title: Generalized Methods for User-Centered Brain-Computer Interfacing

contributor:
Becker, Suzanna
Computational Engineering and Science

subject:
brain-computer interface
electroencephalography
mental imagery
neurofeedback
human learning
coadaptation
signal processing
machine learning

abstract:
Brain-computer interfaces (BCIs) create a new form of communication and control for humans by translating brain activity directly into actions performed by a computer. This new field of research, best known for its breakthroughs in enabling fully paralyzed or locked-in patients to communicate and control simple devices, has resulted in a variety of remarkable technological developments. However, the field is still in its infancy, and facilitating control of a computer application via thought in a broader context involves a number of a challenges that have not yet been met.

Advancing BCIs beyond the experimental phase continues to be a struggle. End-users have rarely been reached, except for in the case of a few highly specialized applications which require continual involvement of BCI experts. While these applications are profoundly beneficial for the patients they serve, the potential for BCIs is much broader in scope and powerful in effect. Unfortunately, the current approaches to brain-computer interfacing research have not been able to address the primary limitations in the field: the poor reliability of most BCIs and the highly variable performance across individuals. In addition to this, the modes of control available to users tend to be restrictive and unintuitive (\emph{e.g.}, imagining complex motor activities to answer ``Yes" or ``No" questions). This thesis presents a novel approach that addresses both of these limitations simultaneously.

Brain-computer interfacing is currently viewed primarily as a machine learning problem, wherein the computer must learn the patterns of brain activity associated with a user's mental commands. In order to simplify this problem, researchers often restrict mental commands to those which are well characterized and easily distinguishable based on \emph{a priori} knowledge about their corresponding neural correlates. However, this approach does not fully recognize two properties of a BCI which makes it unique to other human-computer interfaces. First, individuals can vary widely with respect to the patterns of activation associated with how their brains generate similar mental activity and with respect to which kinds of mental activity have been most trained due to life experience. Thus, it is not surprising that BCIs based on predefined neural correlates perform inconsistently for different users. Second, for a BCI to perform well, the human and the computer must become a cohesive unit such that the computer can adapt as the user's brain naturally changes over time and while the user learns to make their mental commands more consistent and distinguishable given feedback from the computer. This not only implies that BCI use is a skill that must be developed, honed, and maintained in relation to the computer's algorithms, but that the human is the fundamental component of the system in a way that makes human learning just as important as machine learning.

In this thesis it is proposed that, in the long term, a generalized BCI that can discover the appropriate neural correlates of individualized mental commands is preferable to the traditional approach. Generalization across mental strategies allows each individual to make better use of their own experience and cognitive abilities in order to interact with BCIs in a more free and intuitive way. It is further argued that in addition to generalization, it is necessary to develop improved training protocols respecting the potential of the user to learn to effectively modulate their own brain activity for BCI use. It is shown through a series of studies exploring generalized BCI methods, the influence of prior non-BCI training on BCI performance, and novel methods for training individuals to control their own brain activity, that this new approach based on balancing the roles of the user and the computer according to their respective capabilities is a promising avenue for advancing brain-computer interfacing towards a broader array of applications usable by the general population.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: La bataille entre la vengeance, la justice et le destin: une étude du personnage mythologique, Electre, de l'antiquité jusqu'au théâtre moderne.

contributor:
Stout, John
French

subject: Electre, mythologie, vengeance, destin, justice, religion, readaptation d'un mythe, eschyle, euripide, giraudoux, sartre

abstract:
In this thesis, I will be looking at the different adaptations of the myth of Electra, throughout time, by studying the following plays: Les Choéphores by Aeschylus, Electre by Euripides, Electre by Giraudoux and Les Mouches by Sartre. The purpose of this thesis is to examine why the character of Electra has sparked so many different versions and adaptations. The thesis discusses the evolution of her character over time and also, the main ideas authors have introduced through their renditions.
	I have shown that with Aeschylus, his primary goal was to write in honour of the god Dionysis, and his entire play centers around praising the gods and following their destiny for humans blindly, without questioning it and without fearing another god’s wrath. Euripides’s play was written to mock that of his predecessor and to portray Electra as the symbol of blind vengeance. I then look at the Electra of Giraudoux where the author suggests that Electra is the symbol of absolute justice and that political rulers should sacrifice their own well-being for that of the nation of which they are in charge. Finally, I study Les Mouches by Sartre, who used his play as a work of resistance against the Occupation in France in the 1940s. His play conveys his existentialist thought strongly and is meant to show the French that despite their defeat, that their liberty would stay intact.
Throughout this study, it is evident that Electra is a timeless character which each author has used and molded to convey his own thoughts and ideas, whether they be religious, political or philosophical. Electra stands as a symbol for many things, but the regard in which she is held is up to the author to portray, according to his intent.

abstract: Thesis

abstract: Master of Arts (MA)


title: GAME THEORETIC APPROACHES TO PETROLEUM REFINERY PRODUCTION PLANNING – A JUSTIFICATION FOR THE ENTERPRISE LEVEL OPTIMIZATION OF PRODUCTION PLANNING

contributor:
Mahalec, Vladimir
Chemical Engineering

subject:
Optimization
Production planning
Game theory
Potential game
Mixed Integer Nonlinear Programming

abstract: This thesis presents frameworks for the optimal strategic production planning of petroleum refineries operating in competition in multiple markets. The game theoretic concept of the Cournot oligopoly is used as the basic competitive model, and the Nash equilibrium as the solution concept for the formulated problems, which are reformulated into potential games. Nonlinear programming potential game frameworks are developed for static and dynamic production planning problems, as well for mixed integer nonlinear expansion planning problems in which refiners have access to potential upgrades increasing their competitiveness. This latter model represents a novel problem in game theory as it contains both integer and continuous variables and thus must satisfy both discrete and continuous mathematical definitions of the Nash equilibrium. The concept of the mixed-integer game is introduced to explore this problem and the theoretical properties of the new class of games, for which conditions are identified defining when a class of two-player games will possess Nash equilibria in pure strategies, and conjectures offered regarding the properties of larger problems and the class as a whole. In all examples, petroleum refinery problems are solved to optimality (equilibrium) to illustrate the competitive utility of the mathematical frameworks. The primary benefit of such frameworks is the incorporation of the influence of market supply and demand on refinery profits, resulting in rational driving forces in the underlying production planning problems. These results are used to justify the development of frameworks for enterprise optimization as a means of decision making in competitive industries.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: This thesis presents a mathematical framework in which refinery production planning problems are solved to optimal solutions in competing scenarios. Concepts from game theory are used to formulate these competitive problems into mathematical programs under single objective functions which coordinate the interests of the competing refiners. Several different cases are considered presenting refinery planning problems as static and dynamic programs in which decisions are time independent or dependent, respectively. A theoretical development is also presented in the concept of the mixed integer game, a game theoretic problem containing both continuous and discrete valued variables and which must satisfy both continuous and discrete definitions of Nash equilibrium. This latter development is used to examine refinery problems in which individual refiners have access to numerous unit upgrades which can potentially improve performance. The results are used to justify a game theoretic approach to enterprise optimization.


title: Microbial Secondary Metabolomics for Natural Product Discovery: Development of metabolomic tools and strategies for the discovery of specialized metabolites from bacteria and endophytic fungi.

contributor:
McCarry, Brian E.
Capretta, Alfredo
Chemistry and Chemical Biology

subject:
Natural Product Discovery
Metabolomics
Bioanalytical Chemistry
Natural Products Chemistry
Mass Spectrometry
NMR
Nonribosomal Peptides
Polyketides
Small Molecule Characterization
Endophytes
Chemoinformatics
Bioinformatics
Drug Discovery
Antimicrobials

abstract: Microbial natural products have been a source for new drugs for many decades and are unrivaled in their capacity to generate not only future therapeutic agents, but also providing key agents for agricultural and industrial use. LC-MS/MS based metabolomic tools and technologies have been developed that can rapidly dereplicate nonribosomal peptides and statistically identify related congeners in an automated nontargeted process from complex natural product extracts with nanogram sensitivity. This data-base search approach is designed to handle linear, cyclic and cyclic-branched nonribosomal peptides from proteinogenic and nonproteinogenic amino acids without genomic data or traditional bioactivity directed fractionation. Chemometric work-flows combined with a comprehensive metabolomic guided discovery strategy were used to profile the chemical space of a diverse collection of understudied fungal endophytes from fruiting plants. This approach allowed for the prioritization of unique isolates and for the focused discovery, isolation and characterization of distinct outlier metabolites by LC-SPE, 1D and 2D NMR, HRMS and single crystal X-ray analysis. These metabolomic tools and strategies have led to the discovery and characterization of 35 new and over 40 known natural products, many of which are biologically active. This thesis with enabling metabolomic tools and novel discoveries has demonstrated the utility of these analytical methodologies as an effective strategy for the untargeted discovery of new natural products from bacteria and endophytic fungi.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Neoliberal Space, Place and Subjectivity in Zadie Smith's NW

contributor:
Brophy, Sarah
English and Cultural Studies

subject: Zadie Smith, Neoliberalism, space, place, class, race, subjectivity, affect, phenomenology

abstract:
Following the literary criticism of Zadie Smith’s NW by critics such as Lynn Wells and Wendy Knepper, this thesis seeks to engage with the social scripts and spatial dynamics of Smith’s fourth novel. I argue that NW is concerned with the neoliberalization of both real and virtual spaces, emphasizing the consequent effects of neoliberalism on agency and subjectivity and highlighting the neoliberal advancement of hyperindividualism and securitization over social responsibility and solidarity. Much detail is given to NW’s exploration of race, class and social mobility at the tail-end of the global financial crisis of 2007-08. NW’s fragmented four-part narrative channels a perspectival approach to space and place by delineating its structure through the four separate subjectivities of the main characters.
	I contextualize my thesis alongside Paul Gilroy’s cultural criticism of contemporary British multiculturalism, conviviality and melancholia, while also anchoring NW’s spatial concerns to Jeff Malpas’s spatial philosophy and Emily Cuming’s explication of British council estates in various forms of contemporary literature. As well, this thesis incorporates the philosophical frameworks of Søren Kierkegaard, Martin Heidegger and Maurice Merleau-Ponty as a guide for recognizing some of NW’s interest in the subjective experience of people and spaces, and to reorient the act of ‘seeing’ as a radical form of agency and mediation in itself. Ultimately, this phenomenological and epistemological approach to interpreting Smith’s fiction creates the potential for meaning to be co-constructed between author and reader, forming a new social vision for the novel as artform.

