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Recent Submissions
Commuting, Spatial Allocations, and Inequalities
(University of Waterloo, 2024-11-14) Yu, Aidi
This thesis examines the complex relationships between commuting times, wage disparities, gender differences, and urban spatial distribution, through the lens of three interconnected studies. The first chapter investigates the relationship between commuting times, wages, and the gender wage gap, with a focus on controlling for occupational choice endogeneity. Using data from the American Community Survey (ACS) and the Occupational Information Network (O*Net), the study highlights how gender differences significantly influence the positive correlation between commuting time and wages, especially among full-time working homeowners in U.S. cities. Through quantile regression analysis, it reveals that while men's returns on commuting diminish as income rises, the commuting gender gap remains relatively constant across the wage distribution. The second chapter delves deeper into the gendered impacts of commuting on wage disparities, addressing the endogeneity of commuting times. By constructing instrumental variables based on exogenous city characteristics from the 2016 ACS, the study isolates the causal effects of commuting on wages. The findings suggest that marital status drives the gender difference in commuting premiums, with married women and single men demanding higher wages to compensate for longer commutes. This chapter contributes to a broader understanding of wage-commute trade-offs and the socio-economic consequences of commuting time. The third chapter explores the interplay between job flexibility, residential location sorting, and wage determination through a monocentric city model. The model incorporates both high- and low-skilled workers and employs a bid-rent framework to determine housing prices and the spatial distribution of labour. The study finds that high-skilled workers' job flexibility significantly impacts their commuting decisions and urban spatial sorting patterns. In low-flexibility settings, high-skilled workers tend to live near the central business district, earning higher wages to offset the high cost of central real estate and commuting. Conversely, increased job flexibility enables these workers to relocate to more distant, affordable areas, thereby reducing the equilibrium skill premium. Together, these chapters provide a comprehensive analysis of how commuting, gender, and job flexibility interact to shape wage patterns and urban spatial structures in contemporary cities.
Ocular Effects of Scleral Lens Wear on Dry Eye Patients
(University of Waterloo, 2024-11-14) Otchere, Heinz
Purpose: Dry eye disease (DED) is among the most complex ocular surface diseases to treat. Complaints of ocular discomfort and dryness are common in DED patients and in contact lens wearers. The use of SL to restore the integrity of the ocular surface in a more severe DED has become increasingly accepted among eye care practitioners. However, little is known about this treatment regimen and its impact on ocular surface in mild to moderate DED. Also, the potential impact of coated SL designs incorporating Hydra-PEG (polyethylene glycol) technology on ocular surface health has not yet been fully investigated. This thesis aimed to address this gap in knowledge and determine whether SL (uncoated or Hydra-PEG) could be used as a viable option for patients who are experiencing milder forms of DED. Over the course of the study, participants were asked to complete DE questionnaires; lens settling and vision, corneal thickness, osmolarity and matrix metalloproteinase 9 (MMP-9) in the pre-corneal tear film were investigated. The study also examined the relationship between the respective parameters and compared the two lens pairs.
Methods and Materials: The study was a prospective, double-masked, randomized, dispensing, crossover clinical trial involving five visits, where 20 subjects with mild to moderate dry eye disease (DED) were enrolled. Eligibility of the participants was confirmed following the Tear Film and Ocular Society (TFOS) Diagnostic Report in the first visit: presence of symptoms using the Ocular Surface Disease Index (OSDI) and Standardized Patient Evaluation of Eye Dryness (SPEED) questionnaires (OSDI ≥ 13, SPEED ≥ 4), plus osmolarity values (> 308 mOsmol/L in either eye or interocular difference of > 8 mOsmol/L) and or a positive MMP-9 result (using InflammaDry® test kit) or both. The second visit involved randomization and dispensing of customized hydra-PEG coated or uncoated SL, where each pair of lenses were worn on a daily wear basis for four weeks. Prior to dispensing the lenses, high contrast (HCVA) and low contrast acuities (LCVA) were recorded. The central corneal clearance (CCC) was measured with VisanteTM OCT to determine lens settling over time. Two standard clinical questionnaires (contact lens impact on quality of life (CLIQ) and contact lens dry eye questionnaire 8 (CLDEQ-8)) and an internally developed wearing habit and subjective rating questionnaire were provided to subjects and completed. The third visit (after 4 weeks) involved follow-up of the first randomized SL, where the lenses were evaluated, and clinical measurements repeated. A wash-out period of at least 48 hours was allowed before dispensing (visit 4) and follow-up (visit 5) of the other pair of SL, using the same procedures, measurement protocols and visit schedule. The SL used in the study were Zen™ RC (Alden Optical, Bausch & Lomb, Lancaster, NY, USA) available in only two diameters (14.80 and 15.40 mm), with a central thickness of 250 µm.
