title: INVESTIGATION OF WELD DEFECTS USING THERMAL IMAGING SYSTEM

contributor:
Hamed, Mohamed
Mechanical Engineering

subject: Laser Welding; Emissivity; Laser-based Weld Defects Detection System; Thermal-Imaging based Weld Defects Detection System; Gaussian Heat Source Model.

abstract: Continuous welding is one of the prominent techniques used in producing seamless piping used in many applications such as the mining and the oil and gas industries.  Weld defects cause significant loss of time and money in the piping production industry. Therefore, there is a need for effective online weld defects detection systems. A laser-based weld defects detection (LBWDD) system has been developed by the industrial partner. However, the current LBWDD system can only detect some geometrically based weld defects, but not material inhomogeneity such as voids, impurities, inclusions, etc. The main objective of this study is to assess the predictability of a thermal imaging-based weld defects detection system (TIBWDD) using an IR camera that can be integrated with the current LBWDD system. The aim of the integrated detection system is to be able to detect a wider range of weld defects. A test rig has been designed and used to carry out a set of emissivity (ε) calculation experiments considering three different materials – Aluminum 5154 (Al), Stainless Steel 304L (SS), and Low Carbon Steel A131 (LCS) with two surface finishes 0.25 μm (FM) and 2.5 μm (RM), which are relevant to  pipe welding operations. Al showed least change in ε varying from 0.162 to 0.172 for FM samples and from 0.225 to 0.250 for RM samples from 50°C to 550°C. LCS showed highest change in ε varying from 0.257 – 0.918 for FM samples and from 0.292 to 0.948 for RM samples. SS showed a consistent increase in ε for both FM and RM samples. Experimental and numerical analysis have been carried out mimicking two sets of possible weld defects investigating defect size, Dh, and distance between effect and sample surface,  δ. Results showed  that the δ based defects that are located  within 3 mm can be detected by the IR camera. Defects with Dh = 1. 5 mm can be detected by the IR camera with and without glass wool. Laser welding simulations using 2D and 3D Gaussian heat source models have been carried out to assess the predictability of a set of possible weld defects. The heat source models have been validated using experimental data. Three sets of defects were considered representing material-based inhomogeneity, step and inclined misalignment defects. For material-based inhomogeneity in thin plates all defects located at 1.25 mm from the surface are found detectable as ΔT (temperature difference obtained on surface) > ΔTmin (detectability limit of TIBWDD system). For inhomogeneity defects in thick plates, except defects of 2.5 mm in square size all other defects were found detectable as ΔT > ΔTmin. All step misalignment defects were detected for thin and thick plates. In the case of inclined misalignment defects, for thin plates, the misalignment error in the thin plate had to be at least 0.275 mm to be detected. In the case of thick plates, the misalignment error had be at least 0.375 mm to be detected.  Overall, results of the present study confirm that thermal imaging can be successfully used in detecting material-based and geometry-based weld defects.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: SOURCE IMAGING IN BRAIN-COMPUTER INTERFACES FOR COMMUNICATION

contributor:
Becker, Suzanna
Connolly, John
Computational Engineering and Science

abstract:
Brain-computer interfaces (BCIs) have incredible potential to allow people with limited communication or no ability for speech to be able to communicate. A BCI can acquire brain signals, analyze them, and interpret them into commands or words. A binary set of mental tasks can be mapped into two words, such as Yes and No, to enable a user to answer a binary tree of questions and sufficiently create a communication system. Although motor imagery tasks are the most established control signals used in the context of asynchronous BCI, they are not suitable for a non-negligible percentage of the users. This issue, known as BCI illiteracy, has been shown to improve when individuals are given greater latitude in the choice of mental tasks employed in operating a BCI. However, differentiating the activation pattern of non-conventional mental imageries (MI) is more challenging than motor imagery. Therefore, finding a good feature space in which machine learning and classification methods can be applied to the data is crucial. While the standard in EEG-based BCIs is to directly analyze the electrode space signals, the measurements are greatly contaminated by the volume conduction effect. To address this issue, a novel approach is to map the EEG signals from electrode space into spatial coordinates of the brain to achieve more distinctive features. Hence, this research is intended to investigate (1) the performance difference of a sensor vs. a source space-based motor-imagery BCI and (2) the effectiveness of source localization using beamforming in non-conventional mental imagery decoding for communication BCI.
Firstly, the efficacy of feature extraction in sensor and source space was experimentally compared via using the Linearly Constrained Minimum Variance (LCMV) beamformer and common spatial patterns (CSP) in a two-class motor-imagery paradigm. The analysis suggests that the LCMV beamformer is informing the classifier with meaningful features and state-of-the-art classification accuracies are achieved by the proposed method.
Secondly, to make individual optimization of BCI control strategies possible, on a participant by participant basis, the most separable control signals among six MI tasks were identified using spectral and connectivity measures extracted from beamformed sources without prior knowledge on the relevant brain regions/networks. It is demonstrated that beamforming can reveal at least one pair of highly classifiable mental commands specific to the participant which can further be employed in the online setup.
Therefore, it is concluded that source space EEG analysis using beamforming, applied to a wide range of mental imagery tasks to select the most separable pair, constitutes a promising framework for further development of BCI systems for communication.

abstract: Thesis

abstract: Master of Science (MSc)


title: New Bounding Methods for Global Dynamic Optimization

contributor:
Khan, Kamil
Chemical Engineering

subject:
Global Optimization
Ordinary Differential Equations
Bounding Methods

abstract:
Global dynamic optimization arises in many engineering applications such as parameter estimation, global optimal control, and optimization-based worst-case uncertainty analysis. In branch-and-bound deterministic global optimization algorithms, a major computational bottleneck is generating appropriate lower bounds for the globally optimal objective value. These bounds are typically constructed using convex relaxations for the solutions of dynamic systems with respect to decision variables. Tighter convex relaxations thus translate into tighter lower bounds, which will typically reduce the number of iterations required by branch-and-bound. Subgradients, as useful local sensitivities of convex relaxations, are typically required by nonsmooth optimization solvers to effectively minimize these relaxations. This thesis develops novel techniques for efficiently computing tight convex relaxations with the corresponding subgradients for the solutions of ordinary differential equations (ODEs), to ultimately improve efficiency of deterministic global dynamic optimization.

 Firstly, new bounding and comparison results for dynamic process models are developed, which are more broadly applicable to engineering models than previous results. These new results show for the first time that in a state-of-the-art ODE relaxation framework, tighter enclosures of the original ODE system's right-hand side will necessarily translate into enclosures for the state variables that are at least as tight, which paves the way towards new advances for bounding in global dynamic optimization.

Secondly, new convex relaxations are proposed for the solutions of ODE systems. These new relaxations are guaranteed to be at least as tight as state-of-the-art ODE relaxations. Unlike established ODE relaxation approaches, the new ODE relaxation approach can employ any valid convex and concave relaxations for the original right-hand side, and tighter such relaxations will necessarily yield ODE relaxations that are at least as tight. In a numerical case study, such tightness does indeed improve computational efficiency in deterministic global dynamic optimization. This new ODE relaxation approach is then extended in various ways to further tighten ODE relaxations.

Thirdly, new subgradient evaluation approaches are proposed for ODE relaxations. Unlike established approaches that compute valid subgradients for nonsmooth dynamic systems, the new approaches are compatible with reverse automatic differentiation (AD). It is shown for the first time that subgradients of dynamic convex relaxations can be computed via a modified adjoint ODE sensitivity system, which could speed up lower bounding in global dynamic optimization.

Lastly, in the situation where convex relaxations are known to be correct but subgradients are unavailable (such as for certain ODE relaxations), a new approach is proposed for tractably constructing useful correct affine underestimators and lower bounds of the convex relaxations just by black-box sampling. No additional assumptions are required, and no subgradients must be computed at any point. Under mild conditions, these new bounds are shown to converge rapidly to an original nonconvex function as the domain of interest shrinks. Variants of the new approach are presented to account for numerical error or noise in the sampling procedure.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THE DESIGN AND EVALUATION OF A KNOWLEDGE TRANSLATION TOOL FOR PREGNANT SOUTH ASIANS AND THEIR PRIMARY CARE PHYSICIANS:  USING A SCALABLE APPROACH TO ADDRESS A PUBLIC HEALTH CHALLENGE IN A PRIORITY POPULATION

contributor:
Anand, Sonia
Health Research Methodology

subject: Knowledge Translation Science & Practice

subject: Life course Epidemiology

subject: Mixed Methods Research

subject: Prenatal Health

abstract:
This study, which is focused on addressing the rising prevalence of gestational diabetes mellitus (GDM) in South Asians begins from the perspective that the development of diabetes has scope across public health and anthropology. The onset and progression are rooted within social determinants of health and cultural practices. Similarly, pregnancy—which is a crucial component of the life course—is a time where not only nutrients are shared between mother and child, but also when knowledge is exchanged, and cultural ways are imparted to the pregnant person from their friends and family. Within the South Asian community of Southern Ontario, recent public health evidence demonstrates a high rate of GDM where 1 in 3 South Asians will develop the condition. Babies born to GDM mothers are of higher birthweight and percent body fat than those of non-GDM mothers. Interventions to prevent GDM are important because GDM itself is a risk factor for postpartum obesity, diabetes, and atherosclerosis in the mother, and also because infants with more adipose tissue are more likely to become insulin resistant in adolescence and develop diabetes and cardiovascular disease as adults.
	Discussions to strengthen the public health response to this challenge can incorporate evidence-based counselling tools (e.g., easily scalable knowledge translation (KT) tools) that can be used by prenatal clinicians providing primary care. Given that diet and physical activity can be influenced not only by an individual locus of control, but also by familial interactions/networks and cultural/traditional foods and expectations, there is a need to better understand and weave in these experiences.  I sought to better understand 1) the prenatal lifestyle counselling experiences of South Asians and their family doctors; and 2) the KT tools that have been designed and used in this population; then I used these learnings to develop and evaluate a conceptually-informed, evidence-based KT tool for pregnant South Asians and their family physicians.
	This dissertation begins with an introduction of patient and provider experiences with lifestyle change. I then present a systematic review and narrative synthesis of prenatal KT tools designed for South Asians. This is followed by a case report that outlines the process taken to develop a patient-facing and provider-facing KT tool (‘SMART START’). Next, I include the design and evaluation of a mixed methods pilot evaluation study of ‘SMART START.’ Finally, I culminate with an epilogue that ties in lessons learned and challenges that were overcome throughout the conduct of this work. The concluding chapter also includes a link to a video that captures the story behind this dissertation and the documentation of how all the aforementioned pieces are nested within and built upon one another.

