VictorJuiz/thesis huggingface dataset:
The Medical Necessity of Orthodontic Care: A Qualitative Study

Introduction: The medical necessity of orthodontic care is not a widely agreed upon concept. Without an operational definition of medically necessary orthodontic care (MNOC), priority setting of funds for orthodontics remains a challenge.Purpose: The purpose of this study was to explore factors that might be used to discern MNOC as perceived by stakeholders in orthodontics. Methods: Sixteen participants were interviewed regarding their perceptions of MNOC. Interviews were transcribed, coded, and analyzed for themes. Results: Participants identified dental, medical, psychosocial, and funding factors which must be considered when discerning MNOC. This highlights the complex interplay between the dental profession, funders, society, and individual patients in understanding MNOC. Conclusions: A contemporary decision-making process which considers the viewpoint of all stakeholders should be developed to ensure that resource allocation and priority setting are effectively securing coverage for those with true need in the context of health, wellbeing, and quality of life.

Keywords: Dentistry
Health
Medical
Necessity
Orthodontics
Public
Advisor: Quiñonez, Carlos
Resolving Subclonal Variation in Pancreatic Ductal Adenocarcinoma with Single Cell Whole Genome Sequencing

Pancreatic ductal adenocarcinoma (PDA) is a lethal disease that presents at an advanced stage, and the mutational processes that drive progression are poorly understood. Whole genome duplication (WGD) is a hallmark of many tumour types, increases in frequency in late-stage tumors and predicts poorer overall patient survival. The genome-wide instability that occurs during WGD can promote tumor progression, but little is known about these events at the subclonal level. We performed single cell whole genome sequencing (scWGS) on 10,286 cells from 8 primary PDA tumours and inferred ploidy and genomic copy numbers for each cell. WGD was identified in 5/8 tumours (63%), 2 of which were clonal and 3 and subclonal. Clustering of copy number profiles revealed 2-5 distinct subclones per tumour, though no trend of WGD+ tumours being more diverse was observed. Phylogenetic inference reveals WGD+ clones follow a punctuated pattern of evolution, where many copy number aberrations (CNAs) were acquired rapidly in bursts with few or no intermediate cells. These data show WGD is more common in primary PDA than previously understood and a major driver of rapid CNA accumulation.

Advisor: Notta, Faiyaz
Asymmetry in Bilateral Cochlear Implant Stimulation Levels affect Access to Inter-aural Level Cues in Children

This thesis assessed asymmetrical stimulation levels in bilateral cochlear implants(CIs) and its limits on spatial hearing in children. Children with bilateral CIs rely on inter-aural level differences(ILDs) for binaural cues, but this does not achieve normal spatial hearing. The first hypothesis was that asymmetrical levels would affect ascending areas of the afferent bilateral auditory pathways. Asymmetrical left vs. right auditory nerve responses predicted asymmetric unilateral brainstem responses and a larger bilateral brainstem response but did not predict behavioral lateralization. The second hypothesis was that sensitivity to ILDs would be limited by asymmetric programming and hearing history. Early cortical responses demonstrated sensitivity to changes in ILD, with an effect of acoustic hearing experience and programmed levels. Asymmetric programming, but not cortical detection or experience, affected behavioral lateralization. While asymmetric stimulation levels impact binaural processing, they do not fully predict how children adapt to perceive spatial information from bilateral CIs.

Keywords: Auditory Development
Binaural Hearing
Cochlear Implants
Electrophysiology
Pediatrics
Advisor: Gordon, Karen A
Novel Strategies to Extend In Situ Lung Preservation In An Uncontrolled DCD Large Animal Model

Clinical series reported successful transplantation of uDCD lungs preserved by pulmonary inflation up to 3h postmortem. We investigated the additive effects of in situ intrapleural cooling and sevoflurane perconditioning on lung grafts in a porcine uDCD model. After uDCD induction, donors were allocated to: (1) control, (2) topical cooling, or (3) sevoflurane group. Lungs were preserved for 6h, then assessed on EVLP. The group with best performance was evaluated by allotransplantation in a second phase. Intrathoracic temperature <15°C was achieved within 1h in intervention groups. All lungs in group 1 failed on EVLP. Group 3 outperformed group 2 during 6h-EVLP and presented lower levels of pro-inflammatory cytokines. Post-transplant graft assessment in group 3 showed excellent oxygenation. Preservation of uDCD lungs with sevoflurane, static lung inflation and intrapleural cooling maintains good function up to 6h postmortem, with excellent early post-transplant performance. These interventions could potentially expand clinical utilization of uDCD lungs.

