Theses

Permanent URI for this collectionhttps://uwspace.uwaterloo.ca/handle/10012/6

The theses in UWSpace are publicly accessible unless restricted due to publication or patent pending.

This collection includes a subset of theses submitted by graduates of the University of Waterloo as a partial requirement of a degree program at the Master's or PhD level. It includes all electronically submitted theses. (Electronic submission was optional from 1996 through 2006. Electronic submission became the default submission format in October 2006.)

This collection also includes a subset of UW theses that were scanned through the Theses Canada program. (The subset includes UW PhD theses from 1998 - 2002.)

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Soft Labels for Training and Evaluating Semantic Segmentation Models
(University of Waterloo, 2026-04-17) Jamali, Nima
Despite notable advances in network architectures and representation learning, most semantic segmentation pipelines continue to rely on hard ground-truth labels and evaluation metrics originally designed for binary masks. This assumption is misaligned with real-world data, where object boundaries are often ambiguous, annotations are noisy, spatial downsampling aggregates multiple semantic classes, and uncertainty is frequently encoded through void labels that are ignored during training and evaluation. As a result, both learning objectives and evaluation criteria do not faithfully reflect the underlying semantic structure and uncertainty of the data. In this thesis, we study semantic segmentation in settings where the ground-truth labels are not necessarily hard, but instead may be uncertain. We refer to this formulation as soft-label semantic segmentation. We treat this problem in a unified, end-to-end manner encompassing label generation, training, and evaluation. To generate soft labels, we propose a geometry-aware downsampling strategy called Weighted Average Pooling (WAP ) for semantic segmentation masks. WAP produces smooth and probabilistically valid soft labels at arbitrary resolutions by constructing spatially varying weights based on geometric relationships and spatial proximity. As a result, the generated soft labels are resolution-agnostic, preserve the underlying probabilistic structure of the annotations, and avoid artifacts commonly introduced by conventional downsampling methods. In addition, this work motivates the need for evaluation metrics that operate directly on probabilistic segmentation outputs. To this end, we introduce several principled relaxations of the soft intersection-over-union (soft IoU) metric that provide faithful extensions of standard IoU to soft-label settings. We further introduce void replacement strategies that assign soft class distributions to void pixels based on spatial context, enabling uncertain regions such as ambiguous boundaries and thin structures to be incorporated directly into the supervision signal. Extensive experiments on the PASCAL VOC 2012 dataset demonstrate that WAP produces more faithful soft labels than conventional approaches, particularly in scenarios involving thin structures and complex spatial arrangements. The proposed soft IoU relaxations offer improved interpretability and better alignment with hard-label evaluation, while the void replacement strategies perform comparably to hard-label baselines, indicating that incorporating soft supervision in uncertain regions does not compromise segmentation quality. Together, these contributions establish a principled framework for generating, training, and evaluating soft labels in semantic segmentation.
Targeted Gene Delivery to Astrocytes Using Intelligent Phagemid-Assembled Gene Expression (iPhAGE) Technology for Neuronal Regeneration
(University of Waterloo, 2026-04-17) Ffrench, Anna
Neurodegenerative diseases, stroke, and brain injuries lead to progressive neuronal loss, with limited treatment options focused mainly on symptom management rather than regeneration. A major challenge in developing effective therapies is the lack of safe and efficient gene delivery systems capable of targeting cells in the central nervous system. This project addresses this gap by developing a novel gene therapy approach using the Intelligent Phagemid-Assembled Gene Expression (iPhAGE) platform, an innovative bacteriophage-based system designed to deliver reprogramming transcription factors to astrocytes. The iPhAGE system, derived from M13 miniphagemids, offers high transfection efficiency, large cargo capacity, low immunogenicity, and blood-brain barrier permeability, making it an ideal tool for targeted gene delivery. This research involves constructing plasmids carrying the NeuroD1 gene under astrocyte-specific and universal promoters, producing and characterizing miniphagemids, and evaluating their transfection efficiency in resting and activated A7 cells. Neuronal reprogramming is assessed through PSA-NCAM neuronal marker analysis, a marker associated with early neuronal differentiation, used to evaluate phenotypic changes following NeuroD1 delivery. Key methodologies include designing and validating precursor and helper plasmids, producing miniphagemids, and characterizing them using restriction digestion, MADLS, and transfection assays. The outcome of this project was the establishment and initial evaluation of the iPhAGE-based gene delivery framework for astrocyte-to-neuron reprogramming. This work assesses the main components of the iPhAGE system, including vector construction, miniphagemid production, and astrocyte reprogramming using neuronal markers, therefore establishing a groundwork for future optimization.
Advancing the Conditional Source-Term Estimation (CSE) Framework for Turbulent Combustion Modeling and Application to Alternative Aviation Fuels
(University of Waterloo, 2026-04-16) Mahdipour Dilmaghani, Amir Hossein
The aviation sector faces increasing pressure to reduce greenhouse gas emissions and pollutant formation while meeting projected growth in global air traffic. Alternative aviation fuels (AAFs), including oxygenated fuels and hydrogen, represent promising pathways toward cleaner combustion, provided that their complex chemistry--turbulence interaction can be accurately predicted. Numerical simulation plays a critical role in this effort, but its reliability depends on the availability of combustion models that are both computationally efficient and sufficiently accurate for complex fuels and turbulent flow regimes. This thesis focuses on the development, assessment, and extension of the Conditional Source-term Estimation (CSE) model for the simulation of turbulent non-premixed flames, with particular emphasis on alternative aviation fuels. First, several CSE formulations are systematically evaluated, including traditional Tikhonov-regularized inversion and a Bernstein-polynomial-based approach, with the aim of improving numerical stability, accuracy, and computational efficiency. Next, a new CSE framework incorporating direct integration of detailed chemical kinetics is introduced, eliminating the reliance on pre-tabulated chemistry and enabling more robust predictions for fuels and conditions that are not well represented by conventional chemistry manifolds. The proposed developments are validated against well-documented laboratory-scale turbulent jet flames, including methane, dimethyl ether (DME), and hydrogen flames, covering different fuels and flow scenarios. The effects of differential diffusion are incorporated into the CSE-direct chemistry framework for hydrogen flames, addressing a key limitation of previous CSE implementations. An adaptive and automated CSE ensemble definition strategy is also presented and tested in large eddy simulation (LES) to capture local extinction dynamics. Overall, this work advances the CSE methodology by enhancing its flexibility, physical fidelity, and applicability to alternative aviation fuels. The results demonstrate that CSE with direct chemistry integration can achieve accurate turbulence–chemistry interaction predictions while maintaining computational efficiency, thereby providing a viable modeling framework for future simulations of advanced combustion systems relevant to sustainable aviation.
