Theses

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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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Device-Algorithm Co-Optimization of TiOₓ-based Resistive Switching Devices
(University of Waterloo, 2025-06-05) Shi, Yu
The rapid advancement of artificial intelligence (AI) and growing demand for high-performance computing have exposed key limitations in von Neumann architectures, particularly energy inefficiency and data movement bottlenecks. Resistive Random Access Memory (RRAM) has emerged as a promising candidate for next-generation memory technologies, offering non-volatility, high integration density, and the potential for energy-efficient Compute-In-Memory (CIM) architectures. This thesis focuses on the development and optimization of TiOₓ-based RRAM devices, with a particular emphasis on their application in CIM systems. The work begins with a comprehensive exploration of the device characteristics of TiOₓ-based RRAM, including the influence of electrode materials, oxygen stoichiometry, and physical dimensions on device performance. Through interface engineering and material stack optimization, we achieve significant improvements in forming voltage, endurance, and retention, enabling low-power operation and high reliability. The optimized devices exhibit stable bipolar switching behavior with forming voltages below 1.5 V and operation currents under 100 μA, making them suitable for integration with advanced CMOS technologies. Building on the optimized device performance, we propose a state-aware multi-bit programming algorithm that significantly reduces the number of programming steps and improves the efficiency of multi-bit operations. The algorithm leverages the state-dependent conductance modulation of RRAM devices, enabling precise control over resistance states and mitigating the effects of fast relaxation and retention loss. Additionally, we introduce an electrical annealing method to further enhance the long-term stability of multi-bit programming, demonstrating its effectiveness in extending the refresh period for CIM applications. To bridge the gap between device-level optimization and system-level implementation, we present a back-end-of-line (BEOL) integration process for TiOₓ-based RRAM devices on CMOS chips. The integration process is validated through the successful fabrication and characterization of 1T1R arrays, demonstrating reliable resistive switching behavior and compatibility with existing CMOS technologies. This integration paves the way for the development of RRAM-based CIM macros, which combine RRAM arrays with peripheral circuits for high-performance AI computing. Finally, we discuss future directions for device optimization, hardware-aware CIM design, and system-level integration. Key challenges include reducing programming current, improving retention stability, and developing reconfigurable CIM architectures for emerging AI workloads. The insights and methodologies developed in this thesis provide a foundation for the continued advancement of RRAM technologies and their integration into next-generation computing systems. In summary, this thesis contributes to the field of RRAM-based CIM by addressing critical challenges in device optimization, multi-bit programming, and CMOS integration. The proposed solutions not only enhance the performance and reliability of RRAM devices but also provide a pathway for their practical implementation in energy-efficient AI hardware.
What’s In a Post? Adolescents’ Social Media Response Motivations, Perceptions of Response Motivations, and the Role of Individual Characteristics
(University of Waterloo, 2025-05-30) Bowman-Smith, Celina
As the questions of ‘why’ and ‘how’ adolescents use social media are more informative for understanding socio-emotional outcomes than the amount of time spent on social media, there have been recent calls for experimental studies of youths’ social media experiences. In the present studies, I examined what responses adolescents hoped to receive from others, and the degree to which other users could detect these wanted responses from their social media posts and the characteristics of youth associated with such motivations and perceptions. I further examined the themes, linguistic features, and emotional valence adolescents included in their social media content, and examined relations between the generated content and the characteristics of posters associated with motivations and perceptions. Adolescents (ages 13-16; N=103) participated in a simulated Instagram task where they created social media posts and indicated the degree to which they hoped to receive engagement, advice, support, or entertainment from others for each post, as well as the level of insight they felt they had into their own motivations. Adolescents reported wanting others to engage and be entertained more than they wanted to receive advice and support. Adolescents’ individual characteristics (i.e., social media use, peer relationships, empathy, mood, and emotion regulation) differentially related to what they hoped to receive from others. In a second phase, adolescents (ages 13-17; N = 88) viewed posts from others and rated what they felt the poster had hoped to receive. While the posters’ report and viewers’ ratings correlated, for all response options, adolescent viewers perceived that the poster wanted less of a response than the poster indicated wanting. In the content analysis (816 posts, N = 102), adolescents tended to create social media content that included little to no emotion words, disclosed very little/nothing to a moderate amount of personal information, was literal in its communicative intent, and tended to convey a congruent affect between caption and picture. These features suggest adolescents tend to create social media posts that are consistent with social media norms to avoid emotional posting or disclosing sensitive information to large online audiences. Adolescents’ individual characteristics (i.e., empathy, online and offline peer experiences, emotion regulation skills, mood, and social media use) were associated with their created social media content. Together findings highlight the variability in motivations for social media use based on adolescents’ characteristics and suggest a mismatch between motivations from posters and perceptions from online viewers. This work adds to a growing body of literature examining how adolescents navigate their complex, and increasingly online, communicative interactions.
Using CRISPR/Cas9 to screen an Autographa californica multiple nucleopolyhedrovirus vector genome for gene essentiality in the production of a HIV-Gag virus like particle
(University of Waterloo, 2025-05-28) Sung, Christopher
The baculovirus expression vector system (BEVS) has been widely used for producing recombinant proteins and virus-like particles (VLPs) due to its high protein expression, ability for some complex post translational modifications (PTMs), and high scalability. Of particular interest is the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV), which is the most used virus for the BEVS. This baculovirus is amenable to genetic modifications, yet other than replacing or removing a few genes, this baculovirus has not seen major modifications. A hypothesis in the Aucoin lab centers around the idea that more product can be made if less resources are funnelled away from this goal [1]. Recently, a transfection-infection (TI) assay has been described [2], where the baculovirus genome can be scrutinized. Briefly, a stable Sf9 cell line expressing Cas9 (Sf9Cas9) [3], which has been shown to produce similar levels of green fluorescent protein and baculovirus as the native/parental Sf9 cells, is transfected with a plasmid hosting a single guide ribonucleic acid (sgRNA) targeting a specific baculovirus genomic sequence and subsequently infected with a baculovirus vector that is able to express a gene of interest/reporter product. However, given the large genome of the baculovirus, and the number of genes that can be scrutinized, higher throughput methodologies are required. This work addresses some of the engineering challenges related to the scale of the T-I assay and the associated analyses. These changes are then implemented and used to evaluate the essentiality of 21 late or very late genes in AcMNPV to produce BV and VLPs. More specifically, the effect of targeting these specific genes is being examined when expressing an enveloped virus-like particle under the control of the p6.9 promoter. Moving the T-I assay from a 6-well plate (2.5x106 cells/well in 2mL of media), to a 12-well plate required a change in cell seeding density (0.9x106cell/well in 0.8mL of media) to obtain similar infection and production dynamics. Further, using a human immunodeficiency virus (HIV) group specific antigen (Gag) fused with a green fluorescent protein (GFP) virus-like particle (VLP), or Gag-GFP for short, the effect of targeting genes could be assessed on the release of VLPs in the culture supernatant using flow cytometry. Dilutions of cell culture supernatant in a 96-well plate allowed dilutions to be done in parallel, which increased the throughput of VLP quantification using a 96-well plate compatible flow cytometer. Although VLP concentrations were consistently 10%-20% higher when diluted in the plate condition compared to microcentrifuge tubes, this amount was deemed to be acceptable due to the consistent effect. Furthermore, VLP stability over a 7-hour period was tested. It was found that VLPs started degrading 1.5 hours after initial dilution. This was found to be long enough for 15 samples to be run through the flow cytometer at a time and maintain VLP integrity. Controls were assessed for the T-I assay. One negative control involved only infecting cells with the baculovirus coding for Gag-GFP (infected control). A second negative control involved the use of transfection reagent without any plasmid followed by infection with the baculovirus coding for Gag-GFP (transfection reagent control). A third negative control involved a complete transfection step with a plasmid coding for a sgRNA that was not directed towards any baculovirus sequence. The latter is referred to a scrambled sequence control (or scrambled control for short). A fourth control involved a complete transfection step with a plasmid coding for mKate2, which is a red fluorescent protein (mKate2 control). It was observed that the transfection reagent control, the scrambled control, and the mKate2 control produced higher amounts of budded virus compared to the infected only control. Not only did we determine that that the transfection reagent increased infectious baculovirus in our assay, we determined that the scrambled control was the most appropriate control for the T-I assay. Of the 21 genes scrutinized as part of this work, deletion of lef-2, bion, lef-1, pkip and lef-11 all lowered budded virus production, which was consistent with previous studies. Deletion of pif2 lowered budded virus but has been previously reported to be non-essential. Deletion of ptp, Ac4, pk1, and fgf showed some indication that budded virus production was impaired, but failed to consistently meet the threshold for significance at a 95% confidence interval across all constructs tested. Deletion of v-ubi, Ac38, lef-12, and Ac51, which were previously reported to have lower levels of budded virus upon gene deletion, were found to have no effect in our study. Finally, Ac19 and env displayed no effects on budded virus and VLP production. These final two genes are possible candidates for genes that may be non-essential and should be screened further.
