VictorJuiz/thesis huggingface dataset:
Learning in Games with Side Information

This work regards Nash equilibrium-seeking in multi-player finite games. We present a discrete-time algorithm that can be adapted to leverage two forms of side information – a local/global split in the utility structure, where we assume that each player can track the actions of its neighbors and knows the form of its local utility, and unplayed action payoff measurements, where we suppose that players may be capable of observing their hypothetical payoffs for some actions they didn’t play – when it is available. We use stochastic approximation to prove that, under mild assumptions, the induced mixed strategies of all players convergence to a perturbed Nash equilibria in games where utilities satisfy certain negative monotonicity properties. We also analyze modifications of the proposed algorithm and prove associated results. All presented results are supported with simulations of certain representative games which illustrate that faster convergence can be obtained when side information is exploited.

Keywords: Finite Games
Game Theory
Learning in Games
Multi-Agent Reinforcement Learning
Advisor: Pavel, Lacra
Identification of Protein Interactors of a Pathological TDP-43 C-Terminal Fragment Using Quantitative Mass Spectrometry

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons (MN) in the brain and spinal cord. ALS is pathologically classified by cytoplasmic inclusions of the normally nuclear TAR-DNA binding protein 43 kDa (TDP-43) in patient MNs. TDP-43 a DNA/RNA binding protein that is recruited to stress granules (SG) to sequester mRNA non-essential to survival. We have discovered a splice variant of TDP-43 with a mass of 35 kDa (TDP-35) that is toxic to MNs and is recruited to SGs upon expression in cultured cells. Here, I used affinity purification mass spectrometry (AP-MS) method to identify the protein interactors of TDP-35 in SGs. The failure of BioID fusion tags to replicate our TDP-35 SGs led me to confirm the validity of our EGFP tagged TDP-35 behaviour. As well, the AP-MS protocol I developed serves to guide future investigation into TDP-35 SGs and identified tubulin subunits as potential TDP-35 interactors.

Keywords: ALS
HEK293T
Immunoprecipitation
Mass Spectrometry
TDP-35
TDP-43
Advisor: Robertson, Janice
Mesh Independent Large-Eddy Simulation of Hydrogen Combustion in Compromised Nuclear Facilities

The use of high-fidelity simulations methods based on large-eddy simulation are useful in understanding and assessing the safety hazards associated with hydrogen release in nuclear power plants. However, due to the separation of scales between the domain, large-scale turbulence and its interaction with the thin flame fronts of hydrogen flames, the use of static, unchanging meshes result in impractically high computational costs. For this reason, the use of the mesh-independent Integral Length Scale Approximation (ILSA) subfilter-scale model in combination with an anisotropic block-based Adaptive Mesh Refinement (AMR) technique is proposed and examined for performing LES on turbulent premixed hydrogen flames. This technique is applied to lean premixed hydrogen-air mixtures within closed vessels, a problem relevant to hydrogen safety applications in nuclear facilities. Simulation results derived from these models are compared with experimental data from the THAI HD tests to assess the capabilities of the combined approach.

Keywords: Hydrogen combustion
Large-eddy simulation
Nuclear safety
Advisor: Groth, Clinton P.T.
Commitments Counter Publics: The (un)Importance of Romantic Intimacy in the Lives of Gay Emerging Adults

The desire for a monogamous marriage has long been one of the characteristics that has been assigned to emerging adults, despite criticisms regarding a lack of queer representation. In answer to this, Berlant’s notion of the counter public has been utilized. Using grounded theory, interviews with 12 gay men who frequent counter public spaces in urban Toronto have been examined in order to understand how these men conceptualize successful adulthood, with monogamy and marriage as the privileged forms of romantic intimacy. These men generally rejected the notion that marriage and monogamy were necessary for success, articulating that romantic and sexual intimacy were separate and that the existence of extradyadic partners within a romantic relationship was desirable and strengthened the relationship with their romantic partner. Such a finding forces scholars, professionals, and the wider LGBTQ+ community to revisit the way romantic intimacy in the emerging adulthood years is studied and practiced.

