VictorJuiz/thesis huggingface dataset:
The ‘Paper and Pencil’ Operations of Interdisciplinarity: Interdisciplinary Integration as Information Practice

Interdisciplinary research produces innovative solutions to complex problems by integrating information from multiple disciplines. At present, despite the positioning of integration as the defining activity of interdisciplinarity, interdisciplinary work tends to be evaluated on the basis of final outcomes, at the expense of a clear understanding of what interdisciplinary integration actually is. This thesis problematizes this outcome focus and makes the case for a practice-focused approach, using conceptual modeling and network analysis of the data holdings of in-progress interdisciplinary research projects to explore how researchers integrate data from multiple disciplines. These case studies demonstrate that even in ostensibly interdisciplinary research, data tend to be analyzed in disciplinary silos, leaving any integration that occurs to take place in an ad-hoc, after-the-fact fashion. The adverse implications of this finding on interdisciplinarity are discussed, and a framework for the repositioning of integration as a research practice is proposed as a potential solution.

Keywords: Information Practice
Interdisciplinarity
Meta-Research
Research Practice
Advisor: Alexander, Rohan
Anti-degradative Self-etch Adhesive to Preserve Bonded Interfaces

Objective: Investigate the effect of adding drug-silica co-assembled particles containing Octenidine Dihydrochloride (DSPs) into a commercial self-etch adhesive (SE) on the degradation of resin-dentin interface aged in simulated human salivary esterase (SHSE). Methods: Miniature short rod specimens (mini-SR) were fabricated from human dentin bonded to composite using unmodified commercial SE (negative control), SE+10%w/w calcined particles without drug (CDSP-SE) (positive control) or SE+10% w/w DSPs (DSP-SE) (experimental). Specimens were tested for interfacial fracture toughness (FT) and fracture mode after incubation for 0, 30, or 180-days in SHSE. Media were analyzed for presence of resin degradation by-product 2,2-Bis[4(2,3-hydroxypropoxy)phenyl]propane (BisHPPP). Results: FT among all specimens and periods were similar (p>0.05). Fracture plane for all groups moved from dentin to resin layer over time, with the control groups significantly more into resin and with more BisHPPP in their media (p<0.05). Conclusion: The incorporation of DSPs and CDSPs into SE appears to preserve the resin layer of SE interfaces.

Keywords: Hybrid layer preservation
interfacial fracture toughness
resin
self-etch adhesive
Advisor: Finer, Yoav YF
The Effects of Seasonality on Ecological Interactions Between Fishes in Different Thermal Guilds

Seasonality may play a crucial, yet understudied, role in structuring species interactions. I used acoustic telemetry, stomach contents, and stable isotopes to determine the seasonal niche overlap of a native cold-water species (lake trout) and a range-expanding warm-water species (smallmouth bass) in two northern temperate lakes. I found that niche overlap between lake trout and smallmouth bass was the highest in the spring, when both species were active and using littoral resources. In contrast, lake trout and smallmouth bass spatially partitioned their niches in the summer. Activity diverged during the winter, with lake trout remaining active with a littoral diet, while smallmouth bass activity was minimal. This thesis demonstrates that both temporal (seasonal activity) and spatial (habitat and diet) niche components structure species interactions and suggests that the impacts of smallmouth bass on lake trout may be greatest in the spring, a season that may lengthen due to climate change.

Keywords: acoustic telemetry
coexistence
fish
seasonality
stable isotope
trophic niche
Advisor: McMeans, Bailey C
A Real-time Robotic System for the Continuous Automation of Single Cell Surgery and Embryo Biopsy

The success rates of manually performed embryo biopsies in Preimplantation Genetic Diagnosis (PGD) are low due to human errors, excessive embryo damage and prolonged surgery times. To increase the procedure the success rate, a robotic system for the biopsy of early-stage 2-cell embryos is proposed. The system consists of robotic manipulators, a camera, sensors, a laser, and set of end-effector tools to perform different procedures on the embryo. The system is comprised of six continuous phases, implemented successively, with neither manual intervention nor software interruption. All six phases are under image-based feedback control and use linear and nonlinear controllers to move micromanipulators with high precision, reject external disturbances, and follow reference trajectories accurately. Significantly, this leads to very rapid processing of embryos. Experimental results on 2-cell and 4-cell cleavage stage embryos validate the effectiveness of the methods proposed.