Practical Distributed Key Generation and Signatures
(University of Waterloo, 2026-04-16) Komlo, Chelsea
Threshold schemes are a critical cryptographic primitive that allows a set of n total parties and a threshold of at least tparties to collaborate to jointly perform some function, such as generating key material or issuing a digital signature. Threshold schemes allow for improved robustness in the case of failure, and distribute trust among many parties. In particular, the security of the scheme assumes t−1 players are corrupted, and so can deviate arbitrarily from the protocol. The security of the scheme ensures that in spite of a subset of corrupted players, the scheme can provide important properties such as robustness, unforgeability, or indistiguishability from some target distribution. In this work, we examine the special cases of distributed key generation and threshold signing. In particular, we present constructions that optimize for considerations that are important to implementations in practice. Such considerations include simplicity, network round efficiency, computational and bandwidth efficiency, and low use of broadcast channels. Firstly, we present FROST, a Flexible Round-Optimized Schnorr Threshold signature scheme. FROST improves upon prior threshold Schnorr signature schemes in that signatures can be generated with only two network rounds among participants, while remaining secure against concurrent adversaries. We show that FROST is secure under the Algebraic One-More Discrete Logarithm (ℓ-AOMDL) assumption in the Random Oracle Model (ROM). Secondly, we present Storm, a simplified three-round distributed key generation protocol (DKG). Storm presents a simplified alternative to prior DKGs with a similar security model, assuming the Discrete Logarithm Problem (DLP) is hard, and provides a generic construction that may be applicable beyond discrete-logarithm assumptions. Finally, we present Arctic, a two-round deterministic threshold Schnorr signature scheme. Arctic allows signers to remain stateless, with the exception of persisting state of their long-lived signing keys. Arctic requires a slightly weaker trust model in that it assumes the majority of signers are honest, but shows improved efficiency over alternative deterministic threshold Schnorr signature schemes for small signing coalitions (fewer than 25 signers). We show that Arctic is secure assuming DLP in the ROM.
Development of Cross-Conjugated Polymers for Sensing Applications
(University of Waterloo, 2026-04-16) Zhao, Naixin
Conjugated polymers are an important class of materials for electronic applications. Compared to conventional inorganic semiconductors, they offer mechanical flexibility, solution processability, and tunable electronic properties. Recently, the research interest in polymer-based sensing technology has grown considerably due to the increasing demand from emerging fields such as the Internet of Things (IoT), smart packaging, and healthcare electronics. Sensors based on conjugated polymers have demonstrated promising performance towards various stimuli such as liquid chemicals, gaseous compounds, and temperature. However, they still suffer from several limitations, including insufficient stability, reversibility, and manufacturing challenges. This thesis aims to address these issues through the exploration of novel material designs based on cross-conjugated building blocks, which have received less research interest compared to linear conjugated structures due to their inherent lower carrier mobility. For sensing applications, their unique ability to transform into a linear conjugated structure under specific stimuli could be beneficial for enhanced sensor sensitivity and selectivity. Additional design strategies are employed for enhanced sensing performance, including the incorporation of hydrogen-bonding sites for reversible sensing and the development of intrinsically conductive polymers to eliminate the need for external dopants, potentially improving device stability. In the first part of the study, dihydropiperazine (DHP) is chosen as the target cross-conjugated building block. A novel building block bisindolin-dihydropiperazine (IDHP) is developed and further copolymerized with a thienothiophene (TT) unit to constitute the cross-conjugated polymer, PIDHPTT. IDHP monomer exists as a cross-conjugated lactam but converts to a conjugated lactim form within the polymer. Neighboring DHP units in the lactim form facilitate this process through π-bridges, demonstrating a vinylogous effect, which has previously only been observed in small molecules. The OH groups in the lactim DHP interact more strongly with fluoride ions (F-) than other halides (Cl-, Br-). A water-gated organic field effect transistor (WGOFET) sensor based on PIDHPTT shows excellent sensitivity (LOD = 0.28 μM) and selectivity for fluoride ions over other halide ions, in addition to excellent reversibility and high stability in ambient and aqueous environments, demonstrating the potential of this polymer design for aqueous chemical sensing applications. Next, two thiophene-flanked DHP-based polymers, PTDbT-ET and PTDbT-T, are developed and synthesized with the eco-friendly DArP method. Incorporation of tri-ethylene glycol (TEG) side chain significantly raises their HOMO energy level higher than the ambient oxygen oxidative potential, enabling spontaneous doping by oxygen gas in the presence of moisture. Due to the higher abundance of TEG groups in PTDbT-T, it possesses a larger energy trap between its HOMO and oxygen oxidative potential, forming a more stable charge transfer complex (CTC) and can maintain its conductivity by storing in a moisture-free environment. When tested toward volatile organic compound (VOC) gaseous analytes, PTDbT-T-based chemiresistive sensors demonstrate excellent repeatability and stability, in addition to high sensitivity and selectivity to ethanol (LOD = 3.07 ppm) over other alcohol species, demonstrating the potential of this alternative strategy to develop dopant-free conductive polymers for chemiresistive gas sensor applications. In the second part of the study, a novel cross-conjugated polymer and the first polymeric analogue of a quinhydrone-like charge-transfer complex with intrinsic conductivity, poly(3,4-dihydroxythiophene-alt-thiophene-3,4-dione) (P(HOT-DOT)), is designed and synthesized. The ammonia-coordinated polymer P3 generates a perfectly balanced 1:1 donor-acceptor architecture that promotes self-doping and stabilizes polarons with spontaneous air oxidation. The polymer exhibits a narrow bandgap, broad near-infrared absorption, and high intrinsic conductivity (∼0.29 S cm-1), enabled by an ultrasmall π-π stacking distance (3.25 Å) despite its cross-conjugated backbone. Flexible temperature sensors fabricated from P3 show high stability, rare positive temperature coefficient (PTC) behavior, and reproducible and linear thermal responses over multiple cycles (TCR = 0.113 ± 0.00045%/°C). Ongoing and future studies of this material should focus on expanding other basic coordination groups for higher material stability and targeting unique electronic properties for high-performance organic electronics applications.