abstract: Thesis

abstract: Master of Arts (MA)


title: Offspring cannibalism and parental care in the plainfin midshipman fish

contributor:
Balshine, Sigal
Psychology

subject:
Behaviour
Ecology
Evolution
Parental Care
Cannibalism
Fish
Marine
Intertidal

abstract: Cannibalism of offspring is a common yet seemingly paradoxical phenomenon observed across a wide variety of taxa. Behavioural ecologists have been particularly interested in understanding this behaviour within the context of parental care. This is because, superficially, offspring cannibalism appears counterproductive to the goals of a caring parent, which are often achieved by nurturing and protecting their young. Despite the prevalence of offspring cannibalism in many taxa, we still have a poor evolutionary understanding of this intriguing behaviour. Many hypotheses have been proposed explaining why parents may terminate and consume offspring, however, empirical tests of these hypotheses frequently return mixed results, and few examples exist in which multiple hypotheses for cannibalism have been tested using the same model study system. Over the course of my PhD thesis, I tested different cannibalism hypotheses in a novel study organism, the plainfin midshipman fish (Porichthys notatus), a species of paternal care-giving toadfish that frequently engages in offspring cannibalism. I first characterized the factors that underlie male reproductive success in this species to provide a broader understanding of their reproductive ecology and a background for the cannibalism studies in my later chapters. I showed that both male size and nest size are important correlates of male reproductive success (e.g. mate attraction, egg acquisition, and rearing success) in this system, and that morphological, physiological, and ecological variables can also have an impact on reproductive success (Chapter 2). Next, I conducted a series of field and laboratory studies to uncover the factors that select for offspring cannibalism in this species. In particular, I investigated whether offspring cannibalism serves to replenish dwindling energy reserves and/or occurs when paternity over a brood is likely to be low. I showed that although plainfin midshipman males endure a long and energetically taxing parental care period, they cannibalize offspring most frequently early in the breeding season, the time period when the males are in their best body condition but when male-male competition is also at its peak (Chapter 3). Using a direct comparison of males that had recently cannibalized offspring versus those that had not, I showed that the males with the lowest energy reserves were actually the least likely to have offspring in their digestive tracts, suggesting that offspring cannibalism is not driven by immediate energetic need (Chapter 4). I then tested whether males assess their paternity using direct or indirect offspring cues, and showed that males use the act of a nest take-over as reliable indirect cues of their paternity over a brood (Chapter 5). Altogether, my results further our understanding of the reproductive ecology of the plainfin midshipman fish, and provide a foundation upon which to assess and test between cannibalism hypotheses in this species and others. My thesis work demonstrates the advantage of studying multiple cannibalism hypotheses in a single study system, and through this approach we can gain a more accurate evolutionary understanding of how the phenomenon of offspring cannibalism is maintained in different species.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Measuring the Ratio of Storm-Deposited Gutter Casts, Upper Cretaceous Gallup Sandstone, New Mexico, USA

contributor:
Bhattacharya, Janok
Earth and Environmental Sciences

subject:
Gallup Sandstone
Gutter casts
New Mexico
Tempestites

abstract: Understanding unconventional petroleum reservoirs and HALO plays, areas outside existing production zones which are made up of thin-bedded or heterolithic intervals, has gained in importance in recent years with the continual demand for energy and the increased development of such prospects. Heterolithic units within deltaic successions host vast quantities of oil and gas that often go unexploited due to a lack of understanding of the sandstone shape, morphology and continuity within such reservoirs. The purpose of this work is to examine the thin-bedded units within the Late Cretaceous prodelta successions of the Gallup Sandstone in the Shiprock area of New Mexico in order to quantify the fundamental processes responsible for the deposition of these sands and to perform a correlation for such heterolithic deposits.  Rock Ridge and Sanostee show heterolithic deposits, within parasequences 5a and 7a of the Gallup sandstone, and were analyzed, using measured sections and photomosaics, near the Shiprock area in order to compare the heterolithics in different stratigraphic settings. Five measured sections were collected at the centimeter scale in order to observe every facies change at a high resolution.  Facies associations, such as tempestites, turbidites, and hyperpycnites, were used to identify dominant processes of deposition. Corresponding net-to-gross calculations yielded the sandstone percentage of each section with the result that storm-dominated beds present at Sanostee yielded the highest percentage of sand content. Two high resolution gigapan photomosaics of each heterolithic exposure were collected in order to perform a correlation of all the sandstones observed within the measured sections, across the entire exposure. Results show that dominant process of deposition varies along strike. Towards Sanostee, in the south, storm-waves are dominant while farther north rivers exert greater influence. However, the presence of large scale storm-deposited gutter casts at Sanostee has significant implications for lateral and vertical continuity of sandstones in comparison to the more tabular sandstone facies found at Rock Ridge. These guttered facies have a major impact on net-to-gross and vertical conductivity due to their high degree of amalgamation and therefore may signify important areas for prospecting in such heterolithic reservoirs. Furthermore, the presence of large scale gutters beneath a sharp-based shoreface is indicative of a Falling Stage Systems Tract, leading to the conclusion that Parasequence 7a-6d were affected by forced regression.

abstract: Thesis

abstract: Master of Science (MSc)


title: Optimal Control of a Commuter Train Considering Traction and Braking Delays

contributor:
Sirouspour, Shahin
Electrical and Computer Engineering

subject:
Control systems
Automatic control
Delay systems
Feedback
Motion planning
Optimal control
Rail transportation

abstract:
Transit operators are increasingly interested in improving efficiency, reliability, and performance of commuter trains while reducing their operating costs. In this context, the application of optimal control theory to the problem of train control can help towards achieving some of these objectives. However, the traction and braking systems of commuter trains often exhibit significant time delays, making the control of commuter trains highly challenging. Previous literature on optimal train control ignores delays in actuation due to the inherent difficulty present in the optimal control, and in general, the control, of input-delay systems.

In this thesis, optimal control of a commuter train is presented under two cases: (i) equal, and (ii) unequal time delays in the train traction and braking commands.

The solution approach uses the economic model predictive control framework, which involves formulating and solving numerical optimization problems to achieve minimum mixed energy-time optimal control in discretized spatial and time domains. The optimization problems are re-solved repeatedly along the track for the remainder of the trip, using the latest sensor measurements. This would essentially establish a feedback mechanism in the control to improve robustness to modelling errors. A key feature of the proposed methods is that they are model-based controllers, they explicitly incorporate model information, including time delays, in controller synthesis hence avoiding performance degradation and potential instability. To address the issue of input-delays, the well-established predictor approach is used to compensate for input-delays. The case of equal traction-braking delays is treated in discretized spatial domain, which uses an already developed convex approximation to the optimization problem. The use of the convex approximation allows for robust and rapid computation of the optimal control solution. The non-equal traction-braking delays scenario is formulated in time domain, leading to a nonconvex optimization problem. An alternative formulation for minimum-time optimal control problems is presented for delay-free systems that simplifies the solution of minimum-time optimal control problems compared to conventional minimum-time optimal control formulations. This formulation along with the predictor approach is used to help solve the train optimal control problem in the case of non-equal traction-braking delays. The non-equal traction-braking delay controller is compared with the equal traction-braking delay controller by insertion of an artificial delay to make the shorter delays equal to the longer delay. Results of numerical simulations demonstrate the validity and effectiveness of the proposed controllers.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Role of Randomized and Non-Randomized Studies in Knowledge Synthesis of Health Interventions.

title: Randomized and Non-Randomized Studies in Health Syntheses

contributor:
Schunemann, Holger
Health Research Methodology

subject:
Systematic Reviews
Clinical Trials
Randomized Trials
Clinical Guidelines
GRADE
Evidence Syntheses
Knowledge Syntheses

abstract: PhD thesis assessing the role of non-randomized studies with randomized in evidence syntheses of health interventions.

abstract:
Randomized studies (RS) are considered the best source of evidence for knowledge syntheses (e.g., systematic reviews, health technology assessments, health guidelines, among others) about healthcare interventions. Historically, non-randomized studies (NRS) have been usually discarded from knowledge syntheses of interventions due to their intrinsic risk of bias and confounding, and they are used only when RS are considered unfeasible or unethical to conduct. With better research methods in observational studies and new tools for the evaluation of risk of bias, NRS are more likely to be a helpful source of information when used as replacement, sequential, or complementary evidence. This, together with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach, provide an opportunity for guiding decisions about using RS and NRS in knowledge synthesis and increasing our certainty in a body of evidence.
This work aims to improve research synthesis methods by assessing the role and use of RS and NRS in knowledge syntheses using GRADE. This can help health professionals, researchers, guideline developers, and policy-makers build better and more complete healthcare recommendations.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
All recommendations about healthcare interventions (from common medicines to strategies to prevent diseases) should ideally come from an adequate synthesis (e.g., systematic reviews) of the least biased studies. Many researchers and authors of health syntheses consider randomized studies (RS), the ‘gold standard’ to demonstrate if an intervention is truly effective. Unfortunately, they are not always available, feasible, or ethical to conduct. Non-randomized studies (NRS), also called observational studies, can potentially provide complementary evidence for a research question. Unfortunately, they are usually considered of poorer quality because of their intrinsic nature of being prone to bias and confounding. In most circumstances, authors of syntheses discard these types of studies from the outset, without considering their potential for providing evidence that could complement or even replace that from randomized studies.
This work aims to improve this situation by offering methods for evaluating the appropriateness of integrating both RS and NRS, guiding authors and researchers in cases where this is possible, hence increasing the certainty in a body of evidence and help all stakeholders reach decisions.


title: Design, Optimization, and Testing of a Combined Tri-Axial Polarized Energy Dispersive X-Ray Fluorescence and Energy Dispersive X-Ray Diffraction System for Biological Sample Classification

contributor:
Farquharson, Michael
Medical Physics

abstract:
The examination of biological samples yields information regarding the function and structure of the sample tissue. Many non-destructive methods are employed to interrogate biological samples, helping to further our understanding of these complex systems.

