VictorJuiz/thesis huggingface dataset:
Development and Validation of a Clinical Prediction Tool for Estimating the Risk of 1-year Mortality among Hospitalized Patients with Dementia

Advance care planning (ACP) has an established benefit among dementia patients though may happen infrequently, which could contribute to goal-discordant end-of-life care. A prognostic tool could serve as a trigger for ACP. We sought to develop and test a clinical tool to predict the risk of 1-year mortality among hospitalized dementia patients. Population-level linked healthcare administrative databases in Ontario were used. In a cohort of 235667 patients hospitalized from 2009-2017, we developed a tool with 76 predictor variables (sociodemographic factors, comorbidities, previous interventions, functional status, nutritional status, admission-specific information, previous healthcare utilization). In a cohort of 62909 patients hospitalized from 2018-2019, the tool demonstrated acceptable discrimination (c statistic=0.796). It demonstrated acceptable calibration in the validation cohort (mean relative difference=-3.29%) and subgroups of meaning to clinicians and policy-makers. This model could be integrated into electronic medical records as an automated prognostic tool, which could prompt ACP among hospitalized dementia patients.

Keywords: clinical decision rules
dementia
epidemiology
hospitalization
mortality
prognosis
Advisor: Wentlandt, Kirsten
Assessment of Commuting Pauli Product Grouping Measurement Techniques in the Presence of Noise

Measuring quantum observables by grouping terms that can be rotated to sums of only products of Pauli ˆz operators (Ising form) is proven to be efficient in near-term quantum computing algorithms.This approach requires extra unitary transformations to rotate the state of interest so that the measurement of a fragment’s Ising form would be equivalent to measurement of the fragment for the unrotated state. These extra rotations allow one to perform a fewer number of measurements by grouping more terms into the measurable fragments with a lower overall estimator variance. However, previous estimations of the number of measurements did not take into account non-unit fidelity of quantum gates implementing the additional transformations. Through a circuit fidelity reduction, additional transformations introduce extra uncertainty and increase the needed number of measurements. Here we consider a simple model for errors introduced by additional gates needed in schemes involving grouping of commuting Pauli products. For a set of molecular electronic Hamiltonians, we confirm that the numbers of measurements in schemes using non-local qubit rotations are still lower than those in their local qubit rotation counterparts, even after accounting for uncertainties introduced by additional gates.

Keywords: Chemical Physics
Quantum Chemistry
Quantum Computing
Quantum Information
Quantum Mechanics
Variational Quantum Eigensolver
Advisor: Izmaylov, Artur F
Investigating the Effects of IDO1 Inhibition on the Recovery of Motor Coordination, Memory and Mood Following TBI

Traumatic brain injury (TBI) is caused by mechanistic forces that impact the brain, leading to neuronal damage and deterioration. Secondary injuries, such as neuroinflammation, can cause further damage and neurological dysfunction. The enzyme indoleamine 2,3 dioxygenase 1 (IDO1) catalyzes the rate-limiting step in the kynurenine pathway (KP) which produces both neuroprotective and neurotoxic metabolites and may contribute to secondary injury mechanisms. We hypothesized that PF-06840003, an IDO1 inhibitor, would decrease secondary injury, improving motor, memory and mood recovery following the fluid percussion injury (FPI) model of TBI. Rats underwent either FPI or sham injury and were treated orally with PF-06840003 or vehicle. PF-06840003 treatment resulted in improved performance on long-term visuospatial memory and anxiety-like behavioural tests but not on sensorimotor tests. This suggests the KP may play a role in neurological dysfunction after TBI and should be further investigated as a potential therapeutic target to improve recovery.

