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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The Feasibility of Applying Pescatourism to the Small-scale Fisheries in Japan
(University of Waterloo, 2024-09-13) Song, Yinghao
Small-scale fisheries (SSFs) often receive insufficient attention and are undervalued by governments and the public worldwide, including coastal areas in Japan. The small-scale fisheries communities in Japan face various problems such as ageing population, low income, and environmental degradation. In light of this, Pescatourism, a popular type of fishing tourism in Europe, has the potential to alleviate the vulnerabilities and adhere to the current sustainable regulations in Japan. Japan is also expanding its Umigyo industry, which enables fishers to engage in economic activities utilizing all regional marine-related resources. This initiative encourages SSF communities to develop their tourism industry as an element of Umigyo, providing tourists with an immersive experience of fishers’ lives in these communities, similar to Pescatourism. Thus, this study aims to explore the extent of the existence of SSF communities in Japan and the potential role of Pescatourism in addressing their vulnerability and creating governance arrangements for viability. Case studies, including literature reviews, observations, semi-structured interviews and focus group discussion (FGD) were conducted in five ports in Shizuoka Prefecture and Miyagi Prefecture in Japan. There are gradually increasing SSF tourism markets supported by legislation, owing to the recognised economic, ecological, and social benefits from stakeholder cooperations in Japan. This study can help reflect Japan's efforts and attempts at achieving viability in SSF tourism and its adaptation to Pescatourism, with governance concerns.
Revival: A study of regeneration for unitised curtain walls in healthcare sector
(University of Waterloo, 2024-09-13) Billa, Anmol
This study examines the circular potential and limitations of current aluminium unitised curtain wall facades, primarily through strategies such as reuse, refurbishment, and remanufacture. Despite being widely used in commercial buildings, including healthcare facilities, curtain walls present significant challenges in performance, adaptability, and sustainability. The research aims the critical issue of embodied carbon and resource depletion associated with these facades, particularly in the context of Toronto's healthcare infrastructure, which is undergoing extensive renovations. Buildings contribute immensely to environmental disruption, accounting for a significant portion of energy consumption, waste generation, and carbon emissions. The construction industry is working to reduce operational carbon emissions and enhance occupant safety. However, there is little focus on embodied carbon and the act of valuable materials in the early design phase, particularly in complex facade systems where high-carbon-intensity materials are found in curtain walls, such as aluminium and glass. To address global issues, the development of Toronto's healthcare infrastructure from the 1970s onwards, with ongoing renovations focusing on its building envelope systems, has become a potential model for studying, analysing, and applying sustainable practices. Hospitals like SickKids, Mount Sinai Hospital, and Toronto General Hospital are in the process of sustainably upgrading their building exteriors. This process includes updating their curtain wall and window-wall systems with material substitution and modular designs. It's crucial to incorporate end-of-life plans for new products and strategies for older ones to combat the "take-make dispose" culture", especially in Toronto's healthcare sector. A forensic analysis, including a Life Cycle Analysis (LCA), is being carried out to measure the quantity and quality of curtain walls and window wall systems and to assess the potential carbon emissions produced by facilities like the Patient Support Centre (Research site) at SickKids. Also, a mixed-method approach, combining interviews with international facade and material experts and case studies, is being used to investigate the possibility of implementing circular practices. The Design for Disassembly practice is customised and adapted to the research site (Patient Support Centre building), reflecting the opportunity and limitations of the curtain walls and offering guidance for handling such complex facade systems. The study found that while downcycling unitised curtain wall components is possible, achieving true circularity through reuse and remanufacturing is hindered by factors such as poor thermal performance, complex disassembly, and limited compatibility with new building designs. While the research demonstrates the potential for upcycling certain components, it highlights the need for a paradigm shift toward building better envelope systems that prioritise disassembly, adaptability, and material recovery. The findings emphasize the importance of developing alternative facade systems that better align with circular economy principles and exploring policy incentives to encourage their adoption. By uncovering the current unitised curtain wall systems, this research contributes to a broader understanding of the challenges and opportunities for achieving circularity in the building industry. The findings provide valuable insights for policymakers, designers, and building owners seeking to reduce the environmental impact of the built environment.
A New Tightly-Coupled Dual-VIO for a Mobile Manipulator with Dynamic Locomotion
(University of Waterloo, 2024-09-12) Xu, Jianxiang
This thesis presents a novel approach to address the challenges encountered by a mobile manipulator engaged in dynamic locomotion within cluttered environments. The proposed technique involves the use of a dual monocular visual-inertial odometry (dual-VIO) strategy, which integrates two independent monocular VIO modules, one at the mobile base and the other at the end eﬀector (EE). These modules are intricately coupled at the low level of the factor graph to provide a robust solution. The approach leverages arm kinematics to treat each monocular VIO as a positional anchor in relation to the other, thereby introducing a soft geometric constraint during VIO pose optimization. This mechanism eﬀectively stabilizes both estimators, mitigating potential instability during highly dynamic locomotions. The performance of the proposed approach has been rigorously evaluated through extensive experimental testing, directly comparing it to the concurrent operation of independent dual Monocular VINS (VINS-Mono). The envisaged impact extends beyond the speciﬁc application, as the approach may lay the groundwork for multi-VIO fusion and enhanced system redundancy within the realm of Active-SLAM (A-SLAM).