Keywords: 3D Reconstruction
Automatic biopsy
Image-feedback control
Real-time
Robotic manipulation
Single-cell surgery
Advisor: Mills, James K
Towards Better Algorithms for the Public Sector: Developing Computational Narrative Analysis Methodology to Unpack Biases in Child Welfare Systems

The child welfare sector is an underfunded, understaffed, high-stakes arena where erroneous decisions by caseworkers can lead to child abuse tragedies or traumatic separations between children and their birth parents. To combat these issues, the child welfare sector employs decision-making algorithms using administrative data purportedly to objectively assess a child's maltreatment risk, which have been found to be biased. This research tackles this problem space by conducting computational text analysis on casenotes from a child welfare agency to understand hidden work practices by caseworkers and daily power dynamics that have critical implications in the design of algorithmic systems. Casenotes used in this study are highly contextual, containing rich narrative information on the experiences of frontline caseworkers and their detailed dealings with families involved with child welfare services. The study highlights the need to support sociotechnical systems by accounting for bureaucratic, policy-related constraints and latent power dynamics.

Advisor: Guha, Shion
Longevity of Metal-Acrylic Implant-Supported Fixed Complete Dental Prostheses: A Retrospective Study

Objective: To assess the longevity and survival of metal acrylic implant-supported complete fixed dental prostheses (MA-ICFDPs). Material and methods: This retrospective cohort study included patients treated with MA-ICFDPs at the University of Toronto. Data analyses were carried out to determine rate of complications, and survival analyses were carried out for refurbishing and failure of prosthesis. Results: A total of 156 MA-ICFDPs were included, with a mean follow-up of 9.3 ± 4.8 years. A total of 38 (24%) prostheses were refurbished after an average of 7.8 ± 4.9 years. A total of 18 (11%) prostheses failed, the most common reason being the failure of supporting implants. There was increased hazard ratio (HR) between bruxism for both refurbishing (HR= 3.1, 95% CI= 1.8-5.1, P<.001) and failure of prostheses (HR=2.1, 95% CI= 1.0-4.3, P=0.46). Conclusions: MA-ICFDPs have a good long-term prognosis. Refurbishing is a common repair procedure carried out to address extensive wear.

Keywords: implant-supported fixed complete dental prostheses complications
implant-supported fixed complete dental prostheses success
implant-supported fixed complete dental prostheses survival
multivariate analysis
refurbishing
retread
Advisor: Azarpazhooh, Amir
Chvartszaid, David
Biodegradable Hyaluronic Acid Hydrogel Embolization Microspheres for Osteoarthritis

Osteoarthritis, the most common degenerative joint disease, is driven by inflammation caused by abnormal blood vessels. Embolizing these vessels with particulates can reduce the patient’s pain for ~4 years. A limitation in this emerging field is the unpredictable blockage and dangerous off-target effects caused by commercial particulates. To overcome this, the thesis investigates a hyaluronic acid (HA) hydrogel particle as an embolic agent. It has a high enough yield strength to withstand the shear stress in a vessel, a degradation time of 56±4 hours, and the ability to reduce the risk of blood clot formation. Methylene blue as a surrogate drug was encapsulated into the particles at 6.3±1.7 μg/mg of HA, with 99.8±0.3% cumulative release in vitro over 46 hours. This work produced and characterized a HA hydrogel particle for use of an embolic agent for knee osteoarthritis.