Keywords: Behavioural testing
IDO1 inhibitor
Indoleamine-2-3-dioxygenase
Neuroinflammation
PF-06840003
Traumatic Brain Injury
Advisor: Reid, Aylin
The Neural Correlates of Dystonia and Impaired Inhibitory Control in Pediatric Stroke Patients

Dystonia affects over 20% of pediatric ischemic stroke survivors and is associated with cognitive impairments. However, it remains unclear whether dystonia is solely a motor disorder or if other cognitive impairments are involved. We investigated the functional and structural profiles of post-stroke patients during a motor inhibitory control task, focusing on differences between those with and without dystonia. Using MEG and DTI, we analyzed task-induced brain activity and the structural integrity of the corticospinal tract. Our results suggest that successful motor control relies on the integration of higher order frontal and motor processes, alongside basic motor functions, and that dystonia patients may have impairments in these higher order functions. Furthermore, our study found evidence of functional reorganization beyond motor execution in higher order frontal areas. This multimodal approach provides insight into motor impairment after stroke in children and may inform effective therapeutic interventions to improve outcomes.

Keywords: Dystonia
Inhibitory control
MEG
MRI
Pediatric stroke
Advisor: Cheyne, Douglas
Dlamini, Nomazulu
Using Natural Language Processing and Machine Learning to Analyze Admission Criteria of a General Internal Medicine Short Stay Unit

Short Stay Units (SSU) have been created to minimize emergency department overcrowding and aid in the patient flow process of hospitals. The best way to determine admission criteria into such units remains to be a challenge as not all hospitals operate the same. We apply 3 machine learning algorithms to predict the length of stay (LOS) of all General Internal Medicine (GIM) patients at Toronto General Hospital based on patient flow and emergency room triage assessment data from January 2019 to December 2019. Of these patients, 46% of them had a LOS of less than 72 hours and of those patients 51% were GIM patients. To aid in the potential implementation of a GIM SSU, we investigate into the predictors of the best performing model. Performance metric precision was calculated and found to be 0.77 for the best performing model (Random Forest) after hyperparameter tuning and feature selection. The features affecting admission criteria for a potential GIM SSU were found to be the following: age, pulse, blood pressure, respirations, day of admission, and chief complaint. Predictive key words for patients with a LOS of less than 3 days were also identified.

Keywords: Admission Criteria
General Internal Medicine
Machine Learning
Natural Language Processing
Patient Flow
Short Stay Unit
Advisor: Carter, Michael
The Trajectory and Posttraumatic Transformations of Suicide Bereavement: A Focus on the Experiences of Chinese Canadians

Suicide survivors have lost a loved one to suicide and often experience unique challenges when processing the loss. Addressing a gap in research, this study aims to understand Chinese Canadians’ lived experiences of suicide bereavement. This grounded theory qualitative study involved 11 self-identified Chinese Canadians who had lost loved one(s) to suicide. The findings suggest that when intertwined with questions of “why the person chose suicide” and “what if I had noticed their struggles”, participants reported intensified feelings of shock, sadness, and guilt. The stigma around suicide in Chinese culture exacerbated suicide survivors’ challenges. Contrastingly, strong social support served as a facilitator to counter the negative impact of stigma. Suicide survivors reported increased mental health awareness and strengthened interpersonal relationships following the suicide loss. Both challenges and growth following the death were identified by participants. Study limitations, clinical implications, and directions for future research are discussed.

Keywords: Chinese
Chinese culture
Post-traumatic growth
Qualitative research
Suicide Bereavement
Suicide Survivor
Advisor: Tsang, Ka Tat
Eaton, Andrew
Strategies for Resolving Functional States in Complex Proteins

Guanine nucleotide-binding protein (G protein) coupled receptors (GPCRs) are a large family of proteins that mediate many physiological responses, notably sensory and neuronal signalling, and cell homeostasis. Nearly one-third of approved prescription pharmaceuticals target GPCRs for their druggability and dispersion across the body and hence are essential to study. Biophysical techniques (i.e., NMR and fluorescence) provide detailed information regarding GPCR functional states and conformational dynamics associated with their activation and pharmacology. While these spectroscopic methods often reveal a complex conformational ensemble, it is often difficult to resolve conformers based solely on their electrostatic microenvironments. Here we evaluated two novel tags, for NMR and fluorescence applications. In the former case, we implemented and tested a new thiol-reactive fluorinated lactim/lactam tautomer (ITFPA) exhibiting unprecedented chemical shift sensitivity to polarity. In the latter case, we performed preliminary studies on a solvatochromic fluorophore (PM3_6), whose emissions are also known to depend on microenvironment.

