This dissertation examined the impact of species, physiological age and spacing on tree form and branching at a Nelder experiment located near Rolleston, Canterbury. Two species were compared, Pinus radiata and Eucalyptus nitens, at a range of stockings from 271 stems/ha to 40,466 stems/ha. Within the P. radiata, two different physiological ages were compared. Stocking and species significantly affected (p-value <0.05) tree height, diameter at breast height (DBH), crown depth, branch mortality, branch angle, branch size and internode length. Only stocking was statistically significant for crown width, and height from the ground was also statistically significant for branch angle and branch mortality. DBH, crown width, crown depth, branch size and branch survival decreased with increasing stocking for both species. Branch angle and average internode length increased as stocking increased for both species, and branch angle and average internode length also increased as you moved away from the base of the tree. DBH, average internode length and branch size were significantly larger for P. radiata across all stockings, however branch mortality and branch angle were significantly larger for E. nitens. Physiological age was not statistically significant for any aspects of tree form or branching examined in this study.

With the start of the Large Hadron Collider(LHC) at CERN, we will obtain a new understanding of the physics beyond our current limits. New discoveries will be made; but we will require a deeper understanding, which the LHC machine, being a hadron collider, will not be able to elucidate. Instead, we will need an e+e- collider to make precision measurements of the newly discovered phenomena. Electroweak symmetry breaking and the origin of fermion and boson masses are fundamental issues in our understanding of particle physics. The essential piece of electroweak symmetry breaking - the Higgs boson - will probably be discovered at the LHC. If there are one, or more, Higgs boson(s) precise measurements of all properties of the Higgs will be very important. In this thesis I present two measurements of Standard Model Higgs boson properties in the context of the International Linear Collider (ILC) at √s = 500 GeV, using the proposed International Linear Detector (ILD). First a performance study of ILD to measure the branching ratios of the Higgs boson with mH = 120 GeV, where the Higgs boson is produced with a Z-boson via the Higgsstralung process, and the Z decays into e+e- or μ+μ-. It will also be essential to study the Higgs Yukawa coupling. Therefore, in the second part of this thesis, I present a study of e+e- → tt¯H with the aim of making a direct measurement of the the top-Higgs coupling, using the semi-leptonic nal state and mH of 120 GeV. I show that the top-Higgs coupling can be measured with an accuracy of better than 28%.

The metanephric kidney consists of two types of epithelia; the Wolffian duct-derived ureteric bud and the nephrogenic components that originate from mesenchymal-toepithelial transitions in the metanephric mesenchyme. The ureteric bud forms when inductive signals from the metanephric mesenchyme stimulates the evagination of an epithelial tube from the Wolffian duct into the mesenchyme. Reciprocal signalling between the ureteric bud and the metanephric mesenchyme regulates the branching of the ureteric bud and the induction of nephron formation. Inductive and inhibitory signalling of ureteric bud growth and branching has been shown by several protein families, however, the mechanical aspects of ureteric bud branching and nephrogenesis are largely unknown. I investigated the roles of Rac1-GTPase and Rho-kinase during kidney development. These proteins are important regulators of the cytoskeleton where Rac1 is a promoter of actin filament polymerisation and Rho-kinase directly stimulates the formation and contraction of actin-myosin stress fibres. Using a cell-permeable inhibitor, Rac1 was inhibited with no effects on nephron formation or subsequent segmentation and patterning. Inhibition of active Rac1 significantly reduced the level of ureteric bud branching and also resulted in lower proliferation rates. Rho-kinase was similarly targeted using two inhibitors. Rho-kinase inhibition had important effects on nephron formation and nephron maturation. Inhibition of Rhokinase resulted in decreased levels of nephron formation and severely morphologically abnormal nephrons. The formation of apical-basal polarity was disturbed as was the development of the visceral and parietal epithelia; precursors of the renal corpuscle. Inhibition of Rho-kinase led to abnormal formation of the proximal-distal axis and abnormal segmentation of the nephron. The effects of Rho-kinase inhibition were partially mimicked by direct targeting of actin-myosin contractions using a myosin-ATPase inhibitor. This demonstrated that Rho-kinase is necessary during multiple stages of nephrogenesis and maturation, at least in part, as a result of its ability to regulate actin-myosin contraction. These results show that Rac1 and Rho-kinase play important roles during several aspects of kidney development and highlights the significance of further investigating the mechanisms involved during kidney organogenesis.

