VictorJuiz/thesis huggingface dataset:
Development of a Novel Feedback System to Guide Skill Acquisition for Brain-Computer Interface Control

A brain-computer interface (BCI) enables control of external devices via modulation of neural activity. Currently, BCI use is limited as many users struggle to produce neural modulations that are machine-discernible. Recent evidence suggests ineffective user-training may be partially responsible. Here, we present and evaluate a feedback interface to improve BCI user-training. The system provides feedback derived from recently proposed Riemannian geometry metrics. First, we explore the validity of these metrics for user evaluation by assessing their relation to classifier performance. Regression models showed the metrics were able to account for 45% - 59% of inter-subject variation in classification accuracy for different classifiers. Second, we evaluate whether users improve performance in feedback interpretation tasks using the proposed system over classifier feedback. Using signal detection theory, we find the proposed system significantly outperforms the classifier system in all interpretation tasks. The results suggest the system should be explored further in real BCI-training scenarios.

Keywords: Brain-Computer Interface
EEG
Instructional Feedback
Learning
Motor Imagery
Riemannian Geometry
Advisor: Chau, Tom
Investigating the Roles of UVRAG and EGFR in Skeletal Muscle Homeostasis

Skeletal muscle autophagy is implicated in the maintenance of skeletal muscle mass and function that is critical to sustain mobility and regulate metabolism, particularly with aging. Mice with skeletal muscle-specific deletion of ultraviolet radiation resistance-associated gene (UVRAG) displayed accelerated sarcopenia, impaired skeletal muscle function, and accumulation of epidermal growth factor receptor (EGFR) by six months of age. Constitutively active EGFR expression (EGFRL858R) in UVRAG deficient skeletal muscle led to further detrimental defects in function. Relative gene expression of markers involved in skeletal muscle and mitochondrial function that were abnormal in UVRAG deficient skeletal muscle were unchanged by concomitant EGFRL858R mutation. Rather, enhanced EGFR signaling with EGFRL858R mutation led to defects in skeletal muscle fiber type determination that further deteriorated muscle function in UVRAG-deficient mice. Overall, UVRAG and EGFR signaling together are critical in the maintenance of skeletal muscle mass and function with aging, with distinct roles in skeletal muscle homeostasis.

Keywords: aging
EGFR
mitochondrial homeostasis
sarcopenia
skeletal muscle
UVRAG
Advisor: Woo, Minna
Role of Salinity, Genotypic Variation, Microbial Communities, and Algae on the Elimination of Benzotriazole by Duckweed Lemna minor

Benzotriazole is an emerging contaminant incompletely removed by wastewater treatment plants. This work investigated several environmental factors that may influence the transformation of benzotriazole by wetland model plant duckweed Lemna minor, including salinity, variation among duckweed genotypes, microbial communities, and algae Chlorella vulgaris. Results show that high salinity (10 g/L) reduced the phytotransformation (transformation by plant) of benzotriazole. Intermediate salinity (0.8 g/L) modulated the formation of phototransformation (transformation driven by light) products aniline and 3-aminophenol. Microbial inoculation promoted the formation of a phytotransformation product, benzotriazole acetyl-alanine. Variation among duckweed genotypes in transforming benzotriazole suggests that constructed wetlands could be designed to increase benzotriazole depletion and reduce effluent toxicity by selecting appropriate duckweed genotypes. Algae also depleted benzotriazole, but it did not influence the depletion kinetics by duckweed in a symbiotic manner. Other plants and algae could potentially phytotransform benzotriazole as the proposed pathways are shared among plants and algae.

Keywords: algae
benzotriazole
constructed wetlands
duckweed
phytotransformation
Advisor: Passeport, Elodie
Exact and Heuristic Approaches to Batching-and-scheduling for the Composites Manufacturing Problem

The process of manufacturing composite materials is a complex problem that lacks robust and scalable solutions. This thesis aims to characterize that process and offer solutions by defining and solving a novel optimization problem, the Composites Manufacturing Problem (CMP), and its abstraction, the Two-Stage Bin Packing and Hybrid Flowshop Scheduling Problem (2BPHFSP). The CMP involves batching and scheduling jobs in a four-stage flowshop with time-varying resource requirements. The 2BPHFSP offers a simplified version of the CMP which allows us to focus on the key complexities of the CMP and deepens our understanding of the problem. By extending state-of-the-art techniques from a wide literature body, we construct solution approaches using techniques from Mixed Integer Programming, Constraint Programming, Logic-Based Benders Decomposition, heuristic algorithms, genetic algorithms, and constrained-clustering algorithms. Empirical analyses were performed for both problems on randomly generated instances based on real data from our industrial collaborator.