Results: Eighteen females and two males, mean age 29.10 ± 7.48 years, participated in the study. The overall OSDI and SPEED scores were 36.45 ± 17.08 and 12.50 ± 4.03 respectively. There was no significant difference in the CLIQ and CLDEQ-8 scores between uncoated and coated SL. In terms of wearing habit and subjective ratings, no statistically significant differences were observed in any of the parameters (wear time, dryness, burning, vision, and comfort). This suggests that the use of hydra-PEG coated SL did not show greater performance compared to the uncoated SL. The central corneal clearance (CCC) at the dispensing visit was 260 ± 40 (range: 200 - 300 µm) for both lens pairs. This significantly reduced to 190 ± 40 µm (lens settling: 70 ± 42 µm) for the uncoated SL and 200 ± 30 µm (lens settling: 70 ± 43 µm) for the coated SL at the follow-up visits, (all, p < 0.001). Comparing the CCC for the two lens pairs at the follow-up visits, no significant difference was observed, thus, the lens pairs settled at similar rates. In terms of HCVA and LCVA between the two lens pairs at both the dispensing and follow-up visits, there were no significant differences between them. Also, no significant correlations were found comparing the CCC with HCVA and LCVA of each lens pair at both visits. The CCT at the baseline and follow-up visits were: baseline: 560.55 ± 32.28 µm, post wear of uncoated SL: 557.65 ± 32.10 µm, and post wear of coated SL: 560.50 ± 34.02 µm. There were no significant differences for either lens type for central corneal thickness (CCT) at the baseline and follow-up visits (all, p > 0.05). Also, no significant correlations between CCC and CCT were observed at baseline or follow-up visits. These results demonstrated there were minimal corneal hypoxic effects when these SL were worn on a daily wear basis. For osmolarity measures, there was a statistically significant difference between the baseline and follow-up visit for the coated lenses (311.00 ± 14.86 vs 302.85 ± 7.96 mOsmol/L; p = 0.04). While this is statistically significant, the clinical relevance of this small difference remains questionable. Comparing the two lens pairs, no significant difference was found at all visits. The inflammaDry® test results indicated that 80 % of the participants tested positive for elevated MMP-9 at the baseline visit. There was a reduction in MMP-9 positive test results following the SL wear, however, there were no significant differences between the baseline and follow-up visits for each lens pair. Comparing the two lens pairs, no significant difference was observed. For either lens, no correlation was observed between osmolarity and MMP-9 test results.
Conclusion: There is a potential for using SL to manage symptoms in subjects suffering from mild to moderate DED, as the overall wearing habit and subjective ratings showed > 70 % of lens tolerance among the study cohort. SL wear over the month of wear in this cohort induced little change to the cornea or conjunctival tissue. Furthermore, SL may appear to marginally reduce tear film osmolarity, however, further studies are needed to confirm this result and its impact on subjective dryness. The clinical phenomenon of lens settling needs further investigation, especially on its impact on conjunctival morphology. In this cohort of subjects of mild to moderate DED, the hydra-PEG coating technology did not show superior performance over the uncoated lens for any of the factors assessed.
Keywords: dry eye disease. scleral contact lens, hydra-PEG, osmolarity, inflammadry, cornea
Safe Memory Reclamation Techniques
(University of Waterloo, 2024-11-14) Singh, Ajay
This dissertation presents three paradigms to address the challenge of concurrent memory reclamation, manifesting as use-after-free errors that arise in concurrent data structures using non-blocking techniques. Each paradigm aligns with one of our three objectives for practical and safe memory reclamation algorithms.
Objective 1: Design memory reclamation algorithms that are fast, have a bounded memory footprint, and are easy to use — requiring neither intrusive changes to data structures nor specific architecture or compiler support. These algorithms should also deliver consistent performance across various workloads and be applicable to a wide range of data structures. To achieve this, we introduce the neutralization paradigm with the NBR (Neutralization-Based Reclamation) algorithm and its enhanced version, NBR+ (Optimized Neutralization-Based Reclamation). These algorithms use POSIX signals and a lightweight handshaking mechanism to facilitate safe memory reclamation among threads. By relying solely on atomic reads and writes, they achieve bounded garbage and high performance with minimal overhead compared to existing algorithms. They are straightforward to implement, similar in reasoning and programming effort to two-phased locking, and compatible with numerous data structures.