abstract: Dissertation

abstract: Candidate in Philosophy


title: The Depiction of Abandoned and Lamenting Women in Catullus, Vergil and Ovid

contributor:
Pietropaolo, Mariapia
Classics

subject:
Latin Literature
Lamenting
Abandoned
Catullus, Vergil and Ovid

abstract:
My study focusses on the laments expressed by Ariadne and Dido in the poems of Catullus,
Vergil and Ovid. My study examines the evolution of the character type of the lamenting woman from its Greek origins and portrayal to its presentation in Catullus 64, Aeneid 4 and Heroides 7 and 10. The scholarship and theories of Elizabeth Harvey, Rebecca Armstrong, Bridgitte Libby, Laurel Fulkerson and Sharon James were essential for my understanding and interpretation of these poems. I also consider the implications of male poets writing ventriloquized female voices. Over the course of three chapters, I argue that each of these authors contributes to the development and establishment of a new Romanized theme of the seduced and abandoned lamenting woman and character type. It is evident in each depiction of Ariadne and Dido that the authors build on the standard characterizations in Greek epic and tragedy, and that from these models a new type of lamenting woman emerged. With this project I intend to make a contribution to our understanding of the issues involved in the poetic portrayal of male and female voices in the context of the classical literary tradition of lamenting.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: The aim of this thesis is to examine the motif of the lament of abandoned women in Latin poetry. My study focusses on the laments expressed by the characters of Ariadne and Dido in the ancient poems of Catullus, Vergil and Ovid. My study examines the evolution of the character type of the lamenting woman from its Greek origins and portrayal to its presentation in Catullus 64, Aeneid 4 and Heroides 7 and 10. Over the course of three chapters, I argue that each of these authors contributes to the development and establishment of a new Romanized theme of the seduced and abandoned lamenting woman and character type. With this project I intend to make a contribution to our understanding of the issues involved in the poetic portrayal of male and female voices in the context of the classical literary tradition of lamenting.


title: Dy2ScNbO7: a study of the effect of a disordered B-site on the spin ice magnetism typically seen in dysprosium pyrochlores

title: Dy2ScNbO7: the magnetism of a mixed B-site pyrochlore

contributor:
Wiebe, Christopher
Luke, Graeme
Physics and Astronomy

subject:
Magnetism
Pyrochlore
Geometric Frustration
Spin Ice
Heat Capacity
AC Suceptibility
Muon Spin Relaxation

abstract: The thermodynamics of disorder have been studied for hundreds of years, with physicists using entropy to quantitatively connect the macroscopic properties of a system to its microscopic multiplicity (disorder). Here, we consider the effect of disorder in magnetic materials. The pyrochlore oxides (A2B2O7), comprised of a bipartite lattice of corner-sharing tetrahedra, have been central to the study of geometric frustration for the past several decades. Pyrochlores, in which the A-site is occupied by the magnetic cation dysprosium, tend to exhibit spin ice ordering down to low temperatures, in spite of chemical perturbations to the B-site lattice. With the motivation of this study being the investigation of how adding B-site disorder to the traditional Dy2ScNbO7 form of Dy-pyrochlores, a stoichiometric mixture of Sc-3+ and Nb-5+ was used to synthesize Dy2ScNbO7, the pyrochlore material that is central to this thesis work. We show using magnetometry, heat capacity, muon spin relaxation, and inelastic neutron scattering that the mixed B-site pyrochlore Dy2ScNbO7, does not adopt the spin ice ground state. The low temperature spin dynamics are much faster than other analogous dysprosium pyrochlores, the residual entropy is significantly smaller than that predicted for a spin ice and there are low-lying crystal field excitations. These results all indicate that the B-site disorder appears to destroy the predicted Ising anisotropy of dysprosium.

abstract: Thesis

abstract: Master of Science (MSc)


title: Investigating the Role of Shroom3 in Kidney Development

contributor:
Bridgewater, Darren
Medical Sciences

subject:
Kidney Development
Nephron formation
Shroom3
Nephron progenitor cells

abstract: Nephrons develop from a specialized group of mesenchyme cells known as the nephron progenitors. Nephron progenitors can very dynamic as they can self-renew, migrate, and change their cell morphology. These alterations are essential for orientating and organizing select cells for progression through various stages of nephrogenesis. However, the underlying mechanisms that drive these dynamic morphological changes are not fully understood. Shroom3 is an actin-binding protein that regulates cell shape changes by modulating the actin cytoskeleton. In mice and humans, mutations in Shroom3 are associated with poor nephron function and chronic kidney disease. Despite these findings, the underlying mechanisms of Shroom3 function and how genetic mutations contribute to abnormal nephron formation are unclear. Here, we investigated functional roles for Shroom3 in the nephron progenitor population by analyzing E13.5 and E18.5 Wildtype and Shroom3 deficient mice (termed Shroom3-/-). First, using in-situ hybridization (ISH) and immunofluorescence (IF), we confirm Shroom3 expression in select nephron progenitors. Next, we demonstrated abnormal cell shape and abnormal nephron progenitor cell clustering using H&E staining and Pax2 immunofluorescence. We showed a reduction in nephron progenitor cell numbers and decreased cell length in E13.5 Shroom3-/- kidneys. Using markers of cell orientation, we discovered altered cell orientation in some but not all nephron progenitor cells. While analyzing the cell cytoskeleton, we also demonstrated the abnormal distribution of F-actin in Shroom-/- nephron progenitors. Lastly, immunofluorescence and transmission electron microscopy analysis of Shroom3-/- nephron progenitors confirmed the abnormal shape and reduced filopodia-like thin actin-based membrane protrusions. Our findings conclude that Shroom3 is essential for maintaining and regulating nephron progenitor cell morphology. Taken together, these findings could help explain why Shroom3 mutations are highly associated with kidney disease.

abstract: Thesis

abstract: Master of Science in Medical Sciences (MSMS)


title: An Investigation of Asymmetric Pricing “In the Small” in the Retail Grocery Sector

contributor:
Ray, Sourav
Business

subject: Asymmetric Pricing, Rational Inattention, Strategic Obfuscation, Retailing, Dynamic Pricing; Price Rigidity

abstract:
This dissertation studies asymmetric pricing in the small (APIS), where small price increases outnumber small price decreases, the asymmetry disappearing for larger price changes; and the corresponding reversed phenomenon (APIS-R).  Current evidence suggests retailers deploy these pricing practices despite menu costs and potential consumer concerns.  There is also evidence that inflation is only a partial contributor to the phenomena.  These point to possible strategic intent driving these retail pricing practices.  However, there are only a few papers in the domain, and none specifically address the cross-sectional and longitudinal variations.  Further, existing results are mostly based on a single retailer, limited products, short time span, and legacy datasets dating back to the 1980s and 1990s, leaving their current relevance unsettled.  Recent papers also question if small price changes are measurement artifacts.
This dissertation addresses these gaps by analyzing several large contemporary datasets – a scanner dataset with more than 79 billion price observations and a matching consumer panel dataset with more than 50,000 participating panelists.  Our key results imply the pricing practices can be retailers’ strategic responses to the cognitive tasks faced by consumers.
Chapter 1 is a general introduction to the thesis.  Chapter 2 sets up the fundamentals of the phenomena and reports robust evidence of APIS and APIS-R across the retail price spectrum.  Chapter 3 examines the cross-sectional variations of the phenomena and finds that APIS and APIS-R are associated with product characteristics such as purchase frequency and category price level, as well as retail format such as HILO or EDLP.  Chapter 4 explores the longitudinal variations and finds that business cycles are a major time-varying factor influencing retail practices of APIS and APIS-R.  Chapter 5 concludes with reflections on the findings, implications for theory and practice, limitations, and suggestions for future studies.

abstract: Dissertation

abstract: Candidate in Philosophy

abstract: This dissertation studies asymmetric pricing in the small (APIS), where small price increases outnumber small price decreases, the asymmetry disappearing for larger price changes; and the corresponding reversed phenomenon (APIS-R).  There are only a few papers in the domain, and none explain their cross-sectional and longitudinal variations.  Existing results are mostly based on a single retailer, limited products, short time span, and legacy datasets dating back to the 1980s and 1990s, leaving their current relevance unsettled.  Recent papers also question if small price changes are measurement artifacts.  This dissertation addresses these gaps by analyzing several large contemporary datasets.  The research finds robust evidence of both APIS and APIS-R in the retail price spectrum, and provides explanations for their cross-sectional variation, across products and retailers, as well as longitudinal variations, across business cycles.  The results indicate the pricing practices can be retailers’ strategic responses to the cognitive tasks faced by consumers.