Keywords: ex-vivo lung perfusion
lung transplantation
sevoflurane
uncontrolled DCD
Advisor: Cypel, Marcelo
The Association of Postoperative Anemia with Adverse Outcomes in Patients Undergoing Cardiac Surgery: A Retrospective Cohort Study

Anemia is a common blood disorder in cardiac surgery patients. While many studies demonstrated a relationship between preoperative anemia and adverse outcomes, few have explored postoperative anemia in this manner. This single-centre retrospective cohort study included 4608 elective cardiac surgery patients and was undertaken to assess the prevalence of postoperative anemia, to identify potential risk factors, and to examine the influence of postoperative anemia on outcomes. Nearly half (48%) of patients developed postoperative anemia. Significant risk factors were female sex, older age, lower BMI, preoperative anemia, poor kidney function, unstable cardiac symptoms, and longer procedure times. Postoperative anemia was a significant predictor of acute kidney injury (odds ratio 1.41; 95% CI 1.09-1.82) and longer hospital stay (ratio of means 1.04; 95% CI 1.00-1.08). The data suggest that postoperative anemia is a highly prevalent and important risk factor for adverse events in cardiac surgery. Therefore, research into potential therapies is necessary.

Keywords: Anemia
Cardiac surgery
Advisor: Karkouti, Keyvan
Multi-dimensional Mereotopology based on Algebraic Topology

This study centers on investigating and setting necessary conditions for building a spatial ontology. In the qualitative formalization of space, researchers typically adopt either a point-set or an algebraic topology viewpoint. Some incorporate dimensionality, while others do not. A significant research gap exists in determining whether the current characterizations share the same ontological commitments or semantic requirements. We thus introduce a novel mathematical structure thatserves as a unifying platform for boundaries in both multi-dimensional and non-dimensional mereotopologies. Beyond the dimensional aspects, we explore spatial characterizations from the angle of Euclidean geometries. We initially focus on the familiar two-dimensional space, before expanding our perspective to encompass a more general concept of space: manifolds. By utilizing an amalgamation of mereology with graph theory, we can formally define and comprehend certain graph types using first-order-logic axioms. This not only enhances our understanding of these graphs but also opens up new avenues for more complex explorations in spatial ontology.

Advisor: Gruninger, Michael
Designing a Good Place: Culturally Safe Virtual Care for Chinese Canadian Prostate Cancer Survivors through Community-based Participatory Methods

Cultural adaptations of digital health interventions have been posited as a pathway to relieve resource constraints in an era of thinning healthcare services, while increasing access to care for communities made vulnerable. However, in settler colonial nation-states such as Canada, this approach may problematize “minority” culture and identity as the cause of structural health inequities. This research programme sought to qualitatively (1) explore the perceptions and experiences of Chinese Canadian prostate cancer survivors with follow-up and virtual care to identify structures that influenced their care (Study 1), and (2) develop and evaluate a community-based, culturally safe adaptation of the patient-facing Ned Clinic application (Study 2). Rather than adapting interventions using cultural sensitivity or competency, we demonstrate that by shifting paradigms, resurfacing the desires of our relations, and designing for relational accountability and cultural safety, we may be able to regenerate places of caring through digital health for more communities instead.

