title: Evolutionary Genomics from Ontogeny to Phylogeny

contributor:
Singh, Rama S.
Biology

subject: ontogeny, phylogeny, divergence, evolution, species

abstract: Much speculation has been made about the relative importance of changes in developmental regulation of gene expression in determining major phylogenetic patterns observed both in extant and extinct species. However, most of these hypotheses have been formulated based on data obtained from the comparison of very distantly related organisms (e.g., between animal phyla). Another approach to answering questions about development (ontogeny) in the context of evolution (phylogeny) is to observe how developmental patterns diverge between closely related species, in order to obtain a better understanding of the population level processes underlying phyletic change. With the intent of addressing this possibility, the principle work outlined in this thesis investigated patterns of divergence between closely related species of Drosophila at the level of both the nucleotide coding sequence as well as gene expression levels in the context of ontogeny. The results show that the stage during which genes are expressed has a significant impact on their patterns of divergence, acting both to constrain (earlier stages) and accelerate (later stages) their rates of evolution - the latter being largely the result of sexual selection pressure. However, we also find that intermediate stages of fly development, such as metamorphosis, may experience a greater degree of conservation of the elements regulating gene expression than other stages. Nonetheless, we do find evidence that both gene expression and coding sequences may be subject to similar selection pressures, yet there also appears to be substantial uncoupling of the two, as evidenced by our observation of stage-specific, autonomous patterns of hybrid misexpression manifested in interspecific hybrids. The data presented herein shed new light on patterns of divergence between species, specifically with regards to how various selection pressures affect different stages of ontogeny.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Factors Influencing Consumer Attitudes Towards Biometric Identity Authentication Technology within the Canadian Banking Industry

contributor:
Head, Milena
Business Administration

subject: biometrics, authenticating, identity, Canadian, banks, consumer

abstract:
 Biometrics is the science of measuring either physiological (i.e. fingerprint, iris) or behavioural (i.e. gait, signature) characteristics for the purpose of determining or authenticating one's identity. While there has been considerable research conducted with respect to the technical aspects of biometrics, very little attention has been paid to consumer acceptability of this technology. The research presented here is a first step towards filling that void.

 As such, a series of three studies were undertaken. The first study was a qualitative analysis that identified what avenues of exploration Canadian banks considered to be the most salient with respect to consumer perceptions of biometric authentication technology. This analysis consisted of semi-structured interviews with subject matter experts. The second study was also qualitative and asked consumers from across Canada what they perceived as potential benefits and concerns with biometric authentication technology being used to access their bank accounts. Based upon the results of these two studies, which were further informed by a review of technology adoption literature, a third quantitative study was carried out in which a proposed research model was tested. This model identified both contextual antecedents and innate traits that may influence consumer attitudes towards using biometrics to access their bank accounts via an automated teller machine (ATM). In addition, the aspects of control and voluntariness were manipulated, through the presentation of various scenarios, to examine their effects upon both attitude as well as the direct antecedents of privacy and security concerns and usefulness. The proposed model was assessed using structural equation modeling. In addition, ANOV As and qualitative answers to open ended questions were examined to provide further insight as to what will enhance or impede consumer acceptance of biometric technology.

 The findings suggest that the contextual factors of privacy and security concerns and usefulness have a bigger impact upon attitude as compared to innate personality traits. In addition, while voluntariness appears to have no effect, control has a significant impact upon attitude as well as privacy and security concerns and usefulness. Based upon these results, implications for theory and practice are discussed, and suggestions for future research are presented. It is hoped that this initial research spurs additional interest in examining consumer acceptability of biometrics in terms of both private and public sector applications.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Forcing the Immovable One to the Ground: Revisioning a Major Deity in Early Modern Japan

contributor:
Benn, James A.
Religious Studies

subject:
Japanese religion
Fudō Myōō
Japanese deity
Naritasan Temple
miracle tale literature

abstract:
This dissertation examines early modern (seventeenth-mid-nineteenth century) Japanese religion through a study of a cult devoted to the popular deity Fudō Myōō ("The Immovable King of Illumination") at Naritasan Temple (also known as Shinshōji Temple) in Shimōsa Province (present-day Chiba Prefecture). It discusses how Naritasan developed a distinctive corpus of miracle tale literature centered around its sacred statue of Fudō, and how these tales interwove doctrinal and sectarian traditions with local geography and history to produce a regionally-specific brand of the deity. This process of individuation became central to the creation of Naritasan's identity and religious activities, its promises of material and spiritual rewards, and to the way stories were used to spread
the cult among the populace through recreational and commercial enterprises. I demonstrate how these narratives can thus be read in light of the temple's evolution and socio-economic changes affecting early modern Japan as a whole. By employing a locally-based and trans-sectarian approach to the study of the Fudō cult at Naritasan, this dissertation seeks to illuminate a number of issues: how the temple used miracle tales to domesticate and transform Fudo into a trademark "Narita Fudō", a process central to the religious and commercial identities of temples; how the Narita Fudo was not static but evolved over time to became an object of worship shared across a variety of religious and popular traditions; and finally, how the deity therefore resists convenient categorizations afforded him by modern scholarship, thus challenging the ways we understand one of Japan's oldest and most important deities.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Dynamic Analysis of Substructures with Account of Altered Restraint When Tested in Isolation

contributor:
Metzger, D.
Behdinan, K.
Mechanical Engineering

subject:
isolated substructure
dynamic loading
boundary conditions
impact analysis methodology
impact velocity
mass

abstract:
The objective of this research is to simulate the response of an isolated substructure such that the response of the substructure in isolation would be the same as the substructure within the structure. Generally, the behaviour of an isolated subsystem (substructure) subjected to dynamic loading is different than the behaviour of the same substructure within a system (structure). This is primarily caused by the boundary conditions that are imposed on the substructure from the surrounding subsystem in the entire structure. A new systematic approach (methodology) is developed for performing impact analysis on the isolated substructure. The developed technique is fundamentally based on enforcing the mode shapes around the boundary of the substructure in the full structure to be similar to the mode shapes of the isolated substructure. This is achieved by providing a consistent adjustment to the loading conditions (impact velocity and mass) to account for the loss of restraint at the interface with the full structure. Another important aspect of this research is experimental validation of proposed method. This method allows the experimental testing of an isolated substructure since the testing is performed by impacting the isolated substructure with an appropriate mass and velocity. In the finite element analysis, the structure is analyzed, and then the isolated substructure simulation is performed using the developed technique. The results obtained from the numerical simulations, for both the substructure in situ and the substructure in isolation, are compared and found to be in good agreement. For instance, the effective plastic strains, kinetic and internal energies for the substructure within the structure and the substructure in isolation range from 7% to 12% discrepancies between two analyses.
The numerical simulations of a full structure are verified by performing a series of
experimental impact tests on the full structure. Finally, the experimental applicability of
the technique is studied and its results are validated with FE simulation of substructure in
isolation. This problem of experimentally testing an isolated substructure had previously
not been addressed. The comparisons of FE simulation and experimental testing are made
based on the deformed geometries, out-of-plane deflections and accelerometer readings.
For example, the out-of-plane deformations from the FE analysis and the experimental
test were determined to be within 7% to 9%. The experimental validation and numerical
simulations indicates the technique is reliable, repeatable and can predict dynamic
response of the substructures when tested in isolation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Looking and seeing: How do school-aged children with and without developmental coordination disorder integrate vision and attention during visuomotor performance?

contributor:
Missiuna, Cheryl
Health Sciences

subject: developmental coordination disorder, school-age, selective visual attention, eye tracking, visual difficulties, internal models

abstract: This dissertation explores how children with and without developmental coordination disorder (DCD) ‘look’ and ‘see’: how they integrate vision and attention to guide arm and hand movements during a visuomotor task. Chapter 1 provides the thesis context, reviewing the vision and attention literature, outlining the role of these processes in motor performance, and reviewing what is known about vision and attention in children with DCD. Chapter 1 includes a discussion on eye tracking to measure visual attention, and outlines the thesis purpose and objectives.Chapter 2 focuses on children with DCD, detailing their presentation and clinical management. This chapter serves to increase the reader’s understanding of the difficulties children with DCD experience, and to demonstrate the need for intervention to prevent the profound consequences that can impact their quality of life. Chapter 3 presents a study that explores how children with and without DCD employ vision and attention to accomplish a visuomotor task in a natural setting, using a novel eye tracking design. Highlighted here are important differences during visuomotor task performance: compared to their peers, children with DCD did not use predictive gaze to attend to relevant task objects, but rather used vision to guide their arm/hand throughout the task. Chapter 4 outlines lessons learned from using an eye tracker with children with DCD, describing the children for whom eye tracking was not reliable, and discussing equipment and participant factors that impact eye tracker use. Recommendations for future research using eye tracking with the DCD population are provided. Finally, Chapter 5 discusses the clinical and research implications of the studies conducted here. Insights gained regarding visual attention differences between children with and without DCD are discussed in the context of interventions to improve health outcomes in children with DCD and the design of future eye tracking studies.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: THE PROBLEM OF ARTHRITIS IN THE MAYAN MUNICIPALITY OF CHANKOM, MEXICO: A SITUATIONAL ANALYSIS FOR DEVELOPING A COMMUNITY-BASED REHABILITATION PROGRAM

title: A SITUATIONAL ANALYSIS OF ARTHRITIS IN CHANKOM

contributor:
Richardson, Julie
Rehabilitation Science

subject:
Community based rehabilitation
Indigenous populations
Mexico
Mixed Methods
Participatory Action Research
Mexico

