VictorJuiz/thesis huggingface dataset:
Capturing Realistic Architectures for Field Programmable Gate Array Optimization

The use of FPGAs is growing, and with it the need for open-source CAD tools that are customizable and easily accessible. Benchmarking is crucial for the development of these tools, as it helps identify areas for improvement and evaluate updates and new features. This thesis presents a VPR-compatible architecture description of Intel’s Stratix 10 device for use as a benchmarking test case in FPGA CAD flows. The capture is used to benchmark the performance of VPR in terms of quality of results (QoR), runtime, and resource utilization, as compared to Quartus Prime 21.2. The results show a significant gap in packing and placement runtime, but a smaller overall runtime and smaller memory footprint for VPR. In terms of QoR, VPR performed noticeably worse with longer wirelength and smaller frequency on average. The major causes for VPR’s slow packing runtime are investigated and potential future directions for improvements are proposed.

Advisor: Betz, Vaughn T
A Maximum Entropy Principle for the Brain

In this work, we attempt to provide a theoretical rationale, rooted on biological grounds, for the anatomical organization of neurons in the brain. We propose a maximum entropy principle for the brain, inspired by Merzenich's work on neuroplasticity and Hebb's and Edelman's postulate for brain development. We show that when one maximizes the joint entropy of neuronal diameter and length constrained by neurophysiological elements of power, resource, space, and time, one arrives at a maximum entropy joint distribution conforming to a joint gamma distribution often reported in the literature. Then, using graph theory, we show how biological neuronal networks may self-organize topologically to maximize entropy and exhibit properties of a Rentian scaled small-world architecture to accompany learning and memory formation often observed in in vivo and in vitro neuronal networks across different species. This thesis is an attempt to show how the brain unfolds in a structured and lawful manner such that it embeds these laws into its anatomy to make learning and memory formation possible. It attempts to show that these fundamental elements of everyday life are mapped to the structural and topological level, which can be explained through an inference model from maximizing Shannon's entropy subject to biological constraints. In the hope of advancing the engineering of truly intelligent robotics, we believe that translating brain dynamics with mathematical and physical laws can pave the way for the future.

Keywords: Artificial intelligence
Brain
Engineering
Entropy
Neuroscience
Robotics
Advisor: D'Eleuterio, Gabriele G.D
Performance-Based Seismic Assessment of Moment-Resisting Frame Structures Retrofitted with Viscoelastic Plastic Dampers

Despite the incorporation of inelastic mechanisms to dissipate energy during seismic activity, buildings designed to current standards can still sustain significant damage. Older buildings, lacking proper seismic detailing, are particularly vulnerable to global instability. To mitigate financial losses and promote sustainability, researchers are seeking ways to enhance the seismic resilience of structures. One promising solution is the implementation of visco-elastic dampers, which provide supplemental damping and enhance a structure's ability to withstand wind and earthquake forces. Researchers at the University of Toronto have successfully integrated visco-elastic-plastic dampers into high-rise concrete buildings. Following their success, the potential for incorporating these dampers into mid-20th century high-rise moment-resisting frame structures was explored, resulting in estimated improvement in building performance. A general design process was established to optimize damper configurations for specific performance objectives.

Keywords: Seismic Design
Structural Engineering
Viscoelastic Dampers
Advisor: Christopoulos, Constantin
Caregiver Mental Health and Caregiver-Mediated Intervention in Autistic Children: An Integrated Approach

Caregivers of autistic children participating in caregiver-mediated interventions (CMI) (e.g., Social ABCs) face high levels of stress. Interventions such as acceptance and commitment therapy (ACT) may help alleviate stress. This study utilized reflexive thematic analysis to 1) understand mental health needs of caregivers participating in the Social ABCs; and 2) identify caregivers’ perspectives on the benefits and disadvantages of ACT, and its potential application to early intervention. Semi-structured interviews with Social ABCs participants revealed the need for social support, culturally sensitive care, emphasis on caregivers’ own wellness needs and the link between child success and caregiver wellness. ACT participants felt supported and revealed a new focus on prioritizing their own needs. Recommendations were made on integrating ACT with early intervention. These findings highlight the mental health need of caregivers participating in CMIs, and provide a starting point for integrating mental health intervention within early intervention.

