VictorJuiz/thesis huggingface dataset:
Organoid Generation from Circulating Tumor Cells Isolated from Esophageal Adenocarcinoma Patients

Esophageal adenocarcinoma (EAC) is diagnosed in nearly 40% of patients when their cancer has already metastasized. Circulating tumor cells (CTCs) play a critical role in the metastatic cascade and need to be investigated in the context of EAC, but these need to be expanded due to their scarcity in blood. Studies in other cancers have successfully generated CTC-derived organoid (CTCDO) models and thus in this study we developed an EAC CTCDO model. We validated commonly used CTC isolation methods and were able to demonstrate that CTCs isolated using these can be cultured to generate organoids. We observed that these structures undergo growth arrest but are able to regenerate. We further confirmed the presence of and obtained the counts of CTCs within our cultures. This exciting preliminary CTCDO model holds great promise and potential to better understand the biology of EAC and personalize therapies for EAC patients.

Advisor: Yeung, Jonathan C
Advancing Wildfire Research Through Big Data, Artificial Intelligence and Emerging Image Processing Algorithms

More and larger wildfires in northern Canada are causing environmental damage, releasing stored carbon, and forcing residents to relocate. With climate change factors such as warmer winters and broader spread of damaging insects, Yukon is experiencing earlier, longer, and more intense wildfire seasons. This paper furthers our understanding of wildfire severity mapping by: (1) assessing advancements in remote sensing data, cloud geoprocessing platforms and emerging image processing algorithms for wildfire burned area mapping, (2) conducting a driver analysis of wildfire severity in Yukon using the LandTrendR temporal segmentation algorithm, the Google Earth Engine cloud geoprocessing platform, and a deep neural network, and (3) analyzing the influences that a diverse series of climate, topographic, ecological and fire history variables had on wildfire severity. These new techniques and tools, enhancing the accuracy of burn severity models, could improve Canadian and global forest management practices, potentially reducing the impact of severe wildfires on humans.

Keywords: automated machine learning
deep learning
forest fire
Google Earth Engine
LandTrendR
wildfire severity
Advisor: He, Yuhong
Promoting Online Learning in Primary Schools in Rural China

In response to the global impact of the Covid-19 pandemic, China introduced a national online education program catering to students in both urban and rural areas. The abrupt transition from traditional in-person education to online learning has posed numerous challenges, especially concerning the quality of learner-instructor interactions. This study explored the role of instructional design in enhancing these interactions and, consequently, improving the online learning experience for rural primary school students. Additionally, the research investigated the specific challenges rural primary school students and their instructors face while adapting to online education. By providing insights into how instructional design can be harnessed to address these challenges, this study contributed to the field of online education, particularly for rural primary schools. The findings offered guidance to policymakers, educators, and instructional designers working to enhance online learning experiences in similar contexts.

Keywords: K-12 Education
Online Education
Primary School Education
Rural Online Education in China
Advisor: Lui, Michelle
A Tailored Fit: Design and Evaluation of a Website Structure Self-Tailoring Option for Older Adults

Older adults are increasingly turning to online sources for health information. In doing so they face unique combinations of barriers which must be considered when creating websites. Linear and matrix information architecture structures can be used to address certain barriers faced by older adults. This thesis describes the design and evaluation of a health information website which allows older adults to choose, or self-tailor, between a linear and matrix structure. The study also evaluated the role that user involvement, in the form of a focus group, had on users’ satisfaction and experience with the final website design. The findings indicate that older adults are able to successfully select their preferred structure when self-tailoring and that having the option to self-tailor gives older adults a greater sense of control over their experience. The findings also demonstrate that the focus group led to design changes which were received positively by subsequent website users.

