title: Feature-Oriented Design Pattern Detection in Object-Oriented Systems

contributor:
Sartipi, Kamran
Computing and Software

subject: feature-oriented, design pattern detection, object-oriented systems, two-phases, software

abstract:
 Identifying design pattern instances within an existing software system can support understanding and reuse of the system functionality. Moreover, incorporating behavioral features through task scenario into the design pattern recovery would enhance both the scalability of the process and the usefulness of the design pattern instances. In this context, we present a novel method for recovering design pattern instances from the implementation of system behavioral features through a semi-automatic and multi-phase reverse engineering
process.

 The proposed method consists of a feature-oriented dynamic analysis and
a two-phase design pattern detection process. The feature-oriented dynamic analysis works on the software system behavioral features' run-time information and produces a mapping between features and their realization at class level. In the two-phase design pattern detection process, we employ an approximate matching and a structural matching to detect the instances of the target design pattern described in our proposed Pattern Description Language (PDL), which is an XML-based design pattern description language. The correspondence between system features and the identified design pattern instances can
facilitate the construction of more reusable and configurable software components.
Our target application domain is an evolutionary development of software product line which emphasizes on reusing software artifacts to construct a reference architecture for several similar products. We have implemented a prototype toolkit and conducted experimentations on three versions of JHotDraw systems to evaluate our approach.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Leaders and Followers Among Security Analysts

contributor:
Veall, Mike
Kanagaretnam, K.
Statistics

subject: leaders, followers, security analysts, attributes, discriminant analysis, logistic regression model

abstract:
 We developed and tested procedures to rank the performance of security analysts according to the timeliness of their earning forecasts. We compared leaders and followers among analysts on various performance attributes, such as accuracy, boldness, experience, brokerage size and so on. We also use discriminant analysis and logistic regression model to examine what attributes have an effect on the classification. Further, we examined whether the timeliness of forecasts is related to their impact on stock prices. We found that the lead
analysts identified by the measure of forecast timeliness have a greater impact on stock price
than follower analysts. Our initial sample includes all firms on the Institutional Brokers
Estimate System (I/B/E/S) database and security return data on the daily CRSP file for the
years 1994 through 2003.

abstract: Thesis

abstract: Master of Science (MSc)


title: Relative Efficiency of Adjusted and Unadjusted Analyses when Baseline Data are Partially Missing

contributor:
Walter, Stephen
Statistics

subject: relative efficiency, adjusted, unadjusted, analyses, baseline data, missing, ANOVA

abstract:
 Many medical studies are performed to investigate the effectiveness of new treatments (such as new drugs, new surgery) versus traditional (or placebo) treatments. In many cases, researchers measure a continuous variable at baseline and again as an outcome assessed at follow up. The baseline measurement usually has strong relationship with post treatment measurement. Consequently, the ANCOVA model using baseline as covariate may provide more powerful and precise results than the ANOVA model.

 However, most epidemiologic studies will encounter the problem of missing covariate data. As a result, the patients with missing baseline measurements will be excluded from the data analysis. Hence, there exists a tradeoff between the ANOVA with full data set and the ANCOVA with partial data set.

 This study focuses on the variance of the estimator of treatment means difference. In practical situation, the standard error of the estimator obtained from the ANCOVA model with partially missing baseline relative to the standard error obtained form the
ANOVA with full data relies on the correlation between baseline and follow-up outcome, the proportion of the missing baseline, and the difference of the group means on the baseline. In moderate sample size studies, it is also affected by the sample size.

 The theoretically required minimum correlations for the ANCOVA model were calculated to obtain the same precision with the ANOVA model assuming the missing proportion, sample size and difference of group means on covariate are available. The minimum correlation can be obtained through checking the reference table or figures.

 The figures of asymptotic relative efficiencies provide the asymptotic variance and the length of the confidence intervals of the estimated difference obtained from the ANCOVA model relative to the ANOVA model for all the range of the correlation between baseline and follow up.

abstract: Thesis

abstract: Master of Science (MSc)


title: Reverse Engineering of Scientific Computation FORTRAN Code

contributor:
Carette, Jacques
Wassyng, Alan
Computing and Software

subject: reverse engineering, scientific computation, FORTRAN code, programming languages, algorithm

abstract:
 In this day and age, many companies struggle with the maintenance of legacy scientific
software systems written in outdated programming languages. These languages use low-level control structures, algorithmic operations and cumbersome syntax that make the true meaning of an algorithm difficult to understand. To make matters worse, the process of reverse engineering the algorithm to specification often involves a considerable amount of manual work which is error-prone and time-consuming.

 This thesis explores a completely automated method of reverse engineering. We apply this method to FORTRAN77 linear algebra software. This software is transformed to an extension of FORTRAN77, which we call Fortran-M. This language allows for high-level mathematical constructs such as sums, products and vector and matrix operations. To serve as a proof-of-concept for this method, we have developed a tool which uses a combination of pattern matching on the source code's abstract syntax tree to recognise low-level control structures, and symbolic analysis to determine the meaning of loops. Once a pattern has been recognised, or a loop's invariant found, we apply transformations to the syntax tree, thus creating a Fortran-M equivalent.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Time-Dependent Scaling Solutions in D Dimensional Supergravity

contributor:
Burgess, C.
Physics

subject: time-dependent, scaling, solutions, dimensional supergravity

abstract: We look for time-dependent solutions to a general class of supergravity models in an arbitrary amount of dimensions. Previously, many static solutions of these models have been found and studied, of which a subclass of these solutions support membrane-like configurations. While many properties of these solutions are known, their dynamics - and therefore stability - are not. We follow this motivation, and investigate the possibility of time dependent solutions that will also support this membrane configuration. Under various conditions, it turns out this is the case, bringing a better understanding to the stability of these branes. In addition, the form of the time dependence found suggest possible applications of supergravity to cosmological models.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Role of Feedback in Astrophysics

contributor:
Couchman, H. M. P.
Wadsley, J. W.
Physics and Astronomy

subject: role, feedback, astrophysics, energy, particle, artificial thermal conductivity, wave, fluid quantities

abstract:
 In very high resolution galaxy simulations, the supercomputers of today offer the possibility of enough resolution to capture the bubble of a supernova, though not the originating star itself. Modeling the energy released as originating from a single SPH particle initially arranged amongst a grid of particles requires the introduction of an artificial thermal conductivity term that allows the SPH method to resolve the thermal energy discontinuity inherently present in such a scenario. Such an artificial thermal conductivity is implemented in the SPH code GASOLINE. Resolution tests show that the method is insensitive to resolution changes when determining the radius of the Sedov-Taylor blast wave, and that the numerical solution agrees with the analytic prediction R = βE^1/5ρ0^-1/5t^2/5. The peak density at the shock is lower than the actual value of four times the ambient density, though it is found to scale with resolution. The density of the interior of the shock, near the center of the
supernova remnant is found to be elevated compared to the value expected from the Sedov-Taylor solution, but this too is resolution dependent, and with increased resolution the central density converges towards the expected value of zero. The fluid quantities pressure and velocity are also found to be in good agreement with the profiles predicted by the analytic solution.

abstract: Thesis

abstract: Master of Science (MSc)


title: Stellar Structure in Scalar-Tensor Gravity

contributor:
Burgess, Cliff
Physics and Astronomy

subject: stellar structure, scalar-tensor, gravity, Newtonian polytropes, mass, radius, density

abstract:
Stellar structure is investigated within the framework of scalar-tensor gravity. Novel
perturbative analytical results are obtained for constant-density stars and for Newtonian
polytropes in the quadratic model with coupling function A(Φ) = exp(αΦ+1/2βΦ^2). They are compared to full numerical calculations, and possible applications to main-sequence stars, white dwarfs, and the Chandrasekhar mass are indicated. It is found that Buchdahl's theorem is violated in Brans-Dicke theory for stars with exponentially-decaying density profiles. However, the mass-to-radius ratio M/R tends to the constant-density value in a certain limit. It is observed that for β < 0, there exists a maximum value of η = P0/ρo for constant-density stars, where P0 and ρ0 are the central pressure and density, respectively. It is conjectured that if such a maximum value also exists for other equations of state, and is less than the constant-density maximum value, then knowledge of P/ρ in the centre of a star can be used to constrain β.

abstract: Thesis

abstract: Master of Science (MSc)


title: Preparing Health Professions Students to Care for Older Adults: Exploring Experiences with an E-learning Course

contributor:
Jung, Bonny
Health Science Education

abstract:
As the population of older adults increases over the next 20 years, students in
health professions programs must be equipped with the knowledge, skills, and attitudes
required to care for older adults. Unfortunately, some students hold negative attitudes
towards older adults, which can negatively affect older patients. In order to prepare
students to provide care for older adults, this study piloted an e-learning course that
covered communication with older adults, common stereotypes of aging, and information
about the typical versus atypical aging processes.
The purpose of this thesis study was to explore the experiences of health
professions students with the course with respect to attitudes towards older adults and
collaborative care. A mixed methods design was used and participants were students
from health professions programs (medicine, occupational therapy, nursing). The initial,
quantitative strand sought to determine the influence of the course on attitudes towards
older adults, according to a geriatrics attitudes survey. The qualitative strand followed
with the intent to add meaning to the quantitative results; it explored participants’
experiences with the course and older adult care, and consisted of interviews with the
participants.
Although quantitative findings did not reveal a change in attitudes as measured by
the geriatric attitudes survey, the participants did report increased knowledge about older
adult care after completing the course. The participants’ experiences in older adult care
were consistent with theories in the literature, such as the informal curriculum in older
adult care. The participants also reported integrating knowledge from the course into their learning, which is encouraging as there is little evidence to show that online interventions
result in changes in behaviour and/or patient care. Overall, online interventions, such as
the course in this study, have the potential to improve older adult care through increased
knowledge about aging and collaborative care, and the translation of this knowledge into
practice.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
As the population of older adults increases, students in health professions
programs (medicine, occupational therapy, nursing, etc.) must be prepared to care for
older adults. Unfortunately, some students hold negative attitudes towards older adults,
which can negatively affect older patients. The purpose of this thesis was to explore
students’ experiences with an e-learning course that aimed to prepare them for older adult
care. The students completed a survey before and after the course to measure their
attitudes towards older adults. They were also interviewed about their experiences with
the course. Although quantitative findings did not reveal a change in attitudes, the course
did increase their knowledge about older adult care. Some of the students integrated this
knowledge with other learning experiences. Overall, this course has the potential to
improve older adult care by increasing health profession students’ knowledge about
aging, which might influence how they care for patients in practice.