abstract:
Disability and arthritis in Mexico are important public health problems. There is a need to develop rehabilitation interventions aimed at reducing the prevalence and disabling effects of arthritis in low socioeconomic communities in this country. This thesis reports findings from the initial execution of a mixed-methods participatory research program. This program was designed to develop, implement and evaluate a community-based rehabilitation program to decrease disability of people living with arthritis in the municipality of Chankom, a low-income rural Mayan community located in Southeast Mexico.
Epidemiologic results showed a high prevalence of arthritis in Chankom associated with low levels of wealth and high body mass index. In addition, arthritis was associated with a higher prevalence of disability in this municipality. Further results showed that people who live with osteoarthritis in Chankom perform standardized and real-life activities with significant levels of disability. This disability was associated with levels of wealth, pain, muscle strength, self-efficacy, and physical activity. Ethnographic results showed that: a) arthritis reduces the health-related quality of life of people in Chankom through a process of disablement, b) people living with arthritis need access to culturally sensitive healthcare, and c) there are availability, attainability and acceptability barriers to accessing culturally sensitive health services in this municipality, which result from power imbalance between indigenous and non-indigenous people.
The work presented in this thesis is the extensive examination of the problems associated with arthritis in Chankom, using quantitative and qualitative methods. Our findings justify the need to develop health policies and interventions to prevent and decrease the disabling effects of arthritis in this marginalized community. Moreover, these findings will support the creation of a culturally sensitive, community-based rehabilitation program, as a multi-level strategy to promote social development and improve health-related quality of life of people living with arthritis in the municipality of Chankom.

abstract: Thesis

abstract: Candidate in Philosophy

abstract: There is a need to develop rehabilitation interventions aimed at reducing the onset and disabling effects of arthritis in poor areas of Mexico. This thesis reports findings from the initial implementation of a research project designed to decrease disability of people living with arthritis in Chankom, a poor rural Mayan community located in Southeast Mexico. These findings show that arthritis is common in Chankom and it is related to having problems performing usual activities, which reduce people’s quality of life. People living with arthritis in Chankom need culturally appropriate healthcare services; however, they don’t obtain these due to different barriers associated with their indigenous background. Consequently, it is necessary to design health policies and interventions to decrease the disabling effects of arthritis in Chankom. The findings of this thesis will help creating a rehabilitation program that increases access to appropriate healthcare, improving function and quality of life of Chankom’s inhabitants.


title: Molecular Modelling of Voltage-Gated Potassium, Sodium and Calcium Channels Complexed with Metal Ions and Small-Molecule Ligands

contributor:
Zhorov, Boris S.
Biochemistry and Biomedical Sciences

subject: voltage-gated, potassium, sodium, calcium, channels, ligands, ion,

abstract: Voltage-gated potassium, sodium, and calcium channels play fundamental roles in cell physiology. They are targets for numerous drugs that are used to treat pain, cardiovascular, autoimmune, and other disorders. Atomic-resolution structures of ion channels and their complexes with ligands are necessary to understand the mechanisms of drug action of ligands. Electrophysiological and crystallographic studies have advanced our understanding of ion channels, but the binding sites, access pathways, and the mechanism of state-dependent action of medically important drugs remain unclear. During my graduate studies, I investigated the structure-function relationships of voltage-gated ion channels and their complexes with drugs by using energy calculations with experimental constraints. My work has helped resolve controversial interpretations of experiments addressing structural similarity between prokaryotic and eukaryotic K+ channels. Our model of the open Shaker K+ channel was confirmed by the later published X-ray structure of Kv1.2. Our Cav2.1 model reinterprets substituted-cysteine accessibility experiments, validates the proposed alignment between K+ and Ca2+ channels, and suggests a similar folding of voltage-gated K+ and Ca2+ channels. These results allowed me to model eukaryotic K+ and Na+ channels in the resting and open/slow-inactivated states, and to predict the binding sites of local anaesthetics, correolide, and chromanol 293B. In these studies, we proposed the involvement of metal ions in the binding of nucleophilic drugs and suggested that the deficiency of permeating ion(s) in the outer pore of the slow-inactivated channels stabilizes the ligands. Simultaneous studies of K+, Na+, and Ca2+ channels were advantageous because the information acquired from one family of ion channels was relevant to other families. My studies contributed to the growing knowledge about ion channels by offering structural information and suggesting mechanisms for the action of drugs.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Cubature Kalman Filtering Theory & Applications

contributor:
Haykin, Simon
Electrical and Computer Engineering

subject: Bayesian, filtering, posterior density, cubature, Kalman filter,

abstract:
 Bayesian filtering refers to the process of sequentially estimating the current state of a complex dynamic system from noisy partial measurements using Bayes' rule. This thesis considers Bayesian filtering as applied to an important class of state estimation problems, which is describable by a discrete-time nonlinear state-space model with additive Gaussian noise. It is known that the conditional probability density of the state given the measurement history or simply the posterior density contains all information about the state. For nonlinear systems, the posterior density cannot be described by a finite number of sufficient statistics, and an approximation must be made instead.

 The approximation of the posterior density is a challenging problem that has engaged many researchers for over four decades. Their work has resulted in a variety of approximate Bayesian filters. Unfortunately, the existing filters suffer from possible divergence, or the curse of dimensionality, or both, and it is doubtful that a single filter exists that would be considered effective for applications ranging from low to high dimensions. The challenge ahead of us therefore is to derive an approximate nonlinear Bayesian filter, which is theoretically motivated, reasonably accurate, and easily extendable to a wide range of applications at a minimal computational cost.

 In this thesis, a new approximate Bayesian filter is derived for discrete-time nonlinear filtering problems, which is named the cubature Kalman filter. To develop this filter, it is assumed that the predictive density of the joint state-measurement random variable is Gaussian. In this way, the optimal Bayesian filter reduces to the problem of how to compute various multi-dimensional Gaussian-weighted moment integrals. To numerically compute these integrals, a third-degree spherical-radial cubature rule is proposed. This cubature rule entails a set of cubature points scaling linearly with the state-vector dimension. The cubature Kalman filter therefore provides an efficient solution even for high-dimensional nonlinear filtering problems. More remarkably, the cubature Kalman filter is the closest known approximate filter in the sense of completely preserving second-order information due to the maximum entropy principle. For the purpose of mitigating divergence, and improving numerical accuracy in systems where there are apparent computer roundoff difficulties, the cubature Kalman filter is reformulated to propagate the square roots of the error-covariance matrices.
The formulation of the (square-root) cubature Kalman filter is validated through three different numerical experiments, namely, tracking a maneuvering ship, supervised training of recurrent neural networks, and model-based signal detection and enhancement. All three experiments clearly indicate that this powerful new filter is superior to other existing nonlinear filters.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Do Efficacy Claims in Pharmaceutical Sales Visits Vary by Approved Product Information or National Policy?

contributor:
Holbrook, Anne
Global Health

subject:
health policy
health services research
primary care
pharmaceutical promotion
comparative regulatory policy

abstract:
Introduction: Pharmaceutical sales visit claims of drug efficacy can influence physician prescribing. Efficacy claims may be susceptible to exaggeration in promotions for drugs approved on the basis of surrogate outcomes. They may also be different in countries with different sales visit regulations.

Objectives: To compare the frequency of physician-reported claims of serious morbidity or mortality benefit in promotions for drugs approved on the basis of surrogate outcomes (where claims are unwarranted) with those approved on the basis of serious morbidity or mortality. Additionally, to compare the frequency of unwarranted claims of serious morbidity or mortality benefit by country of promotion.

Methods: From 2009 to 2010, primary care physicians in Canada, France, and the United States reported via pre-set questionnaires on claims of serious morbidity or mortality benefit in consecutive cardiovascular drug promotions. Promoted drugs were either 1)  approved on the basis of surrogate outcomes, or 2)  approved on the basis of serious morbidity or mortality. Using generalized estimating equations, the frequency of reported efficacy claims was compared between the two promotion types. The frequency of unwarranted claims drug benefit was also compared by country.

Results: 448 promotions were analyzed. Claims of serious morbidity or mortality benefit were reported in 156/347 (45%) promotions for drugs approved on the basis of surrogate outcomes and 72/101 (71%) promotions for drugs approved on the basis of serious morbidity or mortality, p<0.001. Despite stricter sales visit regulations, unwarranted claims of serious morbidity or mortality benefit for drugs approved on the basis of surrogate outcomes were reported most frequently in France (59%) compared to Canada (46%), p=0.2 or the United States (26%), p=0.02.

Conclusions: Across countries, unwarranted claims of drug benefit were frequently reported in promotions for drugs approved on the basis of surrogate outcomes. These claims amount to off-label promotion and contravene national sales visit regulations.

abstract: Thesis

abstract: Master of Science (MSc)


title: Efficient Sensitivity Analysis and Design Optimization of Photonic Devices

contributor:
Bakr, Mohamed H.
Li, X.
Electrical Engineering

subject: optimization, photonic devices, sensitivity, gradient,

abstract: Pages (41,133,161,209) were omitted from the thesis as they were completely blank pages.

abstract:
 In this thesis, we propose efficient approaches for design optimization of passive
and active photonic devices. These approaches are based on utilizing gradient based
optimization algorithms for efficient optimization of photonic devices. Some of the
proposed approaches obtain the required gradient (sensitivity) information efficiently
using adjoint variable method (AVM) applied directly to the exploited numerical
techniques. Other approaches are based on formulating the design problem as an
optimization problem using convex programming. These approaches utilize the gradient-based
interior point method (IPM) for solving the design.