A combined Polarized Energy Dispersive X-Ray Fluorescence and Energy Dispersive X-Ray Diffraction system was designed, tested, and optimized for the purpose of classifying biological samples. This system is capable of determining the elemental composition and structural components present within a biological sample. Using two energy dispersive techniques allowed for decreased data acquisition times, and a single x-ray source to be used by both setups.

The system was optimized to improve its performance when measuring biological samples. The x-ray fluorescence spectrometer uses metallic secondary targets that allow for low minimum detection limits in transition metals, which are usually very important to biological tissue function. The x-ray diffraction spectrometer was also optimized to examine structures commonly found in biological samples, while still providing an adjustable range of measurable momentum transfers. Other optimizations performed on both systems provided significant improvements when measuring biological samples.

The functionality of the combined system was tested by measuring several sets of tissue samples. Two sets of cancerous breast tissues, were examined to determine measurable differences between healthy and abnormal tissue. A set of rat organs overloaded with iron were also measured to examine the high customizability and sensitivity of the x-ray fluorescence spectrometer. Lastly, a series of calibration samples were measured to determine minimum detection limits of commonly found elements. All measurements agreed with published literature, and the combined spectrometers showed an improvement in both accuracy and speed over other available spectrometers when measuring biological samples.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Detailed Thin-bedded Facies Analysis of Mancos C in the Upper Mancos Shale, New Mexico

contributor:
Bhattacharya, Janok
Geography and Earth Sciences

subject:
Thin-beds
Mudstones
Shale
Facies Analysis
Sedimentology
Geology

abstract: Fine grained sediments were common in epicontinental seas, with shallow slopes, such as the Cretaceous Western Interior Seaway.  However, proposed mechanisms for offshore mud transport, such as turbidity currents, tempestites, and hyperpycnal flows, require significant slopes.  A core from the Upper Mancos Shale, Mancos C, located in the San Juan Basin of New Mexico was analysed to determine the dominant transport processes bringing sediment offshore.  A detailed facies analysis was conducted, over 54 m of slabbed core, using sedimentological data, such as grain size, type of sedimentary structures, bed thickness, lithology, clay content, fossils, ichnofacies, and degree of bioturbation.  The facies observed in the core show that multiple processes, including ignitive turbidity currents, hypopycnal and hyperpycnal flows, and tempestites, were responsible for the deposition of the Mancos C core.  The resuspension of mud on the inner shelf by storm waves also played a key role in moving mud further offshore.  Tidal influence within the Mancos C was relatively small.

abstract: Thesis

abstract: Master of Science (MSc)


title: INFANT FEEDING IN HIV IN CANADA: PROVIDER PERSPECTIVES

title: INFANT FEEDING IN HIV IN CANADA:  An exploration of Healthcare Provider Perspectives: Knowledge, Attitudes and Practices Survey and Clinical and Research Priority Setting Meeting

contributor:
Smieja, Marek
Health Research Methodology

subject:
HIV
infant feeding
breastfeeding
HIV stigma
risk tolerance
knowledge translation

abstract: Infant Feeding in HIV in Canada is an increasingly challenging and confusing aspect of clinical care for providers and patients due to differences in recommendations in Canada compared to low income countries.  The frequency of breastfeeding occurring in Canada is not documented or known, and is shrouded in stigma because of fear of criminalization or child apprehension in the midst of a culture where ‘breast is best’ messaging dominates.  Breastmilk transmission data comes from observational and randomized controlled trials completed in low resource settings, which may not be generalizable to Canadian clinical settings.  Previous literature has not explored provider perspectives on this issue, especially in high resource settings. We developed a survey to explore the knowledge, attitudes and practices of adult and pediatric HIV care providers in Canada.  This survey explores the provider knowledge levels, risk tolerance and perceived stigma pertaining to infant feeding in HIV.  Using exploratory analysis including descriptive statistics and regression modelling, we developed scales on the above listed three subject areas.  The overall opinions of providers were that formula feeding should remain the recommendation due to the potential risk to the infant; and that women should be supported to access formula and resources to overcome barriers to formula feeding.  Providers varied in their risk tolerance and the degree of stigma they perceived associated with infant feeding for their patients.  Providers did not feel that breastfeeding is a criminal matter, but in some circumstances they would consider involving child protection services.  Focus group consultation with women living with HIV, provided insight into the experiences, and clinical and research priorities for women living with HIV on infant feeding.  A provider meeting was organized to discuss the challenges and resources pertaining to infant feeding in Canada across the provinces.  Providers described diverse patient populations with differing needs.  Using a World Café model for discussion, priority needs were decided through consensus including the need for knowledge translational resources to convey information to women living with HIV on infant feeding, and the need for evidence based consensus clinical management guidelines was evident.  Quantifying the frequency of breastfeeding occurring in Canada by women living with HIV will help to understand how often this issue is encountered.  A preliminary qualitative approach to understanding infant feeding issues for women living with HIV using focus groups is described.  However, further exploration in a community based approached is needed to explore the needs and challenges faced by families affected by HIV around infant feeding.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Infant Feeding in HIV in Canada is an increasingly challenging aspect of clinical care.  Information on breastmilk transmission comes from studies completed in lower income countries, and this may not be applicable to the Canadian HIV setting.  Previous literature has not explored provider perspectives on this issue, especially in high-income countries like Canada. In this knowledge, attitudes and practices survey of HIV care providers in Canada, the main findings were that formula feeding should remain the recommendation due to the potential risk of HIV infection occurring in the baby, however women should be supported to access formula and resources to overcome barriers to formula feeding.  Providers do not feel that breastfeeding is a criminal matter, but in some circumstances may consider involving child protection services.  We performed community consultation using focus groups to understand some of the issues women face with infant feeding, some of the clinical solutions they would support, and research questions and knowledge translation they would want undertaken.  A provider meeting to discuss the challenges pertaining to infant feeding in Canada demonstrated that although populations differ, the need for knowledge translational resources to convey information to women living with HIV on infant feeding was universal.  Furthermore, the need for evidence based consensus clinical management guidelines would improve the quality of care provided.


title: INVESTIGATION OF AN ADAPTATION-INDUCED TACTILE SPATIAL ILLUSION: PSYCHOPHYSICS AND BAYESIAN MODELING

contributor:
Goldreich, Daniel
Psychology

subject:
tactile perception
adaptation
tactile illusion
psychophysics
two-point perception
Bayesian
sensory adaptation
repulsion illusion
Bayes
Bayesian inference
touch
perceptual illusion
human psychophysics
somatosensory
vibrotactile adaptation
anesthesia
Bayesian perceptual model
EMLA
spatial perception
aftereffect

abstract: Sensory adaptation is an important aspect of perception. A seemingly non-beneficial consequence of adaptation is that it produces perceptual illusions. For instance, following focal adaptation, the perceived separation between stimuli straddling the adapted attribute or region is often exaggerated. This type of illusion, known as perceptual repulsion, is both a consequence of and a clue to the brain’s coding strategies and how they are influenced by recent sensory events. Adaptation-induced perceptual repulsion has been well documented in vision (e.g. the tilt aftereffect) and to a lesser extent in audition, but rarely studied in touch. The present thesis investigated the effects of adaptation on tactile spatial perception using a combination of human psychophysics and computational modeling. In a two-interval forced choice task, participants compared the perceived separation between two point-stimuli applied on the forearms successively. The point of subjective equality was extracted as a measure of perceived two-point distance. We showed that tactile spatial perception is subject to an adaptation-induced repulsion illusion: vibrotactile adaptation focally reduced tactile sensitivity and significantly increased the perceived distance between points straddling the adapted skin site (Chapter 2). This repulsion illusion, however, was not observed when the intervening skin was desensitized with topical anesthesia instead of vibrotactile adaptation, suggesting that peripheral desensitization alone is insufficient to induce the illusion (Chapter 3). With Bayesian perceptual modeling, we showed that the illusion was consistent with the hypothesis that the brain decodes tactile spatial input without awareness of the adaptation state in the nervous system (Chapter 4). Together, the empirical and theoretical work furthers the understanding of dynamic tactile spatial coding as the somatosensory system adapts to the sensory environment. Its main findings are consistent with the adaptation- induced repulsion illusions reported in vision and audition, suggesting that perception in different sensory modalities shares common processing features and computational principles.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Sensory adaptation can shape how we perceive the world. In this thesis, we showed that the perception of space in touch is pliable and subject to the influence of adaptation. Psychophysical testing in human participants showed that vibratory adaptation induced an illusion that expanded the perceived distance between stimuli on the skin. This illusion provides clues into how information about space in touch is normally processed and interpreted by the brain. In addition, we developed a computational model that used a powerful statistical framework – Bayesian inference – to probe touch on a theoretical basis. To the best of our knowledge, the present thesis provides the first combined psychophysical and computational study on the effects of adaptation on tactile spatial perception. Our findings suggest that touch shares some common information processing principles with vision and hearing, and adaptation plays a functionally similar role in mediating this process across the senses.


