VictorJuiz/thesis huggingface dataset:
Development of an Impedance Bioresistor for Protein Quantification targeted towards COVID-19 Prognosis

The COVID-19 pandemic claimed over 6 million lives worldwide. Nucleic Acid Amplification tests and Antigen tests identify infections but are incapable of determining disease prognosis. Assessing disease prognosis is crucial for the effective allocation of limited resources. This study conceptualizes and optimizes a low-cost, fieldable, and user-friendly point-of-care electrochemical impedance bioresistor (IBR) that enables monitoring of COVID-19 disease progression and severity. A 35:1 ZIF-8 metal-organic framework film containing 5 mg/mL bovine serum albumin and 5μg biotinylated antibodies form the chemiresistive channel between two parallel gold leaf electrodes. Following exposure to streptavidin-HRP, the change in impedance is measured using a potentiostat. Time scan and electrochemical impedance measurements are used to detect and quantify the interaction to guide the optimization of the sensor design. This label-free sensing platform is intended to give clinicians an affordable way to monitor diseases and allocate limited resources, ultimately aiming to reduce the COVID-19 mortality rate.

Keywords: Biosensor
Disease diagnostics
Electrochemical
Label-free detection
Metal-organic frameworks
Point-of-care (POC) device
Advisor: Ogata, Alana
Payload Software Interface Development and Testing for the NorSat-TD Microsatellite Mission

Smaller nano- and microsatellites have become ideal platforms for validating new space technologies before their widespread use. The Space Flight Laboratory (SFL) at the University of Toronto Institute for Aerospace Studies (UTIAS) has developed several satellite platforms featuring heritage subsystem designs that can be adapted to accommodate a variety of novel payloads. Software interfaces provide an important final link between payloads and other subsystems and help to support all payload functions. This thesis presents the contributions of the author in developing and testing payload software interfaces for the NorSat-TD microsatellite mission which launched in April 2023. Ground and on-board computer software interfaces were created to support all required functions for two of the mission’s novel payloads. In addition, a generic test script was created to streamline the development of automated tests for new payloads. All payload tests were created from this template and used throughout development of the spacecraft. Furthermore, all of NorSat-TD's payloads and their software interfaces are currently functioning as intended and working to meet their on-orbit mission objectives.

Keywords: microsatellite
norsat-td
payload
sfl
software interface
utias
Advisor: Zee, Robert E
CMP: A Filesystem Metadata Compression Framework For Data Intensive Workloads

The growing demand of data-intensive applications, represented by machine learning, coupled with rapidly expanding datasets, have precipitated significant challenges in metadata caching system for large-scale, distributed filesystems. Traditional in-memory metadata caches are increasingly inadequate due to the sheer volume of files and the non-localized data access patterns typical of such workloads. To address these challenges, this thesis presents the Compressed Metadata Pool (CMP), a novel, mid-layer solution that compresses the in-memory inode cache for distributed filesystems. Designed for seamless integration, CMP imposes no modifications on client-side software, server hardware, or stored data, offering a modular upgrade path for existing inode-based filesystems. Structurally, CMP adopts a block-based architecture, allowing for the accommodation of multiple compression algorithms, thereby providing adaptability to a range of workload characteristics. Specifically, CMP leverages the Base-Delta-Immediate (BDI) compression algorithm, striking an optimal balance between compression efficiency and latency overhead, a feature especially beneficial for machine learning tasks. To resolve the decompression and recompression issue that may arise during inode updates, CMP employs the extra slots for few incompressible inodes after updates. Further enhancing its robustness, we introduce two supplementary optimizations—grouping and relaxation—that target dynamic datasets. Implemented and evaluated within the Lustre filesystem, CMP’s performance under simulated machine learning training workloads revealsup to 3.66× improvement in metadata cache capacity while maintaining a latency overhead of less than 15%. Overall, CMP offers an effective and modular approach to extend metadata services for filesystems coping with large-scale datasets and data-intensive workloads.