 The AVM aims at efficiently obtaining the sensitivity information using the numerical technique. This technique requires a solution of an additional simulation of the adjoint system. The information obtained from the original and the adjoint simulation is sufficient to obtain the response and the sensitivity of the response with respect to all the design parameters. The AVM technique differs for different numerical method.

 The obtained sensitivity using the AVM approach is not only useful for exploiting gradient based optimization for design optimization, but also for yield and tolerance analyses of the newly proposed designs.

 We proposed a second order accurate approach to obtain the sensitivity information using finite difference time domain (FDTD) technique. This approach utilizes the AVM to efficiently obtain the sensitivity information. This approach is exploited for efficiently obtaining the sensitivity of the power reflectivity and coupling coefficient of various devices. This approach has been also utilized for obtaining the sensitivity of the dispersion characteristics of different guided wave structures.

 We also introduce a novel approach for sensitivity analysis of photonic devices
using the beam propagation method (BPM). This approach is simple and easy to
implement. It exploits the existing factorization of the system matrices for efficient
calculation of the sensitivity of the required objective function. This approach is also
utilized for sensitivity analysis of the vectorial modal properties of different guided wave
structures. This approach is also exploited for sensitivity analysis of various surface
plasmon devices.

 This AVM approach is also exploited to propose a novel design of an optical switch with wide working wavelength band and compact size. The switch is based on the self imaging theory in multimode waveguide with a refractive index has approximate
parabolic profile. The design problem is formulated as two stage optimization procedure.
The optimization algorithm exploits the efficiently obtained sensitivity information from
a BPM simulation. The final design has interesting characteristics.

 An efficient approach is also proposed to obtain the sensitivity of the energy levels and wavefunctions of different quantum structures obtained using time dependent and time independent Schrodinger equation. This approach is exploited for design optimization of different quantum well lasers.

 We also propose a convex formulation for the design problem of multilayer optical coatings. This formulation allows for efficient design of structures with large
number of layers in fractions of a second without an initial design.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Performances of different estimation methods for generalized linear mixed models.

contributor:
Bolker, Ben
Mathematics and Statistics

subject: Mixed models, Laplace approximation, adaptive Gauss-Hermite quadrature, penalized quasi-likelihood, lme4, glmmML

abstract:
Generalized linear mixed models (GLMMs) have become extremely popular in recent years. The main computational problem in parameter estimation for GLMMs is that, in contrast to linear mixed models, closed analytical expressions for the likelihood are not available. To overcome this problem, several approaches have been proposed in the literature. For this study we have used one quasi-likelihood approach, penalized quasi-likelihood (PQL), and two integral approaches: Laplace and adaptive Gauss-Hermite quadrature (AGHQ) approximation. Our primary objective was to measure the performances of each estimation method. AGHQ approximation is more accurate than Laplace approximation, but slower. So the question is when Laplace approximation is adequate, versus when AGHQ approximation provides a significantly more accurate result. We have run two simulations using PQL, Laplace and AGHQ approximations with different quadrature points for varying random effect standard deviation (Ɵ) and number of replications per cluster. The performances of these three methods were measured base on the root mean square error (RMSE) and bias. Based on the simulated data, we have found that for both smaller values of Ɵ and small number of replications and for larger values of and for larger values of Ɵ and lager number of replications, the RMSE of PQL method is much higher than Laplace and AGHQ approximations. However, for intermediate values of Ɵ (random effect standard deviation) ranging from 0.63 to 3.98, regardless of number of replications per cluster, both Laplace and AGHQ approximations gave similar estimates. But when both number of replications and Ɵ became small, increasing quadrature points increases RMSE values indicating that Laplace approximation perform better than the AGHQ method. When random effect standard deviation is large, e.g. Ɵ=10, and number of replications is small the Laplace RMSE value is larger than that of AGHQ approximation. Increasing quadrature points decreases the RMSE values. This indicates that AGHQ performs better in this situation. The difference in RMSE between PQL vs Laplace and AGHQ vs Laplace is approximately 12% and 10% respectively.

In addition, we have tested the relative performance and the accuracy between two different packages of R (lme4, glmmML) and SAS (PROC GLIMMIX) based on real data. Our results suggested that all of them perform well in terms of accuracy, precision and convergence rates. In most cases, glmmML was found to be much faster than lme4 package and SAS. The only difference was found in the Contraception data where the required computational time for both R packages was exactly the same. The difference in required computational times for these two platforms decreases as the number of quadrature points increases.

abstract: Thesis

abstract: Master of Science (MSc)


title: Essays on Household Savings and Finances

contributor:
Contoyannis, Paul
Economics

subject: household, savings, finances, retirees, income, taxation, economic,

abstract:
 My doctoral dissertation is composed of an introductory chapter followed by five
independent chapters on household savings and finances.

 After the introductory chapter, the second chapter investigates the living standards of Canadian retirees and the adequacy of their financial preparations. We explore the responses of Canadian retirees to subjective survey questions administrated in General Social Surveys and in the 1975 Retirement Survey. Our results show that a significant portion of Canadians report enjoying life more after retirement compared to before retirement. Moreover, in 2002, three quarters of retired Canadians indicated being at least as satisfied with their finances as they were in the year prior to retirement. The most significant correlate of financial dissatisfaction that our analysis uncovers is involuntary retirement and, in particular, involuntary retirement associated with poor health.

 The third chapter revisits a long standing question of whether households with higher lifetime income save a larger fraction of their income. The major difficulty in empirically assessing the relationship between lifetime incomes and saving rates is finding a credible proxy for lifetime income. Taking advantage of the unique
characteristics of the Canadian Family Expenditure Survey data, we construct reliable
lifetime income proxies. Our empirical analysis suggests that the estimated relationship
between saving rates and lifetime incomes is sensitive to the instrument used to proxy
lifetime income. Nevertheless, our preferred estimates indicate that, except for the poorest households (who simply do not save), saving rates do not differ substantially
across lifetime income groups.

 The fourth chapter examines the effect of taxation on households' portfolio allocation decisions. The key challenge in empirically assessing this relation is to find a substantial and plausibly exogenous source of variation in marginal tax rates. We use variation in marginal tax rates across households with the same total earnings, which arise in progressive income tax systems with individual taxation. Employing the
Canadian Survey of Household Finances, we find statistically significant but
economically modest responses to differential taxation.

 The fifth chapter investigates the problems associated with the estimation of intertemporal allocation parameters via linearized Euler Equations. We solve and simulate life-cycle consumption models in different economic environments and perform Monte Carlo experiments with these simulated data. Our results suggest that problems associated with the estimation of linearized Euler equations are strongly related to the assumed economic environments. In particular, the validity and relevance of conventional instruments used in the estimation depend on the concavity of the underlying policy rules, which in turn follows from features of the economic environment.

 The final chapter reviews the economic literature on the saving behavior of lower income households. Our discussion focuses on the motives shaping the saving behavior of low-income households. In addition to the standard economic framework
used for analysis of this kind, the Life-Cycle/Permanent Income Hypothesis, we also
discuss insights from "behavioral" economics. We review the international evidence on a
variety of policies designed to stimulate savings among low income households.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Formulations and Exact Solution Methods For a Class of New Continous Covering Problems

contributor:
Wesolowsky, George O.
Business

subject: Problem Formulations

subject: Exact Solution

subject: Continous Covering Problems

subject: Planar Expropriation problem with non-rigid rectangular facilities

subject: nonlinear

abstract:
This thesis is devoted to introducing new problem formulations and exact solution methods for a class of continuous covering location models. The manuscript includes three self-contained studies which are organized as in the following.

 In the first study, we introduce the planar expropriation problem with non-rigid rectangular facilities which has many applications in regional planning and undesirable facility location domains. This model is proposed for determining the locations and formations of two-dimensional rectangular facilities. Based on the geometric properties of such facilities, we developed a new formulation which does not require employing distance measures. The resulting model is a mixed integer nonlinear program. For solving this new model, we derived a continuous branch-and-bound framework utilizing linear approximations for the tradeoff curve associated with the facility formation alternatives. Further, we developed new problem generation and bounding strategies suitable for this particular branch-and-bound procedure. We designed a computational study where we compared this algorithm with two well-known mixed integer nonlinear programming solvers. Computational experience showed that the branch-and-bound procedure we developed performs better than BARON and SBB both in terms of processing time and size of the branching tree.

 The second study is referred to as the planar maximal covering problem with single convex polygonal shapes and it has ample applications in transmitter location, inspection of geometric shapes and directional antenna location. In this study, we investigated maximal point containment by any convex polygonal shape in the Euclidean plane. Using a fundamental separation property of convex sets, we derived a mixed integer linear formulation for this problem. We were able to identify two types of special cuts based on the geometric properties of the shapes under study, which were later employed for developing a branch-and-cut procedure for solving this particular location model. We also evaluated the resultant bound quality after employing the afore-mentioned cuts.

