VictorJuiz/thesis huggingface dataset:
Evaluating the Role Of Hippocampal Inputs to the Mammillary Nuclei In Spatial Memory

This study sets the stage for an investigation into the role of subiculum efferents to the mammillary bodies (MB) in spatial navigation. We characterized baseline behaviour of male and female C57BL/6 mice (n = 11) in an egocentric and allocentric spatial escape assay using a Barnes maze. Egocentric testing revealed escape to a previously memorized shelter location can be encoded after a brief exploration under red light condition and that an animal’s position relative to the shelter is constantly updated for goal-directed flight. Allocentric testing revealed mice can encode a shelter location to effectively utilize distal cues for goal-directed escape. Finally, anatomical tracing experiments reveal MB-projecting subicular neurons are organized topographically such that axons originating from the dorsal or ventral subiculum terminate in the dorsal or ventral regions of the medial MB respectively. Parallel pathways may represent a functional differentiation of subicular inputs to the MB.

Keywords: Allocentric Navigation
Egocentric Navigation
Hippocampus
Mammillary Bodies
Spatial Memory
Spatial Navigation
Advisor: Kim, Junchul
Takehara-Nishiuchi, Kaori
The Impacts of the Great Recession on Systolic Blood Pressure in the United States: A Population Health Perspective

Despite the importance of socioeconomic status for health, there are inconsistent conclusions over the health impacts of the Great Recession. One potential reason is that smaller, more pervasive, individual-level changes in health could have occurred and pushed populations towards poorer distributions of health overall, but no studies have used a distributional approach. Thus, this dissertation asks: Can distributional perspectives provide additional insights into the health impacts of the Great Recession? In conducting three studies, I find: i) heterogeneity among the methods used in the literature, but none appropriate for distributional outcomes; ii) a decomposition analysis of distributional outcomes provides more insights than that of mean outcomes; and iii) that while mean systolic blood pressure (SBP) improved for most American adults, a distributional approach reveals that SBP may have worsened overall for some. This work applies a distributional perspective to provide more comprehensive insights into the health impacts of recessions.

Keywords: Decomposition methods
Economic recession
Great Recession
Social determinants of health
Systolic Blood Pressure
Advisor: Siddiqi, Arjumand AS
Oscillatory Basis of Working Memory Function and Dysfunction in Children with Epilepsy

Working memory (WM) deficits are prevalent in children with epilepsy. The causes of these impairments remain elusive. In the current work, we leveraged intracranial recordings from the hippocampi and epileptogenic zones of children with epilepsy performing a WM task to probe the oscillatory basis of WM function and dysfunction in children with epilepsy. First, we demonstrated that low-frequency phase resetting of hippocampal oscillations occurred in response to stimulus presentation, and the precision of the phase angle was associated with optimal WM processing, as indexed by faster reaction times. Second, enhancement of coordinated interactions between the hippocampi and WM-related networks occurred concurrent to phase resetting. Finally, the occurrence of transient epileptic activity was associated with prolonged reaction times, attenuated low-frequency hippocampal phase resetting, and alterations in interregional low-frequency connectivity. This dissertation presents evidence that may guide the development of future treatments aimed at improving memory function in children with epilepsy.

Keywords: Epilepsy
High-frequency oscillations
Hippocampi
Interictal epileptiform discharges
Neural oscillations
Working memory
Advisor: Ibrahim, George M
Use of High-concentration Chlorhexidine (Prevora®) for Reduction in ‘Need for Surgery’ in Patients with Periodontitis

AbstractIn this clinical study, we studied the effects of treating patients with Prevora® following initial scaling and root planing (SRP) as an adjunct in order to assess whether this treatment would improve clinical disease parameters beyond SRP alone. Our results showed that there was a statistically significant reduction in BOP from 32.8% to 22.9%, reduction in mean probing depths (PD) of 0.25 ± 0.01mm and a gain in mean clinical attachment level (CAL) of 0.27 ± 0.02mm. However, for sites with PDs of 4-6mm, an average reduction of 0.73 ± 0.07mm was observed; for sites with ≥ 7mm PD, an average reduction of 1.11 ± 0.48mm. More importantly, we found a significant decrease in the number of teeth that would have required surgical treatment from 111 teeth to 58 teeth; a 48% decrease in the total number of teeth that would have required surgical treatment.