Keywords: Batching
Composites Manufacturing
Constraint Programming
Heuristics
Optimization
Scheduling
Advisor: Beck, J C
Investigating the Gut Microbiome, Metabolomic Signatures, and Metabolic Dysfunction in Antipsychotic Naïve Patients

Antipsychotics (APs) are the treatment cornerstone for psychotic spectrum disorders (PSDs) but have severe metabolic side-effects. Gut microbiome (GMB) and metabolomic profiling may explain these. This thesis comprises two 12-week studies. In study one, 6 AP-naïve (cases) and 6 healthy participants (HCs) completed baseline GMB and metabolic assessments, repeated at 6 and 12 weeks for cases. At baseline, alpha diversity and genera level differences were found between groups. Over the three months of AP treatment, genera changes were observed and a positive correlation between triglycerides and Actinobacteria change was noted. In study two, 24 cases and 5 HCs completed metabolomic and metabolic assessments. Cases had lower acylcarnitine levels and differences in fatty acids compared to HCs. Baseline aspartic acid was higher for cases who gained weight. The GMB and metabolome may provide biomarkers for PSDs, intrinsic metabolic abnormalities, and help predict/monitor AP induced metabolic side-effects.

Keywords: Antipsychotics
Gut Microbiome
Metabolic Dysfunction
Metabolomics
Psychotic Spectrum Disorders
Advisor: Hahn, Margaret K
Evaluation of Muscle Texture and Motor Unit Abnormalities after Experimentally Induced Sensitization using Capsaicin

Central sensitization describes a state of central nervous system hyperexcitability causing pain hypersensitivity. The impact of central sensitization on muscle structure and neurophysiology is unclear. This work aimed to determine the effect of experimentally induced central sensitization on muscle structure, motor recruitment, motor unit action potential characteristics and upper limb movement. Twenty healthy participants were randomized to receive topical capsaicin – to induce central sensitization acutely – or placebo. Ultrasound images, surface electromyography(sEMG), intramuscular electromyography (iEMG), and movement data were acquired before and after treatment. Capsaicin-induced sensitization resulted in significant changes in ultrasound image texture features, motor unit recruitment pattern (sEMG) and motor unit variability (iEMG). Movement analysis revealed capsaicin-induced changes in acceleration variability, suggesting changes in anterior horn cell excitability affecting efferent output. Overall, this thesis advances understanding of central sensitization manifestation, a requisite for developing quantitative criteria to diagnose central sensitization and chronic widespread pain.

Keywords: Central Sensitization
Intramuscular Electromyography
Motor Unit
Recruitment
Surface Electromyography
Advisor: Kumbhare, Dinesh A
Olfactory Discrimination in Caenorhabditis elegans

Caenorhabditis elegans (C. elegans) is an organism with only 302 neurons (in the adult hermaphrodite) and only two pairs of (bilaterally symmetrical) neurons detect attractive volatile odourants. Despite its simple neuroanatomy, C. elegans can perform olfactory discrimination between two odourants when both are detected almost exclusively by a single pair of neurons. ARR-1 (Beta-Arrestin) desensitizes the receptors detecting the two odourants in an activity-dependent manner; this allows for odourant-specific adaptation and olfactory discrimination. An arr-1 null strain of C. elegans is unable to discriminate intra-neuronally (when both odours are detected by the same pair of neurons), but is able to discriminate inter-neuronally (when odours are detected by separate pairs of neurons). This work characterizes the mechanism of intra-neuronal olfactory discrimination in C. elegans, which has been mysterious since it was first decribed by Bargmann et al in 1993.