Keywords: Filesystem
Memory Compression
Metadata
Advisor: Pekhimenko, Gennady
Clinical and Functional Neuroimaging Characteristics of Older Adults with Subjective Cognitive Decline

Subjective cognitive decline (SCD) is conceptualized as a preclinical stage of Alzheimer's disease (AD) in which individuals perceive memory decline despite normal cognitive performance. This thesis aims to identify clinical and functional neuroimaging markers to characterize SCD individuals before AD onset. SCD and Mild Cognitive Impairment (MCI), a prodrome to AD, reported increased frequency and severity of memory lapses and health anxiety compared to the cognitively unimpaired (CU) group. SCD reported increased state and trait anxiety and neuroticism compared to the CU group. SCD individuals who have perception of lower memory ability expressed more health anxiety, trait anxiety, and neuroticism. Within the SCD group, reduced posterior default mode network (DMN) and increased anterior DMN functional connectivity were observed. Limitations include lacking AD biomarkers or longitudinal follow-up to establish SCD as a preclinical AD group. This thesis serves as a platform to continue developing markers of SCD due to preclinical AD.

Keywords: Default Mode Network
Functional Magnetic Resonance Imaging
Memory Complaints
Memory Functioning Questionnaire
Psychological Symptoms
Subjective Cognitive Decline
Advisor: Mah, Linda
Growth Factor Regulation of Neuroblastoma Migration and Invasion

Neuroblastoma (NB) is the most common extracranial pediatric cancer with a five-year survival rate of less than 50%. It arises from neural crest precursors in tissues such as the adrenal gland. Metastatic NB is often fatal with common sites including bone, bone marrow and brain. Our laboratory previously developed a mouse model of NB to study metastasis to the bone and the brain, isolated tumor cells from these metastatic sites and identified genes regulating their metastatic behavior. Since neural crest-derived cells often use receptor tyrosine kinases (RTKs) and their ligands to proliferate and migrate, I hypothesized that NB cells also use these proteins to metastasize. To address this, I performed mass spectroscopy analysis of NB cell surface proteins and scRNA-seq to identify RTKs and their ligands enriched in hypermetastatic NB cells as compared to less metastatic parental cells. I identified four RTKs, PDGFRA, PDGFRB, EGFR, and FGFR1 and found that the PDGFRB ligand PDGFBB mediated the migration and invasion of the hypermetastatic cells without markedly affecting the parental cells. These findings suggest that NB cells use PDGF to mediate part of the metastatic process.

Keywords: Biophysics
Cancer
Neuroblastoma
Advisor: Irwin, Meredith
Applying Human Factors to Reduce Healthcare- Associated Infections Caused by Face Touching

Canada is currently facing a critical healthcare worker (HCW) shortage, in part resulting from absenteeism due to healthcare-associated infection. Face touching is a behaviour that HCWs engage in frequently and is one way for HCWs to infect themselves. While personal protective equipment has been found to decrease face touching, current solutions are insufficient and the behaviour still occurs. I conducted a literature review and full-scale interview study with emergency room, intensive care unit, and operating room nurses to investigate how human factors can be applied to create solutions to reduce face touching behaviours among HCWs. Interviews were analyzed thematically and revealed HCWs’ perceptions, needs, desires, constraints, attitudes, and beliefs surrounding face touching and related solutions and key differences between the participant groups. Key considerations for the design of face touching solutions were identified, along with potential strategies for reducing the likelihood of face touching by HCWs.

Advisor: Chignell, Mark
The Relationship between Compulsory Schooling Policy, Educational Equity and Student Achievement in Turkey and Portugal

AbstractCompulsory schooling laws are used as a policy tool for promoting educational equity and access to education, especially for disadvantaged students. However, the evidence regarding the impact of these laws on decreasing inequalities is not consistent. This paper uses PISA data from 2009 and 2015—before and after compulsory schooling policy changes in Turkey and Portugal in 2012—to examine changes in the math achievement of students with low and high socioeconomic status (SES). The results suggest the impact of compulsory schooling laws can vary depending on the context as SES achievement gaps decline in Turkey but do not change in Portugal. As there is little previous quantitative research conducted about these reforms in Turkey and Portugal, this study will contribute to the comparative literature by providing recent evidence about the role of compulsory schooling policy change on socioeconomic inequalities in middle-income countries with their unique challenges and opportunities.