Advisor: Matsuura, Naomi
Novel Problems and Challenges in Language-based Conversational Recommender Systems

Language-based Conversational Recommender Systems (CRSs) have attracted growing attention as they allow users to express and interactively refine their preferences in natural language. However, there exist open problems in CRSs relating to the challenges users face when articulating accurate natural language preferences and the underlying technologies required to facilitate language-based interactions. Our first contribution addresses the challenge that users have trouble specifying preferences with the right level of specificity. We propose a clarification-based extension of a critiquing-based interaction workflow for CRSs that outperforms state-of-the-art models. In our second contribution, we explore the novel issue of unintended bias in language model-driven conversational recommendation by proposing novel bias evaluation metrics and performing source of bias analysis. In summary, this thesis investigates novel and important challenges in the deployment of language that can help users express their preferences more accurately and allow the identification and resolution of bias that arises in language-model-driven CRSs.

Keywords: Bias and Discrimination
Clarification-based Critiquing
Contextual Language Models
Conversational Recommendation Systems
Distributional Latent Embedding
Language-based Conversational Recommendation Systems
Advisor: Sanner, Scott SS
suPAR to Risk-stratify Children with Malaria

Severe malaria is a leading global cause of childhood morbidity and mortality, particularly in sub-Saharan Africa. However, current malaria diagnostic tests do not reliably identify children at risk of severe disease and death. Host immune and endothelial activation contribute to severe malaria pathogenesis. Soluble urokinase-type plasminogen activator receptor (suPAR) is a marker of these pathways. Here, in a large cohort of Ugandan children with Plasmodium falciparum infection, we showed that suPAR levels at first clinical presentation are associated with disease severity and mortality. Furthermore, suPAR improved the predictive accuracy of a validated malaria clinical scoring system. We provide the first clinical evidence in a large prospective cohort that suPAR is a reliable marker to risk-stratify children with severe and fatal malaria. Together, our data provide proof-of-concept for prospective trials evaluating whether suPAR point-of-care measures can enhance triage, management and outcome of children with malaria in low-resource community settings.

Keywords: malaria
mortality outcome
prognostic marker
risk-stratification
soluble urokinase-type plasminogen activator receptor (suPAR)
triage
Advisor: Kain, Kevin C
The Role of Canadian Bison Producers in Conserving the Plains (Bison bison bison) and Wood (Bison bison athabascae) Bison

This project examines the curious tension between conservation and commercial livestock production in a case study of Plains bison (Bison bison bison) and Wood bison (Bison bison athabascae) in Canada. Despite a population of nearly 200,000 individuals, bison in Canada are species of conservation concern as over 90% exist in commercial production rather than for ecological conservation. Where conservation goals for bison include preserving wildness, genetic diversity, and ecological function, ranchers typically prioritize profits through artificial selection and intensive management. However, the Canadian Bison Association (CBA) — an organization committed to protecting the industry — has taken strides to identify with conservation. Interviews with CBA representatives and bison ranchers were conducted to understand the creation of and participation in conservation initiatives, as well as perspectives on the future of bison in Canada. Overall, the results inform bison conservation and contribute to the literature on stakeholder values in cross-jurisdictional wildlife conservation.

Keywords: Collaboration
Conservation
Plains Bison
Ranching
Stakeholder values
Wood Bison
Advisor: Olive, Andrea
Cell-ECM Interaction Regulates Inflammatory Signaling through Tension-Mediated Control of IL-1 Receptor

Cells in the human body experience and integrate a wide variety of environmental cues. Recent interests in tissue stiffness has shown that mechanical properties of tissue drive key biological processes and facilitate disease development. In order to probe their mechanical microenvironment, cells employ many molecular sensors including focal adhesions and the actin cytoskeleton. In this thesis, I show that attachment to the extracellular matrix through focal adhesions upregulates interleukin-1 receptors on the plasma membrane. Such regulation is mediated by increased cytoskeletal tension that controls the local membrane distribution of the receptor. In addition, cells cultured in stiff 3D matrices and those mechanically coupled to neighboring cells display higher amounts of interleukin-1 receptors on the cell surface, suggesting that mechanical properties of the microenvironment can regulate inflammatory pathways at the receptor level. Together, my data reveal the key role of tissue mechanics in regulation of inflammatory signaling and tissue fibrosis.

