title: Mechanisms Underlying the Immunopathology in Heterologous Pulmonary Infection

contributor: Medical Sciences (Molecular Virology and Immunology Program)

subject:
Influenza virus
Bordetella parapertussis
polymicrobial infection
IL-1 beta
immunopathology
exaggerated neutrophilia
Medical Immunology
Medical Immunology

abstract: Despite the advanced knowledge of the mechanisms of influenza infection and improved vaccines, Influenza A Virus still causes a life-threatening respiratory disease, especially during pandemics. Past investigations have proposed a synergism between Influenza A virus and a simultaneous or subsequent bacterial superinfection as the predominant cause of death. The recent development of animal models to study these heterologous infections has shed light onto the diverse mechanisms by which Influenza A Virus may increase the susceptibility to contract a secondary bacterial infection. These studies suggested an important role for the innate immune system in mediating such disease. We developed a model of heterologous infection combining Influenza A Virus and Bordetella parapertussis that demonstrated a critical role for MIP-2 to drive pulmonary neutrophilia in the pathology associated with bacterial superinfection of influenza. However, the origin of this increased MIP-2 production and the mechanisms underlying the immunopathology remained to be elucidated. The present studies proposed IL-1β overproduction as the upstream cause of the increased MIP-2 production observed in heterologous infection. This exaggerated IL-1β production was likely related to the increased bacterial burden observed in heterologously infected mice. This study also demonstrated that reduction in IL-1β production by blockade of the inflammasome seemed to provide an improvement in the clinical symptoms and the immunopathology of the disease. Thus, interventions to attenuate the exacerbated bacterial burden and the inflammatory responses derived from the subsequent IL-1β overproduction should be further investigate as possible therapeutic approaches to treat bacterial superinfections.

abstract: Master of Science (MSc)


title: INFERENCE FOR A GAMMA STEP-STRESS MODEL UNDER CENSORING

contributor:
Balakrishnan, Narayanaswamy
Computational Engineering and Science

abstract:
In reliability and life-testing experiments, one of the popular and commonly used strategies, that allows manufacturers and designers to identify, improve and control critical components, is called the Accelerated Life Test (ALT). The main idea of these tests is to investigate the product's reliability at higher than usual stress levels on test units to ensure earlier failure than what could result under the normal operating conditions. Stress can be induced by such factors as voltage, pressure, temperature, load or cycling rate.

ALT are applied using different types of accelerations such as high usage rate in which the compressed time testing is done through speed or by reducing off times. Another type of acceleration is the product design where the life of a unit can be accelerated through its size or its geometry. Stress loading is another type of acceleration that is applied using constant stress, step-stress, progressive stress, cyclic stress or random stress. Here, we discuss the step-stress model, which applies stress to each unit and increases the stress at pre-specified times during the experiment allowing us to obtain information about the parameters of the life distribution more quickly than under normal operating conditions.

In this thesis, we present the simple step-stress model (the situation in which there are only two stress levels) when the lifetimes at different stress levels follow the gamma distribution when the data are (Chapter 2) Type-II censored, (Chapter 3) Type-I censored, (Chapter 4) Progressively Type-II censored, and (Chapter 5) Progressively Type-I censored, as well as a multiple step-stress model under Type-I and Type-II censoring. The likelihood function is derived assuming a cumulative exposure model with gamma distributed lifetimes. The resulting likelihood equations do not have closed-form solutions, and so they need to be solved numerically. We then derive confidence intervals for the parameters using asymptotic normality of the maximum likelihood estimates and the parametric bootstrap method. In each case, the performances of the methods of inference developed here are examined by means of Monte Carlo simulation study and are also illustrated with some numerical examples.

abstract: Doctor of Philosophy (PhD)


title: NEUTRON STARS AND BLACK HOLES IN SCALAR-TENSOR GRAVITY

contributor:
Burgess, Cliff
Physics and Astronomy

subject: Scalar-Tensor Gravity

subject: Scalar Hair

subject: Stellar Structure

subject: Spontaneous Scalarization

subject: Double Black Hole Binaries

subject: Quasar OJ287

subject: Cosmology, Relativity, and Gravity

subject: Elementary Particles and Fields and String Theory

subject: Cosmology, Relativity, and Gravity

abstract:
The properties of neutron stars and black holes are investigated within a class of alternative theories of gravity known as Scalar-Tensor theories, which extend General Relativity by introducing additional light scalar fields to mediate the gravitational interaction.

It has been known since 1993 that neutron stars in certain Scalar-Tensor theories may undergo ‘scalarization’ phase transitions. The Weak Central Coupling (WCC) expansion is introduced for the purpose of describing scalarization in a perturbative manner, and the leading-order WCC coefficients are calculated analytically for constant-density stars. Such stars are found to scalarize, and the critical value of the quadratic scalar-matter coupling parameter βs = −4.329 for the phase transition is found to be similar to that of more realistic neutron star models.

The influence of cosmological and galactic effects on the structure of an otherwise isolated black hole in Scalar-Tensor gravity may be described by incorporating the Miracle Hair Growth Formula discovered by Jacobson in 1999, a perturbative black hole solution with scalar hair induced by time-dependent boundary conditions at spatial infinity. It is found that a double-black-hole binary (DBHB) subject to these boundary conditions is inadequately described by the Eardley Lagrangian and emits scalar dipole radiation.

Combining this result with the absence of observable dipole radiation from quasar OJ287 (whose quasi-periodic ‘outbursts’ are consistent with the predictions of a general-relativistic DBHB model at the 6% level) yields the bound |φ/Mpl| < (16 days)-1 on the cosmological time variation of canonically-normalized light (m < 10−23 eV) scalar fields at redshift z ∼ 0.3.

abstract: Doctor of Philosophy (PhD)


title: The Log Analysis in an Automatic Approach

contributor:
Maibaum, Tom
George Karakostas, Alan Wassyng
Computing and Software

subject:
analysis
automatic
log
program
software
source
Computer Engineering
Computer Engineering

abstract:
Large software systems tend to have complex architecture and numerous lines of source code. As software systems have grown in size and complexity, it has become increasingly difficult to deliver bug-free software to end-users. Most system failures occurring at run-time are directly caused by system defects; therefore diagnosis of software defects becomes an important but challenging task in software development and maintenance.

A system log is one available source of information from a software system. Software developers have used system logs to record program variable values, trace execution, report run-time statistics and print out full-sentence messages. This makes system logs a helpful resource for diagnosis of software defects. The conventional log analysis requires human intervention to examine run-time information in system logs and to apply their expertise to software systems, in order to determine the root cause of a software defect and work out a concrete solution. Complex software systems can generate thousands of system logs in a relatively short time frame. Analyzing such large amounts of information turns out to be extremely time-consuming. Automated techniques are needed to improve the efficiency and quality of the diagnostic process.

This thesis presents an automated approach to diagnosis of software defects, combining source code analysis, log analysis and sequential pattern mining, to detect anomalies among system logs, diagnose reported system errors and narrow down the range of source code lines to determine the root cause. We demonstrate that, by implementation, the methodology provides a feasible solution to the diagnostic problem.

abstract: Master of Applied Science (MASc)


title: AN AGENT–BASED COMPUTATIONAL MODEL FOR BANK FORMATION AND INTERBANK NETWORKS

contributor:
Grasselli, Matheus R.
Computational Engineering and Science

subject:
Agent Based Model
bank formation
interbank networks
social measures
systemic risk
contagion
Evolution
Finance
Laboratory and Basic Science Research
Other Economics
Evolution

abstract:
The aim of this thesis is to study the role of banking in society and the effect of the

interbank market on the performance of the banking system.

It starts by reviewing

several studies conducted on empirical banking networks and highlighting their salient

features in the context of modern network theory. A simulated network resembling the

characteristics documented in the empirical studies is then built and its resilience is

analyzed with a particular emphasis in documenting the crucial role played by highly

interconnected banks.

It is our belief that the study of systemic risk and contagion in a banking system

is an integral part to the study of the economic role of banks themselves. Thus the

current work focuses on the fundamentals of banking and aims at identifying the

necessary drivers for a dynamical setup of the interbank market.

Through an agent–based model, we address the issues of bank formation, bank runs

and the emergence of an interbank market. Starting with heterogeneous individuals,

bank formation is viewed as an emergent phenomenon arising to meet the needs for

investment opportunities in face of uncertain liquidity preferences. When banks work

in isolation (no interbank market), in the long run and through a long experience with

bank failures, banking turns into a monopoly or a market with few players.

By equipping banks with their own learning tools and allowing an interbank market

to develop, fewer bank failures and a less concentrated banking system are witnessed.

In addition, through a scenario analysis, it is demonstrated that allowing banks to

interact does not weaken the banking system in almost all the cases, and improves

the performance on multiple occasions.

The work is concluded by studying the effects of a banking system on individuals

and the economy in what is called social measures. We establish that the effects

of banking on social measures such as consumption level, consumption inequality

between individuals, long term investment and economic waste, varies significantly

based on the structure of the society.

abstract: Doctor of Philosophy (PhD)


title: Shedding Light on the Formation of Stars and Planets: Numerical Simulations with Radiative Transfer

contributor:
Wadsley, James
Physics and Astronomy

subject:
Planet Formation
Protostellar Discs
Brown Dwarfs
Star Formation
Numerical Simulations
Radiative Transfer
Other Astrophysics and Astronomy
Other Astrophysics and Astronomy

abstract:
We use numerical simulations to examine the fragmentation of protostellar discs via gravitational instability (GI), a proposed formation mechanism for gas-giant planets and brown dwarfs. To accurately model heating and cooling, we have implemented radiative transfer (RT) in the TreeSPH code Gasoline, using the flux-limited diffusion approximation coupled to photosphere boundary cooling. We present 3D radiation hydrodynamics simulations of discs that are gravitationally unstable in the inner 40 AU; these discs do not fragment because the cooling times are too long. In prior work, one of these discs was found to fragment; however, we demonstrate that this resulted from an over-estimate of the photosphere cooling rate. Fragmentation via GI does not appear to be a viable formation mechanism in the inner 40 AU.

We also present simulations of GI in the outer regions of discs, near 100 AU, where we find GI to be a viable formation mechanism. We give a detailed framework that explains the link between cooling and fragmentation: spiral arms grow on a scale determined by the linear gravitational instability, have a characteristic width determined by the balance of heating and cooling, and fragment if this width is less than twice their Hill radius. This framework is consistent with the fragmentation and initial fragment masses observed in our simulations. We apply the framework to discs modelled with the commonly-used beta-prescription cooling and calculate the critical cooling rate for the first time, with results that are consistent with previous estimates measured from numerical experiments.