Keywords: Autism spectrum disorder
Caregiver
Caregiver-mediated intervention
Early intervention
Mental health
Parent
Advisor: Penner, Melanie
Maternal Deaths using Ontario Coroner's Data: A Latent Class Analysis

Though rare in Canada, maternal death during or after pregnancy is an often-preventable event with far-reaching consequences. This study sought to identify distinct profiles of women who died during or after pregnancy. All deaths in pregnancy, or within a year thereafter, were identified using Office of the Chief Coroner for Ontario database, from January 1, 2004, to December 31, 2020. Variables related to the social and clinical circumstances surrounding the deaths were abstracted in a standardized manner. A latent class analysis (LCA) was performed to identify distinct profiles. Among 273 deaths identified, injury (22.0%) was the leading cause of death. LCA optimally identified three distinct subgroups, namely, (1) in-hospital deaths arising during birth or soon thereafter (52.7%); (2) accidents and unforeseen obstetric complications also resulting in fetal or infant demise (26.3%); and (3) out-of-hospital suicides occurring postpartum (21.0%). These findings highlight the need for policy aimed at reducing peri-pregnancy mortality.

Keywords: coroner
latent class analysis
maternal mortality
medical examiner
pregnancy
severe maternal morbidity
Advisor: Ray, Joel G
Critical Oxygen Tension of Synaptic Arrest, an Anoxia Defense Mechanism in Western Painted Turtle (Chrysemys picta bellii) and Common Goldfish (Carassius auratus)

The partial oxygen pressure at which an organism is no longer able to aerobically support its cellular energetic (ATP) demand is defined as the critical oxygen tension (Pcrit). Western painted turtles and goldfish are model vertebrates of anoxia tolerance, able to balance a decreased ATP supply and demand through various physiological methods including synaptic arrest, whereby GABAergic signaling causes a shunting inhibitory effect, depolarizing the neuronal membrane and increasing chloride conductance. The Pcrit of synaptic arrest for both fish and painted turtle was previously unknown, though unpublished results from our own lab predicted them to be around 30 torr for turtles. These results seemed oddly high, though my results corroborate these findings. Using nonlinear regression models, I observed Pcrit for turtle being observed at 21 torr, and 27 torr for goldfish. My findings suggest the Pcrit of synaptic arrest is higher than what is typically expected of hypoxia tolerant animals.

Keywords: critical oxygen tension
electrophysiology
goldfish
neurons
synaptic arrest
western painted turtle
Advisor: Buck, Leslie T
Process Design, Techno-Economic Analysis, and Life Cycle Assessment of Adipic Acid Production from Lignin

This thesis examines the environmental and financial aspects of lignin-derived adipic acid production. Process modelling and material and energy balances were used to conduct a techno-economic assessment (TEA) and life cycle assessment (LCA) to determine the economic and environmental impacts of this process. Three lignin-derived adipic acid production cases were evaluated and appeared profitable and economically robust with an expected capital cost of $99.9M to $100.1M, with IRRs ranging from 69% to 86%. The lignin-derived adipic acid production cases have life cycle GHG emissions ranging from 0.772 to 0.795 kg CO2 eq/kg adipic acid while conventional production emits 12.9 kg CO2 eq/kg adipic acid. The lower CO2 emissions for lignin-derived adipic acid production, when compared to conventional production, is consistent with other studies, however, GHG emission values can vary significantly due to study assumptions such as facility location, electrical grid, treatment of biogenic carbon, adipic acid yield, and chemical inputs.