Techniques to learn constraints from demonstrations
(University of Waterloo, 2025-05-27) Gaurav, Ashish
Given demonstrations from an optimal expert, inverse reinforcement learning aims to learn an underlying reward function. However, it is limiting to assume that the reward function fully explains the expert behaviour, since in many real world settings the expert might be acting to satisfy additional behavioural constraints. Recovering these additional constraints falls within the paradigm of constraint learning from demonstrations. Specifically, in this work, we focus on the setting of inverse constraint learning (ICL), where we wish to learn a single but arbitrarily complex constraint from demonstrations assuming the reward is known in advance. For this setting, we first provide a framework to learn an expected constraint from constrained expert demonstrations. We then show how to translate an expected constraint into a probabilistic constraint and additionally extend the proposed framework to learn a probabilistic constraint from constrained expert demonstrations. Here, an expected constraint refers to a constraint that bounds the cumulative costs averaged over a batch of trajectories to be within a budget. Similarly, a probabilistic constraint upper bounds the probability that cumulative costs are above a certain threshold. Finally, we provide convergence guarantees for the proposed frameworks. Following these approaches, we consider the complementary challenge of learning a constraint in a high dimensional state-action space. In such a setting, the constraint function may truly depend only on a subset of the input features. We propose using a simple test from the hypothesis testing literature to select this subset of features in order to construct a reduced input space for the constraint function. We also discuss the implications of using this approach in conjunction with an ICL algorithm. To validate our proposed approaches, we conduct experiments with synthetic, robotics and environments based on real-world driving datasets. For feature selection, we test our approach by considering environments with varying state-action space sizes.
Data-driven patient scheduling for speech and language therapy
(University of Waterloo, 2025-05-27) Mirhashemi, Parmida
The demand for pediatric Speech-Language Pathology (SLP) services has increased significantly, particularly after COVID-19, leading to extended wait times and limited access to timely intervention for children with speech and language delays. Traditional scheduling models, including continuous scheduling and Specific Timely Appointments for Triage (STAT), while beneficial in some respects, often struggle to meet growing demands without additional resources. Block scheduling has emerged as a potential alternative, offering high-intensity therapy sessions within structured periods to reduce wait times and align treatment with critical developmental windows. However, block scheduling’s rigid framework poses challenges in adapting to fluctuating patient needs and resource constraints. This study develops a mathematical model aimed at optimizing block scheduling in SLP clinics, balancing treatment intensity, wait times, and operational resources. The model leverages real-world variables, such as patient arrival rates and therapist availability, to inform decisions on block length and sequencing, enhancing the efficiency of SLP services without adding to clinician workload. This approach addresses key limitations in current scheduling methods, offering a flexible framework that supports timely intervention during crucial developmental stages. Our findings suggest that optimized block scheduling can reduce administrative burdens, improve service accessibility, and lead to better outcomes for pediatric patients requiring SLP intervention.
The Effect of Acute Intermittent Hypercapnia and Exercise on Ventilatory Chemosensitivity and Cardiovascular Function
(University of Waterloo, 2025-05-27) Rynne, Paige
Ventilatory long-term facilitation (vLTF) is a form of respiratory plasticity triggered by intermittent hypoxia (IH) in the presence of CO2 (1,2,4,34). The manifestation of vLTF following intermittent hypercapnia (IHc) without concurrent hypoxia – particularly in combination with exercise- remains unclear. This study evaluated the physiological effects of IHc and moderate-intensity exercise on cardiovascular function and ventilatory control in the resting and exercising states. Twenty healthy participants (10F) completed a three-visit protocol, including two experimental exposures to either IHc (PETCO2 +5mmHg for 40s, intersped with 20s normocapnic normoxia) or continuous room air (control), each followed by an exercising and resting observational period (~45 minutes in total). At rest, the cardiovascular response to IHc was not found to be different from control. During exercise, heart rate (HR) increased following IHc and mean arterial pressure (MAP) significantly decreased (HR: +12bpm, p < 0.001; MAP: -8mmHg, p = 0.006), while both appeared stable in the time-matched control. Exercising peripheral hypercapnic chemosensitivity (PHC) appeared constant over time with IHc (+14 ± 25%), contradicting the significant decrease observed with control (-8 ± 20%, p = 0.017). While ventilation (V̇E) increased across both states following IHc relative to control, only resting V̇E was disproportionate to metabolic demand, as reflected by a lower %ΔV̇E/%ΔV̇CO2 ratio relative to control. These findings suggest the presence of exercise with IHc may have a modulatory role in the development or expression of cardiorespiratory plasticity, as well as implicating sensory long-term facilitation (LTF) as a contributor to vLTF. Finally, a progressive amplification in V̇E over the course of IHc, independent of CO2 stimulus intensity, is consistent with early-stage chemosensory gain. Collectively, these findings demonstrate that IHc without hypoxia can elicit key indicators of vLTF.