RT is fundamentally important in the star formation process. Non-ionizing radiation heats the gas and prevents small-scale fragmentation. Ionizing radiation from massive stars is an important feedback mechanism and may disrupt giant molecular clouds. We present methods and tests for our implementation of ionizing radiation, using the Optically-Thin Variable Eddington Tensor method.

abstract: Doctor of Philosophy (PhD)


title: Gaussian Robust Sequential and Predictive Coding

contributor: Jiankang Zhang, Sorina Dumitrescu, Lizhong Zheng

subject:
Extremal inequality
Gauss-Markov source
minimax theorem
predictive coding
saddle point
sequential coding
Electrical and Electronics
Electrical and Electronics

abstract: Video coding schemes designed based on sequential or predictive coding models are vulnerable to the loss of encoded frames at the decoder end. Motivated by this observation, in this thesis we propose two new coding models: robust sequential coding and robust predictive coding. For the Gauss-Markov source with the mean squared error distortion measure, we characterize certain supporting hyperplanes of the rate region of these two coding problems. The proof is divided into three steps: 1) it is shown that each supporting hyperplane of the rate region of Gaussian robust sequential coding admits a max-min lower bound; 2) the corresponding min-max upper bound is shown to be achievable by a robust predictive coding scheme; 3) a saddle point analysis proves that the max-min lower bound coincides with the min-max upper bound. Furthermore, it is shown that the proposed robust predictive coding scheme can be implemented using a successive quantization system. Theoretical and experimental results indicate that this scheme has a desirable \self-recovery" property. Our investigation also reveals an information-theoretic minimax theorem and the associated extremal inequalities.

abstract: Doctor of Philosophy (PhD)


title: Spatial Clutter Intensity Estimation for Multitarget Tracking

contributor:
Kirubarajan, Thiagalingam
Electrical and Computer Engineering

subject:
multitarget tracking
clutter estimation
spatial intensity
point process
Controls and Control Theory
Signal Processing
Controls and Control Theory

abstract: In this thesis, the problem of estimating the clutter spatial intensity function for the multitarget tracking algorithms has been considered. In many scenarios, after the signal detection process, measurement points provided by the sensor (e.g., sonar, infrared sensor, radar) are not distributed uniformly in the surveillance region as assumed by most tracking algorithms. On the other hand, in order to obtain accurate results, the multitarget tracking algorithm requires information about clutter’s spatial intensity. Thus, non-homogeneous clutter spatial intensity has to be estimated from the measurement set and the tracking filter’s output. Also, in order to take advantage of existing tracking algorithms, it is desirable for the clutter estimation method to be integrated into the tracker itself. In this thesis, the clutter is modeled by a non-homogeneous Poisson point (NHPP) process with a spatial intensity function g(z). To calculate the value of the clutter spatial intensity, all we need to do is estimating g(z). First, two new methods for joint spatial clutter intensity estimation and multitarget tracking using the Probability Hypothesis Density (PHD) Filter are presented. Then, based on NHPP process, multitarget multi-Bernoulli processes and set calculus, the approximated Bayesian method is extended to joint the non–homogeneous clutter background estimation and multitarget tracking with standard multitarget tracking algorithms, like the Multiple Hypothesis Tracking (MHT) and the Joint Integrated Probabilistic Data Association (JIPDA) tracker. Finally, a kernel density method is proposed for the clutter spatial intensity estimation problem. Simulation results illustrate the performance of the above algorithms, both in terms of the false track number and the true track initialization speed. All proposed algorithms show the ability to improve the performance of the multitarget tracker in the presence of slowly time varying non–homogeneous clutter background.

abstract: Doctor of Philosophy (PhD)


title: Shape Coexistence in ¹⁵¹Gd

contributor:
Johns, M.W.
Physics

subject: Physics Physics

abstract:
The level structure of the odd-A transitional nucleus ¹⁵¹Gd has been studied by means of the ¹⁴⁹Sm(α,2n)¹⁵¹Gd reaction through ϒ-ray singles, ϒ-ray angular distributions, ϒ-ϒcoincidence and conversion electron measurements.

A number of rotational band-like structures have been observed, indicating that the nucleus is deformed when produced in this reaction. A rotational band built on one of the states populated in the reaction conforms well to present theory and indicates that the nucleus has a large deformation when this state is populated. The order bands are not well explained by present theory, although a much smaller nuclear deformation is indicated.

The implication is that the Nilsson model, in its present stage of development, is inadequate for treating nuclei such as ¹⁵¹Gd. Further theoretical work is necessary particularly in the treatment of multiple particle states where j is not a good quantum number and the core is not a rigid rotor.

abstract: Doctor of Philosophy (PhD)


title: Contemporary Challenges to Quinean Ontology

contributor:
Griffin, Nicholas
Garrett, Brian
David Hitchcock, Mark Vorobej
Philosophy

subject: Ontology Metametaphysics Existence Quine Carnap Metaphysics Metaphysics

abstract: In this master’s thesis I defend a Quinean approach to ontology. I first describe the Quinean approach as consisting of three steps and three theses. All three theses have been challenged in the contemporary literature. In each chapter I describe one such challenge, and then provide a response. The first challenge states that ontology is actually easy. Proponents of this challenge include Matti Eklund’s maximalist, as well as Amie Thomasson. In response, I argue that the maximalist cannot consistently determine whether abstract entities exist. I also argue that Thomasson’s account involves a certain slide in logic and is, in certain cases, ontologically uninformative. I then turn to the second challenge, which states that traditional ontological questions are not even worth pursuing. Here I discuss the work of Rudolf Carnap and of Jonathan Schaffer. I argue that Carnap fails to provide a cogent argument for the meaninglessness of ontological questions. Furthermore, I argue that one should not adopt Schaffer’s Aristotelian view of metaphysics and ontology. I do so by constructing an argument, logically parallel to one of Schaffer’s own, to demonstrate that there are no fundamental grounds. Finally, I consider the challenge posed by an ambiguity in ‘existence’. According to Eli Hirsch, such an ambiguity results in verbal disputes. Hirsch argues that the remedy is to adopt ordinary English. In response, I accept that ‘existence’ is ambiguous. But I deny that this poses a significant problem for Quinean ontology.

abstract: Master of Philosophy (MA)


title: ASPECTS OF HUMAN RHINOVIRUS INFECTION IN HOSPITALIZED AND NON-HOSPITALIZED INDIVIDUALS

contributor:
Mahony, James
Smieja, Marek
Mossman, Karen
Medical Sciences

subject:
rhinovirus
epidemiology
viral load
diagnostics
qPCR
Clinical Epidemiology
Virology
Clinical Epidemiology

abstract:
Human rhinovirus (HRV) is a single-stranded RNA virus responsible for causing the common cold and exacerbating chronic respiratory diseases. HRV is the most common cause of acute respiratory illness. Unfortunately, difficult culturing conditions and perceived mild symptoms have limited our understanding of HRV. This thesis characterizes fundamental aspects of HRV such as viral load in different patient populations, prevalence and diversity of HRV, and severity and duration of infection.

We developed an HRV qPCR assay to quantitate HRV in clinical isolates. We used this assay to measure viral loads in hospitalized and community members. We found that HRV viral loads were similar regardless of age and need for hospitalization. Viral loads were significantly lower amongst individuals with asymptomatic HRV infection than symptomatic HRV infection. Next, we determined the prevalence and diversity of HRV in children and adults. We found that HRV is the most common respiratory pathogen in September-October in both children and adults. A broad range of HRV genotypes can be found circulating amongst children and adults; however HRV C is more prevalent in children. Furthermore, we investigated the association of HRV C duration and severity of illness. Among otherwise healthy individuals, HRV C did not persist longer than HRV A/B, nor was the viral load significantly different. In hospitalized children, HRV C was not more associated with an asthma or wheeze diagnosis. Overall, our data suggest that viral loads do not predict the severity of illness, HRV C commonly occurs in children, and behaves like other HRV species.

abstract: Master of Science (MSc)


title: Lateral Gene Transfer in Operons and Its Effects on Neighbouring Genes

contributor:
Golding, G. B.
Finan, T. M.
Evans, B.
Biology

subject:
Bioinformatics
Computational Biology
Lateral Gene Transfer
Bioinformatics
Bioinformatics

abstract: Prokaryotes evolve, in part, by lateral gene transfer (LGT). This transfer of genetic material is likely important in the evolution of operons, a group of genes that are transcribed as a single mRNA. Genes that are transferred may then be integrated into genomes by homologous recombination. In this thesis, it was proposed that homologous recombination is the mechanism of integration of laterally transferred genes into operons. To investigate this proposal, a phylogenetic tree of Bacillus was inferred using DNA sequence alignments. LGT was inferred using a parsimony algorithm, and operons were inferred using OperonDB. Homologous recombination breakpoints were identified by permutation tests, GENECONV and maximum chi square algorithm. The results indicate that there is evidence for integration of functionally annotated genes into operons by homologous recombination. There are several laterally transferred genes that have recombination breakpoints before the start codon or after the stop codon of the genes. It was also proposed in this thesis that LGT causes an increase in the rate of evolution of genes that are neighbours of laterally transferred genes. To investigate this proposal, genes that are neighbours of laterally transferred genes in Bacillus were identified. These genes were classified as upstream or downstream genes to the LGT event. Genes that are not neighbours of laterally transferred genes were also identified as a control. Selection and the rate of evolution was studied using maximum likelihood models implemented in CodeML of PAML. Genes under positive selection were inferred using likelihood ratio tests. The results indicate that only a few neighbouring genes were under positive selection, and the rate of evolution of the neighbouring genes was slightly higher than that of the non-neighbouring genes. The high rates of evolution of the neighbouring genes are likely due to relaxed selection on the neighbouring genes.