Keywords: Fluorescence
G-protein coupled receptors
Nuclear Magnetic Resonance
Solvatochromic Fluorophore
Tautomer Tag
Advisor: Prosser, Robert Scott
Design and Optimization of a 1.5m Telescope Balloon Borne Gondola

GigaBIT is the successor of the Balloon-Borne Imaging Testbed (SuperBIT), a 1.5m telescope that operates in the stratosphere. The GigaBIT gondola must support a telescope almost double the size of SuperBIT while still adhering to the mass restrictionset forth by its predecessor as it will be launched with the same balloon. This presents the challenge of designing a lightweight gondola, strong enough to survive the necessary structural safety requirements and rigid enough to allow for sub-arcsecond pointing. This thesis explores the design process and development of the gondola. This was done using topological optimization to determine the optimal structural geometry of the gondola’s frames. From there, a design was produced, analyzed and amended rigorously following static analysis results to adhere to the mandatory design specifications set forth by the Gondola Structural Design Requirements. This design represents a foundation for future balloon-borne astronomy.

Keywords: Balloon Borne Imaging
Design for Manufacturing
Material Approximation
Stratospheric Ballooning
Structural Design
Topology Optimization
Advisor: Damaren, Christopher J.
Netterfield, C. Barth
Duration of Diaphragmatic Inactivity after Endotracheal Intubation of Critically Ill Patients

There is a recognized pathophysiological association between mechanical ventilation (MV) and respiratory muscle dysfunction, particularly the diaphragm and is associated with adverse outcomes. In this study, we aimed to assess the duration of absent or excessively low diaphragm activity after intubation by continuously measuring the electrical activity of the diaphragm (EAdi) soon after intubation in critically ill patients and assessed the relationship between EAdi and diaphragm activity on ultrasound. We hypothesized that resumption of activity was influenced by disease severity and sedation management. Sixty-nine patients were analyzed, the median time to EAdi recovery was 22 hours. Prolonged duration of EAdi suppression was associated with sedative agents and controlled modes of ventilation, but severity of illness was not. We found that low levels of diaphragm electrical activity are common in the early course of mechanical ventilation, and it may be related to clinician behaviour and sedation prescription.

Advisor: Brochard, Laurent
The Lattice Model of Fragmentation Modes: A Multilevel Selection Model of a Major Transition in Individuality

A multicellular organism is a group of cooperating cells. But wherever there is cooperation, there is the temptation to cheat. Cancer cells are cheating cells. On a cellular level there is selection for cells that replicate faster, even if it is to the detriment of the organism. Given this phenomenon, what has facilitated and maintained the transition to multicellular life? The unicellular bottleneck has been hypothesized as an adaptation to deal with these cheating cells by increasing kinship among cells in the organism and purging lineages of cancer cells. Meanwhile, competition between organisms may favour larger offspring. I created a simulation to investigate the most adaptive life history strategies given the trade-off between different selective forces acting on propagule size. This model provides insight into a major transition in individuality, and in particular, the evolution of clonal, multicellular life cycles.