Keywords: Compulsory education policy
equity
Portugal
socioeconomic status
student achievement
Turkey
Advisor: Chmielewski, Anna Katyn
Roofstock and the Millennial Remote Landlord: A Case Study of Post-crisis, Platform-mediated Retail Investment in Single-family Rental Housing

Millennials are the generation of “forever renters”: a cohort of aspiring homeowners facing exorbitant housing prices and stagnant wages. With homeownership out of reach for many, millennial consumers are being targeted to become investors in the single-family rental (SFR) market. Digital property technologies – online platforms for real estate investment known as “PropTech” – are creating bespoke marketplaces for young, first-time investors to become digital landlords in lieu of personal homeownership. This research focuses on one firm, Roofstock, an Oakland-based PropTech startup recently valued at $1.9 billion, which is incorporating young, inexperienced investors into the SFR market with retail consumer products. I explore the platform business model in structuring digital rentier relations for remote landlords and tenants and the significance of platform technologies naturalizing high-risk digitally-mediated investments. Finally, I discuss the implications for a growing class of millennial remote landlords in leveraging market power and building housing wealth through alternative investing pathways.

Keywords: Millennials
Platform real estate
Property Technology
Remote landlord
Single-family rental housing
Advisor: Buckley, Michelle
Occupancy Grid Mapping via Resource-Constrained Robotic Swarms: A Collaborative Exploration Strategy

This Thesis considers the use of robotic swarms with limited exteroceptive and inter-robot sensing capabilities for exploring and mapping unknown environments. It presents a novel collaborative exploration strategy that directs the resource-constrained swarm toward unexplored areas in the environment by dividing the swarm into two teams: landmark robots and mapper robots, respectively. The former directs the latter toward ‘promising’ frontiers in the environment enabling efficient frontier-based exploration. The landmark robots are optimally positioned to maximize new information added to the map while also adhering to connectivity constraints. The mapper robots are decentralized and use random motion to explore the local area surrounding the landmark robots. Through this decoupling of the swarm into two separate teams, directing the swarm to new areas of the environment can be addressed separately from exploring and mapping that new area. The performance of the exploration and mapping strategy has been validated through extensive simulations.

Keywords: exploration
motion control
occupancy grid map
swarm mapping
Swarm robotics
Advisor: Benhabib, Beno
Nejat, Goldie
Brain-Cognition Associations in Late-Life Depression or Mild Cognitive Impairment: An Analysis of Gray and White Matter Integrity

Most older adults with late-life depression (LLD) exhibit cognitive impairment and a third meet diagnostic criteria for mild cognitive impairment (MCI). While LLD is a risk factor for developing Alzheimer’s dementia (AD), the mechanisms remain unclear. In Study 1, we systematically reviewed the literature to synthesize the published associations between structural brain alterations and cognition in LLD or LLD+MCI. The current literature is characterized by limitations: basic cognitive measures, univariate models, small sample sizes, and quasi-absence of participants with LLD+MCI. These findings guided the design of Study 2: we assessed the multivariate associations between structural brain alterations and cognition in a sample (N=283) of participants with LLD, MCI, or LLD+MCI, and controls. Gray matter atrophy in specific regions predicted worse memory, language, and processing speed; global reduced white matter tract integrity predicted worse executive function and processing speed. These findings remained significant in MCI/LLD+MCI, but not LLD or HC groups.

Keywords: Cognition
Depression
Geriatric
Magnetic resonance imaging
Mild cognitive impairment
Neuroimaging
Advisor: Mulsant, Benoit H.
LiNO₃-Poly(vinyl Alcohol) (PVA) Solid Polymer Electrolytes: Properties, Longevity and Application for Electrochemical Capacitors

Neutral pH polymer electrolytes are promising for future thin solid energy storage technologies including electrochemical capacitors (ECs), enabling environmentally benign, leakage-free and flexible form factors without bulky packaging. In this thesis, LiNO₃-poly(vinyl alcohol) (PVA) polymer electrolyte was studied and compared to the liquid baseline. Examining ionic conductivity at ambient and low temperatures, an optimal LiNO₃-PVA composition with a molar ratio of 2,500:1 demonstrated high ionic conductivity of 40 mS cm-1, and remained functional at -40 °C. The long-term stability of the polymer electrolytes revealed a strong connection between electrolyte water content and ionic conductivity. Raman spectroscopy indicates that the chemical bonding, structure, and conductivity of LiNO₃-PVA are linked to aqueous LiNO3 concentration rather than PVA. Key water levels in the electrolyte have been identified. The enabled solid electric double layer capacitors (EDLCs) had a wide voltage range of 1.6 V and 76% capacitance retention at -40 °C, surpassing aqueous counterparts.