title: The Effect of Temperature on Unbonded Fiber-Reinforced Elastomeric Isolators

contributor:
Tait, Michael
Civil Engineering

subject:
base isolation
seismic isolation
low temperature
bridge
fibre-reinforced
elastomeric isolator

abstract:
During strong ground motions, structures equipped with base isolation systems have been shown to have their seismic demand significantly reduced, mitigating adverse effects such as damage and loss of life. More recently, the fiber-reinforced elastomeric isolator (FREI) has been investigated as a relatively new type of isolator for the base isolation of structures. Constructed from alternating layers of elastomer and carbon-fiber cloth, FREI can be produced in large pads that can be cut to any desired size and shape when required.
In bridges, FREI can to be used in an unbonded application (U-FREI) by placing them between the bridge deck and the piers. Experimental and numerical investigations have shown U-FREI as a viable option for the isolation of bridges. However, experimental studies have been limited to room temperature testing. In North America, climates vary drastically across the continent. Northern climates, such as those existent in Canada, are capable of reaching extremely low temperatures. Thus, base isolated bridges in these regions require isolation systems that perform adequately at cold temperatures.
The studies presented in this dissertation have been completed in order to investigate the effects that low temperatures have on U-FREI used in bridge structures. An experimental program was conducted that evaluated the behaviour of U-FREI. It was found that U-FREI performed adequately under lateral displacements expected during a seismic event, and provided acceptable response under vertical and rotational testing that is typical of normal bridge operation. Using these results, a numerical model for U-FREI was then updated to account for the effects of low temperature. The model was combined with a bridge model to evaluate the seismic response of a bridge structure isolated with U-FREI subjected to low temperatures. A substantial reduction in seismic demand was achieved, even under the most severe conditions tested.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: THE EFFECTS OF AN UNEXPECTED VISUAL PERTURBATION ON HAND PATH TRAJECTORIES IN MANUAL OBSTACLE AVOIDANCE

contributor:
Lyons, James
Kinesiology

subject:
manual obstacle avoidance
autism spectrum disorder
multiple process model
ASD
visual perturbation
motor planning

abstract:
Perturbations to the upper limb in aiming tasks act to force individuals to modify their movements using online control processes. Individuals are able to successfully counteract these mechanical and perceptual perturbations to accurately acquire a specific target goal. What is less well understood is how individuals self-initiate a change to their trajectory during obstacle avoidance.  A series of two studies were conducted to better understand the effects of a visual perturbation when performing two-dimensional sliding aiming movements during a manual obstacle avoidance task when a second set of obstacles appeared unexpectedly along the preferred, optimal trajectory. On each trial, a planned obstacle appeared at 25%, 50% or 75% of the movement amplitude. On some trials, a second set of obstacles appeared early or late in the movement to force participants to make online corrections or adapt their preferred trajectory to successfully reach the specified target. Results revealed that the mere possibility of the unexpected second obstacles influenced the overall trajectory and movement kinematics (i.e., whether that second obstacles appeared or not). Despite performing the movement in the same amount of time, participants executed a more lateral avoidance trajectory and reached higher accelerations later and further into the movement. We suggest that this pattern of behaviour is indicative of an optimal movement strategy such that the potential for an online correction resulted in individuals planning for the worst-case scenario.
The presentation of a case-study for an individual with autism spectrum disorder (ASD) provides insight into potential differences in obstacle avoidance tasks when compared to a matched control. Despite relative differences in execution behaviour, the individual with an ASD successfully completed the task. This provides potential support for the sparing of motor execution processes within this population.
Taken together, we suggest that optimal movement strategies may be better defined on a more individual basis. That is, what is optimal for one population might not be optimal for another.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: It is well known that individuals are able to successfully aim to targets in environments that are both predictable and unpredictable. Additionally, these trajectories are successfully modified in the presence of an expected obstacle resulting in a change to the optimal movement to incorporate the location of the obstacle. What is less understood, however, is how individuals respond to the sudden onset of an obstacle along the optimal trajectory. This thesis characterizes these behaviours using a manual obstacle avoidance task wherein obstacles unexpectedly appear to obstruct the preferred movement pathway. The behavioural response to this perturbation is indicative of the performance of more cautious movements, adapted for the worst-case scenario. On average, individuals compromise between the biomechanical and computational demands of the task to execute wide trajectories that do not need to be updated during movement execution, a response that is potentially identified in an autism spectrum population.


title: Investigation of sediment pathways in Hidden River Cave, Kentucky

contributor:
Maclachlan, John C.
Eyles, Carolyn H.
Earth Sciences

subject: Sedimentology Karst Caves Kentucky

abstract: Karstic cave systems are intricately related to surficial processes and the study of cave sediments is a growing field of research. Sediment deposits in caves are protected from surficial weathering processes, and are therefore often preserved. Cave sediments have applications in studies for paleoclimatic reconstruction, contaminant transport, and paleoflood and stream incision rates, making them valuable contributors to other areas of geoscience. Hidden River Cave is an active, multi-level cave system in the town of Horse Cave, Kentucky with over 33 km of mapped passages. A history of anthropogenic impacts on the cave system include uses for hydroelectric power generation, a water source, and a show cave until it closed in 1943 due to severe contamination from domestic and industrial waste. This study reports on the analysis of sediment cores collected from the cave system which show distinct concentrations of metals within the sediment from chrome plating plant effluent. Relative concentrations of metals in the core record were obtained using an ITRAX core scanner, and were observed to decrease moving downstream from the chrome plating plant contamination source.  Sediment core analysis allows depositional patterns in the cave system to be observed and related to historic surficial processes. The chronology of sedimentation events was determined using Pb-210 analysis of core sediment and indicates a strong connection between historical contaminating events in the town of Horse Cave and cave sediment deposition. Sediment core analysis has thus allowed depositional patterns in the cave system to be determined and related to historic surficial processes. These findings can be applied to enhance understanding of the combined effects of landscape evolution and anthropogenic impacts which may be used to inform decision making processes for communities overlying both Hidden River Cave and other karstic cave systems.

abstract: Thesis

abstract: Master of Science (MSc)


title: On Clustering: Mixture Model Averaging with the Generalized Hyperbolic Distribution

contributor:
McNicholas, Paul
Statistics

subject:
clustering
finite mixture model
model averaging
generalized hyperbolic distribution
Occam's window
Bayesian model averaging
Statistics

abstract: Cluster analysis is commonly described as the classification of unlabeled observations into groups such that they are more similar to one another than to observations in other groups.  Model-based clustering assumes that the data arise from a statistical (mixture) model and typically a group of many models are fit to the data, from which the `best' model is selected by a model selection criterion (often the BIC in mixture model applications). This chosen model is then the only model that is used for making inferences on the data.  Although this is common practice, proceeding in this way ignores a large component of model selection uncertainty, especially for situations where the difference between the model selection criterion for two competing models is relatively insignificant.  For this reason, recent interest has been placed on selecting a subset of models that are close to the selected best model and using a weighted averaging approach to incorporate information from multiple models in this set. Model averaging is not a novel approach, yet its presence in a clustering framework is minimal.  Here, we use Occam's window to select a subset of models eligible for two types of averaging techniques: averaging a posteriori probabilities, and direct averaging of model parameters.  The efficacy of these model-based averaging approaches is demonstrated for a family of generalized hyperbolic mixture models using real and simulated data.

abstract: Thesis

abstract: Master of Science (MSc)


title: SOIL-TRANSMITTED HELMINTH INFECTIONS IN HONDURAS: MAPPING INFECTION PREVALENCE AND IMPLICATIONS FOR HEALTH CARE REGIONALIZATION

contributor:
Yiannakoulias, Niko
Geography

subject:
Soil-transmitted helminth infections
Health care regionalization
Epidemiology
Honduras

abstract: Soil-transmitted helminth (STH) (A. lumbricoides, T. trichiura and hookworm) infections are a significant public health concern in Honduras. These infections are treatable using inexpensive anthelmintic medications, however long-term control and eradication will require large investments in public and private sanitation infrastructure. Importantly, both types of interventions are targeted towards high-risk populations and regions rather than individuals. The goal of this thesis is to contribute to improving the efficiency of soil-transmitted helminth control efforts in Honduras. In our first study, we use multiple regression analyses to identify determinants of STH infections and generate estimates of A. lumbricoides, T. trichiura and hookworm infection prevalence, as well as recommended deworming frequencies, for each of Honduras’ 298 municipalities. Our estimates suggest that prevalence of all three infections has declined over time, however 75% of municipalities still require annual or semi-annual deworming. In our second study, we quantify how the type of region used for measuring prevalence and allocating resources can impact the success and efficiency of public health programs. More specifically, we compare administrative regions to alternative zoning schemes at the same geographic scale. Our findings suggest that regions designed to be homogeneous with respect to prevalence can be more efficient than existing municipalities (at the same scale) for distributing resources. This research has implications on future control efforts.