Artificial selection of Stutzerimonas stutzeri MBI-RS3 towards enhanced nitrogen fixation in presence of ammonia and oxygen
(University of Waterloo, 2025-05-27) Tello Yepes, David Felipe
Food security is a primary concern for every region of the world. Today, the agricultural sector relies heavily on artificial fertilizers to maintain crop production and yield. This has an unsustainable dependency that has exceeded the planetary boundary for nitrogen fertilizer usage for decades. Biologically, nitrogen nutrition can be provided by nitrogen fixation carried out by bacteria in the rhizosphere of crops. Nitrogen fixation is done by an enzyme called nitrogenase. This enzyme converts biologically inaccessible N2 from the atmosphere and into NH4, which is then readily available in the soil. Nitrogenase expression and activity are heavily downregulated by oxygen and biologically available nitrogen, making it challenging for bacteria to balance respiration, proliferation, and nitrogen fixation when subject to levels of oxygen and nitrogen. Bacteria capable of nitrogen fixation can be endosymbiotic or free-living. Endosymbiotic nitrogen-fixing bacteria interact specifically with legume plants by triggering nodulation. Free-living nitrogen-fixing bacteria can colonize legume and non-legume rhizospheres, opening possible environments where free-living nitrogen-fixing bacteria can survive and fix nitrogen. Free-living nitrogen-fixing bacteria are exposed to a wide range of oxygen and nitrogen concentrations, forcing them to adapt more extensively than endosymbiotic nitrogen-fixing bacteria. The genetic modification of free-living nitrogen-fixing bacteria can give an advantage in the race against artificial fertilizers, contributing to a more sustainable and resilient agriculture. Stutzerimonas stutzeri MBI-RS3 is a free-living bacterium that is capable of fixing nitrogen. This thesis focuses on exposing strain MBI-RS3 to UV energy, targeting a 99% kill rate and generating random mutations in the 1% survivors. A plasmid construct carrying a fusion of nif promoter and gus was developed. The UV-irradiated culture was recovered, transformed with a reporter gene plasmid pFT1NP and screened for blue colonies. Forty-three isolates were recovered and cryopreserved. Six candidates (FT11, FT16, FT22, FT34, FT38, FT40) were characterized by β-Glucuronidase assay, identifying mutant FT11 as the sample with the strongest nif gene expression. MBI-RS3 wildtype and mutants were inoculated in tomatoes, soybeans, and canola to assess their plant growth-promoting activity in different conditions. This showed a stronger performance of the mutant groups (FT11, FT16, FT22, FT38) compared to the wild-type in tomatoes, with higher shoot dry weight production. Mutant FT11 and FT22 showed some potential to make up for the decrease in nitrogen fertilizer use while maintaining yield. Mutants FT16 and FT 40 showed more pod and shoot dry weight in soybeans than wildtype in the presence of Bradyrhizobium sp. The MBI-RS3 wild-type was the best performer in terms of dry weight production of canola pods and shoots. These results demonstrate that not only MBI-RS3 wild-type but also some mutants exhibit plant growth-promoting activity, with a particular focus on nitrogen nutrition. Furthermore, in the tomato and soybean rhizosphere, the mutants induce higher yields and biomass production compared to the wild-type. All MBI-RS3 6 mutants and wild type were assessed by acetylene reduction assay to confirm nitrogenase activity, but only the MBI-RS3 wildtype strain showed ethylene production.
Quickest Change Detection in Nonlinear Hidden Markov Models Using a Generalized CUSUM Procedure
(University of Waterloo, 2025-05-27) Li, Dongchang
Fault diagnosis in modern aircraft engines is crucial for monitoring due to the rising need for high performance and safety. Early detection of system changes within a controllable range can prevent significant breakdowns. It's essential to track jet engine states and detect real-time dynamic mode shifts. This thesis explores change detection theories and procedures to handle dynamic instabilities in jet engines. We use the Moore-Greitzer equation to model flow and pressure changes in axial-flow compressors, specifically focusing on a reduced planar system. The research addresses QCD problems in nonlinear hidden Markov models, using pressure rise coefficients as observational data. The standard QCD scheme doesn't apply, so we employ the generalized CUSUM procedure, where the post-change distribution depends on an unknown change point, despite its non-recursive nature. We adopt standard filtering theory to approximate log-likelihood ratios with particle methods. To manage computational costs, we adjust the CUSUM-like procedure with an assumption of immediate change to enable recursion. This research focuses on how changes in the system excite shifts from a steady state to a new equilibrium or periodic oscillations. We assess the performance of generalized CUSUMs with particle filters through random simulations in surge modes of the Moore–Greitzer model with external forcing. Observations reveal similarities and differences between generalized CUSUMs and a special CUSUM that assumes immediate change, influenced by phase errors and the relationship of the steady state to the limit cycle. Signal noise mitigates the phase effects of the limit cycle. This research addresses change detection in the Moore-Greitzer PDE model, where disturbances in axial flow at the compressor inlet are combined with a modified ODE system. We simulate the PDE system by obtaining time series from a finite-dimensional Moore-Greitzer system using the Fourier spectral method. Employing proper orthogonal decomposition (POD), we reduce model dimensions while maintaining fidelity with fewer basis functions. The reduced model is validated by reconstructing the PDE system with $N$ POD modes capturing about 95% energy of the full model in $L^2$ inner product and $H^1$ Sobolev spaces. We examine generalized CUSUM statistics to detect dynamic changes, using POD bases and particle filters, with simulations showing the effectiveness of CUSUM statistics using {\em in situ} and {\em a priori} POD modes. Validated reduced models implement the generalized CUSUM for stall detection in stochastic systems, showing that the generalized CUSUM statistics are more effective and robust than recursive CUSUM-like procedures.
Leveraging Emerging Data Center Technologies to Build High-Performance Data Stores
(University of Waterloo, 2025-05-27) Alquraan, Ahmed
Distributed in-memory storage systems play a critical role in supporting modern applications and meeting their performance, reliability, and scalability requirements. Current in-memory storage systems adopt three design decisions that limit their performance and efficiency. First, these systems rely on the write-ahead log to guarantee data consistency and tolerate failures. The write-ahead log enforces a strict sequential ordering on operations that is often unnecessary for many applications, introducing a performance bottleneck. Second, these systems are designed for traditional, server-centric hardware, overlooking potential design optimization of emerging hardware capabilities and rendering them incompatible with the recently proposed hardware-disaggregated architecture. Third, their disaster recovery mechanisms are designed under the assumption of complete time asynchrony across machines, resulting in either a large data loss window or a significant performance overhead. This thesis explores a fundamentally different design space for building high-performance, replicated in-memory storage systems. First, to address the inefficiency of the write-ahead log, this thesis explores a novel system design that forgoes the write-ahead log and builds the Logless, Linearizable Key-Value storage system (LoLKV). By removing the log, LoLKV eliminates the serialization bottleneck and unnecessary memory copy operations, achieving a higher level of concurrency and improving resource utilization. LoLKV relies on one-sided RDMA to efficiently replicate data. Evaluation results demonstrate that LoLKV achieves 1.7–10× higher throughput and 20–92% lower tail latency compared to state-of-the-art RDMA-based systems. Second, to address the performance challenges of current storage systems on the hardware-disaggregated architecture, I propose SplitKV, a low-latency linearizable key-value store designed for the hardware-disaggregated architecture. SplitKV leverages one-sided RDMA for communication with memory nodes, ensuring that memory nodes remain completely passive. SplitKV co-designs the replication protocol with the data structures of the system to minimize the number of RDMA operations required to process client requests. Evaluation results show that SplitKV achieves 2.6–21× higher throughput and 80–89% lower latency compared to Sift, the state-of-the-art disaggregated key-value store. Finally, to address the shortcomings of current disaster recovery mechanisms, I leverage modern data center time synchronization hardware and protocols to build Slogger, a new disaster recovery system. Slogger achieves near-zero data loss and guarantees prefix linearizability at the backup site. Slogger uses continuous asynchronous replication to minimize the overhead on the system. Slogger employs a watermark service to guarantee the linearizability of the backup site while avoiding across-shard coordination. Evaluation experiments show that Slogger reduces the data loss window by 50% compared to the incremental snapshotting approach.