Keywords: Counter public
Emerging adulthood
Gay men
Monogamy
Queer theory
Advisor: McCready, Lance
Phonetic Accommodation to Hypernasal Speech

Speech accommodation is a process in which an individual’s speech becomes more (convergence) or less (divergence) similar to their interlocutor’s speech. Individuals diverge to increase distance and reduce commonality between conversation partners (Shepard, Giles, Le Poire, 2001) based on social biases (Babel, 2010). Hypernasality is a negatively perceived (Blood Hyman, 1997; Watterson, Mancini, Brancamp, Lewis, 2013) speech disorder resulting from an excessive amount of acoustic energy emanating from the nasal cavity (Zajac Vallino, 2017). Since it is theorized that individuals diverge in negative social contexts (Shepard et al., 2001) and that hypernasality is negatively perceived (Blood Hyman, 1997; Watterson et al., 2013), we hypothesized that speakers would diverge from hypernasal speech. Speakers read sentences in response to hearing pre-recorded sentences with modelled hypernasal and typical speech. Results indicated that speakers inconsistently converged to typical levels of nasality and consistently diverged from hypernasal speech.

Keywords: Communication Accommodation
Hypernasality
Nasalance
Nasality
Phonetic Accommodation
Speech Disorders
Advisor: Bressmann, Tim
Pardo, Jennifer
Investigating Cortical Dopamine Release due to a Cognitive Challenge in Clinical High-risk: A [11C]FLB457 Positron Emission Tomography Study

Evidence from several lines of research suggests decreased dopamine release in the prefrontal cortex as the neural correlate of cognitive deficits in schizophrenia, key features of the disease and strong predictors of later functional status. However, there are currently no in-vivo studies examining cortical dopamine function in the clinical high risk (CHR) stages of schizophrenia, despite the large amount of preclinical and clinical evidence pointing to the cortical hypodopaminergic hypothesis. The main aim was to investigate cognitive task-induced cortical dopamine function in CHR participants using positron emission tomography imaging with [11C]FLB457 radiotracer in a two-scan paradigm. There were no statistically significant differences in cognitive task-induced cortical release as quantified by [11C]FLB457 radiotracer displacement between healthy controls and CHR participants. This is the first in vivo study to illustrate that the cortical hypodopaminergic state observed in schizophrenia may not be present in its putative high-risk state.

Keywords: Cognition
Dopamine
Imaging
Prodromal
Schizophrenia
WCST
Advisor: Mizrahi, Romina
Automatic Segmentation and Three-dimensional Reconstruction of Fascicles in Peripheral Nerves

Computational studies can be used to support the development of peripheral nerve interfaces, but currently use simplified models of nerve anatomy that do not accurately represent anatomical conditions. To better quantify and model neural anatomy across the population, we have developed an algorithm to automatically reconstruct accurate peripheral nerve models from histological cross- sections. We acquired serial median nerve cross-sections from human cadaveric samples. We developed a processing pipeline involving four steps: registration, detection, segmentation, and reconstruction. While our algorithm could not always outperform simplified anatomical models, it nonetheless provided useful anatomical information that would otherwise be lost. Fascicle detection by convolutional neural network worked particularly well and can be applied to histological images as is. The other components of the pipeline need improvements in order to build truly accurate models. This work provides a baseline from which to progress toward a fully automatic approach to constructing peripheral nerve models.

Keywords: 3D Reconstruction
Automatic Segmentation
Neural Anatomy
Neural Interfaces
Neural Networks
Peripheral Nerves
Advisor: Zariffa, José
Agur, Anne
Histone Variant H2A.Z's Effects on Nicotine Locomotor Sensitization and Reward

Epigenetic modifications are key regulators of neural plasticity and are implicated in various forms of experience-induced changes in behavior, including memory and addiction. Histone variants are newly identified epigenetic regulators of neural plasticity and the histone variant H2A.Z has been shown to regulate memory formation, suggesting a potential role in other types of plasticity. The goal of this thesis was to determine whether H2A.Z regulates the development of preference (index of reward) and sensitization to nicotine by isolating the unique contributions of two H2A.Z-encoding genes, H2afv and H2Afz. Using conditional-inducible knockout mice for each gene, we showed that H2Afv deletion eliminated conditioned place preference (CPP) and locomotor sensitization to nicotine, whereas H2Afz deletion selectively impaired locomotor sensitization. This is the first study to demonstrate a gene-specific effect of H2A.Z on behavior and to implicate H2A.Z in regulating responses to psychostimulants, suggesting that H2A.Z may contribute to risk for nicotine addiction.

