VictorJuiz/thesis huggingface dataset:
Assessment of Commuting Pauli Product Grouping Measurement Techniques in the Presence of Noise
Keywords: Chemical Physics
Quantum Chemistry
Quantum Computing
Quantum Information
Quantum Mechanics
Variational Quantum Eigensolver

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.
Investigating the Effects of IDO1 Inhibition on the Recovery of Motor Coordination, Memory and Mood Following TBI
Keywords: Behavioural testing
IDO1 inhibitor
Indoleamine-2-3-dioxygenase
Neuroinflammation
PF-06840003
Traumatic Brain Injury

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.
The Neural Correlates of Dystonia and Impaired Inhibitory Control in Pediatric Stroke Patients
Keywords: Dystonia
Inhibitory control
MEG
MRI
Pediatric stroke

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.
Using Natural Language Processing and Machine Learning to Analyze Admission Criteria of a General Internal Medicine Short Stay Unit
Keywords: Admission Criteria
General Internal Medicine
Machine Learning
Natural Language Processing
Patient Flow
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.
The Trajectory and Posttraumatic Transformations of Suicide Bereavement: A Focus on the Experiences of Chinese Canadians
Keywords: Chinese
Chinese culture
Post-traumatic growth
Qualitative research
Suicide Bereavement
Suicide Survivor

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.
Strategies for Resolving Functional States in Complex Proteins
Keywords: Fluorescence
G-protein coupled receptors
Nuclear Magnetic Resonance
Solvatochromic Fluorophore
Tautomer Tag

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.
Design and Optimization of a 1.5m Telescope Balloon Borne Gondola
Keywords: Balloon Borne Imaging
Design for Manufacturing
Material Approximation
Stratospheric Ballooning
Structural Design
Topology Optimization

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.
The Lattice Model of Fragmentation Modes: A Multilevel Selection Model of a Major Transition in Individuality
Keywords: cancer
life cycles
multicellularity

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.
Towards a Nanoscale Flow Cytometry Assay of Circulating Extracellular Vesicles for Maternal Health Trajectories
Keywords: Extracellular vesicles
HLA-G
Liquid biopsy
Nanoscale flow cytometry
PLAP
Preeclampsia

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.
The Effects of Dairy and Non-dairy Aternatives on Post-prandial Gycemia and Appetite in Healthy Young Adults
Keywords: Appetite
Dairy
Glycemia
Metabolic responses
Plant-based alternatives

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.
Debunking the International Student Problem: Redefining Plagiarism as Culturally Specific Behaviours for Demonstrating Widely Held Moral Values
Keywords: academic integrity
Canadian higher education
cultural capital
ideal types
international students
plagiarism

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.
Efficient Hyperreduction by Empirical Quadrature Procedure with Constraint Reduction for Large-scale Parameterized Nonlinear Problems
Keywords: Constraint reduction
Empirical quadrature procedure
Hyperreduction
Parameter sampling
Reduced order modeling

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.
Digital Systems for Closed-Loop Neuromodulation Research
Keywords: Multi-Electrode Array
Neural Probe
Partial Reconfiguration
Python HDL

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.
Fragile-X Mental Retardation Autosomal Homolog 1 and Glycogen Synthase Kinase 3 Regulation by Antipsychotics
Keywords: Antipsychotics
D2R
Fxr1
GSK3
Schizophrenia

Schizophrenia is defined by varying symptoms between patients that all lead to impaired quality of life. An underlying cause of schizophrenia is thought to be a dysregulated dopamine system, with dopamine related antipsychotics being the first form of care. Current treatment options for patients are limited to chronic antipsychotic use which all target dopamine receptor D2. Part of D2 signalling involves downstream proteins, like Akt and GSK3β. GWAS studies have recently implicated FXR1, a protein downstream of GSK3β, as a risk factor for schizophrenia. This thesis looks at the changes in downstream effectors of D2 due to chronic antipsychotic treatment to elucidate the role of FXR1 in schizophrenia management. Using qPCR and western blot techniques, no significant changes were seen in downstream protein or gene levels due to chronic antipsychotics. However, these results do show promise as this study was underpowered and future research should be done to confirm these findings.
The Role of Transforming-growth Factor Beta 1 and Platelet-derived Growth Factor in Right Ventricular Remodeling in Response to Right Ventricular Pressure and Volume-loading
Keywords: Cardiology
Congenital heart disease
Fibrosis
Hypertrophy
Right ventricle
Tetralogy of Fallot