 In the third study, we discuss the dynamic planar expropriation problem with single convex polygonal shapes. We showed how the basic problem formulations discussed in the first two studies extend to their diametric opposites, and further to models in higher dimensions. Subsequently, we allowed a dynamic setting where the shape under study is expected to function over a finite planning horizon and the system parameters such as the fixed point locations and expropriation costs are subject to change. The shape was permitted to relocate at the beginning of each time period according to particular relocation costs. We showed that this dynamic problem structure can be decomposed into a set of static problems under a particular vector of relocations. We discussed the solution of this model by two enumeration procedures. Subsequently, we derived an incomplete dynamic programming procedure which is suitable for this distinct problem structure. In this method, there is no need to evaluate all the branches of the branching tree and one proceeds with keeping the minimum stage cost. The evaluation of a branch is postponed until relocation takes place in the lower-level problems. With this postponing structure, the procedure turned out to be superior to the two enumeration procedures in terms of tree size.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A Political Economy of Protest: Ethical and Ethnographic Sensibilities of Contemporary Anti-Capitalism

contributor:
O'Brien, Robert
Political Science

subject: anti-capitalist, protest, contemporary, ethical, ethnographic, International Relations

abstract:
 This work explores the importance anti-capitalist protest in the
contemporary international system. In doing so, I address some of the
practical, philosophical and ethical considerations of academic
depictions of protest through examples in Toronto, Canada and Seoul,
South Korea. Drawing on fieldwork at protest sites in both places, I
focus on forms of contemporary anti-capitalism through a political
economy of 'Capital' and the inherent contestation of contemporary
political decision making. I outline how it is important to develop
subjective accounts of political protest that utilize ethical and
psychoanalytic insights to come to terms with the tension between
conformity and resistance. Contrasting what I call 'militant
masculinties' of protest with 'alternative masculinities' of anticapitalism,
I problematize some of the commonly held assumptions about
the distinction between activism and academic efforts. Instead, I
demonstrate how the methodological insights of an 'ethnographic
sensibility' can benefit International Relations scholarship by
discussing the possibilities and limits of political participation in
the contemporary capitalist system. This research seeks to contribute
to debates about political subjectivity and political activism through
an examination of the efforts to challenge economic decision making
power that rests in the hand of a few supposed experts. This thesis is
an effort to democratize the way we think about participation in the
site of protest, in order to encourage popular and academic engagement
with the local and global struggles taking place across the world.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Recent Advances in Heteroatom-Stabilized Carbanion Chemistry

contributor:
McNulty, Jim
Chemistry

subject:
modified Peterson olefination
new reactions
carbanion chemistry

abstract:
An efficient, stereoselective method for the synthesis of α-phosphonoenamines based on
a modified Peterson olefination was developed. The carbanion derived from Diethyl 1-dimethylamino-1-trimethylsilylmethanophosphonate reacted with aromatic or aliphatic
aldehydes selectively eliminating in Peterson fashion to deliver functionally rich α-phosphonoenamines. A highly efficient method was developed for the one-carbon homologation of aldehydes to carboxylic acid derivatives employing the reaction of a 1, 1-bis-dimethylphosphonate derivative with the aldehyde and controlled acid hydrolysis of the derived α-phosphonoenamine intermediate. The reaction of bis(trimethylsilyl)chloromethane with s-BuLi was found to proceed via transmetallation rather than deprotonation yielding the nucleophilic bistrimethylsilylmethyl anion quantitatively which reacted readily with aldehydes
providing a general entry to vinylsilanes. The reaction of α-silylated ylides with non-enolizable aldehydes proceeded via selective Peterson-type elimination, in contrast to prior literature reports, providing a direct route to synthetically useful vinylphosphonium salts. The chemoselective formation of trialkylbenzyl phosphoranes in water and their Wittig reaction with aromatic and aliphatic aldehydes provided a practical, stereoselective and environmentally benign route to valuable trans-stilbenes and alkenes. The synthesis of
the phytoalexin resveratrol was described. In addition, the method allowed for a gramscale
synthesis of the anticancer agent DMU-212 utilizing no organic solvent at any stage. A direct synthesis of 1,3-dienes and 1,3,5-trienes from the reaction of semi-stabilized ylides and a range of saturated and unsaturated aldehydes was reported in water as solvent, employing sodium hydroxide as base. The water-soluble phosphine oxide side product was removed simply by aqueous partitioning of the organic products.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Predictors of First Ambulation During Hospitalization Among Patients Admitted For Acute Myocardial Infarction

contributor:
Markle-Reid, Maureen
Nursing

subject:
acute myocardial infarction
timing of first ambulation
predictors of first ambulation
retrospective cohort study
Hamilton Health Sciences
patient and care related factors

abstract:
Purpose: To determine the timing of first ambulation during hospitalization among patients admitted for acute myocardial infarction (AMI) and to identify the predictors of first ambulation.
Methods: This retrospective cohort study included 500 AMI patients admitted during 2004 to one of three hospitals that form the Hamilton Health Sciences Corporation in Hamilton, Ontario, Canada. The patients were randomly selected from a total of 1,014 charts from the Hamilton Health Sciences Computerized Health Records (SOVERA). Using a chart abstraction tool, the following data were collected from each patient's chart: demographic information, past medical history, treatment, complications, and patterns of ambulation while in hospital. The primary outcome was first ambulation, defined as the first time patients walked during their hospital stay. Secondary outcomes included heart rate at discharge and mortality during hospitalization. The relationship between patient and care-related factors and the time of first ambulation after AMI was explored through a time to event analysis using Cox regression; the associations were expressed as hazard ratios. The fit for the proportional hazard model was assessed and a stratified proportional hazard model was performed for age.          Results: Of the 500 charts, 60 were excluded. Of the 440 patients who were included in the final analysis, 340 (77.3%) walked during hospitalization. One hundred fifteen (26.1 %) walked during the first 48 hours (early walking), 98 (22.3%) walked between 49-96 hours (intermediate walking), and 127 (28.9%) walked after 96 hours (late walking). A total of 100 patients (22.7%) were categorized as non-walkers. Factors that emerged in the survival analysis that were positively associated with early ambulation after AMI and that proved the proportionality on the assessment of the fit of the model were: having a family history of cardiovascular disease (HR 1.33; 95% Cl 1.00, 1.44; p=0.05), receiving thrombolysis (HR 1.47; 95% Cl 1.11, 1.49; p=0.007), receiving nitroglycerin (HR 1.51; 95% Cl 1.19, 1.93; p<0.001 ), and taking calcium channel blockers (HR 1.58; 95% Cl 1.22, 2.05; p<0.001 ). Factors that were negatively associated with early ambulation after AMI were age >59 years (HR 0.98; 95% Cl 0.97, 0.99; p<0.001 ), having an arrhythmia in-hospital (HR 0.48; 95% Cl 0.22, 0.94; p=0.04), taking inotropic drugs (HR 0.72; 95% Cl 0.53, 0.98; p<0.001 ), and undergoing coronary artery bypass surgery (HR 0.51; 95% Cl 0.33, 0.78; p=0.002). Conclusion: There is variability in the timing of first ambulation among patients hospitalized with an AMI. Furthermore, those who walked early were more likely to have a family history of cardiovascular disease, have received thrombolysis, and be taking nitroglycerin or calcium channel blockers. Those least likely to walk early were older (>59 years), were more likely to have had an arrhythmia inhospital, to be taking inotropic drugs, and to have undergone coronary artery bypass surgery.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Genomic and Physiological Effects of Waterborne Copper Exposure in Zebrafish, Danio Rerio

contributor:
McClelland, Grant
Biology

subject: waterborne metals

subject: tropical freshwater species

subject: zebrafish

subject: henotypic plasticity in gene and protein expression

subject: waterborne Cu toxicity

subject: protective ions

subject: mixed metal contamination

subject: tissue metal accumulation

abstract:
Little is known regarding the impact excessive waterborne metals, like copper (Cu), have on tropical freshwater species. Zebrafish (Dania rerio) only recently became popular as a tool for environmental monitoring, due to their fully sequenced genome. Despite this, little was known regarding the ionoregulatory physiology of zebrafish. I first examined the impact softwater acclimation has on the ionoregulatory capacity of zebrafish, and identified a high degree of phenotypic plasticity associated with changes in both gene and protein expression, which highlighted the need for proper experimental design for studies involving pre-acclimation to softwater.
I then examined the acute and chronic effects of waterborne Cu exposure under the influence of both softwater conditions and the addition of protective ions (Na+ & Ca2+) . On an acute timeframe, I found that Na+ provided a greater protective effect than
Ca2+ in reducing Cu uptake, which was mimicked during chronic exposure, although the transcriptional effects were not as clear cut. I found that although Na+ and Ca2+ provided protective effects from Cu accumulation, there were still tissue specific and global
changes at the transcript level, as determined by microarray analysis. Furthemore, this set of experiments identified the metal- and stress- induced transcriptional effects due to Cu exposure, which is key to identifying gene endpoints of chronic Cu exposure.
A final experiment went further and looked at the effects of mixed metal contamination, examining chronic waterborne Cu exposure with interactive effects of elevated dietary Fe on gene expression and tissue metal accumulation. Not only did this experiment highlight that gene expression is not necessarily reflected in protein abundance/activity, but also demonstrated that high dietary Fe can significantly alter the transcriptional expression pattern of Cu transporters in the gill, liver, and gastrointestinal tract. This thesis has made significant steps in identifying viable gene endpoints of Cu toxicity.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Duplicate Gene Evolution and Expression After Polyploidization

contributor:
Evans, Ben J.
Biology

subject:
gene duplication
clawed frog Xenopus
retained expression of gene duplicates
evolutionary genomics
comparative transcriptomics
microarrays