Keywords: Empirical study that tells us about how people use a system
Human-Computer Interaction
Information Architecture
Older Adults
User Experience Design
Website Design
Advisor: St-Cyr, Olivier
Locating the Political and Spiritual in Three Plays by Métis/Dene Playwright Marie Clements: the Unnatural and Accidental Women, Copper Thunderbird, and Tombs of the Vanishing Indian

This work examines the dramaturgical relationship between the political and spiritual layers of three of Marie Clements’ plays: the Unnatural and Accidental Women, Copper Thunderbird, and Tombs of the Vanishing Indian. I introduce the playwright and the three plays, my relationship to the plays, Clements’s craft and Indigenous dramaturgy, Indigenous spirituality as it pertains to the play, and my political approach, which includes Marxist-influenced feminist materialism. I then separate the three plays into the spiritual and political narratives for a close and individual reading of each. I argue that by bringing the spirit world directly onstage and weaving together both traditional and material worlds, Clements provides her characters with a timeless connection to the wisdom of ancestors and history with which to confront the consequences of colonialism and settler capitalism on their lives. In doing so, she alleviates her characters’ isolation and dislocation, allowing them (and the audience) to transcend their circumstances and (re) imagine an Indigenous futurity.

Keywords: Clements
Dramaturgy
Indigenous
Performance
Playwriting
Advisor: Eacho, Douglas
A Net-Decomposing Parallel Field-Programmable Gate Array Router

Routing is the final step in the FPGA CAD tool flow and has a significant impact on runtime and quality of results. The most common algorithm used for FPGA routing, PathFinder, has proven difficult to accelerate by parallelization since it was introduced in 1995. We introduce two parallel routers extending the PathFinder-based AIR router in VPR 8, which is the fastest serial routerto date. The baseline router is based on the widely applied technique of recursive bi-partitioning. The improved router applies a range of novel net decomposition methods on top of recursive bi-partitioning to increase scalability. We obtain a speedup of 1.42x with 4 threads compared to VPR 8 on the Titan benchmark set with the baseline router and a speedup of 1.72x with 4 threads with the improved one (with 1.1% increase in critical path delay). The improved router is able to obtain a speedup of 1.82x with 4 threads with 1.4% increase in critical path delay when flat, or combined inter- and intra-cluster routing is enabled. Both routers are deterministic and serially equivalent. Implementations are made available as a part of the open-source VTR framework.

Keywords: CAD
EDA
FPGA
parallel routing
Advisor: Betz, Vaughn
Investigating Heterogeneity in the Long-term Maintenance of Cellular Phenotype Following Ionizing Radiation

Ionizing radiation (IR) is commonly used to kill cancer cells by causing DNA damage. Cells initiate DNA repair pathways and cell cycle arrests to suppress cell death, and the differential activation of these pathways can lead to several distinct fates in neighbouring irradiated cells. Some cells die rapidly by apoptosis, some proliferate indefinitely, while others activate another mode of cell death or permanently exit the cell cycle into senescence. We established scRNA-seq data analysis pipelines for tracing transcriptionally heterogeneous fates in vitro, and my preliminary data demonstrate separable gene expression when a homogeneous cell population (MCF10A cells) is irradiated. My work is focused on establishing a long-term live-cell imaging assay for tracing the diverse fates of irradiated cells at the single-cell level. Using this system, the timepoint, frequency, and state of cell divisions can be observed in normal and pharmacologically modified conditions, and we traced fate outcomes in cells irradiated during different cell cycle phases as DNA damage burden increases, as classical DNA damage response kinases are inhibited, and when cell fate is artificially directed towards different modes of death. Through fate mapping of single-cells, I envision this system as an aid to establishing novel deterministic features of IR-induced cell fate outcomes, identifying candidate pathways associated with fate emergence for further investigation, and guiding novel avenues for rationally shaping heterogeneity in fate following IR. This will provide a deeper understanding of why some cells are responsive to treatment, activating favorable modes of cell death, while others are left behind to repopulate a tumor and drive local cancer recurrence after treatment.

