valable en grande dimension. La condition sur la dimension de l'espace ambiant est discutée à travers le calcul, sous des hypothèse de régularité faibles pour le mécanisme de branchement, de la dimension de packing du range total du processus. / This thesis investigates some fractal and pathwise properties of branching processes with continuous time and state-space. Informally, this kind of process can be described by considering the evolution of a population where individuals reproduce and die over time, randomly. The first chapter deals with the class of continuous branching processes with immigration. We provide a semi-explicit formula for the hitting times and a necessary and sufficient condition for the process to be recurrent or transient. Those two results illustrate the competition between branching and immigration. The second chapter deals with the Brownian tree and its local time measures : the level-sets measures. We show that they can be obtained as the restriction, with an explicit multiplicative constant, of a Hausdorff measure on the tree. The result holds uniformly for all levels. The third chapter study the Super-Brownian motion associated with a general branching mechanism. Its total occupation measure is obtained as the restriction to the total range, of a given packing measure on the euclidean space. The result is valid for large dimensions. The condition on the dimension is discussed by computing the packing dimension of the total range. This is done under a weak assumption on the regularity of the branching mechanism.

On s'intéresse dans cette thèse au modèle de la marche aléatoire branchante, un système de particules qui évoluent au court du temps en se déplaçant et se reproduisant de façon indépendante. Le but est d'étudier le rythme auquel ces particules se déplacent, dans deux variantes particulières de marches aléatoires branchantes. Dans la première variante, la façon dont les individus se déplacent et se reproduisent dépend du temps. Ce modèle a été introduit par Fang et Zeitouni en 2010. Nous nous intéresserons à trois types de dépendance en temps : une brusque modification du mécanisme de reproduction des individus après un temps long ; une lente évolution de ce mécanisme à une échelle macroscopique ; et des fluctuations aléatoires à chaque génération. Dans la seconde variante, le mécanisme de reproduction est constant, mais les individus subissent un processus de sélection darwinien. La position d'un individu est interprétée comme son degré d'adaptation au milieu, et le déplacement d'un enfant par rapport à son parent représente l'héritage des gènes. Dans un tel processus, la taille maximale de la population est fixée à une certaine constante N, et à chaque étape, seuls les N plus à droite sont conservés. Ce modèle a été introduit par Brunet, Derrida, Mueller et Munier, et étudié par Bérard et Gouéré en 2010. Nous nous sommes intéressés dans un premier temps à une variante de ce modèle, qui autorise quelques grands sauts. Dans un second temps, nous avons considéré que la taille totale N de la population dépend du temps. / In this thesis, we take interest in the branching random walk, a particles system, in which particles move and reproduce independently. The aim is to study the rhythm at which these particles invade their environment, a quantity which often reveals information on the past of the extremal individuals. We take care of two particular variants of branching random walk, that we describe below.In the first variant, the way individuals behave evolves with time. This model has been introduced by Fang and Zeitouni in 2010. This time-dependence can be a slow evolution of the reproduction mechanism of individuals, at macroscopic scale, in which case the maximal displacement is obtained through the resolution of a convex optimization problem. A second kind of time-dependence is to sample at random, at each generation, the way individuals behave. This model has been introduced and studied in an article in collaboration with Piotr Mi\l{}os.In the second variant, individuals endure a Darwinian selection mechanism. The position of an individual is understood as its fitness, and the displacement of a child with respect to its parent is associated to the process of heredity. In such a process, the total size of the population is fixed to some integer N, and at each step, only the N fittest individuals survive. This model was introduced by Brunet, Derrida, Mueller and Munier. In a first time, we took interest in a mechanism of reproduction which authorises some large jumps. In the second model we considered, the total size N of the population may depend on time.