abstract: Thesis

abstract: Master of Science (MSc)


title: The Educational Impact of the Evaluation Tool for Child Life Interns:  A Mixed Methods Study

contributor:
McConnell, Meghan
Health Science Education

subject:
assessment
evaluation
clinical education
in-training evaluation
clinical internship

abstract:
Background:  The Association for Child Life Professionals (ACLP) requires those seeking to become a Certified Child Life Specialist (CCLS) complete a minimum of 480 hours of supervised clinical experience prior to the certification exam.  Trainees’ skills are evaluated using the Evaluation Tool for Child Life Interns.  This tool consists of 54 skill-based items scored with a 7-point Likert-based rating scale (with a Not Applicable (NA) option) and space for open-ended narrative feedback.  Skill based items are within three separate domains:  Assessment, Intervention and Professional Responsibility.  There are no published research studies available to date on the use or effectiveness of the tool.
Purpose:  This study seeks to explore the educational impact of the tool using two sources of data: frequency of NA ratings across the three domains and narrative feedback from preceptors in comment sections of the tool.
Methods:  Using an explanatory sequential mixed methods design, quantitative data (proportion of NA ratings) and qualitative data (preceptors’ comments) from evaluation tools obtained from 45 learners spanning the academic years 2011 – 2016 at McMaster University’s Post Graduate Diploma Program in Child Life.   Mean proportion of NAs was evaluated using a 2 (time: internship 1 and internship 2) x 3 (domain: assessment, intervention and professional responsibility) two-way repeated measures analysis of variance ANOVA. Qualitative data was explored using thematic analysis of preceptors’ narrative comments for skill-based items where at least 1 NA rating was selected.
Results:  Analyses of quantitative data revealed NA ratings to be substantially greater in the professional responsibility domain (22%) relative to both assessment (<1%) and intervention (3%) domains (p-value < 0.001).  There was no main effect for time.  Qualitative analyses showed that the use of NA was primarily due to the intern not having the opportunity to experience or demonstrate the skill being rated.  Four themes emerged from the thematic analysis of narrative feedback (constructive feedback, action plans, clinical examples with patients and families, little to no opportunity for skill development).
Conclusion:  The Evaluation Tool for Child Life Interns offers quantitative and qualitative feedback to child life learners with benefits and challenges to its use.  The subtasks in the assessment and intervention domains represent child life practice across various placement sites.  Within the professional responsibility domain, skills being assessed require further review through stakeholder input to ensure they reflect current practice.  The narrative feedback provided by preceptors is detailed and constructive.  The tool is discouraged for use as a single summative assessment to make decisions of competency and is recommended for formative and summative use as one method of feedback within a program of assessment.

abstract: Thesis

abstract: Master of Science (MSc)


title: RHYTHM AND “RESILIENCE”: BLACK YOUNG ADULTS AND POETRY

contributor:
Sinding, Christina
Social Work

subject:
race
youth
young adults
Black
poetry
spoken word
rap
Tupac
resilience
identity
impact
storytelling
entreprenurship
social justice

abstract: Many Black young adults engage with poetry in its various forms on a regular basis. This interview study explores the reasons why eight Black young adults have decided to partake in poetry and examines how poetic practices have permeated the lives of those who actively engage with the art form. Critical race theories and narrative approaches were used to complete this work. These specific theoretical frameworks and research methodologies were applied as their major tenants allow for consideration of race, marginalization, social justice and storytelling. The work begins with a historical look at poetry in relation to present day poetics. The experiences of the participants involved are then featured. Finally, the author examines the most common themes expressed in the conversations she shared with the young adults. Through poetry, Black young adults were able to 1) find a release for their emotions and experiences 2) form and understand their identities and 3) have an impact their surroundings. Although the Black young adults involved in this research speak about the need for support, the lack thereof has not hindered them from sharing their poetry or speaking eloquently about how poetry has affected them.

abstract: Thesis

abstract: Master of Social Work (MSW)


title: Quantifying the Contribution of Environmental and Genetic Factors to the Variation in Melanin Production Among Strains of Cryptococcus neoformans

contributor:
Xu, Jianping
Biology

subject: Cryptococcus neoformans, melanin, LAC1

abstract: Cryptococcus neoformans is a basidiomycetous yeast capable of causing fatal meningoencephalitis in immunocompromised individuals. Naturally found worldwide in association with pigeon droppings, C. neoformans produces melanin pigments that play a protective role in both natural and physiological settings. Significant variation in the level of melanin production has been observed among natural populations of C. neoformans, although the factors behind this phenotypic variation remain unclear. In my project, I quantified the level of melanin production in 54 strains of C. neoformans  and characterized the change in melanin response to three common stressors encountered by C. neoformans  in natural and clinical environments: thermal, oxidative and nitrosative stresses.  Using this data, I assessed the contribution of genetic factors, environmental factors and genotype-environmental interactions to the observed variance in melanin. The analysis revealed that over 50% of the variance in melanin was attributable to genetic differences among the strains. I identified three single nucleotide polymorphisms (SNPs) in the LAC1 gene, which is essential for melanin synthesis, to be significantly associated with melanin production in thermal and oxidative stresses. One of the SNPs is predicted to cause an amino acid change (P182A/T) in a putative catalytic domain of the Lac1 protein. The genotype-environment interactions were also found to contribute to a significant proportion of the variance in phenotype. In the majority of tested stress conditions, environmental factors only contributed to a small amount of variance ranging from 5-15%. These results highlight the complex interplay of genetic, environmental and interaction factors that contribute to an observable phenotype. C. neoformans is a model fungal pathogen whose ability to produce melanin is a well-established virulence factor. The results from this project contribute to our understanding of the evolutionary trajectory and regulation of melanin production in C. neoformans.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The yeast, Cryptococcus neoformans, is naturally found worldwide in soil and pigeon droppings, and causes fatal infections in people with a weakened immune system. It produces dark melanin pigments that aid the yeast in neutralizing the immune response of the infected host. My project sought to characterize the variation in melanin levels found among natural populations of C. neoformans and to determine the factors that contribute to this variation.  I identified genetic differences between the strains to be the biggest cause of variation in melanin levels. Changes in the LAC1 gene which is essential for melanin synthesis, were found to shape the melanin production significantly when the yeast is exposed to stressful conditions. Interactions between genes and the environment were also revealed to be a significant contribution to the observed differences in melanin levels. These results highlight the complex interplay of factors that shape the expression of observable traits.


title: Compound Conceptual Relations in Working Memory: Effects of Relation Priming in Immediate Serial Recall

contributor:
Service, Elisabet
Cognitive Science of Language

subject:
working memory
conceptual relations
compound words
compound semantics
immediate serial recall
short-term memory

abstract: The conceptual relation theory postulates that English noun-noun compound words (e.g., snowman) have an underlying predicate structure that is not present in the surface form, but is recovered during compound processing (e.g., man made of snow). The relational nature of constituent binding in compound words marks them as a linguistic construction that is distinct from both the simplex words (monomorphemic) and other complex words (derived and inflected words) previously examined in the context of verbal working memory. In short-term memory research, a growing body of evidence suggests that semantic properties of words influence verbal recall; however, such effects have not been examined in the context of compound conceptual relations. The present study investigated the possible effects of compound conceptual relations in verbal working memory via an immediate serial recall task. The task was designed to examine whether sharing of an individual relation leads to facilitative or inhibitory effects for compounds associated with that relation and, more generally, whether this semantic property of compound words contributes to their recollection from short-term memory. Evidence from the serial recall experiment suggested an effect of compound relation priming in working memory. Relational similarity between recall list items appeared to inhibit recall performance. The thesis discusses how this may be the result of increased competition between compound constituents as a result of heightened constituent-level activation during word recall. This effect was not observed in relations that appeared to be overly general, suggesting that the effect is only present when compound words are matched according to salient, sufficiently specified relations.

abstract: Thesis

abstract: Master of Science (MSc)


title: Molecular & Biological Characterization of the POZ-ZF Transcription Factor KAISO in Intestinal Homeostasis

title: Finding a Niche for KAISO in the Intestinal Epithelium

contributor:
Daniel, Juliet M.
Biology

subject:
Intesine
Notch signalling
Inflammation
Kaiso

abstract:
We recently reported that intestinal-specific overexpression of the POZ-ZF transcription factor Kaiso produced two prominent phenotypes in 1-year old mice: Kaiso transgenic (KaisoTg) mice presented with chronic intestinal inflammation, and an increase in secretory cell types – a trait typical of Notch signalling inhibition. Despite these findings however, the factor(s) responsible for Kaiso-mediated inflammation and secretory cell increases had not been elucidated. The primary goal of this thesis was to begin filling in this knowledge gap, by shedding mechanistic insight on Kaiso’s role in governing these two prominent phenotypes.
	First, we elucidated Kaiso’s role in the Notch signalling pathway and found that Kaiso inhibited the expression of the Notch1 receptor, and its ligand Dll-1, but promoted the expression of the Jagged-1 ligand. We postulated that the Kaiso-mediated reduction in Dll-1 might be responsible for the increase in secretory cell types, whereas Kaiso-mediated regulation of Jagged-1, which is dispensable for cell fate decisions, may be implicated in colon cancer progression. Importantly, we also found that Kaiso’s effects on Notch pathway inhibition occurred prior to the onset of chronic intestinal inflammation.
	Our analyses of the chronic inflammatory phenotype in KaisoTg mice demonstrated that Kaiso overexpression drives pathogenic neutrophil-specific recruitment (as evidenced by increases in neutrophil-specific enzymatic activity, the formation of crypt abscesses, and augmented expression levels of the neutrophils-specific chemokine, MIP2); an increase in the pore-forming Claudin-2; reduction of the cell adhesion protein E-cadherin; and abnormal intestinal epithelial repair mechanisms. Together, these findings imply that the pathogenesis of Kaiso-mediated intestinal inflammation is a multi-factorial process.
	A secondary goal of this thesis was to initiate studies to elucidate how the Kaiso binding partner, Znf131, might play a role Kaiso-mediated transcriptional regulation. We found that Znf131 indirectly associated with several Kaiso target genes, including Cyclin D1 (CCND1). Importantly, Znf131 activated a minimal CCND1 promoter previously shown to be inhibited by Kaiso. Moreover, Kaiso overexpression attenuated Znf131-mediated transcriptional activation and Znf131 expression in intestinal cells. Together, these findings hint that Znf131 and Kaiso may exert opposing biological functions, which may have implications in Kaiso-mediated intestinal homeostasis and disease.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Unravelling the biological roles of Kaiso in triple negative breast cancers

title: Biological roles for Kaiso in triple negative breast cancers

contributor:
Daniel, Juliet
Biology

subject:
Kaiso
triple negative breast cancer

abstract:
Recent studies indicate a correlation between high expression of the POZ-ZF transcription factor Kaiso, and the aggressiveness of the triple negative breast cancer (TNBC) subtype. However, little is known about the biological roles of Kaiso in TNBC tumorigenesis and metastasis, which laid the foundation for this thesis. To elucidate Kaiso’s role in TNBC, we generated stable Kaiso depletion in two well-established TNBC cell lines – MDA-MB-231 and Hs578T – using RNA interference technology. Intriguingly, we observed that Kaiso depletion delayed the tumor onset of MDA-MB-231 but not Hs578T cells, and led to the reduced expression of the c-Myc oncoprotein in MDA-MB-231 but not Hs578T cells. We postulate that this reduction in c-Myc expression is partly responsible for the delayed tumor onset observed in MDA-MB-231 cells. Additionally, loss of Kaiso expression resulted in increased apoptosis of both MDA-MB-231 and Hs578T cells in vitro and in vivo, which was accompanied by reduced expression of the DNA repair protein BRCA1. Remarkably, bioinformatic analysis revealed that high Kaiso and BRCA1 mRNA expression correlates with the reduced survival rates of TNBC patients.