Intermittent Interaction with Fabrication Devices
(University of Waterloo, 2024-09-12) Wall, Ludwig Wilhelm
Personal fabrication devices such as fused deposition modeling 3D printers are fairly slow, often produce lots of waste, and a fully automated fabrication process can take away the cognitive value of crafting something by hand. Interactive fabrication is instead often limited in scope or fidelity of the fabricated items as it requires constant user guidance. However, intermittent user interactions during the fabrication process are sufficient to alleviate downsides of the fabrication process, and direct user involvement can provide a similar personal connection as crafting does. This thesis explores the space of intermittent user interactions in between automated and interactive fabrication. An initial investigation enables physical user interactions during ongoing fabrication processes to reduce internal support material waste. A study with fabrication experts reveals sources of waste and a desire to intervene to take sustainable action. To address external support material as an additional source of waste we investigate more complex or more frequent user interactions. A technical evaluation quantifies the trade-off between increased user involvement and material savings. We investigate frequent interaction during fabrication by enabling sewing on unmodified 3D printers. Our technical evaluation situates the design space of fabricated seams next to traditional stitch patterns. We then examine the spectrum of user involvement during fabrication as a whole through parametric partial assembly tasks. The qualitative analysis of our survey reveal the perceived value of intermittent interaction, scheduling preferences, and design guidelines how systems can offer effective manual interaction options.
Effects of Trastuzumab on Alternative Splicing in HER2+ BT474 Breast Cancer Cells
(University of Waterloo, 2024-09-12) Piticaru, Benjamin
Alternative splicing (AS) is a fundamental process that enhances transcriptomic diversity and protein isoform complexity in eukaryotic cells. Deregulation of AS plays a critical role in various diseases, particularly cancer, where erroneous splicing patterns contribute to oncogenesis, tumor progression, and therapeutic resistance. Human epidermal growth factor receptor (HER)2, overexpressed in more than 20% of breast cancers, has clinical relevance in AS. The humanized monoclonal antibody (mAb) Trastuzumab has been used for decades to fight HER2+ breast cancer with positive results. However, there are many unknowns surrounding the mechanism of this drug and the effects it has on alternative splicing. Next generation long read sequencing technologies like Oxford Nanopore allow researchers to sequence full length transcripts. The ability to sequence long intron/exon spans and repeating regions enables long read sequencing technology to provide new insights into the AS patterns of genes. Identifying AS events is important for understanding changes in function and pathways affected by differing conditions (e.g., drug treatment, diseased cells). Software tools tailored to long read data like Long-read Isoform Quantification and Analysis (LIQA), Full-Length Alternative Isoform Analysis of RNA (FLAIR), FLAME, and Nanosplicer enhance data analysis abilities to detect AS events. They analyze sequencing data by mapping reads to genomes, identifying splice junctions, and clustering AS events. These tools then compare AS events between conditions (e.g., treated vs. untreated cells) to pinpoint significant AS variations. Accurate transcriptome sequencing is vital for research in drug development and diagnostics. The optimization of sequencing methods is an ongoing endeavour that requires continuous development. A chapter of this thesis compares the impact of omitting polyadenylation (poly(A)) enrichment in Oxford Nanopore Technologies (ONT)’s direct complementary deoxyribonucleic acid (cDNA) sequencing protocol to improve library prep efficiency and sequencing accuracy. Analysis indicated that excluding poly(A) selection does not negatively affect sequencing metrics but enhances read length and enables the sequencing of histone messenger ribonucleic acid (mRNA). Further, significant differences in poly(A) tail lengths between selected and unselected samples were found, suggesting a bias against shorter tails with enrichment. Gene composition and unique gene identification remain consistent across conditions. These findings support the potential advantages of omitting poly(A) enrichment in transcriptome sequencing while advocating for further validation. With optimized methods, the impact of Trastuzumab on AS profiles in BT474 and SKBR3 cell lines was tested. Using ONT long-read sequencing, significant AS events were identified in response to Trastuzumab treatment. The findings reveal differential isoform expression in genes involved in cellular signaling, RNA processing, and stress response pathways. Notably, nuclear paraspeckle assembly transcript 1 (NEAT1) and pre-mRNA processing factor 38B (PRPF38B) exhibited distinct AS patterns across multiple cell lines, suggesting HER2-mediated regulatory mechanisms. This study underscores the utility of ONT sequencing and high throughput data processing as an effective and efficient means for explaining complex AS landscapes affected by therapeutic treatments.