Roadway Illumination Level Assessment for Driver Safety and Comfort: A Multimodal Human Factors Evaluation of Visual Behavior, Physiological Arousal, and Driving Performance in a High-Fidelity Driving Simulator
(University of Waterloo, 2026-04-16) Abdalla, Shene
Nighttime driving remains a major road safety concern because reduced illumination can impair visibility, delay hazard detection, and increase visual strain. Although roadway lighting is intended to improve safety, greater brightness does not always produce better driving conditions. Excessive illumination may introduce glare, discomfort, and unnecessary energy use without meaningfully improving driver response. This thesis investigates how different nighttime illuminance levels influence driver safety and comfort by examining their relationship with multimodal safety-related measures, with the aim of identifying the illumination level that best supports visual detection, driving performance, physiological stability, and perceived visibility, comfort, and safety. A controlled mixed-design experiment was led in a high-fidelity virtual driving simulator using a replicated real-world street environment under three nighttime illuminance levels, low, medium, and high, established in accordance with roadway lighting standards. Thirty licensed drivers participated in the study, equally divided between younger adults aged 20 to 45 years and older adults aged 65 years and above. Driver response was evaluated using a multimodal framework integrating eye-tracking (Time to First Fixation (TTFF), Dwell Time), simulator-based driving measures (PRT, Speed, Hazard-related Deceleration), physiological markers (Heart Rate (HR), Electrodermal Activity (EDA)), subjective ratings of perceived visibility, comfort, and safety, and qualitative feedback. The results showed a clear relationship between illuminance level and driver response. Low illuminance was associated with delayed visual detection, slower hazard response, higher physiological arousal, and poorer ratings of visibility, comfort, and safety. Increasing illuminance from low to medium improved TTFF and PRT, enhanced perceived visibility and comfort, and supported greater physiological stability, whereas increasing illuminance from medium to high produced little additional benefit and occasionally introduced glare-related discomfort. Older adults showed higher physiological arousal and more conservative braking behavior than younger adults, but both age groups followed the same overall pattern across illuminance levels. Overall, the findings show that effective nighttime roadway lighting is not achieved by maximizing brightness, but by selecting an illumination level that supports visual effectiveness, driver response, comfort, and physiological stability. Among the conditions examined, medium illuminance provided the most favorable overall balance for safer and more efficient driving. These findings provide practical guidance for roadway lighting design and planning by suggesting that moderate illumination may offer the most effective balance between safety, comfort, and physiological stability.
Personality, Individuality, and the Social Lives of Bats
(University of Waterloo, 2026-04-16) Ryan, Caleb
Individual animals are unique and often differ substantially in their behaviour. Explaining how and why behavioural variation persists among individuals is central to behavioural ecology and requires methods that can capture both stability and uncertainty in complex data. In this thesis, I use a modelling approach to estimate the repeatability of behaviours observed from subjective assessments, standardized personality assays, and long-term monitoring of social interactions in the wild. Using bats as a study system, I investigate the extent of individual behavioural variation, how consistent differences contribute to sociality, and how individuality persists over evolutionary time. In Chapter 2, “Conserving cryptic complexity: Bats with broker roles structure the maternity societies of an endangered bat species”, I examine how individuals with distinct social roles contribute to the cohesion of Little Brown Bat (Myotis lucifugus) maternity colonies. I use a permutation-based network analysis to determine the positions of individuals in the social network across multiple years. My results reveal that a small subset of individuals can consistently act as brokers, meaning they bridge otherwise disconnected roost-area subgroups and maintain population-level social cohesion. Given that the same phenomenon is observed in two separate maternity societies of different sizes, this result suggests that these individualized social roles may be a feature of little brown bat sociality. Further, these results simulate how the loss of a small number of individuals from bat populations post-white-nose syndrome could have devastating impacts on social cohesion. This highlights the need to protect surviving individuals that persist on the landscape following population collapse. In Chapter 3, “Experimentally quantified personality traits are consistent across multiple years yet cannot explain observed differences in the social behaviour of bats on the landscape”, I test whether consistent individual differences in social behaviour among Little Brown Bats are linked to personality. Here I combine Bayesian social relations models of network structure with Bayesian hierarchical models of personality test scores to statistically propagate uncertainty from both social network estimates and behavioural assays into a joint analysis. I find strong evidence that behavioural tendencies are repeatable within individuals across multiple years. This finding is consistent with the concept of personality. However, assayed personality traits do not predict individual differences in social network positions, despite the repeatability of both. These findings suggest that personality and social network position, though both individually consistent, may be shaped by different processes. In Chapter 4, “Statistically upset: Fear response as a species-typical behaviour among neotropical bats”, I extend my behavioural comparison to apply a subjective personality assay to quantify fear-response behaviour in >3400 individuals from 55 Neotropical bat species across four countries. Using Bayesian hierarchical and phylogenetic mixed models, I investigate the sources of among-individual behavioural variation across species at multiple levels. I find that fear-response exhibits weak phylogenetic signal, with closely related species often differing markedly. I also find that species-typical fear-responses remain consistently distinct across geographic regions, suggesting that fear-response is a result of species-level differences and not shared environmental factors. None of the explanations for variation in fear-response investigated yielded positive results. That is, neither individual physiology nor species’ ecological and social traits explained the observed variation. Finally, I show that consistent individual differences are detectable across species, suggesting that species-level divergence in fear-response may arise through the accumulation of within-species individuality.