Further characterization of the Kaiso-depleted cells revealed that loss of Kaiso expression strongly inhibited the metastatic abilities of MDA-MB-231 and Hs578T cells. Importantly, Kaiso depletion led to decreased TGFβ-receptor I and II (TGFβRI and II) expression that is essential for the activation of the TGFβ signaling cascade. Concomitantly, suppressing Kaiso led to reduced TGFβ signaling. As increased TGFβRI expression is independently associated with the poor prognostic outcome of breast tumors, and the TGFβ signaling pathway is highly involved in breast tumor metastasis, we hypothesize that Kaiso functions together with TGFβRI and the TGFβ signaling cascade to promote TNBC metastasis.

An additional goal of this thesis was to investigate the role of Kaiso in the prevalence of TNBC in women of African ancestry (WAA) compared to Caucasian women – since increased Kaiso expression is implicated in the poor survival outcomes of breast cancer patients of African ancestry relative to their Caucasian counterparts. Using tissue microarray and immunohistochemical analyses, we revealed for the first time a high nuclear expression of Kaiso in TNBC tissues of WAA (Nigerian, Barbadian, African American) compared to TNBC tissues of Caucasian women. Collectively, these findings unveiled functional oncogenic roles for Kaiso in the tumorigenesis and metastasis of TNBC, and revealed a plausible link between high Kaiso expression, high African ancestry and the predisposition of young WAA to TNBC.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Clustering Matrix Variate Data Using Finite Mixture Models with Component-Wise Regularization

contributor:
McNicholas, Paul D
Statistics

subject:
Mixture models
Matrix variate distributions
Accelerometers
Pediatrics

abstract:
Matrix variate distributions present a innate way to model random matrices. Realiza-
tions of random matrices are created by concurrently observing variables in different
locations or at different time points. We use a finite mixture model composed of
matrix variate normal densities to cluster matrix variate data. The matrix variate
data was generated by accelerometers worn by children in a clinical study conducted
at McMaster. Their acceleration along the three planes of motion over the course of
seven days, forms their matrix variate data. We use the resulting clusters to verify
existing group membership labels derived from a test of motor-skills proficiency used
to assess the children’s locomotion.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigating the Gut Microbiome in Psychiatric Illness

contributor: Medical Sciences (Division of Physiology/Pharmacology)

subject:
Microbiome
Anxiety
Depression
Bipolar Disorder

abstract: The global burden of mental health disorders is rising with the world health organization recently having recognized major depressive disorder as the leading cause of disability worldwide. Nearly one in five Canadians are now estimated to struggle with a mental health disorder and Generalized Aanxiety Ddisorder (GAD) Mmajor Ddepressive Ddisorder (MDD) and Bbipolar Ddisorder are three of the most prevalent. Despite significant research into the disorders’ cause, the pathophysiology and underlying etiology of these diseases remains largely undiscovered. Recent research has highlighted the potential role of the gut microbiota in mental health, in particular in connection with anxiety. Our research aims to investigate this link in a cohort of GAD, MDD and bipolar patients recruited through the Anxiety Treatment and Research Centre at St. Joseph’s Healthcare in Hamilton, as well as through the University Health Nnetwork in Toronto. 71 GAD, 18 MDD, 17 euthymic MDD and 23 Bipolar patients provided fecal samples from which DNA was extracted, following which the V3 region of the 16S rRNA gene was amplified and sequenced using the Illumina Miseq platform. Sequencing data was analyzed through an in-house pipeline to construct community profiles of patients and age and sex matched healthy controls. My work involved analyzing the data to identify signature organisms that might identify putative disease associated microbial communities for further hypothesis generation about possible roles in disease. Furthermore, an extensive culturing effort was undertaken to identify and characterize some of the Bacteroides strains which were enriched in the GAD patient population. This study presents novel insights into some of the organisms that may be markers for a number of different diseases as well developing a better understanding of the Bacteroides that were correlated with anxiety.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Mental hHealth disorders including Ggeneralized Aanxiety Ddisorder (GAD), Mmajor Ddepressive Ddisorder (MDD) and Bbipolar Ddisorder (BD) affect somewhere between five and ten percent of Canadians, with the Wworld Hhealth Oorganization recently labeling MDD the leading cause of disability worldwide. Despite decades of research,  on these disorders we still have a poor understanding of what factors may contribute to causing these disorders their underlying mechanisms of actionetiology. Another hallmark of many mental health conditions are increased rates of gastrointestinal symptomsor digestive distress relative to the healthy populatioindividualsn. Recently, there has been a great deal of research about how the trillions of bacteria that live in the digestive tract play a role in neuronal brain development and behaviour. This study aimed to better understand which the organisms reside iinn the digestive tract of mental health patients in hopes of better understanding how some of these organisms could be contributing to patients’ poor mental health. Additionally, through better understanding the nature of these communities, recommendations could potentially be made about therapeutic interventions to restore a healthy community.


title: DISSOLUTION KINETICS OF CALCIUM ALUMINATE IN STEELMAKING SLAGS

contributor:
Dogan, Neslihan
Materials Science and Engineering

subject:
Steelmaking
calcium treatment
calcium aluminate
confocal scanning laser microscope
inclusions
dissolution

abstract:
Inclusion removal is critical for the production of clean steel. A better understanding of removal processes require knowledge of the effect of process parameters on dissolution kinetics. The present research focuses on the kinetics of calcium aluminate inclusion dissolution in relevant steelmaking slags that contain CaO, Al2O3 and SiO2.
In-situ observation of inclusion dissolution in slag is conducted using a high temperature, confocal scanning laser microscope (HT-CSLM). The particles used in this experimental work are produced in the laboratory and the production technique is explained in detail. The change in particle size is recorded with time and the effects of temperature, slag composition and inclusion morphology are investigated. The images are extracted from video and they are analysed to record the change in equivalent radius of a single particle during the dissolution process. The original and normalized dissolution data is used to determine the dissolution mechanism and to improve existing dissolution models.
It has been found that an increase in temperature increases the dissolution rate. At 1550°C and 1600°C, there is no product layer formation at the slag-inclusion interface and so, the dissolution process is faster. Slag composition shows a significant influence on the dissolution kinetics due to differences in the dissolution driving force and viscosity. Additionally, the dissolution rate depends on the morphology of inclusion as available reaction sites vary significantly.
Rate limiting steps are discussed based on the shrinking core model and diffusion in stagnant fluid model. It is shown that the rate limiting step for dissolution is the diffusion
v
through a product layer at 1500°C whereas it is mass transfer in slag at 1550°C and 1600°C. The diffusion coefficient of alumina is obtained by applying a one-dimension diffusion model. The calculated results varied between 5.5×10-11 and 2.6×10-10 m2/s depending on experimental conditions. Slag viscosity was found to be an important parameter for the modelling of the dissolution process. A modification to the correlation between the correction coefficient and slag viscosity was proposed. This modification improved the prediction of the dissolution path for calcium aluminate and alumina inclusions in steelmaking slags. This novel study provides an understanding of dissolution mechanisms and it offers data on the dissolution rate of CA2 inclusions in the slags related to the process of steelmaking. The results from this work can be used by steelmakers to aid in process design.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract:
The present work is a pioneer study on the dissolution of calcium aluminate particles in liquid oxide mixtures using the unique real-time observation approach. Experiments were conducted to provide a better understanding of the effects of various steelmaking conditions on inclusion removal during the refinement of liquid steel.
An existing dissolution model is further refined by introducing an additional parameter that is correlated to the properties of oxide mixtures. It has been found that the dissolution model can be applied not only to calcium aluminate inclusions but also to alumina inclusions. Hence, the approach proves the potential university nature of the dissolution model.
A clear understanding of the dissolution kinetics of inclusions helps to optimize the current steelmaking routes and enhance the removability of inclusions. Steel with a minimum amount of inclusions has better properties from all aspects, which improves its applicability in all fields.