title: Interdisciplinary Mental Health Professionals' Definition and Implementation of Evidence-Based Practices

contributor:
Law, Mary
Rehabilitation Science

subject:
Evidence-Based Practice
Mental Health
Interdisciplinary Treatment

abstract: Evidence-based practice was originally defined by Sackett et al. (1996) as the use of current research evidence, clinical expertise and client wishes in making clinical decisions.  To date, several studies have outlined facilitators and barriers to evidence-based practice implementation in mental health treatment settings.  Few have studied evidence-based practice implementation in interdisciplinary mental health treatment settings.  This research explored how clinicians working in interdisciplinary mental health treatment settings 1) define evidence-based practice, 2) report on factors influencing evidence-based practice implementation, and 3) perceive the promoters and barriers to evidence-based practice implementation.  This research analyzed data from three studies.  In the quantitative portion 233 clinicians participated in an online survey.  Descriptive results indicated that clinician scores for knowledge (understanding of and confidence in evidence based-practice) and attitude (positive opinion about evidence-based practice) were high.  However, descriptive results also indicated that scores for outcome (perceived impact of evidence-based practice) were moderate and scores for behaviour (frequency clinicians access research evidence) were low.  Further analysis showed that nearly 50% of evidence-based practice outcome was explained by education, profession, knowledge and attitude, and approximately 15% of clinician behaviour was explained by knowledge.  In the qualitative portion 8 clinicians were interviewed.  The results showed that half of the clinicians defined evidence-based practice as research evidence and the other half defined it as research evidence with clinical expertise and client preferences.  The interviews identified four components essential to evidence-based practice implementation: creating conditions; accessing evidence; motivating practice; reflecting critically.  The interviews also uncovered four tensions clinicians experienced central to evidence-based practice: valuing research evidence vs. clinical expertise; fidelity vs. customization; defining roles vs. role sharing; implementing evidence-based practice vs. managing clinical workload pressures.  The findings across the studies highlighted the importance of knowledge, evidence, access and time to optimize evidence-based practice implementation.  The results showed that evidence-based practice implementation could be facilitated by a more unified definition, clearer expectations on the part of clinicians and organizations, and a shift in focus from education to behaviour change and monitoring implementation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Evidence-based practice involves using research evidence to make decisions about client treatment.  The purpose of this project was to examine how different mental health professionals in the same setting define and implement evidence-based practice.  This research was conducted using two online surveys of over two hundred clinicians and face-to-face interviews with eight clinicians.  The surveys found that clinicians had an understanding of evidence-based practice and positive opinions about evidence-based practices but saw moderate impact of evidence-based practice and infrequency in searching for research evidence.  The research found that reasons for impact included: education, profession, knowledge and attitude. One cause for search infrequency was knowledge.  The interviews found that about half defined evidence-based practice as only research evidence and the other half as research evidence, clinician experience and client wishes.  The interviews also illuminated the process of putting evidence-based practice into place and some areas of tension.  Similarities across all of the research were the importance of knowledge, access to evidence and time to engage in evidence-based practice.


title: Optimization of Magnetic Susceptibility Measurements on Ultrathin Films

contributor:
Venus, D.
Physics

subject: optimization, magnetic susceptibility, measurements, ultrathin films, vibrations, plane, transverse

abstract:
The magnetic properties of ultrathin magnetic films can be investigated in situ by the temperature dependent magnetic ac susceptibility x(T) using an optical technique - the surface magneto-optic Kerr effect (SMOKE). The performance of the ac susceptibility measurements depends primarily on the optical setup used to detect the Kerr effect and on the mechanical stability of the system. Modifications to the optical setup and the sample holder have significantly reduced the influence of noise due to mechanical vibrations. It has
been found that the signal-to-noise ratio has been improved by at least a factor of 2.5 with respect to the previous setup, giving a detection limit of 15 nrad/Oe. This improvement makes measurements on antiferromagnetic ultrathin films feasible. Their susceptibility response has been estimated to be around 20-30 nrad/Oe. As a test study for the performance of the improved setup, transverse susceptibility measurements on 2 ML Fe/W(110) ferromagnetic ultrathin films are presented. These transverse susceptibility signals show interesting features. They have a narrow linewidth and are larger than expected from anisotropy considerations and other work. Also, it has been found that the in-plane and
out-of-plane transverse susceptibilities arise from different mechanisms. Several scenarios that might explain the origin, size and shape of the observed signals are discussed.

abstract: Thesis

abstract: Master of Science (MSc)


title: Metabolism First or Genes First? Investigation of Theories about the Origin of Life

contributor:
Higgs, Paul G.
Physics and Astronomy

subject: metabolism, genes, investigation, energies, theories, origin of life, molecules, inheritance, RNA

abstract:
 Popular theories about the origin of life can be classified to two classes: metabolism first or genes first. As a metabolism first theory, the lipid world theory, in which non-covalent assemblies of lipids, such as micelles and vesicles store information in the form of a non-random molecular composition, has been proposed to investigate the possibility of inheritance without genes. Our models assume that interaction occurs between nearest neighbour molecules only, and account for spatial segregation of molecules of different types within the assembly. We also draw a distinction between a self-assembly model, in which the composition is determined by mutually favourable interaction energies between the molecules, and a catalytic model, in which the composition is determined by mutually favourable catalysis. We show that compositional inheritance occurs in both models, although the self-assembly case seems more relevant if the molecules are simple lipids. In the case where the assemblies are composed of just two types of molecules, there is a strong analogy with the classic two-allele Moran model from population genetics. This highlights the parallel between compositional inheritance and genetic inheritance. We also investigated the polymerization reactions which may bridge the gap between simple organic molecules and the beginning of the RNA world,
which belongs to the class of genes first theories. We found that different from normal
chemical systems, catalysts for the polymerization system can shift the equilibrium
toward longer polymers. Together with RNA's potential as catalyst, the RNA polymerization system may form a feedback loop which makes the formation of functional RNA molecules easier, and come more close to the beginning of RNA world.

abstract: Thesis

abstract: Master of Science (MSc)


title: Validation and Inferential Methods for Distributional Form and Shape

contributor:
Balakrishnan, Narayanaswamy
Mathematics and Statistics

subject:
Operational risk
Goodness-of- fit
Limiting distributions
Convergence
Bump-hunting
Curvature
Kernel density estimation
Multimodality
Asymptotic properties of tests
Hypothesis testing
Monte Carlo methods
Point estimation

abstract: This thesis investigates some problems related to the form and shape of statistical distributions with the main focus on goodness of fit and bump hunting.  A bump is a distinctive characteristic of distributional shape. A search for bumps, or bump hunting, in a probability density function (PDF) has long been an important topic in statistical research. We introduce a new definition of a bump which relies on the notion of the curvature of a planar curve. We then propose a new method for bump hunting which is based on a kernel density estimator of the unknown PDF. The method gives not only the number of bumps but also the location of their centers and base points. In quantitative risk applications, the selection of distributions that properly capture upper tail behavior is essential for accurate modeling. We study tests of distributional form, or goodness-of-fit (GoF) tests, that assess simple hypotheses, i.e., when the parameters of the hypothesized distribution are completely specified. From theoretical and practical perspectives, we analyze the limiting properties of a family of weighted Cramér-von Mises GoF statistics W2 with weight function psi(t)=1/(1-t)^beta (for beta<=2) which focus on the upper tail. We demonstrate that W2 has no limiting distribution. For this reason, we provide a normalization of W2 that leads to a non-degenerate limiting distribution. Further, we study W2 for composite hypotheses, i.e., when distributional parameters must be estimated from a sample at hand. When the hypothesized distribution is heavy-tailed, we examine the finite sample properties of W2 under the Chen-Balakrishnan transformation that reduces the original GoF test (the direct test) to a test for normality (the indirect test). In particular, we compare the statistical level and power of the pairs of direct and indirect tests. We observe that decisions made by the direct and indirect tests agree well, and in many cases they become independent as sample size grows.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Field-Induced Phase Transitions of Block Copolymers

subject: field-induced, phase transitions, block copolymers, soft materials, ordered structures, linear response theory

abstract:
 Block copolymers are a class of soft materials which can self-assemble into a variety
of ordered structures. One method to induce new structures is the application of an external field such as an electric field. Previously, studies of the field-induced phase transitions are based on the assumption that the structural change follows certain symmetry pattern or simply using real-space numerical methods. The goal of the current project is to develop a simple analytic method to predict the structural change. Our approach is based on a linear response theory, in which the external field is taken as a perturbation and the lowest-order contribution to the solution is computed. We applied our method to the Landau-Brazovskii theory which is valid close to the order-disorder transition point of diblock copolymers. The result shows that there will be an additional term to the order parameter as a response to the
external field. The structural change can be predicted by a new Fourier expansion of the order parameter. As an example, we examined the structural change of a body-centered cubic phase under an applied electric field.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Model for a Fractionalized Quantum Spin Hall Effect

contributor:
Lee, Sung-Sik
Kallin, Catherine
Physics

subject: fractionalized, quantum spin hall effect, electron, Hubbard, bilayer, lattice

abstract:
 Effects of electron correlations on a two dimensional quantum spin Hall system are studied. We examine possible phases of a generalized Hubbard model on a bilayer honeycomb
lattice with a spin-orbit coupling and short range electron-electron repulsions at half filling, based on the slave rotor mean-field theory. The phase diagram of the model is found for a special case where the interlayer Coulomb repulsion is comparable to the intralayer Coulomb repulsion.