Keywords: DNA damage
fate tracking
heterogeneous fate
ionizing radiation
single cell
Advisor: Harding, Shane M.
The FORWomen Qualitative Study: Substance Use Treatment Experiences of Forensic and Non-Forensic Women

Biopsychosocial factors influence women’s substance use (SU), like sex differences, higher rates of concurrent mental illnesses, and sociocultural expectations affecting treatment engagement, resulting in a more vulnerable profile compared to men. Furthermore, women involved with the criminal justice system (CJS) experience more complex trauma, leading to higher rates of post-traumatic stress disorder and other challenges. This project aims to identify barriers to treatment-seeking, useful/inconvenient components of treatment, perspectives on women-only group settings, and other opinions on treatment. Forensic and non-forensic women from the Center for Addiction and Mental Health in Toronto, Canada were interviewed using qualitative semi-structured interviews. Ten overarching themes were identified: (1) SU history; (2) Barriers to help-seeking; (3) Facilitators for treatment initiation; (4) Knowledge on SU and mental health; (5) Addressing practical difficulties to attendance; (6) Intervention components; (7) Peers and group settings; (8) Influence of staffing; (9) Gender-specific concerns, and; (10) Supporting long-term recovery.

Keywords: forensic mental health
lived experiences
qualitative
secure services
substance use
women's health
Advisor: George, Tony
Cryopreservation of Myoblasts in Paper-based Scaffolds for Inter-laboratory Studies of Skeletal Muscle Health

Three-dimensional tissue-engineered models are poised to facilitate progress in understanding skeletal muscle pathophysiology and identify novel therapeutic agents to improve muscle health. Yet, barriers to widespread adoption of such models include: methodology complexity, limited throughput, and requirement of cell culture expertise and/or specialized instruments, reagents, or software. To alleviate these barriers, our group engineered a 24-well model to study muscle endogenous repair (MEndR) that can be easily imaged and integrates with semi-automated image analysis pipelines. However, MEndR still requires user seeding experience and a high number of cells, reducing its throughput. Therefore, I first demonstrate our work scaling MEndR to a 96-well footprint (mini-MEndR), augmenting its ease-of-use and throughput. Second, I develop a standard operating procedure for the cryopreservation of muscle cell progenitors in mini-MEndR and validate that it preserves cell viability, differentiation, and function. Taken together, cryopreservation in mini-MEndR offers researchers an “off-the-shelf” platform for studying skeletal muscle health.

Keywords: Cryopreservation
Drug Discovery
Higher-Throughput
In Vitro
Regeneration
Skeletal Muscle
Advisor: McGuigan, Alison P
Gilbert, Penney M
Linearly-scalable R-2R Multiply-and-accumulate Architecture for AI Edge Devices

From the cloud to the user-end, Artificial Intelligence (AI) edge devices have been receiving increasing attention thanks to its benefits including privacy, low latency, and efficient use of bandwidth. However, traditional computing architectures such as CPU and some existing AI accelerator cannot meet the tight energy budget of future AI edge applications. Researchers have been focusing on an emerging computing architecture, computation-in-memory (CIM), which improves both memory access and computation efficiency. This thesis presents a current-domain compute-in-memory (CIM) architecture for acceleration of AI edge inferencing. A novel multiply-and-accumulate (MAC) scheme is introduced by exploiting the R-2R resistor ladder as a binary-weighted current recombiner. The area and power of the proposed scheme scale linearly as numerical precision increases for both input activation and weight. Computation latency is maintained single cycle. A prototype in 22nm FD-SOI CMOS process achieves 2.2ns system latency, 56TOPS/W energy efficiency and 4TOPS/mm2 area efficiency with 6-bit input activation and 8-bit weight.

Keywords: Analog Computation
Artificial Intelligence
CMOS
In-memory
Advisor: Liscidini, Antonio A
Breakdown of the Apical Spectrin Network Leads to Endothelial Dysfunction and Vascular Stiffening in Pulmonary Arterial Hypertension