It is well known that in contrast to the Prisoner's Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. (authors' abstract)

The development of organs such as the lung and kidney occurs by branching morphogenesis. Changes in the cytoskeletal architecture, cell-cell adhesion and cell polarity are necessary for the formation of new branches. Interactions and reciprocal signalling between epithelial and mesenchymal cells mediate these organised cell movements that give rise to a complex system of tubes suitable for the transport of gas or fluids. Mutations that disrupt formation of either the correct number, or shape of epithelial branches, affect lung function. This, in turn, can lead to congenital abnormalities such as cystadenomatoid malformations, pulmonary hypertension or lung hypoplasia. Defects in lung architecture are also associated with adult lung disease, particularly in cases of idiopathic lung fibrosis. Identifying the signaling pathways that drive epithelial tube formation will likely shed light on both congenital and adult lung disease. This study shows that mutations in the planar cell polarity (PCP) genes: Celsr1; Vangl2 and Scribble, lead to disrupted lung development and defects in lung architecture. Examination of Vangl2 mutant kidneys reveals similar impairment of branching morphogenesis. Detailed histological and immunocytochemical analysis reveals that lungs from Celsr1Crsh/Crsh, Vangl2Lp/Lp and ScribbleCrc/Crc mice are small and misshapen with fewer branches, and by late gestation exhibit thickened interstitial mesenchyme and defective saccular formation. Moreover, epithelial integrity is disrupted, cytoskeletal remodeling perturbed and mutant endoderm does not branch normally in response to the chemoattractant FGF10. In ex-vivo culture, inhibition of Rho kinase, an important downstream effector of the PCP signaling pathway, can mimic the branching defects observed in these three mouse mutants. Furthermore, all three proteins are present in restricted spatial domains within lung epithelium. ScribbleCrc/Crc lungs, the most severely affected line, exhibit additional defects in components of the tight and adherens junctions; this in turn affects lumen diameter. These findings show that components of the PCP pathway: Celsr1; Vangl2 and Scribble are required for normal foetal lung development, thereby revealing a novel signalling pathway critical for this process. Examination of postnatal mice was not possible as homozygous mutations result in embryonic lethality. However, an assessment of Vangl2Lp/+ mice reveals that loss of a single copy of Vangl2 is enough to cause defects in embryonic lung development that persist into adult life, affecting lung function. Similarly, Vangl2Lp/+ mice show a small but significant reduction in kidney glomeruli.

Nowadays, the web services and mobile technology advance to a whole new level. These technologies make the modern communication faster and more convenient than the traditional way. People can also easily share data, picture, image and video instantly. It also saves time and money. For example: sending an email or text message is cheaper and faster than a letter. Interactive communication allows the instant exchange of feedback and enables two-way communication between people and people, or people and computer. It increases the engagement of sender and receiver in communication. Although many systems such as REDCap and Taverna are built for improving the interactive communication between the servers and clients, there are still common drawbacks existing in these systems. These systems lack the support of the branching logic and two-way communication. They also require administrator’s programming skills to function the system adequately. These issues are the motivation of the project. The goal is to build a framework to speed up the prototype development of mobile application. The MABIC support the complex workflow by providing conditional logic, instantaneous interactivity between the administrators and participants and the mobility. These supported features of MABIC improve the interaction because it engages the participants to communicate more with the system. MABIC system provides the mobile electronic communication via sending a text message or pushing a notification to mobile’s device. Moreover, MABIC application also supports multiple mobile platforms. It helps to reduce the time and cost of development. In this thesis, the overview of MABIC system, its implementation, and related application is described.

