VictorJuiz/thesis huggingface dataset:
Ex Vivo Perfusion Decellularization and Recellularization of Rat Hindlimbs for Vascular Composite Allotransplantation
Keywords: Decellularization
Recellularization
Regenerative Medicine
Tissue Engineering
VCA

Traumatic injuries, tumor resections, and large burns significantly impact patient quality of life and cause functional deficits due to volumetric soft tissue loss and musculoskeletal damage. Vascular composite allotransplantation (VCA) is an emerging surgical reconstructive avenue in transferring multiple, complex tissues as a composite subunit from donors to recipients. Although promising, significant side effects due to long-term immunosuppression regimens significantly impede the clinical implication of VCA. Tissue engineered composite tissues developed using decellularization and recellularization represent a solution. Herein, we established an ex vivo perfusion decellularized composite rat hindlimb and demonstrated cell clearance while maintaining tissue structure. We subsequently recellularized the vascular and muscle compartments simultaneously, demonstrating cell engraftment, survival, and evidence of a regenerated neo-endothelium and nascent myotube muscle formation. We furthered our ex vivo perfusion bioreactor design by incorporating electrical stimulation to advance towards re-functionalization. Altogether, our findings substantiate a proof-of-concept tissue engineered small animal model for VCA.
The Role of PDGFRα+ Mesenchymal Niche Cells in Intestinal Stem Cell Homeostasis and Tumorigenesis
Keywords: Disease
Homeostasis
Intestinal cancer
Mesenchymal niche cells
Stem cells
Stromal cells

Colorectal cancer is the world’s third most common and second deadliest cancer. Intestinal tumors are characterized by mutations of Apc, leading to Wnt signaling overactivation in intestinal stem cells (ISCs). Tightly associated with ISCs, mesenchymal niche cells (MNCs) and their signaling interactions with epithelium are poorly understood. Aiming to uncover the identity of MNCs, single-cell RNA sequencing studies have implicated cells expressing the Platelet-derived growth factor receptor α (PDGFRα), which is involved in cell recruitment, proliferation, and differentiation. My project focuses on PDGFRα+ MNC signaling and epithelial cross-talk in adult intestinal stem cell homeostasis and tumorigenesis. My work has revealed that tumor-associated MNCs have differences from homeostatic MNCs in their ability to stimulate stem cell growth. Lastly, PDGFRα signaling might be critical during adult homeostasis since gene deletion possibly confers a competitive disadvantage. Altogether, my work demonstrates the involvement of PDGFRα+ M.N.C. signaling in intestinal tumorigenesis and homeostasis.
Design and Simulation of Microfluidic Chip for Detection of Bacteria
Keywords: Bacteria
Diffraction Sensing
Point-of-Care
Pre-concentration

Bacterial infections and associated diseases are of high importance to be addressed in a timely yet efficient manner. In recent years, increasing antimicrobial resistance statistics around the world and a very slow rate of improvement of bacterial diseases in low-resource environments necessitates practical ways to address the issue with a reliable technique.Microfluidics merged with diffraction sensing pose a great potential for point-of-care diagnostics, specifically for capturing and concentrating the bacteria from its host such as drinking water. This study proposed an efficient technique for bacteria concentration and trapping using microfluidics. We studied the behavior of fluid and particles then adjusted corresponding parameters. While several designs were explored, we focused on periodic structures of dimensions compatible with the diffraction-based detection method invented in our group. Doubled Herringbone showed outstanding results, Reversed Herringbone and Simple Herringbone designs performed reliably (capturing bacteria with 72.3%, 54.5%, and 51.8% efficiency respectively).
Mapping Toxin-Host Interactions: A Novel Application of TurboID to AB Bacterial Toxins
Keywords: Clostridial toxins
Diphtheria
protein engineering
TcdB
toxin

Toxins are proteins secreted by bacteria that target host cells and impair cellular function. Significant knowledge gaps remain as to how existing and emerging toxins exploit host factors or processes. In this thesis, I present the first application of enzyme-catalyzed proximity labelling with TurboID to class AB bacterial toxins, introducing a new tool to uncover host-toxin interactions. Fusions of TurboID to the active domain of TcdB, and the related toxin TcsL, biotinylated proximal proteins at the plasma membrane, including members of Rho GTPase signaling cascades and the actin cytoskeletal network. I also present the first application of TurboID paired with mass spectrometry to identify cell surface receptors with recombinant fusions of a prey protein and the biotinylating enzyme. Using this novel approach, I present supporting evidence for the role of LRP1 as a receptor for TcdB.
COVID-19 as a glitch in time: Park-use in a Pandemic and the ‘Revolving Door of Emergencies’ in Toronto’s St. James Town
Keywords: COVID-19
displacement
gentrification
housing
policy
public space