Recently, a critical role for a spectrin cytoskeletal network in sensing of shear and regulation of vascular stiffness has been described in systemic endothelial cells. The loss of spectrin resulted in the disappearance of apical caveolae, dysregulated eNOS activation, and a lack of calcium response to shear. Since spectrin can be broken down in vivo by calpain, which is activated in pulmonary arterial hypertension, I hypothesized that spectrin breakdown may represent a key mechanism underlying endothelial dysfunction.I report an increased prevalence of spectrin digesting proteases and spectrin breakdown products in the lungs of monocrotaline treated rats, along with decreased levels of caveolin-1 and a reduction in apical caveolae, a trend that was reversed by administration of calpeptin, a calpain inhibitor. Calpeptin was also shown to be protective against severe pulmonary hypertension in MCT rats. Furthermore, I determined that the knockdown of spectrin in endothelial cells results in internalization of caveolin-1 and impaired endothelial responses to shear. My studies detail a critical role for the spectrin cytoskeleton in the development of endothelial dysfunction and highlight the therapeutic potential of preventing its breakdown via calpain inhibition.

Keywords: Breakdown
Endothelial Dysfunction
Pulmonary Hypertension
Spectrin
Advisor: Goldenberg, Neil M
VR Drama Therapy

This thesis delves into the scarcely explored domain of Virtual Reality Drama Therapy (VR DT), an innovative intersection that merges the capabilities of VR with the foundational principles of traditional Drama Therapy. The study aims to bridge the existing knowledge gap in this area, delivering a comprehensive understanding of its potential benefits, applications, and limitations. The core methodology implemented encompassed a literature review and theoretical analysis, specifically within three academic fields: Drama Therapy, VR Therapy, and VR Drama. The research scrutinizes the fundamentals of Drama Therapy and the therapeutic and performative potentials of VR, culminating in a theoretical framework for VR DT. Although limitations are acknowledged, the conclusions indicate VR's unique features can amplify the therapeutic interventions’ scope, presenting an inventive and immersive therapeutic paradigm. This thesis provides a preliminary guide for implementing VR DT, paving the way for further research and practical applications in Drama Therapy contexts.

Keywords: Drama Therapy
Psychodrama
Theatre Therapy
Virtual Reality
VR Drama
VR Therapy
Advisor: Eacho, Douglas
Optimizing Fabrication and Validating Performance of InAs Nanowire Field-Effect Transistors for Enhanced Chemical Sensing

As the demand for advanced sensing technologies is growing in multiple industries, Nanowire Field-Effect Transistors (NWFETs) have recently shown great promise as highly sensitive, rapid, and portable chemical detectors. The large surface-to-volume ratio and the confined transport allow perturbations occurring at the surface of nanowires to affect the entire cross-section of the structure. This thesis presents an exploration into the performance enhancement and optimization strategies of InAs NWFETs, with the core intention of contributing to the realization of next-generation sensing electronics. The fabrication procedure has been optimized to significantly improve usable device yield. A new detection limit has been established in the proof-of-concept measurement of streptavidin in the liquid media. Commercialization and large-scale production perspectives and challenges are discussed.

Keywords: biosensing
InAs
NWFET
sensor
Advisor: Ruda, Harry E
The Performance Cost of Disintegrated Manycores: Which Applications Lose and Why?

Recent industry manycores have transitioned to disintegrated designs with multiple chips within a package. Disintegration can make larger and higher performance systems economically viable by reducing cost, but introduces additional network bandwidth and latency bottlenecks which harms performance. Ideally, cost savings outweigh disintegration slowdown. This thesis presents the first study, to our knowledge, of the disintegration performance penalty across a diverse suite of applications and a characterization of what properties of applications impact this penalty. We find high variance in disintegration slowdown (performance penalty normalized to equivalently sized monolithic design) across applications. Some disintegrated applications lose almost half their performance. We identify that metrics relating to the network-on-package bandwidth and data sharing are correlated with disintegration slowdown. Disintegration constrains the network where it crosses between chips, and these categories of metrics either measure network pressure or measure data sharing, which causes network pressure.