title: EXTREME TOLERANCE IN THE EUTARDIGRADE SPECIES HYPSIBIUS DUJARDINI

contributor:
Stone, Jonathon
Biology

subject: Astrobiology Extreme-Tolerance Tardigrada

abstract:
Tardigrades are microscopic animals that can survive exposure to multiple extreme conditions. This remarkable ability makes them suitable laboratory model organisms for conducting biological to astrobiological research. Whereas tardigrade extreme-tolerance research has been focused predominantly on their ability to endure extreme desiccation, responses to other extraordinary conditions (i.e. hypergravity, pH, radiation and low temperature) remain un-described. These extreme tolerance research areas, in addition to life history traits, were documented in our studies on the eutardigrade species Hypsibius dujardini.
We found that specimens tolerated extreme g-equivalent forces (i.e., 16060g) and radiation levels (i.e. 5 kGy), with decreased survivorship at increased accelerations and radiation doses. Radiation induced bystander effects (RIBEs) manifested as a threshold response, with the threshold value between 3 and 5 kGy. Extreme acidic (pH 1 and 2) and alkaline (pH 11 to 14) conditions caused death instantaneously, while exposures to pH 4, 6, 8, 9, and 10 were tolerated. Tardigrade eggs reared at 0 °C for 4 days developed relatively slowly, diminishing their biological age relative to their chronological age. Extending cold exposure (0 °C) time (days = 10, 20 and 40) decreased incubation time (days = 3, 2 and 1, respectively) at 22 °C; lengthening cold exposure time led to decreased growth in juveniles and lowered survivorship in adults, suggesting that costs are associated with increasing incubation time at 0 °C.
Tolerance to hypergravity, large radiation doses and a wide-range in pH conditions support the notion that tardigrades are suitable organisms for astrobiological research, particularly in exploring parameters associated with potential transfer and habitability in extreme environments. RIBEs in adult tardigrades and the ability for tardigrade embryos to alter their ‘biological clocks’ based on exposed cold temperature duration have applications in biological research. Characterizing molecules involved in bystander signaling and response and biological clock adjustments during development could have important implications for improving biological practices such as radiotherapy and cryopreservation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: While interest in tardigrade extreme tolerance research has increased over the last decade, many research areas continue to be underrepresented or non- existent. And, while recognized tardigrade species have been increasing steadily in number, fundamental biological details, like individual life history traits, remain unknown for most. The main objectives in this thesis therefore were to survey the life history traits for the freshwater tardigrade species Hypsibius dujardini, increase knowledge about its extreme-tolerance abilities and describe its utility in astrobiological and biological studies. Research involved tardigrade tolerance to hypergravity, pH levels and radiation exposure (and associated radiation-induced bystander effects) as well as responses to temperature changes during development. Findings reported in this dissertation provide new data about H. dujardini, thereby narrowing the information gap that currently exists in the literature for this species.


title: EARLY STAGE WATER CAP OXYGEN CONSUMPTION TRENDS WITHIN THE FIRST COMMERCIAL SCALE OIL SANDS PIT LAKE, BASE MINE LAKE.

contributor:
Warren, Lesley A
Earth and Environmental Sciences

subject:
Geochemistry
Oil sands
Pit Lake

abstract:
Bitumen exploitation in Alberta’s oil sand region generates considerable amounts
of waste including tailings and process-affected water that needs reclamation. Water
capped tailings technology (WCTT) is currently being assessed as a potential wet
reclamation strategy in the oil sand by the commission of Base Mine Lake (BML), the first
commercial scale Pit Lake. Pit Lakes consist of ~40m of fluid fine tailings (FFT) deposited
in old mine pit covered with a ~10m water cap. In order to be successful, pit lakes much
achieve the ecological roles of a natural lake, which includes colonization of the water by
macrofauna therefore necessitating the water cap to be oxic. Due to the reductive nature of
the tailings, oxygen consuming constituents (OCC) such as methane, sulfide and ammonia
are released from the FFT into the water cap potentially posing a threat to the success of
the reclamation. Additional seasonal effects such as stratification and ice cover may further
affect oxygen consumption by isolating parts of the water cap therefore allowing
accumulation of OCC. Results shows that BML thermally stratifies during the summer and
winter and that oxygen persist throughout the water cap despite reaching low level at the
FFT-water interface (FWI) during summer. Consistent with the FFT acting as an OCC
source, aqueous CH 4 and NH 4+ concentrations were highest closer to the FWI, decreasing
upwards into the water cap. Using linear regression CH 4 was shown to be an important
OCC during the summer of 2015 while NH 4+ and CH 4 were both important for the summer
of 2016 highlighting the emergence of nitrification in BML. Detailed analysis of seasonal
data revealed that accumulation of OCC below the hypolimnion depletes oxygen and favors
methanotrophic activity. Results from both studies suggest that methanotrophs have a
competitive advantage at low oxygen levels against nitrifiers.

abstract: Thesis

abstract: Master of Science (MSc)

abstract:
Bitumen extraction in Alberta’s oil sand region generates substantial amounts of
waste including tailings that needs reclamation. Pit Lakes have been proposed as a
reclamation strategy, where tailings are deposited into a mined-out pit and covered with a
water cap. To achieve the reclamation goal, the lake must be able to sustain life and must
therefore maintain an oxic water cap. The underlying tailings poses a threat to the
oxygenation of the lake because of the constant release of compounds that have the
potential to consume oxygen. Additional seasonal effects due to temperature change may
further affect oxygen consumption by isolating parts of the water cap. In this thesis the
results of two years of field sampling and analyses show that despite active oxygen
consumption from tailings-released compounds, oxic status is achieved in the upper layer
of the lake during summer and under ice.


title: Hegemonic Masculinity and Violence in Nic Pizzolatto's "True Detective: Season One"

contributor:
Savage, Anne
English

subject: television gender masculinity violence

abstract: This paper examines the relationship between hegemonic masculinity and violence within American society as seen in the HBO television show, True Detective. Ultimately, it claims that violence is a necessary aspect of hegemonic masculinity and that this violence not only affects the feminine other but also is destructive for men.

abstract: Thesis

abstract: Master of Arts (MA)


title: Gene-environment interactions in obesity: current evidence and future directions

contributor:
Meyre, David
Health Research Methodology

subject:
Gene-environment interaction
Genetic
Obesity
Lifestyle
Environment

abstract:
Background: Obesity is a multifactorial disease caused by the interplay of environmental and genetic risk factors. With the prevalence of obesity more than doubling since 1980, this disease has become a global epidemic. The objectives of this research were to (1) review the current evidence of gene-environment interactions (GEI) in the field of obesity, (2) investigate novel GEI involving sedentary behaviour, sleep duration and alcohol consumption, (3) assess GEI using a cumulative environmental risk score, and (4) provide an overview of methodological weaknesses in GEI studies and provide suggestions for future directions.

Methods: The data for the gene-environment interaction analyses were collected from the EpiDREAM study: a cohort study including participants of six ethnic backgrounds from 17 countries worldwide. A subset of 17 423 participants with complete genotype and phenotype information was included in the analysis. Twenty-three obesity predisposing single nucleotide polymorphisms (SNPs) were analyzed independently and as a genetic risk score (GRS). Linear regression models were used to analyze these interactions.

Results: Heritability, monogenic and polygenic obesity studies provide converging evidence that obesity-predisposing genes interact with a variety of environmental exposures including physical activity and diet patterns. In the EpiDREAM cohort, we found that increased sedentary time did not interact with obesity predisposing SNPs or the GRS to modulate BMI. The interaction between sedentary time and physical activity was also not significant. We observed a U-shaped association between sleep duration and BMI and sleep duration did not appear to moderate the impact of the obesity predisposing SNPs or the GRS. However, we did observe an alcohol x FTO rs1421085 interaction, whereby increased alcohol consumption attenuated the impact of FTO rs1421085 variation on BMI. We also found that the combined effect of several environmental risk factors significantly modified the effect of FTO rs3751812 on BMI. Specifically, we found that the effect of the FTO rs3751812 SNP on BMI was over two times greater among those in the highest quartile of environmental risk compared to those in the lowest quartile. The GRS did not interact with any of the exposures tested.

Discussion: Our results indicate that sedentary behaviour did not moderate the impact of obesity predisposing genes, while alcohol consumption decreased the impact of variation in FTO rs3751812 on BMI. We also observed that variation in FTO rs3751812 interacted with a cumulative environmental risk score to moderate BMI. The growing body of GEI evidence has provided a deeper understanding of obesity aetiology and may have tremendous applications in the emerging field of personalized medicine and individualized lifestyle recommendations. Although the number of gene-environment interaction analyses has increased rapidly across multiple disciplines, addressing methodological concerns such as statistical modeling, confounding, biological assumptions and measurement precision will be necessary to fully exploit the potential of the GEI field. With the development of new methodological and measurement techniques such as hypothesis-free genome wide interaction studies and deep phenotyping, it may be possible to translate the information from GEI studies into public health policy and personalized medicine for obesity and other complex human diseases.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: A predator-prey model in the chemostat with Ivlev functional response

contributor:
Wolkowicz, Gail
Mathematics

subject:
predator-prey system
chemostat
global dynamics
Hopf bifurcation
Ivlev functional response

abstract: It has been shown that the classical Rosenzweig-MacArthur predator-prey model is sensitive to the functional form of the predator response.  To see if this sensitivity remains in the highly controlled environment of the chemostat, we use a predator-prey model with three trophic levels and a Holling type II predator response function.  We first focus on the analysis of the model using an Ivlev functional response.  Local and global dynamics are studied, with global stability of the coexistence equilibrium point obtained under certain conditions.  Bifurcation analysis reveals the existence of a stable periodic orbit that appears via a super-critical Hopf bifurcation.  The uniqueness of this periodic orbit is explored.  Finally, we make comparisons between the dynamics of the model with Ivlev response and Monod response, both of which have nearly identical graphs.  The same sensitivity to functional form is observed in the chemostat as in the classical model.

abstract: Thesis

abstract: Master of Science (MSc)


title: Mass Loss and Preprocessing of Galaxies Traversing Group Environments

title: Mass Loss and Preprocessing of Galaxies in Groups

contributor:
Parker, Laura C.
Wadsley, James
Physics and Astronomy

abstract:
Groups and clusters of galaxies are environments that can significantly influence the evolution of galaxies within them. On average, as galaxies are accreted onto these structures, blue, spiral, star-forming galaxies are transformed into red, elliptical, quiescent galaxies. A number of physical environmental processes can affect the various components of galaxies and each process leaves a signature on their dark matter, gas and stellar content. Additionally, a natural result of the hierarchical growth of structure in the Universe is that more massive clusters accrete smaller groups of galaxies, which may already have exerted an environmental influence on their members. These galaxies may therefore be preprocessed in smaller groups before their final accretion. The implication of preprocessing is that some of the environmental effects attributed to clusters may in fact be established in the group environment.