Use of Physiologically-Based Pharmacokinetic Modelling To Support Dose Optimization in The Critically Ill
(University of Waterloo, 2024-09-12) Dubinsky, Samuel
Critical care is a subspeciality of medicine that incorporates a multidisciplinary approach for patient care in a heterogeneous population. The wide array of etiologies to critical illness may result in disturbances to homeostasis and organ function. This variability in host-response may impact the pharmacokinetics (PK) of an individual, resulting in potential differences in drug exposure compared to a healthy counterpart. The high mortality rates of critically ill patients are thought in part to be due to altered drug exposure, resulting in suboptimal dosing or adverse effects. The complexity and heterogeneity of critical illness limits the feasibility of conventional PK studies for dose determination in this population. Furthermore, current “one-dose-fits-all” approaches in pharmacotherapy overlook the interplay between drug physicochemical properties and pathophysiology towards altered PK in the critically ill. Methods incorporating pharmacometrics have advanced our understanding of this relationship, however current approaches may require robust data sets to inform dose-exposure relationships and limit extrapolations to untested clinical scenarios. Methods incorporating physiologically-based pharmacokinetic (PBPK) modelling are encouraging to overcome some of the current challenges and knowledge gaps towards optimizing drug therapy in critically ill patients. PBPK models leverage mechanistic principles to incorporate knowledge of physiology and drug physicochemical properties to provide a simulation-based approach to drug PK. Knowledge of drug PK and physiology in healthy adults may be adjusted to account for differences in age (i.e adults to children), or disease (i.e. critical illness), to predict drug exposure. As these methods leverage known prior information, it enables a more proactive approach in predicting drug PK in clinical settings when data sampling is sparse, such as the critically ill. This thesis aims to apply state-of-the-art mechanistic modelling strategies to advance pharmacotherapy in critically ill adults and in children receiving extracorporeal life-saving technology. The objectives are to (1) analyze the PK data in critically ill children receiving continuous renal replacement therapy (CRRT), (2) evaluate the extraction of drugs via CRRT utilizing a closed-loop ex-vivo study design, and (3) develop PBPK models to optimize drug dosing in various presentations of critical illness. The first objective included a systematic review to evaluate our current understanding of drug PK in critically ill children receiving CRRT. Several knowledge gaps were identified, which were to be addressed within the second objective by incorporating a closed-loop study design to isolate the drug-CRRT circuit interaction. This ex-vivo¬ approach was the first of the holistic methodological solution towards which this thesis aims to achieve. Knowledge gained from the ex-vivo studies may be integrated into a PBPK model structure to provide a mechanistic understanding of drug PK, allowing for prospective dose predictions in untested scenarios. Within this work, it was identified that 40% of PK studies conducted in critically ill children receiving CRRT focused on antimicrobials. Furthermore, only 50% of studies included in the final analysis provided dosing guidance based upon PK findings in this population, representing several knowledge gaps to support clinicians in dosing guidance at the bedside. Anakinra and cefazolin were targeted as drugs of need for dosing guidance in patients receiving CRRT. Ex-vivo studies were conducted to investigate the drug-circuit interaction. Both anakinra and cefazolin, were efficiently removed from plasma upon the completion of the experiment, rendering a sieving coefficient of 0.34 and 0.31, respectively. A PBPK model for anakinra was developed to predict the PK in children receiving concurrent CRRT and extracorporeal membrane oxygenation (ECMO). Upon applying the results from the ex-vivo experiment, PBPK model predictions successfully described anakinra PK amongst critically ill children enrolled in a prospective, opportunistic study. Overall anakinra exposure was similar amongst children receiving ECLS compared to those who are not, supporting the hypothesis that renal dose adjustments in this population may not be required. The work herein this thesis seeks to advance the application of PBPK in supporting pharmacotherapy to a diverse group of critically ill patients. In doing so, a mechanistic representation of cefazolin drug concentrations in the central nervous system (CNS) through PBPK was performed. Cefazolin cerebrospinal fluid (CSF) concentrations were accurately predicted, and simulated CSF:plasma ratios fell within a 1.5 fold-error compared to observed values. Dosing simulations demonstrate that a continuous infusion of 10 g/day may be required to achieve pharmacodynamic response towards methicillin-susceptible Staphylococcus aureus in treating infections in the CNS. This thesis aims to articulate the multiplicity of PBPK to support dosing guidance in the critical care setting. Several knowledge gaps were identified, and the methods applied aim to address some of the current limitations of conventional PK studies in this population. PBPK modelling efforts such as these have the potential to improve generalizability, and efficiently conduct PK studies in a highly vulnerable patient population by reducing the number of participants required and applying a more proactive approach to dose determination in untested clinical scenarios.
Towards Feshbach Resonances in the S-WAVE Channel
(University of Waterloo, 2024-09-12) Del Franco, Paul
Ultracold molecules offer unique opportunities for studying quantum phenomena. This thesis presents work undertaken to repair and optimize an older experimental setup which last studied Feshbach resonances in the p-wave channel for ultracold Sodium-Lithium (NaLi) molecules. The primary focus of this work was on the process of repairing and reconfiguring the molecule machine back to a working state. This involved the repair of the optical systems which provide the laser light at the required frequencies. The characterization of the dual species atomic beam, leading to the replacement of the Sodium (Na) and Lithium (Li) sources. The re-optimization of the Zeeman slower current and light alignment. The alignment, configuration and optimization of the magneto optical trap, along with configuration of the transfer processes to the magnetic trap. Significant effort was dedicated to evaporative cooling, where we reached near quantum degeneracy temperatures for both species. With both ultracold gases, we optimized the transfer into an optical dipole trap where we could sweep a magnetic field to produce Feshbach molecules. Progress was made towards Stimulated Raman Adiabatic Passage (STIRAP) for efficient transfer into the triplet ground-state. Although the final step in the STIRAP process was not completed, the successful detection of Feshbach molecules was achieved. This work provides a solid foundation for future experiments, including the completion of the triplet ground-state molecule formation and enhanced stability which will allow for the exploration of s-wave Feshbach resonances in NaLi + NaLi collision complexes. This thesis contributes to the understanding of ultracold molecular interactions and offers insight into the problems encountered in the process of restoring and optimizing a complex experimental apparatus.