Keywords: Chlorhexidine
Periodontitis
Periodontology
Prevora
Treatment
Varnish
Advisor: Tenenbaum, Howard
Goldberg, Michael
Effects of Maternal High Fat Diet and Milk-derived Exosome Supplementation on DNA Methyltransferase 1

Maternal high fat diet (mHFD) exposure during perinatal life shapes offspring’s neurodevelopment trajectories. mHFD also influences the bioactive composition of maternal milk, including milk-derived exosomes (MDEs), nanovesicles that transport functional microRNAs (miRNA). miRNA-148/152 regulate DNA methyltransferase-1 (DNMT1), enzyme that catalyzes DNA methylation modifications, which in turn downregulates fat-mass and obesity-associated (Fto) gene via promoter hypermethylation. The main objectives of this thesis were: 1) examine the effects of mHFD exposure on DNMTs and Fto expressions in postnatal day 7 rats and 2) investigate MDE-supplementation effects on DNMTs and Fto expressions using a human microglia cell line. DNMT1 and Fto transcript abundances remained unchanged in the PVN and ventral hippocampus but decreased in the retroperitoneal fat of mHFD offspring. In microglia, MDE-supplementation resulted in increased DNMT1 expression only. These findings indicate that DNMT1 and Fto exhibit tissue-specific sensitivity to mHFD exposure in neonates, and that DNMT1 is altered by MDE-supplementation in microglia.

Keywords: DNA methyltransferases
Epigenetic programming
Maternal obesity
Microglia cell culture
Milk-derived exosomes
Neurodevelopment
Advisor: McGowan, Patrick O.
Self-supervised Semantic Learning of LiDAR Point Clouds for Large-scale Scene Understanding

Semantic segmentation is a challenging task in the robotic vision community to classify various objects in a scene. While recent works employ supervised learning approaches using hand-annotated examples, these training samples are often costly to obtain. In this thesis, we present a self-supervised semantic learning method for large-scale scene understanding. Our offline method retrieves point cloud annotations by combining a mapping and localization solution with ray-tracing algorithms. Through multi-session navigation experiences in the same environment, our method labels points into four semantic classes: ground, non-movable, long-term movable, and short-term movable. These semantic labels allow us to train a semantic segmentation network without any hand annotations, which can then be used online. For qualitative and quantitative analysis, we demonstrate our method on a simulation dataset. We also provide a qualitative evaluation of a real-world dataset. Furthermore, by semantically filtering out movable points, results show that our method improves existing localization performance.

Keywords: Deep Learning
Point Cloud
Robotics
Semantic Learning
Advisor: Barfoot, Tim
Kelly, Jonathan
Less Than the Sum of its Parts: Viewing Parts of Faces Increases Subsequent Attractiveness Ratings of the Original Wholes

People’s general expertise with faces leads them to quickly process them as wholes rather than as collected sums of their parts. Here, I tested whether judgments of facial attractiveness (one of the most socially consequential attributes of a face) change when such holistic processing is disrupted. Participants in three studies rated faces as more attractive after perceiving their constituent features separately. Repeated exposure to the features and local-processing dominance did not explain this benefit, which improved ratings of attractive faces more than unattractive faces. Disruptions of holistic processing thus positively affect how perceivers view facial attractiveness.

Keywords: attractiveness
face perception
holistic processing
Advisor: Rule, Nick
The Role of Geospatial Factors and Distance on Timely Physician Follow-up after a First Hospitalization Discharge with a Diagnosis of a Schizophrenia Spectrum Disorder: A Retrospective Population-based Cohort Study

Timely follow-up after a hospitalization for a schizophrenia spectrum disorder (SSD) is an important quality indicator. We examined the proportion of physician follow-up within 7 and 30 days of a first hospitalization discharge for a SSD by health administrative region in Ontario. The effect of distance between a person’s residence and discharging hospital on follow-up was estimated using multilevel models. We identified 6,382 incident hospitalizations for a SSD between January 1, 2012 and March 30, 2019. Only 14.2% received follow-up care with a psychiatrist within 7 days and 49.2% received follow-up care with a psychiatrist within 30 days. These proportions varied between regions. Although distance was not associated with psychiatrist follow-up within 7 days of discharge, increasing distance was associated with reduced odds of follow-up within 30 days of discharge. Geospatial factors may impact post-discharge care and should be considered in further evaluation of quality of care in this population.