L'un des défis auxquels sont confrontés les producteurs de fruits est de réussir à maintenir d'année en année un équilibre entre croissance végétative et production. La productivité des arbres fruitiers au cours des années est étroitement liée à leur développement. Intégrer les caractères architecturaux dans les programmes de sélection pourrait donc, améliorer la régularité de production et aider à optimiser la gestion des cultures. Dans cette thèse, nous avons étudié le déterminisme génétique des caractères architecturaux chez l'olivier (Olea europaea L. subsp. Europaea), en incluant le développement végétatif et reproducteur. L'olivier a un grand intérêt en raison de l'importance de l'huile d'olive et des olives dans l'alimentation humaine. L'étude a porté sur une descendance issue du croisement entre les variétés 'Olivière' et ‘Arbequina' qui a été cultivée en verger dans deux environnements contrastés. En premier lieu, nous avons étudié le déterminisme génétique de la croissance et ramification des arbres durant la phase juvénile sur un site en considérant trois échelles d'observation: arbre, unité de croissance et entrenœuds. Les interactions entre les facteurs liés à l'ontogénie de l'arbre ainsi que les facteurs génotype et environnement ont été prises en compte. Des modèles génétiques, incluant les effets année de croissance et/ou ordre de ramification, environnement, génotype et leurs interactions respectives, ont été construits en intégrant une fonction de variance et une structure de covariance lorsque cela était nécessaire. Après une étape de sélection de modèle, les facteurs impactant significativement l'architecture de l'arbre ont été identifiés et les valeurs d'héritabilité au sens large ont été estimées. Ces résultats nous ont permis de définir à quel moment au cours de l'ontogenèse de l'olivier et à quelle échelle d'observation, les caractères de croissance et ramification sont déterminés génétiquement. De plus, cette étude a permis d'investiguer la plasticité des caractères architecturaux et leur stabilité entre environnements contrastés. Enfin, les changements associés à l'acquisition des facultés reproductives ont été observés. Quand tous les descendants ont atteint l'âge adulte, j'ai étudié les bases génétiques du développement reproducteur. La stratégie était basée sur (i) une décomposition d'un sous échantillon d'unités de croissance localisées à la périphérie de la couronne de l'arbre en variables quantitatives liées à la fois aux processus de floraison et fructification en relation avec leur croissance et ramification (ii) une évaluation annuelle du rendement des arbres durant quatre années. L'observation d'arbres 'ON' ou ‘OFF' pour une année donnée a révélé des tendances de production régulière vs irrégulière au sein de la descendance. Après avoir développé une nouvelle carte génétique, une recherche QTLs associés aux caractères reproductifs a été réalisée. Des QTLs présentant les effets des deux parents et des co-localisations ont été identifiés. Cette étude a mis en évidence le schéma de développement de l'olivier pendant les phases juvénile et mature mettant en évidence l'existence de gradients ontogéniques se traduisant par des caractères héritables qu'à la périphérie de l'arbre. Une stratégie de phénotypage adaptée aux caractéristiques architecturales de l'olivier a été proposée. Enfin, les descendants montrant une supériorité intéressante par rapport à leurs parents ont été identifiés. Ces génotypes pourraient être valorisés dans les programmes de sélection futurs pour la création de variétés innovantes. / One of the most challenging questions that fruit growers are facing is to maintain trees in a stable balance between production and vegetative growth from year to year. Fruit trees productivity over years is closely linked to their development. Integrating architectural traits in breeding programs could thus, optimise cultivation management and improve bearing regularity. Here, we investigate the genetic determinism of architectural traits in the olive tree (Olea europaea L. subsp. europaea) including vegetative and reproductive behaviour. The olive tree raises high interest because of the importance of olive oil and olives in the human diet. The segregating population under study derived from a cross between ‘Olivière' and ‘Arbequina' cultivars and was grown on two orchards under contrasting environments. First, we investigated the genetic determinism of juvenile growth and branching traits in one site at three different scales: whole tree, growth unit and internodes. Interaction between tree ontogeny, genetic and environmental factors were considered. Genetic models, including the year of growth, environment, genotype effects and their interactions, were built with variance function and covariance structure of residuals when necessary. After a model selection step, morphogenetic factors impacting significantly tree architecture were identified and heritabilities were estimated. These finding allow us to define when during the olive tree ontogeny and at which observation scale, growth and branching traits are under genetic influence. Moreover, progenies plastic response to contrasted environments was highlighted and traits showing significant genotype-by-environment effect were identified. Changes over time associated to the acquisition of reproductive competence were further observed. Once all progenies attempt adulthood, we studied the genetic basis of reproductive behaviour. Our strategy was based on (i) a decomposition of adult growth units at the crown periphery in quantitative variables related to both flowering and fruiting process in relation to their growth and branching (ii) an annual assessment of individual trees yield. The observation of ‘on' or ‘off' olive trees in a given year over four years revealed patterns of regular vs. irregular bearing. After developing a new genetic map, a QTL mapping was carried out on reproductive traits, leading to the identification of QTLs with effects from both parents and co-localizations. This study gives an overview of olive tree development during juvenility and maturity periods showing the existence of ontogenic trends, which result in traits heritable mostly at the tree periphery. A phenotyping strategy adapted to its architectural characteristics is proposed. Finally, progenies showing interesting superiority in comparison to their parents were identified and could constitute interesting sources for innovative materials in future selection programs.