title: Assurance Case Templates: Principles for Their Development and Criteria for Their Evaluation

contributor:
Wassyng, Alan
Computing and Software

abstract:
An Assurance Case (AC) captures and presents explicit reasoning associated with assuring critical properties of a software-intensive system, such as safety. This thesis contributes specifically to how we build effective ACs, and how we can evaluate the quality of an AC. Rather than simply add yet another set of patterns to the existing AC literature, we developed ten principles for constructing ACs from existing safety and security standards. This is our first
contribution in this thesis. An Assurance Case Template (ACT) is a complete assurance case that guides the development of systems within a product line. In most cases, safety-critical systems have to comply with existing standards. Thus, an ACT that complies with a relevant standard can be used to guide development of systems that must comply with that standard. We applied our principles to ISO 26262 (functional safety for automotive vehicles) and SAE J3061 (cyber-security), and used the resulting ACT's specialization in a case study to guide us to pre-emptively mitigate against potential vulnerabilities in automotive over-the-air update implementations. A vital attribute of an AC is to facilitate the identification of fallacies in the validity of any claim. There is considerable published research related to confidence in ACs, which primarily relates to a measure of the soundness of reasoning. Evaluation of an AC should be more general than measuring confidence and should consider multiple aspects of the quality of an AC. Standard evaluation criteria could play a significant role in making the evaluation process more systematic. Another contribution of this research is the identification of effective evaluation criteria for ACs. Concerning this, we developed five criteria for structure evaluation and seven criteria for content evaluation of an assurance case. A final contribution of the thesis is the development of detailed AC evaluation methods that use the aforementioned evaluation criteria from the perspective of the developer of the AC as well as from the perspective of an external reviewer. The evaluation criteria and methods are applied in a simple case study to demonstrate how they may be used in practice.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract:
This thesis contributes specifically to how we build effective Assurance Cases (ACs) for safety-critical systems, and how we can evaluate the quality of an AC. An Assurance Case (AC) captures and presents explicit reasoning associated with assuring critical properties of a software-intensive system, such as safety. Concerning this, we defined principles to develop an Assurance Case Template (ACT) that complies with a standard and applied those principles to
ISO 26262 (functional safety for automotive vehicles) and SAE J3061 (cybersecurity).
An Assurance Case Template (ACT) is a complete assurance case that guides the development of systems within a product line. Later we used the resulting ACT's modification in a case study to guide us to pre-emptively mitigate against potential vulnerabilities in automotive over-the-air update implementation. Furthermore, we defined effective evaluation criteria for an
AC and developed a systematic evaluation process to make it less subjective.


title: The Ethics of Heritable Non-Therapeutic Human Genome Editing

contributor:
Binik, Ariella
Humanities

subject:
genome editing
ethics

abstract: This thesis considers the moral permissibility of heritable non-therapeutic human genome editing. That is, genetic changes that seek to alter the genes of future generations for enhancement and aesthetic reasons. Some examples include genetic changes to muscle mass, cognitive abilities, eye colour, hair texture, skin colour, and so on. Given relevant moral considerations, I argue that the case against heritable non-therapeutic human genome editing is stronger than the case in favour.

abstract: Thesis

abstract: Master of Philosophy (MA)


title: The Effects of Texture on Perceived Step Height

contributor:
Sekuler, Allison
Bennett, Patrick
Psychology

abstract: Falls on stairs are a leading cause of injury and accidental death among older adults. Elliot and colleagues (2015) suggested that high-contrast gratings on step risers could increase perceived step height, thereby encouraging people to lift their feet appropriately to clear steps and reduce the likelihood of a fall. The present study attempted to replicate these findings and investigate the effects of contrast and context on perceived step height in young adults. In all experiments, stimuli were line drawings of a three-step staircase. Experiment 1 measured the perceived height of steps that contained high contrast textures (i.e., vertical square wave gratings) with different spatial frequencies. Grating contrast was manipulated in Experiments 2 and 3. In Experiment 4, stimulus context was varied by removing the top two steps of the staircase.  In each experiment, participants were shown two images in randomized order on each trial: one contained the texture on the bottom step (test step) and the other did not (reference step). Participants judged which image contained the taller bottom step. The height of the reference step varied across trials using the method of constant stimuli, and the point of subjective equality was derived from psychometric functions that were fit to the data. We found that the presence of the texture increased the perceived height of the step and that the size of the effect was nearly constant across spatial frequencies. In addition, the perceived height of the step was greater with low contrast textures than high contrast textures. Finally, removing context reduced the perceived height. These results suggest that the perceived height of a step can indeed be affected by placing a texture on the step riser, which might lead to a safer stepping strategy.

abstract: Thesis

abstract: Master of Science (MSc)


title: Determining the number of classes in latent class regression models

contributor:
McNicholas, Paul
Mathematics and Statistics

subject:
latent class analysis
class enumeration
latent variable models
mplus
simulations
classifcation
mixture models
categorical data
model selection
latent class regression
latent classes
covariates
measurement non-invariance
direct effects

abstract: A Monte Carlo simulation study on class enumeration with latent class regression models.

abstract:
Latent class regression (LCR) is a statistical method used to identify qualitatively different groups or latent classes within a heterogeneous population and commonly used in the behavioural, health, and social sciences. Despite the vast applications, an agreed fit index to correctly determine the number of latent classes is hotly debated. To add, there are also conflicting views on whether covariates should or should not be included into the class enumeration process. We conduct a simulation study to determine the impact of covariates on the class enumeration accuracy as well as study the performance of several commonly used fit indices under different population models and modelling conditions. Our results indicate that of the eight fit indices considered, the aBIC and BLRT proved to be the best performing fit indices for class enumeration. Furthermore, we found that covariates should not be included into the enumeration procedure. Our results illustrate that an unconditional LCA model can enumerate equivalently as well as a conditional LCA model with its true covariate specification. Even with the presence of large covariate effects in the population, the unconditional model is capable of enumerating with high accuracy. As noted by Nylund and Gibson (2016), a misspecified covariate specification can easily lead to an overestimation of latent classes.

Therefore, we recommend to perform class enumeration without covariates and determine a set of candidate latent class models with the aBIC. Once that is determined, the BLRT can be utilized on the set of candidate models and confirm whether results obtained by the BLRT match the results of the aBIC. By separating the enumeration procedure of the BLRT, it still allows one to use the BLRT but reduce the heavy computational burden that is associated with this fit index. Subsequent analysis can then be pursued accordingly after the number of latent classes is determined.

abstract: Thesis

abstract: Master of Science (MSc)


title: Decision Analysis in Shared Decision Making for Thromboprophylaxis During Pregnancy (DASH-TOP) Study

contributor:
Xie, Feng
Health Research Methodology

subject:
Decision analysis
Shared decision-making
Thrombosis
Pregnancy

abstract:
Decision analysis is a quantitative approach to decision-making that could bridge the gap between decisions based solely on evidence and the unique values and preferences of individual patients, a feature especially important when existing clinical evidence cannot support clear recommendations and there is a close balance between harms and benefits for the treatment options under consideration. Low molecular weight heparin for the prevention of venous thromboembolism (VTE) during pregnancy represents one such situation. The objective of this thesis is to explore the use of a decision analysis intervention for shared decision-making for thromboprophylaxis during pregnancy.
This thesis begins with a scoping review that explores the ways in which decision analysis has been used to inform shared decision-making encounters, highlighting key challenges for implementing and evaluating this type of intervention. This is followed by a protocol that presents the methodology of an explanatory sequential mixed methods pilot study for the Decision Analysis in SHared decision making for Thromboprophylaxis during Pregnancy (DASH-TOP) tool. This tool was pilot tested through interviews of eligible women in Canada and Spain who were facing the treatment decision for the prevention of VTE in the antenatal period. While the tool was well received by patients, more effective ways of obtaining patient preferences and presenting the decision analysis results are required to enhance shared decision-making interactions. Finally, this thesis concludes with a reflection on the lessons learned from developing and evaluating a decision analysis intervention for shared decision-making.
The insights from this research have informed the development of an integrated online shared decision-making tool for VTE in the antenatal period, which the DASH-TOP team plans to evaluate in a randomized controlled trial. It is hoped that this information will also provide guidance to researchers interested in developing or evaluating decision analysis interventions for other clinical decisions.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)


title: Creating An Editor For The Implementation of WorkFlow+: A Framework for Developing Assurance Cases

contributor:
Wassyng, Alan
Lawford, Mark
Computing and Software

subject:
Assurance Case
Safety Engineering
Model-Driven Engineering
Domain Specific Language
ISO 26262
Workflow+
Sirius
Eclipse Modeling Framework
Ecore
Safety Case

abstract:
As vehicles become more complex, the work required to ensure that they are
safe increases enormously. This in turn results in a much more complicated
task of testing systems, subsystems, and components to ensure that they are
safe individually as well as when they are integrated. As a result, managing
the safety engineering process for vehicle development is of major interest to all
automotive manufacturers. The goal of this research is to introduce a tool that
provides support for a new framework for modeling safety processes, which can
partially address some of these challenges. WorkFlow+ is a framework that was
developed to combine both data flow and process flow to increase traceability,
enable users to model with the desired granularity safety engineering workflow
for their products, and produce assurance cases for regulators and evaluators
to be able to validate that the product is safe for the users and the public.
With the development of an editor, it will bring WorkFlow+ to life.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Model applications on nitrogen and microplastic removal in novel wastewater treatment

contributor:
Kim, Younggy
Civil Engineering

subject:
Wastewater treatment
Nitrigen removal
Microplastic
Numerical modeling
Model calibration