Attentional effects on visual-tactile crossmodal enhancement at early stages of cortical processing
(University of Waterloo, 2024-09-12) Salazar, Esteban
Sensory processing can be facilitated through bimodal interactions between relevant visual-tactile sensory inputs in order to achieve goal-oriented behaviours. While the specific neural mechanisms contributing to this modulation remain unclear, the dorsolateral prefrontal cortex (DLPFC) may have a role in regulating the observed processing facilitation seen in the somatosensory cortex (S1), though the extent is not yet clear. We used electroencephalography (EEG) to observe the temporal contributions of visual priming to the enhancement of S1 responses. We hypothesized that inhibiting DLPFC cortical activity would result in a diminished facilitation of tactile processing in S1 (represented by the P50), observed by a visual-tactile stimuli onset with a 200-300 ms time delay. Somatosensory modulation was inferred through amplitude and latency shifts in tactile event-related potentials (ERPs) recorded while participants performed a sensory integration task that required scaled motor responses dependent on the amplitudes of tactile and visual stimuli. Tactile stimuli were discrete vibrations (25 Hz) presented to the left index finger, visual stimuli were presented as a central horizontal bar on a computer screen at varying heights, and graded motor responses were made by squeezing a pressure-sensitive rubber bulb. Healthy adults completed a training session to become familiar with the stimulus-response relationships for both visual and tactile stimuli prior to completing a task where pairs of discrete stimuli with random amplitudes were presented: Tactile-tactile (TT, 500 ms each, 30 ms ISI), visual-tactile with a 200-300 ms delay (vTd 200-300 ms), and visual-tactile with a 300-400 ms delay (vTd 300-400 ms). Stimuli pairs were administered in a block setting, where each block contained 60 trials, with 20 trials for each of the discrete stimuli presented in a randomized order. The study design consisted of 10 blocks, with a short transcranial magnetic stimulation (TMS) intervention at the halfway mark. Participants were randomly assigned to either an intervention group (n=16) or control group (n=16) where TMS modalities of theta burst stimulation (TBS); continuous TBS (cTBS) was given to the intervention group and intermittent TBS (iTBS) was given to the control group, both applied to the right DLPFC. Results revealed that P50 upregulation observed in condition vTd (200- 300 ms) is significantly lower following cTBS on the right DLPFC but still greater than unimodal TT stimulation. Following iTBS, bimodal facilitation was observed in condition vTd (300-400 ms) for P50 and N70. These findings improve our understanding of the role right DLPFC plays regarding crossmodal facilitation observed in visual-tactile processing.
Towards Standardized Evaluation in Differentially Private Image Classification: A Critical Approach
(University of Waterloo, 2024-09-10) Kodeiri, Sara
This thesis critically examines differentially private machine learning (DPML) in image classification, addressing recent critiques about the effectiveness of current techniques and the validity of existing benchmarks. We focus on three key questions: the accuracy of current benchmarks in measuring DPML progress, the impact of public pre-training datasets on DPML model performance, and strategies for unifying future research efforts. Our study introduces standardized benchmark datasets and evaluation settings using two medical image datasets as private data sources. We assess various DPML methods across different scenarios, including those with no public data, training from scratch, and fine-tuning approaches. The main contributions include: proposing standardized benchmark datasets and evaluation settings, conducting a validation study of previous DPML techniques, and introducing a moderated public leaderboard to track progress in DPML. This research aims to provide a comprehensive assessment of DPML in image classification, offering insights into existing methods and suggesting future research directions in machine learning and privacy.
Fabrication of atomic force microscope probes with high aspect ratio silicon tips, silicon/silicon nitride cantilevers and stair-shaped handles
(University of Waterloo, 2024-09-10) Pan, Aixi
The atomic force microscope (AFM) is a versatile tool with promising applications in biomedical detection, optical spectroscopy, and material characterization. However, its widespread utilization faces challenges due to limitations in conventional fabrication methods of commercially available probes. Specifically, the standard tips may not meet the requirements for scanning deep or narrow structures accurately, and the rectangular handle design can block a portion of the reflected laser signal, leading to inconsistent feedback. Overcoming these limitations is crucial for expanding the utility and unlocking the full potential of AFM in diverse scientific and technological applications. In this thesis, we propose innovative strategies to enhance the scanning performance of AFM probes with high aspect ratio (HAR) tips and stair-shaped handles. Chapter 3 explores four distinct silicon (Si) AFM tip fabrication methods, each offering unique advantages and contributions to the field. The first method (Section 3.1) integrates non-switching pseudo-Bosch etching with wet sharpening techniques to achieve an exceptional aspect ratio of 1:135, marking a significant advancement in tip fabrication. The second method (Section 3.2) introduces an innovative approach utilizing tapered silicon oxide (SiO2) masks to fabricate Si nanocones with extraordinary apex measuring just 3.54 nm. The third method (Section 3.3) explores a novel two-step cryogenic etching process to yield a controllable tip profile with a slight taper angle of 2.2°. The fourth method (Section 3.4) combines the Bosch process with the pseudo-Bosch process, incorporating periodic oxygen (O2) shrinking steps. This approach achieves a remarkable tip apex sharpness of 20 nm, pushing the boundaries of nanofabrication capabilities. Chapter 4 details the fabrication of a stair-shaped Si handle to mitigate laser blocking. Two techniques are described: one leveraging the loading effect and RIE-lag to attain stage heights of 71 μm, 151 μm, 168 μm, and 287 μm, while the other employs pseudo-grayscale lithography with a titanium (Ti) mask, yielding final stages of 52 μm, 83 μm, 161 μm, and 211 μm. Both these methods are applicable for practical AFM probe fabrication without laser blocking. Chapter 5 delves into the mass fabrication of all-Si HAR AFM probes, merging tips fabricated by the O2 shrinking method with handles fabricated using the loading effect and RIE-lag. Furthermore, Chapter 6 explores the adoption of silicon nitride (SiNx) as an alternative to Si for cantilevers. Amorphous low-pressure chemical vapor deposition (LPCVD) SiNx offers benefits such as low spring constants and precise deposition control, resulting in thin and low-spring constant cantilevers. This configuration minimizes damage to the sample and tip, making it ideal for delicate samples. By combining a SiNx cantilever with a Si tip, the probe capitalizes on both tip apex and thin cantilever advantages, facilitating accurate AFM imaging with high resolution while preventing false images on fragile samples.