Le chêne sessile (Quercus petraea) est une essence majeure de la sylviculture française. Sa ramification, phénomène de mise en place des rameaux, a pour origine unique les bourgeons proventifs axillaires mis en place lors de l'élongation des pousses annuelles (PA). On distingue la ramification séquentielle (les branches séquentielles) et la ramification épicormique. L'ontogénèse des épicormiques, c'est-à-dire le passage d'un bourgeon épicormique à un rameau épicormique plus complexe tel qu'un gourmand, picot ou broussin est encore peu connue. Les rameaux laissent dans le bois des marques, les traces raméales, qui peuvent fortement déprécier la qualité du bois. Etudier l'ontogénèse des rameaux épicormiques du chêne passe par un suivi longitudinal ou une analyse rétrospective des PA, ou par une dissection de l'arbre et une observation des traces raméales. Pour s'affranchir de ces méthodologies fastidieuses nous avons utilisé la tomographie à rayons X qui permet une étude exhaustive de toutes les traces raméales d'un billon, de leur ontogénèse ainsi que la reconstruction du billon en 3D. Les études menées au cours de cette thèse ont permis de mettre en évidence un important effet de l'arbre qui confère à chacun d'entre eux sa propre capacité à mettre en place et maintenir des épicormiques. Plus un arbre présente d'épicormiques dans son jeune âge, plus il en présentera quelques années plus tard. Cette tendance est modulée par la sylviculture actuelle, comme le maintien d'une végétation d'accompagnement qui joue sur les réserves en eau et carbohydrates de l'arbre, et la sylviculture passée, notamment les éclaircies fortes ayant favorisé les émissions de gourmands. Cependant la sélection précoce des arbres objectifs présentant le moins de formations épicormiques est une recommandation sylvicole de première importance dans le but de produire davantage de bois d'œuvre de la meilleure qualité possible. Une stratégie d'intégration de ces résultats dans le simulateur de croissance Fagacée est proposée. / Sessile oak (Quercus petraea) is a major tree species of the French forestry. Its branching, i.e. the phenomenon of twigs implementation, has a unique origin: the proventitious axillary buds set during the annual shoot (AS) elongation. We distinguish the sequential branching and the epicormic branching. Epicormic ontogeny, i.e. transition from a bud to a more complex epicormic twig as an epicormic shoot, a picot or a burl is still little known. The mark left by these twigs in the wood, the rameal trace, can depreciate its commercial value. The study of the epicormic twigs ontogeny is possible with a longitudinal follow-up or a retrospective analysis of an AS, or a dissection of the tree and an observation of the rameal traces. To free ourselves from these tedious methodologies, we used RX computed tomography which allows an exhaustive survey of all the rameal traces of a log, their ontogeny as well as the 3D reconstruction of the log. This PhD allowed to show the important effect of the tree which confers on each one its capacity to set up and maintain epicormics. The more numerous the epicormics were at young stage, the more numerous the epicormics are several years later. This trend is modulated by the actual forest operations, as the maintaining of an accompanying vegetation which play on water and carbohydrates reserve; and by past forest operation as epicormic shoot emission favoured by strong thinning. Nevertheless, the early selection of the crop trees with the few epicormic formations is a silvicultural advice of first importance in order to produce more timber wood of the best quality. A strategy of inclusion of these results in the growth simulator “Fagacées” is proposed.