abstract:
Gene duplications can facilitate genetic innovation, reduce pleiotropy and catalyze reproductive incompatibilities and speciation. Therefore, the molecular and transcriptional fate of duplicate genes plays an important role in the evolutionary trajectory of entire genomes and transcriptomes. Using the polyploid African clawed frog Xenopus, I have investigated mechanisms that promote the retained expression of duplicate genes (paralogs) after whole genome duplication. The studies herein estimated molecular evolution and characterized expression divergence of thousands of duplicate genes and a singleton ortholog from a diploid outgroup. In this thesis, I have discussed the multiple mechanisms for the retention of duplicate genes in a polyploid genome and examined the potential effects that gene characteristics before duplication have on the odds of duplicate gene persistence. I have also explored the use of microarrays for comparative transcriptomics between duplicate genes, and between diverged genomes.
The main objectives of my thesis were to better understand the genetic mechanisms that promote the retained expression of gene duplicates. My research utilized the duplicated genome from the allopolyploid clawed frog Xenopus. Genome duplication in clawed frogs offers a compelling opportunity to study factors that influence the genetic fates of gene duplicates because many paralogs in these frogs are of the same age, permitting one to control for the influence of time when evaluating the impact of duplication. My work has major impacts on several biological fronts including evolutionary genomics and comparative transcriptomics, and also on technical aspects of using microarrays. I have provided among the most comprehensive studies of its kind, in terms of examining molecular and regulatory aspects of thousands of expressed duplicates of the same age, and exploring various alternative hypotheses to explain how these genes are retained.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Activation of Sterol Regulatory Element Binding Protein-2 By Endoplasmic Reticulum Stress

contributor:
Austin, Richard
Medical Sciences

subject:
Protein
Sterol Regulatory Element Binding
Cell
Cellular Cholesterol Homeostasis
SREBP
Endoplasmic Reticulum
Unfolded Protein Response

abstract:
 Cellular cholesterol homeostasis is a fundamental and highly regulated process. Transcription factors known as sterol regulatory element binding proteins (SREBP) are responsible for the expression of many genes involved in the uptake and biosynthesis of cholesterol. SREBP activation and lipid dysregulation has been associated with cellular endoplasmic reticulum (ER) stress and the activation of the unfolded protein response (UPR). Our lab has previously reported a relationship between ER stress and SREBP activation causing lipid dysregulation and hepatic steatosis. This project was designed to elucidate the mechanism of ER stress-induced SREBP activation and determine its relationship with cellular pathologies associated with ER stress and lipid accumulation. My research has examined the mechanism by which ER stress activates SREBP-2 in various cell lines, including epithelial and macrophage cells. This research revealed that
(1) ER stress-induced SREBP-2 activation is not dependent on caspases and occurs through the conventional sterol-mediated proteolytic pathway; (2) the mechanism of ER stress-induced SREBP-2 activation is sensitive to changes in ER calcium; (3) ER stress is associated with SREBP-2 activation and lipid dysregulation in a model of renal injury; and ( 4) ER stress-induced SREBP activation in vitro is not associated with lipid accumulation in macrophage foam cells.

 This project has also offered me the opportunity to further enhance our understanding of the mechanism by which ER stress causes SREBP activation in a sterolindependent manner.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: SYNTHESIS, STRUCTURAL CHARACTERIZATION, SPECTROSCOPIC STUDIES AND COMPUTATIONAL INVESTIGATIONS OF 1,2,5-TELLURADIAZOLES AND THEIR SUPRAMOLECULAR ASSEMBLIES

contributor:
Vargas-Baca, Ignacio
Chemistry

subject: supramolecular synthon

abstract: The use of Te-N-C heterocycles as supramolecular building blocks was investigated. The propensity of the heavy main-group elements to engage in secondary bonding interactions motivated a survey of the literature that identified the supramolecular association patterns that are most frequent in the crystal structures of tellurium compounds. A notation was proposed to classify those supramolecular synthons. The shortest Te-N secondary bonding distances are observed in the crystals of 1,2,5-chalcogenadiazoles which assemble the virtual four-membered ring [Te-Nb. Detailed computational investigations (OFT) established that the Te-N secondary bonding interactions are stabilized by a combination of electrostatic and Lewis acid-base covalent contributions. The study also indicated that the [Te-N] 2 supramolecular synthon meets the requirements of strength, directionality and reversibility that are necessary in supramolecular chemistry. A general method was developed for the synthesis of a wide variety of telluradiazoles. These compounds were used in experiments that probed the ability of steric effects to disrupt the self-assembly and select dimers instead of ribbon polymers. Derivatives resulting from the addition of Lewis acids and bases were also investigated. Photoelectron spectroscopy confirmed the details of the calculated electronic structures of benzo-2, 1,3-chalcogenadiazoles and mass spectrometry provided evidence of the association of these molecules in gas phase. A molecular mechanics method was parameterized to reproduce the structural features of the [Te-N]2 supramolecular synthon and, using this information, envision new supramolecular architectures based on 1,2,5-telluradiazoles. The use of the [Te-N]2 supramolecular synthon in the design and function of materials with properties such as thermochromism and nonlinear optical responses was demonstrated. Preliminary findings also highlighted the potential use of this approach in molecular materials that conduct electricity.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THE ROLE OF SEMEN TRANSFORMING GROWTH FACTOR BETA 1 IN MODULATING IMMUNE RESPONSES DURING HIV-1 INFECTION

title: IMMUNE RESPONSES TO SEMINAL TGF-BETA 1

contributor: Medical Sciences (Molecular Virology and Immunology Program)

subject:
Semen
TGF-Beta 1
HIV-1
Female Genital Tract
Male Genital Tract
Epithelial Cell
Mucosal Immunity

abstract: Thirty five million people are currently living with HIV-1 today with women accounting for half of infected individuals globally. Sexual transmission is the main route of HIV transmission with approximately 40% of HIV infections occurring when the mucosal lining of the female genital tract (FGT) is exposed to HIV in semen from an infected male partner. Seminal plasma (SP), the fluid portion of semen, is a complex fluid which plays an immunomodulatory role in the FGT for successful conception, largely due to its high concentrations of TGF-β1. Several factors in SP from HIV-uninfected men have been shown to either inhibit or enhance HIV infection in target cells, however it is not clear how SP from HIV infected men would modulate genital epithelial cells (GECs), the first cells that encounter HIV in the FGT. The overall goals of this thesis were to compare inflammatory and regulatory cytokine concentrations in SP from HIV-uninfected and infected men, and subsequently compare GEC cytokine responses following exposure to SP from HIV-uninfected and HIV-infected men. I also investigated how SP and TGF-β regulated cytokine production and barrier function in GECs in the presence of HIV. The results summarized in this thesis demonstrated that HIV infection leads to different cytokine profiles in SP, based on stage of HIV-1 infection. HIV-infected men in acute stage contained higher levels of proinflammatory cytokines in their SP compared to HIV-uninfected and chronically infected men (CI men) which subsequently lead to higher levels of proinflammatory cytokines from GECs compared to CI men. In the follow up to this study we found that active TGF-β, which was found in higher concentrations in SP from CI men and led to decreased inflammatory response from GECs, was compartmentalized between blood plasma and seminal plasma. Higher levels of active TGF-β in SP correlated with decreased semen viral load and the immune activation marker sCD14 leading us to believe that ART-naive CI men in our cohort were naturally controlling their immune activation status, as active TGF-β levels were lower in ART-treated men. Short-term exposure of GECs to SP from CI men or TGF-β at comparable concentrations to SP protected the GEC barrier against HIV by decreasing inflammatory cytokines and preventing tight junction breakage. However, long-term exposure to TGF-β in the presence of HIV further increased inflammation in GECs suggesting a biphasic role for TGF-β in the FGT. This body of work summarized in this thesis demonstrates for the first time how semen from HIV-infected men modulates FGT epithelial cell cytokine responses and barrier function, an important consideration in the design of local therapeutic strategies to protect the FGT against HIV infection.

abstract: Thesis

abstract: Doctor of Philosophy (Medical Science)


title: Investigation into the Role of Glycogen Synthase Kinase-3 in Hyperglycemia-Induced Atherosclerosis

contributor:
Werstuck, Geoff H.
Biochemistry and Biomedical Sciences

subject: hyperglycemia, glucosamine, diabetes, fatty acid, chain,

abstract:
 Diabetes mellitus is a major independent risk factor for cardiovascular disease and stroke. However, the molecular and cellular mechanisms by which diabetes contributes to the development of vascular disease are not fully understood. We have shown that conditions of hyperglycemia are associated with accumulation of intracellular glucosamine, a downstream metabolite of glucose. Our findings indicate that elevated levels of intracellular glucosamine can promote inflammation and lipid accumulation - the hallmark features of atherosclerosis - in vascular cells and HepG2 cells.

 Here I demonstrate that exposure of HepG2 cells to the branched chain fatty acid, valproic acid, increases cellular resistance to glucosamine-induced lipid accumulation and nuclear factor-KB activation. In vivo I show that hyperglycemic apolipoprotein E-deficient (ApoE-/-) mice fed a diet supplemented with 625 mg/kg valproic acid have significantly reduced lesion volumes relative to non-supplemented controls. Valproate supplementation has no apparent effect on the plasma levels of glucose, or lipids, nor does it affect the expression of ER chaperones. Significant reductions were observed in total hepatic lipids(> 50.4%) and hepatic glycogen synthase kinases (GSK)-3β activity (> 55.8%) in mice fed the valproate supplemented diet.

 In vitro I demonstrate that valproic acid directly inhibits GSK-3α/β. Also pretreatment with novel GSK-3 inhibitors protects primary mouse hepatocytes from glucosamine-induced unesterified cholesterol accumulation. I further establish the role of GSK-3 by showing that GSK-3-deficient mouse embryonic fibroblasts do not accumulate unesterified cholesterol after glucosamine treatment. Dietary supplementation with 2-ethylbutyric acid, a novel and potent GSK-3 inhibitor in vitro, did not reduce lesion development in hyperglycemic ApoE-/- mice and significantly increased atherosclerosis in normoglycemic mice. This may be a side effect attributed to multiple cellular pathways controlled by GSK-3 .