Keywords: arrestin
Caenorhabditis elegans
olfaction
olfactory adaptation
olfactory discrimination
Advisor: van der Kooy, Derek
Endocannabinoid Metabolism in Posttraumatic Stress Disorder: Preliminary Results from a Neuroimaging Study with the Novel Fatty Acid Amide Hydrolase Probe [C-11] CURB

Background: Preclinical studies suggest that levels of Fatty Acid Amide Hydrolase (FAAH)—the catabolic enzyme for the endocannabinoid anandamide—may be elevated in the amygdala in posttraumatic stress disorder (PTSD). However, the status of FAAH in vivo in posttraumatic stress disorder remains unknown. Methods: Healthy subjects (n=29) and individuals with PTSD (n=16) completed a positron emission tomography scan following injection of the FAAH probe [C-11]CURB. Results: We find no evidence for elevated [C-11]CURB binding in PTSD. Instead, we find marginally lower [C-11]CURB binding in whole brain (-9.38%, p=0.079) and significantly lower [C-11]CURB binding in the amygdala (-14.50%, p=0.020) in PTSD subjects. [C-11]CURB binding did not correlate with PTSD symptomatology. Conclusion: Our data provide preliminary evidence contrary to preclinical literature, suggesting that FAAH may be lower in people with PTSD. These findings have implications for treatment strategies targeting this enzyme (i.e. FAAH inhibitors) in PTSD.

Keywords: Endocannabinoid System
Fatty Acid Amide Hydrolase
Neuroimaging
PET imaging
Posttraumatic Stress Disorder
Advisor: Boileau, Isabelle
Development and Validation of an Automated Video-Based Analysis Tool to Identify Motor Impairment in Preterm Infants

Introduction: The objective of this project was to explore automated technology as an alternative to clinical General Movements Assessment (GMA) for early identification of motor impairment (MI), including cerebral palsy (CP), in preterm infants. Methods: A systematic review evaluated gaps in current automated technologies. A 2D video-based automated tool was developed for infants

Keywords: cerebral palsy
computer vision
general movement assessment
motor impairment
movement recognition
preterm infant
Advisor: Shah, Vibhuti
Computational Fluid Dynamics Simulation of Tubular Scaffold Re-cellularization inside Perfusion Bioreactors

Humans suffer from tracheal pathologies such as malignancy, traumatic injury, and stenosis. Tissue engineering provides a viable treatment method by substituting a damaged trachea with an engineered graft that uses the recipient’s own cells to reduce the rate of transplant rejection by the recipient’s immune system. This requires a re-cellularization with cells harvested from the recipient. Bioreactors are designed to assist us in re-cellularization to distribute cells uniformly on the lumen tracheal. Currently, a lack of understanding of the bioreactor hydrodynamic and cell-seeding environment is a major obstacle for obtaining viable tracheal grafts. The complexity of cell behavior and modelling assumptions have led to significant differences between experimentally observed and computationally predicted results. In this study, we implement and compare a series of computational models of increasing complexity, incorporating previously neglected physical mechanisms, to improve the predictive ability of the models.

Keywords: CFD
DPM
Recellularization
Advisor: Amon, Cristina
Mental Health Care for Common Perinatal Mental Disorders: What Do Fathers Need?

Purpose: The purpose of this study was to understand fathers’ decision making processes around help-seeking for symptoms of common perinatal mental disorders. Methods: Using a cross-sectional survey, we recruited a large sample of fathers to identify their decision making needs and preferences for mental health services, in accordance with the Ottawa Decision Support Framework. Results: Our results revealed that fathers’ knowledge about mental disorders was relatively high. Knowing how a mental disorder impacts child development was an important reason to seek treatment. Only 50% of fathers reported being comfortable disclosing symptoms to a healthcare provider, and the preferred disclosure settings were an online survey or primary care provider. Fathers with a history of a perinatal mental disorder had greater acceptability towards pharmacotherapy, compared to fathers with no history. Conclusions: Our findings support the need for the design of targeted decision support to optimize fathers’ engagement in mental health services. Conclusions: Our findings support the need for the design of targeted decision making support that overcomes obstacles to help-seeking among fathers and optimizes their engagement in mental health services in the perinatal period.