abstract: Master of Biological Science (MBioSci)


title: The Type 1 Fimbrial Adhesin Mediates the Interaction of Adherent-Invasive Escherichia coli with the Host

contributor:
Coombes, Brian K.
Dawn Bowdish, Karen Mossman
Biochemistry

subject: AIEC

subject: NRG857c

subject: LF82

subject: FimH

subject: macrophage

subject: CD-1

subject: Pathogenic Microbiology

subject: Pathogenic Microbiology

abstract: Crohn’s Disease is a chronic inflammatory bowel disease characterized by an overzealous immune response to a microbial trigger in genetically susceptible individuals. Although this microbial trigger is unknown, Escherichia coli with adherent and invasive properties (Adherent-Invasive Escherichia coli, AIEC) is preferentially enriched in a proportion of Crohn’s Disease patients. AIEC can adhere to and invade intestinal epithelial cells and replicate intracellularly within epithelial cells and macrophages in vitro. One important colonization factor expressed by AIEC is the type 1 fimbrial adhesin protein FimH. FimH mediates colonization of CEABAC10 transgenic mice and can bind several host cell receptors including the macrophage receptor CD48 in vitro indicating a potential role for FimH in macrophage interaction. However, it was not known whether FimH contributed to phagocytosis of AIEC or colonization of wild-type mice. Here we show that FimH enhances early intracellular AIEC levels in vitro and colonization in vivo. We found that deletion of fimH may reduce intracellular AIEC burden at 2 hours post-infection and that this effect was modulated by bacteria opsonisation. Using a competitive index assay, we show that a ΔfimH mutant is unable to chronically colonize CD-1 mice at the same levels as the parental strain. Our results demonstrate that FimH is an important AIEC colonization factor and may increase interaction with macrophages. Identifying factors such as FimH which contribute to colonization and persistence will further our understanding of AIEC survival strategies within the host. Development of therapeutics targeting FimH may provide a means to reduce harmful bacteria overgrowth particularly after surgical intervention.

abstract: Master of Science (MSc)


title: The Origin of Life by Means of Autocatalytic Sets of Biopolymers

contributor: An-Chang Shi, Jonathan R. Stone, Jonathan Dushoff

subject:
Origin of Life
RNA world
autocatalytic sets
ribozyme
stochastic simulation
Biological and Chemical Physics
Biology
Biological and Chemical Physics

abstract: A key problem in the origin of life is to understand how an autocatalytic, self-replicating biopolymer system may have originated from a non-living chemical system. This thesis presents mathematical and computational models that address this issue. We consider a reaction system in which monomers (nucleotides) and polymers (RNAs) can be formed by chemical reactions at a slow spontaneous rate, and can also be formed at a high rate by catalysis, if polymer catalysts (ribozymes) are present. The system has two steady states: a ‘dead’ state with a low concentration of ribozymes and a ‘living’ state with a high concentration of ribozymes. Using stochastic simulations, we show that if a small number of ribozymes is formed spontaneously, this can drive the system from the dead to the living state. In the well mixed limit, this transition occurs most easily in volumes of intermediate size. In a spatially-extended two-dimensional system with finite diffusion rate, there is an optimal diffusion rate at which the transition to life is very much faster than in the well-mixed case. We therefore argue that the origin of life is a spatially localized stochastic transition. Once life has arisen in one place by a rare stochastic event, the living state spreads deterministically through the rest of the system. We show that similar autocatalytic states can be controlled by nucleotide synthases as well as by polymerase ribozymes, and that the same mechanism can also work with recombinases, if the recombination reaction is not perfectly reversible. Chirality is introduced into the polymerization model by considering simultaneous synthesis and polymerization of left- and right-handed monomers. We show that there is a racemic non-living state and two chiral living states. In this model, the origin of life and the origin of homochirality may occur simultaneously due to the same stochastic transition.

abstract: Doctor of Philosophy (PhD)


title: The Impact of Exercise-Induced Hormonal Changes on Human Skeletal Muscle Anabolic Responses to Resistance Exercise

contributor:
Phillips, Stuart
Kinesiology

subject:
skeletal muscle
hypertrophy
testosterone
growth hormone
resistance exercise
muscle protein synthesis
Exercise Science
Exercise Science

abstract:
There is a prevalent belief that acute hormone responses to resistance exercise mediate adaptations in skeletal muscle hypertrophy; however, there is little supporting evidence. We conducted studies to examine the relationship between acute hormonal increases after resistance exercises and subsequent changes in muscle anabolism.

We tested the hypothesis that exercise-induced responses of anabolic hormones—growth hormone (GH) and testosterone—would enhance rates of myofibrillar protein synthesis (MPS) after an acute bout of resistance exercise, and would augment muscle hypertrophy after training. We concluded, however, that resistance exercise-induced increases in putative anabolic hormones do not enhance MPS or hypertrophy.

We also examined whether rates of MPS would be attenuated in women (compared with men) after resistance exercise, due to their lack of post-exercise testosteronemia. We reported similar increases in MPS in men and women; post-exercise testosterone responses in women, which were 45-fold lower than men, did not attenuate elevations in MPS.

Collectively, our work leads to the conclusion that the acute rise in hormones such as testosterone and GH has very little bearing on MPS and hypertrophy responses to resistance exercise. Instead, the rise in these hormones appears to be a non-specific response to exercise stress rather than a response that is important for muscle anabolism. Contrary to widely used principles, our data suggests that exercise programs should not be designed based on nuances in the post-exercise hormonal milieu. Alternatively, understanding local mechanotransduction, which is directly linked to muscle fibre loading, will reveal the processes that drive human exercise-mediated muscle hypertrophy.

abstract: Doctor of Philosophy (PhD)


title: CHARACTERIZATION AND APPLICATION OF SELF-PHOSPHORYLATING DEOXYRIBOZYMES

contributor:
Li, Yingfu
Biochemistry

subject: quadruplex

subject: biosensor

subject: DNAzyme

subject: SELEX

subject: Biochemistry, Biophysics, and Structural Biology

abstract: The process of in vitro selection has led to the isolation of many catalytic DNA molecules, called deoxyribozymes, which can catalyze a range of biologically-relevant reactions. Despite these advances, questions still remain as to why DNA, which seems more suited to information storage than catalysis can efficiently catalyze chemical reactions. In this thesis, a group of deoxyribozymes that can catalyze their own phosphorylation using NTP substrates are used a model system to study how DNA is able to fold into complex structures necessary for catalysis. Using a variety of structural probing techniques, these studies elucidated a common secondary structure shared by three deoxyribozymes, which do not appear to share a common ancestor sequence. This suggests that this motif may be most efficient motif to catalyze self-phosphorylation by DNA. It also more generally demonstrates that DNA can undergo convergent evolution to reach the same complex folding arrangement. A fourth deoxyribozyme was found to fold into a complex tertiary structure containing a novel quadruplex-helix pseudoknot motif. The finding of this pseudoknot and comparison with other quadruplexes found in other functional nucleic acids led us to investigate whether these stable motifs could be incorporated into nucleic acid libraries to improve the process of in vitro selection and give researchers a better chance of isolating functional nucleic acids. Design and characterization of structured libraries revealed that DNA libraries could be made in which the majority of sequences are folded into quadruplex arrangements. The incorporation of this quadruplex scaffold into DNA sequence libraries may ease the isolation of functional nucleic acids that contain this useful structural motif. In the final part of this thesis, a self-phosphorylating deoxyribozyme was converted from a tool for study of DNA structure to a sensor for GTP and Mn2+, demonstrating that deoxyribozyme substrates can be converted into targets for biosensors.

abstract: Doctor of Philosophy (PhD)


title: A Philosophical Examination of the Instrumental Conception of the Epistemic Rationality of Human Doxastic States

contributor:
Hitchcock, David
Vorobej, Mark
Garrett, Brian
Philosophy

subject:
epistemic rationality
epistemic justification
instrumentalism
epistemic goals
epistemic value
Epistemology
Epistemology

abstract:
The instrumental conception of epistemic rationality is the view according to which beliefs, or doxastic states generally, are epistemically rational insofar as they promote the achievement of an epistemic goal, and they are epistemically irrational to the extent that they fail to promote such a goal. The thesis that I defend here is that the instrumental conception is not satisfactory as a general account of epistemic rationality.

I proceed by examining a number of reasons one might offer for accepting the instrumental account, and I find them wanting. I also consider various ways of formulating the epistemic goal, attempting to determine the best one, in order to show the instrumental conception in its best light. I consider and reject the attempt to ground the instrumental conception on the proper function of our cognitive systems. Finally, I consider three arguments against the instrumental conception of epistemic rationality, and some objections to them. I conclude that, even shown in its most favourable light, the instrumental conception cannot give us a satisfactory general account of epistemic rationality.

abstract: Doctor of Philosophy (PhD)


title: The (Nested) Word Problem: Formal Languages, Group Theory, and Languages of Nested Words

contributor:
Boden, Hans U.
Nicas, Andrew J.
Valeriote, Matthew
Mathematics

subject:
geometric group theory
formal languages
automatic groups
word problem
algorithmic properties of group
nested words
Algebra
Geometry and Topology
Theory and Algorithms
Algebra

abstract: This thesis concerns itself with drawing out some interesting connections between the fields of group theory and formal language theory. Given a group with a finite set of generators, it is natural to consider the set of generators and their inverses as an alphabet. We can then consider formal languages such that every group element has at least one representative in the language. We examine what the structure of the language can tell us about group theoretic properties, focusing on the word problem, automatic structures on groups, and generalizations of automatic structures. Finally we prove new results concerning applications of languages of nested words for studying the word problem.

abstract: Master of Science (MSc)


title: Aerobic Exercise Intensity Affects Skeletal Muscle Myofibrillar Protein Synthesis and Anabolic Signaling in Young Men

subject:
aerobic exercise
myofibrillar protein synthesis
protein synthesis
mTOR
Exercise Science
Exercise Science

abstract: Aerobic exercise can stimulate mixed muscle protein synthesis (MPS) acutely post-exercise; however, the types of proteins synthesized as a result of aerobic exercise are not known by studying changes in mixed MPS. We aimed to study the effect of aerobic exercise intensity on the 4 and 24 h post-exercise fractional synthesis rate (FSR) of myofibrillar proteins. Using a within-subject design, eight males (21 ± 1 years, VO2 peak: 46.7 ± 2.0 mL kg-1 min-1) underwent 2 trials with a primed constant infusion of L-[ring-13C6]phenylalanine in the fasted state for each work-matched exercise intensity (LOW: cycling for 60 min at 30% Wmax and HIGH: 30 min at 60% Wmax). Muscle biopsies were obtained to determine resting, 4 and 24 h post-exercise myofibrillar FSR. We also studied the phosphorylation of signaling proteins involved in protein synthesis at each time point using immunoblotting methods. Phospho-p38Thr180/Tyr182 was greater at 4.5 h after exercise compared to 0.5, 24 and 28 h post-exercise (p < 0.05). Additionally, a strong trend was present for phospho-mTORSer2448 (p = 0.056) with 0.5 h post-exercise phosphorylation significantly higher after HIGH than after LOW exercise (p < 0.05). Myofibrillar protein synthesis was stimulated 1.5–fold 0.5 – 4 h post-exercise (p < 0.05), returning to rest in the LOW condition 24 h post-exercise, while 6 out of 8 subjects maintained increased myofibrillar FSR 24 h post HIGH exercise (p < 0.05). The increase in myofibrillar FSR 0.5 – 4 h post-exercise was correlated with phospho-mTORSer2448 0.5 h post-exercise (r = 0.698, p < 0.01), indicating the role of this signaling pathway in myofibrillar protein synthesis. It is concluded that aerobic exercise has an effect on myofibrillar protein synthesis and intensity may play a role in the duration of this response.

