VictorJuiz/thesis huggingface dataset:
FCRC: A Fully Connected Recurrent Convolutional Network for Recommendation
Keywords: AI
Graph Convolutional Network
Knowledge Graph
Machine Learning
Recommendation
Recommender

In pursuit of superior recommendation performance, it is compulsory to leverage information that goes beyond simple user-item interaction histories. Traditional supervised learning recommenders, like factorization machines (FM), collect both userand item attributes to enhance their recommendation while treating each interaction as an independent data instance. Later research showed that interaction histories can be effectively organized into a knowledge graph (KG), thereby exploiting the data’s spatial information and interconnectedness. Although these KG-equipped methods are capable of superior performance, the advent of KGs, caused prevalent literature to bifurcate into item or user attribute models. By exploiting only a single knowledge domain, such models forego additional performance. This work combines both knowledge domains into a single Fully Connected Recurrent Convolutional Neural Network (FCRC). Specifically, a method for concurrently leveraging both knowledge domains into a single graph is presented, alongside a novel recurrent pooling approach for improved message passing throughout the graph.
Reuse-Aware Temporal Partitioning of Data-Flow Graphs on a Coarse-Grained Reconfigurable Array
Keywords: CGRA
Data-Flow Graphs
Temporal Partitioning
Tight coupling

We design, implement and evaluate an Integer Linear Programming (ILP) model to partition dataflow graphs (DFGs) that exceed the resource capacity of a Coarse-Grained Reconfigurable Array (CGRA) based system, called T-CGRA. T-CGRA tightly couples the CGRA to system memory, which gives rise to partitioning concerns not addressed in prior work. First, it leverages the opportunity to reuse a cache line to multiple load nodes in a DFG partition. This results in an increase in throughput by up to 56% compared to when reuse is ignored. Second, T-CGRA has a limit on concurrent memory transactions that can be issued, which the model enforces. This leads to a reduction of up to 33% in throughput. Third, the inter-partition reads/writes are modeled for correctly measuring communication traffic, as opposed to inter-partition edges, which a bulk of the prior work has done. This leads to an increase in throughput of up to 48%.
Development of a Cell-mediated Passive Immunization System for Protection against SARS-CoV-2 Infection
Keywords: Cell therapy
COVID-19
Monoclonal antibody
Neutralizing antibody
Passive immunization
SARS-CoV-2

Immunologically impaired individuals respond poorly to vaccination, underscoring the need for alternative strategies to protect these vulnerable populations from COVID-19. The work contained in this thesis combines cell and monoclonal antibody engineering in an attempt to overcome the transient protective immunity afforded by passive monoclonal antibodies. Here, both mouse and human pluripotent stem cells engineered for safety and allogeneic acceptance were genetically modified to secrete potent SARS-CoV-2 neutralizing biologics (nBios). When transplanted subcutaneously, transgenic mouse embryonic stem cells and their differentiated derivatives deliver a supply of protective nBio titers for long periods of time in vivo, resulting in high and persistent plasma SARS-CoV-2 neutralizing activity. Altogether, this work establishes the foundation for a novel approach to passive immunization by demonstrating the potential for long-lived ‘off-the-shelf’ cell products that secrete neutralizing antibodies to confer sustained passive prophylaxis against current and future viral pathogens.
Performance of Pillar Wrapping Cable Slings in Block Cave Mines
Keywords: block cave extraction level support
ground support
instrumented cable slings
pillar wrapping

Pillar wrapping refers to a ground support system that uses rope or cable slings. It is commonly used to support the drawpoint pillars in the extraction level of block cave mines. An instrumentation study was conducted at the New Afton Mine to quantitatively assess the field performance of pillar wrapping used in the B3 Extraction Level. Instrumented cable slings were installed at two drawpoints to capture the behavior of the support system through cave initiation and propagation. Key factors that influence the performance of cable slings during early stages of the caving process were determined through the analysis and interpretation of the field data. A series of practical recommendations have been provided for designing and implementing cable slings and a comprehensive monitoring system to be used in the extraction level of block cave mines.
Automated Real-time 3D Visual Servocontrol of Single Cell Surgery
Keywords: 3D computer vision
image processing
object detection
single cell surgery
visual servoing