Master of Science / Department of Industrial and Manufacturing Systems Engineering / Todd Easton / Integer Programs (IP) are a class of discrete optimization that have been used commercially to improve various systems. IPs are often used to reach an optimal financial objective with constraints based upon resources, operations and other restrictions. While incredibly beneficial, IPs have been shown to be NP-complete with many IPs remaining unsolvable. Traditionally, Branch and Bound (BB) has been used to solve IPs. BB is an iterative algorithm that enumerates all potential integer solutions for a given IP. BB can guarantee an optimal solution, if it exists, in finite time. However, BB can require an exponential number of nodes to be evaluated before terminating. As a result, the memory of a computer using BB can be exceeded or it can take an excessively long time to find the solution. This thesis introduces a modified BB scheme called the Octanary Branching Algorithm (OBA). OBA introduces eight children in each iteration to more effectively partition the feasible region of the linear relaxation of the IP. OBA also introduces equality constraints in four of the children in order to reduce the dimension of the remaining nodes. OBA can guarantee an optimal solution, if it exists, in finite time. In addition, OBA has been shown to have some theoretical improvements over traditional BB. During computational tests, OBA was able to find the first, second and third integer solution with 64.8%, 27.9% and 29.3% fewer nodes evaluated, respectively, than CPLEX. These integers were 44.9%, 54.7% and 58.2% closer to the optimal solution, respectively, when compared to CPLEX. It is recommended that commercial solvers incorporate OBA in the initialization and random diving phases of BB.

Estudamos um sistema de partículas a tempo discreto cuja dinâmica é a seguinte. Considere que no instante inicial sobre cada inteiro não negativo há uma partícula, inicialmente inativa. A partícula da origem é ativada e instantaneamente ativa um conjunto aleatório contíguo de partículas que estão a sua direita. Como regra, no instante seguinte ao que foi ativada, cada partícula ativa realiza esta mesma dinâmica de modo independente de todo o resto. Dizemos que o processo sobrevive se em qualquer momento sempre há ao menos uma partícula ativa. Chamamos este processo de Firework, associando a dinâmica de ativação de uma partícula inativa a uma infecção ou explosão. Nosso interesse é estabelecer se o processo tem probabilidade positiva de sobrevivência e apresentar limites para esta probabilidade. Isto deve ser feito em função da distribuição da variável aleatória que define o raio de ação de uma partícula. Associando o processo de ativação a uma infecção, podemos pensar este modelo como um modelo epidêmico. Consideramos também algumas variações dessa dinâmica. Dentre elas, variantes com partículas distribuídas sobre a semirreta dos reais positivos (nesta vertente, existem condições para as distâncias entre partículas consecutivas) e também com as partículas distribuídas sobre vértices de árvores. Estudamos também para esses casos a transição de fase e probabilidade de sobrevivência. Nesta variante os resultados obtidos são funções da sequência de distribuições dos alcances das explosões e da estrutura dos lugares onde se localizam as partículas. Consideramos também variações do modelo onde cada partícula ao ser ativada, permanece ativa durante um tempo aleatório e nesse período emite explosões que ocorrem em instantes aleatórios. / We studied a discrete time particle system whose dynamic is as follows. Consider that at time zero, on each non-negative integer, there is a particle, initially inactive. A particle which is placed at origin is activated and instantly activates a contiguous random set of particles that is on its right. As a rule, the next moment to what it has been activated, each active particle carries the same behavior independently of the rest. We say that the process survives if the amount of particles activated along the process is infinite. We call this the Firework process, associating the activation dynamic of a particle to an infection or explosion process. Our interest is to establish whether the process has positive probability of survival and to present limits to this probability. This is done according to the distribution random variable that defines the radius of infection of each active particle, Associating the activation process to an infection, we think this model as a model epidemic. We also consider some variations of this dynamic. Among them, variants with particles distributed over the half line (there are conditions for the distances between consecutive particles) and also with particles distributed over the vertices of a tree. We studied phase transitions and the correspondent survival probability. In this variant the results depend on the sequence of probability distributions for the range of the explosions and on the particles displacement. We also consider a variation where each particle after activated, remains active during a random time period emitting explosions that occur in random moments.