Design, Fabrication, and Testing of Assistive Mobility Solutions for Health Care Facilities
(University of Waterloo, 2024-09-10) Braimah, Maltiti
The movement of people, medication, and equipment in health care is a crucial part of the workflow, however, it is also an area that causes significant physical strain to the workers. This thesis proposes a design which is used to retrofit existing medical beds and carts with motorized modules that reduce the amount of force required for a worker to move equipment within hospitals and long-term care homes. The unique design makes use of mechatronic design principals to offer reliable and effective solutions to mobility problems in health care environments. Though available motorized beds and carts exist, they tend to be expensive as they are integrated in the bed and cart designs, thus requiring new equipment to be purchased. This is not always possible as it requires a large initial investment, while also introducing a foreign piece of equipment that workers must learn to use. The designed solution solves this by considering the existing design of medical equipment and adding technology to its frame to vastly reduce the costs. Adding onto the established medical designs allows for the electromechanical assembly to be the focus of the retrofit, coupling its additional functionality to familiar equipment. In this thesis, modules for improving beds and carts are designed, fabricated, and tested. The mechatronic design of the bed establishes a set of components and parameters that are successful in allowing for locomotion in indoor environments without the need for significant muscle exertion. The thesis scope details the mechanical design and electric and pneumatic component selection of the bed for a platform created to allow for manual, assistive, and autonomous controls. Using the experience and observations made while designing the bed platform, a more general assistive cart design is created. The cart offers a streamlined module that offers longitudinal torque assistance and can be paired with a wider range of medical equipment. An assistive handle allows for a seamless control experience on the assistive cart, wherein the assistive torque provided by the motorized module can be scaled by sensing the force exerted on the handle. This is observed to reduce the force needed to push a cart, and significantly decreases the effort needed to maneuver a heavy cart. The cart is also proven to be effective in its intended environment through limited prototype use in Grand River Hospital. An alternative cart is also designed, which can couple and detach from carts. This solution allows for a large fleet of similar carts to be powered using one product, rather than requiring a module for each cart.
Harmony in Highrises for Humans and their Loyal Companions: A canine inclusive design guideline for best practices
(University of Waterloo, 2024-09-10) Wong-Chun-Sen, Matthew
The idea of a house has always been present since the beginning and as humanity underwent evolutionary transitions over the course of history, so did the understanding of what a house is. Architecturally, while houses have modernized with regard to construction methods, materiality, and technology, the essence of a home seems to have remained the same. At first glance, many who read the previous statement do not see anything wrong with it, but take a second and dig a little deeper and you will begin to realize the underlying issues within. If modern homes can be defined as permanent or semi-permanent spaces used as residences for one or more human occupants, which is clearly driven by the necessities of people, then what happens when society evolves? If the people change, shouldn’t the essence of a home change with it and be reflected in the architecture? In the last few decades, there has been a noticeable surge in the canine population in North America, a trend that further accelerated in the wake of the 2021 pandemic (Institute 2022). While the concept of dog-inclusive architecture is still in its infancy, a comprehensive synthesis can be attained by exploring the realms of both canine behavioral psychology and selective architectural philosophies. Notable figures like Aldo Van Eyck and Jane Jacobs have contributed their spatial design philosophies in public realms (Jacobs 2011), serving as foundational references. Though they didn't specifically address dogs, Eyck, for instance, explored the concept of affordances – the possibility of action - through his playground designs (Strauven 2007). Additionally, and arguably more importantly, the work of Jakob von Uexküll, a Baltic German biologist, delves into animal behavior studies and introduces the concept of Umwelt, acknowledging the unique subjective worlds of animals and humans (Uexküll 2010). Uexküll argued that different species perceive and engage with their environments differently, emphasizing the importance of comprehending these distinct perspectives to truly understand animal experiences (Uexküll 2010). Therefore, to successfully create an architecture for both humans and dogs, we must first recognize the shift society underwent to coexist with dogs and then understand their Umwelt. This thesis aims to tackle the social neglect towards our dogs as their presence has grown in our society and challenges what the new fundamental ingredients are that structure the essence of what a modern home should be. Specifically, this research will investigate how to create a canine-inclusive design guide for high-density North American urban landscapes, by reimagining high-rise residential architecture in order to improve the everyday quality of life for our canine companions. Concepts such as inclusivity, sustainability, and building science will be considered to help guide the research, which eventually will culminate in a final design proposal in Toronto’s Liberty Village as a successful canine inclusive example. It is our responsibility as Architects to understand the fundamental distinction between a house and a home, recognizing that both are integral to the creation of successful designs. While this thesis attempts to offer a fresh perspective on architecture, it also seeks to emphasize the profound significance of the bond between humanity and our loyal canine companions - between “man-kind” and “man’s best friend”.