In this thesis, we concentrate on the final masses and mass loss experienced by galaxies in dense environments and the degree to which they are preprocessed. Using galaxy analogues in a dark matter simulation, we investigate the phenomena of mass segregation and mass loss occurring in groups and clusters and find that tidal effects dominate their halo mass evolution. A large fraction of these galaxy analogues are preprocessed, resulting a large proportion of their total mass loss occurring \emph{before} they are accreted by their final host haloes. We also conduct a high-resolution hydrodynamical simulation of a galaxy group to study the detailed mass loss of individual galaxies in dark matter, gas and stars. We find, again, that tidal stripping dominates the mass loss experienced by these galaxies and that it removes large amounts of dark matter and diffuse gas, while leaving most of their stellar content intact. This differential mass loss results in these galaxies having significantly different stellar mass-to-halo mass (SMHM) relations compared to field galaxies or galaxies that were accreted individually. This work stresses the important role preprocessing plays in galaxy evolution within dense environments and emphasizes the challenges of using galaxy observations containing mixed populations to constrain the effects of evolutionary mechanisms.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Beliefs that Matter: Workplace Religiousness and Spirituality Across Cultures

contributor:
Hackett, Rick D.
Business

subject:
belief
cross-cultural
measurement
psychology of religion
religiousness
workplace spirituality
cognitive science
conceptualization
methodology
integral theory
sanctification
sense-making

abstract: This dissertation takes a sharp methodological turn from prior research on religiousness, spirituality, and culture in organizations by making advances in the study of the structure and role of workplace religio-spiritual beliefs, combining a critical review, theory building, and two empirical sections. The research is based on the premise that the study of individual psychology has yet to address the cross-cultural and domain-specific nature of religio-spiritual beliefs that come to mind naturally in everyday work situations. First, after a case is made for the study of religio-spiritual beliefs, a critical review of the literature provides a comparison of 90 content-based measurement models, and is followed by implications for improving future measurement and research. Second, a conceptual discussion recommends a way forward for a domain-specific conceptualization of religiousness and spirituality and sets a framework for improving methodology, drawing from grounded theory, integral theory, and sense-making methodology. Third, a bottom-up exploration of the religio-spiritual beliefs induced by a variety of workplace situations is conducted through interviews of informants from six major faith traditions, plus the spiritual-but-not-religious. From the analysis, workplace situations, associated beliefs, and mental modules are structured according to the four quadrants of the Workplace Integral Model, each quadrant typified by a different workplace-grounded existential dilemma. Fourth, a higher level of religio-spiritual cognition is accessed through a sense-making methodology, revealing why and how work-related thoughts, self-concepts, and experiences become imbued with religio-spiritual significance, as illustrated in eight modes arranged on a Religio-Spiritual Sense-Making Circumplex. It is hoped that these findings can help set a foundation for future progress with research methods, measurement models, and theory building focused on the religio-spiritual thoughts of a diversity of people in the workplace.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Investigating the use of T cells engineered with a T cell antigen coupler (TAC) receptor as cellular carriers of oncolytic maraba virus

title: TAC-engineered T cells as carriers of oncolytic virus

contributor:
Bramson, Jonathan
Medical Sciences

subject: Oncolytic Virus, T cell, immunotherapy, virus loading, cancer

abstract: The field of immuno-oncology has made tremendous advances in the treatment of cancer. Adoptive cellular transfer (ACT) of tumor-specific T cells and oncolytic viruses (OVs) are powerful anti-tumor agents, but each modality faces significant challenges. Despite the promise of ACT against hematological malignancies, success has been limited in solid tumors. OVs preferentially lyse tumor cells, but have difficulty overcoming antiviral host factors when delivered systemically – therapeutic doses must therefore be quite high to achieve tumor delivery. One means of overcoming viral neutralization is by loading OV onto cellular carriers prior to treatment. Since engineered T cells and OVs both possess anticancer activity, and since viruses naturally associate with nearby circulating immune cells, employing T cells engineered with a T cell antigen coupler (TAC) receptor as viral carriers may offer an ideal combination. Our studies indicated that loading oncolytic maraba virus (MRB) onto T cells – engineered with a TAC receptor targeting HER2 – had no impact on the functionality or receptor expression of these T cells. OV loaded on the surface of these TAC-T cells enabled killing of a variety of tumor targets that may be otherwise resistant to TAC-T cell therapy. Efficacy remains to be elucidated in vivo using xenograft murine models due to the lack of a protective antiviral immune response, which ultimately resulted in encephalopathy. These observed toxicities were likely model-specific, as MRB has shown to be highly attenuated in healthy tissues of wild type models. While conceptually attractive, using TAC-T cells as viral carriers to deliver a multi-pronged, one-pot antitumor therapy directly to the site of the tumor requires further evaluation before considering human studies.

abstract: Thesis

abstract: Master of Science (MSc)


title: Sorption Modelling of Np(IV), Np(V), and Pd(II) on Illite and Montmorillonite Under High Ionic Strength Conditions

contributor:
Nagasaki, Shinya
Engineering Physics

subject:
Sorption
Palladium
Neptunium
Model
LFER
High Ionic Strength
PHREEQC

abstract:
A database is being developed by the NWMO that will be capable of predicting
sorption for key elements of interest onto crystalline and sedimentary rocks in the highly
saline groundwaters and porewaters at DGR depths in Ontario, Canada. Pd(II), Np(IV), and
Np(V) have all been identified as elements of interest by the NWMO. Sorption experiments
of Pd(II) were conducted on illite, bentonite, and shale to investigate the effects that ionic
strength (I), and pH have on sorption. Na-Ca-Cl solutions ranging from 0.01 – 6.0 M I with
pH values between 3 and 9 were considered under aerobic conditions at 25°C for sorption
testing conditions. Sorption data for Pd(II), Np(IV), and Np(V) was used with 2SPNE SC
and 2SPNE SC/CE models developed in PHREEQC to model sorption onto illite and
montmorillonite at different values of I and pH. These models were also used to test
proposed reaction constants from various sources in the existing literature, and to establish
and propose optimized surface complexation constants of our own. Optimized reaction
constants were compared with the LFER to determine its validity across all test conditions.
The LFER was found to not adequately describe sorption of Pd(II), Np(IV), or Np(V) on
either illite or montmorillonite. The JAEA TDB, R04, and R07 THEREDA were all tested
along with the Davies, Debye-Hückel, SIT, and Pitzer computational methods in order to
determine their overall accuracy. The JAEA TDB using the SIT computational method was
found to not be capable of modelling Np(IV) onto illite or montmorillonite in 4.0 M I.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: UNDERSTANDING BIKE SHARE CYCLIST ROUTE CHOICE BEHAVIOR

contributor:
Scott, Darren
Geography

subject:
Active Travel
Bike Share
Cycling
Dominant Route
Route Choice
Shortest Path
Path-Size Logit

abstract:
This thesis examines the existence of a dominant route between a hub pair and factors
that inﬂuence bike share cyclists route choices. This research collects 132,396 hub
to-hub global positioning system (GPS) trajectories over a 12-month period between
April 1, 2015 and March 31, 2016 from 750 bicycles provided by a bike share program
(BSP) called SoBi (Social Bicycles) Hamilton. Then, a GIS-based map-matching
toolkit is used to convert GPS points to map-matched trips and generate a series of
route attributes. In order to create choice sets, unique routes between the same hub
pair are extracted from all corresponding repeated trips using a link signature tool.
The results from t statistics and Path-size logit models indicate that bike share cyclists
are willing to detour for some positive features, such as bicycle facilities and low traﬃc
volumes, but they also try to avoid too circuitous routes, turns, and steep slopes over
4% though detouring may come with a slight increase in turns. This research not
only helps us understand BSP cyclist route preferences but also presents a GIS-based
approach to determine potential road segments for additional bike facilities on the
basis of such preferences.

abstract: Thesis

abstract: Master of Science (MSc)


title: Exploring Retributive School Discipline Practices in Ontario: Voices of the Suspended and Expelled

contributor:
Joseph, Ameil
Social Work

subject:
school discipline
suspension
expulsion
youth
voice

abstract: Through an analysis of 7, semi-structured, one-on-one, open-ended interviews and relying on methodological principles from interpretive social science (ISS) and critical social sciences (CSS) this graduate thesis uncovers the voices of youth who have been suspended and/or expelled from a public secondary school in Ontario. Youth in this study spoke to the impact that being suspended and/or expelled had on school climate through describing the adverse changes that they experienced in regards to their relationships with their peers, and school professionals. A unique contribution from my study is a participant’s description of an experience of suspension, which I interpreted as being caused by, the behavioural targeting of a student living with a disability. Many of the participants also explained how the use of disciplinary procedures that rely on sending a student home from school for x amount of days can affect students’ academic progress and success. Furthermore, the similarities between the treatment of disciplined students in the education system, and the treatment of criminal offenders in the justice system found in this study, included: the use of punitive discipline, increased surveillance, and the involvement of the police in disciplinary processes. The youth in this study recognize that the use of suspension and expulsion does not dig beneath the surface and address the root of the problem, and agree that this approach to school discipline is ineffective in regards to correcting behaviour. Finally, all of the youth in this study suggested the development and implementation of more supportive approaches to addressing and preventing unsafe and inappropriate behaviour in schools that aim to keep students in school while resolving the problem.

abstract: Thesis

abstract: Master of Social Work (MSW)