Keywords: cancer
life cycles
multicellularity
Advisor: Osmond, Matthew M
Towards a Nanoscale Flow Cytometry Assay of Circulating Extracellular Vesicles for Maternal Health Trajectories

Preeclampsia is a hypertensive disorder characterized by the onset of high blood pressure and high protein in urine. However, no test is available clinically for the diagnosis of preeclampsia. In pathological studies, measurements derived from extracellular vesicles (EVs) circulating in maternal blood during pregnancy have emerged. This thesis demonstrates the use of blood-circulating EVs; specifically, EVs found in plasma have lower variability in expression than serum samples, regardless of patient classification. Placental Alkaline Phosphatase (PLAP) and Human Leukocyte Antigen G (HLA-G) were biomarkers used to distinguish between low-risk full-term and preeclamptic pregnancies, creating a novel placental liquid biopsy. Notedly, HLA-G positive EVs and EVs co-expressing PLAP and HLA-G showed significant differences in concentration amongst preeclamptic patients and patients undergoing amniocentesis procedures. High HLA-G expression was noted as early as five weeks gestation, suggesting the possibility of detecting potentially abnormal pregnancies as early as the first trimester for maternal health trajectories.

Keywords: Extracellular vesicles
HLA-G
Liquid biopsy
Nanoscale flow cytometry
PLAP
Preeclampsia
Advisor: Leong, Hon
The Effects of Dairy and Non-dairy Aternatives on Post-prandial Gycemia and Appetite in Healthy Young Adults

The hypothesis that dairy products will reduce post-prandial glycemia (PGG) and appetite more than their plant-based alternatives before and after a fixed size meal in healthy young adults was explored. Experiment one compared one-serving of Greek yogurt or cheddar cheese to their plant-based alternatives. Experiment two compared one-serving of 2% milk, vanilla soy beverage, vanilla almond beverage, cheddar cheese, and vegan cheese. In experiment one, PPG was reduced by premeal consumption of Greek yogurt and cheddar cheese compared to their plant-based alternatives. In experiment two, PPG differed among dairy products and their plant-based alternatives. Similarly, post-prandial appetite and appetite responses during the second meal were product dependent. Overall, premeal consumption of semi-solid and solid dairy food resulted in lowered PPG than their plant-based alternatives. Future research is necessary to determine components in dairy products and their plant-based alternatives that contribute to PGG, insulin responses, and appetite control.

Keywords: Appetite
Dairy
Glycemia
Metabolic responses
Plant-based alternatives
Advisor: Anderson, G. Harvey
Utilizing Mobile Monitoring to Predict the Spatial Distribution of Urban Air Temperature and Associations of Marginalization at a Microscale in Mississauga, Ontario

This thesis has two main objectives: to determine if the model based on continuous collection of air temperature observations could produce better performing results than a semi-stationary collection to estimate a microscale surface of urban air temperature, and second, to investigate the spatial associations between marginalization and air temperature in Mississauga, Ontario, Canada. The first objective was achieved by sampling air temperature by mobile monitoring, then comparing the performance of models generated from continuous collection and semi-stationary using regression kriging. Results demonstrated that the model generated from the air temperature data from continuous collection performed better. The second objective was achieved by expanding our air temperature results from the first objective and using ordinary least squares (OLS) regression and simultaneous autoregressive (SAR) modelling techniques to understand the associations between marginalization and air temperature. Results demonstrated that the spatial differences in urban air temperature in Mississauga do not align with marginalization.

Advisor: Adams, Matthew D
Debunking the International Student Problem: Redefining Plagiarism as Culturally Specific Behaviours for Demonstrating Widely Held Moral Values

Academic misconduct is a global issue in higher education, but literature from Western countries like Australia, the United States, and the United Kingdom, seem to frame it as an “international student problem”. This assumption is both essentialist and racist, absolving the institution of responsibility in the teaching and learning relationship. In this study, I debunk this concept as a complex, socially constructed issue that naturalizes the academic cultural capital of the white, Western middle-class. I do so through a comparison of Eastern, Western, and African ideal types for normative constructions of academically honest behaviours. In comparing each type to the International Center for Academic Integrity’s values for academic integrity, I encourage Western faculty and institutions of higher education to realize their joint responsibility with students in maintaining academic integrity so that international students can be better supported towards academic success.