Strain-Balanced InGaAs/InAlAs Superlattices on InP(111)B for Terahertz Photoconductive Antennas
(University of Waterloo, 2025-05-27) Hosseini Farahabadi, Seyed Ali
Terahertz time-domain spectroscopy (THz-TDS) systems hold great promise for next generation communication, imaging, sensing, and metrology applications, all of which demand stringent performance requirements. Extending the deployment of THz-TDS systems beyond research laboratories into practical field applications requires the development of cost-effective and portable systems compatible with 1550 nm femtosecond fiber-coupled lasers. InGaAs/InAlAs photoconductors grown on InP(001) have emerged as strong candidates for efficient THz signal generation and detection. However, further material modifications are necessary to optimize their performance. One promising strategy involves growing InGaAs/InAlAs superlattices (SLs) along crystal orientations other than [001], such as [111], which can significantly influence their electronic and optical properties. Despite this potential, the growth and characterization of InGaAs/InAlAs SLs on (111)-oriented InP substrates remain underexplored due to intrinsic growth complexities and financial constraints. Addressing this gap, the present work investigates the molecular beam epitaxy (MBE) growth of InGaAs/InAlAs SLs on InP(111)B substrates. Through rigorous theoretical design, controlled MBE growth, and detailed structural and electrical characterization, we successfully achieved an atomically smooth, strain-balanced InGaAs/InAlAs SL on InP(111)B at 450°C for the first time. Leveraging the polar nature of the [111] orientation and strain engineering, simulations revealed a strong piezoelectric field of 153 kV/cm across the SL. This systematic approach enabled a detailed analysis of how structural parameters— such as indium composition and layer thickness—affect carrier dynamics, evaluated using time-resolved pump-probe spectroscopy at 1550 nm. Complementary absorption measurements indicated an enhanced absorption coefficient reaching 5195 cm⁻¹, while Hall effect characterization showed carrier mobility as high as 2756 cm²/Vs. These findings mark a crucial step toward achieving low-temperature-grown InGaAs/InAlAs structures with subpicosecond carrier lifetimes. While high-quality SLs were realized at 450°C, the impact of lower growth temperatures on structural quality remained unclear and warranted further investigation. To this end, two 50-period InGaAs/InAlAs SLs—one nominally lattice-matched and the other strain-balanced—were grown on InP(111)B substrates, with the growth temperature systematically reduced from 450°C to 200°C. Cross-sectional scanning transmission electron microscopy (STEM) revealed that lowering the temperature from 450°C to 400°C led to the formation of various defects and stacking faults within the SL grown at 400°C. Further temperature reduction resulted in spatial modulation of interfaces, the formation of microtwins, and phase separation in both the InGaAs and InAlAs layers. A comparative study of strain-balanced SLs grown on (001)- and (111)-oriented substrates under identical conditions showed that while high crystalline quality could be preserved on InP(001), maintaining structural integrity on InP(111) requires careful temperature-specific optimization. Building on these findings, we evaluated the sensitivity of InGaAs and InAlAs crystal quality to the temperature using two novel SLs with modulated growth temperature profiles. In the first structure, InGaAs and InAlAs layers were grown at 450°C and 200°C, respectively; in the second, the respective growth temperatures were reversed. The first SL exhibited a well-defined structure, although the InGaAs-on-InAlAs interfaces appeared slightly more diffuse than the InAlAs-on-InGaAs counterparts. These results suggest that growing InGaAs at 450°C can help mitigate interface roughness introduced by low-temperature InAlAs growth, thereby preserving SL integrity throughout the growth process. Despite the structural imperfections observed in SLs grown entirely at low temperatures on InP(111)B, these structures remained functional for THz photoconductive applications. This promising behavior led to a further investigation of carrier dynamics using strain-balanced InGaAs/InAlAs SLs grown on stationary substrates with varied indium compositions in the wells and barriers. Remarkably, trapping times as short as 1 ps and carrier lifetimes as fast as 4 ps were achieved without relying on complex Be doping schemes. Collectively, these advancements provide new insight into the controlled growth of InGaAs/InAlAs SLs on InP(111)B substrates, paving the way for the development of high performance electronic and photonic devices operating at telecommunication wavelengths.
Influence of Indium Contamination from E-waste on Cell Behaviour
(University of Waterloo, 2025-05-27) Eskandari, Ali
Recent trends show a massive increase in the production of electronic waste (e-waste) worldwide. These e-waste materials often contain heavy metals whose biological impact on human health and the environment is unknown. One of these contaminants is indium, which can be found in many e-waste materials such as solar panels and liquid-crystal displays (LCDs). This thesis investigates how indium affects the functionality, behaviour, morphology, and viability of live mammalian cells. Two types of cells are used in this work: human dermal fibroblast cells (GM5565) and Vero cells (CCL81) isolated from C. aethiops kidney of an African green monkey (Cercopithecus aethiops). Cell adhesion is an essential biological function for division, migration, signalling, and tissue development. Although it has been demonstrated that this cell function can be modified by using nanometer-scale surface topographic structures, it remains unknown how contaminants such as indium (III) ions might influence this specific cell behaviour. Different tissues and organs, such as skin, muscle, and cornea, consist of cells organized in specific patterns that support their function. It is, therefore, important to understand how external cues, such as engineered surfaces or chemical contaminants, can influence the organization and morphology of cells. Two different indium compounds that are commonly seen in both extracting and recycling indium are indium sulfate (In2(SO4)3) and indium chloride (InCl3). These are two of the main sources of indium that humans are regularly exposed to, and can result in potential long-term harmful effects on human health. This thesis investigates the effect of indium on mammalian cells by exposing cells to different concentrations of each of these indium compounds and measuring an array of cell function indicators such as viability, production of Reactive Oxygen Species (ROS), cell alignment, cell morphology, and focal adhesion protein expression. In this thesis, first, the influence of indium chloride on cell adhesion characteristics is investigated, and the morphology of the adherent cells and their mitochondrial reticulum is characterized on cell culture dishes and nanopatterned surfaces using fluorescence confocal microscopy and scanning electron microscopy. Results showed that exposure to indium chloride decreased cell viability, affected cell alignment, had detrimental effects on the behaviour of human fibroblasts, and adversely impacted their mitochondrial morphology. Next, the impact of indium sulfate on cell viability, production of ROS, morphology, and alignment behaviour on tantalum/silicon oxide parallel line/trench surface structures is studied. Cell morphology and orientation on the engineered surfaces are characterized using fluorescence confocal and scanning electron microscopy. Results again confirmed that average cell viability decreased, the concentration of cellular ROS increased, and cell alignment and mitochondrial morphology were adversely affected. Finally, a study on the impact of indium chloride and indium sulfate on Vero cells is presented to investigate the effect of these contaminants on cell viability, ROS production, morphology, and alignment on tantalum/silicon oxide parallel line/trench surface structures. Results showed that when Vero cells were cultured in media containing indium chloride, the cell viability decreased by ∼35% on average, ROS concentration increased, and the cell geometry and alignment were again affected. The impact of indium chloride and indium sulfate on focal adhesion proteins was also studied using the Western blotting technique. The results showed that focal adhesion kinase (FAK) expression increased with increased concentration of indium in the media, and paxillin phosphorylates, while α−actinin stayed unchanged. All of these results confirm that indium has a negative effect on both human dermal fibroblast cells (GM5565) and Vero cells (CCL81) functionality. Their viability dropped to about 65%, and the ROS production increased. The morphology of cells changed to a more compact and circular shape. The alignment of GM5565 cells on the parallel patterns decreased with an increase in indium concentration, while Vero cells’ alignment on patterns in sizes of less than 1 μm increased. It also revealed that indium solutions alter the signalling pathway in Vero cells that are involved in forming focal adhesions.