Keywords: epigenetics
H2A.Z
Nicotine
reward
sensitization
Advisor: Zovkic, Iva
The Proportion of Female Students in Canadian Undergraduate Engineering Programs by Institution and Sub-discipline

Science, Technology, Engineering and Math (STEM) fields in many countries continue to experience difficulties attracting and retaining women. In Canada, the proportion of female students in engineering is considerably lower than the proportion of female students in higher education. Using Tinto’s theories concerning social and academic integration, this study investigated the relationships between the proportion of female undergraduate engineering students, and the proportion of female faculty, and policies addressing gender representation. Using descriptive statistics, this study analysed proportions of female students and faculty in Canadian engineering programs and established that distinct and persistent differences exist in these proportions among schools and among sub-disciplines. As these results suggest that institutional factors can influence the proportion of female students within engineering programs, this study has laid the foundation for future qualitative research to investigate what institutional factors could attract and retain more women in Canadian engineering schools.

Keywords: education
engineering
equity
faculty
female
gender
Advisor: Wheelahan, Leesa
A Retail Robot Architecture using ContextSLAM for Locating Products in Crowded Unknown Environments

Retail environments often create stress on shoppers due to confusing layouts, difficulty to locate products and crowding. These stresses can prevent shoppers from purchasing all their intended items. This can be detrimental to their well being as well as financially damaging to the store. To address these concerns, this thesis presents a retail robot architecture that can explore and locate requested products in an unknown, crowded, environment. Furthermore, a novel mapping algorithm entitled contextSLAM is presented, which creates contextually rich maps of crowded environments to aid in localisation and exploration. ContextSLAM was validated in simulation then implemented in the full retail architecture. The full system was then validated through a battery of experiments where it was tasked with finding requested products in both a mock retail environment and a grocery store. These experiments were conducted in both uncrowded and crowded settings to ensure repeatability and robustness.

Keywords: Contextual Mapping
Retail Robotics
Robot Architecture
Simultaneous Mapping and Localisation
Advisor: Nejat, Goldie
Reading the Linguistic Landscape: Fostering Newcomer Children's Language Awareness and Identity Positioning

This case study investigated newcomer English language learner (ELL) children’s perspectives on and interpretations of their linguistic landscape (LL), as well as the influence of LL-based activities on their language awareness and learning, identity negotiation, and sense of belonging. With the children as co-researchers, creative-driven methodology was implemented through carefully designed class activities including children’s photography, VLP (visual, lexical, and pragmatic) analyses, research conversations, and the creation of visual art (map making) as a form of identity text. The findings included 1) the types of LL that children were attracted to, 2) children’s interpretations of their multilingual LL and 3) the influence of specifically developed activities on ELL children’s meaning-making processes, language learning, language awareness, and identity positioning. Overall, the findings suggested that increasing multilingual signage would support ELL children’s language awareness, strengthen their sense of identity and belonging, and would create opportunities for L1 and L2 incidental language learning.

Keywords: children as co-researchers
creative methodologies
identity negotiation
language awareness
linguistic landscape
multilingualism
Advisor: Labrie, Normand
Investigating Batch-to-batch Variability and Stability of Enamel Matrix Proteins Preparations used in Periodontal Surgery (Emdogain®)

Emdogain®, a porcine-derived Enamel Matrix Derivative (EMD), is a promising biological mediator used in the regeneration of lost periodontium, a direct result of periodontitis. However, several clinical studies have demonstrated inconsistencies regarding Emdogain®’s therapeutic results. We hypothesize that a reason for inconsistent clinical results stems from a variability in the product’s protein content resulting from the inherent variability in the harvested enamel matrix, presence of enzymes and effects of storage conditions. Emdogain® protein composition was assessed using tandem mass spectrometry (TMS), silver stained SDS-PAGE and western blotting. Enzyme activity was examined using a fluorescence enzyme assay. TMS identified all major Enamel matrix proteins (EMPs) and enzymes. No definitive effects of temperature and time were observed through SDS-PAGE, western blotting or TMS. Nonetheless, TMS analysis did show differences in abundances of certain EMPs between batches. Enzymatic activity was detected in most samples, with significant differences in activity between batches.