This project uses park restrictions implemented during the COVID-19 lockdowns in Toronto as an entry point to examine the relationship between park use and housing conditions, focusing specifically on St. James Town, the most densely populated neighbourhood in Canada. Drawing upon interviews, as well as analysis of municipal policies and archival documents, I find that closures of outdoor spaces in St. James Town went beyond the standard COVID park restrictions implemented in the rest of the city, limiting available outdoor spaces for residents for three years. COVID park restrictions represented both a physical and temporal displacement for residents who experienced the lockdowns as a multi-scaled process of infrastructural abandonment. The targeting of green spaces, together with an increase in building maintenance issues and feeling of abandonment by decision makers made people feel like they had to leave the neighbourhood to access to social supports and an increased quality of life.
Identification of Novel Protein Abundance Fold Changes in Rett Syndrome in Neural Progenitor Cells and Neurons
Keywords: iPSC
proteomics
Rett Syndrome

Rett Syndrome (RTT) is a neurological disorder primarily caused by mutations in MECP2 (methyl-CpG-binding protein 2), a global modulator of transcription and translation. RTT has been well-studied at the RNA level, but despite the known effects of MECP2 on translation, RTT has been poorly studied at the protein level. To address this, I performed whole cell and membrane-enriched tandem mass tag-labeled mass spectrometry on neural precursor cells (NPCs) and neurons derived from a RTT patient induced pluripotent stem cell line. I quantified over 5000 proteins and found over 250 misregulated in RTT NPCs and neurons, many of which were not previously detected in RTT including CRABP1, a retinoic acid shuttling protein and marker of cell fate. The analysis of both whole cell and membrane-enriched neurons also identified a potential mislocalization phenotype not previously described in RTT. Overall, this work provides novel targets for RTT research and therapeutic development.
Health and Wellness Impacts of Being on the Land for Indigenous Peoples in North America
Keywords: Environmental Contaminants
Environmental Health
Indigenous Health
Land-based activities
Obesogens
Traditional activities

Indigenous people globally face disparate chronic health outcomes when compared to non-Indigenous counterparts. In Canada, First Nations people experience higher rates of obesity and associated conditions. The causes behind this are multifactorial and include colonialism alongside various social determinants of health. Being on the land (traditional lifestyle) can have numerous benefits, including an attenuating effect on obesity associated conditions. This thesis explored being on the land in two prongs. Chapter 2 is a systematic review conducted to explore the diverse health experiences related to traditional physical activities for Indigenous youth worldwide. Overall, the literature described numerous emotional, mental and spiritual benefits of traditional physical activity, including familial and communal relationships. This research shows the importance of including traditional physical activity in future programs. Chapter 3 examined the association between selected morphometry measures and body burdens of persistent organic pollutants (POPs) and toxic metals in seven communities of Eeyou Istchee. Results indicated a negative association between cadmium with various obesity measures in both males and females. Null associations were found between POPs and morphometry.
Assessment of Depression in Kidney-Pancreas Transplant Recipients: PROMIS Depression Item Bank with Computer Adaptive Testing
Keywords: Depression
Kidney-Pancreas Transplant
PROMIS CAT
Psychosocial
Validation

Kidney-pancreas transplant recipients (KPTRs) experience physical and psychological symptoms, despite improvements in survival and quality-of-life. Routine assessment of depressive symptoms using patient-reported outcome measures may identify KPTRs requiring clinical assessment and support. Validity and reliability of the PROMIS Depression Computer Adaptive Test (PROMIS-D CAT) was assessed. A cross-sectional, single-center convenience sample of KPTRs completed PROMIS-D CAT and additional legacy measures. PROMIS-D CAT demonstrated excellent validity and reliability. PROMIS-D CAT also had excellent discrimination in identifying KPTRs with potentially significant depressive symptoms. Results provide supporting evidence for the validity and reliability of PROMIS-D CAT to characterize depressive symptom severity among KPTRs.
Investigation of Material-Process-Structure-Property Relationships for Lignocellulosic Nanofibril Reinforced Polylactic Acid Composites
Keywords: Biodegradable
Biopolymer
Cellulose
LCNF
Packaging
PLA