abstract: Excessive release of nitrogen (e.g., ammonia and organic nitrogen) into natural water systems can cause serious environmental problems such as algal blooms and eutrophication in lakes and rivers, threating the aquatic life and ecosystem balance. Membrane aerated biofilm reactor (MABR) and anaerobic ammonia oxidation (Anammox) are new technologies for wastewater treatment with an emphasis on energy-efficient nitrification and denitrification. Microplastic (MP) is an emerging contaminant in wastewater and sludge treatment that has a negative effect on the environment and public health. For these relatively new technologies and contaminants, mathematical models can enhance our understanding of the removal mechanisms, such as reaction kinetics and mass transport. In this study, mathematical models were developed and utilized to simulate the removal of nitrogen and MP in biological reactions in wastewater treatment processes. Firstly, a comprehensive MABR model was developed and calibrated using a pilot-scale MABR operation data to estimate the important process parameters where it was found that biofilm thickness, liquid film thickness and C/N ratio are key parameters on nitrification and denitrification. Secondly, a mathematical model for Anammox process was developed and calibrated using previous experimental results to simulate the wastewater treatment using Anammox process, reflecting the importance of dissolved oxygen on the nitrogen removal using Anammox bacteria. Thirdly, a granule-based Anammox mathematical model was built and calibrated using other simulation results from previous Anammox studies, showing the significance of operational conditions (e.g., granule diameter and dissolved oxygen) on the success of Anammox enrichment process. Fourthly, an enzyme kinetic mathematical model was constructed and calibrated with lab-scale experiments to simulate the MP reduction using hydrolytic enzymes under various experimental conditions where it was found that anaerobic digesters can be an innovative solution for MP removal during the wastewater treatment processes. Based on the main findings in this study, it can be concluded that mathematical models calibrated with various experimental results are efficient tools for determining the important operational parameters on the nitrogen and MP removal and helping in the design and operation of large-scale removal applications.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Nitrogen and microplastic (MP) are serious contaminants in wastewater that can cause critical environmental and public health problems. Nitrogen can cause algal blooms, threatening the aquatic ecosystem while MP can be ingested by the biota (e.g., fish and seabirds), causing serious damage in the food chain. Nitrogen removal in the conventional biological wastewater treatment is relatively expensive, requiring high energy cost and large footprint for the wastewater treatment facilities. MP removal is also difficult in the conventional wastewater and sludge treatment processes. Therefore, new technologies, including membrane aerated biofilm reactor (MABR), anaerobic ammonia oxidation (Anammox) and hydrolytic enzymes processes, are implemented to improve the nitrogen and MP removal with a reduced energy and resources consumption in wastewater and sludge treatment processes. Numerical models are considered as an efficient tool for better understanding of these novel technologies and the competitive biological reaction in these technologies coupled with accurate estimation of process rates of the reactions. In this thesis, different numerical models were developed and calibrated to estimate the important model parameters, assess the effect of operational conditions on the removal mechanisms and determine the dominant parameters on the removal of nitrogen and MP in the wastewater treatment processes. These numerical models can be used for better understanding of the removal mechanisms of nitrogen and MP, helping in the design and operation of removal systems and addressing novel technologies in large-scale nitrogen and MP removal applications.


title: SHYNESS AND SOCIAL COGNITIVE PROCESSES IN EARLY CHILDHOOD: BIOLOGY, HETEROGENEITY, AND DEVELOPMENT

contributor:
Schmidt, Louis
Psychology

abstract: Shyness is an anxious preoccupation with the self in real or imagined social situations, and can be expressed situationally and temperamentally. Although state and trait shyness have been previously examined in the context of social cognitive outcomes such as Theory of Mind (ToM) and prosocial processes in early childhood, relatively little work has considered 1) the role of self-regulatory capacity in these relations, and 2) the longitudinal and transactional relations between shyness and prosocial behaviors. Chapters 2, 3, and 4 of this dissertation include empirical investigations that aim to address these gaps in the literature. In Chapter 2, I contextualized the previously reported positive relation between expressions of positive shyness and ToM by revealing that this relation may only exist in children with relatively high physiological self-regulatory capacity, as measured by baseline respiratory sinus arrhythmia (RSA). Similarly, in Chapter 3, I demonstrated that only children with high temperamental shyness and low baseline RSA appear to experience the performance deficits that lead to relatively lower cognitive empathic response. Finally, in Chapter 4, I reported a longitudinal relation between early shyness and later affective empathic response. This study also detected a mediating influence of instrumental helping on this longitudinal relation. Collectively, these studies extend and further contextualize relations between individual differences in shyness and developing social cognitive outcomes in early childhood. This dissertation also considers and explores heterogeneity in types of shyness, expressions of state shyness, and prosocial behaviors; highlighting that not all shy children experience similar outcomes and not all children express shyness in the same way.

abstract: Dissertation

abstract: Doctor of Science  (PhD)

abstract: Shyness is an anxious preoccupation with the self in real or imagined social situations, and can be expressed situationally and temperamentally. Individual differences in children’s state and trait shyness have been previously examined in the context of self-other understanding and prosocial behaviors, such as helping and empathy. However, we know relatively little about how shyness affects these behaviors over time or at different levels of children’s self-regulation. This dissertation provides evidence that more adaptive expressions of shyness can be beneficial for children’s self-other understanding in the context of high self-regulation. However, children’s understanding of others’ negative emotions can be constrained by temperamental shyness in the context of low self-regulation. Finally, early temperamental shyness can have long-term, rather than concurrent, effects on later empathic functioning. Collectively, this dissertation contextualizes relations between individual differences in shyness and developing social outcomes in early childhood.


title: IMMUNE SYSTEM MODULATION BY LOW DOSE IONIZING RADIATION

contributor: Dr. Carmel Mothersill, Dr. Colin Seymour

subject: Low dose ionizing radiation; adaptive response to radiation; bystander effects; genomic instability; immune responses

abstract:
The historical narrative and our understanding about the low dose effects of radiation on the immune system has changed drastically from the beginning of the 20th century to now. A paradigm shift from the DNA target hit model to the one that also considers non-targeted effects (NTE) has attracted a lot of interest recently. Investigations to delineate mechanisms of NTE in the biological tissue have been carried out by various research groups where radiation induced genomic instability (RIGI), bystander effect (RIBE) and abscopal effect (AE) are the effects with most evidence available. This thesis addresses the question of whether low dose ionizing radiation (LDIR) stimulates or suppresses the immune system and how NTEs contribute to this immune modulation by adopting a two-pronged approach where first a narrative review constituting the introduction and literature review was performed followed by a systematic review using PRISMA guidelines to synthesize existing LDIR literature.
This was prompted by our recent discovery that UVA photons are emitted by the irradiated cells and that these photons can trigger bystander effects in unirradiated recipients of these photons. Given the well-known association between UV radiation and the immune response, where these biphotons may pose as bystander signals potentiating processes in deep tissues as a consequence of ionising radiation, it is timely to revisit the field with a fresh lens. After reviewing various pathways and immune components that contribute to the beneficial and adverse effects induced by LDIR, it was found that these modulations can occur by way of NTE. However, the exact mechanistic underpinnings are still unclear and the literature examining low to medium dose effects of ionising radiation on the immune system is complex and controversial. Early work was compromised by lack of good dosimetry while later work mainly focuses on the involvement of immune responses in radiotherapy which typically uses high dose radiation. There is a lack of research in the LDIR/NTE field focussing on immune responses although bone marrow stem cells and lineages were critical in the identification and characterisation of NTE. This may be in part, a result of the difficulty of isolating NTE in whole organisms which are essential for good immune response studies. Models involving inter organism transmission of NTE are a promising route to overcome these issues. It is concluded that the simple question of whether LDIR stimulates or suppress the immune system is not as simple as initially hypothesized. An attempt was made to analyze if LDIR shifts the balance to immune suppression or enhancement via systematic review but, due to too many differences in the experimental methods in the current radiation and immune studies, a cookie-cutter answer was not possible. However, this thesis did point out the areas of concern such as lack of standardised tools in the field of radiobiological experimental research and quality of methods used which requires urgent attention.

abstract: Thesis

abstract: Master of Science (MSc)


title: A μSR Study of Current-Induced Destruction of Order in 1% Ti Doped Ca2RuO4

contributor:
Luke, Graeme
Physics and Astronomy

abstract:
Due to its electrically activated phase transition from an insulator to a metal, Mott
insulator Ca2RuO4 is a material with great potential in researching phase transitions
and application of bolometric devices. Although pure Ca2RuO4 is very unstable and
thus difficult to obtain in bulk, single-crystal form, a 1% doping of Ti for Ru stabilizes
the material with minimal influence on its magnetic and electrical properties. This thesis
uses μSR techniques to look at a single crystal of 1% Ti doped Ca2RuO4 under current in
order to investigate the magnetic ordering of the material in its metallic state. From this
we determine that Ca2RuO4 undergoes a destruction of long-range order when under
sufficient current to induce its metallic state if one assumes adequate cooling power of
the cryostat. In order to confirm the cooling power of the cryostat used, analyses on
the Joule heating from the sample was performed, yielding mixed results, causing the
question of whether this data was collected below the currentless ordering temperature
of Ca2RuO4 to go unanswered.