Residual lesions in repaired Tetralogy of Fallot (rTOF) induce chronic right ventricular (RV) pressure- and volume-loading which can lead to maladaptive RV remodeling and dysfunction. Recent work has found that pro-fibrotic, transforming-growth factor β1 (TGFβ1) and platelet-derived growth factor (PDGF) are upregulated in RV hemodynamic overloading models. However, the functional impact and underlying mechanisms of RV fibrosis are poorly defined. Therefore, we hypothesize that TGFβ1 and PDGF induce RV fibrosis which drives RV dysfunction in RV pressure and volume-loading conditions. Utilizing a pulmonary artery band and pulmonary regurgitation in vivo model, to mimic residual lesions found in rTOF, we administered a potent dual inhibitor of TGFβ1 and PDGF, Tranilast (TRN). Our study shows that TRN reduced RV fibrosis and/or hypertrophy in PAB and PR models, which were associated with improved RV function. These results form a basis that TGFβ and PDGF signaling are key drivers of RV dysfunction.
Integration Experiences of Kenyans in North America: A Case Study on Canada and the USA
Keywords: Immigration
intergration
Trans migration

This thesis examines the integration experiences of Kenyan immigrants in North America, with a primary focus on Canada and the US. The study employs a qualitative methodology and integration and transnational theory to investigate the different experiences of Kenyan immigrants in both nations, as well as the factors affecting their integration. Findings indicate that although Kenyan immigrants to North America encounter language, cultural and social capital obstacles, they are also able to find a sense of community and belonging. Despite these challenges, the study shows that Kenyans have used a variety of tactics to disrupt the obstacles and seize the chances that North America has to offer. This thesis offers significant insights into the ways in which immigrants from Kenya manage their life in their new cultures and helps our knowledge of the integration experience of those immigrants in North America. Additionally, through this study, both the positive and negative impacts of transnationalism are determined and examined.
Assessing Astrocyte Function in Bipolar Depression
Keywords: Astrocytes
Bipolar Depression
Bipolar Disorder
MAO-B
PET imaging

Bipolar Disorder (BD) is a chronic mental disorder characterised by episodes of hypomanic/manic, depressed, or mixed mood. Monoamine oxidase B (MAO-B) is an enzyme that is associated with oxidative stress in the brain and is found in astrocytes, a type of glial cell. Reports suggest neuroinflammation in BD may be associated with astrocyte dysfunction. The aim of this pilot positron emission tomography (PET) study was to evaluate MAO-B volume distribution (VT) as an index of astrocyte activity in the prefrontal cortex, and anterior cingulate cortex of adults with BD depression using the radiotracer, [11C]SL2511.88. Recruitment was conducted at the Centre for Addiction and Mental Health (CAMH), Toronto from January 2021 and is ongoing. Findings indicated reduced MAO-B VT in participants with BD depression (n=4) compared to healthy controls (n=20), suggesting astrocyte loss/dysfunction. Further investigations are required to confirm whether reduced MAO-B VT is associated with the neuropathology of BD depression.
Modeling and Comparison of Parallel Heuristic Algorithms for Trade Optimization
Keywords: Genetic Algorithm
neighborhood search
Optimization
promotion
Simulated Annealing
trade

This thesis proposes a mathematical optimization model for the trade optimization (TO) problem, considering various general features and key performance indicators (KPIs) from both commodity suppliers and retailers' perspectives. It also introduces parallel models for genetic algorithm (GA), simulated annealing (SA), and large-scale neighborhood search (LNS) to solve the TO problem. The study aims to evaluate and compare the performance of these heuristic optimization algorithms in terms of convergence behavior, solution quality, and robustness. The contributions include a novel optimization model, a parallel framework implemented using Python, and a comprehensive evaluation of different heuristic optimization algorithms in the TO context. Experimental results indicate that the suggested parallel framework greatly improves both the convergence rate and the quality of the solution. Overall, among the three algorithms, SA exhibits the most superior performance. The study provides insights and guidelines for solving complex optimization problems in the context of trade optimization.
Osteochondral Allograft Transplantation: Tissue Storage and Surgical Factors Using an Ovine Model
Keywords: Allograft
Osteochondral
Tissue Storage
Transplant

An effective surgical treatment for large cartilage lesions is Osteochondral Allograft Transplantation (OCAT). The method and duration of cadaveric donor tissue storage prior to transplantation can reduce chondrocyte viability, which is directly correlated to negative clinical outcomes. Active research aims to increase chondrocyte viability at extended durations of storage. Effects of long-term storage were investigated by quantifying changes in ovine cartilage explants after storage in a proprietary, DMEM-based media known as MOPS. OCAT surgical techniques can also negatively impact cartilage quality. This thesis investigated the relationship between increased graft press-fit and insertion forces and resulting cell viability, using both human and ovine tissues. Finally, 3D-printed drill guides were developed for placement of osteochondral grafts in a pre-clinical ovine model. This thesis highlights interdependent factors that influence donor cartilage quality in OCAT, as well as identifying species differences that are important to consider when interpreting results from the pre-clinical ovine model.