Ce travail est consacré à l'étude de limites d'échelle de différentes fonctionnelles de marches aléatoires sur un arbre de Galton-Watson, potentiellement en milieu aléatoire. La marche aléatoire que nous considérons sur cet arbre est une marche aux plus proches voisins récurrente nulle, dont les probabilités de transition dépendent de l'environnement. Plus particulièrement, nous étudions la trace de la marche, c'est-à-dire le sous-arbre constitué des sommets visités par celle-ci. Nous considérons d'abord le cas où dans un certain sens l'environnement est à variance finie, et nous montrons que bien renormalisée la trace converge vers la forêt brownienne. Nous considérons ensuite des hypothèses plus faibles, et nous montrons que la fonction de hauteur de la marche (c'est-à-dire la suite des hauteurs prises par la marche) converge vers le processus de hauteur en temps continu d'un processus de Lévy spectralement positif strictement stable, et que la trace de la marche converge vers l'arbre réel codé par ce même processus. La stratégie employée pour établir ces résultats repose sur l'étude d'un type d'arbres que nous introduisons dans cette thèse : ceux-ci sont des arbres de Galton-Watson à deux types, l'un des types étant stérile, et à longueur d'arête. Notre principal résultat concernant ces arbres assure que leur fonction de hauteur satisfait un principe d'invariance, similaire à celui vérifié par les arbres de Galton-Watson simples. Ces arbres trouvent également une application directe dans les arbres de Galton-Watson multitype à infinité de types, un lien explicite entre les deux nous permettant de montrer qu'ils satisfont également le même principe d'invariance. / This work is devoted to the study of scaling limits of different functionals of random walks on a Galton-Watson tree, potentially in random environment. The randow walk we consider is a null recurrent nearest-neigbout random walk, the probability transition of which depend on the environment. More precisely, we study the trace of the walk, that is the sub-tree made up of the vertices visited by the walk. We first consider the case where in a certain sense the environment has finite variance, and we show that when well-renormalised, the trace converges towards the Brownian forest. We then consider hypotheses of regular variation on the environement, and we show that the height function of the walk (that is the sequence of heights in the tree of the walk) converges towards the continuous time height process of a spectrally positive strictly stable Lévy process, and that the trace of the walk converges towards the real tree coded by this very process. The strategy used to prove these two results is based on the study of a certain kind of trees that we introduce in this thesis: they are Galton-Watson trees with two types, one of which being sterile, and with edge lengths. Our main result about these trees states that their height functions satisfies an invariance principle, similar to that verified by simple Galton-Watson trees. These trees also find a direct application in multitype Galton-Watson trees with infinitely many types, as an explicit link between these two kind of trees allow us to show that they satisfy also the same invariance principle.

Le fil conducteur de cette thèse, composée de trois parties, est la notion de branchement.Le premier chapitre est consacré à l'arbre de Yule et à l'arbre binaire de recherche. Nous obtenons des résultats d'oscillations asymptotiques de l'espérance, de la variance et de la distribution de la hauteur de ces arbres, confirmant ainsi une conjecture de Drmota. Par ailleurs, l'arbre de Yule pouvant être vu comme une marche aléatoire branchante évoluant sur un réseau, nos résultats permettent de mieux comprendre ce genre de processus.Dans le second chapitre, nous étudions le nombre de particules tuées en 0 d'un mouvement brownien branchant avec dérive surcritique conditionné à s'éteindre. Nous ferons enfin apparaître une nouvelle phase de transition pour la queue de distribution de ces variables.L'objet du dernier chapitre est le graphe d'Erdős–Rényi dans le cas critique : $G(n,1/n)$. En introduisant un couplage et un changement d'échelle, nous montrerons que, lorsque $n$ augmente les composantes de ce graphe évoluent asymptotiquement selon un processus de coalescence-fragmentation qui agit sur des graphes réels. La partie coalescence sera de type multiplicatif et les fragmentations se produiront selon un processus ponctuel de Poisson sur ces objets. / This thesis is composed by three chapters and its main theme is branching processes.The first chapter is devoted to the study of the Yule tree and the binary search tree. We obtain oscillation results on the expectation, the variance and the distribution of the height of these trees and confirm a Drmota's conjecture. Moreover, the Yule tree can be seen as a particular instance of lattice branching random walk, our results thus allow a better understanding of these processes.In the second chapter, we study the number of particles killed at 0 for a Brownian motion with supercritical drift conditioned to extinction. We finally highlight a new phase transition in terms of the drift for the tail of the distributions of these variables.The main object of the last chapter is the Erdős–Rényi graph in the critical case: $G(n,1/n)$. By using coupling and scaling, we show that, when $n$ grows, the scaling process is asymptotically a coalescence-fragmentation process which acts on real graphs. The coalescent part is of multiplicative type and the fragmentations happen according a certain Poisson point process.

This master thesis is focused on stress-strain analysis abdominal aortic aneurysm using ANSYS software. The model of abdominal aortic aneurysm are based on CT scans of five specific patients. The branching arteries are included to the model and one goal of this thesis is decision about their influence of the wall stress. In this thesis was used a hyperelastic materiál model, which is based on mechanical tests done on human arterial samples.