Knee Extensor Capacity Utilization and Stair-gait Biomechanics in Younger and Older Adults
(University of Waterloo, 2025-05-27) Rinaldi, Daniel
Stair-gait is a more challenging task than level-gait, particularly for older adults. Both ascending and descending stairs require greater lower extremity joint ranges of motion, vertical ground reaction forces, and external knee flexion moments than level-gait. Safe and efficient performance while negotiating stairs is largely dependent on adequate knee extensor muscle function. However, age-related declines to muscle quantity, quality, and function contribute to limitations in physical function and independence during activities of daily living, such as stair-gait. Consequently, compensatory movement strategies employed by the trunk may be a key mechanism by which those with reduced muscle function adapt to large knee joint demands encountered in daily activity. The large demands imposed by stairs paired with reduced muscle function among a growing ageing population poses a substantial threat to quality of life. A few studies have investigated knee extensor muscle utilization, a concept that describes the proportion of the maximal available capacity of the knee extensors that is used to complete a task. Knee extensor muscle utilization is greater in older adults compared to younger adults during walking and other tasks. A number of studies also demonstrate knee extensor muscle capacity utilization is larger during stair ascent and descent compared to level walking in both young and older adults. However, little data compare knee extensor muscle capacity utilization between young and older adults on stair negotiation; and no study has determined whether this is related to sagittal plane trunk kinematics. This study aimed to compare knee extensor capacity utilization during stair ascent and descent in older adults versus younger adults. A secondary aim was to determine if this knee extensor capacity utilization is related to sagittal plane trunk kinematics. Twenty-five healthy young adults (n = 16) aged 18-30 years and healthy older adults (n = 9) aged 45-70 years were recruited primarily from the University of Waterloo and surrounding communities. Three-dimensional kinematics and kinetics were captured while participants ascended and descended a custom-built 4-step staircase using a high-speed motion capture system as well as floor- and step-embedded force plates, respectively. Knee extensor capacity utilization was calculated from maximal voluntary isometric and isokinetic contractions via dynamometry and peak external knee flexion moments measured in the stance phase of stair-gait for both stair ascent and descent. A two-tailed Welch’s t-test was used to determine if there was any difference in knee extensor capacity utilization between the healthy young adults and healthy older adults. A Pearson-Product Moment Correlation test was used to determine the relationship between knee extensor capacity utilization and the peak trunk flexion angle during the stance phase of stair-gait. Healthy older adults exhibited significantly greater knee extensor capacity utilization compared to healthy younger adults (p = 0.02), but not while descending stairs (p = 0.62). Knee extensor capacity utilization was not associated with peak sagittal trunk flexion angles during the stance phase of stair ascent (r = -0.06; p = 0.77) or stair descent (r = -0.31; p = 0.14). Findings demonstrate that healthy older adults utilize a greater amount of their available knee extensor capacity than healthy younger adults during stair ascent but not during stair descent. KECU was not associated with peak trunk flexion while either ascending or descending the stairs. Overall, findings further support for stair ascent being more challenging for older adults than younger adults. This study provides insight into the impact of knee extensor weakness while negotiating stairs.
Characterization of Microbial Communities of the Utikuma Region Study Area (Alberta, Canada)
(University of Waterloo, 2025-05-26) Kwok, Arnold
Understanding the drivers of bacterial communities and the dynamics of boreal ecosystems is critical for safeguarding water quality and ecosystem resilience in the face of environmental change. This study investigates the interplay between cyanobacterial dynamics and ecohydrologic factors in the Utikuma Region Study Area (URSA) of northern Alberta. Cyanobacteria play a pivotal role in oxygenic photosynthesis and nutrient cycling, yet their unchecked proliferation can lead to harmful algal blooms with significant ecological and economic consequences. Field sampling was conducted in 34 URSA ponds using a two-phase filtration process designed to capture both larger microbial and picocyanobacterial cells. DNA was extracted and analyzed through 16S rRNA gene sequencing, with taxonomic assignments derived from the curated CyanoSeq 1.3 database and complementary methods. Advanced bioinformatics pipelines provided high-resolution community profiling, while statistical analyses—including redundancy analysis and PERMANOVA—linked microbial diversity patterns to water chemistry parameters (e.g., pH, nutrients, trace metals) and ecohydrologic variables such as hydrologic relief areas, hydrologic units, and wildfire disturbances. Key findings indicate that environmental factors explain up to 23.9% of the variance in microbial composition based on clr-transformed RDA. Notably, landscape-scale drivers and wildfire history significantly influenced community structure, with their interactions accounting for up to 30.1% of the variance (PERMANOVA). Dominant phyla observed included Pseudomonadota, Bacteroidota, Actinomycetota, Cyanobacteriota, and Verrucomicrobiota, while analysis of 165 cyanobacterial Amplicon Sequence Variants highlighted taxa such as Prochlorococcaceae and Aphanizomenonaceae. These results, while based on a specific sampling period, provide valuable foundational insights into the relationships between ecohydrologic drivers and microbial community structure for a region previously uncharacterized in this regard. This work sets the stage for further research to refine taxonomic methods and inform targeted water quality management strategies in boreal ecosystems.