Advisor: Saville, Bradley
MacLean, Heather
Learning based Communication and Sensing with Reconfigurable Intelligent Surface

Reconfigurable intelligent surface (RIS) can intelligently manipulate the impinging electromagnetic wave to improve the wireless propagation environment between the transceivers. New communication algorithms need to be explored as conventional algorithms are difficult to deploy in RIS-assisted networks due to the passive structure of the hardware. This thesis focuses on finding deep learning-based approach to address two challenging problems in RIS-assisted networks, namely 1) user scheduling in densely populated networks and 2) uplink localization via active sensing. To address the former problem, this thesis shows that graph neural networks can be used to schedule users and design RIS configurations to achieve high overall throughput while ensuring user fairness. For the latter problem, this thesis shows that long short-term memory networks can be used to design the RIS to gradually narrow down the search area to locate the user. Numerical results show that the proposed learning-based approaches outperform existing conventional approaches.

Keywords: Deep Learning
Neural Network
Reconfigurable Intelligent Surface
Resources Allocation
Wireless Communication
Advisor: Yu, Wei
Maturation of Movement-Related Brain Activity and Motor Control in Early Childhood

The neural development of motor control in early childhood is poorly understood. This thesis attempts to fill gaps in our knowledge by examining movement-related brain activity, motor skill assessments and white matter changes in children aged 6 to 10 years. Magnetoencephalographic (MEG) recordings of brain activity were collected during visuomotor and passive movement paradigms. Responses were found to be highly variable across participants during both tasks. However, clear trends were noted for movement-evoked fields during passive movements (MEFI - MEFIII) in the contralateral sensorimotor cortex. Increases in amplitude of the MEFs were also correlated with an increase in motor skills, as measured with the MABC-2. The development of white matter changes (fractional anisotropy, FA and mean diffusivity, MD) in the corticospinal tract revealed increases in FA and decreases in MD with age and the opposite with MABC-2. Further research is required confirm relationships between age and motor skills neural development.

Keywords: Brain development
MEG
Motor development
Advisor: Cheyne, Douglas
Towards the Development of Long-term Watershed Managment Plans: Retrospective Analysis and Forecasting of Hydraulic and Phosphorus Loading Trends in the Bay of Quinte

My study presents a modelling framework that can aid in our understanding of tributary total phosphorus and streamflow trends in the Bay of Quinte, Area of Concern. Retrospective analysis of riverine P concentrations signifies the success of local remediation efforts to mitigate the impact of point sources, but we also found a recent increase in the impact of nonpoint-source pollution. Global Circulation Models predict a seasonality shift, whereby spring freshet occurs earlier in the year accompanied by higher flow rates in the local creeks for the winter and early spring. This prediction implies that the timing when the exogenous nutrient masses enter the system may not necessarily be conducive to stimulating the primary productivity, but the GCM projections of intense summertime precipitation also suggest a propensity for higher frequency of extreme runoff during the period of the year, when the Bay of Quinte is more susceptible to undesirable ecological shifts.

Keywords: Bay of Quinte
Climate Change
Eutrophication
Global Climate Modelling
Hydrological Modelling
SWAT
Advisor: Arhonditsis, George
Magnetic Induced Vibration to Aid Miniature Surgical Scissors Cutting

Untethered magnetic surgical scissors have the potential to alleviate dexterity challenges plaguing surgeons during minimally invasive surgery. The lack of a tether affords these scissors to not take up limited ports and to possess a high degree of autonomy to access constrained spaces within the human body. However, due to limitations of magnetic actuation, untethered scissors have limited cutting torque and are difficult to control. This work attempts to address these issues through magnet placement design optimization for a greater degree of control and implementation of magnetic vibration induced cutting to promote crack formation in cutting targets. Alongside these scissors' improvements, a novel scissors evaluation technique independent of cutting force was developed to support performance comparison between vibration and no vibration cutting. Experimentation with novel vibrational capable scissors has shown that, under controlled conditions, vibrational cutting can be beneficial to small scale surgical scissors cutting. The combination of a vibrational slicing motion with cutting torque maintains the clean cutting capability of a pure torque based cutting while also enabling cutting of high fracture toughness agar (up to 5% concentration by weight concentration) in 10~s at a frequency of 10~Hz. This work aims to improve the quality of minimally invasive surgery through improving controllability and cutting abilities of surgical scissors.