The examination of bacteriophage M13-based miniphagemids as a platform for the delivery of genetic material for neuronal applications
(University of Waterloo, 2026-04-16) St Jean, Jesse
M13-derived vectors have been shown to deliver foreign genetic material in vitro as well as bypass the blood-brain barrier, offering a promising approach to gene therapy applications that target the brain. Miniphagemid particles combine the capsid architecture of M13, which enables cellular targeting through peptide display, with a minimized genetic sequence, creating a highly modular vector. Despite the potential of these particles, their novelty and unique biology have limited the examination of their interaction with neuronal cells. This thesis examines the tailoring of miniphagemid particles to neuronal applications though neuropeptide display and transcriptional control. The outlined changes did not result in a significant increase in transfection efficiency in neuronal cells, instead revealing the unsuitability of the promoter used and ssDNA. Although, the specific application to neuronal cultures was unsuccessful, the use of a novel characterization method in miniphagemid particle analysis, specifically multi-angle dynamic light scattering, illustrated a substantial issue in current production methods; highlighting the current overreliance on functional quantification methods and supporting multi-angle dynamic light scattering as a physical method to determine miniphagemid particle purity.
Effects of Heat Treatment on the Temperature Coefficient of Resistivity of Laser Fabricated NiCr Flexible Sensors
(University of Waterloo, 2026-04-15) Almomani, Hashem
Advancements in automation, flexible electronics and embedded sensing systems has increased the demand for specifically designed and customizable sensors. This includes thin film resistive sensors with customizable electrical properties and long-term stability. Nickel chromium (NiCr) alloys are widely used in resistive sensors due to their chemical stability, high resistivity, and low temperature coefficient of resistivity (TCR); however, controlling TCR remains a challenge in novel sensor fabrication methods, such as laser ablation. Laser ablation offers a promising alternative to conventional lithography-based fabrication due to its low process complexity, rapid prototyping capabilities, and compatibility with flexible substrates. In this work, NiCr thin films were heat treated over a range of temperatures and hold times to modify their electrical and microstructural properties. Following heat treatment, the thin film samples were hot pressed between two polyimide sheets and patterned into flexible resistive sensors using UV laser ablation. The laser fabrication process was optimized through investigation of processing parameters, including laser power, number of passes, and environmental factors. The influence of these parameters on feature geometry, resistance control, and fabrication repeatability was evaluated, and laser fabricated sensors were benchmarked against commercially manufactured resistive sensors. Heat treatment was found to significantly reduce the magnitude of TCR, while improving resistance stability. Microstructural and compositional changes were characterized using scanning electron microscopy, energy dispersive x-ray spectroscopy, and x-ray photoelectron spectroscopy. The results indicate that surface compositional changes and oxidation influence electrical properties more than bulk changes in thin films. These findings demonstrate that pre-fabrication heat treatment is an effective strategy for tailoring the TCR of laser fabricating NiCr thin film sensors for flexible sensor applications.
Some results on hypersymplectic structures
(University of Waterloo, 2026-04-14) Petcu, Amanda
A conjecture of Simon Donaldson is that on a compact 4-manifold X⁴ one can flow from a hypersymplectic structure to a hyperkähler structure while remaining in the same cohomology class. To this end the hypersymplectic flow was introduced by Fine–Yao. In this thesis the notion of a positive triple on X⁴ is used to define a hypersymplectic and hyperkähler structure. Given a closed positive triple one can define either a closed G₂ structure or a coclosed G₂ structure on 𝕋³ × X⁴. The coclosed G₂ structure is evolved under the G₂ Laplacian coflow. The coflow descends to a flow of the positive triple on X⁴, which is again the Fine–Yao hypersymplectic flow. In the second part of this thesis we let X⁴ = ℝ⁴ ∖ {0} with a particular cohomogeneity one action. A hypersymplectic structure built from data invariant under this action is introduced. The Riemann and Ricci curvature tensors are computed and we verify in a particular case that this hypersymplectic structure can be transformed to a hyperkähler structure. The notion of a soliton for the hypersymplectic flow in this particular case is introduced and it is found that steady solitons give rise to hypersymplectic structures that can be transformed to hyperkähler structures. Some other soliton solutions are also discussed.