This study explores polylactic acid (PLA)-based composites reinforced with lignocellulosic nanofibrils (LCNF) processed by spray drying (SD), freeze drying (FD), solvent exchange (SE), and solution transfer (ST) via polyethylene glycol (PEG). The LCNF ranged from near-spherical in the SD LCNF to fibrillar in SE LCNF. SE and FD LCNF agglomerated significantly which inhibits their ability to improve crystallization kinetics and tensile properties. SD LCNF, by its dispersed nature, facilitates high nucleation density, leading to crystallization-induced tensile enhancement. ST LCNF self-assembled into core-shell structures with PEG localizing at the LCNF/PLA interface, reducing agglomeration, yielding significant rheological modification, and greatly enhancing toughness. LCNFs processed by these methods impart differing morphologies that give rise to varying degrees of dispersion and agglomeration, which impacts downstream structures that form after processing and give rise to observed properties. Such material-process-structure-property relationships are foundational in the intelligent design of novel bio-based and biodegradable packaging materials.
Reciprocal Stimulation of HMGB1 and TGF-β in Pulmonary Fibroblasts – Implications for Pulmonary Arterial Hypertension
Keywords: Fibroblasts
HMGB1
Inflammation
Pulmonary Arterial Hypertension
TGF-β
Vascular Remodeling

A characteristic hallmark of pulmonary arterial hypertension (PAH) involves vascular remodeling and cellular dysfunction of the pulmonary vasculature. In addition to endothelial dysfunction, the outer adventitial layer of pulmonary vessels is a key site for immune cell activation and inflammatory initiation. The danger signal high mobility group box-1 (HMGB1) and the cytokine transforming growth factor beta (TGF-β) have long been recognized as critical mediators of PAH. With this in mind, we aimed to assess the relationship between HMGB1 and TGF-β signaling with respect to disease-related phenotypes in resident pulmonary artery adventitial fibroblasts (PAAF). We demonstrate that extracellular HMGB1 induces the secretion of TGF-β from PAAF in vitro, and inversely, TGF-β promotes intracellular protein expression of HMGB1, potentially via SMAD3 signaling. Our results introduce a mechanistic positive-feedback loop between HMGB1 and TGF-β on PAAF, progressively driving inflammation and vascular remodeling in PAH.
Development of a Robotic System for Femoral Artery Puncture and Access
Keywords: Endovascular
Femoral Artery
Robot
Robotics
Surgery
Ultrasound

Femoral access is used to complete endovascular procedures and is the recommended treatment for conditions such as stroke and cardiovascular diseases. These treatments are very time-sensitive and should ideally be performed within 3 hours to minimize long-term adverse effects. In addition to being time-sensitive, the procedures are highly complex and currently can only be performed by well-trained medical professionals. These factors are most significant in rural areas or underserved communities, where there is a shortage of healthcare professionals and the evacuation time to a hospital is the longest. If these procedures are to be performed in these areas, a device capable of completing the entire procedure with minimal human intervention is required. This thesis aims to accomplish this by developing a robotic system capable of US-guided needle puncture into the femoral artery, followed by the advancement of a guidewire.
The Guidance Signal Building Algorithm: A Method to Guide Neural Abstractive Summarization
Keywords: Natural Language Processing
Semantic Spaces
Transfer Learning
Transformers
Word Embeddings

The pervasiveness of large language models has been met with polarizing perspectives from the public. Calls for regulation from prominent institutions have increased the necessity to control the output of these models or perhaps align their learning, understanding, and generative capabilities with the values current societies deem important. The Guidance Signal Building algorithm builds a "guidance" feature using the XSum dataset as input. The guidance feature uses Text Rank and Parts of Speech Tagging to locate and store keywords from the document feature. The keywords are concatenated to the source document and summary features for the T5 transformer model. T5 is fine-tuned on the task of text summarization. After training, concatenation of the keywords did not prove to be an effective method of guidance. The training process illuminates recommendations for potentially adjustments to causal language modeling and masked language modeling by adding a guidance objective.
Grounding the Design of a Supportive Post-Hospital Discharge Intervention in the Experiences and Perspectives of Sudden Cardiac Arrest Survivors and Family Members
Keywords: experience-based co-design
out-of-hospital cardiac arrest
qualitative research
sudden cardiac arrest
survivorship

