To supplement and modify the diagnosis and clinical research of B-cell Chronic Lymphocytic Leukemia (B-CLL), a new method based on cell imaging and image processing was developed and applied to the B-CLL patient samples. The fluorophore-labelled leukemia cells were clearly visualized, reflecting the positive/negative expression of the corresponding surface markers and their distribution. Computer algorithms were devised and used to analyze a large number of images. The fluorescence intensity of the labelled antibodies on a given cell directly reflects the expression of the corresponding surface markers. The morphology and size of leukemia cells were not identical even in the same patient’s sample and the size variation does not correlate with the number of surface markers. The amount of each surface marker was approximately fixed for each patient, but there were some relationships, for instance, the number of CD19 and CD38 markers were correlated to each other. The heterogeneous expression of surface markers confirmed an assumption that surface markers have their preferred membrane positions. One of the most important results is that the cell imaging and our image processing method has provided an alternative and reliable way to diagnose B-CLL and new insights in the prognosis of subtype of B-CLL.

Canada’s official languages policy makes English and French the country’s official languages in federal institutions. The policy has succeeded in fostering equitable representation of both official languages groups in the federal public service and has improved capacities for the public service to serve the citizenry in its official language of choice. It is a puzzle however, that despite these advances, the Canadian federal public service continues to operate predominantly in English when both official languages on paper are equal languages of work. To explore this puzzle this dissertation asks: why, despite the promise of the Official Languages Act (OLA) 1969 for choice in language of work and the OLA 1988 that made the choice a claimable right, is there inequitable access to French as a language of work in the federal public service? Framed through a historical institutionalist approach and layering, this project analyzes the implementation of the official languages program in the federal public service from 1967-2013. This thesis argues that the implementation of the official languages program could not challenge the federal public service’s path dependency to operate predominantly in English. By analyzing the roles of actors and institutions that influenced the process, this dissertation finds that lack of structural change, inadequate managerial engagement and a false sense that official languages are engrained in the public service, can explain the persistence of English as the dominant language of work.

Every single day, lots of users actively participate in social media sites (e.g., Facebook, YouTube, Last.fm, Flicker, etc.) upload photos, videos, share bookmarks, write blogs and annotate/comment on content provided by others. With the recent proliferation of social media sites, users are overwhelmed by the huge amount of available content. Therefore, organizing and retrieving appropriate multimedia content is becoming an increasingly important and challenging task. This challenging task led a number of research communities to concentrate on social tagging systems (also known as folksonomy) that allow users to freely annotate their media items (e.g., music, images, or video) with any sort of arbitrary words, referred to as tags. Tags assist users to organize their own content, as well as to find relevant content shared by other users. In this thesis, we first analyze how useful a folksonomy is for improving personalized services such as tag recommendation, tag-based search and item annotation. We then propose two new algorithms for social media retrieval and tag recommendation respectively. The first algorithm computes the latent preferences of tags for users from other similar tags, as well as latent annotations of tags for items from other similar items. We then seamlessly map the tags onto items, depending on an individual user’s query, to find the most desirable content relevant to the user’s needs. The second algorithm improves tag-recommendation and item annotation by adapting the Katz measure, a path-ensemble based proximity measure, for the use in social tagging systems. In this algorithm we model folksonomy as a weighted, undirected tripartite graph. We then apply the Katz measure to this graph, and exploit it to provide personalized tag recommendation for individual users. We evaluate our algorithms on two real-world folksonomies collected from Last.fm and CiteULike. The experimental results demonstrate that the proposed algorithms improve the search and the recommendation performance, and obtain significant gains in cold start situations where relatively little information is known about a user or an item