Keywords: Chinese Canadian
Cultural adaptation
Digital health
Health informatics
Prostate cancer
Structural competency
Advisor: Pham, Quynh
Exploring the Experiences of Racialized Lawyers Within Law Firms and Their Impact on Career Wellbeing

The upward mobility of racialized lawyers within Canadian law firms continues to lag behind that of their White counterparts. Available data suggests that the underrepresentation of racialized lawyers within the highest echelons of firm leadership may be closely linked to rate of attrition. This study used semi-structured interviews to gain an in-depth understanding of the subjective experiences of racialized lawyers working within Canadian law firms. These experiences were examined under the lens of theories about career wellbeing and the existence and persistence of racial inequity within organizations to understand their affect on racialized lawyers’ career wellbeing and, therefore, shed light on why racialized lawyers may be more likely to leave law firms than their White counterparts. This analysis suggested that experiences unique to or more common amongst racialized lawyers within Canadian law firms can negatively affect their career wellbeing, which can in turn lead to decreased organizational commitment and overall wellbeing.

Keywords: attrition
career wellbeing
diversity
inclusion
law firms
racialized lawyers
Advisor: Chen, Charles P
Theory Embedded Learning

Theory Embedded Learning (TEL) combines theoretical principles with machine learning to solve Engineering problems. It offers a middle ground between principle-driven and learning-based approaches. Principle-driven approaches rely on assumptions to inject prior knowledge, to simplify the problem for analytical solvability, and the solution is represented by mathematical relations the solution should satisfy. Learning-based approaches, on the other hand, require minimal assumptions and use parameterized black-box functions without any prior knowledge. TEL modifies principle-driven approaches by retaining assumptions that represent prior knowledge while removing unnecessary assumptions for solvability. It achieves solvability through gradient based optimization, representing the solution with parameterized mathematical relationships. Therefore, TEL benefits from the flexibility of learning-based approaches and the rigidity of principle-driven approaches, without any unnecessary assumptions made for solvability. This work identifies TEL solution approach as well as introduces three original instances of TEL for solving problems in optimal control, derivative pricing and combinatorial optimization.

Keywords: Combinatorial Optimization
Finance
Machine Learning
Reinforcement Learning
Advisor: Lee, Chi-guhn CGL
Rehabilitative Outcomes Following Childhood Stroke

A staggering 41-75% of children demonstrate impairments in speech and language functioning following stroke. A crucial stage for recovery occurs during post-stroke rehabilitation, however, little research has described speech and language outcomes throughout rehabilitative recovery. This dissertation explored the post-acute speech and language outcomes following childhood stroke through 1) a scoping review investigating the neural mechanisms driving speech and language recovery post-stroke and 2) a case series outlining speech and language outcomes across rehabilitation. Study 1 revealed a rudimentary accounting within the literature of speech and language profiles of children post-stroke; limited by varied and limited assessment batteries, inconsistent reporting of lesion location to speech and language functioning, a dearth of functional neuroimaging studies and a lack of information regarding speech and language functioning throughout rehabilitation. Study 2 describes three unique participant profiles of speech and language outcomes following childhood stroke across rehabilitation. Finally, future work is indicated and discussed.

Advisor: Beal, Deryk S.
Morgan, Angela T.
VLR: Scalable Failure-Tolerant Routing Based on Virtual Topologies

The Internet of Things (IoT) transforms industries by interconnecting a wide range of products, systems, sensors, vehicles, etc., leading to improved productivity and efficiency, reduced expenses, and new business directions. These large, dynamic networks consisting of heterogeneous devices call for scalable routing solutions that require minimal configuration and supervision. However, the current Internet's hierarchical architecture demands sufficient communication infrastructure and manual configurations, whereas typical ad-hoc routing protocols face scalability issues due to high memory consumption and control traffic overhead. In response to these challenges, this thesis introduces Virtual Link Routing (VLR), a distributed, scalable network routing scheme based on location-independent identifiers that is compatible with any link layer. VLR can leverage any structured virtual topologies that satisfies the greedy property, but the ring topology stands out because of its simplicity, configurability, efficient memory-stretch trade-off. Based on a ring overlay, we present a self-organizing VLR protocol that avoids network-wide flooding and periodic route probing while ensuring loop-free routing even in times of network instability. VLR exhibits robust performance in simulations comprising up to 10 000 nodes, highlighting its competence in achieving timely convergence after node/link failures or network partitions.