Evaluating the Impact of Fan Design and Air Speed on User and Nearby Occupants’ Thermal Comfort in a Shared Office
(University of Waterloo, 2026-04-13) Bayode, Kehinde
Personal Comfort Systems (PCS) are increasingly recognized for their potential to improve individual thermal comfort and reduce building energy demand. ASHRAE Standard 55 defines PCS as a device, under the control of the occupant, intended to heat and/or cool individual occupants without affecting the thermal environment of other occupants. Desk fans are common PCS cooling devices, but their use in shared workspaces raises questions about the differential impact on the primary user and nearby occupants. Limited empirical evidence exists on how local air speed and fan technology jointly influence thermal, airflow, and acoustic domains among occupants. To address these gaps, a human-subject experiment involving 40 participants was conducted, paired into 20 pairs: P1 as the fan primary user and P2 as a nearby occupant. Two desk fan designs (conventional-blade and bladeless) were tested at high and low-speed settings. Participants provided repeated comfort assessments at each fan speed condition. The results indicate that both fan technology and operating speed significantly affect the alignment or divergence of comfort between P1 and P2. At low speed, both fan types produced strong convergence, with both occupants reporting neutral thermal sensation, slight satisfaction, and a shared perception of air movement as “just right.” In contrast, at high speed, the bladed fan resulted in divergence: P1 perceived the airflow as “too breezy” and preferred less air movement, while P2 reported no change despite experiencing breezy conditions. Conversely, the bladeless design reduced this asymmetry. At all speeds, both P1 and P2 reported neutral thermal sensation and consistent satisfaction. For primary users, both fan types enhanced thermal comfort at both speeds. The bladed fan was effective only at low speed, as high speed produced a “too breezy” sensation, whereas both speeds were acceptable for the bladeless fan. Despite these advantages, the bladeless fan introduced acoustic disturbance to the environment. High-speed bladeless was perceived as more annoying than the bladed fan, with the P2 group reporting higher annoyance (85%) than the P1 group (65%). This suggests that the high-frequency profile of the air multiplier technology is intrusive, especially for nearby occupants in shared environments. For shared workspaces with mechanical cooling, a low-speed fan setting is recommended. This configuration minimizes acoustic annoyance for both fan technologies (0-5% annoyance) while maintaining high thermal satisfaction for primary users and minimal intrusion into the environment of nearby occupants.
Investigating mitochondrial microRNAs in response to metabolic disruption
(University of Waterloo, 2026-04-13) Robichaud, Karyn
Aquatic and terrestrial environments are dynamic due to natural and anthropogenic sources, including pollutants, thermal variability, and hypoxia. These stressors or perturbations can result in changes to energetic demands of animals resulting in metabolic stress. As a major energy transduction site within cells, mitochondria can respond to alterations in environmental conditions and metabolic stress by changing their physiology. Specifically, mitochondrial oxidative phosphorylation may change during stress, resulting in altered oxygen consumption rates and efficiency of energy transduction. These plastic responses of mitochondria can be regulated by post translational modifications to proteins; however post-transcriptional regulation of genes may also alter mitochondrial physiology. Genes can be post-transcriptionally regulated by microRNA; microRNAs are small, non-coding RNA molecules that canonically suppress mRNA expression, and thus protein expression. MicroRNAs regulate nuclear encoded genes in response to a variety of physiological stressors, however microRNA can also redistribute subcellularly into mitochondria. Mitochondria contain their own genome which encodes proteins involved in oxidative phosphorylation, therefore mitochondrial microRNAs (mitomiRs) can also regulate mitochondrial gene expression in response to stress. The overall goal of this thesis was to investigate mitomiRs in animals and predict their potential role in regulating mitochondrial function in response to metabolic stress. Most research on mitomiRs prior to this thesis was conducted in mammals, and with respect to disease. Therefore, this thesis aimed to compare mitomiRs across species, identify whether mitomiRs change in abundance with exposure to different stressors, and predict mitomiR mRNA targets. It was hypothesized that mitomiR abundances differ based on environmental changes (stressor type, stressor duration) and inherent differences (species, sex), resulting in changes to mitochondrial function during metabolic stress. Chapter 2 investigated the mitomiR profiles of zebrafish (Danio rerio) brains under control conditions and during acute exposure to two known metabolic stressors (hypoxia and elevated temperature). Exposure to each stressor resulted in distinct mitomiR profiles, where two mitomiRs were differentially abundant during hypoxia, and another mitomiR had altered abundance during thermal stress. The predicted nuclear targets of these mitomiRs were mainly involved in metabolic pathways, with many distinct predicted targets. Furthermore, brain mitochondrial respiration was only altered during thermal stress, and results indicated a potential decrease in ATP synthesis efficiency. Overall, brain mitochondrial respiration and mitomiR abundances had stressor-specific effects. Chapter 3 investigated whether venlafaxine, an antidepressant commonly found in wastewater effluent, altered zebrafish brain mitochondrial respiration and mitomiR abundances. In vitro, this study first confirmed that venlafaxine suppressed brain mitochondrial respiration. Then, an acute time-course exposure was conducted using zebrafish. In vivo, venlafaxine had minimal effects to brain mitochondrial respiration, however, three mitomiRs were differentially abundant based on exposure, sex, and time sampled. Changes to mitomiR abundance may have been due to their host gene expression, circadian rhythm, and venlafaxine exposure. Chapter 4 utilized three species of wild fish (Etheostoma spp.), to determine if they responded similarly to chronic exposure to wastewater effluent outfall in the Grand River, Waterloo, with respect to mitomiR abundances and mitochondrial function. Wild rainbow (Etheostoma caeruleum), fantail (E. flabellare), and Johnny darters (E. nigrum) were collected from up and down stream of the Waterloo wastewater treatment plant, then liver mitomiR abundances and mitochondrial cytochrome c oxidase activities were measured, and species-specific differences were detected. Results indicated that these darter species had species-specific changes to mitomiR abundances and mitochondrial enzyme activity when living downstream of the Waterloo wastewater treatment plant. Chapter 5 provided a comparative study between vertebrate taxa using a mammal that experiences drastic changes in mitochondrial respiration during torpor and interbout euthermia hibernation states. During torpor, mitochondrial respiration is suppressed and returns to summer values during interbout euthermia. This study profiled mitomiRs in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) during summer and hibernation. Changes in mitomiR abundances were detected during hibernation, and mitomiRs had predicted effects that may indicate their involvement in regulating changes to mitochondrial respiration and function during hibernation. The major finding of this thesis was that mitomiRs are differentially abundant based on stressor, sex, and species, despite some conservation of mitomiRs among species studied. This thesis also predicted targets for differentially abundant mitomiRs within mitochondrial and nuclear genomes, and measured changes in mitochondrial enzyme activities and respiration in fish to provide context for how mitomiRs may aid in regulating mitochondrial function. Overall, this thesis contributed to knowledge of mitomiRs and how they show distinct abundance patterns using a variety of comparative approaches.