Keywords: magnetic robot
magnetic vibration
scissors cutting
Advisor: Diller, Eric
Trace Element Loss in Pyrite at Different Pressure and Temperature

Pyrite is a common accessory mineral in orogenic gold deposit, one of the most important sources of gold that is valuable for economic geology all around the world. Although ore fluid sources are debated by researchers, metamorphic fluid source is the most popular model recently. During syngenetic and/or early diagenetic formation, pyrite is enriched with gold and trace elements that are present in the water column. When the metamorphism starts, later pyrite overgrowths replace earlier pyrite, and some trace element and gold are released to fluids that may precipitate as a free gold in cracks or as a rim around the pyrite. If the metamorphism reaches high grade (Greenschist and/or Amphibolite facies), pyrite converts into pyrrhotite, and gold and associated trace elements are released to metamorphic fluids to form ore deposit. But this model is only based on the interpretation of pyrite and pyrrhotite with the optical petrography.In this study, pyrite was converted to pyrrhotite experimentally, and determine which trace elements are released or retained and in what quantities. To do this a piston cylinder apparatus was used to apply pressure and variety temperatures. After the conversion, reductant pyrrhotite was analyzed by scanning electron microscopy (SEM) to check amount of pyrrhotite produced, and laser ablation inductively coupled plasma mass spectrometry (LA-ICP MS) to determine which trace element.

Keywords: conversion
metamorphism
Pyrite
pyrrhotite
trace elements
Advisor: GREGORY, Daniel David
Paediatric Crohn's Disease: The Impact of First Maintenance Therapy

Background: Tumour necrosis factor-a antagonist (aTNF) therapy is increasingly used as primary therapy to induce and/or maintain remission of Crohn’s disease (CD). Aim: This study compared outcomes with immunomodulator (IM) versus aTNF-based first maintenance therapy in paediatric CD. Methods: This study analyzed data from the Canadian Children IBD Network (CIDsCaNN) inception cohort study. Children with newly diagnosed luminal inflammatory CD receiving IM or aTNF-based first maintenance therapy were included in this analysis. The primary outcome was 18-month sustained steroid-free clinical remission and intestinal healing on first maintenance therapy. Propensity score matching was used to match children on baseline characteristics who received aTNF therapy or IM as first maintenance. Results: The primary outcome was more often met with aTNF vs IM maintenance. Conclusion: aTNF was superior to IM as first maintenance therapy in paediatric luminal CD. This was true even before matching, despite greater CD activity among children receiving aTNF therapy.

Keywords: Crohn's Disease
Inflammatory Bowel Disease
Advisor: Nguyen, Geoffrey
Towards Fail-in-Place Server Operation in Cloud Platforms

Hardware failure in datacenters is becoming a more challenging problem as the size of datacenter increases. Current cloud platforms handle hardware failures by sending technicians for an immediate repair, which becomes inefficient and unsustainable at scale. For example, each technician is responsible for maintaining 1,000 servers on average in modern datacenters. The number of technicians scales linearly with the size of datacenters under immediate service model. Moreover, future datacenter designs confine servers into closed-space environments to increase power efficiency. Forexample, Microsoft has been experimenting with encapsulating servers into sealed containers that are placed on the ocean floor. Immediate service becomes infeasible with such design; instead, a paradigm shift to the Fail-in-Place is required, where no repairs are performed until the entirecluster is decommissioned. This thesis introduces Tetra, a novel design of datacenter stacks that provides support for hosting VMs when hardware failures occur. Under air-cooled datacenters, Tetra employs repair batching with tunable repair frequency to improve efficiency. Tetra aligns with denser datacenter trend by reducing required technicians to scale sublinearly with the number of servers. As a first attempt atimplementing the Fail-in-Place paradigm, Tetra supports closed-space server environment design byforegoing repairs on components that fails most frequently. Under evaluations with real-world data, Tetra reduces operation costs on fan-cooled datacenters by reducing repairing needs by 80% while maintaining Service Level Objectives (SLOs) in key performance metrics. With immersion-cooled technology and future server designs, Tetra eliminatesthe need for repairs without having any impact on VM scheduling.