Automating the cell surgery processes is a potential solution to eliminate human involvement and promote the development of cell surgery. Here, we propose a real-time 3D visual servocontrol system for single cell surgery with the experimental results of single cell microinjection of an embryo and analysis of experimental data. Real time 3D image processes are a necessary requirement, since during cell surgery, when a micropipette contacts the embryo, the embryo is deformed, repositioning the internal components of the cell to be injected. An innovative 3D edge extraction algorithm is demonstrated for the real time 3Ds image processes. Visual servocontrol of the cell surgery process acquires the real-time target cell blastomere 3-dimensional position which is used to maneuver the micropipette under real-time closed-loop feedback control. The automated embryo microinjection process is conducted using the proposed real-time 3D visual servocontrol system, which is proven to be a potential solution for microinjection automation.
Beyond Landscape: Self-Expression in Xie Lingyun’s (385–433) Music Bureau Poetry and Imitation Poems Series
Keywords: Imitation
Medieval China
Music Bureau
Self-expression
Xie Lingyun

The Southern Dynasties poet Xie Lingyun 謝靈運 (385–433) is known as the pioneer of Chinese landscape poetry (shanshui shi 山水詩). Scholarly attention has been focusing on the accomplishments of Xie Lingyun’s landscape poetry and his philosophical thoughts; meanwhile, studies of his other poetic works are relatively few. While scholars argue that the writing of imitation poems was from the perspective of literary criticism, and the motivation was to express the inheritance and respect of Jian’an建安 (196–220) literature and Music Bureau (yuefu 樂府), they neglect the poet’s self-expression of writing styles and emotions. The thesis will concentrate on Xie Lingyun’s lesser-studied imitation poetry. It argues that the poems demonstrate the poet’s distinctive writing styles, personality traits and sentiments. This thesis aims to interpret Xie Lingyun’s imitative poem series and music bureau poetry as a form of self-expression that will reveal individual and diverse values and meanings.
GATA6: A Molecular Regulator of Pancreatic Tumour Growth and Phenotype
Keywords: Basal-like
Classical
CRISPR
GATA6
Pancreatic Cancer
Pancreatic Subtypes

Pancreatic ductal adenocarcinoma (PDAC) has been classified into two main transcriptional subtypes, Basal-like and Classical. The Classical subtype correlates with GATA6 expression, and ~16% of tumors show amplification in GATA6. The goal of this project is to understand the role of GATA6 as a molecular regulator of the Classical subtype. Competition assays show loss of GATA6 reduced cell fitness. Gene expression analysis showed GATA6 was integral in maintaining Classical gene expression and loss led to shifts towards more Basal-like expression and pathways. Despite a transcriptional shift towards Basal-like expression, phenotypic characteristics of the Basal-like subtype were notably absent (i.e., no EMT, MYC expression, or aggressive growth). This data suggests that loss of GATA6 is not sufficient to cause a full Basal-like phenotype and may lead to a transitional state that does not offer the same growth advantages as being in a full Basal-like state.
A Maximum Entropy Principle for the Brain
Keywords: Artificial intelligence
Brain
Engineering
Entropy
Neuroscience
Robotics

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.
Performance-Based Seismic Assessment of Moment-Resisting Frame Structures Retrofitted with Viscoelastic Plastic Dampers
Keywords: Seismic Design
Structural Engineering
Viscoelastic 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.
Caregiver Mental Health and Caregiver-Mediated Intervention in Autistic Children: An Integrated Approach
Keywords: Autism spectrum disorder
Caregiver
Caregiver-mediated intervention
Early intervention
Mental health
Parent

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.
Maternal Deaths using Ontario Coroner's Data: A Latent Class Analysis
Keywords: coroner
latent class analysis
maternal mortality
medical examiner
pregnancy
severe maternal morbidity

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.
Critical Oxygen Tension of Synaptic Arrest, an Anoxia Defense Mechanism in Western Painted Turtle (Chrysemys picta bellii) and Common Goldfish (Carassius auratus)
Keywords: critical oxygen tension
electrophysiology
goldfish
neurons
synaptic arrest
western painted turtle

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.
Learning based Communication and Sensing with Reconfigurable Intelligent Surface
Keywords: Deep Learning
Neural Network
Reconfigurable Intelligent Surface
Resources Allocation
Wireless Communication

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.
Maturation of Movement-Related Brain Activity and Motor Control in Early Childhood
Keywords: Brain development
MEG
Motor development

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.
Towards the Development of Long-term Watershed Managment Plans: Retrospective Analysis and Forecasting of Hydraulic and Phosphorus Loading Trends in the Bay of Quinte
Keywords: Bay of Quinte
Climate Change
Eutrophication
Global Climate Modelling
Hydrological Modelling
SWAT

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.
Magnetic Induced Vibration to Aid Miniature Surgical Scissors Cutting
Keywords: magnetic robot
magnetic vibration
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.
Trace Element Loss in Pyrite at Different Pressure and Temperature
Keywords: conversion
metamorphism
Pyrite
pyrrhotite
trace elements

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.
Paediatric Crohn's Disease: The Impact of First Maintenance Therapy
Keywords: Crohn's Disease
Inflammatory Bowel Disease

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.