An Ecologically Inspired Constraint-Based Approach to AI System Design: Reshaping Clinical Uncertainty in Paediatric Sepsis
(University of Waterloo, 2026-04-13) Tennant, Ryan
In paediatrics, sepsis is a high-stakes, safety-critical challenge for clinicians to recognize and respond to, where a sick child can look stable until they are not, and where diagnostic definitions, symptom baselines, and care pathways vary across children and healthcare settings. This variability creates uncertainty in the clinical environment and limits the extent to which artificial intelligence (AI) and machine learning-based prediction tools can support clinical decision-making when the goal is to classify sepsis. In this dissertation, we position paediatric sepsis as a structurally uncertain domain and argue for an ecologically inspired, constraint-based approach to AI system design that learns and visualizes (1) the boundaries of physiological functioning and (2) the boundaries of the socio-technical system, to support clinically justified decisions under uncertainty in such non-specific contexts. To ground this work, we first synthesize the paediatric sepsis prediction literature through a scoping review. We find substantial heterogeneity in endpoint definitions, datasets, validation practices, prediction timing, and performance reporting. We also find limited attention to human factors considerations, such as workflow integration, interface design, and interaction design, despite their potential for clinical decision support, which fundamentally motivates the research of this dissertation. We then examine how clinicians experience and manage uncertainty about paediatric sepsis. Through semi-structured interviews with registered nurses, respiratory therapists, pharmacists, nurse practitioners and physicians in Canada about their experiences with paediatric sepsis recognition and response, we develop a domain-grounded account of uncertainty conceptualization and a sensemaking-action cycle model. This work extends the established uncertainty constructs from Naturalistic Decision Making by identifying two sources specific to paediatric sepsis: indeterminate clinical trajectories and operational constraints, including how emotional & intuitive anchoring shapes constructing readiness to act. We also describe AI-associated uncertainty concerns, including how and when predictions may reshape clinical judgement. Next, we establish the paediatric sepsis work domain constraints for recognition and response through Cognitive Work Analysis (CWA), conducting a tri-model Work Domain Analysis of the biological, clinical, and AI-augmented clinical work domains, and a Control Task Analysis of decision-making. We also apply this modelling to compare classification- and constraint-based prediction architectures and translate the constraints into an interactive Ecological Interface Design (EID) concept. Our resulting EID includes a configurable display of a baseline-relative trajectory forecast and AI-based uncertainty-aware cues to support the “gut feeling” of early paediatric sepsis recognition and escalation, and how and when to use model predictions at the bedside, respectively. Finally, we formatively evaluate the constraint-based approach in simulated paediatric sepsis scenarios with clinicians in individual and team-based contexts. Across outcomes, including clinical concern, confidence, trust, and sensemaking, our results suggest the trajectory forecast most strongly influences interpretation and action planning and is more validating of preparatory clinical action when the prediction is concordant with clinical reasoning. While AI-based uncertainty elements do not generally yield quantitative differences in outcomes in our evaluation format, they are perceived as potentially valuable for ongoing AI system use; however, mixed perceptions indicate the need for further research to improve their interpretability and usability at the bedside. Taken together, our findings support the promise of further investigating the constraint-based approach toward AI system design in supporting resilience and clinical judgement in paediatric sepsis. Overall, this dissertation demonstrates why the safe integration of AI into high-stakes healthcare cannot be purely data-driven. By conceptualizing uncertainty before introducing predictive algorithms and by applying CWA to anticipate how predictions may reshape clinical judgement, this research provides a framework for more responsible system design. Our approach supports a thorough examination of domain complexity and clinical judgement, informs decisions about whether and how an AI system should be developed and how prediction information should be introduced, and grounds clinical AI in human factors, ensuring these systems respond to genuine clinical needs.
Topics in Arithmetic Dynamics
(University of Waterloo, 2026-04-13) Zhong, Xiao
This thesis comprises four papers completed during my doctoral studies at the University of Waterloo and is organized into three chapters. The first chapter concerns preimage problems and dynamical cancellation, incorporating the papers “Dynamical Cancellation of Polynomials,” published in the Bulletin of the London Mathematical Society, and “Preimages Question for Surjective Endomorphisms on (P1)^n,” published in the New York Journal of Mathematics. We investigate stabilization phenomena for the set of rational points occurring in the preimages of invariant subvarieties under algebraic dynamical systems. In the special case in which the subvariety is the diagonal subvariety in P1 × P1 and the dynamics is given by a pair of rational functions (f, f), the problem reduces to a dynamical cancellation question. We also obtain a generalization of dynamical cancellation to the setting in which the dynamics are generated by a semigroup of polynomials. The second chapter contains the joint paper with Chatchai Noytaptim, “A Finiteness Result for Common Zeros of Iterates of Rational Functions,” published in International Mathematics Research Notices. Addressing a question posed by Hsia and Tucker concerning finiteness properties of greatest common divisors of polynomial iterates, we prove that if f, g belong to C(X) and are compositionally independent rational functions, and c belongs to C(X), then, apart from a few explicit exceptional families with f and g in Aut(P1_C), there exist only finitely many λ in C for which there is an n satisfying f^n(λ) = g^n(λ) = c(λ). The final chapter presents my recent preprint, “Polynomial Endomorphisms of A2 with Many Periodic Curves.” We show that for any regular polynomial endomorphism of positive degree on P2, every family of curves containing a Zariski dense set of periodic curves must be invariant under some iterate of the map. This establishes a weaker form of the Relative Dynamical Manin-Mumford Conjecture of DeMarco and Mavraki in the setting where the endomorphism is fixed in the family of dynamical systems, and may also be viewed as a dynamical Manin-Mumford statement on the moduli space of divisors. As an application, we classify all regular polynomial endomorphisms of P2 that admit infinitely many periodic curves of bounded degree.