Inspired by Gould, who claimed life would be arriving at a different outcome each time it were allowed to run from the same beginning, I have attempted to determine the repeatability of the adaptive course of one Pseudomonas fluorescens lineage. In addition, my study aimed to establish whether the likelihood of parallel evolution of the two synonymous single-nucleotide substitutions was contingent upon a prior motility-impairing deletion or a prior increase in fitness. Further, the study was designed to provide empirical data addressing the long-standing question of the effect of starting fitness on the ensuing rate of adaptation. Although no exact replay of the initial evolutionary trajectory was observed, I have demonstrated that gtsB, but not gtsC gene, is likely to be a mutational hotspot under the low glucose with a recovery of two undescribed mutations in gtsB. My data are consistent with a notion that substitutions in gtsB may be contingent upon Δ35kB(fliJ-PFLU4466) motility-impairing deletion, but not the fitness increase associated with it. Finally, the features of the adaptive landscape of P. fluorescens in the minimal glucose provide languid support for Fisher’s hypothesis of a decrease in adaptation rate with the rise in the starting fitness. Taken together, these original results reinforce the non-negligible role of history in shaping the outcomes of biological evolution and call for caution in attempting a formulation of rigid predictive models of evolutionary change. Inspiré par les travaux de Stephen J. Gould qui affirmait que la vie sur terre arriverait à une forme différente si elle repartait à zéro, je présente ici mes travaux où je teste la reproductibilité du cours adaptatif d’une lignée expérimentale de Pseudomonas fluorescens. L’objectif de cette étude était de déterminer si la probabilité que deux mutations synonymes évoluent en parallèle est affectée par la présence d’une délétion affectant la motilité de la bactérie ou de l’augmentation de la valeur sélective de celle-ci. De plus, le design expérimental de cette étude permet de tester si la valeur sélective initiale d’une population affecte le taux d’adaptation de cette même population. Bien d’une reproductibilité exacte du cours adaptatif initial ne fut pas observée, je démontre que le gène gtsB est probablement un « hotspot »mutationnel permettant l’adaptation à de bas niveau de glucose, ayant trouvé deux mutations dans ce site; alors que le gène gtsC ne l’est pas. Mes données sont également conséquentes avec le fait que les mutation dans le gène gtsB dépendent de l’effet de la délétion Δ35kB(fliJ-PFLU4466) affectant la motilité de la bactérie, mais non de l’augmentation de la valeur sélective qui y est associée. Finalement, la forme du plateau adaptative associé à de bas niveaux de glucose chez P. fluorescens supporte l’hypothèse émise par Fisher qui stipule que le taux d’adaptation d’un organisme diminue avec la valeur sélective initiale qui y est associée. L’ensemble de ces résultats supporte le rôle non-négligeable de l’histoire de vie d’une population en ce qui attrait à l’évolution future de cette même population. Aussi, ces résultats appelle à la prudence quand vient le temps de formuler des modèles prédictifs des changements évolutifs d’une population.

This thesis addresses the growing privatization of the US forces through the Revolution in Military Affairs and the War in Iraq and its implications for the purpose of mobilization and individual military commitment conceptualize by the US warrior ethos. Creating a dialogue between the literature on Private Military Companies and the US warrior ethos, this thesis aims at providing a comprehensive understanding of the values sustaining the warrior ethos and how they are jeopardized by the emergence of new actors in the battlespace. I argue that this commercial turn in the US military erode the warrior ethos by placing business consideration ahead of great personal risk and ultimately raises doubts about civic responsibilities and democratic control of US military affairs.

This thesis focuses on the development of method to the photochemical synthesis of niobium nanoparticles (NbNP) using Irgacure 907 (I-907) photoinitiator. This investigation is composed of two parts; whereas the mechanistic study of formation of particles was investigated first, and then followed by particles property characterization. By studying the mechanism of formation we were able to obtain knowledge on how to control the size of NbNP. This knowledge provided us with ability to generate a library of nanoparticles with the varying sizes. Furthermore, the study of I-907 photoproducts has given insight for an alternative method for the synthesis of NbNP using a milder reducing agent, 4-(methylthio)benzaldehyde (MSBA). Exposure of NbNP to air causes their oxidation leading to the formation of niobium oxide nanoparticles (NbONP). The oxidation of NbONP was characterized with variety of techniques (XPS, EDS and HRTEM) that demonstrated the core-shell structure of the nanoparticles. These methods indicated that the core is metallic Nb0 and the shell is the niobium oxide, Nb2O5. Since Nb2O5 is known be a strong Brønsted acid, we tested the Brønsted activity of NbONP with pH sensitive dye coumarin-6 (C6) (monitored using fluorescence and UV-vis). The results of these spectroscopic experiments indicated that NbONP can protonate C6, thus serving as confirmation for the acidity of NbONP. Furthermore, particles with varying sizes were tested with C6 to check if the difference in size affects the acidity. It was observed that the particles with the larger sizes have the strongest acidity and the particles of smaller sizes are less acidic.