Keywords: Ad-hoc routing
Internet of Things
Overlay networks
Scalable routing
Virtual links
Advisor: Liebeherr, Jorg
Evaluation of Land-Atmosphere Nitrogen Cycling in CLASSIC at the Single-Site Level

The objective of this study was to evaluate Canadian Land Surface Scheme Including Biogeochemical Cycles (CLASSIC) simulations following the implementation of the nitrogen (N) cycle and compare these model outputs with observations of fluxes of reactive N (Nr) species in preparation for future coupling with the atmospheric component of the Canadian Earth System Model (CanESM). The model was forced using two deposition data sets, one observation-based (NADP) and the other model-based (TRENDY), at two FLUXNET towers, US-Ha1 and US- UMB. Elevated N deposition led to higher Nr emissions, and this was emphasized for N deposited as NO3-. Observations of NO and N2O fluxes at each site and other locations across the globe showed variability depending on forest type, which CLASSIC could not represent. Volatilization to ammonia is a significant contributor to gaseous N loss from the land and its description in CLASSIC is sensitive to soil pH.

Keywords: CLASSIC
Environmental Chemistry
Modelling
Nitrogen cycle
Advisor: Murphy, Jennifer G
Leveraging Cellular and Bluetooth Sensor Data for Enhanced Urban Travel Time Predictions

As urban areas continue to expand, the integration of smart city technologies and robust traffic control systems become essential in creating sustainable and safe living environments for all citizens. Efficient traffic management and advanced city planning are crucial for transforming urban centers into smart cities, ensuring smooth mobility and heightened safety for their residents. Many researchers have explored the domain of travel time prediction, with the majority focusing on trajectory tracking, often neglecting the broader perspective at the city level. While there are a few who shift their attention to city-wide travel time, they typically rely on individual GPS signals to learn and formulate predictions. Predicting at the city level presents a couple of challenges: firstly, the vast area to be covered, and secondly, ensuring accuracy in predictions while maintaining user privacy. Our research introduces two cutting-edge machine-learning models for city-level travel time prediction: the Network Insight Model and the Integrated Mobility Model. The former operates based on the count of unique cellular devices within a cell site to formulate its predictions. In contrast, the latter draws from both Bluetooth sensor data and network cellular count data to generate its estimates. The primary aim of these models is not just to offer precise insights into travel time patterns but also to ensure the flexibility of model deployment in varied situations. By integrating city-wide information, our models not only provide a detailed analysis of specific areas but also capture the broader context of the entire urban landscape. This approach further enables the models to identify and analyze correlations between various road intersections. Leveraging our innovative methods ensures that city travel becomes significantly convenient as the travel times are predicted accurately under varying circumstances. Our approach not only empowers city planners with essential data but also offers a comprehensive view of city dynamics. By identifying which road networks face higher traffic volumes, planners can design road development plans to reduce commute time, ultimately creating a city that is both comfortable and safe for its residents.

Advisor: Leon-Garcia, Alberto ALG
Encounter and Event

This thesis sheds light on the transcendent nature of the performative act and its relationship with the audience's experience. It argues that a successful performance must surpass the immediate situation and rely on the encounter between the viewer and the performance. The transformative experience of performance allows the viewer to engage with it, leading to disintegration and deconstruction within the drama itself. The performative act enables individuals to act under unbearable circumstances, achieving the impossible and realizing the unattainable actual event. The viewer's perception of the performance is integral to its unfolding, and the encounter between the viewer and the performance represents a harmony between sensory signs and truth-making processes. This text emphasizes the significance of the performative act as an event and its impact on the audience's perception. The synthesis of European post-structuralist theories, including phenomenology and psychoanalysis, helps to explain the political potential of postdramatic theatre, particularly for the possibility of recognition in non-universalist/pluralist democracies.