Keywords: cloud computing
data centers
Advisor: Schroeder, Bianca BS
Social Anxiety and Friendship Quality: The Role of Anger Suppression

Social anxiety has been linked to poor friendship quality, although it remains unclear why this association exists. The present study investigated anger suppression as a possible mechanism by which social anxiety influences friendship quality. 115 participants completed self-report measures of social anxiety, depression, anger suppression, self-criticism, and friendship quality. After controlling for depression, higher social anxiety was found to be associated with greater anger suppression. In addition, greater anger suppression was associated with poorer friendship quality. However, contrary to what was hypothesized, social anxiety was not significantly associated with friendship quality after controlling for depression. A moderated mediation analysis was conducted to determine if self-criticism moderated the mediated relationship between social anxiety, anger suppression, and friendship quality through its effects on the relationship between social anxiety and anger suppression. Evidence for moderated mediation was not found. These findings provide insight into the social and emotional functioning of individuals with social anxiety, thus illuminating potential targets for intervention and areas for future research.

Keywords: anger suppression
emotional expression
friendship quality
self-criticism
social anxiety
Advisor: Watson, Jeanne
Implementing a Thermal Proteome Profiling Assay to Probe Off-Target Effects of Novel GID4 Binder

Thermal proteome profiling (TPP) is a chemoproteomic approach to identify the protein:small molecule interactors. It relies on shifts in thermal stability of proteins when a small molecule binds to them. This is done by creating thermal denaturation curves at the scale of the proteome and finding proteins that have changes in denaturation or “melting” temperature. In this thesis, I first implemented a TPP pipeline and optimized it with previously published compounds methotrexate and staurosporine. I later used TPP on a novel GID4 binder. GID4 is the substrate binding domain of the CTLH complex, a conserved RING E3 ligase complex found across eukaryotic species. GID4 is responsible for binding to a peptide motif known as a “degron” and recruit it to the RING domain of the E3 ligase so it can be ubiquitinated. Through a collaboration with the Sicheri lab, we found 2 lead compounds (Cmpd67 and Cmpd88) that bind to GID4. Of the two compounds, Cmpd88 had the highest affinity and was cell permeable. With TPP, I found 15 potential interactors of Cmpd88 with GID4 being the compound significantly shifting the most. These results will inform future efforts to use Cmpd88 in a therapeutic context such as targeted protein degradation.

Keywords: CTLH Complex
Thermal Proteome Profiling
Advisor: Gingras, Anne-Claude
Rost, Hannes
Investigating the Use of Circulating Tumour DNA for Sarcoma Management

Sarcomas are a heterogeneous group of cancers, many with high rates of recurrence and metastasis, leading to significant morbidity and mortality. Due to a lack of early diagnostic biomarkers, by the time recurrent disease can be clinically detected it is often extensive and difficult to treat. ctDNA can potentially be used to monitor disease recurrence, progression, and response to treatment. Since ctDNA is present in extremely low quantities detection requires highly sensitive methodologies. Droplet digital PCR is highly sensitive, and capable of detecting and quantifying ctDNA; however, it is limited in that it can only be used to target one tumour variant at a time. mPCR-amplicon sequencing overcomes this issue by investigating multiple tumour variants simultaneously, although it is not as sensitive as ddPCR. ctDNA was detected in plasma collected at two different time points, indicating that ctDNA analysis has the potential to be used to monitor disease progression.

Advisor: Andrulis, Irene