SYMMETRY OF HIP, KNEE AND ANKLE JOINT POWER DURING CYCLING WITH AND WITHOUT PAIN FROM KNEE OSTEOARTHRITIS
(University of Waterloo, 2024-09-10) Currie, Daniel
Knee osteoarthritis (OA) is one of the most common chronic conditions in Canada (Bombardier et al., 2011). Commonly, the pain caused by knee OA is unequal between knees, which can lead to asymmetry of movement and joint power in daily activities. With hip and knee extensors generating the greatest proportion of power during cycling, it is unclear how the body will compensate if there is a painful knee (Elmer et al., 2011). The purpose of this study was to investigate if seat height, workload and, any difference in knee pain, affected asymmetry of power between hips, knees and ankles during cycling. Asymmetry was defined as the difference between the dominant versus non-dominant leg. It was hypothesized that bilateral joint power would become more symmetrical as seat height increased, workload decreased and any difference in knee pain decreased. Twenty-six participants aged 45-75 years, with and without knee OA completed six cycling bouts at three seat heights (20°, 30°, 40° minimum knee flexion angle) and two workloads (40W and 75W) on a commercial fit-bike (Pro 1, Purely Custom, USA). Self-reported knee pain on the Numeric Pain Rating Scale (NPRS) was recorded for each knee before the first bout and after each bout. Three-dimensional kinematics were collected with a commercial motion capture system (Optotrak Certus, NDI, Canada) and synchronized three-dimensional kinetics were collected with commercial instrumented 3-axis pedals (Science to Practice, Slovenia). Joint angles and power were calculated in Visual3D (HAS-Motion, Germantown, USA) for the full bout. From that full bout, a one-minute portion was selected. Then revolutions in that one-minute were averaged to one pedal cycle using custom Python code. Seat height and workload did not have a significant effect on symmetry of joint power. A significant relationship was found between hip, knee and ankle joint power difference and knee pain difference. The leg with the more painful knee produced less power than the opposite leg (p < 0.001, both workloads). Evaluating asymmetry for each joint revealed an interesting pattern. The more painful knee produced more joint power than the less painful knee (p = 0.003, 75W workload). The hip and ankle in the leg with the more painful knee produced less power than the contralateral joints (p < 0.001, both workloads). These results demonstrated the relationship between lower limb joint power and knee pain during cycling and in turn, how these joints could contribute power in the presence of knee pain. These findings are also relevant to rehabilitation clinicians, because they show rehabilitation could aim to boost the power produced by healthy joints to offload a symptomatic joint.
Theory and Results on Restarting Schemes for Accelerated First Order Methods
(University of Waterloo, 2024-09-10) Pavlovic, Viktor
Composite convex optimization problems are abundant in industry, and first order methods to solve them are growing in popularity as the size of variables reaches billions. Since the objective function could be possibly non-smooth, proximal gradient methods are one of the main tools for these problems. These methods benefit from acceleration, which uses the memory of past iterates to add momentum to the algorithms. Such methods have a O(1/k^2) convergence rate in terms of function value where k is the iteration number. Restarting algorithms has been seen to help speed up algorithms. O'Donoghue and Candes introduced adaptive restart strategies for accelerated first order methods which rely on easy to compute conditions, and indicate a large performance boost in terms of convergence. The restart works by resetting the momentum gained from acceleration. Their strategies in general are a heuristic, and there is no proof of convergence. In this thesis we show that restarting with the O'Donoghue and Candes condition improves the standard convergence rate in special cases. We consider the case of one-dimensional functions where we prove that the gradient based restart strategy from O'Donoghue and Candes improves the O(1/k^2) bound. We also study the restarting scheme applied to the method of alternating projections (MAP) for two closed, convex, and nonempty sets. It is shown in Chapter 6 that MAP falls into the convex composite paradigm and therefore acceleration can be applied. We study the case of MAP applied to two hyperplanes in arbitrary dimension. Furthermore we make observations as to why the restarts help, what makes a good restart condition, as well as what is needed to make progress in the general case.
Deep Learning-Based Probabilistic Hierarchical Reconciliation for Hydrological and Water Resources Forecasting
(University of Waterloo, 2024-09-10) Jahangir, Mohammad Sina
Accurate, probabilistic, and consistent forecasts at different timescales (e.g., daily, weekly, monthly) are important for effective water resources management. Considering the different timescales together as a hierarchical structure, there is no guarantee that when forecast models are developed independently for each timescale in the hierarchy, they will result in consistent forecasts. For example, there is no guarantee that one-seven day(s) ahead forecasts from one model will sum to a weekly forecast from another model. Significant efforts have been made in the time-series forecasting community over the last two decades to solve this problem, resulting in the development of temporal hierarchical reconciliation (THR) methods. Until recently, THR methods had yet to be explored for hydrological and water resources forecasting. The main goal of this research is to introduce THR to the field of hydrological and water resources forecasting and to merge it with the latest advancements in deep learning (DL) to provide researchers and practitioners with a state-of-the-art model that can be used to produce accurate, probabilistic, and consistent multi-timescale forecasts. To achieve this goal, this research follows three interconnected objectives, each including a main contribution to the field of DL-based hydrological forecasting. In the first main contribution of this research, the potential of THR to produce accurate and consistent hydrological forecasts was verified for the first time in hydrology through a large-scale precipitation forecasting experiment using 84 catchments across Canada. Three THR methods were coupled with three popular time-series forecasting models (exponential time-series smoothing, artificial neural network, and seasonal auto-regressive integrated moving average) for annual precipitation forecasting at monthly (12-steps ahead), bi-monthly (6-steps ahead), quarterly (4-steps ahead), 4-monthly (3-steps ahead), semi-annual (2-steps ahead), and annual (1-step ahead) timescales. It was confirmed that not only does utilizing THR guarantee forecast consistency across all timescales, but it can