Development and Initial Validation of the Haptic Experience Inventory (HXI)
(University of Waterloo, 2026-04-13) Shi, Tianzheng
Haptic Experience (HX) encompasses distinct quality criteria specific to haptic inter- actions, yet no standardized instrument exists to measure it. This makes understanding and evaluating HX challenging. This thesis reports on the development and validation of the Haptic Experience Inventory (HXI), a questionnaire measuring HX. An item pool of 50 items is developed through theoretical construction, expert reviews (N=10), and cog- nitive interviews (N=9). These items are then subjected to exploratory and confirmatory factor analysis using data from 591 participants across in-person and online studies, cov- ering vibrotactile, force-feedback, and mid-air devices. Eventually, a 20-item HXI with five dimensions is established: Autotelics, Realism, Involvement, Harmony, and Discord. The HXI converges with theory and shows strong reliability, validity, and measurement invariance, suggesting it is effective across deployed modalities and contexts. The HXI provides empirical evidence about the structure of HX and offers a robust, standardized tool for assessing haptic feedback in research and practice. Ongoing efforts to develop and validate a French version of the HXI are also reported.
Characterizing the effects of diel temperature fluctuations on thermal and hypoxia tolerance in adult zebrafish
(University of Waterloo, 2026-04-10) Clow, Tanner
Aquatic ecosystems naturally experience temperature fluctuations, which are often accompanied by shifts in dissolved oxygen. However, climate change has exacerbated the prevalence and magnitude of these fluctuations, often leaving organisms exposed to sub-optimal conditions. Due to their inherent relationship, these abiotic factors are thought to share common signalling pathways (cross-talk) and protective mechanisms (cross-tolerance) that confer cross-protection. Much of what we understand about the effect of temperature on fish originates from static exposures, despite physiological performance differing in fluctuating environments. Therefore, in this study, I aimed to determine whether diel temperature fluctuations influence thermal and hypoxia tolerance, while simultaneously characterizing the underpinning molecular and biochemical adjustments. Three experimental series were conducted, during which adult zebrafish were acclimated to either static control conditions (27ºC) or a thermal flux (23-33ºC) for approximately two weeks. Following the acclimation, I quantified whole-animal tolerance (critical thermal maximum and time to loss of equilibrium), heat-shock response genes (heat-shock proteins; hsp70 and hsp90αα), hypoxia response genes (hypoxia-inducible factor 1 alpha: hif-1αb; insulin-like growth factor binding protein: igfbp1), microRNAs (let-7d-5p, miR-301c-5p, miR-29a, miR-22b-3p), heat-shock proteins (Hsp70 and Hsp90α), and enzymatic activity (lactate dehydrogenase: LDH; citrate synthase: CS; pyruvate kinase: PK) in the brain and liver tissue. Together, the data suggest that fish acclimated to diel thermal variability exhibit distinct molecular and biochemical responses that may be involved in the observed increase in thermal and hypoxia tolerance
Optimizing Weld Geometry for High-Speed Wire-Fed Laser Welding of Thin-Gauge Press-Hardened Steel
(University of Waterloo, 2026-04-10) Embleton, Andrew
As the automotive industry continues to prioritize fuel efficiency and performance, the demand for stronger, lighter materials, such as press-hardened steel (PHS) increases in vehicle design. This research examines the impact of high-speed wire-fed laser welding parameters on the final weld bead geometry for thin-gauge Al-Si coated PHS sheets used as tailor welded blanks. The primary objective is to determine the optimal laser welding parameters that consistently produce defect-free welds, with reinforcement and undercut values not exceeding 10% of the material thickness, while achieving the highest possible travel speeds. A comparative analysis is conducted on key welding parameters including laser spot diameter size, laser power, wire feed speed, travel speed, and sheet gap size to establish best practices for laser welding in thin-gauge press-hardened steels. To identify the individual contribution of each laser welding parameter on the final weld geometry, a variety of welding conditions are tested such that the individual influence of each specific welding parameter is isolated and compared against macroscopic weld cross-sectional measurements, primarily focusing on the degree of excess reinforcement and undercut. It is shown for welding 1 mm thick Al-Si coated PHS blanks that utilizing a laser spot diameter size of 0.6 mm, a laser power of 4500 W, a wire feed speed of 2.75 m/min, a travel speed of 8 m/min and a sheet gap size of 0.04 mm consistently produced welds with geometry not varying by more than 10% of the base materials thickness for undercut and excess reinforcement. These findings provide a better understanding of laser welding parameters required for welding Usibor®1500 at higher welding speeds.