abstract: Thesis

abstract: Master of Science (MSc)


title: Dynamical Modification of a Primordial Population of Binaries in Simulations of Star Cluster Formation

title: Primordial Binaries and Star Cluster Formation

contributor:
Sills, Alison
Harris, William E.
Physics and Astronomy

subject:
astronomy
computational astrophysics
star clusters
binary stars

abstract:
Most star formation in galaxies takes place in embedded clusters, within Giant Molecular
Clouds (GMCs). Stars also generally form as part of binary star systems, with almost
all massive stars having at least one close companion. Binaries shape the physical properties
of older star clusters by setting their central density and ejecting low-mass stars,
but also play a role during cluster formation by modifying the mechanical and radiative
feedback from massive stars and shedding enriched material in the cluster’s gas reservoir.
Conversely, dynamical interactions between stars in dense stellar environments are
known to form, modify, and destroy binary systems. In consequence, the populations
of binaries observed in the Galactic field and in old stellar clusters are understood to
be shaped by a combination of the physics of star formation and subsequent dynamical
interactions in embedded clusters, although the relative importance of these processes
remains unknown. In this thesis, we implement a prescription for an initial population of
binaries in the coupled N-body and radiation hydrodynamics star cluster formation code
Torch, and investigate how this initial population is modified in the earliest stages of
cluster formation, while gas and stars coexist. As an ansatz for the initial population of
binaries, we use the properties of main-sequence binaries in the Galactic field. We first
perform a suite of simulations initialized from a 10^4 M⦿  cloud, in which the simulations
only differ by their stellar content (i.e. presence or absence of an initial population of
binaries, and stochasticity of star formation). We compare the populations of binaries
identified 1.2–2 Myr after the onset of star formation and find that an initial population
of binaries is needed at all masses to reproduce the multiplicity fraction observed in
main-sequence stars. We also show that this initial population is modified in a systematic
manner before the effects of feedback from massive stars shape the gas. We further
find evidence of both preferential formation and preferential destruction of binaries via
dynamical interactions. The net effect of these interactions shifts the distributions of
primary masses and semi-major axes to lower values, and the distributions of mass ratios and eccentricities to larger values. In a second time, we perform simulations with different
virial parameters and initial turbulent velocity patterns, and find that the trends
previously identified are robust to those changes in our initial conditions. We however
find that both the virial parameter and the initial turbulent velocity pattern have a
strong influence on the star formation rate, and therefore on the rapidity with which
the distributions are modified. We conclude that dynamical interactions in embedded
clusters are important for shaping the populations of binaries observed in the MilkyWay,
thus opening the floor to future investigations of the impact of binaries on star cluster
formation.

abstract: Thesis

abstract: Master of Science (MSc)


title: On the Asymptotic Rate-Distortion Function of Multiterminal Source Coding Under Logarithmic Loss

contributor:
Chen, Jun
Electrical and Computer Engineering

subject:
Multiterminal source coding
rate-distortion theory
logarithmic loss

abstract:
We consider the asymptotic minimum rate under the logarithmic loss distortion constraint. More specifically, we find the asymptotic minimum rate expression when given distortions get close to 0. The problem under consideration is separate encoding and joint decoding of correlated two information sources, subject to a logarithmic loss distortion constraint.
We introduce a test channel, whose transition probability (conditional probability mass function) captures the encoding and decoding process. Firstly,  we find the expression for the special case of doubly symmetric binary sources with binary-output test channels. Then the result is extended to the case where the test channels are arbitrary. When given distortions get close to 0, the asymptotic rate coincides with that for the aforementioned special case. Finally,  we consider the general case and show that the key findings for the special case continue to hold.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Quantifying Trust in Deep Learning Ultrasound Models by Investigating Hardware and Operator Variance

contributor:
Noseworthy, Michael
Biomedical Engineering

subject: Ultrasound, Deep Learning, Machine Learning, K-Means Clustering, Trust, Hardware Variance, Operator Variance

abstract:
Ultrasound (US) is the most widely used medical imaging modality due to its low cost, portability, real time imaging ability and use of non-ionizing radiation. However, unlike other imaging modalities such as CT or MRI, it is a heavily operator dependent, requiring trained expertise to leverage these benefits.

Recently there has been an explosion of interest in artificial intelligence (AI) across the medical community and many are turning to the growing trend of deep learning (DL) models to assist in diagnosis. However, deep learning models do not perform as well when training data is not fully representative of the problem. Due to this difference in training and deployment, model performance suffers which can lead to misdiagnosis. This issue is known as dataset shift. Two aims to address dataset shift were proposed. The first was to quantify how US operator skill and hardware affects acquired images. The second was to use this skill quantification method to screen and match data to deep learning models to improve performance.

A BLUE phantom from CAE Healthcare (Sarasota, FL) with various mock lesions was scanned by three operators using three different US systems (Siemens S3000, Clarius L15, and Ultrasonix SonixTouch) producing 39013 images. DL models were trained on a specific set to classify the presence of a simulated tumour and tested with data from differing sets. The Xception, VGG19, and ResNet50 architectures were used to test the effects with varying frameworks. K-Means clustering was used to separate images generated by operator and hardware into clusters. This clustering algorithm was then used to screen incoming images during deployment to best match input to an appropriate DL model which is trained specifically to classify that type of operator or hardware.

Results showed a noticeable difference when models were given data from differing datasets with the largest accuracy drop being 81.26% to 31.26%. Overall, operator differences more significantly affected DL model performance. Clustering models had much higher success separating hardware data compared to operator data. The proposed method reflects this result with a much higher accuracy across the hardware test set compared to the operator data.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: The Effect of School Closures on Housing Prices in Hamilton, Ontario

contributor:
Paez, Antonio
Geography and Earth Sciences

subject:
housing
econometrics
spatial analysis
spatial regression
schools
real estate

abstract:
Is school accessibility a valued good, and do school closures affect house prices?
This thesis applies two different methods of hedonic regression analysis, augmented
by spatial regression methods, to a dataset of Hamilton real estate
transactions (2005-2017) to investigate whether the closure of a school in an
urban neighbourhood negatively affects house prices in that closed school
catchment.
Evidence is found that school accessibility is a valued good, and that the closure
of a primary school will negatively affect house prices from the period of closure
announcement through several subsequent quarters. The use of spatial analysis
corrects for bias in coefficient estimates.

abstract: Thesis

abstract: Master of Arts (MA)

abstract:
Do homebuyers pay a premium to be located closer to a school, and do school
closures affect house prices?
An analysis of Hamilton real estate transactions (2005-2017) finds evidence
that houses closer to schools sell for more, and that a primary school closure
has a negative impact on local house sale prices.


title: Unwrapping the Emporium: Hudson’s Bay Company and the Legacy of Department  Store Management in the Global Culture of Retailing

contributor:
Weaver, John C.
History

subject:
Canadian History
Transnational History
Department Stores
Consumerism and Consumption
Globalization
Retailing and Retail History
Business History
Hudson's Bay Company (HBC)
Branding and Marketing
Management History
Managerial Techniques
Internationalization
E-commerce
Nationalism
Corporate Identity

abstract: Between the 1850s to the 1960s, the department store emerged as a prominent retail format worldwide. As a retail format, the department store model broke away from pre-existing retailer and consumer conceptions of shopping and the shopping environment. Store leaders placed their focus on creating an uplifting mode of consumerism that perpetuated the department store as an ‘experience.’ However, behind the department store’s ‘magical’ façade, store management preplanned and manipulated consumer interactions with every part of the store. The managerial techniques managers used allowed these institutions to become an epicentre of consumerism and urban culture globally. The department store has lost its reputation as a vibrant shopping location in the digital age, and retailers and consumers alike have disregarded it as solely a monument of retail nostalgia. Nonetheless, today’s retailers still have much to learn from the ways department store leaders innovated. The management techniques used in department stores can provide insight into these institutions’ successes and pitfalls when navigating changing retail circumstances. If the department store is used as a tool of managerial know-how for retailers in the digital age, it could allow other retailers to sustain a semblance of the department store’s longevity, commercially and culturally. Hudson’s Bay, a remaining store in the Canadian department store industry, features as a case study to highlight the extent to which department store leaders designed and managed their stores.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This thesis examines the department store’s legacy as a tool of managerial know-how for retailers in the digital age. From the 1890s to the 1960s, department stores were an epicentre of consumerism and urban culture in locales worldwide. Department store management crafted store environments to create a ‘magical’ atmosphere for customers while calculating every consumer interaction with the store behind the scenes. Over the twentieth and twenty-first centuries, increased retail competition has forced many stores to close, often leaving visual façades as the sole reminders of some defunct stores. Yet, the extensive management techniques used inside and outside stores provide insight into how this retail format achieved prominence, how its leaders responded to competitors, and how department store management techniques can contribute to current retail discussions despite its continued decline.


title: From Physical Activity to Brain Activity: An Exercise Science and Functional Neuroimaging Study of Pediatric Concussion