 Besides the conventional quantum spin Hall phase and a broken-symmetry insulating phase, we find a new phase, a fractionalized quantum spin Hall phase, where the quantum spin Hall effect arises for fractionalized spinons which carry only spin but not charge. Experimental manifestations of the exotic phase and effects of fluctuations beyond the saddle point approximation are also discussed.

 We finally study a toy Bose-Hubbard model for the charge sector of the theory to gain some insight into the phase diagram away from the special Coulomb repulsion values.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Novel Hybrid Aerial/Ground Mobile Manipulator

contributor:
Sirouspour, Shahin
Electrical and Computer Engineering

abstract: This research is concerned with the mechanical design of a mobile manipulating un- manned ground vehicle (MM-UGV) coupled with an existing commercial unmanned aerial vehicle (UAV) to create a novel hybrid aerial/ground mobile manipulator. A hybrid robotic system capable of manipulating in both aerial and ground environments is a new research direction for field robotics. The hybrid system has the potential of stimulating new research and engineering challenges as well as providing multipurpose robotic systems for industrial applications. A bilevel optimization-based strategy is presented for making important design choices, such as the selection of gear ratios, electric DC motors, manipulator link lengths, and UGV base length. The objective is to minimize the overall mass of the MM-UGV such that hybridization given certain constraints is possible. Constraints related to workspace, dynamic tip-over stability, actuator torque/force limits, and battery properties are incorporated into the formulation in order to ensure maneuverability of the system. Design specifications such as the expected range of end-effector forces, operating surface grade, and various position, velocity and acceleration variables are input to the optimization problem. The resulting problem is formulated as a robust mixed integer bilevel nonlinear program (MINBP), in which some of the constraints are derived from maximization/minimization over the operational variables to ensure constraint satisfaction in all possible ground/air operation scenarios. Optimizing over the operational variable space is a novel technique compared to current research that focuses on optimizing robotic mechanical components for a single trajectory. The Branch-and-Sandwich Bilevel optimization algorithm (BASBL) was used to find a solution to the optimization problem. A parallelized version of the algorithm was implemented and deployed on an IBM BladeCenter computer cluster. Speedup and parallel efficiency of the algorithm show significant improvement over the serial approach. Improving the run time of the optimization is critical for iterative engineering design with different input parameters. A prototype using an optimal set of design parameters is constructed and results of a preliminary flight experiment are reported. The proposed design optimization methodology is rather general and could be applied to other robotic systems.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Integrating Mass Spectrometry and Computational Chemistry: A Study of Dissociation Reactions of Radical Cations in the Gas Phase

contributor:
Terlouw, Johan K.
Chemistry

subject: mass spectrometry, computational chemistry, dissociation reactions, radical cations, gas phase, electron, ionization

abstract:
 The organic ions studied in this thesis were generated in the rarefied gas phase of the mass spectrometer by electron ionization of selected precursor molecules. The characterization of their structure and reactivity was probed by using a variety of tandem mass spectrometry techniques. These include metastable ion spectra to probe the dissociation chemistry of the low energy ions and collision experiments to establish the atom connectivity of the ions. The technique of neutralization-reionization mass spectrometry (NRMS) was used to probe the structure and stability of the neutral counterparts of the ions. Computational results involving the CBS-QB3 model chemistry formed an integral component in the interpretation of the experimental findings.

 The above approach was used to study proton-transport catalysis in the formaldehyde elimination from low energy 1,3-dihydroxyacetone radical cations. Solitary ketene-water ions, CH2=C(=O)OH2·+, do not readily isomerize into its more stable isomer, CH2=C(OH)2·+. A mechanistic analysis using the CBS-QB3 model chemistry shows that metastable 1,3-dihydroxyacetone radical cations will rearrange into hydrogen-bridged radical cations [CH2C(=O)O(H)-H•••OCH2]·+, where the CH2=O will catalyze the
transformation of CH2=C(=O)OH2·+ into CH2=C(OH)2·+.

 Metastable pyruvic acid radical cations, CH3C(=O)COOH·+, have been shown to undergo decarboxylation to yield m/z 44 ions, C2H4O·+, in competition with the formation of CH3C=O+ + COOH· by direct bond cleavage. Collision induced dissociation experiments agree with an earlier report that oxycarbene ions CH3COH·+ are formed but they also suggest the more stable isomer CH3C(H)=O·+ may be co-generated. Using the CBS-QB3 model chemistry, a mechanism is proposed to rationalize these results.

 Next, the isomeric ions CH3O-P=S·+ and CH3S-P=O·+ were characterized and differentiated by tandem mass spectrometry. Metastable CH3O-P=S·+ and CH3S-P=O·+ ions both spontaneously lose water to yield m/lz 74 cyclic product ion [-S-CH=]P·+. Using the CBS-QB3 model chemistry a mechanism is proposed for the water loss from CH3O-P=S·+ and CH3S-P=O·+. Our calculations also show that these two isomers communicate via a common intermediate, the distonic ion CH2S-P-OH·+, prior to the loss of water.

 The final component of this work details the computational study addressing the long standing question on the mechanism for the water elimination from metastable ethyl acetate radical cations. The CBS-QB3 results show that low energy ethyl acetate ions isomerize into ionized 4-hydroxy-2-butanone prior to the loss of water.

abstract: Thesis

abstract: Master of Science (MSc)


title: GLaDOS: Integrating Emotion-Based Behaviours into Non-Player Characters in Computer Role-Playing Games

type: Software Thesis

contributor:
Carette, Jacques
Computing and Software

subject:
Replayability
Non-Player Character Believability

abstract:
Non-Player Character (NPC) believability is a game aspect that can be exploited to increase a game's replayability, but little research has been conducted on the topic. One method for enhancing a NPC's believability is to integrate human-like behaviours into their design, so that they react to players in a realistic and interesting way. A large part of human behaviour can be explained by their emotions; therefore it was selected as the inspiration for the GLaDOS system.

Two psychological theories of emotion, Lazarus's cognitive appraisal and Plutchik's psycho-evolutionary synthesis, guided the design of the GLaDOS system, although several components are not unique to these theories. An implementation of the design was created as a "mod" for the popular CRPG "The Elder Scrolls V: Skyrim" to test its feasibility within the context of a commercial game. This task required an additional psychological model, PAD space, to map appraisal values to emotion codes and intensities. Feasibility testing was done via a user study to determine if the GLaDOS system increases player engagement when compared to the original game. While the objective analysis found that there were no significant differences between the two versions, subjective participant responses expressed a strong affinity for the GLaDOS system. Since player engagement is inherently subjective, it is encouraging to see positive responses from participants. This indicates that the GLaDOS system, and NPC believability in general, is one aspect of video games that has the potential to increase a game's replayability and should be investigated further.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Realistic video game characters are a desirable game component to increase a game's value. Even if the game's ending does not change, realistic character behaviours encourage players to replay a game multiple times to see what happens along the way. This is closer to tabletop games where players know the game's outcome, but still play because no two sessions are alike. Despite its advantages, few developments have been made towards realistic game characters. An easily recognizable factor of human decision-making and behaviour is emotion and integrating emotion into character design is one way to improve their realism. The GLaDOS system is a proof-of-concept product that incorporates psychological models of emotion into its design. To test its impact on player engagement, the system was implemented as an extension for the popular computer game "The Elder Scrolls V: Skyrim". Preliminary test results are promising and show that further development could prove fruitful.


title: THERMAL ENHANCEMENT OF BENTONITE-BASED GROUTING MATERIAL BY USING CARBON FIBERS IN GROUND HEAT PUMP SYSTEM

contributor:
GUO, PEIJUN
Civil Engineering

abstract:
With regard to the global climate changes, green energy and smart resource consumption are highly demanded. There is a great opportunity to make the applications of Ground Heat Pump Systems (GHPS) that take the advantage of green and renewable geothermal resources to save energy consumption, more popular.
In GHPS, the thermal performance of bentonite-based grouting material is a key factor that affects the system efficiency. This research focuses on the enhancement of thermal conductivity and specific heat capacity of bentonite-based grouting material by adding different types and volumetric fractions of carbon fiber. A standard bentonite-sand mix set as a baseline grout was used to assess the additives’ effect. Five carbon fiber types supplied by Asbury Carbons, AGM94-0.1mm/3mm/6mm, AGM95-6mm, and AGM99-0.15mm, were investigated in this research. The volumetric fractions of carbon fibers added to the baseline grout ranged from 0.5% to 1.25%.
The laboratory research results demonstrated that the grout thermal conductivity could be increased efficiently by adding higher volumetric percentage and longer carbon fibers. Also, it was found that the greater the fiber aspect ratio, the higher the grout thermal conductivity was. AGM94-6mm carbon fiber had the best enhancement effect on grout thermal performance among the five fibers, although shorter carbon fibers performed more consistently. AGM95-6mm carbon fiber had a similar performance to AGM94-3mm fiber due to their close aspect ratio and its relative softness. The addition of carbon fibers was not found affect the specific heat capacity of composite grouting material significantly.
A series of on-site bench scale experiments from McClymont & Rak Engineers Inc. was conducted for the potential industrial value of this composite grouting material in GHPS field. Numerical models of this bench scale experiment were also built and simulated using ABAQUS/CAE v6.14. The results were found to be consistent with what is obtained from the field experiments.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Architecture-Based Software Evolution: A Multi-Dimensional Approach