Rigorous Security Proofs for Practical Quantum Key Distribution
(University of Waterloo, 2026-04-08) Tupkary, Devashish Jayant
This thesis is concerned with the rigorous security analysis of practical Quantum Key Distribution (QKD) protocols, using a variety of modern proof techniques. Throughout, the emphasis is on mathematical rigor across a wide range of security proof frameworks. We begin by presenting a security proof for variable-length QKD protocols against IID collective attacks, which represents the first such result for generic QKD protocols. We then show that this analysis can be lifted to hold against coherent attacks by an adversary, using the postselection technique. In doing so, we extend the application of the postselection technique to practical QKD protocols, and resolve a long-standing flaw in the method, thereby placing its application to QKD on a rigorous mathematical footing. We next study security proofs based on entropic uncertainty relations. These proofs proceed by bounding the so-called ``phase error rate", using the observed statistics available in the actual protocol. All known methods of bounding the phase error rate require strong assumptions on hardware: namely, that all detectors have exactly equal probability of detection. This renders these security analysis inapplicable to practical QKD scenarios. We show that such phase error rates can be bounded even when detectors are imperfect and only approximately characterized. This resolves a long-standing well-known open problem of nearly two decades, and renders this proof technique applicable to realistic scenarios. We then study security proofs using the recently obtained marginal-constrained entropy accumulation theorem, and obtain a highly rigorous and general result for the security analysis for practical QKD protocols. Most importantly, the proof is constructed in a transparent and self-contained manner, and is designed to be a key ingredient in certification efforts for QKD. Moreover, it can be easily modified to apply to other protocols of interest, and to device imperfections and side-channels. We also revisit the assumptions on authentication traditionally made in QKD security analyses, which assume that all classical messages are delivered faithfully and on time, without any aborts. We show that these assumptions are generally unrealistic, and that adopting realistic authentication assumptions necessitates a modification of both the standard QKD security definition and the corresponding security analysis. However, under mild and easily satisfied protocol design conditions, security under realistic authentication can be reduced to the usual idealized setting. As a result, existing QKD security proofs can be lifted to the realistic authentication setting with only a minor protocol modification. A distinctive feature of this thesis is its unified presentation of multiple major QKD security proof frameworks using consistent protocol descriptions and notation. This first-of-its-kind treatment enables direct comparison and contrast between different approaches, a perspective that is often obscured when these techniques are developed in isolation. Consequently, this work is intended not only as a collection of new technical results, but also as a pedagogical reference for understanding rigorous security analysis in quantum key distribution.
Physically-Based Simulation and Visualization of Optical Phenomena Elicited by Negative Refraction
(University of Waterloo, 2026-04-08) Steinfield, Scott
Metamaterials characterized by a negative refractive index are being the object of intense research across a broad range of fields, from mathematics and physics to photonics and engineering. Nonetheless, the development of materials exhibiting this property in the visible spectral domain remains challenging. This situation, along with their potential transformative role in new technological advances, has motivated the scientific community to instrumentally employ computer graphics software to visually explore their interactions with light. In this work, we contribute to the initiatives in this area by describing a white-box methodology aimed at the physically-based simulation and visualization of optical phenomena elicited by these materials. We demonstrate its suitability to applications, both within and outside computer graphics, through the rendering of images depicting these phenomena under different optical scenarios, including those not examined in the literature to date.
Application of Latent Class Analysis to Examine the Association Between Allostatic Load and Profiles of Perceived Stress and Lack of Support Among Firefighters in the Waterloo Region
(University of Waterloo, 2026-04-08) Adejumo, Seun
Background and Objectives Firefighters are often exposed to significant occupational hazards due to the demanding nature of their work. They are repeatedly exposed to trauma, physical strain, and emotional pressure because they are daily faced with fire rescue calls that involves live and properties. Such exposures make firefighters vulnerable to events that cause both physical and psychological stress. The cumulative effect of occupational stress among firefighters over the course of their career leads to wear and tear of their body system, and this has negative impact on their health outcomes. Additionally, their perception of stress may influence how they process and respond to everyday demands, which in turn could change their psychological resilience, quality of sleep, emotional regulation, and overall well-being. The effects of perceived stress may be further compounded when social support, which is meant to be a resiliency factor is lacking. With these points in mind, this thesis proposed a new paradigm of using validated instruments from the domains of psychosocial stress (PSS-10, SOOS-14) and social support (MS-PSS, SSS-FF) to develop a multidimensional profile, which we called Perceived Stress and (lack of) Support. In particular, this thesis used Latent Class Analysis as a means of modeling Perceived Stress and (lack of) Social Support Profiles (PSSP) via the aforementioned variables. This new concept of PSSP was motivated and applied to data gathered from firefighters in the City Waterloo. With these data, we examined the association between our proposed PSSP, and physiological stress captured by an Allostatic Load Profiles (ALP; developed for the same participants by Elliot 2024). This approach provided an understanding of how perceived stress and lack of social support can co-exist and their association with physiological wear and tear in this high-risk population. Methods This study used male-only data from the firefighter’s study in Waterloo. Latent class analysis (LCA) was applied to identify PSSP based on validated psychosocial indicators. Then, the ALP that was previously developed from physiological biomarkers in the same male-only data was used as the outcome variable in logistic regression models to examine its association with PSSP as the predictor variable. Furthermore, these models sequentially adjusted for relevant occupational and behavioural confounders which included length of service, sleep disturbance, alcohol use, exercise, and smoking. Finally, sensitivity analyses were conducted to assess the stability of the aforementioned objectives when using the pooled study sample, which included both male and female firefighters. Results For the male-only sample, approximately 50% of firefighters were classified into the elevated-ALP, while 70.1% were classified into the high-PSSP. The pooled sample had about 25.4% of firefighters with elevated ALP and 65.1% high PSSP class. Logistic regression results for the male-only sample indicated a positive association between elevated-PSSP and high-ALP; however, this association was not statistically significant in unadjusted (OR = 1.25, 95% CI: 0.38 – 4.51) and adjusted models (OR range 1.01 – 1.10). Adjusted models controlled for length of service, sleep disturbance, alcohol use, exercise, and smoking. Sensitivity analyses yielded similar results with narrow confidence intervals (CI), but still not statistically significant. Conclusion This study expands understanding of occupational stress in firefighters by showing that perceived stress and lack of social support co-occur as a distinct psychosocial profile. The association between the ‘high perceived stress and lack of social support’ profile and ‘elevated allostatic load’ profile was consistently positive, regardless of adjustment for confounders. Future research should build on these findings by using longitudinal designs and larger samples to inform occupational health interventions that simultaneously reduce stress and strengthen support systems within this unique sample.

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