title: EXERCISE, NEUROIMAGING, AND PEDIATRIC CONCUSSION

contributor:
Timmons, Brian W
Medical Sciences

subject:
Concussion
Exercise science
Neuroimaging
fMRI

abstract:
Concussion management is changing. Recent years have marked a sea change, with the former rest-is-best approach being supplanted by an exercise-is-medicine mindset. Despite this, important questions remain unanswered in the pediatric exercise-concussion literature. The overarching aim of this thesis was to examine the effects of exercise on outcomes beyond concussion symptoms, and build our understanding of the relationship between pediatric concussion and physical activity.
Four studies were performed to this end. First, per a systematic review, we found that randomized trials on the effects of exercise on neuroimaging and cognitive outcomes remain limited. Studies suggest that exercise may improve brain structure and function post-concussion, while data with respect to cognitive outcome were mixed. Second, we provided the first evidence that the functional neuropathology of pediatric concussion differs by sex at 1 month post-injury, with females demonstrating impairment not observed in males. Namely, only females with concussion showed patterns of both hyper-connectivity (between the lateral pre-frontal cortex & inferior frontal gyrus, lateral pre-frontal cortex & lateral occipital cortex, and the posterior cingulate cortex & cerebellum; all p-corrected <0.05) and hypo-connectivity (between the anterior cingulate cortex & precuneus, anterior cingulate cortex & cingulate gyrus, and posterior cingulate cortex & paracingulate gyrus; all p-corrected <0.05). Third, we provided the first accelerometer-based characterization of physical activity and sedentary time in children with concussion in comparison to 1:1 matched healthy controls. Relative  to healthy controls, children with concussion were more sedentary, with a mean difference [MD] of 38.3 minutes/day (95% confidence interval [CI] 11.2 to 65.4, p<0.01), and they also performed less light (MD -19.5 minutes/day, CI -5.3 to -33.7, p<0.01), moderate (MD -9.8 minutes/day, CI -5.7 to -13.8, p<0.001) and vigorous physical activity (MD -12.0, CI -6.9 to -17.2, p<0.001); greater physical activity deficits were observed in females with concussion. Fourth, per the first study to employ both accelerometry and functional neuroimaging in pediatric concussion, we found that intra-network connectivity of the default mode network was associated with subsequent accelerometer-measured light (F(2, 11) = 7.053, p = 0.011,  Ra2 = 0.562; β = 0.469), moderate (F(2, 11) = 6.159, p = 0.016,  Ra2 = 0.528; β = 0.725), and vigorous (F(2, 11) = 10.855, p = 0.002,  Ra2 = 0.664; β = 0.792) physical activity. This study provides the insight into a potential link between brain activity and physical activity in pediatric concussion. The next wave of exercise and physical activity research in concussion needs to move beyond symptom studies, employ sex-specific analyses, understand the impact of exercise on brain function, and consider interventions that increase habitual physical activity. Doing so is necessary for exercise to become medicine for concussion patients.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Until a few years ago, the advice children received after a concussion (or mild brain injury) was to rest until they no longer had symptoms. But the way concussions are being treated is changing. Scientists have found that exercising soon after a concussion can lessen symptoms. It is no longer thought that rest-is-best. Instead, it is now believed that exercise-is-medicine. But there are still important questions about the role of exercise after a concussion that have not been answered. The four studies in this thesis had the goal of answering some of those questions. In the first study, we found that while exercise improves symptoms after a concussion, we know less about how it impacts the brain and our ability to think. From the second study, we learned that a concussion impacts the brains of boys and girls in different ways, and that girls may have longer lasting brain changes after a concussion than boys. Our third study showed that after a concussion, girls take part in less physical activity than boys throughout the day. The fourth study suggests that there may be a link between brain activity and physical activity in children with a concussion. This thesis adds to our knowledge of the role of exercise in concussion. It also raises some important questions that should be answered by new studies in the near future.


title: Towards EEG-based biomarkers of large scale brain networks

contributor:
Becker, Suzanna
Neuroscience

subject:
EEG
fMRI
Machine Learning
Brain Networks
Graph theory

abstract:
Several major functional networks in the brain have been identified, based on sub-regions in the brain that display functionally correlated, synchronous activity and perform common cognitive functions. Three such brain networks (default mode network - DMN, central executive network - CEN, and salience network - SN) form a tri-network model of higher cognitive functioning and are found to be dysregulated in a number of psychopathologies, such as PTSD, autism, schizophrenia, anxiety, depression, bipolar disorder and fronto-temporal dementia (FTD). Current therapies that improve the patient’s cognitive and behavioural states are also found to re-normalize these dysregulated networks, suggesting a correlation between network dysfunction and behavioural dysregulation. Hence, assessing tri-network activity and its dynamics can be a powerful tool to objectively assess treatment response in such psychopathologies. Doing so would most likely rely on functional magnetic resonance imaging (fMRI), as one of the most commonly used modalities for studying such brain networks. While fMRI allows for superior spatial resolution, it poses serious challenges to widespread clinical adoption due to MRI's high operational costs and poor temporal resolution of the acquired signal. One potential strategy to overcome this shortcoming is by identifying the activity of these networks using their EEG-based temporal signatures, greatly reducing the cost and increasing accessibility of using such measures. This thesis takes a step towards improving the clinical accessibility of such brain network-based biomarkers.

Doing so first required the exploration of a popular EEG-based method currently being used to study brain networks in mental health disorders - Microstates. This work uncovered flaws in the core assumptions made in assessing Microstates, necessitating the development of an alternate method to detect such network activity using EEG. To accomplish this, it was important to understand the healthy dynamics between the three brain networks constituting the tri-network model and test one of the core predictions of this model, i.e. the SN gates the DMN and CEN activation based on interoceptive and exteroceptive task demands. Probing this question next uncovered mechanistic details of this process, discovering that the SN co-activates with the task-relevant network. Using this information, a novel machine learning pipeline was developed that used simultaneous EEG-fMRI data to identify EEG-based signatures of the three networks within the tri-network model, and could use these signatures to predict network activation. Finally, the novel machine learning pipeline was trialed in a study investigating the effects of lifestyle interventions on the network dynamics, showing that CEN-SN synchrony can predict response to intervention, while DMN-SN synchrony can develop in those that fail to respond. The understanding of healthy network dynamics gathered from the earlier study helps interpret these results, suggesting that the non-responders persistently activated DMN as a maladaptive strategy.

In conclusion, the studies discussed in this thesis have improved our understanding of healthy network dynamics, uncovered critical flaws in currently popular methods of EEG-based network analysis, provided an alternative methodology to assess network dynamics using EEG, and also validated its use in tracking changes in network synchrony. The identified EEG signatures of widely used functional networks, will greatly increase the clinical accessibility of such brain network measures as biomarkers for neuropathologies. Monitoring the level of network activity in affected subjects may also lead to the development of novel individualized treatments such as brain network-based neurofeedback interventions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Synergistic activity in specific brain regions gives rise to large-scale brain networks, linked to specific cognitive tasks. Interactions between three such brain networks are believed to underlie healthy behavior and cognition, and these are found to be disrupted in those with mental health disorders. The ability to cheaply and effectively detect these networks can enable routine network-based clinical assessments, improving diagnosis of mental health disorders and tracking their response to treatment. The first study in this thesis found major flaws in a popular method to assess these networks using a suitably cheap imaging method called electroencephalography(EEG). The remainder of the thesis addressed these issues by first identifying healthy patterns of network activity, followed by designing a novel method to identify network activity using EEG. The final study validates the developed method by tracking network changes after lifestyle interventions. In sum, this thesis takes a step towards improving the clinical accessibility of such brain network-based biomarkers.


title: GETTING US ALL ON THE SAME PAGE: A SCOPING REVIEW OF SHARED MENTAL MODELS IN ACUTE CARE MEDICAL TEAMS

contributor:
Monteiro, Sandra
Health Science Education

subject:
Team Cognition
Health Science Education
Shared Mental Models

abstract: Purpose: Shared mental models (SMMs) represent commonly held understandings of task and team related knowledge within a team. Thought to facilitate implicit and adaptive coordination without the need for explicit communication, the construct has been thoroughly studied in non-health care settings. There has been increasing interest in the topic in the healthcare setting, but recent reviews have found that the construct is poorly defined and has significant heterogeneity in how it is measured (Floren et al., 2018). We conducted a scoping review examining the construct of SMMs in medical teams within the acute care setting. Method: Following the Arksey and O’Malley (2005) framework, five data bases were searched: Medline, CINAHL, PsychInfo, Web of Science, and Embase. Eligible studies examined SMMs in the context of medical teamwork in the acute care setting. Definitions, methods, and general study characteristics were examined. Results: Of the 1397 articles retrieved, 25 met eligibility criteria. The studies encompassed a variety of areas of clinical practice. There was no common definition for SMMs across the studies examined. The majority of studies (20/25) used quantitative methods with surveys, questionnaires, and observation being the most common. Conclusions: The construct of the SMM is poorly defined in the setting of acute care medical teams. Although many standard types of SMM measurement exist, few of the studies used these common methods. The lack of direct measurement of SMMs, especially in the case of observation, questions the validity of these studies. We propose a definition for SMMs in this context and a path forward for studying SMM in the acute care setting.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Health care is a team sport and as health care systems become more complex, teamwork becomes increasingly important. However, a team of experts does not make an expert team and highly effective teams possess a particular set of characteristics that allow them to perform high quality care. One characteristic that is receiving an increasing amount of attention is the Shared Mental Model. The purpose of this study was to examine what is already known about these shared mental models in the context of acute care medical teams. This study will act as a launching point for future research exploring how teams think and how it impacts the quality of care they can provide.


title: Wavelength Dependent Free-Carrier Absorption Pump/Probe Spectroscopy of Silicon

contributor:
Kleiman, Rafael
Engineering Physics

abstract: The wavelength dependence on the free carrier absorption (FCA) cross-section has been explored using pump-probe spectroscopy. Until now the determination of the cross-section over a wavelength range using a completely optical method of carrier injection has yet to be done. For the first time, measurements are done at wavelengths less than 1000 nm which contributes to the overall measurement range of 935 to 2500 nm. In most cases, the work presented here agrees with literature values that have been reported at single wavelengths for optical injection methods. However, when compared to literature that uses non-optical injection methods, such as the introduction of dopants, there is a clear discrepancy between the methods. The cross-section for non-optical methods is roughly twice that when compared to the optical method though the curvature is consistent throughout. We believe this discrepancy comes from how carriers are scattering within doped and lightly doped materials. Since the process of FCA requires a momentum-conserving scattering event to occur, the dominant scattering mechanism must influence the magnitude of the FCA cross-section in some way. FCA upon optical injection is dominated by electron-hole scattering whereas FCA upon injection by dopants is facilitated through impurity scattering. As the doping level increases, not only will there be more carriers to collide with and scatter, but the process also introduces charge donor or acceptor atoms that can act as additional scattering sites resulting in a naturally higher cross-section.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: p14 viral fusion protein driven cell-cell fusion induces micronuclei formation and a STING-dependent interferon response