abstract: Master of Science in Kinesiology


title: The James Thomason School in Northern India, 1822-1853: A Biographical and Administrative Study

contributor:
Johnston, Charles Murray
History

abstract: This dissertation attempts to show Haileyburians - students of the East India College - at the peak of their influence in India. This is done by an examination of the so-called Thomason 'school' at work in Northern India in the two decades before the Mutiny. This serves the purpose, moreover, of shedding light on a relatively neglected period of British India. The writings - private and published - of Haileyburians themselves provide the principle source of narrative, analysis, and interpretation.

abstract: Doctor of Philosophy (PhD)


title: A Study of the Pseudotypes of Vesicular Stomatitis Virus and Murine Leukemia Viruses

contributor:
Prevec, L. A.
Biology

subject: Biology Biology

abstract:
Superinfection of murine leukemia virus infected cells with VSV produces a certain proportion of pseudotype particles which have the genome of VSV and envelope antigen characteristics of murine leukemia virus, i.e. these particles cannot be neutralized by anti-VSV antiserum. Pseudotypes of VSV and Friend murine leukemia virus have been neutralized by anti-FLV antiserum. These particles do not form plaques on the cells which are already infected with any of Friend-, Moloney-, Rauscher- or Gross murine leukemia viruses. This shows that this interference effect is an envelope mediated phenomenon which is common to all four of these murine leukemia viruses.

At a high MOI of VSV infection the yield of VSV(FLV) pseudotype particles is reduced suggesting that this is due to direct inhibitory effect of VSV on FLV protein synthesis as well as on the host cell protein synthesis.

Pseudotype particles have been shown to possess the same density and probably the same sedimentation coefficient values as normal VSV, but they have a tendency to form aggregates with non-pseudotype material more readily than do VSV(VSV) particles.

In the studies of intracellular events involved in the synthesis of FLV specific glycoproteins, it has been shown that FLV glycoprotein is available for pseudotype production some 9 hours after FLV infection. The input FLV genome does not appear to act as a m-RNA for the glycoprotein in these experiments. Addition of actinomycin D after VSV superinfection does not reduce the yield of VSV (FLV) pseudotype synthesis significantly showing that concurrent DNA-dependent transcription is not needed for pseudotype formation. Effect of actinomycin D on pseudotype production in chronically infected FN-3T3 cells has shown that either the m-RNA or the glycoprotein itself is stable during 6 hour time prior to VSV infection.

Experiments with glucosamine have shown that the majority of the FLV glycoprotein necessary for pseudotype production in chronically infected cells is synthesized after VSV infection.

An interesting possibility that unintegrated "proviral" DNA may be capable of being transcribed and giving rise to FLV glycoprotein is suggested by experiments with ethidium bromide.

abstract: Doctor of Philosophy (PhD)


title: Fusing the C-terminal tridecapeptide of hirudin to α1-proteinase inhibitor M358R accelerates its rate of thrombin inhibition

contributor:
Sheffield, Bill
Jeffrey Weitz, Patricia Liaw
Medical Sciences

subject:
blood
coagulation
anticoagulants
serpins
hirudin
Medical Biochemistry
Medical Molecular Biology
Other Medicine and Health Sciences
Medical Biochemistry

abstract:
The serpin α-1 proteinase inhibitor (API) normally only impacts the coagulation cascade through its ability to inactivate factor XIa. However, the point mutation (Met to Arg) at position 358 results in a potent thrombin inhibitor, API M358R. This mutation also enhances this serpin’s ability to inhibit the anticoagulant protein, activated protein C (APC) and hence this property limits its therapeutic potential. As a result, various modifications to this protein have been engineered in order to enhance its specificity towards thrombin. Previously, the Heparin Cofactor II (HCII) N-terminal tail, HCII 1-75, which binds exosite 1 of thrombin, was tethered to the N-terminus of API M358R, creating HAPI M358R. Although this change did not alter anti-APC activity, it did augment the anti-thrombin activity of API M358R. In addition, further changes in the reactive center loop, the region that interacts with the thrombin active site, resulted in a significant reduction in APC activity while maintaining antithrombotic activity similar to HAPI M358R; this variant was termed HAPI RCL5.

Preliminary experiments were performed with the C-terminal tridecapeptide of Hirudin Variant 3 (HV3) to determine its exosite 1 binding capacity compared to HCII 1-75. Three different variants of this peptide were tested: one with a hexahistidine tag (H6HV354-66), another that also had a hexa-glycine C-terminal addition (H6HV354-66G6) and a third without either addition. All were found to bind exosite 1 with a greater affinity than HCII 1-75. Thus, the H6HV354-66G6 peptide was fused to API M358R and API RCL5 in hopes of creating an inhibitor with heightened specificity compared to HAPI M358R and HAPI RCL5, respectively.

HV3API M358R and HV3API RCL5 were expressed in a bacterial system and purified by nickel-chelate and ion exchange chromatography. Second order rate constants for the inhibition of thrombin and APC by the API variants and fusion proteins were determined. The K2 values for α-thrombin inhibition ranged from 186 M-1min-1 to 22 M-1min-1 with an order of inhibitory potency observed as follows: HAPI M358R > HAPI RCL5 > HV3API M358R > HV3API RCL5>API RCL5 > API M358R.

The ability of recombinant chimeric serpins to bind thrombin exosite 1 in a manner independent of RCL-thrombin active site interactions was also investigated through competitive inhibition of the binding of active site-inhibited thrombin to immobilized HCII 1-75. It was found that the order of exosite 1 binding affinity was HV3API RCL5 > H6HV354-66G6> HCII 1-75 > HAPI RCL5. Our results indicate that fusing the C-terminal tridecapeptide of HV3 to API variants enhanced their ability to inhibit thrombin, but to a lesser extent than fusing the N-terminal 75 residues of HCII. This finding likely reflects a requirement for the exosite 1-binding motif of the fusion protein to bind exosite 1 in a way that allows for subsequent optimal active site attack on the RCL by the serpin moiety of the fusion protein. In general, this work provides a second novel example of how the activity of a thrombin-inhibitory serpin can be enhanced by fusion to an exosite-1 binding motif.

abstract: Master of Health Sciences (MSc)


title: STRUCTURE, SURFACES, AND COMPOSITION OF CATALYTIC NANOPARTICLES FROM QUANTITATIVE ABERRATION CORRECTED TRANSMISSION ELECTRON MICROSCOPY

contributor:
Botton, Gianluigi
Materials Science and Engineering

subject:
electron microscopy
catalysts
nanoparticles
Other Materials Science and Engineering
Other Materials Science and Engineering

abstract: Proton exchange membrane fuel cells (PEMFC) are a technology of high interest for the automotive and power generation industry. The catalyst layer plays a critical role in fuel cells as it is responsible for catalyzing hydrogen oxidation and oxygen reduction to generate electricity. The current challenge in catalyst development is to produce highly active and economical catalysts. This challenge cannot be overcome without an accurate understanding of catalyst surfaces and morphology since the catalytic reactions occur on the surface active sites. Transmission electron microscopy (TEM) is an excellent tool to understand the structures of the nanoparticles down to the atomic level in determining the relationship with the catalyst’s performance in fuel cell applications. Platinum (Pt) is one of the best commercially available catalysts for PEMFC due to its highly active, inert, and relatively stable properties. However, Pt is a rare precious metal due to its low abundance and high demand. Further research is aimed at developing highly active and more economical catalysts in order to mass produce PEMFC. A strategic approach is to use platinum bimetallic alloys, which greatly reduce the platinum loading as they enhance the oxygen reduction reaction. A detailed understanding of the nanoparticle surface is critical as the catalyst surface strongly determines its catalytic activity. Furthermore, another challenge in utilizing fuel cells is the life-time of the catalysts. It is known that electrochemical cycling affects Pt alloys. As a result, the understanding of the effect of electrochemical treatments on the catalyst’s v morphology and composition is key to improving the fuel cell’s performance and durability. This thesis demonstrates that through the use of TEM, useful insights regarding the morphology, surfaces, and compositions of the catalysts can be gained and contribute to the improvement in catalyst development for next generation fuel cells.

abstract: Master of Applied Science (MASc)


title: Image and Video Resolution Enhancement Using Sparsity Constraints and Bilateral Total Variation Filter

contributor:
Shirani, Shahram
Patriciu, Alexandru
Electrical and Computer Engineering

subject:
Contourlet Transform
Sparsity
Image interpolation
Video Resolution Enhancement
Deinterlacing
Bilateral Total Variation Filter
Electrical and Computer Engineering
Signal Processing
Electrical and Computer Engineering

abstract:
In this thesis we present new methods for image and video super resolution and video deinterlacing. For image super resolution a new approach for finding a High Resolution (HR) image from a single Low Resolution (LR) image has been introduced. We have done this by employing Compressive Sensing (CS) theory. In CS framework images are assumed to be sparse in a transform domain such as wavelets or contourlets. Using this fact we have developed an approach in which the contourlet domain is considered as the transform domain and a CS algorithm is used to find the high resolution image. Following that, we extend our image super resolution scheme to video super resolution. Our video super resolution method has two steps, the first step consists of our image super resolution method which is applied on each frame separately. Then a post processing step is performed on estimated outputs to increase the video quality. The post processing step consists of a deblurring and a Bilateral Total Variation (BTV) filtering for increasing the video consistency. Experimental results show significant improvement over existing image and video super resolution methods both objectively and subjectively.