Advisor: Plootnikov, Sergey V
The Neurophysiological Effects of Intermittent Theta-burst Stimulation in Treatment-resistant Depression

Objective: To investigate the neurophysiological effects of intermittent theta-burst stimulation (iTBS) in patients with treatment-resistant depression (TRD) when two daily iTBS sessions are delivered separated versus contiguous, and between responders versus non-responders. Methods: Transcranial magnetic stimulation- electroencephalography (TMS-EEG) was recorded at baseline and post-iTBS from a triple-blind trial 1:1 randomized separated: contiguous iTBS schedule. TMS-evoked potential components (N45, N100, P60, area under curve) were analyzed. Results: N100 amplitude decreased from baseline regardless of treatment schedule (F(1, 106.02=5.20, p=0.02). iTBS responders showed decreased N100 amplitude from baseline (F(1,102.13)=11.30, p=0.001, pcorrected=0.0004), and higher post-iTBS N45 amplitude (F(1, 94.14)=4.11, p=0.045, pcorrected=0.016). Conclusions: Our results provide evidence of iTBS effects on TMS-EEG measures in TRD. These findings uncover potential neurophysiological mechanisms suggesting that iTBS may enact antidepressant effects in part by restoring the balance between cortical inhibition and excitation.

Keywords: depression
electroencephalography
neurophysiology
TBS
TMS
TRD
Advisor: Voineskos, Daphne
Blumberger, Daniel
The Platformization of TikTok: Examining TikTok’s Boundary Resources

A fast-growing international success, ByteDance’s short video platform TikTok is an exceptional case study for examining how digital platforms expand infrastructurally and accumulate power. Unlike most leading social media companies, TikTok is a mobile-first platform (i.e., its web services are auxiliary to its mobile application), and it is not owned by an American or Chinese tech titan—Google, Apple, Facebook (now Meta), Amazon, and Microsoft (GAFAM) or Baidu, Alibaba, and Tencent (BAT) (Kaye, Chen, and Zeng 2021). Yet it has achieved popularity comparable to major players in the social media ecosystem, and now grapples with balancing the interests of end-users with those of ‘platform-dependent’ institutional actors, including cultural producers. With this thesis, I interrogate how TikTok manages this challenge by studying the platform’s evolution through its boundary resources—i.e., the technical tools and informational resources and regulations that facilitate the creation of apps and services in relation to the platform (Eaton et al. 2015). This work serves as a response to calls from media scholars to view platforms as processes and to further social media historiography (Poell, Nieborg, and van Dijck 2019; Helmond and van der Vlist 2019). More specifically, this thesis contributes to the literature on platform studies because it focuses on an understudied aspect of platform power: boundary resources.

Keywords: boundary resources
cultural production
platformization
social media platforms
TikTok
Advisor: Nieborg, David
Facilitating Floorplan-based Design for Heterogeneous FPGAs

Field Programmable Gate Arrays (FPGAs) are used for many applications due to their flexibility and reconfigurable nature. However, traditional FPGA implementation flows have been unable to keep pace with the increasing size and complexity of FPGA designs, adversely impacting designer productivity. As a result, some techniques have been used to make FPGA implementation flows more modular. These techniques often require the use of floorplan constraints. The goal of this thesis was to add the ability to implement FPGA designs with floorplan constraints to VPR, an open-source FPGA CAD tool. We present the algorithms that were implemented to allow VPR to run with floorplan constraints. We evaluate VPR flows with a variety of floorplan constraint scenarios across 3 FPGA architectures and 32 benchmark circuits. We found that VTR was able to adhere to a variety of floorplan constraints while maintaining comparable quality of results.