 In conclusion, I have identified a pathway involving glucosamine-induced cellular dysfunction that leads to accelerated hyperglycemia-associated atherosclerosis. This pathway involves GSK-3, which regulates glucosamine-induced unesterified cholesterol accumulation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Democracy After the Charter

contributor:
Waluchow, Wilfrid
Philosophy

subject: Charter of Rights, legislation, judicial, democracy, voter

abstract:
 The adoption of the Canadian Charter of Rights and Freedoms has marked a revolutionary change to our legal and political institutions and practices. While parliament used to have the final say in defining the details and limits of the rights of Canadians, the Supreme Court is now the ultimate arbiter of our rights as it has the authority to determine the meaning of the Charter and decide when legislation contradicts the letter and spirit of the Charter. The question of whether the entrenchment of the Canadian Charter of Rights and Freedoms and the subsequent practice of Charter-based judicial review are beneficial developments to our political culture is the topic of this dissertation. I argue that entrenched Charters of rights in general, and the Canadian Charter of Rights and Freedoms in particular, are unnecessary in mature democracies which already have adequate institutions and practices which protect rights. My central claim is that Charters of rights and judicial review are not only unnecessary, but they are also fundamentally undemocratic; Charters and judicial review limit the ability of citizens, acting through their democratic representatives, to make important decisions concerning rights.

 First I explore Jeremy Waldron's rights-based critique of Charters of rights and judicial review to argue that Charters and judicial review are undemocratic and then defend Waldron's critique against three major arguments which claim that Charters and judicial review do not necessarily conflict with our commitments to democracy and might also be mandated by our democratic principles. Then I explore two major consequentialist arguments supporting Charters of rights and judicial review: the "tyranny of the majority" argument, and the institutional argument. I critique these two influential arguments and conclude that the fear of the "tyranny of the majority" is an exaggerated fear based on simplistic conceptions of "majorities" and "minorities" which does not recognize the limits of majority rule within a parliamentary democracy, while the institutional argument is based upon questionable assumptions of voter and legislative motivations and behaviour. Finally, I argue that Charters of rights and judicial review might subtly undermine our commitments to democracy by reinforcing unrealistic attitudes concerning rights and cynicism toward democratic politics. Furthermore, I argue that Charters of rights and judicial review imply that there are "correct answers" and moral expertise concerning rights debates which also undermine our commitment to democracy. Finally, I offer some democratic alternatives to Charters of rights and judicial review which could help protect rights without having the democratic illegitimacy of Charters and judicial review.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: An Online Input Estimation Algorithm For A Coupled Inverse Heat Conduction-Microstructure Problem

contributor:
Hamed, Mohamed S.
Lightstone, Marilyn F.
Mechanical Engineering

subject: numerical algorithm

subject: recursive

subject: coupled nonlinear inverse heat

subject: heat transfer

subject: chemical vapor deposition

subject: industrial baking

subject: heat flux

subject: thermal

subject: microstructure fields

subject: finite-difference

subject: Runge-Kutta

abstract:
This study focuses on developing a new online recursive numerical algorithm for a coupled nonlinear inverse heat conduction-microstructure problem. This algorithm is essential in identifying, designing and controlling many industrial applications such as the quenching process for heat treating of materials, chemical vapor deposition and industrial baking. In order to develop the above algorithm, a systematic four stage research plan has been conducted.

 The first and second stages were devoted to thoroughly reviewing the existing inverse heat conduction techniques. Unlike most inverse heat conduction solution methods that are batch form techniques, the online input estimation algorithm can be used for controlling the process in real time. Therefore, in the first stage, the effect of different parameters of the online input estimation algorithm on the estimate bias has been investigated. These parameters are the stabilizing parameter, the measurement errors standard deviation, the temporal step size, the spatial step size, the location of the thermocouple as well as the initial assumption of the state error covariance and error covariance of the input estimate. Furthermore, three different discretization schemes; namely: explicit, implicit and Crank-Nicholson have been employed in the input estimation algorithm to evaluate their effect on the algorithm performance.

 The effect of changing the stabilizing parameter has been investigated using three different forms of boundary conditions covering most practical boundary heat flux conditions. These cases are: square, triangular and mixed function heat fluxes. The most important finding of this investigation is that a robust range of the stabilizing parameter has been found which achieves the desired trade-off between the filter tracking ability and its sensitivity to measurement errors. For the three considered cases, it has been found that there is a common optimal value of the stabilizing parameter at which the estimate bias is minimal. This finding is important for practical applications since this parameter is usually unknown. Therefore, this study provides a needed guidance for assuming this parameter.

 In stage three of this study, a new, more efficient direct numerical algorithm has been developed to predict the thermal and microstructure fields during quenching of steel rods. The present algorithm solves the full nonlinear heat conduction equation using a central finite-difference scheme coupled with a fourth-order Runge-Kutta nonlinear solver. Numerical results obtained using the present algorithm have been validated using experimental data and numerical results available in the literature. In addition to its accurate predictions, the present algorithm does not require iterations; hence, it is computationally more efficient than previous numerical algorithms.

 The work performed in stage four of this research focused on developing and applying an inverse algorithm to estimate the surface temperatures and surface heat flux of a steel cylinder during the quenching process. The conventional online input estimation algorithm has been modified and used for the first time to handle this coupled nonlinear problem. The nonlinearity of the problem has been treated explicitly which resulted in a non-iterative algorithm suitable for real-time control of the quenching process. The obtained results have been validated using experimental data and numerical results obtained by solving the direct problem using the direct solver developed in stage three of this work. These results showed that the algorithm is efficiently reconstructing the shape of the convective surface heat flux.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Ultrashort-Pulse Laser Systems Based on External-Cavity Mode-Locked InGaAs-GaAs Semiconductor Oscillators and Semiconductor or Yb:Fibre Amplifiers

contributor:
Haugen, Harold K.
Engineering Physics

subject: ultrashort-pulse, semiconductor, laser, system, InGaAs-GaAs, oscillator

abstract: Pages 10, 46, 126, 142 and 146 have been omitted because they were completely blank.

abstract:
 This thesis describes the development of a tunable, ultrashort-pulse semiconductor-based laser system operating in the 1 μm wavelength region. The design of the oscillator is based on a two-contact long-wavelength InGaAs-GaAs quantum-well semiconductor device containing integrated gain and saturable absorber sections. A key design component of the oscillator is the fabrication of a curved ridge-waveguide in the gain section of the device, which allows the laser to be operated in a compact, linear external cavity. Under conditions of passive or hybrid mode-locking, the semiconductor oscillator can generate pulses of 1 to 10 ps in duration, which are tunable from 1030 to 1090 nm. The oscillator is also capable of being passively mode-locked at harmonics of the cavity round-trip frequency, allowing tuning of the pulse repetition rate from 0.5 to over 5 GHz. Noise measurements on two independently hybridly mode-locked semiconductor lasers reveal that the absolute noise of each laser is dominated by phase noise at frequencies below 10^5 Hz, while amplitude noise dominates at higher frequencies.

Semiconductor and fibre optical amplifiers are used to scale the average power level of the mode-locked pulses. Semiconductor optical amplifiers consisting of narrow-stripe and flared-waveguide designs have been fabricated using the same material structure as that of the mode-locked semiconductor oscillator. Narrow-stripe devices with a length of 800 μm have produced amplified average signal powers of 13 mW, while 1700-μm-long, 2° flared-waveguide devices have produced amplified average signal powers of 50 mW. A fibre-based system consisting of a single-mode double-clad Yb-doped fibre has been constructed to investigate the suitability of a mode-locked diode laser as a seed-source for a Yb:fibre amplifier. Amplified average signal powers of up to 1.4 W have been obtained at the output of the fibre for a launched pump power of 2.1 W. Compression of the amplified pulses using a modified dual-grating compressor yields pulse durations as low as 500 fs and a peak power of up to 1.5 kW.

 Preliminary work is reported on the development of a novel dual-wavelength optical source consisting of two synchronized mode-locked diode lasers and a polarization-maintaining Yb:fibre amplifier. Numerical simulations based on a rate-equation model for the amplifier gain are conducted to investigate the performance characteristics of a Yb:fibre amplifier when operated under dual-wavelength signal amplification. The simulations are used to predict and optimize the performance of the fibre amplifier for two mode-locked semiconductor-seed-oscillators operating at wavelengths of 1040 and 1079 nm. Good agreement is obtained between the simulations and experimental results.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


subject: recursive numerical algorithm

subject: coupled nonlinear inverse heat conduction-microstrucure

subject: heat transfer

subject: heat treating

subject: chemical vapor deposition

subject: industrial baking

subject: inverse heat conduction

subject: heat flux

subject: Runge-Kutta

subject: nonlinear solver

subject: algorithm

abstract:
 This study focuses on developing a new online recursive numerical algorithm for a coupled nonlinear inverse heat conduction-microstructure problem. This algorithm is essential in identifying, designing and controlling many industrial applications such as the quenching process for heat treating of materials, chemical vapor deposition and industrial baking. In order to develop the above algorithm, a systematic four stage research plan has been conducted.

 The first and second stages were devoted to thoroughly reviewing the existing inverse heat conduction techniques. Unlike most inverse heat conduction solution methods that are batch form techniques, the online input estimation algorithm can be used for controlling the process in real time. Therefore, in the first stage, the effect of different parameters of the online input estimation algorithm on the estimate bias has been investigated. These parameters are the stabilizing parameter, the measurement errors standard deviation, the temporal step size, the spatial step size, the location of the thermocouple as well as the initial assumption of the state error covariance and error covariance of the input estimate. Furthermore, three different discretization schemes; namely: explicit, implicit and Crank-Nicholson have been employed in the input estimation algorithm to evaluate their effect on the algorithm performance.