contributor:
Mossman, Karen
Biochemistry and Biomedical Sciences

subject: Stress induced interferon responses

abstract: The innate immune system is the first line of defence against viral infections. Conventionally, innate immune activation begins with the detection of foreign nucleic acids by pattern recognition receptors (PRRs), which triggers a signalling cascade that culminates in the production of interferon (IFN) and other inflammatory cytokines and chemokines. Over the past few years, a number of studies have shown that IFN innate immune responses can also be triggered by stressors, such as membrane perturbations, cytoskeletal perturbations, oxidative stress, and endoplasmic reticulum (ER) stress 1–3. One way that some viruses provoke such stress responses is through membrane and cytoskeletal distortions during enveloped virus particle entry. In some cases, the glycoproteins responsible for virus particle entry can also trigger cell-cell fusion. The potential of cell-cell fusion to induce stress-based IFN responses analogous to those triggered by virus-cell fusion has not been addressed until very recently. To investigate if and how cell-cell fusion may induce antiviral mechanisms and IFN responses we used the reptilian reovirus p14 fusion associated small transmembrane (FAST) protein as a model of cell-cell fusion. We found that p14-mediated cell fusion led to the production of low level IFN and upregulation of interferon stimulated genes (ISGs) in a stimulator of interferon genes (STING) and interferon regulatory factor 3 (IRF3) dependent manner. We also observed that multinucleated cells experienced extensive DNA-damage that led to the accumulation of cytosolic DNA in the form of micronuclei. Micronuclei can be detected by cytosolic DNA PRRs like cyclic GMP-AMP synthase (cGAS) and signal IFN production through the cGAS-STING signalling axis. Additionally, early syncytia formation restricted replication of vesicular stomatitis virus (VSV), herpes simplex virus-1 (HSV), and vaccinia virus (VSV) in an IFN and IRF3 independent, and STING dependent manner, suggesting involvement of either a novel antiviral mechanism or suppression of virus replication and spread by biological changes in syncytial cells, such as cell cycle arrest. This study highlights a key role of DNA sensing pathways in the immune response to cell fusion associated stress and points out the importance of fusion kinetics in the selective advantage of syncytial viruses. Understanding the potential of syncytial cells to induce IFN responses and influence viral replication at a mechanistic level is beneficial to the design of improved oncolytic immunotherapy.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Viruses and their hosts continuously fight each other for survival. The host tries to protect itself from the virus by activating various features of its immune system, while the virus tries to block and evade detection by the immune system. One way that some viruses attempt to bypass the immune system and enhance spread involves expressing proteins that can merge together infected cells with neighboring uninfected cells. Cell-cell fusion disrupts the balanced environment within the cell, which is a form of stress that may activate immune responses. This work investigates if and how host cells may activate the immune system to respond and protect themselves from the cell merging activity of select viruses. We found that the stress associated with existing as a large, fused cell caused DNA damage and fragmentation. These DNA fragments could stimulate key immune sensors and initiate immune responses. We also observed an impaired ability of viruses to infect fused cells, but this restriction was not associated with typical immune responses, suggesting that some other biological change in fused cells created an environment that is not suitable for viral spread. Further investigation is required to fully understand this phenomenon; however, this study highlights some protective mechanisms of the host immune system in response to the stress of viral fusion protein induced cell-cell fusion.


title: TAC Engineered γδ T cells for Multiple Myeloma

contributor:
Bramson, Jonathan
Biochemistry and Biomedical Sciences

abstract: Engineered T cell therapies have had unprecedented success in treating hematological malignancies. However, their use is limited by expensive treatment costs – priced at approximately $500,000 CAD for a single-dose of CAR-T cell therapy. γδ T cells are a candidate for allogeneic engineered T cell therapies, which can be mass manufactured to reduce the cost of goods. In this thesis we investigate γδ T cells engineered with a T cell Antigen Coupler targeting BCMA (BCMA-TAC) for the treatment of Multiple Myeloma – an incurable hematological malignancy. We optimized a manufacturing method to transduce γδ T cells with a GaLV-pseudotyped γ-retrovirus encoding BCMA-TAC and demonstrated that BCMA-TAC γδ T cells rapidly and specifically kill Multiple Myeloma tumour cells. We also investigated the potential for a combination therapy using engineered γδ T cells and monoclonal antibodies. Such a combination therapy may be synergistic, because γδ T cells express CD16 and can respond to antibody opsonized cells via direct cytotoxicity or phagocytosis. While degranulation of BCMA-TAC γδ T cells was enhanced by CD16 stimulation, we did not observe any improvements in direct cytotoxicity against antibody-opsonized tumour cells. Overall, our results demonstrate that BCMA-TAC γδ T cells can directly target and kill Multiple Myeloma tumour cells, but whether monoclonal antibodies can be used to further enhance their anti-tumour properties remains unclear.

abstract: Thesis

abstract: Master of Science (MSc)


title: A Combined Approach to Vulnerability for Research Ethics

contributor:
Binik, Ariella
Philosophy

subject: Vulnerability; Research Ethics; Bioethics;

abstract:
There is a problem associated with the concept of vulnerability for research ethics. This problem is that we must identify populations in need of additional protections while also delineating these protections. Some have argued that the concept is too nebulous to warrant use since an increasing number of individuals may be deemed vulnerable such that virtually everyone is vulnerable in some way. In opposition to this, many have argued that that the concept of vulnerability needs to be more specific. In this thesis, I evaluate the concept of vulnerability in a number of ways. I touch on rejections of the concept, the history of the concept though both research guidelines and research ethics and seek to explore a way forward to a more useable account of vulnerability. I argue that no current account of vulnerability is adequality able to address the challenging questions posed by research trials involving human participants.
	A persuasive account of vulnerability should (1) have a plausible/persuasive definition of vulnerability; (2) figure out what the application of a theory of vulnerability looks like; and (3) what obligations or duties are owed to the vulnerable (and who is responsible for fulfilling these duties). In order to address this, I propose the Combined approach to vulnerability. This approach defines vulnerability as an increased likelihood to incur additional or greater wrongs. The Combined approach functions like a taxonomy and categorizes vulnerability into three groups with the use of layers and restricts the application of these layers with its formal the definition of vulnerability.
	This thesis marks a new novel contribution to the field of research ethics, in the way of a new theory to vulnerability that emerges from the current literature and makes progress towards a more useful concept of duties and obligations owed to the vulnerable grounded communal engagement.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: Vulnerability as a concept is thoroughly debated in the field of research ethics. Some argue that the concept is useless, while others argue that the concept of vulnerability needs to be more specific about who it applies to and why. This thesis situates itself within the latter side of the debate. The Combined approach to vulnerability is my answer to this question. The Combined approach defines vulnerability as an increased likelihood to incur additional or greater wrongs. The Combined approach functions like a taxonomy and categorizes vulnerability into three groups (inherent layers, contextual layers, cascade layers) with the use of the metaphor of layers and restricts the application of these layers with its formal the definition of vulnerability. The main contributions of this approach are its novel combination as well as its new approach to the duties owed to the vulnerable.


title: Towards a Critical History of The Writers' Union of Canada, 1972 - 1992

contributor:
York, Lorraine
English and Cultural Studies

subject:
Canadian Literature
Canadian Literary History
Writers' Union of Canada
Archival Research
Equity
Labour
Literary Activism
Literary Celebrity
Women Writers
BIPOC Writers
Union Organizing
Appropriation

abstract: The Writers’ Union of Canada was founded in November of 1973 “to unite Canadian writers for the advancement of their common interests.” Drawing on extensive archival collections – from both the Writers’ Union and its member authors – this dissertation offers the first critical history of the organization and its work, from pre-founding to the early 1990s, arguing that the Writers’ Union has fundamentally influenced Canadian literature, as an industry, as a community, and as a field of study. I begin by tracing the contextual history of the organization’s founding, interrogating how union organizing, celebrity, and friendship underpin the organization’s work. Chapter One discusses the Writers’ Union’s programs, reforms, and interventions aimed at ‘fostering’ writing in Canada as I argue that the Union was instrumental in building a fiscal-cultural futurity for CanLit. In Chapter Two, I consider the role that women played in this important work, as I highlight the labour of female Union members and the all-female administrative staff, who maintained and supported the organization’s work through its first twenty years. In Chapter Three I draw attention to the stories of, perspectives of, and experiences of BIPOC authors in relation to the Writers’ Union. While the Writers’ Union’s involvement in race relations is often positioned as having ‘begun’ with the Writing Thru Race conference in 1994, this chapter uses the archives to reveal a much longer trajectory of racialized conflict within and around the organization, providing important context for the very controversial and public battles about appropriation and race that would explode in the late 1980s and early 1990s. Throughout this work, I look to see how institutional narratives are deployed and upheld, and to what ends; how successful advocacy work is often effaced and forgotten; how institutional structures function; and how their boundaries and intentions are challenged and developed over time.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: The Writers’ Union of Canada was founded in November of 1973 “to unite Canadian writers for the advancement of their common interests.” Drawing on extensive archival collections – from both the Writers’ Union and its member authors – this dissertation offers the first critical history of the organization and its work, from pre-founding to the early 1990s. I argue that the Writers’ Union has fundamentally influenced Canadian literature – as an industry, as a community, and as a field of study – as I consider how unionism, literary celebrity, and friendship underpinned the organization’s work. This dissertation recuperates and comments on the important volunteer labour of Writers’ Union members in the service of literary labour, gender equity, and racial equity over the organization’s first twenty years.