Keywords: Cross-Sectional Survey
Decision Making
Help Seeking
Men's Mental Health
Perinatal Period
Treatment Preferences
Advisor: Ivers, Noah M.
Vigod, Simone N.
The Effect of β-cell Specific ZnT8 Deficiency on Insulin Secretion

Zinc plays a role in insulin processing, storage, and secretion. Zinc transport processes may be linked to defects in insulin secretion associated with type 2 diabetes (T2D). Indeed, ZnT8, a zinc influx transporter highly expressed in pancreatic β-cells, is associated with T2D risk. Presently, the role ZnT8 plays in diabetes progression and whether altered ZnT8 activity affects T2D risk/treatment is controversial. The effects of ZnT8 knockdown in mouse are modestly to severely deleterious, whereas in humans, ZnT8 loss-of-function haploinsufficiency appears to reduce diabetes risk. A β-cell specific ZnT8 knockout and haploinsufficiency model were developed and examined under normal and metabolically stressed conditions. Mice with reduced ZnT8 did not have significantly impaired glucose homeostasis or β-cell function compared to controls under normal and conditions of acute insulin resistance. Overall, pancreatic β-cell ZnT8 deletion or knockdown did not impair β-cell function, nor was it protective of hyperglycaemia associated with insulin resistance.

Keywords: Beta-cell
Diabetes
Insulin
Slc30a8
ZnT8
Advisor: Wheeler, Michael B
A 3-phase Electric Vehicle Charger Integrated with Dual Inverter Drive

This thesis proposes a 3-phase electric vehicle (EV) charger which reemploys components of a dual inverter drive for charging when the EV is parked. Reemployment of drive components for charging can significantly reduce charging station infrastructure costs. The proposed charger's current source converter basis improves fault detection and prevents motor torque generation during charging. The dual inverter drive allows for integration of mixed energy storage media during driving and reduction of current ripple during charging. The proposed charger was tested through experimentation on a 10kW prototype. Experimental results showed the charger could perform constant-current constant-voltage charging of two isolated energy storage units from a 3-phase grid with >0.99 power factor. Charging wasperformed with balanced DC current passing through the EV's motor windings which prevented torque generation during charging. The prototype achieved an overall efficiency of 93% at rated power while meeting the international grid current harmonics standard IEC 61000-3-12.

Keywords: dual inverter
electric vehicle
integrated charging
onboard charging
Advisor: Lehn, Peter W.
Tuning of Pd Clusters and their Local Environment for CH4 and CO Oxidation Reactions

Pd clusters are active catalysts for oxidation of CH4 and CO, the major components of exhaust gas emissions and significant greenhouse gasses. Addition of Pt enhances the reactivity of Pd for either oxidation reaction by modifying the electronic properties of the Pd. This thesis explored (i) the optimum Pd-to-Pt atomic ratio for CH4 and CO oxidation reactions and (ii) the effects local Pd site environment alteration by confining of the clusters in SSZ-13 zeolite pores and the resulting dynamic interconversions among small and large Pd clusters. The optimal Pt-to-Pd atomic ratio was between 0.2 and 0.3, maximizing Pd-Pt interactions. In SSZ-13 zeolites, reversible re-dispersion was achieved using subsequent treatments under O2 and H2, and 10 kPa O2 partial pressure during CH4-O2 reactions was found to maximize the Pd cluster dispersion. The modifications on Pd clusters explored in this thesis could help produce more active (Pt incorporation into Pd) and stable (Pd supported on SSZ-13) exhaust emission catalysts that are less prone to sintering.

Keywords: Catalysis
Kinetics
Methane Oxidation
Zeolite
Advisor: Chin, Ya-Huei (Cathy)
A Multi-facet Investigation of Impulsivity and Social Cognition in Bipolar Disorder

Research has supported the impairment of both impulsivity and social cognition within bipolar disorder (BD). Despite this, additional research is necessary to clarify the manifestation of the sub-domains of these multi-faceted constructs. This study sought to examine the manifestation of the facets of impulsivity (i.e. trait behavioural) and social cognition (i.e. theory of mind social perception). Performances on validated measures of impulsivity and social cognition from a sample of 26 BD participants and 25 community controls were compared to observe for patterns indicative of impairment. The results of this examination suggest that euthymic and subthreshold BD individuals perform equal to controls regarding behavioural measures of impulsivity, theory of mind, and social perception. At the same time, levels of trait-impulsivity are statistically elevated compared to controls. These results suggest additional variables such as medication, symptom profile, and baseline functioning may mediate/moderate the manifestation of impulsivity and social cognitive impairments.