Objective 2: Eliminate the asymmetric synchronization overhead in existing reclamation algorithms, which often incur costly memory fences while eagerly publishing reservations, as seen in algorithms like hazard pointers and hazard eras. We propose the reactive synchronization paradigm, implemented through deferred memory reclamation and POSIX signals. This mechanism enables threads to privately track memory references (or reservations) and share this information on demand, using the publish-on-ping algorithm. This approach serves as a drop-in replacement for hazard pointers and hazard eras and includes a variant (EpochPOP) that combines epochs with the robustness of hazard pointers to approach the performance of epoch-based reclamation.
Objective 3: Completely eliminate the batching common in current reclamation algorithms to allow immediate memory reclamation, similar to sequential data structures, while maintaining high performance.
We introduce Conditional Access, a hardware-software co-design paradigm implemented in a graphite multi-core simulator. This paradigm leverages cache coherence to enable efficient detection of potential use-after-free errors without explicit shared-memory communication or additional coherence traffic. Conditional Access provides programmers with hardware instructions for immediate memory reclamation with minimal overhead in optimistic data structures.
To validate our claims, we designed and conducted extensive benchmark tests to evaluate all proposed algorithms on high-end machines under various scenarios. We paired these algorithms with several real-world concurrent data structures, representing various memory access patterns, and compared their time and space efficiency against numerous state-of-the-art memory reclamation algorithms, demonstrating significant improvements.
Metal Concentrations in an Arctic Wastewater Wetland: Insights and Innovations from Baker Lake, Nunavut, Canada
(University of Waterloo, 2024-11-14) McPhedran, Bronte
The unique climatic conditions and isolated geographies of Arctic communities present distinct challenges for municipal wastewater treatment. Most communities depend on natural wetlands to provide passive treatment of wastewater; however, increased pressure on these systems from prolonged use, climate change, and intensifying human activity has resulted in the recent development of northern-specific standards for wastewater. These standards, among other objectives, aim to maintain healthy fish populations and diverse aquatic ecosystems, while calling for community consultation, integration of traditional knowledge, and adherence to federal and territorial regulations. A passive wastewater treatment system near Baker Lake, NU, served as a case study to address knowledge gaps regarding ecosystem function and trace metal dynamics in abiotic and biotic ecosystem compartments subject to wastewater inputs. Additionally, this research explored a method for time-resolved analysis of contaminant histories, which is particularly valuable in environments lacking baseline data or where regular monitoring is challenging, including in the Arctic.
Between the summers of 2019 and 2021, a series of lakes that represented wastewater-affected and reference systems were sampled for water, sediment, and fish. Water from wastewater-affected lakes had elevated concentrations of metals (e.g., Mn, Fe, Cu) and increased primary productivity (as inferred from chlorophyll-a concentrations), with persistent hypereutrophic conditions; extremely low dissolved oxygen levels were recorded in the lake closest to wastewater influent. Although sediment analysis near wastewater sources indicated higher levels of Cu and Zn, overall sediment chemistry was similar across all sites. The influence of wastewater on the trophic ecology of Burbot (Lota lota) was minimal, whereas Arctic grayling (Thymallus arcticus) had more enriched (i.e., less negative) δ13C at wastewater-affected sites, suggesting altered energy pathways in lakes that receive nutrients from wastewater. Analyses of metals in muscle tissue revealed lower, although not significant, concentrations of methylmercury – the toxic, biomagnifying form of mercury - in fish from wastewater-affected sites compared to those from reference sites. These lower concentrations of methylmercury in fish muscle tissue occurred despite higher concentrations in abiotic media, potentially because of somatic growth dilution, but more research is necessary. Analyses of trace metals in otoliths revealed distinct multi-element otolith signatures (i.e., Zn, Mn, Cu, Fe, and Pb) between wastewater-affected and reference lakes, and significantly greater concentrations of Fe in a lake receiving wastewater across two reconstructed periods of growth. Together, findings from this research not only fill knowledge gaps regarding the influence of municipal wastewater on cold, oligotrophic freshwater systems in the subarctic, but also highlight the potential uses and limitations of otoliths as markers of wastewater exposures.