For video deinterlacing problem a method has been proposed which is also a two step approach. At first 6 interpolators are applied to each missing line and the interpolator which gives the minimum error is selected. An initial deinterlaced frame is constructed using selected interpolator. In the next step this initial deinterlaced frame is fed into a post processing step. The post processing step is a modified version of 2-D Bilateral Total Variation filter. The proposed deinterlacing technique outperforms many existing deinterlacing algorithms.

abstract: Master of Science (MSc)


title: RETROFITTING SUBURBAN HOMES FOR RESILIENCY: A PROTOTYPE DECISION SUPPORT SYSTEM

contributor:
Baetz, Brian W.
Razavi, Saiedeh
Guo, Yiping
Civil Engineering

subject:
suburbs
suburban
home design
decision support system
energy analysis
Architectural Engineering
Computer-Aided Engineering and Design
Environmental Engineering
Urban, Community and Regional Planning
Architectural Engineering

abstract:
North American suburbs are facing decline and obsolescence. They cannot meet the needs of North America’s ageing society, future climate change, or higher energy prices. Compounded with their negative environmental impact, non-resilient is an appropriate label for North American suburbs.

Resilient suburban communities can be realized through retrofitting to meet current and future needs. Community scale retrofitting is in the early stages of development. House-level retrofitting tools exist but must be synthesized into a useable form for homeowners.

Homeowners arguably have the largest stake in the future of the suburbs for both financial and social reasons. Empowering them with tools to make their suburban home and community more resilient is considered to be desirable.

This thesis empowers homeowners by developing a prototype decision support system (DSS) that will help them (or their contractors) make choices about adapting and retrofitting their home for resilience. This Microsoft Excel-based DSS addresses the following suburban needs: new housing types, reducing the environmental impacts of the home, and decreasing reliance on fossil fuels. The DSS does this through three constituent ‘modules’.

The first module, Dividing Suburban Homes, demonstrates the feasibility of dividing large suburban homes into multifamily dwellings. The second module, Sustainable Additions, selects resilient building materials for housing additions. The last module, Reducing the Home’s Environmental Impact, helps homeowners choose methods for reducing the environmental impact and fossil fuel usage of their home.

Through these three modules, this DSS addresses a considerable number of the current and anticipated issues facing the suburbs.

abstract: Master of Applied Science (MASc)


title: Large-Scale Motion Modelling using a Graphical Processing Unit

contributor:
Kirubarajan, T.
Electrical and Computer Engineering

abstract: The increased availability of Graphical Processing Units (GPUs) in personal computers has made parallel programming worthwhile and more accessible, but not necessarily easier. This thesis will take advantage of the power of a GPU, in conjunction with the Central Processing Unit (CPU), in order to simulate target trajectories for large-scale scenarios, such as wide-area maritime or ground surveillance. The idea is to simulate the motion of tens of thousands of targets using a GPU by formulating an optimization problem that maximizes the throughput. To do this, the proposed algorithm is provided with input data that describes how the targets are expected to behave, path information (e.g., roadmaps, shipping lanes), and available computational resources. Then, it is possible to break down the algorithm into parts that are done in the CPU versus those sent to the GPU. The ultimate goal is to compare processing times of the algorithm with a GPU in conjunction with a CPU to those of the standard algorithms running on the CPU alone. In this thesis, the optimization formulation for utilizing the GPU, simulation results on scenarios with a large number of targets and conclusions are provided.

abstract: Master of Applied Science (MASc)


title: The Effects of Augmented Reality Computing on Microgenetic Place Developments in Unfamiliar Spaces

contributor:
Eyles, John
Geography and Earth Sciences

subject: Augmented Reality

subject: Sense of Place

subject: Virtual Reality

subject: Microgenesis of Place

subject: Virtual Mobility

subject: Information and Communication Technologies

subject: Human Geography

subject: Other Social and Behavioral Sciences

subject: Science and Technology Studies

subject: Human Geography

abstract: Modern virtually mobile technologies, largely facilitated by the Internet, have changed communication modes, methods, and even daily-lived experiences within the past 20 years. The most prevalent medium of virtual mobility, virtual reality (VR) manages information through the creation of analogies of the physical world. Recently, a new mode of computing called augmented reality (AR) has become increasingly ubiquitous through the proliferation of modern mobile handsets. AR utilizes augmentation of the physical realm rather than simulation as a guiding principle, binding together the physical and virtual realms. Through the use of context-aware features such as landmark identification, geodetic data, etc., AR is able to superimpose virtual information onto real-time displays of physical landscapes. It is in this way that AR is the first mode of computing that truly transcends the boundaries of the virtual and physical realms, demonstrating the concept of dual presence. The effects of this new medium of computing on navigation, wayfinding, and especially the developments involved in the creation of sense of place are largely unstudied. A phenomenological exploratory research design is carried out to seek to identify the effects AR facilitation has on respondents’ cognitive developments, including developments in wayfinding and the creation of social representations of place.

abstract: Master of Arts (MA)


title: Quantitative, non-destructive estimates of forest coarse root biomass using 3-D ground-penetrating radar (GPR)

contributor:
Arain, M. Altaf
Boyce, Joe
Morris, William A.
Geography and Earth Sciences

subject:
3-D ground penetrating radar
root biomass
carbon
temperate forest
Pinus strobus
root structure
antenna tilt
vector corrections
Earth Sciences
Geophysics and Seismology
Earth Sciences

abstract:
We evaluated 3-D imaging of coarse root structure and biomass using ground-penetrating radar (GPR). GPR surveys were conducted in a white pine forest in southern Ontario, Canada. GPR profiles were obtained across two test plots (6 and 17 m2 area), using 1-GHz GPR and a MEMS (micro-electro-mechanical systems) accelerometer. Test plot surveys evaluated the effects of micro-topography, soil moisture content, and root diameter and spacing. In addition, with the aid of the outcome of the control test plots two other plots (25 and 400 m2 area) were surveyed with varying line sample spacing to investigate the restraints on resolution brought about by line sampling density.

Accounting for antenna tilt is necessary to determine an accurate and more precise position of root mass. The antenna tilt was >45o pitch, >28o roll and up to 10o yaw due to surface micro-topography of the forest floor. Vector 3-D imaging enhanced the diffraction amplitude (15.5% increase) and centralized the position of the root. Radial surveys provided root continuity and produced better root imaging.

GPR largely underestimates coarse root biomass when a line spacing of 25 cm is used. However similar results are found with smaller line spacing (12.5 cm). A maximum line spacing of 10 cm provided continuous root structure and differentiation of roots spaced 10 cm apart and greater. A sampling line spacing of 5 cm and an inline sampling interval of 0.5 cm in low soil moisture conditions provided the detection of roots that were a minimum of 1.4 cm in diameter.

abstract: Master of Science (MSc)


title: ADVANCED IMAGE AND VIDEO INTERPOLATION TECHNIQUES BASED ON NONLOCAL-MEANS FILTERING

contributor:
Shirani, Shahram
Terence D. Todd, Jian-Kang Zhang
Electrical and Computer Engineering

subject:
De-interlacing
Frame rate up-conversion (FRUC)
View interpolation
Nonlocal-means
Signal Processing
Signal Processing

abstract:
In this thesis, we study three different image interpolation applications in high definition (HD) video processing: video de-interlacing, frame rate up-conversion, and view interpolation. We propose novel methods for these applications which are based on the concept of Nonlocal-Means (NL-Means).

In the first part of this thesis, we introduce a new de-interlacing method which uses NL-Means algorithm. In this method, every interpolated pixel is set to a weighted average of its neighboring pixels in the current, previous, and the next frames. Weights of the pixels used in this filtering are calculated according to the radiometric distance between the surrounding areas of the pixel being interpolated and the neighboring pixels. One of the main challenges of the NL-Means is finding a suitable size for the neighborhoods (similarity window) that we want to find radiometric distance for them. We address this problem by using a steering kernel in our distance function to adapt the effective size of similarity window to the local information of the image. In order to calculate the weights of the filter, we need to have an estimate of the progressive frames. Therefore, we introduce a low computational initial de-interlacing method. This method interpolates the missing pixel along a direction based on two criteria of having minimum variation and being used by the above or below pixels. This method preserves the edge structures and yields superior visual quality compared to the simple edge-based line-averaging and many other simple iv de-interlacing methods.

The second part of this thesis is devoted to the frame rate up-conversion application. Our frame rate up-conversion method is based on two main steps: NL-Means and foreground /background segmentation. In this method, for every pixel being interpolated first we check whether it belongs to the background or foreground. If the pixel belongs to the background and the values of the next and previous frames’ pixels are the same, we simply set the pixel intensity to the intensity of its location in the previous or next frame. If the pixel belongs to the foreground, we use NL-Means based interpolation for it. We adjust the equations of the NL-means for frame rate up-conversion so that we do not need to have the neighborhoods of the intermediate for calculating the weights of the filter. The comparison of our method with other existing methods shows the better performance of our method.

In the third part of this thesis, we introduce a novel view interpolation method without using disparity estimation. In this method, we let every pixel in the intermediate view be the output of the NL-means using the pixels in the reference views. The experimental results demonstrate the better quality of our results compared with other algorithms which use disparity estimation.

abstract: Master of Applied Science (MASc)


title: The Inclusion of Atypical Minorities in Public Policy: Urban Aboriginal Peoples in Canada and Travellers in Ireland

contributor:
Frost, Catherine
Graefe, Peter
Bird, Karen
Political Science

subject:
Urban Aboriginal Peoples in Canada
Irish Travellers
public policy
inclusion
voluntary sector
Public Policy
Public Policy

abstract: This research project asks: to what extent are voluntary organizations included in the policy processes that make decisions regarding the needs and interests of atypical groups? Both urban Aboriginal peoples and Travellers are defined as atypical groups due to their indigeneity and their separate treatment by the state because of cultural differences characterized by nomadism, language and distinctive lifeways preserved by oral traditions. Their marginalization was exacerbated as they transitioned to urban centres after the middle of the twentieth century and the state, although it acknowledged these groups, did not accommodate their needs and interests. In an era of neoliberalism where significant responsibility for welfare has shifted to the voluntary sector, marginalized groups still require disproportionate assistance by the state in policy areas of education, health and housing and they rely on voluntary organizations to provide culturally appropriate programs and services and to advocate for their needs and interests. Applying a scalar analysis, this project isolated three key concepts that are interdependent yet distinct, that are critical to inclusion. First, is incorporation of culturally relevant programs on the micro scale. Second, is atypical group representation in policy processes on the meso scale. And third, their collaboration with government on the macro scale. On balance it appears that urban Aboriginal peoples in Canada have moved closer to inclusion in policy processes due to their success in incorporation, representation and collaboration. In contrast, Travellers in Ireland face greater obstacles in collaborating with government, which impacts on their representation in policy processes and their incorporation of programs and services to meet the needs and interests. The trajectory of these findings suggest that urban Aboriginal peoples will continue to collaborate with government and move closer to goals self-determination while Travellers will continue to struggle against prevailing societal domination to achieve ethnic minority status.