The enzyme carbonic anhydrase (CA) contributes to multiple physiological processes by catalysing the reversible hydration of carbon dioxide. However, regulation of CA activity in response to homeostatic challenges remains poorly understood. The objectives of this thesis were to investigate whether CA is transcriptionally regulated by cortisol in fish and whether post-translational modification (PTM) of CA occurs in fish. The results of an in vivo reporter assay used to investigate potential transcriptional regulation of zebrafish, Danio rerio, cytoplasmic CA (CAc) were inconsistent, and it remains unclear whether zebrafish CAc is regulated transcriptionally by cortisol. Phosphorylation of rainbow trout, Oncorhynchus mykiss, CAc was predicted from in silico analysis of the putative amino acid sequence and confirmed by Western analysis of phosphoprotein levels following in vitro incubation of CA, purified from trout gill, under conditions designed to potentiate endogenous kinases. Again using in vitro incubations designed to potentiate endogenous kinases and phosphatases, changes to the phosphorylation state of CAc were found to modulate its enzymatic properties. These findings suggest that CA activity may be regulated by signalling pathways that activate cellular protein kinases, and future work should focus on identifying these pathways.

Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversial, as is the question of fractionation bias, namely whether one homeologous chromosome is more vulnerable to gene deletion than the other. As a null hypothesis, we first assume deletion events, on one homeolog only, excise a geometrically distributed number of genes with unknown mean mu, and these events combine to produce deleted runs of length l, distributed approximately as a negative binomial with unknown parameter r; itself a random variable with distribution pi(.). A biologically more realistic model requires deletion events on both homeologs distributed as a truncated geometric. We simulate the distribution of run lengths l in both models, as well as the underlying pi(r), as a function of mu, and show how sampling l allows us to estimate mu. We apply this to data on a total of 15 genomes descended from 6 distinct WGD events and show how to correct the bias towards shorter runs caused by genome rearrangements. Because of the difficulty in deriving pi(.) analytically, we develop a deterministic recurrence to calculate each pi(r) as a function of mu and the proportion of unreduced paralog pairs. This is based on a computing formula containing nested sums. The parameter mu can be estimated based on run lengths of single-copy regions. We then reduce the computing formulae, at least in the one-sided case, to closed form. This virtually eliminates computing time due to highly nested summations. We formulate a continuous version of the fractionation process, deleting line segments of exponentially distributed lengths in analogy to geometric distributed numbers of genes. We derive nested integrals and discover that the number of previously deleted regions to be skipped by a new deletion event is exactly geometrically distributed. We undertook a large simulation experiment to show how to discriminate between the gene-by-gene duplicate deletion model and the deletion of a geometrically distributed number of genes. This revealed the importance of the effects of genome size N, the mean of the geometric distribution, the progress towards completion of the fractionation process, and whether the data are based on runs of deleted genes or undeleted genes.

Experiments were completed in order to examine the effects of combined constriction and pier scour. Scour is cited as being a leading cause of bridge failure. It was found that in cases where both constriction and pier scour are present, the sum is greater than the linear addition of each individual case. This is contrary to the current industry assumption which states that the total depth of scour is the linear sum of the constriction and pier scour depth. Velocimetry and scour data were collected enabling comparisons to be made in order to determine how the flowfield influences the equilibrium scour conditions. In addition, experiments were performed examining the effect that the pier shape has on the scour depth and distribution. Since the results are contrary to the assumption used in industry, they are especially important and may help reduce future bridge failures.

The desire to obtain value and justify investments from the different Information Systems in place in organizations has been around for a long time. Organizations constantly theorize and implement different approaches that provide some sort of alignment between their different business objectives and Information Systems. Unfortunately, the environments in which these organizations operate are often dynamic, constantly changing with influence from external and internal factors that require continual realignment of the Information Systems with business objectives to provide value. When businesses evolve, leading to changes in business requirements, it is hard to know what direct Information System changes are needed to respond to the new requirements. Similarly, when there are changes in the Information System, it is not often easy to discern which business objectives are directly affected. Whilst the different Enterprise Architecture frameworks available today provide and propose some form of alignment, in their implementation, they do not show links between business objectives and Information Systems, i.e., indicating what Information System is directly responsible for different business objectives thereby allowing for anticipation and support of changes as the business evolves. This thesis utilizes insights from Business Intelligence and uses the User Requirements Notation (URN), which enables modeling of business processes and goals, to provide a framework that exploits links between business objectives and Information Systems. This Business Intelligence - Enabled Adaptive Enterprise Architecture framework allows for anticipating and supporting proactively the adaptation of Enterprise Architecture as and when the business evolves. The thesis also identifies and models levels within the enterprise where responses to change as the business evolves are needed and the ways the changes are presented. The tool-supported framework is evaluated against the different levels and types of changes on a realistic Enterprise Architecture at a Government of Canada department, with encouraging results.