Keywords: academic integrity
Canadian higher education
cultural capital
ideal types
international students
plagiarism
Advisor: Buckner, Elizabeth
Towards Quality Care: Understanding Mental Health Service Providers in the Non-Insured Health Benefits (NIHB) Program

Mental health-related harms and suicide are significant public health crises among Indigenous populations in Canada, with outcomes being attributed to lasting impacts of colonization, ongoing marginalization, and barriers to accessing services. The Non-Insured Health Benefits (NIHB) program is a federally funded program for First Nation and Inuit people that seeks to address disparities in access to care through services, including mental health counselling, that are not otherwise covered through insurance programs. Despite growing uptake and increasing expenditures for the mental health counselling area, this analysis serves as one of the first evaluations of the program. Data from a nationwide survey for NIHB mental health providers was used to summarize demographic information, assess providers’ beliefs about suicide, and explore the relationship between experience and provider confidence levels. Our growing understanding has lasting implications for policy and practice, including addressing gaps in service delivery and clarifying areas where more training is needed.

Advisor: Ansloos, Jeffrey
Efficient Hyperreduction by Empirical Quadrature Procedure with Constraint Reduction for Large-scale Parameterized Nonlinear Problems

Many engineering applications require rapid and reliable approximations of parameterized nonlinear partial differential equations. Model order reduction (MOR) constructs a low-dimensional model in the offline stage such that we can rapidly calculate outputs for any parameter value in the online stage. For equations with general nonlinearities, MOR requires hyperreduction, which can be computationally expensive. In this work, we improve the offline-efficiency of empirical quadrature procedure (EQP) used for hyperreduction. EQP involves solving a constrained minimization problem, often with a large set of constraints. We propose four modifications to EQP. First, we consider second-order error contributions to achieve smaller error tolerances. Second, we propose a rounding-error stable constraint residual calculation method, reducing offline cost. Third, and most importantly, we develop a constraint reduction method, employing QR factorization to reduce the number of constraints and thus improve offline-efficiency. Fourth, we develop an efficient sampling procedure for problems with high-dimensional parameter spaces.

Keywords: Constraint reduction
Empirical quadrature procedure
Hyperreduction
Parameter sampling
Reduced order modeling
Advisor: Yano, Masayuki
Design and Feasibility Analysis of a Low-Cost Wearable Gait Sensing System

Gait assessment is an essential part of the rehabilitation process for stroke survivors, persons with Parkinson’s disease, lower limb amputees, and other individuals with gait challenges. Current gait analysis methods rely primarily on clinical observations, which are subjective and only moderately reliable, especially when gait deviations are minor. Existing technologies like gait mats and motion capture systems are expensive and require expertise to operate. The objective of this research was to design a low-cost and practical gait sensing system to complement clinical assessments. The proposed solution consists of size-adaptable shoe covers instrumented with force sensing resistors and IMUs as well as a GUI for data processing and visualization. A feasibility study was performed at a rehabilitation centre with lower limb prosthesis users as participants. The study is ongoing but initial results obtained from six participants suggest high levels of both feasibility and acceptability of the technology.

Advisor: Azhari, Faezeh FA
Digital Systems for Closed-Loop Neuromodulation Research

Closed-Loop Neuromodulation (CLN) is a form of adaptive therapy that provides stimulation only when necessary. Clinical trials have shown that, despite several advantages, fundamental insights in pathological state-classification and stimulus application are still needed to realize the full potential of CLN. However, the existing research tools have functional limitations or proprietary restrictions that hinder exploration of state-classification algorithms and stimulation protocols. This thesis presents the design of a digital hardware platform to address these issues. The platform interfaces with neural sensors and enables the development of custom software and firmware for the evaluation of complex algorithms and low-latency applications. In addition, the incorporation of a Python-based hardware description language and partial reconfiguration facilitates the creation of a reusable firmware library for CLN research. An in vitro electrophysiological system using multielectrode arrays and an in vivo multimodal system with an implantable opto-electrode are implemented to demonstrate the capability of the platform.

Keywords: Multi-Electrode Array
Neural Probe
Partial Reconfiguration
Python HDL
Advisor: Valiante, Taufik A
Poon, Joyce