also improve forecast accuracy. DL models are increasingly being used for hydrological modeling, particularly for lumped simulation, due to their ability to capture complex non-linear relationships within hydrological data as well as their efficiency in deployment. Likewise, the application of DL for hydrological forecasting has gained momentum recently. DL models can extract complex patterns from meteorological forcing data (e.g., precipitation) to forecast future streamflow, often leading to forecasts that are more accurate than current conceptual models. However, due to uncertainty in the phenomena affecting hydrological processes, it is necessary to develop accurate probabilistic forecast models to provide insights for informed water management decisions. In the second main contribution of this research, two novel state-of-art sequence-to-sequence probabilistic DL (PDL) models were developed, tested, and applied for short-term (one-seven day(s) ahead) streamflow forecasting in over 75 catchments with varied hydrometeorological properties across both the continental United States (CONUS) and Canada. The two designed models, namely quantile-based encoder-decoder and conditional variational auto-encoder (CVAE) showed superior performance compared to the benchmark long-short-term memory (LSTM) network considering forecast accuracy and reliability. Specifically, CVAE, a generative DL model that can estimate magnitudes of different sources of uncertainty (e.g., aleatoric, epistemic), proved to be effective in producing reliable forecasts for longer forecast lead times (three-seven days ahead). Given the introduction of THR to the field of hydrological forecasting through the first main contribution, there is no guidance on how to couple THR with the latest advancements in DL, especially PDL, to produce accurate, and consistent probabilistic hydrological forecasts. Furthermore, existing methods for combining THR with DL models, particularly PDL models, suffer from several limitations. Firstly, almost all approaches treat THR as a post-processing step. Secondly, existing THR methods often lack adaptability, meaning they are unable to adjust properly to changing data distributions or new information. Finally, there is limited research on implementing probabilistic THR, a crucial aspect for making probabilistic forecasts consistent. As the third main contribution, a hierarchical DL model (HDL) was introduced where THR was integrated directly into the DL model. Specifically, a custom THR layer was developed that can be combined with any DL model, much like a LSTM layer or a linear layer, to produce the proposed HDL. This integrated approach (via the new THR layer) allows any DL model to leverage temporal information across multiple timescales during training, perform probabilistic THR, and be efficient for real-time application. Furthermore, the proposed HDL is based on auto-regressive normalizing flows, a state-of-the-art generative DL model that is more flexible than CVAE in that it can non-parametrically estimate the probability distribution of the target variable (e.g., streamflow). HDL was tested on more than 400 catchments across CONUS for weekly streamflow forecasting at daily (seven-steps ahead) and weekly (one-step ahead) timescales. The performance of HDL was benchmarked against LSTM variants. HDL produced forecasts that had substantially higher accuracy than the LSTM variants and simultaneously generated consistent forecasts at both daily and weekly timescales, without the need for post-processing (as in the vast majority of THR methods). The implementation of THR as a neural network layer allows it to be seamlessly combined with other DL layers. For example, the new THR layer can be coupled with physics-based differentiable routing layers for multi-timescale distributed hydrological forecasting. It is expected that HDL will serve as a benchmark upon which future THR methods will be compared for streamflow forecasting. Furthermore, given the generality of the approach, HDL can be used for forecasting other important variables within hydrology (e.g., soil moisture) and water resources (e.g., urban water demand), as well as other disciplines, such as renewable energy (e.g., solar power).
Towards Dipole Blockade Controlled-NOT Gate Using Ultracold Molecules
(University of Waterloo, 2024-09-10) Byres, Megan
Quantum computing is a promising field that aims to achieve large increases in computational speed by taking advantage of the unique properties of quantum physics. There are many proposals for how it can be implemented in the real world, one of these being the use of Rydberg atoms. Rydberg atoms are limited by the instability of the highly excited Rydberg states, resulting in lifetimes measured in the hundreds of microseconds. Molecules can be used to perform quantum gates with a similar method to Rydberg atoms, and their lifetimes can be several orders of magnitude longer than the lifetimes of Rydberg atoms. This thesis builds on a previous work in which the ideal fidelity of this method was calculated by investigating various real world factors and their implications for the feasibility of molecules as a platform for quantum computing. Additionally, it discusses many changes and improvements to the ovens and larger vacuum system designed to perform these experiments.
A Bridge Over Troubled Waters: Should Canada Allow Mental Illness as the Sole Underlying Medical Condition for Accessing Medical Assistance in Dying?
(University of Waterloo, 2024-09-10) Rossi, Michael
Canada’s Medical Assistance in Dying (MAID) regime was set to expand its eligibility criteria on March 17, 2024, to allow mental illness as an acceptable sole underlying condition (MAID MI-SUMC) until Bill C-62 rapidly received Royal Assent in late February 2024, delaying this expansion until March 17, 2027. Those who oppose allowing mental illness as a sole condition for MAID often cite fears of what would happen in Canada should MAID MI-SUMC become legal. However, proponents counter these claims with relevant facts, statistics, and information to demonstrate that MAID MI-SUMC can be effectively incorporated in Canada. This study uses evidence from countries with MAID but that do not allow MI-SUMC (Australia, New Zealand, and the United States), and countries with MAID MI-SUMC (the Netherlands, Belgium, and Luxembourg) to examine why these countries oppose and allow this legislation, respectively. Using this evidence, this Thesis then focuses on the Canadian context to address the concerns of opponents on why they are adamant that MAID MI-SUMC should not become an acceptable part of Canada’s MAID regime. Incorporating studies conducted by proponents and evidence from permissive jurisdictions helps to find that opponents’ fears are unsubstantiated. Using a rights-based approach, this Thesis observes that the rights of individuals who solely suffer from a mental illness and wish to access MAID are infringed upon, resulting in a call for legislative changes to occur.