abstract: Doctor of Philosophy (PhD)


title: DEVELOPMENT OF ROBUST ANIMAL MODELS FOR VITAMIN C FUNCTION

contributor:
Schellhorn, Herb
Nurse, Colin
Biology

subject:
Vitamin C
animal model
guinea pig
mouse
gene therapy
Biology
Biology

abstract:
Vitamin C inhibits the oxidation of biologically important molecules and may have a potential protective role against cancer, cardiovascular diseases, and aging. Clinically relevant models of vitamin C function are essential for understanding the role of the antioxidant in the pathogenesis of these complex diseases, and its therapeutic potential. In this thesis, we examine ascorbic acid synthesis and deficiency in animal models, and develop these animal models into powerful tools to examine specific questions of vitamin C function. This thesis first presents a review on the existing animal models for antioxidant function in human nutrition, focusing on their clinical relevance in chronic diseases. We concluded that equivocal proof of beneficial effects of high dose antioxidant supplementation has not been established, and further investigations of animal models of antioxidant function are needed to resolve outstanding questions.

We then examined the feasibility and efficacy of an alternative vitamin C delivery method using gene therapeutic lentivirus vectors in a guinea pig model of vitamin C function. The guinea pig exhibits an inactivated gulonolactone oxidase gene (Gulo), which is required for endogenous ascorbic acid synthesis, and as such must acquire vitamin C from the diet. Using a lentivirus vector carrying the mouse Gulo under the murine cytomegalovirus (mCMV) promoter, which was previously developed as a part of my undergraduate thesis, we examined the ability of this gene therapeutic vector to mediate the expression of GULO and the production of ascorbic acid in guinea pigs. At a titre of 1010 viral particles per animal, the life of lentivirus-treated guinea pigs were prolonged by 35 days compared to the scorbutic control, which was given an ascorbic acid-free diet. Ascorbic acid was produced in the liver of the treated guinea pigs, but the amount produced was not sufficient to elevate plasma concentrations or fully correct the metabolic deficiency. We conclude that lenti-mCMV-Gulo is able to mediate the expression of GULO and endogenous production of vitamin C in guinea pigs.

To test the role of vitamin C in cancer etiology and outcome, we are currently in the process of introgressing the Gulo-/- inactivation mutation, developed by Maeda et al. in 2000, from the C57BL/6 strain background into the FVB/N strain background. The FVB/N strain is also the background for several models of erbB2/neu overexpression in human breast cancer, associated with increased metastasis and low patient survival rates. Taken together, this thesis develops two animal models of vitamin C function, which can be employed in future applications.

abstract: Master of Science (MSc)


title: Behaviour of Reinforced Concrete Joints

contributor:
Drysdale, R.G.
Civil Engineering

subject:
Civil Engineering
Civil Engineering

abstract:
No rigorous explanation exists for the behaviour of reinforced concrete joints. The lack of understanding the complex interaction may account for continued use of inadequate joint details particularly for knee joints subjected to opening moments. The object of this research was to provide a better understanding of joint behaviour through a combined experimental and analytical investigation.

In the experimental program, 6 specimens with different types of joint details were tested under opening moment. These details reflected recent recommendations by other investigators and some adaptations of their ideas. The results served as evidence of the ability to produce effective and simple details as well as serving as a basis for evaluating the reliability of the analytical model.

A method of analysis has been developed using the finite element method to model the behaviour of reinforced concrete including the interactions between concrete and steel in the form of bond and dowel forces. One of the principle features of this method of analysis is the built in ability to trace the propagation, location and orientation of cracking. This feature was tested by comparing predicted behaviour of beams failing in shear and flexure with test results. Very good agreement with the well documented phenomena of various modes of cracking and failure provided evidence of the validity of the analytical method.

The analyses of the joints reproduced cracking patterns and sequences as well as capacities which are quite close to the test results. The analytical information helped to identify the primary causes of failure of premature failure and thereby provided a more rational basis for suggesting alternate joint details which will behave much better than inadequate details which are currently recommended.

abstract: Doctor of Philosophy (PhD)


title: Cis-Regulatory Evolution in Salmonella enterica

contributor:
Coombes, Brian K.
Biochemistry

subject:
Salmonella
evolution
infection
Pathogenic Microbiology
Pathogenic Microbiology

abstract: Originally considered the sole providence of protein coding sequences, evolutionary biology has begun to recognize the importance of non-coding DNA in dictating phenotypic adaptation. Exclusively examined in eukaryotic anatomical development, cis-regulatory modifications have the power to alter the spatial-temporal dynamics of gene expression without the plieotropic consequences of protein modification. Owing to the need to integrate horizontally acquired DNA into existing regulatory networks, cis-regulatory mutations may also significantly contribute to prokaryotic evolution. The horizontal acquisition of Salmonella Pathogenicity Island (SPI)-2 led to the evolutionary divergence of Salmonella enterica from S. bongori. Use of the type 3 secretion system encoded in SPI-2 allowed S. enterica to exploit an intracellular host niche offered by immune cells and allowed for its systemic dissemination. Here we identify ancestrally encoded srfN and dalS and demonstrate that through acquisition of a binding site for the SPI-2 regulator, SsrB, they have contributed to the pathoadaptation of S. enterica to the host environment. We also demonstrate that ancestral regulatory networks contribute to the establishment of an expression hierarchy for SPI-2 in vitro and to transcriptional priming in the host lumen prior to invasion. These findings demonstrate that cis-regulatory modifications have significantly contributed to the evolution of S. enterica as an intracellular pathogen.

abstract: Doctor of Philosophy (PhD)


title: Electrodeposition of Organic-Inorganic Films for Biomedical Applications

contributor:
Zhitomirsky, Igor
Materials Science and Engineering

subject:
biomedical implants
coatings
biopolymers
bioceramics
halloysite
Electrophoretic Deposition (EPD)
Polymer and Organic Materials
Polymer and Organic Materials

abstract: Electrochemical methods show great promise in the deposition of biocompatible coatings for biomedical applications with advanced functionality. Consequently, methods of creating coatings of bioactive materials, such as halloysite nanotubes (HNT), hydroxyapatite (HA), chitosan, hyaluronic acid (HYH), poly-L-ornithine (PLO) and poly-L-lysine (PLL) and polyacrylic acid (PAA) have been developed through the use of electrophoretic deposition (EPD). The co-deposition of these materials are achieved at voltages ranging from 5 to 20 V on a 304 stainless steel substrate using suspensions of 0.5 and 1.0 gL-1 biopolymer (chitosan, PAA, PLO, PLL) containing 0.3, 0.5 0.6, 1.0 and 2.0 gL-1 bioceramic (HNT, HA). The resulting films were then investigated to further understand the kinetics and mechanics of deposition, determine their properties, and evaluate their suitability for physiological applications. The films were studied using X-Ray Diffraction (XRD), Differential Thermal Analysis and Thermogravimetric Analysis (DTA/TGA), Scanning Electron Microscopy (SEM), Quartz Crystal Microbalance (QCM) and Linear Polarisation. The results indicate that film thickness, composition and morphology can be controlled and modified at will, and that the deposition of composite films, multilayer laminates and functionally graded films are possible.

abstract: Master of Applied Science (MASc)


title: Existence, Continuity, and Computability of Unique Fixed Points in Analog Network Models

contributor:
Zucker, Jeffery I.
Carette, Jacques
Computing and Software

subject:
analog computation
contraction
smoothies
vanishing delay
computable analysis
Hadamard's Principle
Theory and Algorithms
Theory and Algorithms

abstract:
The thesis consists of three research projects concerning mathematical models for analog computers, originally developed by John Tucker and Jeff Zucker. The models are capable of representing systems that essentially “diverge,” exhibiting no valid behaviour---much the way that digital computers are capable of running programs that never halt. While there is no solution to the general Halting Problem, there are certainly theorems that identify large collections of instances that are guaranteed to halt. For example, if we use a simplified language featuring only assignment, branching, algebraic operations, and loops whose bounds must be fixed in advance (i.e. at “compile time”), we know that all instances expressible in this language will halt.

In this spirit, one of the major objectives of all three thesis projects is identify a large class of instances of analog computation (analog computer + input) that are guaranteed to “converge.” In our semantic models, this convergence is assured if a certain operator (representing the computer and its input) has a unique fixed point. The first project is based on an original fixed point construction, while the second and third projects are based on Tucker and Zucker's construction. The second project narrows the scope of the model to a special case in order to concretely identify a class of operators with well-behaved fixed points, and considers some applications. The third project goes the opposite way: widening the scope of the model in order to generalize it.

abstract: Doctor of Philosophy (PhD)


title: Femtosecond laser irradiation of synthetic single crystal diamond: studies of surface ripples and ablation thresholds

contributor:
Haugen, Harold
Botton, Gianluigi
Fang, Qiyin
Engineering Physics

subject:
diamond
laser ablation
high-speed optical techniques
scanning electron microscopy
surface structure
optical microscopy
ultrashort pulses
Electromagnetics and photonics
Electromagnetics and photonics

abstract: This thesis explores the ablation and texturing of synthetic single crystal diamond under ultrashort laser pulse irradiation in rough vacuum ambient conditions. Experiments were performed with a 1 kHz repetition rate titanium sapphire laser system producing pulses at 800 nm central wavelength and 150 fs pulse duration. First, the production of ordered periodic nanostructures (ripples) on the diamond surface was characterized and the periodicity of these structures was analyzed against irradiation parameters. Ripples were usually found to fall into one of two categories: one with a spatial period near the irradiation wavelength and one with a spatial period near λ/2n, where λ is the central laser wavelength in air and n is the refractive index of diamond at λ. The spatial periods were plotted against irradiation conditions including the peak fluence, number of incident pulses, and the angle of incidence. Unique outcomes arising out of complex irradiation conditions were also explored. Second, the ablation thresholds for single pulse up to 1000 pulse irradiation were determined using the D2 method at both the fundamental central wavelength (800 nm) and the second harmonic (400 nm). The single 800 nm pulse ablation threshold for synthetic single crystal diamond was determined to be 2.3 J/cm2 with an incubation coefficient of 0.54. The single 400 nm pulse ablation threshold was determined to be 1.5 J/cm2 with an incubation coefficient of 0.73.

abstract: Master of Applied Science (MASc)


title: “STANDING ON JELLO”: IMAGES AND EXPERIENCES OF ‘ALTERNATIVE’ SOCIAL WORK

contributor:
Sinding, Chris
Aronson, Jane
Social Work

subject:
social work
alternative
arts-based research
images
social work practice
Social Work
Social Work

abstract:
Grounded in postmodern and social constructionist theories, this research was designed to challenge 'mainstream' views of social work practice. Three social workers with extensive backgrounds in various social work roles were asked to submit individual arts-based representations of 'alternative' social work. The arts-based representations (a story, a tool box, and a medicine wheel) were shared in a focus group where the topics of mainstream and alternative social work were collectively explored. I present an analysis of the representations, offer a brief structural narrative analysis of how the participants talked about mainstream and alternative social work, and explore the dissonance surrounding the term 'alternative social work.'