Strain-Balanced InGaAs/InAlAs Superlattices for 1550 nm-based Terahertz Photoconductive Antennas
(University of Waterloo, 2025-05-26) Entezami, Milad
Terahertz (THz) technology has developed as a transformative tool with critical applications in spectroscopy, imaging, and high-speed communication across diverse fields. Recent advancements have facilitated a transition from conventional photoconductors, driven by laboratory-scale and costly Ti:Sapphire lasers operating at 800 nm wavelengths, toward compact, cost-effective, and industrially viable THz time-domain spectroscopy systems utilizing a fiber-optic platform. Despite these advances, developing high-performance photoconductive materials remains a significant challenge, especially for efficient THz generation and broadband detection at the telecom wavelength of 1550 nm. This research investigates the growth, characterization, and photoconductive properties of strain-balanced InGaAs/InAlAs superlattices grown on InP substrates as promising photoconductive materials for fiber-compatible THz photoconductive sources and detectors. First, fundamental principles underlying photoconductivity, including carrier generation, transport, and recombination, are reviewed, highlighting their critical role in determining overall performance. Recent material engineering strategies targeting THz operation at telecom wavelengths are also discussed. Despite recent advancements, there remains a need for photoconductive materials simultaneously exhibiting enhanced optical absorption, superior carrier transport, and ultrafast recombination lifetimes to enable efficient broadband THz operation. Based on these principles, a theoretical framework describing carrier dynamics for transient THz photocurrent generation and detection is reviewed. This theoretical foundation is complemented by comprehensive experimental studies, including time-resolved pump-probe spectroscopy, Hall effect measurements, optical absorption spectroscopy, and band structure simulations, enabling precise quantification of carrier lifetime, mobility, and optical absorption coefficients. Molecular beam epitaxy was employed to implement a stationary (non-rotating) substrate growth method, enabling precise lateral control of structural parameters across the wafer. The primary contribution lies in strategically balancing compressive strain within InGaAs wells with tensile strain in InAlAs barriers, thereby achieving a net-zero stress condition in each superlattice period. This strain-balancing approach systematically addresses limitations inherent to conventional lattice-matched epitaxy, resulting in significantly enhanced crystal quality in strain-induced superlattices, improved optical absorption at 1550 nm, and optimized electronic transport properties. Experimental results confirm these structural optimizations improve carrier dynamics, essential for high-performance THz devices. Moreover, low-temperature-grown Be-doped strain-balanced superlattices are comprehensively characterized, revealing sub-picosecond carrier recombination lifetimes, increased mobility, and enhanced optical absorption. Detailed structural analyses through high-resolution X-ray diffraction, atomic force microscopy, and transmission electron microscopy identify notable Be-induced interdiffusion effects at interfaces. Lastly, modulation doping strategies are explored to further refine photoconductive properties. By systematically controlling dopant distribution within the superlattice layers, this study reveals the complex interplay among doping, defect formation, and strain, enabling precise tuning of carrier transport and recombination dynamics critical for advanced THz photoconductive applications. This research advances the fundamental understanding of carrier dynamics and transport in strain-balanced photoconductive superlattices and offers practical guidance for developing high-performance, telecom-compatible THz photoconductive materials well-suited for portable pulsed THz spectroscopy and imaging systems.
The Role of the Theory of Planned Behaviour (TPB) and socio-demographics in influencing Pro- climate behaviours
(University of Waterloo, 2025-05-26) Hussain, Mahnoor
The study aimed to investigate the association between demographic factors and components of the Theory of Planned Behaviour (TPB) with the climate change behaviour of the people residing in Canada. The hypotheses of the research focused on the association between socio-demographics of age, gender, race, region, income, language, and education with the intention of the people to act in an environment-friendly way. Moreover, the hypotheses were also concerned with social norms, attitudes, perceived behavioural control, intention, and behaviour of the people. The data of the study was obtained from the survey of Impact Canada, selecting wave 1 responses for the research as it provided information according to the variables required for the study. The data analysis was conducted through Chi-square and Spearman correlation. The findings have provided support for all of the study hypotheses, excluding H6 and H7 which were related to the association of language and race with intention. However, the other hypotheses have been accepted, which implies that demographic factors tend to play a significant role in determining the pro-climate behaviours of the people. In addition, the relevance of TPB has been established through this study as a means of understanding the adoption of environment-friendly behaviours of the people in Canada.
Assessment of the viability of VISR: a mid-wavelength infrared (MWIR) multispectral imaging-based approach for remote flare CE quantification
(University of Waterloo, 2025-05-26) Kaveh, Alireza
In the upstream and downstream petrochemical industry, flaring is a common practice to dispose of the redundant by-products of crude oil extractions, including associated gas and highly reactive volatile organic compounds (HRVOCs), for a variety of regulatory, safety and economic purposes. The current consensus among government regulators and industry experts is that flaring typically occurs at a combustion efficiency (CE) higher than 98%. Recent studies, based on real-world observations and computational simulations, have called this into question. For example, a recent study, based on airborne sampling observations and unlit flare prevalence surveys, reported a mean flare CE of 91%, accounting for both inefficient flaring and unlit flares in the three largest basins in the US. This represents a five-fold increase in fugitive hydrocarbon emissions, primarily comprised of methane, compared to the presumed release rates, highlighting an opportunity for developing robust flare CE monitoring techniques to mitigate the adverse health and environmental impacts of the underappreciated flaring emissions. This study presents a numerical assessment of video imaging spectro-radiometry (VISR), a mid-wavelength infrared (MWIR) multispectral technique, proposed for remote flare combustion efficiency quantification applications. The present analysis utilizes a series of computational fluid dynamics (CFD) simulations of a crosswind steam-assisted industrial flare, with a focus on three aspects: how approximations in the radiometric model impact the local “pixel-wise” CE, the validity of the approach for computing flare global CE using inferred local CE values, and the ability and limitations of VISR instrument to capture fuel that may be aerodynamically stripped from the combustion zone under crosswind conditions. The current assessment is conducted on a simplified version of the VISR instrument model using simulated broadband images generated over spectral bands adjusted for the key absorption features of three main by-products of flare combustion reaction: CO2 (4.2–4.4 µm), CO (4.5–4.9 µm), and CH4 (3.2–3.4 µm). The results highlight the accuracy of the proposed simplified VISR approach in predicting local CE within the VISR region-of-interest (ROI) yet flawed in terms of converting these values into a flare global CE, potentially leading to large biases from the actual flare CE. Ultimately, the VISR technique, due to reliance on mid-wavelength infrared imaging, is inherently incapable of quantifying unburned (cold) methane, allegedly stripped from the flare stack, without participating in the combustion process, due to the presence of a high crosswind over the flare stack, leading to a considerable overestimation of the true flare performance. Keywords: Flares, Combustion Efficiency, Remote Sensing, Verification and Validation, Radiometric Measurements, Uncertainty Analysis, Bayesian Inference.
Characterizing the effects of temperature variation on metabolic capacity in darter fish (Etheostoma spp.)
(University of Waterloo, 2025-05-26) Sinik, Alexandra
With progressive increases in global temperatures from climate change, aquatic ectotherms are particularly at risk, considering they are incapable of maintaining their internal body temperatures. As environmental temperatures increase, metabolic rate rises in ectothermic poikilotherms, with thermal extremes presenting potentially lethal implications. By gaining an understanding of the metabolic functioning of local species, we can draw conclusions on the implications of thermal stress on biochemical responses. Here, we focused on understanding the effect of increased temperatures on enzyme activity in the brain, heart, and muscle tissues of three closely related darter species found in the Grand River of Southern Ontario: Johnny (Etheostoma nigrum: JD), Fantail (Etheostoma flabellare: FTD) and Rainbow darter fish (Etheostoma caeruleum: RBD) to determine whether energetic enzymes are a potential limiting factor in thermal tolerance. Analysis of enzymatic activity of four key metabolic enzymes including lactate dehydrogenase (LDH), pyruvate kinase (PK), malate dehydrogenase (MDH) and citrate synthase (CS) were conducted via enzyme assays through a temperature profile, ranging from 20C to 34C, just past the predetermined critical thermal maximum (CTmax), or upper thermal tolerance, at 30.7C ± 0.9, 31.9C ± 0.6 and 33.3C ± 0.8 for RBD, JD and FTD, respectively (Weber & Craig, 2025). Through modelling enzymatic activity in a segmented regression, breakpoint estimates were found for brain at 22.0C ± 0.8, heart at 22.0C ± 5.0 and muscle at 26.0C ± 4.7 indicating decreases in enzymatic activity at higher temperatures. These results indicate that enzymatic activity in brain and heart tissue is most impacted by increased temperatures as evident by the lower trending breakpoints, suggesting that these tissues may be implicated in defining thermal tolerance limits. Muscle tissue enzymatic activity also decreased at higher temperatures but had a higher trending breakpoint, suggesting compensatory mechanisms. Moreover, breakpoints also occurred far before previously determined CTmax values for these fish, indicating that biochemical processes decline in performance prior to ecological death. Overall, these findings enhance our understanding of the biochemical processes that limit thermal tolerance in these local species, with potential implications for conservational efforts in defining temperatures of concern.