Keywords: Distance
Geospatial
Hospitalization
Quality of care
Schizophrenia
Schizophrenia spectrum disorders
Advisor: Kurdyak, Paul
Machine Learning Models for Traffic Flow Prediction

Many methods of traffic prediction have been proposed over the years, from the time series models over 40 years ago to the latest deep learning models today, which prompts the need for an in-depth comparison and the critical question of whether deep learning offers significant improvements over the traditional methods. This thesis addresses this situation by systematically evaluating the different methods. We first procure a diverse set of traffic data from simulation software and real-world sensors. We then compare the different methods and perform further analysis on the latest deep learning models. Finally, we also consider the task of predicting long-term traffic up to a week in advance. Overall, we demonstrate that deep learning models are effective in short-term prediction. However, the classical random forest regression provides the best performance in both short-term and long-term prediction, which suggests that there is still room for improvement for deep learning methods.

Keywords: Machine Learning
Traffic Prediction
Advisor: Sanner, Scott
Abdulhai, Baher
The Cognitive Processes and Neural Regions Supporting Unitization

Hippocampal damage or dysfunction can result in impairments in relational memory (RM), which is the ability to bind distinct elements into a lasting memory representation. The cognitive strategy, unitization, can mitigate RM impairments by fusing objects into a single unit through a physical interaction. The transverse patterning task was used to determine whether the unitization strategy supported memory above-and-beyond effects of extended practice (EP), and whether strategy transfer occurred. Healthy older adults benefitted from extended practice, and unitization use surpassed EP benefits. Five older adult cases with varying damage to the ventromedial prefrontal cortex, and medial temporal lobe and extended regions, did not benefit from strategy training or EP; suggesting potential roles for these regions in RM and unitization. Neither population showed transfer. Relational memory impairments may be remediated through strategy interventions by aligning with one’s cognitive and neural profiles, and in conjunction with extended practice.

Keywords: aging
amnesia
frontal lobe
memory
relational memory
unitization
Advisor: Ryan, Jennifer D
Driver Scanning Behavior at Urban and Suburban Intersections: An On-road Approach

The safety of Vulnerable Road Users (VRUs), such as pedestrians and cyclists, is highly jeopardized at intersections, with driver inattention being a leading cause. It is not well known (1) where drivers distribute their visual attention at real intersections or how this impacts VRU safety, and (2) how driver attention interacts with different intersection elements from an on-road perspective. This thesis utilizes rich instrumented vehicle data from 26 experienced drivers (13 cyclists and 13 non-cyclists) to quantify drivers gaze distributions at signalized right turns. Key findings include that drivers spent the most time glancing at relevant pedestrians, irrespective of signal status, and that driver attention was heavily skewed toward leftward traffic during red lights. Additionally, this thesis outlines an instrumented study which will examine the effects of Guelph’s suburban road infrastructure on driver scanning behaviour. Reported findings can benefit broad road safety perspectives from urban planning, collision forensics, and more.

Keywords: Eye tracking
Glance allocation
Human factors
Instrumented vehicle
Intersections
Vulnerable road users
Advisor: Donmez, Birsen
Pratt, Jay
Design and Implementation of Open Source Testing Equipment in Engineering Education and Research

Laboratory work teaches students how technical knowledge is applied in practice and has long been recognized as a crucial component of a complete undergraduate engineering experience. The deployment of new laboratory activities is challenging for several reasons, particularly due to resource constraints. Providing students with meaningful hands-on experience became even more challenging in the remote learning environment during the COVID-19 global pandemic. In the work presented, two low-cost, open-source mechanical testing machines were designed, and implemented in engineering education and research. The Universal Mechanical Testing Kit was launched as lab activities in a first-year introduction to materials science class. The Miniature Mechanical Testing Kit was designed as a remote learning tool and used as a lab kit in a third-year engineering design class during the pandemic to provide students with meaningful hands-on experience while learning from home. Other design variations were also implemented in engineering education and research.