Advisor: Eacho, Douglas
Maternal-fetal ABO Blood Group Congruence and Risk of Serious Maternal and Infant/child Infection

During pregnancy, a variety of maternal IgG antibodies are transported across the placenta to the developing fetus, some of which are present at the birth, and protect the neonate against infection. Exposure of the mother and fetus to different (“incongruent”) ABO blood groups may influence maternal antibody formation, and plausibly, affect the risk of serious infection in the infant, and lesser so, the mother. The purpose of this study was to determine if maternal-newborn ABO blood group incongruence vs. congruence is associated with a higher risk of serious infection in the mother, or in her child, within the first 27 days after birth, as well as, from 28 days to 5 years thereafter. This retrospective population-based cohort study was completed at ICES, using linked patient-level datasets. Included were mothers with a singleton hospital livebirth in Ontario from 2008-2022, with known ABO blood groups among the mother and her newborn, and OHIP eligibility at the index birth. The relation between ABO blood group congruence and risk of serious infection was assessed using Cox proportional hazard models, adjusted for relevant covariates, and expressed as adjusted hazard ratios (aHR) and 95% confidence intervals (CI). Relative to congruent maternal-newborn ABO groups, those with incongruent ABO blood groups had an aHR for serious maternal infection of 1.14 (95% CI 0.98-1.35) within 27 days, and 0.95 (95% CI 0.91-0.99) from 28 days to 5 years after birth. The respective aHR for serious infant/child infection were 0.81 (95% CI 0.70-0.92) within 27 days and 0.95 (95% CI 0.93-0.97) from 28 days to 5 years after birth. The results of this study suggest that maternal-fetal ABO incompatibility may influence the short-term risk of infection in the child, and perhaps, the mother, soon after birth.

Keywords: ABO blood group(s)
Infant/child health
Infection(s)
Infectious disease(s)
Maternal health
Advisor: Ray, Joel G
Cohen, Eyal
Multi-Period Index-Tracking Strategies for Investment Portfolios

We introduce an innovative multi-period approach to index tracking for long-term investment portfolios. Unlike conventional tracking methods relying on single-period estimates, we propose a multi-period adaptive receding horizon strategy. The multi-period model mirrors the risk-return dynamics of the index it is tracking while accommodating portfolio manager preferences. This differs from existing multi-period tracking approaches that solely focus on replicating the return profile of an index. Our approach also incorporates cardinality constraints by way of a Penalized Alternating Direction Method of Multipliers (PADM), ensuring efficient optimal portfolio computations. The strategy showcases sustained tracking accuracy, computational efficiency, and adaptability to varying market conditions. We extend the multi-period index tracking model to a goal-oriented strategy that aims to increase the likelihood of attaining a defined wealth goal over a specified investment horizon. Our proposed model consistently outperforms benchmark strategies like Mean-Variance Optimal (MVO) and Equal-Weighted (EW).

Keywords: cardinality constraint
convex optimization
heuristic
index-tracking
multi-period
Advisor: Kwon, Roy
Designing a Synthetic Intron for AAV Capsid Engineering

Introns are often forgotten about in research, as they are typically not included in final proteins. However, their ability to be conditionally spliced out can benefit protein engineering by creating two protein variants from the same DNA sequence. In this research, a synthetic intron was developed that produces two variants; one where the intron is retained (i.e., readthrough), and another where it is spliced out. This creates two protein variants from the same DNA. To realize this concept, three constructs (control, weak splice, and strong splice) were engineered by integrating varying levels of intronic elements, such as, 5’ and 3’ splice enhancers (SEs), and G triplets. These constructs demonstrated that you can tailor splicing by adding intronic elements. These results were verified by microscopy and RT-qPCR. Then, an AAV repcap construct was developed and its splicing was determined by RT-qPCR. This research has many applications, such as rAAV targeting.

Keywords: AAV capsid engineering
g triplets
nanobody
splice enhancers
synthetic intron
Advisor: Truong, Kevin
Brown, Stephen