title: Two Problems in Resource Management: Scheduling with Prediction Errors and Fair Data-Driven Allocation with Limited Data

contributor:
Down, Douglas
Li, Na
Computing and Software

abstract: Resource management is challenging when one needs to allocate scarce or limited resources to different entities with heterogeneous demands. In many practical situations, predictions of relevant quantities are only possible or available. While accurate estimates can certainly allow for better decisions to be made, a key challenge is to extract the maximum benefit when highly accurate estimates are not available (or possible). Even in the presence of reasonable estimates, other factors such as the need for a timely or real-time resource allocation can add to the complexity of the resource management process. This thesis studies two problems in resource management: scheduling with prediction errors and fair data-driven allocation with limited data. These problems both consider scenarios where only estimates of the demand are known and real-time resource allocation is required. In the second problem, the supply for resources is also not known within the decision-making period and is estimated.

abstract: Thesis

abstract: Master of Science (MSc)


title: Psychological Stress Drives an Aberrant IL-22 and Nutritional Immune Response, Favouring an Expansion of Crohn’s Disease-Associated Pathobionts

contributor:
Coombes, Brian
Biochemistry and Biomedical Sciences

subject:
Psychological Stress
Dysbiosis
Adherent Invasive E. coli
IL-22
Nutritional Immunity

abstract: Crohn’s disease (CD) is an inflammatory disease of the gastrointestinal tract attributed to an aberrant immune response to environmental and microbial triggers. Individuals with CD exhibit an enrichment of pro-inflammatory strains of Adherent-Invasive E. coli (AIEC) and often report a relapse of symptoms following a period of acute psychological stress. Despite a known immunosuppressive role, the mechanism by which stress contributes toward the development and progression of intestinal inflammation remains unknown. Here, we use a well characterized model of restraint stress to investigate the influence of psychological stress on host protection against a CD-associated strain of AIEC. We found that stress results in profound intestinal dysbiosis, allowing for a complete dominance of Enterobacteriaceae. Interestingly, while stress alone drives a state of low-grade inflammation and loss of barrier integrity in the gut, in the presence of a pathobiont strain of AIEC, stress drives a substantially heightened inflammatory response which exacerbated the resultant loss of barrier integrity. Moreover, we have found stress induces an augmented nutritional immune response, providing AIEC a competitive niche against commensal bacteria lacking alternative methods of iron uptake. Further, we see that stress-induced glucocorticoids mediate broad apoptosis of the CD45+CD90+ lymphocytic population in the gut. The loss of this population prevents an appropriate IL-22 mediated response to dysbiosis. Accordingly, blocking glucocorticoid signalling or exogenous administration of IL-22 prevents the stress-induced expansion of AIEC. This work underscores the complex nature of psychological stress such that the combination of iron limitation and glucocorticoid mediated immune attrition are simultaneously required for the stress-induced expansion of AIEC. These findings present novel insight into the mechanistic consequences of glucocorticoid signalling on impaired immune function and the provision of an inflammatory environment, resulting in a distinct impact on CD susceptibility. As such, deeper insight regarding the complex underpinnings of CD will assist in efforts to design representative models and will strengthen the discovery of targeted therapeutics.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Crohn’s disease (CD) is an inflammatory disease of the gastrointestinal tract resulting from an exaggerated immune response. CD patients often report a relapse of symptoms following a period of psychological stress and are at an increased likelihood of having pro-inflammatory strains of E. coli within their gut. Here, we use a model of restraint stress to investigate how psychological stress modulates the abundance of bacterial species associated with CD. We found stress results in the limitation of essential nutrients, allowing for an outgrowth of E. coli. Further, stress hormones lead to the loss of a protective immune response in which E. coli expansion can be prevented by blocking these hormones or restoring immune signalling. Together, we conclude that stress leads to immune cell death and creates an iron limited environment that favours E. coli expansion. Such work begins to uncover the functional consequence of stress and its’ role in disease progression.


title: "CanLit" and Capitalism: Canada Reads and the Circulation of Class Politics Through Contemporary Canadian Fiction

subject:
Canadian Literature
Class
Neoliberalism
Capitalism
Canada Reads

abstract: This thesis explores, through a neo-Marxist/cultural materialist lens, how discourses of class conflict in three pieces of contemporary Canadian fiction — Megan Gail Coles’ Small Game Hunting at the Local Coward Gun Club (2019), Tracey Lindberg’s Birdie (2015), and André Alexis’s Fifteen Dogs (2015) — are suppressed in broader public discussions of the texts, particularly on the CBC Radio program Canada Reads. Through close-reading the texts and their respective Canada Reads seasons for how class is operating “equiprimordially” (Ashley Bohrer) — an intersectional conceptualization of class that views class and its relations to other systems of oppression such as race, gender, sexuality, and settler-colonialism as co-constitutive, not separate — I argue that Canada Reads serves as a cultural arm of the neoliberal Canadian state’s project of erasing the political saliency of class conflict so that it may continue to reproduce its conditions of existence. To demonstrate this, I first outline the history of Canadian state cultural policy in relation to class, as well my theoretical framework. I then close read the thesis’s three pieces of fiction to determine how they mobilize class in relation to Canadian state narratives of class. Following this, I close read each book’s respective Canada Reads broadcast to see if class is taken up at all in the discussions. I then examine Canada Reads as a “mass reading event” (MRE) [Danielle Fuller and DeNel Rehberg Sedo] and explore alternative modes of shared reading that escape the nationalist logic of Canada Reads and thus have potential for bringing class discourses forward. Ultimately, the thesis demonstrates that Canada Reads as a model of shared reading is too deeply tied to the liberal humanist values of the Canadian state for any radical class discourse to emerge from it. Radical class discourses in literature that could spur collective, transformative action must come from elsewhere.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: This thesis examines how messages of class conflict in three pieces of Canadian fiction — Megan Gail Coles’ Small Game Hunting at the Local Coward Gun Club, Tracey Lindberg’s Birdie, and André Alexis’s Fifteen Dogs — are suppressed in broader public discussions of each piece, particularly on the CBC Radio program Canada Reads. Reading both the books and the Canada Reads seasons each book appeared on through a neo-Marxist lens that places class in relation to other systems of oppression, such as gender, race, sexuality, and settler-colonialism, I argue that Canada Reads serves as a cultural arm of the neoliberal Canadian state’s project of erasing the political saliency of class conflict — something that it requires in order to reproduce itself. Based on this finding, I turn at the end to alternative models of shared reading that could serve as spaces that recognize class messages in literature.


title: Stochastic Multiperiod Optimization of an Industrial Refinery Model

contributor:
Swartz, Christopher
Chemical Engineering

subject:
refinery planning
stochastic programming
surrogate modelling
generalized Benders decomposition

abstract:
The focus of this work is an industrial refinery model developed by TotalEnergies SE. The model is a sparse, large-scale, nonconvex, mixed-integer nonlinear program (MINLP). The nonconvexity of the problem arises from the many bilinear, trilinear, fractional, logarithmic, exponential, and sigmoidal terms. In order to account for various sources of uncertainty in refinery planning, the industrial refinery model is extended into a two-stage stochastic program, where binary scheduling decisions must be made prior to the realization of the uncertainty, and mixed-integer recourse decisions are made afterwards. Two case studies involving uncertainty are formulated and solved in order to demonstrate the economic and logistical benefits of robust solutions over their deterministic counterparts.

A full-space solution strategy is proposed wherein the integrality constraints are relaxed and a multi-step initialization strategy is employed in order to gradually approach the feasible region of the multi-scenario problem. The full-space solution strategy was significantly hampered by difficulties with finding a feasible point and numerical problems.

In order to facilitate the identification of a feasible point and to reduce the incidence of numerical difficulties, a hybrid surrogate refinery model was developed using the ALAMO modelling tool. An evaluation procedure was employed to assess the surrogate model, which was shown to be reasonably accurate for most output variables and to be more reliable than the high-fidelity model. Feasible solutions are obtained for the continuous relaxations of both case studies using the full-space solution strategy in conjunction with the surrogate model.

In order to solve the original MINLP problems, a decomposition strategy based on the generalized Benders decomposition (GBD) algorithm is proposed. The binary decisions are designated as complicating variables that, when fixed, reduce the full-space problem to a series of independent scenario subproblems. Through the application of the GBD algorithm, feasible mixed-integer solutions are obtained for both case studies, however optimality could not be guaranteed. Solutions obtained via the stochastic programming framework are shown to be more robust than solutions obtained via a deterministic problem formulation.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: COVID-19 & the Opioid Crisis: Harm & Harm Reduction at the Intersection

contributor:
Savelli, Mat
Health and Aging

subject:
covid-19
harm reduction
opioid crisis
Hamilton, ontario
social history
health studies
homelessness
pandemic
encampments
coronavirus
nursing
frontline workers

abstract: This project utilized an interdisciplinary approach to explore what harm and harm reduction meant during intersecting public health emergencies, the opioid crisis and the coronavirus pandemic. Using thematic and historical analysis, I analyzed interviews with frontline workers, news coverage, and municipal government documents to understand how people conceptualized the opioid crisis during coronavirus (and vice versa). On the whole, I found that harm reduction was a central aspect of the efforts against the opioid crisis in Hamilton. However, there were discrepancies in how it was practiced and understood. Generally, harm reduction was presented in municipal government documents as a medical intervention that involved, for example, the provision of new needles and naloxone kits to prevent disease and death. Such a practice was indeed important to address the unique harms at the intersection of COVID and the opioid crisis. However, to frontline workers and activists, harm reduction was a much broader term: it included services that were crucial to daily life, such as food and washrooms; the right to safe housing; and broader social and structural interventions, such as the decriminalization of opioid use. The context of the coronavirus pandemic, which exposed people who use opioids to unique harms, exacerbated the disparity between these definitions: harm reduction was simultaneously presented as a narrow, medical practice and a broad, political intervention.

abstract: Thesis

abstract: Master of Arts (MA)