Keywords: Emdogain
Enamel
Periodontology
Regeneration
Advisor: Ganss, Bernhard
Tenenbaum, Howard
Investigating the Effect of Mild Cognitive Impairment on Brain Activity during Completion of the Clock-drawing Test

There is a lack of quick cognitive assessments for general practitioners to use to screen for MCI, resulting in missed diagnoses. The CDT is essential in assessment of dementia, therefore has potential as a screening tool for MCI. Studies have identified MCI-related behavioural impairment on the CDT, however there is less knowledge regarding the effect of MCI on CDT-related brain activity. This study combined fMRI and an fMRI-compatible tablet to measure brain activity during a naturalistic version of the CDT in an MCI and control cohort. Although patients with MCI performed worse on the CDT, the test did not have adequate sensitivity and specificity to MCI. Patients with MCI exhibited less extensive CDT-related activity in the frontal and parietal lobes relative to controls. Both areas have important cognitive functions for CDT completion, suggesting that reduced activity in these regions may cause the behavioural impairment observed in patients with MCI.

Keywords: Aging
Brain mapping
Clock-drawing
Functional MRI
Mild cognitive impairment
Screening tool
Advisor: Schweizer, Tom A
Determining the Clinical Effects of Photostimulable Phosphor Plate Artifacts on the Interpretation of Periapical Inflammatory Disease

Objectives: This thesis aims to determine the extent that photostimulable phosphor (PSP) plate artifacts hinder the radiologic interpretation of common dental diseases, such as periapical inflammatory disease. Methods: Gold standard radiologic interpretations for periapical inflammatory disease were determined on high-quality clinical radiologic images. PSP plate artifacts were digitally superimposed over these high-quality images to virtually degrade the image. These simulated images were presented to general dentists who were asked for their radiologic interpretation, the confidence in their interpretation, and their opinion on whether to discard the plates. Results: With increasing levels of artifacts, there was a statistically significant reduction in clinicians’ confidence and increase in the proportion of plates discarded (p

Keywords: artifacts
computer simulation
photostimulable phosphor
quality assurance
radiology
Advisor: Perschbacher, Susanne
Moayedi, Massieh
The Leucine Requirement of Older Adult Men Determined by Indicator Amino Acid Oxidation Method

Leucine recommendations for older adults are based on young adult data. When compared to young adults, older adults require more dietary leucine to stimulate muscle protein synthesis, suggesting that age may affect the leucine requirement. We aimed to determine the leucine requirement of men ≥ 60 years using the indicator amino acid oxidation method. Seven men ≥ 60 years were each assigned to receive seven levels of leucine intake ranging from 20 – 120 mg . kg-1 . d-1, in random order. The rate of release of 13CO2 from the oxidation of L-[1-13C]phenylalanine was measured and breakpoint analysis was applied to determine the leucine requirement. The mean leucine requirement for men ≥ 60 years was estimated to be 80 mg . kg-1 . d-1; double the current recommendations. Current leucine recommendations for older adults need to be revisited.

Keywords: Elderly
Essential Amino Acid
Indicator Amino Acid Oxidation
Leucine
Requirement
Advisor: Courtney-Martin, Glenda
Development of an Anthropomorphic Phantom Coronary Artery Network for CT Imaging

In this work, the design of anthropomorphic phantom coronary arteries for optimization of Computed Tomography Coronary Angiography (CTCA) is presented. First, a phantom vascular wall model for minimization of motion artifacts is manufactured. The mechanical properties of porcine coronary arteries and four soft rubber materials were tested and compared to each other, and the wall attenuation of tubular contrast-filled samples was characterized and compared to literature values as well. A coronary artery model was manufactured by segmenting the main coronary arteries from CT images, 3D printing a mold, and coating it in the rubber material with the most appropriate mechanical and CT attenuation properties. In the second part, the feasibility of 3D printing a phantom directly using four flexible commercially available materials is investigated. The CT attenuation properties match ranges for lipid-rich and fibrous plaque; thus the phantom can be used for optimization of non-calcified plaque imaging.