The findings indicate that social workers who are interested in, or identify with alternative social work implement creative strategies to balance many, often conflicting, responsibilities and commitments. At the core of this study is a fundamental ideological tension in how social work is understood. The focus group revealed that what is commonly identified as 'alternative' social work, is judged by these research participants as 'good' social work. Rather than being a form of resistance to mainstream social work, alternative social work appears as a means of implementing participants' visions of effective, responsible and humane practice.

This study highlights how social workers struggle to represent themselves and their (desired) practice in today's political context. Images of 'good practice' offer insight into how social workers can and do respond to neoliberal pressures; these images and participants' reflections on them have potential to widen public and professional consciousness.

abstract: Master of Social Work (MSW)


title: GENETIC DISSECTION OF lin-11 REGULATION IN DIFFERENTIATION OF C. elegans AMPHID SENSORY NEURONS

contributor:
Gupta, Bhagwati P.
Biology

subject:
C. elegans
lin-11
sensory neurons
AVG
Biology
Cell and Developmental Biology
Biology

abstract:
The expression of lin-11 is regulated by enhancers located upstream from, as well as within, lin-11 intronic sequences. Multiple regulatory inputs control the spatiotemporal expression pattern of lin-11. To better understand that process, we have investigated these regulatory enhancers by dissecting two of the biggest intronic sequences of lin-11: intron 3 and intron 7. Using microscopy, we show that the expression of intron 3 is required in ten head sensory neurons and that the expression of intron 7 is required in two head neurons. The truncation of intron 7 revealed that its regulatory sequence may be located within its narrow 98 base pairs (bp) region. We used bioinformatics to predict which putative transcription factor(s) may regulate AVG expression. Using a hypersensitive RNAi mutant strain, eri-1; lin-15b, we tested forty putative transcription factors and quantitated the number of animals in which the molecular marker lin-11::GFP expression is knockdown in AVG interneurons.

Using electrotactic behavioral analysis we show that the speed of lin-11 null allele, n389, is reduced by almost 50%, when compared to that of the wildtype animals, due to amphid sensory neuronal deformities. We determine which conserved domains of lin-11 are required for the proper development of the neuronal and vulval cells via microinjection rescue experiments.

We sequenced eleven lin-11 alleles to determine which conserved domains are affected and the role of each of these domains in the development of vulval and neuronal cells. Our findings suggest that all lin-11 conserved domains are required for proper vulval cell differentiation as well as for proper development of the amphid sensory neurons. Finally, using tissue specific markers we label vulval cells in lin-11 mutants to show that those cells are defective, as judged by the lack of fate-specific markers in the vulval cells.

abstract: Master of Biological Science (MBioSci)


title: Dissent in Jest: The Political Aesthetics of Contemporary Media Humour

contributor:
O`Brien, Susie
O`Connor, Mary
York, Lorraine
English and Cultural Studies

subject:
Cultural Studies
Liberalism
Humour
Dissent
Postmodernism
Critical and Cultural Studies
Critical and Cultural Studies

abstract: This dissertation argues that humour not only constitutes a central aesthetic strategy within contemporary mass media, but can also be understood as a form of cultural production that is central to how we understand our world as a site of value and politics. Drawing on an understanding of liberalism as a politics of “reasonable dissent,” I investigate how humour is thought to operate as an exemplary form of this politics through a consideration of popular and scholarly literature. I then complicate this theoretical and lay consensus regarding humour-as-dissent, through a consideration of the ways in which a range of specific filmic and televisual texts – Jackass, The Office, The Sarah Silverman Program, The Chappelle Show, The Simpsons, South Park, Family Guy, The Daily Show with Jon Stewart, The Colbert Report and Four Lions – produce an aesthetic of humour through the manipulation and mobilisation of textual strategies and affective registers, such as discomfort, absurdity and provocation. Questioning the easy understanding of humour as a means to challenge existing power structures, I instead argue that the currently dominant forms of media humour are better understood as a political aesthetic that opens up new avenues of understanding and critique even as it shuts down and short circuits previously tenable forms of political interpretation. Through an intertwining of close-reading of popular cultural texts and a critical engagement with wider theoretical models of media production and consumption, I thus propose that the aesthetic aspects of mass media, such as humour, can be understood as cultural precursors that inflect the ways in which we can imagine the problems and possibilities of contemporary politics.

abstract: Doctor of Philosophy (PhD)


title: Characterization of CopN (Cpn0324) the Putative Type III Secretion System Plug Protein of Chlamydia pneumoniae

contributor:
Mahony, James
Lori Burrows, Murray Junop
Medical Sciences

subject:
Medical Biochemistry
Medical Biochemistry

abstract:
 Chlamydia pneumoniae is a Gram-negative, intracellular bacterium which utilizes a type III secretion system for virulence. This system injects virulence associated proteins into a host cell and ultimately hijacks host intracellular machinery required for the bacteria to propagate and reproduce. Chlamydia outer protein N or CopN (Cpn0324), is a member of a family of proteins found in pathogenic bacteria, which inhibits premature secretion of effector proteins by plugging the base of the injectisome. The lack of a genetic system to manipulate the bacteria hampers the identification of proteins within the T3S field. The work presented in this thesis establishes the role of CopN as the plug protein of Chlamydia pneumoniae, and examines protein interactions within the individual CopN domains.

The structure of CopN was first explored by limited proteolysis to establish the domain boundaries. We found three domains, an N-terminal, central domain, and C-terminal domain. Next, we used the full length protein as well as a series of truncations to examine the interactions within each domain. Using a subset of the known protein interactions between CopN and other T3S proteins, we found that the proposed chaperones Scc1 and Scc4 bind in the N-terminal region. There were no apparent interactions in the central domain, whereas FliI, FliF, CopD1158-206 and Scc3 all bound within the C-terminal region of CopN. Finally the secretion of CopN in a HeLa cell model was addressed throughout the course of an infection. CopN was detected in the host cell immediately after infection, and then was not detectable again until late infection. Overall, I have characterized the individual domains of CopN and present data to support the role of CopN as the plug protein in the T3SS of Chlamydia pneumoniae.

abstract: Master of Science (MSc)


title: The Regulation of Vascular Wall Cells by a TLR Ligand and Gp130 Cytokines

contributor: Medical Sciences (Molecular Virology and Immunology Program)

subject: Oncostatin M

subject: Lipopolysaccharide

subject: Aortic Adventitial Fibroblasts

subject: Aortic Smooth Muscle Cells

subject: Toll-like Receptor

subject: Interleukin 6.

subject: Biological Phenomena, Cell Phenomena, and Immunity

abstract:
Atherosclerosis is a disease affecting the blood vessels that is inflammatory in nature, and plays an important role in cardiovascular disease (CVD), one of the leading causes of morbidity and mortality worldwide. Oncostatin M (OSM), a member of the IL-6/gp130 cytokine family, has been implicated in atherosclerosis both in mouse models and in humans. OSM synergizes with other stimuli in various systems to regulate cells. Infectious pathogens as well as danger associated host molecules stimulate members of the innate immune system, including Toll-like Receptors (TLRs), to respond in a pro-inflammatory manner to cause cell activation and cytokine release. Experiments were performed to determine whether OSM and LPS (a TLR-4 ligand) synergize in regulation of vascular wall cells in vitro.

Upon stimulation of Aortic Adventitial Fibroblasts from mice (MAAFs) and humans (HAoAFs) as well as Human Aortic Smooth Muscle Cells (HAoSMCs) with LPS in combination with OSM, it was determined that there was a synergistic increase in IL-6 and VEGF levels in the cell supernatants as measured by ELISA compared to either treatment alone. MAAFs were also able to synergistically express KC upon stimulation with LPS and OSM, while in HAoAFs and HAoSMCs, LPS induced IL-8 levels were supressed by OSM. These effects were unique to OSM among gp130 cytokine members, as treatment of these cells with LPS in combination with LIF, IL-6, IL-31, or IL-11 had no marked effects compared to LPS alone. Furthermore, MCP-1 steady state mRNA levels were elevated 6 hours post stimulation with LPS and OSM compared to either treatment alone in HAoAFs and HAoSMCs.

While OSM did not appear to modulate TLR-4 expression, OSM treatment resulted in an increased phosphorylation signal in STAT-1,-3, and -5, as well as Akt in MAAFs and HAoAFs. In addition, combined LPS and OSM stimulation resulted in an increased phosphorylation signal of the MAPK p38 compared to either treatment alone. Furthermore, a neutralizing antibody to the OSMr-β was able to inhibit HAoAF IL-6 responses to PBMC conditioned medium. Together, these findings indicate that OSM and LPS can synergize in vitro to induce the expression of inflammatory factors in vascular wall cells, emphasizing the potential role of OSM, TLR-4 ligands, and adventitial fibroblasts in vascular inflammation.

abstract: Master of Science (MSc)


title: Discovery of conserved motifs in MARCO through evolutionary analyses and molecular biology

contributor:
Bowdish, Dawn
Health Sciences

subject: class A scavenger receptors; evolution; bioinformatics; pattern recognition receptors; innate immunity; molecular biology

subject: Bioinformatics

subject: Molecular Biology

subject: Bioinformatics

abstract:
Of the pattern recognition receptors involved in innate immunity, the class A Scavenger receptors are involved in the recognition and clearance of bacteria, yeast, and senescent molecules. Previous research has implicated the intracellular region of these receptors as essential for the clearance of these substances via endocytosis. In this work, I used a bioinformatic approach to define the evolutionary history of the class A Scavenger receptor family while elucidating areas of conservation within the cytoplasmic domains of these proteins. With this information, in addition to further predictions of post translational modifications and potential docking motifs for interacting proteins, I conducted molecular biology experiments to study the in vitro functionality of the macrophage receptor with collagenous domain (MARCO), a member of the class A Scavenger receptors.