Advisor: Ramsay, Scott
Numerical Modelling and Testing of Recovery Boiler Deposits to Investigate Fracture by Sootblower Jet Impingement

Steam is used to remove deposits that build up on the heat exchanger tubes in a boiler. Fouling causes a reduction in boiler efficiency, and costly sootblower steam is used to remove deposits. A fundamental study of deposit break-up and crack propagation at boiler temperatures was carried out to improve sootblower efficiency. To analyze fracture of deposits, the material properties of a deposit, mainly the fracture toughness KC, needs to be measured. Moreover, the work of fracture, WF, is used to compare the energy required to fracture brittle deposits versus ductile deposits. Finally, the deposits were modelled in FEA to investigate the effects of surface pits on amplifying the maximum principal stresses created by a jet. A small notch was introduced in the model to investigate crack growth through the deposit under jet impingement using the failure criterion K > KC.The fracture toughness of a deposit declined as the temperature of the testing furnace increased due to the decrease in peak load. The deposit samples tested experienced a brittle to ductile transition at 450°C. Ductile deposits (740 J/m2) required four times more energy to fracture compared to a brittle deposit (185 J/m2). The increased WF resulted from the ductile deposits deforming under force, requiring more energy to fracture. The numerical model indicates that a pit significantly amplifies the maximum stresses leading to small microcracks forming upon jet impingement. The fracture model of a microcrack shows that brittle deposits will fail when the stress intensity factor at the crack tip, K is greater than the critical stress intensity factor KC.

Keywords: Deposits
Finite Element Analysis
Fracture toughness
Recovery Boiler
Sintering
Sootblowing
Advisor: Kortschot, Mark
Bussmann, Markus
Making the Road: Community Benefits Organizing in Canada as a Radical Adult Learning Practice

Canadian organizing efforts aiming to democratize the economy are the focus of this study, specifically if and how emancipatory learning is occurring in Community Benefits Agreements (CBA) campaigns and coalitions. It further aims to delineate CBA organizing as a community power-building strategy in the interests of workers and communities. Turning to dialectical frameworks, Cultural-Historical-Activity-Theory (CHAT) enables consideration of organizing as radical adult learning in a Freirian tradition, while critical place inquiry provides a methodological approach that is concerned with the socio-materiality of human practices as shaped by and in place. History and memory methods centre the voice, agency and perspective of the persistently marginalized communities impacted by CBA organizing. Drawing on secondary sources, coupled with my own experience embedded in this movement activity, I provide case studies of five neighbourhood-based CBA campaigns in two Canadian cities: Toronto and Ottawa. The cases show these campaigns build on previous local leadership and community capacity development, while concurrently equipping constituencies for collective deliberation and action. CHAT further enables an activity analysis of CBA organizing environments that suggests an expansive view of place is foundational for community power-building. It further identifies that collective memory, stories and narrative – coupled with an ethical orientation to movement building – hold promise as practices that could enable and amplify the emancipatory potential of organizing. Finally, Indigenous ontologies and axiology are proposed as a potentially profound source of guidance to Canadian organizing efforts challenging oppressive systems and structures while building collective community agency and power from the ground up.

Keywords: collective memory
community benefits
community power
labour community coalitions
organizing
Advisor: Vieta, Marcelo
Sawchuk, Peter
Tryptophan Mutagenesis Studies of the Adenosine A2A Receptor-Toward Next Generation Biosynthetic Labeling of Fluorotryptophan Analogs in Eukaryotic Cell Cultures and Optimizing Dopamine D2 Receptor expression with ExpiCHO system

G-protein-coupled receptors (GPCRs) comprise the largest and most diverse protein superfamily in the mammalian genome.1 Crystallographic and cryo-EM-derived structures provide high resolution structures but lack information regarding activation intermediates and dynamics. Here, we incorporate 5F-tryptophan biosynthetically and employ 19F NMR to investigate the conformational ensembles and functional motions of adenosine A2A receptor(A2AR), a prototypical class A GPCR. The second part of this thesis involves the optimization of expression (in ExpiCHO cells) of the D2R receptor, which represents another class A GPCR for 19F-NMR analysis. Both the A2A expression and D2R expression methodologies were developed with a focus on both cysteine mutagenesis and biosynthetic labeling.