contributor:
Maibaum, Thomas S. E.
Computing and Software

subject: architecture, software, evolution, multi-dimensional, complexity, configuration

abstract:
 Software Evolution is unavoidable because software systems are subject to continuous change, continuing growth and increasing complexity. As software systems become mission-critical and large in size, the complexity in software development is now focused on software evolution rather than construction. In this work, we view a software system as an entity that is evolving throughout its lifetime, during development and maintenance. Based on a broad survey of software evolution approaches, we propose an architecture-based solution for
software evolution, which is defined in terms of evolution specific operations on architectural elements, that is, adding, removing, replacing components and (or) connectors, transforming configurations according to the required changes. In our view of software architectures, connectors are more likely to change since they are the architectural elements which reflect business rules. This work is focused on the evolution of connectors in architectures describing detailed design. Coordination contracts are introduced by Fiadeiro et al. as a realization of connectors at this detailed architecture level, which enables a three-layer architecture to separate concerns of components, connectors and configuration during evolution. Furthermore, to constrain the evolution in a predictable direction, we have established a matching scheme for justifying behavioral relationships between coordination contracts by specification matching based on pre- and postconditions of contracts and methods. A number of specification matches, with various degrees of similarity between the evolved and evolving
contracts, have been developed for system behaviors after evolution operations. Case studies are exhibited give a better understanding of these matches.

abstract: Thesis

abstract: Master of Science (MSc)


title: On The Practice of B-ing Earley

contributor:
Sekerinski, Emil
Computing and Software

subject: Earley's parsing algorithm, grammars, B-Method, Pascal program

abstract:
 Earley's parsing algorithm is an O(n^3) algorithm for parsing according to any context-free grammar. Its theoretical importance stems from the fact that it was one of the first algorithms to achieve this time bound, but it has also seen success in compiler-compilers,
theorem provers and natural language processing. It has an elegant structure, and its time complexity on restricted classes of grammars is often as good as specialized algorithms. Grammars with ϵ-productions, however, require special consideration, and have historically lead to inefficient and inelegant implementations.

 In this thesis, we develop the algorithm from specification using the B-Method. Through refinement steps, we arrive at a list-processing formulation, in which the problems with ϵ-productions emerge and can be understood. The development highlights the essential properties of the algorithm, and has also lead to the discovery of an implementation optimization. We end by giving a concept-test of the algorithm as a literate Pascal program.

abstract: Thesis

abstract: Master of Computer Science (MCS)


title: Algebraic Processors

contributor:
Farmer, William M.
Computer Science

subject: algebraic, processors, IMPS, algorithm, expressions, user-defined

abstract:
 Algebraic simplification is the task of reducing an algebraic expression to a simpler form without changing the meaning of the expression. Simplification is generally a difficult task and may have different meanings according to what the subject considers as "simple" . This thesis starts off by reverse-engineering the concept of algebraic processors in the IMPS interactive mathematical proof system - which is responsible for handling all the algebraic simplification tasks - and discusses its algorithm and usage in detail. Then it explores the idea of algebraic processors as generic programs that can be configured for any type of algebraic structure to simplify expressions of that type by first formalizing the theory of algebraic processors of IMPS and then extending it to provide solutions for related topics. Algebraic processors can be
defined for any user-defined algebra, as long as it conforms to the structure defined in this paper. The processors are defined as external units that can communicate with other mechanized mathematics systems in a trustable fashion and provide a program and a proof of correctness for any requests of simplification. Finally, some related processors such as one for simplification in partial orders and equivalence classes are outlined with some discussion of possible future expansions.

abstract: Thesis

abstract: Master of Science (MSc)


title: Metabolic Flexibility in Children with Obesity: Exercise as a Dynamic Stimulus to Assess Metabolic Health

contributor: Medical Sciences (Division of Physiology/Pharmacology)

abstract: The research in this thesis was completed to advance our knowledge about metabolic flexibility under exercise conditions in children with obesity. The primary objectives of the studies were to determine the validity and reliability of a novel metabolic flexibility test to screen for risk factors associated with type 2 diabetes, including impaired glucose tolerance, dysglycemia, and insulin resistance (Chapter 3 and Chapter 4), and to investigate the effect of 7 days of exercise training on insulin resistance and metabolic flexibility in children with obesity (Chapter 5). Compared to children with normal glucose tolerance, children identified with impaired glucose tolerance did not have reduced metabolic flexibility, which was measured by calculating exogenous carbohydrate oxidative efficiency during exercise (Chapter 3). Despite greater insulin resistance in the children with impaired glucose tolerance, metabolic flexibility was not significantly different between groups. Bivariate analyses showed that metabolic flexibility was not associated with fasting glucose, insulin resistance or beta-cell function in the entire group of participants (Chapter 4). However, when the children were separated by sex, metabolic flexibility was inversely associated with insulin resistance and directly associated with whole body insulin sensitivity index and beta-cell function in boys but not in girls (Chapter 4). The metabolic flexibility test demonstrated good reliability based on an intraclass correlation coefficient of 0.692 (Chapter 4). After 7 days of exercise training in a group of children with obesity, insulin resistance and metabolic flexibility did not improve as hypothesized (Chapter 5). An unexpected observation was the large inter-individual variability in these responses in the early stages of exercise therapy. Altogether, the studies presented in this thesis were the first to examine metabolic flexibility under exercise conditions at baseline and in response to exercise training in children. The studies were also the first to investigate the relationship of metabolic flexibility with fasting glucose and insulin resistance in children, and to assess the reliability of test results when repeating the non-invasive metabolic flexibility test on a separate day. By increasing our general knowledge of metabolic flexibility testing in children, we can better evaluate the clinical utility of the test to screen for risk factors associated with type 2 diabetes in the future.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: An Approach of Integration Testing for Object-Oriented Programs

contributor:
Maibaum, Tom
Computer Science

subject: integration testing, object-oriented programs, inheritance, polymorphism, UML, visual modeling, design

abstract:
 Object-oriented programs have many unique features that are not present in conventional programs, such as Inheritance, Polymorphism, Dynamic binding and Encapsulation, etc. Hence, testing object-oriented programs using only traditional techniques is unlikely to find the faults associated with these features. A study shows that approximately 40% of software errors can be traced to component interaction problems discovered during integration. Integration testing is an important part of the testing process. However, few integration testing techniques have been systematically studied or defined.

 The goal of this research is to develop an approach for automatic test case execution at the integration level. The approach is based on the concept of Coordination Contract, which was developed by J. Fiadeiro and L. Andrade. A coordination contract is a connection between a group of objects. Through contracts, rules and constraints are superposed on the behavior of the participants
without interfering with their implementation. Due to the contract's character, integration test case execution and test result evaluation are suitably implemented by contracts. A tool has been developed to automatically generate the relevant contracts to implement integration test cases generated by some mechanism for test case generation.

 In recent years, more and more software developers use the Unified Modeling Language (UML) and corresponding visual modeling tools to design and develop their application software. So we are using UML sequence diagrams and class diagrams as integration testing specifications. Actually, there
are few practical tools to generate test cases from UML, and even fewer tools to execute test cases. Therefore, the result of this research will play an important role in testing object-oriented programs at the integration level. Our accomplishment makes some progress in the integration testing for object-oriented programs.

abstract: Thesis

abstract: Master of Science (MSc)


title: Surface Currents in Chiral P-Wave Superconductors

contributor:
Kallin, C.
Physics

subject: surface currents, Chiral P-Wave superconductors, spontaneous magnetization, field distribution

abstract:
 It is believed that Sr2RuO4 is a triplet superconductor that breaks time reversal symmetry, and it is expected to have spontaneous magnetization both at the sample edge, as well as at domain walls. Recent magnetic microscopy results place upper limits on the magnetic fields differing from previous theoretical calculations by 2 orders of magnitude. Using a Ginzburg-Landau formalism we investigate the effects of a rough surface as well as parameter choices which differ from the typical weak coupling parameters on the magnitudes of the spontaneous supercurrents and magnetic fields. The dependance on surface roughness is found to be small resulting in only a 20% reduction for the weak coupling parameters. Changing the parameters from weak coupling in addition to pair breaking surface effects is also found to affect the magnitudes of the spontaneous fields weakly, except in certain unphysical parameter regimes. The effects of the surface stabilizing another non-magnetic
order parameter are considered, and give rise to field distributions with similar features to those present at domain walls.