A User-Centered Design Approach to an Artificial Intelligence-Enabled Electronic Medical Record Encounter in Canadian Primary Care
(University of Waterloo, 2025-05-26) Francisco, Krizia
Introduction The Canadian primary care system serves as the first point of contact for patients entering the healthcare system and plays a crucial role in ensuring continuity of care. Primary care clinicians provide a broad range of services, including disease prevention, health promotion, diagnosis, treatment, and coordination of referrals to specialized care. Despite the widespread adoption of electronic medical records (EMRs) in primary care, their development has historically lagged in addressing the specific needs of primary care providers. For example, chronic disease management (CDM) is a core responsibility in primary care. Yet, EMRs have not evolved to incorporate native, CDM-focused tools that align with the complex, long-term nature of managing chronic conditions. With the emergence of artificial intelligence (AI), there is growing recognition of its potential to enhance clinical decision-making, optimize workflows, and improve patient outcomes. Despite these promising advancements, clinicians remain hesitant to adopt AI due to concerns surrounding trust, usability, and seamless integration into existing workflows. Primary care is a complex and dynamic environment where clinicians must balance efficiency with patient-centered care, making it critical for AI systems to align with their needs rather than introduce additional cognitive or administrative burdens. Trust in AI is not inherent; rather, it is a critical factor influencing clinicians' willingness to incorporate AI-driven tools into their practice. Without trust, even the most advanced AI systems risk a lack of adoption, as clinicians must have confidence that these technologies will enhance, rather than hinder, patient care. Concerns around reliability, accuracy, and the ability to align with clinical workflows contribute to skepticism, making AI adoption a complex challenge. Clinicians also worry about unintended consequences for both patient outcomes and professional responsibility, fearing that AI-generated recommendations could lead to issues, including diagnostic errors, inappropriate treatments, or a diminished sense of clinical accountability. Additionally, broader ethical and legal uncertainties further complicate integration, as unresolved questions regarding liability, accountability, and regulatory oversight leave clinicians uncertain about the implications of relying on AI-enabled tools embedded in their EMRs. Without clear governance structures and well-defined safeguards, hesitation around AI use in healthcare will persist, underscoring the need for thoughtful design and policy development. This study investigates how a user-centered design approach can address these challenges, ensuring that AI-enabled EMR encounters enhance, rather than disrupt, the clinician’s role in primary care. Through qualitative engagement with practicing primary care clinicians in Ontario, this research explores the design considerations necessary to address the various concerns that may hinder the adoption of AI-enabled tools in primary care clinical interactions. Methods This research employed a user-centered design approach, incorporating a two-phase semi-structured qualitative interview process with 14 primary care clinicians practicing in Ontario. In the first phase, scenario-based interviews were conducted in which clinicians interacted with a standard EMR encounter module, allowing for the development of an initial sequence model that mapped out the typical workflow clinicians follow during patient encounters. In the second phase, clinicians engaged with AI-enabled mock-ups with the same scenarios as the first. This mock-up included an AI-generated summary encompassing a numeric confidence score, the concept of approve/edit/decline buttons, and underlined actionable steps like selecting medications. Clinicians provided feedback on the AI-enabled EMR encounter mock-ups, highlighting aspects they liked, elements they found distracting, areas where they had reservations about AI inclusion, and other general sentiments. A thematic analysis was conducted from the qualitative interview transcripts, which informed iterative redesigns of the AI-enabled interface. These themes were further explored with the concepts of ease of use and usefulness through the Technology Acceptance Model (TAM), using these concepts to structure design requirements for revised mock-ups. A second round of semi-structured validation interviews was conducted to assess the effectiveness of the redesigned AI-enabled EMR encounter, with results tabulated to capture clinician feedback. Additionally, a System Usability Scale (SUS) was administered to quantify clinicians' perceptions of the redesigned interface, providing a standardized measure of its usability and potential for adoption in primary care settings. Results The initial sequence model was developed to map out a clinician's typical workflow during a clinical encounter, providing a structured understanding of key interactions from patient intake and history-taking to diagnosis, treatment planning, and documentation. This model highlighted key areas in the workflow where AI could support, rather than disrupt, established workflows by aligning with real-world clinician behavior. It also helped identify inefficiencies and moments where AI could provide meaningful assistance without diminishing clinician autonomy. Through thematic analysis, six key themes were identified, contributing to a greater understanding of how AI-enabled EMR encounters can be designed for adoption, including trust and transparency, clinician authority, workflow efficiency, complexity sensitivity, legal and ethical concerns, and human-centered design. Clinicians approach AI with skepticism, expecting trust to be earned through high performance and transparency. They prefer AI that reinforces their authority by providing relevant, non-intrusive support rather than acting autonomously. Trust is further influenced by clarity in AI-generated confidence scores and the ability to audit recommendations. Maintaining clinician decision-making authority is essential. AI is viewed as most beneficial when offering supportive suggestions, such as reminders or preventative care guidelines, while avoiding directive or overly prescriptive actions. AI adoption also depends on complexity sensitivity, where clinicians favor AI-assisted recommendations in straightforward cases like uncomplicated urinary tract infections but remain cautious in complex, nuanced scenarios such as mental health visits, uncovering a potential pathway for further exploration. Workflow efficiency and seamless integration into clinical practice are critical, with clinicians expressing their desire for AI-generated summaries that are concise, patient-centered, and structured to minimize cognitive burden. Implementing unnecessary steps or disrupting existing workflows is seen as a barrier to adoption, as clinicians emphasize their time constraints and high-volume workload, requiring minimal disruption and patient care maintaining priority. Legal and ethical concerns also play a significant role, with clinicians expecting clarity. Clinicians express delineation between AI-generated and clinician-modified content and well-defined policies on liability auditability. Finally, human-centered design remains paramount, with clinicians emphasizing that AI should enhance rather than replace the clinician-patient relationship. AI should be positioned to operate unobtrusively in the background, ensuring efficiency without diminishing clinical judgment or disrupting the clinician and patient interaction during a visit. These findings directly informed the redesigned screens, with ease of use and usefulness from the Technology Acceptance Model (TAM) serving as guides for the redesign requirements. An "AI Assist" button was introduced, allowing clinicians to engage AI support at their discretion rather than imposing AI-driven suggestions on their workflow. This reinforced clinician autonomy and minimized cognitive burden. Additionally, color-coded delineations were implemented to clearly distinguish AI-generated content from clinician-entered data, ensuring transparency while maintaining workflow efficiency. An optional descriptive confidence score feature was incorporated, addressing varying clinician preferences by allowing them to toggle the feature on or off as needed. The language in the AI-generated summary was also adjusted to align with a more supportive narrative in contrast to an overly prescriptive tone. These insights and the thematic analysis results guided the development of redesigned screens, positioning AI to better align with clinicians’ preferences and expectations. The redesigned screens were completed in a way that attempted to reinforce trust, reduce friction between clinicians and AI, maintain flexibility, and reinforce a clinician’s role as the decision-maker. Validation interviews indicated that these design modifications potentially improved usability by positioning AI in the EMR encounter to better align with clinicians’ preferences and expectations, as informed by the thematic analysis, ultimately increasing the likelihood of adoption. Conclusions AI adoption in primary care depends on thoughtful design prioritizing reinforced clinician autonomy, high performance, and seamless workflow integration. While clinicians recognize AI's potential benefits, they remain cautious about unintended consequences. Designing AI as a supportive, rather than directive, tool is key to fostering trust and improving adoption. Future research should focus on real-world implementation, longitudinal studies on AI adoption, and regulatory frameworks that address liability and ethical considerations. Contributions This study contributes to the academic and practical understanding of integrating AI-enabled clinical tools in Canadian primary care EMRs. From a scientific perspective, it advances knowledge on the barriers and facilitators of AI adoption in EMRs, identifying key design principles that can encourage adoption. From a practical standpoint, this study provides concrete design recommendations that can inform AI developers, EMR vendors, and healthcare policymakers. Additionally, this study contributes to the legal and ethical discourse surrounding AI in healthcare by highlighting unresolved questions regarding liability, data privacy, and patient consent. The findings call for regulatory frameworks that protect clinicians from undue legal risks while ensuring that AI systems are accountable, interpretable, and aligned with best medical practices. Finally, this research offers a framework for future AI integration, emphasizing the need for context-sensitive AI models that adapt to case complexity. Through these contributions, this research informs the potential for responsible design and deployment of AI in primary care, ensuring that technology is a sustainable partner in healthcare delivery.