Keywords: A2A
D2
Fluorotryptophan
GPCR
Advisor: Prosser, Robert RS
Development and Characterization of the Femur Window Chamber Model for Leukemia Research

Acute lymphoblastic leukemia (ALL) is an aggressive disease of the bone marrow (BM) microenvironment. Unfortunately, the difficulty of traditional methodologies to access the BM in vivo has thus far limited our understanding of disease biology. This project therefore advances the femur window chamber (FWC) mouse model as a new tool for intravital imaging and study of the representative BM of long bones. Here, I have optimized the FWC technique for longitudinal leukemia studies and demonstrated minimal disruption to the native BM vasculature and immune landscape from the surgery. I have also determined that ALL progression results in significant BM remodelling, including elevated hypoxia levels, reduced vascular perfusion, increased vessel diameter, and a dynamic cycle of immune cell recruitment then suppression. These findings not only establish important preclinical research methodologies that overcome the limitations of traditional assays, but also characterize significant ALL dynamics that could inform future therapeutic strategies.

Keywords: Femur Window Chamber
Fluorescence
Intravital Imaging
Leukemia
Microscopy
Mouse Model
Advisor: DaCosta, Ralph S
Minden, Mark D
Differences in Cortical Thickness between Cognitively Impaired Persons with and without Apathy May Reflect Discrete Mechanisms of Neuropathophysiology

Apathy increases the risk of dementia and is associated with worse outcomes. Deficits in frontostriatal circuits and frontotemporal association areas are associated with apathy in dementia. However, the specific brain regions mediating apathy remain unclear given concomitant neurodegenerative processes. Cognitively impaired (CI) participants with apathy and without apathy from the Alzheimer’s Disease Neuroimaging Initiative matched by demographic, genetic, and cognitive markers were investigated. Differences in region-wise cortical thicknesses were examined by stratified mixed-effects analyses. The right medial orbitofrontal cortex (mOFC) and left rostral anterior cingulate cortex (rACC) were thinner and the left middle temporal cortex (MTC) was thicker in CI participants with apathy compared to matched CI participants without apathy. Supplementary analyses with cognitively normal participants showed that apathy among CI participants was associated with thinner right mOFC and left rACC. Meanwhile, CI participants with apathy had spared atrophy in the left MTC relative to matched CI participants without apathy.

Keywords: Alzheimer's Disease
Apathy
Clinical Research
Dementia
Goal-directed activity
Neuroimaging
Advisor: Graff-Guerrero, Ariel
Assessing the Impacts of Climate Change on Energy Use and Retrofit Potential of Institutional Buildings at the University of Toronto St. George Campus

The average greenhouse gas intensity of institutional buildings at the University of Toronto St. George campus was 69kg eCO2/m2 in 2017-2018. In 2019, in line with the commitment to climate action, the University of Toronto set a goal for all three campuses to reduce the average building GHGI to below 32kg eCO2/m2 by 2030, meaning institutional buildings at the St. George campus must undergo major energy conservation changes to meet this reduction goal. An energy modelling analysis of a typical institutional building at the St. George campus was carried out using OpenStudio and RETScreen to demonstrate how a changing climate impacts the building energy consumption and associated GHG emissions and to further assess building retrofit potential through different individual passive and active energy efficient retrofit strategies and their combined scenarios. The results also provide insights into how different energy modelling simulation results compare in the context of a future climate.

Keywords: Building Energy Simulation
Campus Building
Climate Change
Energy Use Intensity
Greenhouse Gas Use Intensity
Retrofit Measures
Advisor: Touchie, Marianne