abstract: Thesis

abstract: Master of Science (MSc)


title: Apply Modern Image Recognition Techniques with CUDA Implementation on Autonomous Systems

contributor:
Yan, Fengjun
Mechanical Engineering

subject: CUDA SURF FREAK Autonomous GPU

abstract:
Computer vision has been developed rapidly in the last few decades and it has been used in a variety of fields such as robotics, autonomous vehicles, traffic surveillance camera etc. nowadays. However, when we process these high-resolution raw materials from the cameras, it brings a heavy burden to the processors. Because of the physical architecture of the CPU, the pixels of the input image should be processed sequentially. So even if the computation capability of modern CPUs is increasing, it is still unable to make a decent performance in repeating one single work millions of times.
The objective of this thesis is to give an alternative solution to speed up the execution time of processing images through integrating popular image recognition algorithms (SURF and FREAK) on GPUs with the help of CUDA platform developed by NVIDIA, to speed up the recognition time.
The experiments were made to compare the performances between traditional CPU-only program and CUDA program, and the result show the algorithms running on CUDA platform have a significant speedup.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Rigid NON-Donor Pincer Ligands in Organoactinide Chemistry

contributor:
Emslie, David J H
Chemistry

subject:
organometallic chemistry
actinide chemistry
ligand design
uranium

abstract: The coordination- and organometallic chemistry of uranium complexes bearing the non-carbocyclic ancillary ligand XA2 (4,5-bis(2,6-diisopropylanilido)-2,7-di-tert-butyl-9,9-dimethylxanthene) has been developed as a major focus of this thesis. A number of air-sensitive actinide chloro complexes and alkyl derivatives featuring reactive An–C bonds were prepared, and investigated using a variety of structural and spectroscopic analytical techniques, including X-ray diffraction, NMR spectroscopy, elemental analysis, and electrochemical methods. The research described in this thesis serves to expand the currently underdeveloped, fundamental chemistry of actinide complexes supported by non-carbocyclic (i.e. non-cyclopentadienyl) ligands. For example, the use of the prototypical xanthene-based ligand XA2 has led to neutral dialkyl uranium(IV) complexes which a) react with alkyl anions to yield anionic trialkyl ‘ate’ complexes, b) C–H activate neutral pyridines to yield organouranium(IV) species featuring cyclometalated pyridine-based ligands, and c) react with Lewis acids to yield rare examples of cationic monoalkyl uranium(IV) complexes featuring coordinated arene ligands. By altering the nature of the arene solvent/ligand, latent catalytic ethylene polymerization behaviour has also been unlocked in cationic XA2 uranium and thorium complexes, and this development may offer industrial relevance. Additionally, new NON-donor ligand designs featuring bulky terphenyl-based substituents (the "XAT" ligand) as well as 1-adamantyl groups (the "XAd" ligand) have been developed; a family of crystallographically-characterized dipotassium XAT complexes have been prepared which feature unprecedented potassium–alkane interactions, and the XAd ligand has been employed for the development of new organometallic thorium chemistry. The developments described in this thesis contribute to an emerging field and delineate new reactivities and structural motifs, providing important steps forward in organoactinide chemistry.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Colourful Feasibility: Algorithms, Bounds and Implications

contributor:
Deza, Antoine
Terlaky, Tamás
Computing and Software

subject: colourful feasibility, algorithms, bounds, implications, linear combination

abstract:
 Given a point p and d + 1 sets (i.e., colours) of points in dimension d, the Colourful Feasibility Problem is to decide whether there are d + 1 points of different colours containing p in their convex hull; and if yes, find such a point set. The monochrome version of this problem, expressing p as a linear combination of d + 1 points in a set S, can be solved using traditional linear optimization algorithms. The Colourful Feasibility Problem was presented by
Bárány and Onn in 1997, and it is still not known if a polynomial-time algorithm exists. The case where we have d colours in dimension d and no restriction on the size of the sets has been shown to be strongly NP-complete through a reduction of 3-SAT. We define the core of a configuration to be the intersection of the convex hulls of each colour. We start from the important subcase that we call Colourful Core Feasibility Problem where we have d + 1 points of each colour, and p in the core. By Bárány's 1982 Colourful Caratheodory Theorem, a solution is guaranteed to exist, and the problem is to exhibit one. This problem is described by Bárány and Onn as "an outstanding problem on the border line between tractable and intractable problems". Besides applications to combinatorics, The Colourful Feasibility Problem models a situation where we want to select a set of points that is both diverse and representative.

 While we have not found out whether the Colourful Core Feasibility Problem can be solved in polynomial time, our contributions are on both the theoretical and practical performance of algorithms to solve the Colourful Feasibility Problem. The algorithms proposed by Bárány and Onn are essentially geometric, and the complexity guarantees depend crucially on having p inside the core. We consider modifications of these algorithms which update multiple colours at each stage, as well a greedy heuristic where we choose the adjacent simplex of maximum volume in each iteration and a random sampling approach. Our test suite includes unstructured random problems, ill-conditioned problems, problems with a restricted number of solutions and infeasible problems. We conclude that the most robust and nearly fastest algorithm for the Colourful Core Feasibility Problem is the multi-update variant which yields substantial gains over the original ones. Alternative approaches based on nondefinite quadratic optimization problem and positive semidefinite relaxation, and a combinatorial algorithm not depending on having p in the core are also introduced. Finally,
we give the first upper bound for the minimal number of colourful simplices containing a core point and the first improvement of the lower bound since Bárány's result in 1982.

abstract: Thesis

abstract: Master of Science (MSc)


title: Hyperplane Arrangements with Large Average Diameter

contributor:
Deza, Antoine
Computing and Software

subject: hyperplane arrangements, large average diameter, dimension, conjecture

abstract:
 This thesis deals with combinatorial properties of hyperplane arrangements. In particular, we address a conjecture of Deza, Terlaky and Zinchenko stating that the largest possible average diameter of a bounded cell of a simple hyperplane arrangement is not greater than the dimension. We prove that this conjecture is asymptotically tight in fixed dimension by constructing a family of hyperplane arrangements containing mostly cubical cells. The relationship with a result of Dedieu, Malajovich and Shub, the conjecture of Hirsch, and a
result of Haimovich are presented.

 We give the exact value of the largest possible average diameter for all simple arrangements in dimension two, for arrangements having at most the dimension plus two hyperplanes, and for arrangements having six hyperplanes
in dimension three. In dimension three, we strengthen the lower and upper bounds for the largest possible average diameter of a bounded cell of a simple hyperplane arrangements.

 Namely, let ΔA(n, d) denote the largest possible average diameter of a bounded cell of a simple arrangement defined by n hyperplanes in dimension d. We show that

• ΔA(n, 2) = 2[n/2] / (n-1)(n-2) for n ≥ 3,
• ΔA(d + 2, d) = 2d/d+1,
• ΔA(6, 3) = 2,
• 3 - 6/n-1 + 6([n/2]-2) / (n-1)(n-2)(n-3) ≤ ΔA(n, 3) ≤ 3 + 4(2n^2-16n+21) / 3(n-1)(n-2)(n-3)
• ΔA (n, d) ≥ 1 + (d-1)(n-d d)+(n-d)(n-d-1) for n ≥ 2d.
We also address another conjecture of Deza, Terlaky and Zinchenko stating that the minimum number Φ0A~(n, d) of facets belonging to exactly one bounded cell of a simple arrangement defined by n hyperplanes in dimension d is at least d (n-2 d-1). We show that
• Φ0A(n, 2) = 2(n - 1) for n ≥ 4,
• Φ0A~(n, 3) ≥ n(n-2)/3 +2 for n ≥ 5.
We present theoretical frameworks, including oriented matroids, and computational tools to check by complete enumeration the open conjectures for small instances. Preliminary computational results are given.

abstract: Thesis

abstract: Master of Science (MSc)


title: Effect of Support Conditions on the Behavior of Elastomeric Bearings

contributor:
Konstantinidis, Dimitrios
Civil Engineering

abstract:
Many seismic protection techniques have been suggested over the years to mitigate the damaging effects of earthquake shaking. Seismic isolation is an earthquake-resistant design approach where a horizontally flexible layer is introduced at the base of a structure to decouple the structure from the motion of the ground. This is achieved through the installation of special devices called isolators at the base of columns. The concept of using isolators as a practical method has evolved into reality with the development of multilayer elastomeric bearings.
The elastomeric bearings sometimes feature thick steel end plates and are connected to the superstructure and substructure by mechanical mean named bonded application. In buildings, traditional practice places the isolation system at the foundation level and calls for the construction of rigid diaphragms above and below. The flexural rigidity of these diaphragms prevents the isolators from experiencing rotations. However, in some application such as bridge applications, isolation of high-rise buildings and mid-height isolation, it is possible for elastomeric bearings to experience rotation. In another application, the bearings do not have end plates, and shear forces are transferred from the bearing to the superstructure and substructure by the frictional force that develops along the rubber-to--concrete or rubber-to-steel interface named unbonded application. This shear resistance is necessary to provide the bearing with an adequately large vertical stiffness. Since friction plays a dominant role in holding unbonded bearings in place, it is important to predict the effect of slip in this application.
The main objectives of this study are to investigate the rotation effects on the horizontal behavior of bonded elastomeric bearings and study the effect of slip on the vertical behavior of unbonded bearings. To provide a better understanding and quantitative characterization of the behavior of elastomeric isolators under combined loading, an extensive nonlinear 3D Finite Element Analysis (FEA) study has been done. Moreover, three mechanical models available in the literature were modified to capture the effect of rotation on the lateral behavior of elastomeric bearings. In addition, a new macro model to find the lateral stability limit proposed and the results were compared against FEA. In order to study the axial-shear-bending interaction in elastomeric bearings, a setup was built at Applied Dynamic Laboratory to conduct the experimental tests on a 1/4-scale circular bearing. Furthermore, to study the effect of slip on the vertical behavior of unbonded bearings, a closed--form solution including the effects of the elastomer’ s bulk compressibility was provided and compared against FEA result.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THE EFFECTS OF SYNAPSIN II KNOCK-DOWN IN THE RAT MEDIAL PREFRONTAL CORTEX ON ATTENTION

contributor:
Mishra, Ram
Neuroscience

subject:
Schizophrenia
Dopamine
Rodent Model
Hyperfrontality

abstract:
It has been estimated that approximately 300,000 Canadians are afflicted with
schizophrenia (SCZ). Due to the severity of symptoms as well as critical age of onset, the quality of life among SCZ patients can be poor; thus, further therapeutic research is of great interest. In addition to the more-common rodent models of SCZ (amphetamine sensitization, PCP sensitization, etc.), our lab has proposed the medial prefrontal cortex (mPFC) synapsin-II knockdown
(KD) model. Prior to this study, the cognitive effects of mPFC synapsin-II KD had yet to be
reported. Using a 14-day continuous infusion of antisense (AS) deoxyoligonucleotides for
synapsin-II to the mPFC, the results of the KD model have been recreated for further study. The 5-choice-serial-reaction-time-task was utilized to determine the effects of mPFC synapsin-II KD on attention and vigilance. In addition to reductions in both PPI (p<0.05) and social interaction
(p<0.05), as well as hyper-locomotion (p<0.05); rats treated with synapsin II AS performed
significantly worse on the 5-CSRTT than did control (mismatch/aCSF) animals. The AS animals
were significantly less likely to make correct responses (p<0.001), and significantly more likely to commit omissions (p<0.0001) and perseverative responses (p<0.05) than were control animals.
Additionally, an [18F]FDG tracer and PET/CT scans were used to determine differences
in brain metabolism due to synapsin-II KD. Results revealed significant reductions in [18F]FDG among AS treated rats (p<0.05) when compared to control animals. This reduction appeared to be a global result, however it followed 13-days of treatment which may account for the widespread effect. The mPFC synapsin-II KD model of SCZ has showcased cognitive and metabolic effects similar to that of SCZ. These findings, in conjunction with past research, provide evidence for the synapsin-II KD model as a viable rodent model of SCZ. Further research utilizing this model will provide valuable insight into the pathogenesis of SCZ and potential therapeutics.