Keywords: 3D printing
computed tomography
coronary arteries
coronary artery disease
imaging phantom
mechanical properties
Advisor: Naguib, Hani E
Paul, Narinder
Mood-related Differences in Cerebral Blood Flow in Adolescents with Bipolar Disorder

Numerous adult bipolar disorder (BD) studies have examined cerebral blood flow (CBF) in relation to mood, whereas little is known on this topic in adolescents. We enrolled 129 adolescents (mean age 17.34+/-1.42 years), including 72 BD (28 hypomanic/mixed, 19 depressed, 25 euthymic) and 57 healthy controls (HC). Pseudocontinuous arterial spin labeling (ASL) magnetic resonance imaging (MRI) evaluated CBF, using both a region of interest and whole brain voxel-wise approach. Within-BD analysis examined the association of mania and depression severity with CBF. We found differences in terms of CBF between groups with higher CBF in the BD euthymic group than in HC and symptomatic BD in temporal, precentral, and occipital regions. Severity of depressive symptoms in BD was negatively correlated with CBF in the anterior cingulate cortex and temporal regions. Higher CBF in euthymic BD adolescents may reflect developmentally-specific compensatory CBF regulation mechanisms required to maintain euthymia.

Keywords: Adolescents
Bipolar Disorder
Cerebral Blood Flow
Neuroimaging
Psychiatry
Advisor: Goldstein, Benjamin I
Laminar Flow Blunts Hypoxia Signaling in Endothelial Cells: Relevance for the Venous Circulation

Endothelial cells (ECs) dynamically respond to surrounding environmental stimuli. EC hypoxia response is mediated by the hypoxia inducible transcription factors HIF-1a and HIF-2a, that are stabilized under low oxygen conditions and activate hypoxia-responsive genes (such as VEGFA). Veins experience laminar flow and carry de-oxygenated blood. Therefore, ECs in these regions are exposed to shear stress and hypoxia. Curiously, vein ECs do not constitutively activate HIF signaling. Contrastingly, chronic venous disease (CVD) is often characterized by upregulated HIF signaling and changes in flow patterns. We studied the interaction between flow and hypoxia, primarily the effect of shear stress on HIF-mediated hypoxia-response. Profiling ECs exposed to flow and/or hypoxia showed that laminar flow blunts HIF-mediated hypoxia-signaling. Flow-dependent HIF-1a downregulation is KLF2 and KLF4 dependent, whereas HIF-2a is KLF-independent. Flow prevents veins from manifesting a hypoxic response. This data suggests that loss of venous flow activates the HIF-pathway and contributes to CVD pathogenesis.

Keywords: Chronic Venous Disease
Endothelial Cells
Hypoxia
Shear Stress
Advisor: Marsden, Philip A
The Functional Characterization of Anti-CRISPR AcrIIC2Nme

The CRISPR-Cas system is a prokaryotic adaptive immune system that provides protection against foreign genetic elements, such as bacteriophages. Phages have thus evolved a set of small inhibitors called anti-CRISPRs, which bind and inhibit effector Cas proteins. Among the anti-CRISPRs that target the type II CRISPR system, I characterized the anti-CRISPR AcrIIC2Nme. Through structure-guided mutational analyses, I identified a large electronegative surface that is critical for AcrIIC2Nme activity in vivo. In addition, the anti-CRISPR’s binding site was shown to be the bridge helix of Cas9, a highly electropositive region that stabilizes crRNA binding. Lastly, inactive AcrIIC2Nme mutants were shown to bind Cas9 with lower affinity than WT AcrIIC2Nme. These findings present a structurally novel anti-CRISPR that is the first reported to target the bridge helix of Cas9.

Keywords: anti-CRISPR
Bacteria
Cas9
Protein
Advisor: Maxwell, Karen L