Keywords: Chiplets
Disintegrated systems
Multicore architectures
Network-on-chip
Advisor: Jeffrey, Mark C
Patient-Reported Outcomes, Experiences, And Gaps in Care in Adults Undergoing Congenital Heart Disease Interventions

Congenital heart disease (CHD) is the most common congenital defect across Canada, and with advances in medical research and technology, most patients survive up to adulthood. Over the past decade, there has been a shift from surgical to non-invasive percutaneous interventions for adults with congenital heart disease (ACHD). Though patients with ACHD have several psychosocial needs, there is no literature exploring patient-reported outcomes and experiences after receiving an ACHD intervention. In this multi-methods investigation, we explored change in quality-of-life, factors associated with patient experience, and gaps in care after receiving an ACHD intervention in a single high-volume centre. We found that average change in self-reported mental and physical health in the overall sample was not clinically meaningful. However, scores changed in both directions, with most patients experiencing either clinically meaningful improvement or worsening of their mental and physical scores. Generally, patients reported positive care experiences, but emphasized some communication gaps which contributed to unanticipated experiences during and after their procedures. Sex and New York Heart Association functional class, a measure of functional capacity, emerged as important determinants of patient experience. Future analyses with larger sample sizes will explore determinants of improvement and decline in mental and physical health scores, and use more robust qualitative methods to expand on the importance of communication before, during, and after the procedure.

Advisor: Abrahamyan, Lusine
Horlick, Eric
Geometric and Access Time Utilities for a Payload Operations Planning Software

The Payload Operations Planning Software is a tool that satellite mission operators use for handling the deterministic aspects of mission operations, which include schedule validation and searching for observation opportunities. The software is applicable to any Earth observation satellite mission. This work presents the design and implementation of two modules within the planning software, namely the Geometric Utilities and the Access Time Utilities. The Geometric Utilities perform calculations involving ellipsoidal polygons representing area regions on Earth’s surface, spacecraft sensor fields, and specular reflections on Earth’s surface. The Access Time Utilities compute the periods of access between a spacecraft and objects of interest, which are ground stations, ground targets, latitude ranges, polygon areas, and specular points. Both modules are integral to finding observation opportunities. A Technology Demonstration Mission with radio frequency sensing, bistatic radar, and imaging capability is used as an example for describing design and development.

Advisor: Zee, Robert E
EV Assisted Robust Security Constrained ACOPF for N-1 Line and Generator Contingencies

The optimal power flow provides an economically optimal solution under normal conditions. However, when subject to disturbances, this system may fail to operate securely leading to serious consequences. Security constrained optimal power flow (SCOPF) ensures the reliable operation of the power grid following an outage. Corrective SCOPF uses fast response generating units to ensure feasibility of postcontingency scenarios. Future power grids with high integration of electric vehicles will have huge flexible energy capacities which could be used for ancillary services. Modelling EV behaviour can be challenging due to several uncertain factors affecting its operation and availability. This thesis investigates the potential of using EVs for corrective SCOPF of N-1 contingencies using a robust optimization model. The results show the techno-economic benefit of EV-based post-contingency real and reactive power control. There is cost savings up to 5% and the set level of robustness guides the performance of the model under uncertainty.

Keywords: Benders decomposition
Economic feasibility
Electric vehicles (EV)
Line and generator contingency
Robust optimization
Security constrained optimal power flow (SCOPF)
Advisor: Tate, Joseph
Exploring Seasonal Hydrologic Performance of Green Roofs with Various Layering Profiles

Green roofs (GR) are a low impact development approach that utilizes an untapped local to manage both stormwater quantity and quality in urban areas. Adaptations in the retention layer composition are being made to improve water storage capacity and pollutant control. At GRITLab1, extensive GRs were constructed with manufactured retention/detention materials to evaluate the water quantity management compared to traditional, substrate only GR. The inclusion of manufactured layers improved the hydrologic performance of GRs during the growing season, but better performance was seen by the traditional GR in the winter. At GRITLab2, winter snow accumulation and stormwater quality was evaluated for extensive GRswith substrates both with and without biochar amendments and sedum and native vegetation. Over two winters, the type of vegetation, and its cover density, impacted the snow accumulation. The frozen substrate contributed to a decline in the leaching potential of the GR systems.

Keywords: Green Roofs
Low Impact Development
Stormwater Engineering
Water Quality
Water Quantity
Advisor: Drake, Jennifer