abstract: Thesis

abstract: Master of Health Sciences (MSc)


title: An Acrotelm Transplant Experiment on a Cutover Peatland-Effects on Moisture Dynamics and CO2 Exchange

contributor:
Waddington, J. Michael
Geography

subject: acrotelm transplant, experiment, cutover peatland-effects, moisture, dynamics, CO2 exchange

abstract:
 Natural peatlands are an important component of the global carbon cycle representing a net long-term sink of atmospheric carbon dioxide (CO2). The natural carbon storage function of these ecosystems can be severely impacted due to peatland drainage and peat extraction leading to large and persistent sources of atmospheric CO2 following peat extraction abandonment. Moreover, the cutover peatland has a low and variable water table position and high soil-water tension at the surface which creates harsh ecological and microclimatic conditions for vegetation reestablishment, particularly peat-forming Sphagnum moss. Standard restoration techniques aim to restore the peatland to a carbon accumulating system through various water management techniques to improve hydrological conditions and by reintroducing Sphagnum at the surface. However, restoring the hydrology of peatlands can be expensive due to the cost of implementing the various restoration techniques. The goal of this study is to examine a new extraction-restoration technique where the acrotelm is preserved and replaced on the cutover surface. More specifically, this thesis examines the effects of an acrotelm transplant experiment on the hydrology (i.e. water table, soil moisture and soil-water
tension) and peatland-atmosphere CO2 exchange at a cutover peatland.

 The experimental acrotelm restoration technique maintained both high water table and moisture conditions providing sufficient water at the surface for Sphagnum moss. Furthermore, the high moisture conditions and low soil-water tensions compared to an adjacent natural site were maintained well above the measured critical Sphagnum threshold of 33% (-100 mb) VMC further providing favourable conditions for Sphagnum moss survival and growth.

 Peat respiration at the experimental restored acrotelm (110.5 g C m-2) was considerably lower than the natural peatland (144.8 and 203.7 g C m-2). However, gross ecosystem production (GEP) at the experimental site (-54.0 and -34.4 g C m-2) was significantly reduced compared to the natural site (-179.2 and -162.0 g C m-2). Consequently this resulted in a shift towards a net source of CO2 to the atmosphere over the season at the experimental site (78.5 and 56.5 g C m-2) and a sink of CO2 at the natural site (-17.6 and -22.8 g C m-2).

 Light response curves indicated that maximum GEP was considerably lower at the experimental site; however it is likely that the percentage of living and dead vegetation at the plots post restoration had a large control on this lower productivity as plots with more living vegetation had higher overall productivity (GEP). Despite wetter conditions at the experimental site, large diurnal variations in moisture (~30%) were observed suggesting disturbance to the peat structure. Although soil-water retention analysis and physical peat properties indicated that no apparent structural change in peat structure occurred, it is theorized that a change in volume in the capitula may enhance the wetting and drying cycles in moisture. Lateral expansion/contraction within the peat matrix may occur due to spaces (gaps/fissures) left between the replaced acrotelm blocks from the extraction-restoration process promoting large changes in moisture which consequently can affect the gas exchange process at the surface. Large changes in peat and capitual moisture have been shown to affect productivity leading to variable GEP and enhanced respiration, making it important to limit the moisture variability at the surface from a carbon cycling perspective. Therefore it is likely that a combination of both physiological health of the vegetation and wetting/drying cycles contributed to lower GEP, suggesting the importance of limiting disturbance at the surface during the extraction and restoration process.

 The new extraction-restoration technique has potential to return a peatland to both near-natural hydrological conditions and towards a net sink of atmospheric CO2. The replaced acrotelm on the cutover surface aided in maintaining adequate moisture conditions thereby provided adequate conditions for Sphagnum survival and reestablishment. However, the ability of the system to remain a net sink of CO2 as like the natural site was not observed post-disturbance due to differences in productivity. Nevertheless, the experimental site did maintain limited productivity post-extraction indicating that the carbon dynamics of the system was maintained due to this acrotelm restoration process potentially returning the ecosystem towards a natural sink of
atmospheric CO2 over a longer period time.

abstract: Thesis

abstract: Master of Science (MSc)


title: Meteorological Variations and their Impact on NO2 Concentrations in the Toronto-Hamilton Urban Air-Shed, Canada

contributor:
Arain, Altaf
Geography

subject: meteorological variations, NO2 concentrations, Toronto-Hamilton, Urban air-shed, pollution, health

abstract:
 Exposure to traffic-related air pollutants has been found to be damaging to human health. Nitrogen dioxide (NO2) levels, commonly used to indicate traffic-related pollution levels, vary significantly over small areas with higher levels found near sources such as major roads and industrial areas. The temporal and spatial variability in NO2 levels is partly caused by fluctuations in meteorological variables, and better understanding of these: meteorological influences can be used to enhance exposure assessment in health effects models.

 In this study, the interaction between measured hourly NO2 concentrations and climate variables at 11 locations in the Toronto-Hamilton Urban Airshed (THUAS) is examined. Analysis of meteorological data shows that two large urban heat islands (UHI) are present in the THUAS, centred on the downtown areas of Toronto and Hamilton. Lake breezes are found to occur frequently in the region, on up to 50% of summer days at lakeshore locations. These temperature and wind patterns influence NO2 and pollutant distributions. NO2 concentrations are highest in the early morning and late evening. Mean concentrations are highest in winter, although individual 1-hour NO2 concentrations are found to be highest in summer because of higher production rates. Wind direction is the strongest control on hourly NO2 concentration, and temperature and wind speed also have an effect. Seasonal variations in meteorology and emissions mean that the degree of spatial variability in NO2 concentrations changes from season-to-season in the THUAS resulting in variable exposure of urban populations.

 An attempt to improve an existing Land Use Regression (LUR) model, used for predicting nitrogen dioxide (NO2) concentrations and estimating human exposure, was made by incorporating high resolution interpolated observed up- and downwind effects of wind transport on NO2 concentrations around major roadways. Incorporation of observed wind direction effects in the LUR model slightly improved the accuracy of NO2 concentration estimates in densely populated, high traffic, and industrial/business areas in both Toronto and Hamilton. However the short-term nature of initial NO2 concentration data limits the utility of the model in light of the significant seasonal variation in climate parameters in the THUAS and their influence on NO2 transport and distribution.

abstract: Thesis

abstract: Master of Science (MSc)


title: Magnetic Properties of the Pyrochlore Ho2Ru2O7

subject: magnetic properties, pyrochlore, spin ice, lattice, tetrahedra, polycrystalline

abstract:
 In this thesis, we investigated a recent and interesting issue in magnetism; spin ice, which is a term used for systems where there is a analogy between their magnetic structure and the proton structure of water ice. Until now, only three spin ices, Dy2Ti2O7, Ho2Ti2O7, and Ho2Sn2O7, have been discovered. In 2002, Ho2Ru2O7 was proposed as a candidate spin ice by Bansal et al. Given the similar structure and experimental behaviors of Ho2Ru2O7 and known spin ice systems, it has been an issue whether Ho2Ru2O7 is the fourth spin ice.

 In order to determine whether the new candidate is spin ice or not, the magnetic
characteristics of Ho2Ru2O7 have been investigated. The frustrated system Ho2Ru2O7 has a pyrochlore structure with magnetic spins located on lattice of corner sharing tetrahedra. The crystal field originated <1 1 1> anisotropy of this sites and ferromagnetic interaction of spins give the preference of a two spin in and two spin out to a center of the tetrahedra.

 High quality polycrystalline samples were prepared and crystal growth attempts were made, then various measurements have been conducted. DC susceptibility data were used to determine the effective magnetic moment and value of Weiss temperature(θ). Zero field cooled (ZFC) and field cooled (FC) susceptibility data show a small irreversibility below 95K, which indicate ruthenium antiferromagnetic ordering. AC susceptibility measurements show a strong frequency dependence of the susceptibility which is a feature characteristic of spin glass or superparamagnetic materials.

 Specific heat experiments were conducted to also confirm the existence of Ru magnetic ordering at 95 K. The Debye temperature is estimated to be ~441 K.