Fabrication of Silicon Out-of-Plane Microneedles for Potential Drug Delivery and Interstitial Fluid Extraction
(University of Waterloo, 2024-09-10) Hu, Wenhan
Microneedles represent a successful application of MEMS technology, forming minimally invasive platforms for transdermal drug delivery, body fluid sampling, and diagnostics. Silicon microneedles, in particular, are favored due to their exceptional mechanical strength and biocompatibility. This thesis focuses on the three different fabrication methods of silicon microneedles using MEMS techniques. Initially, we fabricated silicon out-of-plane cone-shaped hollow microneedles with sharp apexes and off-axis pores. This process involved backside hole etching and frontside pillar etching via the Bosch process, followed by pillar sharpening using a HF-HNO3 mixed solution. The resulting microneedles were 160 μm high. However, to penetrate the epidermis and access abundant body fluids for health monitoring systems, taller microneedles longer than 500 μm are required. Fabricating these higher microneedles proved challenging due to difficulties in achieving uniform sharpening through wet etching. To address this, we developed a novel method for fabricating silicon out-of-plane hollow microneedles with beveled tips. This method included frontside slope etching, backside hole etching, and frontside pillar etching, combining anisotropic wet etching and dry etching (Bosch process). The resulting microneedles were approximately 600 μm tall with beveled sharp tips. We tested various fundamental functions of these microneedles by connecting the chip to a syringe using a 3D-printed applicator, successfully demonstrating liquid extraction, liquid injection, and simulated drug delivery process. To minimize the impact of inevitable lateral etching during frontside pillar etching in the Bosch process, we proposed sacrificial structures surrounding the pillars to shield them from lateral etching. Testing two types of sacrificial structures, we found both structures could effectively reduce lateral etching, enabling the fabrication of 370 μm high ring pillars with vertical sidewalls. Additionally, grayscale lithography combined with subsequent Bosch processing presents an effective and flexible method for fabricating complex 3D structures like bevels. We first acquired contrast curve for the photoresist before grayscale lithography. Then we used this technique integrating frontside slope etching and frontside pillar etching into a single step, resulting in the fabrication of hollow microneedles measuring 325 μm in height.
Spatial Storytelling Through Augmented Reality: Toronto’s Water and the Technocene
(University of Waterloo, 2024-09-09) Park, Justin Kyung In
This thesis utilizes augmented reality to illustrate visual and spatial stories of the Technocene regarding water in Toronto. The thesis begins by studying the etymology of the Technocene, and it establishes the need for storytelling through this definition. The thesis then assesses different visual storytelling methods to conclude that Augmented Reality(AR) is a practical approach when discussing the Technocene. After determining the need for Augmented reality, the various techniques and technologies of performing Augmented Reality are evaluated to create a technological foundation before designing the stories. The stories of water are then researched and developed into an AR experience by using the criteria to tell a situated and pedagogical story of the Technocene. Throughout the development of the thesis, a criteria system was developed to help guide the design of the outcome for the thesis. Starting with pedagogical storytelling, the thesis utilizes the criteria to review existing research on situated storytelling and formulate a guideline for situated urban storytelling. These metrics are used to review visual storytelling mediums. Derivatives of these two metrics are also used in literature reviews of AR software to help guide the types of AR technologies and software used in designing the thesis. Finally, to assess the designed stories, all of the developed criteria are used to help explore AR opportunities for this thesis. Toronto and its stories of water were chosen for their significance in terms of culture, ecosystem, and geography. Technocene is a multilayered framework that incorporates technology driven by social activities or issues to understand which environmental outcomes are induced by such activity. To visualize these stories, the site had to be an environment that has undergone dense urban growth to easily locate elements of the Technocene. Toronto has abundant city infrastructure and buildings built of engineered materials, being an appropriate site to spawn these stories. Four specific stories of lost rivers, porosity, flooding, and naturalization were chosen because of water’s crucial role in the ecosystem and the geographical abundance of water in Toronto.
Asymmetric Clustering in Federated Continual Learning
(University of Waterloo, 2024-09-09) Zhang, Zehao
Asymmetric clustering represents a critical yet under-explored challenge in Clustered Federated Learning (CFL). Existing methods often compromise data utilization or model accuracy by either separating devices with different data quality into distinct clusters or merging all devices into a single cluster. The need for asymmetric clustering arises in practical scenarios where not all devices contribute equally due to varying data quality or quantity. For example, in healthcare, devices at a research hospital might generate high-quality medical imaging data compared to a small clinic. Asymmetric clustering allows high-quality data sources to enhance the learning of models on devices with lower-quality data without the need for reciprocity, which is crucial in such imbalanced environments. We introduce a novel federated learning technique that enables selective contributions from some devices to others' model training without requiring equal give-and-take. Crucially, our approach excels in the Federated Continual Learning (FCL) setting by addressing temporal heterogeneity and concept drift through its ensemble features. Through detailed empirical evaluations, we validate that our approach not only efficiently generates high-quality asymmetric clustering but also significantly enhances performance in continual learning settings. This adaptability makes it highly suitable for real-world applications where data distributions are not static but evolve over time.

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