Keywords: electrochemical capacitors
LiNO3-PVA
Polymer electrolyte
Solid-state electric double-layer capacitors
Supercapacitors
Advisor: Lian, Keryn K
Distinct Neurodevelopmental Signatures of Sex-Specific Transcriptome-Based Polygenic Risk Scores for Depression

Post-mortem gene expression profiling reveals distinct transcriptomic signatures of major depressive disorder (MDD) in each sex. Leveraging these data, we sought to develop female- and male-specific transcriptome-based polygenic risk scores (tPRS-F and tPRS-M, respectively) and evaluate their impact on regional cortical thickness, cortical surface area, subcortical volume, and depressive symptoms at baseline and 2-year follow-up in a developmental sample of 5002 adolescents (46.6% female, aged 8.9–11.0). In males, tPRS-M was associated with higher symptoms at both time points and thicker posterior cingulate at follow-up. In females, at follow-up tPRS-F was associated with lower volumes of the accumbens area, caudate, and hippocampus, the latter two of which mediated an indirect tPRS-F effect on symptoms. For each score, no effects emerged in the opposite sex. Our findings suggest that sex-specific depression-like shifts in gene expression may contribute to a vulnerability phenotype for future MDD risk via distinct mechanisms in both sexes.

Keywords: depression
development
neuroimaging
polygenic risk score
sex-specific
transcriptomics
Advisor: Nikolova, Yuliya S
Reactions and Fate of Alkyl-Substituted Polycyclic Aromatic Hydrocarbons (AlkPAHs) in the Atmosphere

Recent studies have reported greater abundance of alkyl-substituted polycyclic aromatic hydrocarbons (AlkPAHs) than unsubstituted polycyclic aromatic hydrocarbons (PAHs) in Canada, suggesting their potential importance to environmental health. The levels and impacts of AlkPAHs depend on their oxidative fate, emission factors and several others. Homogeneous oxidation of AlkPAHs has been shown to be faster than PAHs; however, less is known about heterogeneous oxidation rates. In this study, several AlkPAHs and PAHs were exposed to ozone at various time intervals. Observations showed a decrease in AlkPAHs concentrations with increasing ozone concentration with second order kinetics for all compounds. Additionally, AlkPAHs reacted faster with ozone than their analogous PAHs. Moreover, oxidation rates depended on molecular structure with larger alkyl groups increasing the reaction rate with ozone. This thesis highlights the effect of alkylation on the oxidation rate of PAHs which informs the transformation rate of AlkPAHs in the atmosphere in comparison with PAHs.

Keywords: Alkyl substituted polycyclic aromatic hydrocarbons
Heterogeneous oxidation
ozone
polycyclic aromatic compounds
Advisor: Chan, Arthur
Galarneau, Elisabeth
A Randomized, Double-Blinded, Placebo-Controlled Study Evaluating the Effectiveness of Vortioxetine in Treating Reward Dysfunction Among Individuals with Post COVID-19 Condition

Long COVID is a debilitating, heterogeneous condition that impairs function and quality of life. A commonly reported symptom of long COVID is cognitive impairment. Accordingly, it may be hypothesized that reward function is subsequently impaired. Herein, the primary objective of this project was to evaluate the effectiveness of vortioxetine compared to placebo on improving reward function in long COVID using the Effort Expenditure for Rewards Task (EEfRT). A total of 64 individuals completed the EEfRT at baseline and endpoint. There was no significant effect of treatment on hard-task selection over the eight-week period. Accordingly, vortioxetine did not improve reward motivation in this long COVID population. Future studies should evaluate the effect of long COVID on other sub-components of reward. Research in this area should also aim to better understand and characterize the pathoetiology of long COVID and establish robust diagnostic criteria for clinical use.