 μSR measurements were conducted at TRIUMF. The measurements of Ho2Ru2O7 show signatures of ruthenium ordering near 95K and holmium near 1.4K. In agreement with previous neutron scattering experiment we conclude that the ground state of Ho2Ru2O7 is antiferromagnetic rather than spin ice. Presumably the ruthenium ordering acts to preclude the holmium moments entering the spin ice state.

abstract: Thesis

abstract: Master of Science (MSc)


title: k-Fold Systems of Projections and Congruence Modularity

contributor:
Valeriote, Matthew A.
Mathematics

subject: k-fold, systems of projections, congruence modularity, near-unanimity, finite

abstract: Bergman showed that systems of projections of algebras in a variety will satisfy a certain property if the variety has a near-unanimity term. The converse of this theorem was left open. This paper investigates this open question, and shows that in a locally finite variety, Bergman's Condition implies congruence modularity.

abstract: Thesis

abstract: Master of Science (MSc)


title: Origin of tRNA Genes in Trypanosoma and Leishmania and Comparison of Eukaryote Phylogenies Obtained from Mitochondrial rRNA and Protein Sequences

contributor:
Higgs, Paul G.
Theoretical Physics

subject: tRNA, rRNA, Trypanosoma, Leishmania, eukaryote, phylogenies, mitochondrial, protein sequences, genomes, cytoplasm

abstract:
 Two studies are presented in this thesis. First part is about the origin of tRNA genes in
Trypanosoma and Leishmania. These organisms have special mitochondrial DNA, termed kinetoplast DNA (kDNA), which is unique in its structure and function. kDNA is a massive network which is composed of thousands of connected DNA circles. Unlike most other mitochondrial genomes, there is no gene encoding tRNAs in their kDNAs. So all the tRNAs used in mitochondria must be encoded on nuclear genes and transported from the cytoplasm into the mitochondria. So our question of interest is where the tRNA genes in their nucleus come from. We carry out phylogenetic analysis of these genes and the corresponding ones in bacteria, mitochondria and eukaryotic nuclei. There is no evidence indicating gene transfer
from mitochondria to nucleus on the basis of this analysis. These results are consistent with the simplest hypothesis, i.e. that all tRNA genes of Trypanosoma and Leishmania have the same origin as nuclear genes of other eukaryotes.

 The second part is about the comparison of eukaryote phylogenies obtained from mitochondrial rRNA and protein sequences. We carried out phylogenetic analysis for the species which have complete mitochondrial genomes by using both concatenated mitochondrial rRNA and protein sequences. We got phylogenies for three groups, fungi/metazoan, plant/algae and stramenopile/alveolate group. The analysis is useful for the further study of position of the genetic code changes and the mechanisms involved.

abstract: Thesis

abstract: Master of Science (MSc)


title: Developing Platforms for Solid-Phase Bioaffinity Assays Using Nucleic Acid Aptamers

contributor:
Brennan, John
Chemical Biology

abstract: This thesis focuses on devising strategies for immobilizing nucleic acid aptamers on or in solid supports that improve their stability, availability for binding interactions and compatibility with emerging solid-phase bioanalysis applications.  The work begins with the entrapment of labile RNA-based aptamers within a sol-gel derived material for bio-immobilization without the need for extraneous binding molecules or complex conjugation procedures.  A hybrid organic-inorganic material provided the best matrix environment not only for RNA functionality but protection from both nuclease attack and chemical degradation, enhancing long-term stability when compared to solution.  To expand the application of aptamer/sol-gel biohybrids, rolling circle amplification was used to generate long DNA molecules containing concatemeric aptamer sequences.  A high-throughput screen was used to identify materials with macropores that allowed for minimal leaching and high activity and of the entrapped concatemeric DNA aptamers.  The optimal concatemer-entrapped material was used to make monolithic columns for flow-based detection of both small molecules and high molecular weight proteins, thus, broadening the range of analytes that can interact with sol-gel entrapped aptamers to include large macromolecules.  To further expand the utility of concatemeric aptamers, these large molecules were inkjet-printed as “bioinks” on paper as an alternative means of producing paper-based sensing devices in a simple and inexpensive manner.  The large structure of the concatemeric aptamer molecules allowed direct bio-immobilization through strong adsorption on cellulose without the need for surface conjugation or material entrapment.  Although these concatemers remained immobilized after liquid elution over the printing area, they retained sufficient segmental motion for target binding and signaling on the paper surface.  Patterning letters/symbols to create internally-referenced and multiplexed assays for both qualitative and quantitative detection of small molecules and proteins, demonstrated a generic platform for on-demand printing of aptamer-based solid-phase assays in the emerging field of paper-based sensors for on-site detection applications.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Nonparametric Kernel Estimation Methods Using Complex Survey Data

contributor:
Racine, Jeffrey
Economics

subject:
Nonparametric Econometrics
Complex Surveys

abstract: This dissertation provides a thorough overview of the use of nonparametric estimation methods for analyzing data collected by complex sampling plans. Applied econometric analysis is often performed using data collected from large-scale surveys, which use complex sampling plans in order to reduce administrative costs and increase the estimation efficiency for subgroups of the population. These sampling plans result in unequal inclusion probabilities across units in the population. If one is interested in estimating descriptive statistics, it is highly recommended that one uses an estimator that weights each observation by the inverse of the unit's probability of being included in the sample. If one is interested in estimating causal effects, a weighted estimator should be used if the sampling criterion is correlated with the error term. The sampling criterion is the variable used to design the sampling scheme. If it is correlated with the error term, sampling is said to be endogenous and, if ignored, leads to inconsistent estimation. I consider three distinct probability weighted estimators: i) a nonparametric kernel regression estimator; ii) a conditional probability distribution function estimator; and iii) a nonparametric instrumental variable regression estimator.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Sampled-Data Supervisory Control

contributor:
Leduc, Ryan
Software Engineering

subject: sampled-data, supervisory control, theoretical discrete-event systems, algorithms, binary decision diagrams

abstract:
This thesis focuses on issues related to implementing theoretical Discrete-Event Systems
(DES) supervisors, and the concurrency and timing delay issues involved. Sampled-data (SD) supervisory control deals with timed DES (TDES) systems where the supervisors will be implemented as SD controllers. An SD controller is driven by a periodic clock and sees the system as a series of inputs and outputs. On each clock edge (tick event), it samples its inputs, changes states, and updates its outputs. In this thesis, we identify a set of existing TDES properties that will be useful to our work, but not sufficient. We extend the TDES controllability definition to a new definition, SD controllability, which captures several new properties that will be useful in dealing with concurrency issues, as well as make it easier to translate a TDES supervisor into an SD controller. We then establish a formal representation of an SD controller as a Moore Finite State Machine (FSM), and describe how to translate a TDES supervisor to a FSM, as well as necessary properties to be able to do so. We discuss how to construct a single centralized controller, as well as a set of modular controllers and show that they will produce equivalent output. Next, we capture the enablement and forcing action of a translated controller in the form of a TDES supervisory control map, and show that the closed-loop behavior of this map and the plant is the same as that of the plant and the original TDES supervisor. We also show that our method is robust with respect to nonblocking and certain variations in the actual behavior of our physical system. We also introduce a set of predicate-based algorithms to verify the SD controllability property, as well as certain other conditions that we require. We have created
a software tool for verifying these conditions and provide the source code in the appendix. We have implemented these algorithms using binary decision diagrams (BDD). For illustrative purpose, we have produced a set of examples which fail the key conditions discussed in this thesis, as well as a successful application example based on a Flexible Manufacturing System. We also presented the corresponding FSM, translated from the example's supervisors.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Volumes of Balls in Grassmann Manifolds with Applications to Coding Theory

contributor:
Min-Oo, Maung
Mathematics

subject: volumes of balls, Grassmann manifolds, applications, coding theory, algorithm

abstract:
 This thesis develops the Riemannian Geometry of the real and complex Grassmann Manifolds in a notationally accessible way. The canonical volume form is related to explicit
Jacobi Field calculations. The implementation of a packing algorithm based on repulsive
forces is proposed. Standard packing bounds and bounds on the volumes of geodesic balls
are used to test the performance of the algorithm.

abstract: Thesis

abstract: Master of Science (MSc)


title: Atomic Excitation Caused by α-Decay of the Nucleus

contributor:
van Dijk, W.
Nogami, Y.
Physics and Astronomy

subject: atomic excitation, α-Decay, nucleus, particle, quantum

abstract:
 The prevailing theory of Migdal for predicting the excitation probabilities of an atom from α-decay of the nucleus, considers the α-particle, after it has been emitted by the nucleus, as following a classical trajectory and interacting with the atom quantum mechanically. Recently an attempt was made to properly model this quantum mechanical phenomenon, in one dimension, with a quantum wavefunction treatment of the decaying α-particle, but a discrepancy was found between the new predictions and that of the traditional method. In light of this discrepancy, we have studied the various approximations made in that work. Our
results concur with recent follow up work suggesting that agreement should be found between a fully quantum mechanical model and with the classical model of α-particle propagation where the α-particle is treated as a point particle.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigations of the Microbial Communities of the Respiratory Tract in the Elderly and in Cystic Fibrosis via Culture-Dependent and -Independent Approaches

contributor:
Surette, Michael G
Biochemistry and Biomedical Sciences

abstract: The human microbiota is the collection of microorganisms which live on and in the human body. These organisms have been implicated in a host of diseases and disorders and nationwide initiatives have helped us understand their heterogeneity across the population in health. In this work, I investigate the respiratory tract microbiota and its correlations in age and disease. Elderly (≥ 65 years of age) are at a greater risk of respiratory infection; previous studies have shown changes to the elderly gut microbiota which correlate with the health of these individuals. Thus, we investigated the upper respiratory tract in comparison to mid-aged adults to identify statistically different communities within the anterior nares and oropharynx which may be associated with increased respiratory infection risk in this population. Individuals with cystic fibrosis have a lung microbiota which contributes to the onset of pulmonary exacerbations, increased inflammation, which is the greatest cause of patient mortality. However, it is not understood what triggers these events. In this work, we used 16S rRNA gene sequencing to longitudinally identify the lung microbiota in a subset of patients but were unable to identify any consistent correlations in the lung microbiota and pulmonary exacerbation onset. In order to gain a better resolution of these communities, we combined culture-independent sequencing technology with culture-enrichment. We showed that 81.21% of OTUs representing 99.15% of the biomass of the cystic fibrosis lung is culturable and that metagenomic sequencing of these cultured communities provide better taxonomic resolution of the cystic fibrosis lung. Together, this work shows the contributions of the respiratory tract microbiota in age and disease.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The microbes that live on and in us affect our health and can cause disease. Within, I investigate the association of these microbes in the airways. First, we show that the microbes in the noses and throats of the elderly differ from adults. We hypothesize that these differences may be associated with the increased incidence of respiratory infections, such as pneumonia and influenza, in this population. Second, we study the microorganisms that inhabit the lungs of individuals with cystic fibrosis. The bacteria of the lungs are the main cause of disease. In our study, we attempt to identify why these patients go through cycles of extreme sickness and hospitalization, but we were unable to find a cause of this in the microbiota. A follow up study using new techniques provided us with a better resolution of these communities which will help us better understand cystic fibrosis.