Investigation of the therapeutic potential of a new phytoceutical for lymphopenia in Barth Syndrome
(University of Waterloo, 2025-05-26) Chan, John
Background: Barth syndrome (BTHS) is a debilitating X-linked genetic disorder caused by mutations in the gene that encodes for Tafazzin, an enzyme important for cardiolipin (CL) remodeling. This disorder impairs the ability to modify fatty acyl chains on cardiolipin after de novo synthesis, resulting in decreased cardiolipin levels and alterations in cardiolipin fatty acyl composition. Given that CL is crucial for mitochondrial processes, TAFAZZIN mutations lead to abnormal mitochondrial ultrastructure, impaired dynamics, and decreased electron transport chain capacity. As a result, tissues with high energy demands, including the heart, skeletal muscle, and immune system, are most affected by BTHS. While BTHS research has traditionally focused on innate immune dysfunction, recent studies highlight potential adaptive immune impairments. Data from my MSc research demonstrated that transformed B-lymphoblasts derived from individuals with BTHS exhibit significantly reduced growth compared to sex- and age-matched healthy controls. This deficit was partially restored with the endocannabinoid N-oleoylethanolamide (OEA). However, while OEA showed initial promise, it only partially rescued the impaired clonal expansion of these cell lines. In the pursuit of compounds with potentially better efficacy and safety profiles, further investigations turned to a natural phytochemical known for its antioxidant and mitochondrial-modulating properties, which we refer to as Compound X. Aims and Approach: This thesis aimed to evaluate the therapeutic potential of Compound X in treating BTHS-associated lymphopenia. To achieve this, several objectives were examined by comparing responses in both BTHS and healthy B-lymphoblasts. Specifically, we: (1) assessed the effects of Compound X on cell growth using manual cell counting with a hemocytometer; (2) analyzed changes in CL content and composition following Compound X treatment via thin-layer chromatography and gas chromatography (TLC-GC); (3) evaluated the expression of genes involved in CL biosynthesis using RT-qPCR; (4) examined the impact of Compound X on ETC protein subunit levels using immunoblotting; and (5) investigated alterations in mitochondrial ultrastructure and morphology in response to Compound X treatment through transmission electron microscopy (TEM) and immunoblotting of fission and fusion mediators. Results: In the first study, Compound X treatment fully restored the impaired cell expansion of B-lymphoblasts derived from five distinct BTHS donors, bringing the cell number to near levels of healthy controls. This growth improvement was accompanied with significant increases in the maximal coupled state III respiration in BTHS B-lymphoblasts, in which all five tested BTHS donors had increased mitochondrial membrane potential following Compound X treatment. Further analysis revealed that Compound X treatment restored total CL content of BTHS B-lymphoblasts to healthy levels, but did not significantly alter the relative proportions of the major CL fatty acyl species. At the protein level, Compound X treatment reversed the decreased expression of major ETC subunits, including succinate dehydrogenase subunit A (SDHA), cytochrome c oxidase subunit 1 (COX1), and cytochrome c oxidase subunit IV (COXIV). TEM analysis of three distinct BTHS donor cell lines showed that BTHS lymphoblasts had abnormal cristae patterns with smaller total cristae lengths and enlarged mitochondria compared to healthy controls. While Compound X treatment did not significantly increase the length of cristae, it significantly reduced the mitochondrial enlargement in BTHS B-lymphoblasts. Lastly, immunoblotting of fusion mediators revealed elevated OPA1 levels in BTHS lymphoblasts, while analysis of the fission mediator DRP1 revealed elevated phosphorylation of its inhibitory site at Serine 637, both of which were significantly attenuated by Compound X treatment, suggesting a potential role for this compound in restoring mitochondrial dynamics in BTHS B-lymphoblasts. Conclusion: These findings demonstrate for the first time that Compound X effectively rescued the observed impairments in B-lymphoblast cell expansion in BTHS and partially restored BTHS B-lymphoblast mitochondrial function and morphology. However, additional experimentation in both animal models and humans are needed to further validate the therapeutic efficacy of Compound X in BTHS lymphopenia.
Comparative Analysis of MPC and Integrated Skyhook-LQR Controllers for a CDC Damper Suspension System in Passenger Cars
(University of Waterloo, 2025-05-26) Zheng, Huizhe
The performance of vehicle suspension systems is critical for ride comfort, handling stability, and safety. Passive suspensions, while simple and reliable, lack adaptability to road conditions, whereas fully active suspensions provide superior performance but are impractical for passenger vehicles due to high energy consumption. Semi-active suspensions offer a balance by dynamically adjusting damping forces with minimal power requirements, but their effectiveness depends on the chosen control strategy. This study evaluates two advanced control strategies: Model Predictive Control (MPC) and an integrated Skyhook-Linear Quadratic Regulator (LQR) controller. A seven-degree-of-freedom (7-DOF) full-vehicle model is developed using Lagrange’s equations to analyze vehicle dynamics. MPC is formulated as a predictive controller that anticipates road disturbances, while the integrated Skyhook-LQR controller combines classical Skyhook damping with optimal state feedback for improved stability. The controllers are implemented in a CarSim-Simulink simulation environment and tested under various road conditions. To assess real-world feasibility, experimental testing is conducted on a passenger vehicle equipped with semi-active CDC dampers using the Skyhook-LQR controller. The comparative analysis highlights key trade-offs. MPC provides superior predictive control and optimizes suspension performance across multiple axes but requires high computational power, limiting real-time implementation. The integrated Skyhook-LQR controller, while computationally efficient and practical for embedded systems, has limitations in handling complex disturbances. These findings underscore the importance of selecting control strategies based on application requirements. While MPC enhances ride comfort and stability, Skyhook-LQR remains a more feasible real-time solution. This study contributes to the advancement of semi-active suspension technology, offering insights for future vehicle suspension designs.

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