Advisor: McIntyre, Roger S.
Design, Testing, and Verification of Communication Systems for Microsatellite Missions

Microsatellite missions have enabled greater access to space for many, especially for commercial and research applications. The Space Flight Laboratory provides microsatellite platforms that support the goals of such satellite missions. The platforms include the communication subsystem, which allows a connection to be maintained between the operators on the ground and the satellite in orbit. This thesis presents the author's contributions to the communication subsystem of two missions. Firstly, the testing of components within the communication system is presented, identifying test criteria, observations, and results. Secondly, a verification method for the process of estimating the strength of the signal received by the satellite is developed using data collected from satellites in orbit. The method is then used to analyze the performance of a mission. Finally, the preliminary design of a communication system is presented, including considerations for mission-specific requirements.

Keywords: Communication Systems
Microsatellite
Radio Frequency
Advisor: Zee, Robert E.
Queer Visual Practices and Cross-strait Gallery Space

This thesis posits that queer visual practices in mainland China and Taiwan offer not just a mode of critique but a mode of collective resistance across the Taiwan Strait that can enact queer ways of living. The current framework for understanding queer visual practices in the region is built around a representational critique of political and cultural institutions. While this critique offers a lens onto the institutions that can make queer lives unlivable, there is still a need for alternative frameworks that consider the complexity of queer experiences in the region. My thesis addresses this gap by starting with the understanding that cultural and political institutions are deeply engrained in the political and economic flows that cross the Taiwan Strait. By pulling together an archive of exhibitions, documentaries, landscapes, and autoethnographic data, this thesis reads queer visual practices across mainland China and Taiwan as a practice beyond “art” with the potential to imagine alternatives to the contemporary cold war political and capitalist economic structures of violence.

Keywords: Affect
China
Cold War
Queer Marxism
Taiwan
Visual Culture
Advisor: Boland, Alana
Oswin, Natalie
The Role of ADA2 in Monocyte Phenotype and Function

Deficiency of adenosine deaminase 2 (DADA2) is a vasculitis caused by a loss-of-function mutation in the adenosine deaminase 2 (ADA2) gene, which is involved in monocyte-to-macrophage-differentiation. Stimulated DADA2 patients’ and ADA2 knockout macrophages have been shown to produce more pro-inflammatory cytokines, and DADA2 patients have an abnormal ratio of monocyte subtypes. Further investigations into ADA2’s function in primary monocytes present challenges as obtaining DADA2 patient cells pre-treatment can be difficult. To circumvent this, novel models of ADA2 knockdown via siRNA transfection in THP-1 cells and ex-vivo human classical monocytes were established. ADA2 knockdown classical monocytes revealed no alterations in macrophage marker expression. However, upon TLR stimulation, ADA2 knockdown classical monocytes exhibited altered cytokine gene and protein expression. This suggests that ADA2 plays a critical role in regulating cytokine secretion in classical monocytes. These findings provide more insights into the role of ADA2 and DADA2 disease pathogenesis.

Advisor: Yeung, Rae S.M.
Visual Rehabilitation in a Pediatric Population of Patients with Homonymous Hemianopia: A Pilot Study on Immersive Virtual-Reality Stimulation (HH-IVR)

The purpose of this pilot study is to investigate the feasibility and potential treatment effectiveness of Re: Vision, a novel virtual reality (VR) rehabilitation treatment, in children with tumour-induced homonymous hemianopsia (HH), a field loss deficit in the same halves of the visual field of each eye. Ten pediatric patients with HH received 15 minutes of home-based VR stimulation sessions every two days for six weeks, during which they wore a head-mounted display (Oculus Quest 2, Meta) and were tasked to track the movement of a moving target ball in a 3D virtual space. All participants completed the treatment without adverse events—improvement in binocular visual perception and reading speed after treatment was observed in treatment responders. Preliminary results of this pilot study suggest the feasibility and potential treatment effectiveness of the Re: Vision in pediatric patients with tumour-induced HH, which can be further explored and optimized in future studies.

Keywords: Clinical Trial
Hemianopsia
Neuroscience
Pediatric
Virtual Reality
VR
Advisor: Reber, Michael