Keywords: CAD algorithms
Design automation
Field programmable gate arrays
Floorplanning
Advisor: Betz, Vaughn
Ontario English-language Student Achievement and Growth in Math: Examining the Gap between Students with and without Disabilities

This study analyzes the gaps in math achievement and growth between Ontario English-language students classified with and without disabilities. Some research suggests that early identification and intervention for math difficulty can reduce math gaps. Data come from merged Education Quality and Accountability Office (EQAO) and Early Development Instrument (EDI) datasets for the EDI 2005, 2006, and 2008 student cohorts. Descriptive and longitudinal multilevel model analyses indicate that students with disabilities show increasing math gaps between Grade 3 and Grade 6 and decreasing gaps between Grade 6 and Grade 9. The EQAO math score theta values used in this study are not vertically scaled scores but can reveal gaps in students’ capacity to meet provincial math curriculum expectations. The study’s findings demonstrate the importance of examining math gaps between students with and without disabilities to explain the overall decline in Ontario student math achievement between Grade 3 and Grade 6.

Keywords: EDI
EQAO
Mathematics
Ontario
Special education
Student achievement
Advisor: Davies, Robert S
Dhuey, Elizabeth A
VT Generalizing the Teach and Repeat Navigation Framework

Visual Teach & Repeat (VT&R) achieves long-range and long-term autonomous path following through visual topometric mapping and localization. The system requires only a stereo camera for sensing, making it well-suited for many mobile robot applications involving GPS-denied environments. In this thesis, we present VT&R3, a new version of VT&R that generalizes its underlying teach and repeat navigation framework to work with lidar, radar, and possibly any rich sensor. We develop lidar and radar topometric mapping and localization pipelines that enable lidar/radar-based teach and repeat. We further extend the lidar pipeline with the ability to detect obstacles in changing environments, making obstacle avoidance during path following possible. We validate our pipelines through extensive evaluation using real-world datasets, including runtime analysis showing their online operation capability. Our results demonstrate surprising accuracy and robustness of lidar localization across varying weather and seasonal conditions, while radar localization remains competitive and has advantages in computation and storage requirements.

Keywords: localization
mapping
obstacle detection
range sensing
SLAM
Advisor: Barfoot, Timothy D.
The Impact of Recreational Cannabis Legalization and COVID-19 on Injury-related Emergency Department Visits and Hospitalizations in Canada

Background: The effects of recreational cannabis legalization (RCL) in Canada and the COVID-19 pandemic on the rates of injuries in the Canadian population are largely unknown.Methods: An interrupted time series analysis using population-based data from 2010 to 2021 was used to assess the population-level effect of RCL and COVID-19 on rates of emergency department (ED) visits and hospitalizations for injury. The Mantel-Haenszel method was used to estimate weighted odds ratios for injury-related ED visits after RCL only. Results: There were no notable changes in rates of ED visits or hospitalizations for injury after RCL; however, after lockdowns due to COVID-19 began there was an immediate decrease in ED visits for most injury types followed by gradual increases over time. Conclusions: These results have implications for Canadian and international public health policies, health planning, and injury prevention and mitigation measures.

Keywords: COVID-19
emergency department
hospitalization
injury
interrupted time series
recreational cannabis legalization
Advisor: Cusimano, Michael D
Exploring Policy-mandated Building Design Requirements as an Intervention for Waste Diversion in Multi-residential Buildings: A Case Study of the City of Toronto

This research seeks to review a City of Toronto policy which specifies which waste sorting systems must be implemented into multi-residential building designs. The study draws on socio-technical systems and technological fix as theoretical frameworks to gauge how effective the required waste collection systems actually are and how well the users interact with the systems. Semi-structured interviews were conducted with nine property managers with different chute systems to gauge effectiveness. To expand the policy context, interviews with policy makers of design standards of chute designs in five municipalities were also conducted to explore the rationale behind their requirements. Findings show that some municipalities are starting to move away from technological waste chute systems. The technological chute systems were found to be regularly malfunctioning and needing maintenance and were also used incorrectly by residents—all of which led to more contamination. Efforts to increase waste diversion at MRBs through design will need the expertise of occupants and would benefit from more operational standards to understand diversion technology design flaws.

Keywords: chute systems
multi-residential buildings
socio-technical systems
technological fix
waste mangement
Advisor: Maclaren, Virginia