Evolutionary analyses of the 5 class A Scavenger receptors identified a shared ancestry between these proteins and allowed me to postulate that 4 distinct gene du- plication events in addition to subsequent domain fusions, internal repeats, and dele- tions are responsible for the diverse protein structures and functions of this family. Despite some variation in domain structure, I found highly conserved regions across all 5 members, including a negatively charged region in the cytoplasmic domain. Further analyses of MARCO across organisms identified other conserved regions, in- cluding 2 residues predicted to be ubiquitinated, sumoylated, or phosphorylated by in silico predictive methods. However, molecular biology experiments demonstrated that these post translational modifications to not occur in the steady state. Addi- tional in vitro experiments, including isolations of MARCO and an artifical construct containing only the intracellular regions of the protein, were unable to identify any candidate adaptor binding proteins. Further research is needed to determine whether modifications in this region occur in the presence of bound ligands and/or known co-receptors.

abstract: Master of Science (MSc)


title: An Experimental Investigation of Small Angle Scattering of (200-1500 keV) Gamma Rays

contributor:
Prestwich, W.V.
Physics

subject: Physics Physics

abstract:
Differential cross-sections for the small angle (2° - 10º) scattering of 1408.0, 1274.2, 1112.0, 1085.8, 964.0, 778.9, 443.9, 344.3 and 244.7 keV gamma rays from lead, tantalum, cadmium, copper, aluminum and carbon were measured experimentally employing a high resolution gamma ray spectrometer system. An attempt was made to separate the coherent and incoherent components of the scattered radiation. An empirical model was developed to generate the shape or energy distribution of the incoherently scattered gamma rays and was applied to extract these components where these were unresolved. Various correction factors for the coherent and incoherent components have been considered.

The experimental results for the coherent scattering in lead, tantalum, cadmium and copper were compared with the form-factor based numerical computations. Significant deviations have been observed and some of the possible causes are indicated. The present results are compared with the previous measurements, wherever available, on the basis of momentum transfer.

This work reports the first set of systematic measurements of the incoherent scattering cross-sections for small momentum transfers (1.0Åˉ¹ - 10.0Åˉ¹). The experimental incoherent scattering functions are found to be considera0bly lower than the theoretical values for the scatterers of high atomic number.

abstract: Doctor of Philosophy (PhD)


title: LOCALIZATION, TRACKING, AND ANTENNA ALLOCATION IN MULTIPLE-INPUT MULTIPLE-OUTPUT RADARS

contributor:
Kirubarajan, Thia
Reilly, James
Zhang, J. K.
Electrical and Computer Engineering

subject:
MIMO radars
target tracking
sensor management
Signal Processing
Systems and Communications
Signal Processing

abstract:
This thesis concerns with the localization, tracking, and sensor management in the Multiple-Input Multiple-Output (MIMO) radar systems. The collocated and widely-separated MIMO radars are separately discussed and the signal models are derived for both structures.

The first chapter of the thesis is dedicated to the tracking and localization in collocated MIMO radars. A novel signal model is first formulated and the localization algorithm is developed for the derived signal model to estimate the location of multiple targets falling in the same resolution cell. Furthermore, a novel tracking algorithm is proposed in which the maximum bound on the number of uniquely detectable targets in the same cell is relaxed. The performance of the tracking and localization algorithms is finally evaluated using the tracking Posterior Cramer-Rao Lower Bound (PCRLB).

After showing the impact of the antennas position on the localization CRLB, a novel sensor management technique is developed for the collocated MIMO radars in Chapter 4. A convex optimization technique is proposed for the antenna allocation in a single-target scenario. When multiple targets fall inside the same cell, a sampling-based technique is formulated to tackle the non-convexity of the optimization problem.

The third chapter of this thesis also proposes new approaches for detection, localization, and tracking using a widely-separated MIMO radar. A scenario with multiple-scatterer targets is considered and the detection performance of both MIMO and multistatic radars will be evaluated in the designed scenario. To estimate the location of the multiple-scatterer target, a Multiple-Hypothesis (MH) based approach is proposed where the number and the location of multiple targets are both estimated. A particle filter based approach is also formulated for the dynamic tracking by a widely-separated MIMO radar. Finally, the performance of the MIMO radar and the miultistatic radar in detecting and localizing multiple-scatterer targets is studied.

abstract: Doctor of Philosophy (PhD)


title: A Policy Response to Canadian Economic Inequality

contributor:
Zhou, Rachel
Dumbrill, Gary
Social Work

subject:
income inequality
wealth inequality
redistribution
neoliberalism
maximum wage
Robin Hood Tax
Inequality and Stratification
Inequality and Stratification

abstract:
Economic inequality is increasing in Canada and throughout the world. In addition to the equity concerns of distributive justice, growing economic inequality negatively impacts poverty, social cohesion, and the stability of the economy. This master’s thesis undertakes a major literature review to explore the trends in economic inequality and the policies that influence it.

The current increase in economic inequality has been dominated by an increase in the income and wealth of the 1% to which the Occupy movement has drawn significant attention. Policies to directly counter this rise in both before- and after-tax top incomes are critical to combatting economic inequality. In addition to highlighting policies that target the very rich, this thesis examines intersections between traditional social policy and broader public policy in the field of economic inequality. It also argues for increased consideration of economics in social work research and policy practice. Economic inequality should be a concern to social workers alongside poverty.

Policies in four areas are considered: income taxes and transfers, public services, labour market institutions, and capital market interventions. Recommendations are made for the future. Addressing economic inequality through national policy is both possible and advantageous. A comprehensive policy package involving policies from the four areas explored has the potential to reduce economic inequality.

abstract: Master of Social Work (MSW)


title: DO PATIENTS MANAGED WITHIN A TRIAL EXPERIENCE DIFFERENT OUTCOMES THAN THEIR COUNTERPARTS MANAGED OUTSIDE THE TRIAL? A SYSTEMATIC REVIEW AND META-ANALYSIS OF RANDOMIZED AND OBSERVATIONAL STUDIES.

contributor: Clinical Epidemiology/Clinical Epidemiology & Biostatistics

subject:
clinical epidemiology
clinical trial as topic
trial effect
Clinical Epidemiology
Clinical Epidemiology

abstract:
Context: It is unclear whether the construct of a randomized controlled trial (RCT) itself could confer benefit or harm to trial participants beyond any effect of the experimental treatment under study (trial effect).

Objective: To determine whether there is a trial effect appreciated by RCT participants (insiders) compared to similar patients who do not participate (outsiders). Although we are most interested in the pragmatic comparison of insiders to outsiders, we will also conduct the explanatory comparison of insiders to outsiders when the intervention is the same.

Data Sources: We searched electronic health research databases, including CENTRAL (1960-2010), MEDLINE (1966-2010), EMBASE(1980-2010) and PsycINFO (1880- 2010).

Study Selection: Eligible studies included those that reported the outcomes of insiders and a group of parallel or consecutive outsiders and reported the same health outcome at the same endpoint.

Results: We included 147 articles out of the 42493 identified in our initial search. Five out of the 147 studies randomized patients to be insiders or outsiders, the remaining were observational designs. The heterogeneity of our overall result was reduced by grouping studies based on whether the intervention being investigated was effective and whether treatment inside and outside of the RCT was the same or different. There was no significant difference in outcomes between insiders and outsiders when the experimental intervention was ineffective (standard mean difference [95% confidence interval]: -0.03 [-0.1, 0.04]), or when it was effective and received by both insiders and outsiders (0.04 [-0.04,0.13]). If the experimental intervention was effective but was not administered to outsiders, they experienced worse health outcomes (-0.36 [-0.61, -0.12]).

Conclusions: There is no evidence to support any benefit or harm associated with trial participation. There is some evidence that better outcomes are experienced by insiders who had access to effective treatments not offered or available to outsiders.

abstract: Master of Health Sciences (MSc)


title: CHARACTERIZING THE FUNCTION OF HUNTINGTIN IN THE CELL STRESS RESPONSE AS A TARGET FOR DRUG DISCOVERY IN HUNTINGTON’S DISEASE

contributor:
Truant, Ray
Andrews, David W.
Brown, Eric
Biochemistry

subject:
Huntington's Disease
FLIM-FRET
cofilin
huntingtin
live cell imaging
Neurosciences
Neurosciences

abstract: Huntington’s disease (HD) is a devastating autosomal dominant neurodegenerative disorder for which there are no disease modifying treatments. Owing to this are the multiple biological functions of the huntingtin protein and the lack of understanding of the exact pathways being affected in HD. It is clear that the huntingtin protein normally provides anti-apoptotic support and that there are underlying energetic problems and cell stress defects associated with disease. Work from our group has shown that huntingtin acts as a stress sensor and translocates from the endoplasmic reticulum to the nucleus upon cell stress. We therefore hypothesized that huntingtin has a nuclear function in the cell stress response; which would tie together what is currently known about huntingtin, its pro-apoptotic function and the energetic defects of neurodegeneration. In this thesis we describe huntingtin as having a role in the nuclear cofilin-actin rod stress response. Cofilin is an actin binding protein normally involved in actin treadmilling. During stress, cofilin saturates F-actin leading to rod formation which functions to alleviate ATP. We show that this response is impaired in the presence of mutant huntingtin and that the aberrations in this response can be mediated through the enzyme tissue transglutaminase. Little is known about the physiological role and requirement of the cofilin-actin rod response. Therefore we created a system to test if rod formation was required in cells during stress, which indicates if and how targeting this pathway will be possible. We additionally looked at targeting the nuclear import and export properties of the cofilin protein, which directly affect rod formation and may be targetable in cofilin modifying drug discovery efforts. Overall, this work has described a specific and relevant pathway affected by mutant huntingtin and started the process of assessing this pathway as a therapeutic avenue for Huntington’s disease.

abstract: Doctor of Philosophy (PhD)