Keywords: Bipolar Disorder
Impulsivity
Social Cognition
Social Perception
Theory of Mind
Advisor: Goghari, Vina
Gender, Migration, and Newcomer Artists

The art world is grounded in the gendered and undervalued work of social reproduction. Thus, the high female presence in the newcomer arts scene is not circumstantial but a common trait of an increasingly gendered art world. Drawing from dialectical historical materialist anti-racist Marxist-feminism and existing literature, I explore the conditions in which newcomer female artists come to engage with the Toronto art world, and how do their experiences are imbricated with the power relations that constitute a gendered society. Through interviews to eight artists, I present not only a description of these women’s experiences, but their intersection with gender and racial hierarchies and capitalist social relations embedded in the art world in which they wish to be included.

Keywords: art and social reproduction
Gender and Migration
Marxist feminism
Newcomer artist
Advisor: Mojab, Shahrzad
Manipulating the Blood Labyrinth Barrier with Mannitol to Prevent Cisplatin-induced Hearing Loss

AbstractCisplatin is a chemotherapeutic medication that remains in the cochlea indefinitely, causing permanent hearing loss. Mannitol may increase the permeability of the Blood Labyrinth Barrier (BLB) therefore increasing the rate of egression of cisplatin and entry of N-acetylcysteine (NAC): an otoprotective agent. Rats treated with cisplatin, at t=0 hours, were given either mannitol at t=0 hours, mannitol at t=6 hours, NAC alone, or NAC with mannitol. Mannitol at t=0 hours increased cisplatin entry into the inner ear and exacerbated cisplatin-induced hearing loss. Mannitol at t=6 hours did not increase cisplatin entry into the inner ear and preserved inner ear functionality and structure. NAC with mannitol provided greater protection against cisplatin-induced hearing loss than NAC alone. Mannitol injections at t=6 hours reduced cisplatin ototoxicity and enhanced the efficacy of antioxidants. This will provide an important therapeutic strategy to prevent cisplatin ototoxicity, a direct implication in hearing rehabilitation in cisplatin chemotherapy.

Keywords: Antioxidants
Blood Labyrinth Barrier
Cisplatin
Hearing Loss
Mannitol
Pharmacokinetics
Advisor: Le, Trung
Investigating Neuroimaging and Cognitive Correlates of the Glutathione Antioxidant System in Mild Vascular Cognitive Impairment

Mild vascular cognitive impairment (mVCI) is the prodromal stage of vascular dementia and its pathogenesis is less defined in literature. This thesis explored the associations between antioxidant glutathione (GSH), white matter damage, and cognitive deficits. Patients with mVCI (n=23) were recruited from Toronto Rehabilitation Institute’s cardiac rehabilitation program. Increased GSH in the occipital lobe as measured by proton magnetic resonance spectroscopy was associated with greater periventricular white matter hyperintensities in the occipital lobe as measured by magnetic resonance imaging (β=0.629, p=0.029). Conversely, increased plasma glutathione peroxidase was associated with greater deficits in verbal memory (β=-0.587, p=0.010), while increased GSH in the anterior cingulate cortex demonstrated a trending association with greater deficits in verbal memory (β=-0.564, p=0.056). This research suggests that GSH dysregulation may be associated with white matter damage, although findings were limited to the occipital lobe, and the peripheral GSH system may be associated with memory deficits in mVCI.

Keywords: cardiovascular
glutathione
magnetic resonance spectroscopy
neuroimaging
oxidative stress
vascular cognitive impairment
Advisor: Lanctôt, Krista L
Integrating a Neural Network for Depth from Defocus with a Single MEMS Actuated Camera

The prevalence of miniature cameras used in mobile devices such as smartphones or tablets have made different applications possible, including 3D depth mapping. While exploiting the advancements on speed of response in miniature cameras., the use of convolutional neural networks (CNNs) in depth estimation is explored. This thesis details the extensive steps in set-up that is required to gather a dataset using a MEMS actuated miniature camera in order to train a CNN to predict depth maps. Training is completed on the dataset and results of the performance of the CNN is shown. Scenarios where the depth estimation fails or excels are discussed, and possible further steps to take for refinement and improvement of the current results are provided. This project shows the primitive feasibility of integration of the CNN in order to perform depth estimation using the miniature camera using MEMS actuators and provides a proof-of-concept for this feature.

Advisor: Ben-Mrad, Ridha