 The effect of changing the stabilizing parameter has been investigated using three different forms of boundary conditions covering most practical boundary heat flux conditions. These cases are: square, triangular and mixed function heat fluxes. The most important finding of this investigation is that a robust range of the stabilizing parameter has been found which achieves the desired trade-off between the filter tracking ability and its sensitivity to measurement errors. For the three considered cases, it has been found that there is a common optimal value of the stabilizing parameter at which the estimate bias is minimal. This finding is important for practical applications since this parameter is usually unknown. Therefore, this study provides a needed guidance for assuming this parameter.

 In stage three of this study, a new, more efficient direct numerical algorithm has been developed to predict the thermal and microstructure fields during quenching of steel rods. The present algorithm solves the full nonlinear heat conduction equation using a central finite-difference scheme coupled with a fourth-order Runge-Kutta nonlinear solver. Numerical results obtained using the present algorithm have been validated using experimental data and numerical results available in the literature. In addition to its accurate predictions, the present algorithm does not require iterations; hence, it is computationally more efficient than previous numerical algorithms.

 The work performed in stage four of this research focused on developing and applying an inverse algorithm to estimate the surface temperatures and surface heat flux of a steel cylinder during the quenching process. The conventional online input estimation algorithm has been modified and used for the first time to handle this coupled nonlinear problem. The nonlinearity of the problem has been treated explicitly which resulted in a non-iterative algorithm suitable for real-time control of the quenching process. The obtained results have been validated using experimental data and numerical results obtained by solving the direct problem using the direct solver developed in stage three of this work. These results showed that the algorithm is efficiently reconstructing the shape of the convective surface heat flux.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Biochemical And Genetic Studies of Quebec Platelet Disorder

contributor:
Hayward, Catherine P.M.
Medical Sciences

subject:
disorders
bleeding
inherited bleeding disorders
mutations
platelet
coagulation
QPD
Quebec Platelet Disorder
Autosomal Diominant Disorder
urokinase plasminogen activator
uPA
genetic
clot lysis
fibrinolysis
hematuria

abstract: Inherited bleeding disorders can be caused by mutations affecting platelet, coagulation, or fibrinolytic proteins. Quebec platelet disorder (QPD) is a rare, autosomal dominant disorder associated with increased expression of the fibrinolytic enzyme urokinase plasminogen activator (uPA) in platelets. Individuals with QPD experience delayed-onset bleeding after hemostatic challenges that is attenuated with fibrinolytic inhibitor therapy. The aims of this thesis were to: 1) determine if increased platelet uPA contributes to QPD clot lysis in vitro; 2) investigate whether QPD individuals have increased urinary uPA, as some individuals experience hematuria; and 3) map the genetic locus of QPD, and look for the putative mutation. Studies of clot lysis indicated that QPD platelets induce a gain-of-function defect in fibrinolysis when platelets are incorporated into clots. This suggests that accelerated fibrinolysis may contribute to QPD bleeding. Studies of urinary uPA in QPD showed that uPA is not increased, indicating that hematuria in QPD is likely a consequence of increased platelet uPA. This finding also suggests that uPA overexpression in QPD may be megakaryocyte-specific. Linkage studies showed that QPD is strongly linked to a 2 megabase region on chromosome 10 that harbors the uPA gene, PLA U. No mutations in PLA U or its regulatory regions were identified; however, a common haplotype for a 32.5 kilobase region around PLA U, including inheritance of a rare, linked polymorphism, suggests this is the most likely locus for QPD. mRNA studies in QPD platelets showed that QPD selectively increases expression of the linked PLAU allele, without similar increases in megakaryocyte progenitors or in saliva. These findings implicate a cis-mutation near PLA U as the cause of QPD. This thesis provides novel insights on the fibrinolytic abnormality in QPD blood, and on the QPD genetic locus. which will be important for identifying the precise mutation that converts normally prohemostatic platelets to profibrinolytic cells.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: FUNDAMENTAL AND APPLICATION OF SURFACE-INITIATED ATOM TRANSFER RADICAL POLYMERIZATION FOR SURFACE MODIFICATION OF SHEETS AND NANOPARTICLES

contributor:
Zhu, Shiping
Chemical Engineering

subject:
Atom
Atom Transfer
Radical Polymerization
Nanoparticles
ATRP
flurinated polymers
polyhedral oligomeric silsesquioxane
flurinated monomer
trifluoroethyl methacrylate
TFEMA
POSS
POSS-MA
Polymerized
silicon wafer
graft polymers
bromo-2-methylpropionyloxy
undecyltrichlorosilane
PTFEMA
electrochemical
triethoxysilane

abstract:
 A recently developed surface grafting technique, surface-initiated atom transfer radical polymerization (ATRP), has the ability to directly graft polymer chains with controllable chain lengths, densities and functionalities from various kinds of surfaces. This thesis has two main focuses. First is to study the use of this technique in grafting monomers with special structures and functionalities. The other is to apply this technique to the modification of reactive metal surfaces.

 Both of fluorinated polymers and polyhedral oligomeric silsesquioxane (POSS)-containing polymers have very interesting properties. In this thesis, for the first time, a highly fluorinated monomer, 2,2,2-trifluoroethyl methacrylate (TFEMA) and a POSS-containing monomer, POSS-MA were successfully polymerized from silicon wafers by surface-initiated ATRP. This is also the first work to use this technique to graft polymers with bulky, rigid side groups.

 To achieve very high grafting density is a big challenge for surface-initiated ATRP. We designed a novel surface-attachable difunctional initiator, 11-(2,2-bis(2bromo-2-methylpropionyloxy methyl)propionyloxy) undecyltrichlorosilane. With its help, the grafting density of PTFEMA was almost doubled, from 0.48 to 0.86chains/nm2. This is so far the most effective method to increase the grafting density.

 Unlike other kinds of materials, the surfaces of metals are active in electrochemical and acid/base reactions and this reactivity complicates A TRP reactions. With the help of triethoxysilane-based initiator and mild Fe(II)/Fe(III) catalyst system, various acrylic polymers were successfully grafted from flat nickel and copper surfaces by surface-initiated ATRP. This work provided a convenient method to prepare functional polymer coatings with very stable adhesions to the metal surfaces. The same strategy can be extended to the surface modification of a shape-memory-alloy, nitinol.

 Metal nanoparticles were also modified by this technique. Polymer shells were grafted from nickel nanoparticles surfaces. After the polymer grafting, both of the dispersibility and dispersion stability of nickel nanoparticles in appropriate solvents were greatly improved.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Hypoxic Regulation and Function of Hypoxiainducible Factor 2α (HIF-2α) In an Adrenomedullary Chromaffin Cell Line

contributor:
Nurse, Colin A.
Biology

subject:
Biology
Chronic low Oxygen
hypoxia
cell
tissue
organismal survival
HIF
Hypoxia Inducible Factor
transcription factors
rapid degradation
normal oxygen
normoxia
SA
sympathoadrenal
rat adrenomedullary chromaffin cells
MAH cells
ROS
Reactive Oxygen Species
mitochondrial
pharmacological agents
RNAi
catecholaminergic phenotype
MAH
siRNA
DOPA
DDC
decarboxylase
dopamine β hydroxylase
Adenosine
paracrine
extracellular adenosine

abstract: <p> Exposure to chronic low oxygen (hypoxia) leads to a series of adaptive responses involving changes in gene expression that are critical for cell, tissue, and organismal survival. These changes are mediated by an important set of regulators belonging to the hypoxia inducible factor (HIF) family of transcription factors (e.g. HIF-lα, HIF-2α, HIF3α) which undergo rapid degradation during normal oxygen (normoxia) but are rapidly stabilized during hypoxia. While the role of HIF-1α has been extensively studied in many cell types, there have been relatively few studies on the role of HIF-2α, though recent evidence suggests its function maybe tissue specific. This thesis examined the hypothesis that HIF-2α plays a central role in the development and function of catecholaminergic cells of the sympathoadrenal (SA) lineage. The study was aided by use of an immortalized line of rat adrenomedullary chromaffin cells (i.e. MAH cells), derived from fetal SA progenitors, which express several hypoxia-sensitive properties characteristic of native cells in the adrenal gland. In Chapter 2, I investigated the potential contributions of mitochondrial reactive oxygen species (ROS) and 0 2 consumption to HIF-2α induction in MAH cells exposed to chronic hypoxia (2% O(2); 24 hr). In MAH cells, chronic hypoxia caused an increase in HIF-2α induction which was blocked by inhibition of any of the mitochondrial complexes using pharmacological agents, or by specific inhibition of complexes III and IV using RNAi techniques. It was found that in this 0 2-sensitive chromaffin cell line mitochondrial O(2) consumption, rather than changes in ROS, regulated HIF-2α induction during hypoxia. In Chapter 3, I investigated the hypothesized role of HIF-2α in the development of the catecholaminergic phenotype in cells of the SA lineage using the MAH cell line as a model. Mutant MAH cells, with depleted HIF-2α due to siRNA knock-down, showed dramatically lower levels of dopamine and noradrenaline compared to untransfected and scrambled control cells, regardless of whether the cells were cultured under normoxia or chronic hypoxia. This was correlated with a marked reduction in the expression of DOPA decarboxylase (DDC) and dopamine B hydroxylase (DBH), though the expression of tyrosine hydroxylase (TH) was unaffected. Moreover, HIF-2α was able to bind to a region of the DDC gene promoter which contains two putative hypoxia response elements (HREs). These data suggest that a basal level of HIF-2α function is required for the normal developmental expression of DDC and DBH in SA progenitor cells, and that loss of this function leads to impaired catecholamine (CA) biosynthesis. In Chapter 4, I investigated genes regulated by chronic hypoxia in MAH cells, with a focus on those involved in CA metabolism, storage, and secretion. Using microarray analysis combined with QPCR and RNAi knock-down methodology I uncovered several genes, involved in amine vesicular packaging, trafficking and secretion, which were upregulated during chronic hypoxia. One gene specifically, the adenosine A(2A) receptor (A(2A)R) gene, which appears to modulate CA secretion via autocrine or paracrine actions of extracellular adenosine, was dramatically upregulated in chronic hypoxia. Interestingly, this effect was completely abolished in HIF-2α knockdown MAH cells, suggesting a critical involvement of HIF-2α. Chromatin immunoprecipitation (ChIP) assays revealed that HIF-2α bound to the promoter region of the A(2A)R gene which contains a putative hypoxia response element (HRE) immediately upstream of exon 1. Ratiometric fluorescence measurements of intracellular Ca(2+) revealed that adenosine (50 μM) potentiated the high K(+)-evoked rise in [Ca(2+)]i in MAH cells. This effect of adenosine was further enhanced after chronic hypoxia, but was abolished in HIF-2α knock-down cells. In conclusion, these data suggest that HIF-2α is a key regulator of several genes involved in CA biosynthesis, and of others that mediate the facilitatory effects of chronic hypoxia on CA secretion in sympathoadrenal derivatives.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Dominance and Communication in a Cooperatively Breeding Bird