title: An Experimental Implementation of Action-Based Concurrency

contributor:
Sekerinski, Emil
Computing and Software

subject: experimental implementation, action-based, concurrency, objects, ABC Pascal, programming, one-pass compiler, assemble code

abstract:
This thesis reports on an implementation of an action-based model for concurrent
programming. Concurrency is expressed by allowing objects to have actions with a guard and a body. Each action has its own execution context, and concurrent execution is realized when program execution is happening in more than one context at a time. Two actions of different objects can run concurrently, and they are synchronized whenever a shared object is accessed simultaneously by both actions. The appeal of this model is that it allows a conceptually simple framework for designing and analyzing concurrent programs. To experiment with action-based concurrency, we present a small language, ABC Pascal, which is an experimental attempt as a proof of feasibility of such a model, and also meant to help identify issues for achieving reasonable efficiency in implementation. It extends a subset of Pascal that supports basic sequential programming constructs, and provides action-based concurrency as the action-based model prescribes. This work deals with the specification and implementation of ABC Pascal. The one-pass compiler directly generates assembly code, without devoting efforts to optimization. While the code is not optimized, the results that ABC Pascal has achieved in performance testing are so far comparable to mainstream concurrent programming languages.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Total Progeny of a Multitype Branching Process

contributor:
Hoppe, Fred M.
Statistics

subject: total progeny, multitype branching process, matrix theory, functions

abstract: Techniques from algebra and matrix theory are employed to study the total progeny of a multitype branching process from the point of probability generating functions. A result for the total progeny of different types of individuals having identical offspring distribution is developed, which extends the classic Dwass formula from single case to multitype case. An example with Poisson distributed offspring having different distributions of children is given to illustrate that total progeny does not preserve similar structure as Dwass' formula in general.

abstract: Thesis

abstract: Master of Science (MSc)


title: 30S Beam Development and the 30S Waiting Point in Type I X-Ray Bursts

contributor:
Chen, Alan A.
Physics and Astronomy

subject: beam development, waiting point, Type I x-rays bursts, energy generation, radionuclide, particle

abstract:
Nuclear physics tells us a lot about astrophysics, particularly the energy generation in stars. The present work is a thesis in experimental nuclear physics, reporting the results of 30S radioactive beam development for a future experiment directly measuring data to extrapolate the 30S(α,p) stellar reaction rate in Type I X-ray bursts, a phenomena where nuclear explosions occur repeatedly on the surface of accreting neutron stars. On the astrophysics side, the work details basic stellar physics and stellar reaction formalism in Chapter 1, the behaviour of compact stars in Chapter 2, and a full literature review of Type I X-ray bursts in Chapter 3. Nuclear experiments are non-trivial, and the results reported here were not accomplished by the author alone. Stable-beam experiments are technically challenging and involved, but for the case at hand, the halflife of 30S is a mere 1.178 seconds, and in order to measure reaction cross-sections, we must make a beam of
the radionuclide 30S in situ and use these rare nuclei immediately in our measurement.
Particle accelerator technology and radioactive ion production are treated in Chapter 4, and the experimental facility and nuclear measurement techniques are discussed in some detail in Chapter 5. In order to perform a successful future experiment which allows us to calculate the stellar 30S(α, p) reaction rate, calculations indicate we require a 30S beam of
~ 10^5 particles per second at ~ 32 MeV. Based on our recent beam development experiments in 2006 and 2008, it is believed that such a beam may be fabricated in 2009 according to the results presented in Chapters 6 and 7. We plan to measure the 4He(30S,p) cross-section at astrophysical energies in 2009, and some remarks on the planned (α,p) technique are also elucidated in Chapters 5, 6 and 7.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Characterization of Pulse Front Tilt and Spatial Dispersion in 800 NM Femtosecond Lasers

contributor:
Haugen, Harold K.
Physics

subject: characterization, pulse front tilt, spatial dispersion, 800 nm, femtosecond lasers, distortions

abstract:
 This thesis presents a study of diagnostics of pulsed laser systems. Two simple and cost effective devices are constructed that measure common spatio-temporal distortions. The first is a spectrally-resolved knife-edge (SRKE) for spatially and spectrally resolving a laser beam, which enables spatio-temporal distortions to be measured. The second is an interferometric
autocorrelation taken with a 2-photon diode. A lens is used to focus light from the entire cross section of the beam onto the diode. By scanning the diode through the focus, the effects of pulse-front-tilt on focused beam pulse durations can be measured. These techniques are compared with current theoretical models, and with each other, to establish their reliability and practicality, as well as the reliability of the commercial techniques. SRKE is found to be highly sensitive to spatial and angular dispersion, and also able to measure the frequency gradient, although not as precisely. Interferometric autocorrelation is only able to resolve effects on duration. It can detect the presence of significant spatio-temporal distortion, but several scans must be taken as a function of distance from the lens, through the focus.

 A commercially built GRENOUILLE was also tested on pulses compressed with a hollow-capillary-prism pulse compressor. Compression of 800 nm, 50 fs pulses to less than 19 fs was achieved with an overall transmission efficiency of 33%. With further work, efficiency could be increased, and pulse duration decreased.

abstract: Thesis

abstract: Master of Science (MSc)


title: STRUCTURAL FACTORIZATION OF SQUARES IN STRINGS

contributor:
Deza, Antoine
Franek, Frantisek
Computational Engineering and Science

subject:
double square
factorization
inversion factor

abstract:
A balanced double square in a string x consists of two squares starting
in the same position and of comparable lengths. We present a unique fac-
torization of the longer square into primitive components refereed to as the
canonical factorization and analyze its properties. In particular, we examine
the inversion factors and the right and left inversion subfactors. All three
substrings are collectively referred to as rare factors as they occur only twice
in a signi cant portion of the larger square. The inversion factors were es-
sential for determining the classi cation of mutual con gurations of double
squares and thus providing the best-to-date upper bound of 11n=6 for the
number of distinct squares in a string of length n  by Deza, Franek,
and Thierry. The right and left inversion subfactors have the advantage of
being half the length of the inversion factors, thus providing a stronger dis-
crimination property for a possible third square. This part of the thesis was
published  by Bai, Franek, and Smyth.
The canonical factorization and the right and left inversion subfactors are
used to formulate and prove a signi cantly stronger version of the New Periodicity Lemma by Fan, Puglisi, Smyth, and Turpin, 2006, that basically
restricts what kind of a third square can exists in a balanced double square.
This part of the thesis was published by Bai, Franek, and Smyth.
The canonical factorization and the inversion factors are applied to for-
mulate and prove a stronger version of the Three Squares Lemma by
Crochemore and Rytter. This part of the thesis was published by Bai,
Deza, and Franek.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Source apportionment of polycyclic aromatic hydrocarbons in diverse environmental media using receptor and physico-chemical models

contributor:
McCarry, B. E.
Chemistry

subject:
polycyclic aromatic
hydrocarbons
receptor
physico-chemical
environmental media

abstract: This thesis focused on the interpretation of environmental data obtained from chemical analyses of complex and divergent environmental media. Environmental monitoring of pollutants yields large datasets which may be difficult to process using simplistic univariate approaches. Polycyclic aromatic hydrocarbons (PAH) are environmental organic contaminants that have important health implications and are ubiquitous in the environment. These compounds are regularly monitored in all environmental compartments but delineating their impacting sources from analytical data is usually challenging and thus not routinely attempted. The work contained in this thesis discusses how source information can be obtained by the application of (a) qualitative relationships, (b) physico-chemical models dealing with phase change and partitioning, as well as (c) receptor models using factor analysis to P AH data collected in samples from the atmosphere and in suspended sediments. There are unique concepts and new applications embodied in this thesis. They include: (a) The development and definition of a new diagnostic relationship that discriminates between industrial and urban sources of P AH, (b) the integration of qualitative diagnostic correlations with measured concentration data to improve the diagnostic potential of these simple non-multivariate relationships, (c) the integration of local meteorological data with receptor modeling using factor analysis to explicitly identify impacting PAH source regions, and finally (d) the first known instance of the use of a hybridized receptor modeling methodology to explicitly identify, quantify and spatially map the potential source regions of P AH on a hemispheric scale. An additional effect of the work contained herein is that it shows how much information which could be useful to environmentalists and policy-makers in designing effective abatement and control strategies if available is usually left un-extracted from environmental monitoring activities.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)