Microbiology of bentonite clay relevant to a deep geological repository for used nuclear fuel
(University of Waterloo, 2024-11-12) Beaver, Rachel
Nuclear energy is an important source of energy globally, but results in the production of used nuclear fuel. When removed from a nuclear reactor after its useful lifetime, used nuclear fuel is still highly radioactive and must be stored safely for approximately one million years until it returns to the radioactivity level of naturally occurring uranium ore. Canada, along with other countries that have an inventory of used nuclear fuel, is in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. In this system, used nuclear fuel, itself a stable solid, will be stored in copper-coated steel used fuel containers, and placed in bentonite clay buffer boxes made of highly compacted Wyoming MX-80 bentonite. Buffer boxes would then be stacked in placement rooms approximately 500 m below ground in a suitable host rock with spaces between buffer boxes and host rock filled in with a granulated form of bentonite referred to as gapfill material. To ensure the longevity of a DGR, it is important to consider the role that microorganisms could play, particularly through contributing to corrosion of used fuel containers through a process termed microbiologically influenced corrosion. Expected to dominate occurrences of microbiologically influenced corrosion under anoxic conditions, sulfate-reducing bacteria (SRB) are a primary target of research, but rarely live in isolation, thus necessitating the study of microbial communities that could live in the bentonite clay surrounding used fuel containers on a broader scale.
Due to the potentially detrimental role that some microorganisms could play in a DGR, a goal in designing a DGR is to compact bentonite, a type of swelling clay, to a sufficiently high dry density that microbial growth is suppressed upon saturation. The first goal of this thesis was to investigate the bentonite dry density necessary to suppress microbial growth in Wyoming MX-80 bentonite under oxic conditions and gapfill material under both oxic and anoxic conditions. A set of pressure vessel experiments demonstrated suppression of microbial growth under oxic conditions in bentonite compacted to a minimum dry density of 1.4 g/cm3. Under anoxic conditions, growth of heterotrophs was suppressed in pressure vessels with a minimum dry density of 1.45 g/cm3, but culturable SRB persisted in abundances higher than the as-received bentonite starting material in the outer layers of all pressure vessels throughout the full one-year experiment. Additional experiments were conducted to explain the increase in abundance of SRB, which had not previously been observed in other studies. These experiments suggested that the increase in abundance of SRB was likely not inherent to the gapfill material, nor was there evidence for it being a result of differences in SRB medium or in amounts of trace oxygen between studies. In both oxic and anoxic pressure vessels, an initial increase in abundance of culturable heterotrophs was observed prior to complete saturation, presumably as water became available but swelling pressure remained sufficiently low to allow for their growth. Although previously proposed to potentially be associated with a recovery from the viable but not culturable state rather than growth, a follow-up experiment suggested that the initial increase in abundance of culturable heterotrophs was likely a reflection of growth (i.e., cell division).
Dry density is an important consideration in DGR design, but it is not the only physical property that could influence microbial growth within a DGR. Temperature is expected to fluctuate from natural subsurface temperatures of <20°C to temperatures as high as 94°C, and little research has been conducted to explore the potential for microbial growth in bentonite at these elevated temperatures. This thesis includes experiments testing the abundance and community composition of microorganisms adapted to a variety of temperatures in as-received and hydrated bentonite. The results showed a low abundance of culturable microorganisms that survived incubation at 60°C, but 16S rRNA gene profiles dominated by presumably unculturable representatives of the thermophilic family Thermoactinomycetaceae. Hydrated bentonite was additionally incubated at temperatures of 75, 90, and 105°C, but DNA sequencing results did not show a shift in community composition from as-received bentonite, suggesting that the natural as-received bentonite microbial community may not include members adapted to these very high temperatures.
Lab-scale experiments allow for testing of very specific DGR-relevant conditions (e.g., dry density and temperature) and the effect these have on microbial community abundance and composition. However, a DGR is being designed to exist for upwards of one hundred thousand years, which is not a realistic timescale for any experiment. To circumvent this limitation, one approach is to couple lab-scale experiments to the study of natural analogues, which have naturally existed for DGR-relevant timeframes. This thesis presents a study of the Tsukinuno bentonite deposit in Japan, which can serve as a natural analogue to DGR bentonite. In this study, sequencing of DNA extracted from bentonite revealed microbial communities dominated by sequences associated with Thiobacillus, Hydrogenophaga, Comamonadaceae, and Pseudomonas. Although differences in community composition were observed between samples, microbial communities were relatively similar for all four studied cores and at all depths into the clay bed. A series of geochemical parameters were measured to help identify factors that may influence microbial community composition. The abundance of culturable anaerobic heterotrophs was positively correlated with the concentration of nitrate, which could be used by anaerobes for denitrification, and the abundance of culturable aerobic and anaerobic heterotrophs was negatively correlated with the abundance of the clay mineral montmorillonite, increased concentrations of which would increase the swelling capacity of the bentonite. The results presented throughout this thesis will together be useful for incorporation into future models of microbial activity within a DGR and can ultimately be used to inform DGR design.