contributor:
Quinn, James
Balshine, Sigal
Biology

subject:
ethology
ecology
behaviour
evolution
animal
sexual selection

abstract:
Social dominance can influence the allocation of resources in animal groups and
has important consequences for individual fitness. In my thesis, I examined the
structure, formation, maintenance and consequences of dominance, in the
cooperatively breeding pukeko (Porphyrio melanotus melantous: Aves). I first
describe a quantitative analysis of pukeko dominance networks (Chapter 2),
which included one of the first applications of exponential random graph models
in behavioural ecology. This study demonstrated that pukeko form highly ordered
dominance hierarchies, and that dominance relationships were influenced by
both the attributes of individual birds, as well as self-organizational processes
such as winner and loser effects. Additionally, I demonstrated that hatching order
has an important influence on the formation of dominance relationships, with
earlier hatched chicks achieving higher dominance ranks as adults (Chapter 3).
To maintain dominance relationships, pukeko use their red frontal shield as a
‘status signal’, with larger frontal shields indicating more dominant individuals. I
showed that sexual dimorphism in frontal shield size is dramatically different in
two pukeko populations, probably due to differences in the intensity of intrasexual
competition (Chapter 4). Furthermore, by manipulating apparent frontal shield
size, I demonstrated that shield phenotype both influences, and is influenced by,
social interactions (Chapter 5). This bi-directional relationship between signals
and social interactions challenges conventional signalling theory, and has
important implications for how honesty is maintained in this signalling system. Finally, I expanded my findings on pukeko colour traits by exploring interspecific
patterns of bill colouration in over 1600 bird species (Chapter 6). This study
revealed that colourful bills likely evolved as a signal used in competitive
interactions, rather than as a sexual signal. Taken together, my research
provides a significant advancement in our understanding of the complex nature of
dominance in a wild bird, and provides both a methodological and theoretical
basis for future studies on animal social behaviour.

abstract: Thesis

abstract: Doctor of Science  (PhD)


title: Isotopic Investigations of Carbon Cycling And Microbially Influenced Carbonate Precipitation In Freshwater Microbialites And Carbonate-Rich Microbial Mats

title: Microbial Carbon Cycling and Isotope Biosignatures

contributor:
Slater, Gregory F.
Geography and Earth Sciences

subject: microbialites, microbial mats, microbial-mineral, carbonate precipitation, biosignatures, geological record, DIC, inorganic carbon, PLFA, photosynthetic, oxygen, sporadic nodular microbial surface communities

abstract:
Modern microbialites and microbial mats are the focus of ongoing research as they provide an opportunity to understand microbial-mineral interactions during carbonate precipitation and the generation of biosignatures that can inform our interpretation of the geological record. This study determined the natural abundance isotopic compositions ([13]C, [14]C) of the primary carbon pools and microbial communities associated with modern freshwater microbialites located in Pavilion Lake and in carbonate rich microbial mats on the nearby Cariboo Plateau in British Columbia, Canada.

 Natural abundance [14]C analysis of carbon pools associated with the Pavilion Lake microbialites demonstrated that structures were actively growing and that groundwater carbon inputs to the lake and microbialites were minimal. Rather, ambient dissolved inorganic carbon (DIC) was the primary carbon source for both microbial communities
and recent carbonate.

 Isotopic enrichment of calcium carbonate within microbial communities
associated with the microbialites was identified as a biosignature of microbial
photosynthetic influence driving precipitation. Elevated oxygen concentrations and pH within the microenvironment of small, sporadic nodular microbial surface communities was concurrent with in situ precipitation of carbonate with δ[13]C values higher than
predicted abiotic values and δ[13]C of bulk organic matter and phospholipid fatty acids (PLFA) that were consistent with a photosynthetically dominated community. Elevated carbonate δ[13]C values were also noted in the thin surface microbial mat recovered from shallow (11m) microbialites. These samples showed increased biomass during summer sampling periods as compared to deeper samples, consistent with expected high rates of photosynthetic activity due to higher light levels and temperature at these depths. These results contrast other recent studies of modern microbialite systems that identified biosignatures of heterotrophic influences on precipitation of carbonates. PLFA profiles demonstrated that the surface microbial mat community consisting of both photosynthetic and heterotrophic microbes was stable over seasonal and spatial changes in light and temperature. However, changes in microbial biomass with depth and season indicated that microbial activity and growth plays an important role in the development of isotopic biosignatures.

 Biosignatures of high levels of photosynthetic activity were also observed in carbonate, rich microbial mats that exhibited undersaturated p CO2 concentrations during the summer and DIC δ[13]C values enriched above values predicted for isotopic equilibrium with atmospheric CO2. Seasonal and annual shifts in the balance of heterotrophy and autotrophy in the lakes and microenvironment of the mat accounted for observed variations in DIC and associated carbonate δ[13]C values. In contrast to other organic rich microbial mats, bulk organic δ[13]C values were not enriched and the systems did not show evidence of CO2 limitation. Rather, these results indicated that low bulk organic δ[13]C values and large isotopic discriminations can exist under conditions of high DIC concentrations and carbonate content that provide a non limiting carbon source to replenish photosynthetic drawdown.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Predator-Prey Models with Discrete Time Delay

contributor:
Wolkowicz, G.S.K.
Mathematics

subject:
predator-prey model
chemostat
discrete delay
Holling type I
Hopf bifurcation
eigenvalues
second order transcedental equation

abstract:
Our goal in this thesis is to study the dynamics of the classical predator-prey model and the predator-prey model in the chemostat when a discrete delay is introduced to model the time between the capture of the prey and its conversion to biomass. In both models we use Holling type I response functions so that no oscillatory behavior is possible in the associated system when there is no delay. In both models, we prove that as the parameter modelling the delay is varied Hopf bifurcation can occur. However, we show that there seem to be differences in the possible sequences of bifurcations. Numerical simulations demonstrate that in the classical predator-prey model period doubling bifurcation can occur, possibly leading to chaos while that is not observed in the chemostat model for the parameters we use. For a delay differential equation, a prerequisite for Hopf bifurcation is the existence of a pair of pure imaginary eigenvalues for the characteristic equation associated with the linerization of the system. In this case, the characteristic equation is a transcendental equation with delay dependent coefficients. For our models, we develop two different methods to show how to find values of the bifurcation parameter at which pure imaginary eigenvalues occur. The method used for the classical predator-prey model was developed first. However, it was necessary to develop a more robust, less complicated method to analyze the predator-prey model in the chemostat with a discrete delay. The latter method was then generalized so that it could be applied to any second order transcendental equation with delay dependent
coefficients.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Emergency Powers: Addressing the Crisis of Homelessness in a Canadian City

contributor:
Wilton, R. D.
Geography

subject: urban homelessness

subject: social exclusion

subject: managing homelessness in a Canadian city

subject: emergency shelter system

subject: management spaces

subject: chronically homeless men

subject: special care facility

abstract:
Urban homelessness is one of the most blatant forms of social exclusion in
advanced capitalist societies. In Canada, the United States, and the United
Kingdom, homelessness has become particularly entrenched due to systemic forces such as global economic recession, the restructuring of regional economies, the dismantlement of the welfare state, and the erosion of affordable housing that together have pushed more people towards economic marginality and housing insecurity. Despite years of advocacy and 'high profile' government investments, homelessness has persisted as an intransigent social problem. A central purpose of this doctoral thesis is to provide some insight into how homelessness is being 'managed' in one Canadian city. The papers gathered together in this dissertation are based on three years of ethnographic fieldwork (conducted between 2006 and 2009) in a medium-sized, de-industrializing city in the province of Ontario. The specific focus of the thesis is the emergency shelter system. Over the past ten years, a number of new social service models have emerged in response to rising rates of homelessness. As these have been adopted homeless shelter systems in many Canadian cities have undergone significant reconfigurations. This thesis focuses on some of the new 'management spaces' that are emerging in this unfolding policy context. The first paper explores the experiences of voluntary sector organizations and local state authorities. The second paper explores the experiential dimensions of a unique service environment providing emergency shelter and social services. The third paper examines the personal experiences of chronically homeless men as they adapt to life in an innovative 'special care' facility.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)