While advancements in pre-hospital and critical care have contributed to greater sudden cardiac arrest (SCA) survival, advancements in survivorship support remain desperately needed. This research leveraged qualitative methods to conduct step two of an adapted experience-based co-design process. The aim was to gain an understanding of SCA survivor and family perspectives on their previous experiences, challenges, and needs along the first year of their (co-)survivorship journey. Two themes reflect experiences related to challenges and support needs including: 1) navigating new territory without a map and 2) the impact of time and evolution of needs. Within each (theme) are several sub-themes which inform on how to support survivors and families after hospital discharge. Based on the themes identified, a set of considerations for subsequent co-design activities have been produced. The findings inform on SCA survivor and family support needs in the first year after hospital discharge, and how these needs change over time. Moreover, this work highlights how qualitative methods can be used not only to identify and understand SCA survivorship needs, but to inform further action to address such needs as well.
Usability and Feasibility Testing of Eating for Wellness (E4W) – An Image-Recognition Dietary Assessment Application for Adolescents with Obesity
Keywords: adolescent
dietary assessment
mhealth
nutrition
obesity
weight management

Background: Use of image-recognition dietary assessment apps in adolescents with obesity is not well studied.Purpose: To evaluate the usability, feasibility, and preliminary effectiveness of Eating for Wellness (E4W), an mHealth app, in improving dietary intake in adolescents with obesity attending an obesity clinic. Methods: Usability was tested through iterative cycles of patient and healthcare provider interviews with standardized scenario-based tasks. A pilot RCT of 32 adolescents (each enrolled for 1 month) was completed to assess feasibility of implementation and preliminary effectiveness. Results: Usability testing demonstrated that E4W was effective, efficient, and well-liked. Feasibility testing was hindered by technical challenges, patient engagement and adherence to food records, and there was no statistically significant improvement in dietary intake. However, patient acceptance and satisfaction scores were high. Conclusions: E4W was well-received by patients and HCPs. Further research is warranted to determine if E4W can improve dietary intake in adolescents with obesity.
Machine Learning-Assisted Computational Exploration of High Entropy Materials for Hydrogen Energy
Keywords: density functional theory
high entropy alloys
hydrogen
machine learning

Hydrogen fuel can be generated cleanly and used to store and transport energy. Challenges remain regarding the generation and storage of hydrogen, wherein low-cost materials with superior performance represent the final frontier towards ubiquitous adoption of this technology. Multi-principal element materials provide unlimited opportunity for tuning material properties to achieve desired performance goals. This thesis leverages density functional theory simulations and machine learning to both investigate previously synthesized materials and search for new, optimal compositions. Mechanisms of the hydrogen and oxygen evolution reactions were studied by analyzing the stability of intermediates on the active sites. Strategies for exploiting the varying local chemical environments within high-entropy surfaces are presented. Bayesian optimization was applied towards the accelerated discovery of high entropy alloys for hydrogen storage. Fundamental understanding of metal hydride stability was uncovered, and new alloy compositions were proposed.
Quantized Analog Signaling on a Switch Capacitor DAC (SCDAC)-based Transmitter
Keywords: Quantized Analog
Switch Capacitor
Wireless Transmitter

The presence of multiple operative modes and standards in 5G/6G systems set two crucial requirements for the next generations of wireless transmitters (TX): flexibility and high spectral purity. Modern radio frequency (RF) TXs are evolving to become more digital signal processing (DSP) intensive. While the scaling of technology nodes benefits DSPs, certain analog front ends (AFE) of the TX are still limited to conventional architectures, which do not offer great flexibility nor dynamic range. The solution is to use quantized analog (QA) approach to create an AFE which offers a new design space typically not seen in an analog-only AFE This thesis focuses on the design and characterization of a Quantized Transmitter(QTX) using the QA approach. It is the first time that QA signalling has been applied to RF TX designs, where previously this novel architecture has only been applied to RX front-ends. Fundamentally, this QTX uses passive switch-capacitor (SC) networks, including a 6-bit SC-DAC which can achieve an equivalent number of bits (ENOB) of 11 bits using 32 QTX slices. Thanks to the slicing of the signal, multiple channel transmission is possible on this QTX, which serves similar functionality asan RF-DAC without using high sampling rates nor high physical bits. Designed and manufactured in GlobalFoundries’s 22nm FDSOI technology, this QTX achieves an adjacent channel leakage ratio (ACLR2) of -56dBc and an error vector magnitude(EVM) of -35dB for a 15MHz 64-QAM signal. The linearity (SFDR) is also improved by over 10dB after an algorithm is applied to the slice offsets for a single tone test.
A Robust Model Predictive Control Scheme for Slung-load UAS Operating in Confined Flight Space
Keywords: Aerial Robotics
Collision Avoidance
Model Predictive Control
Planning and Control
Uncertainty Disturbance Estimator
Unmanned Aerial Systems

Unmanned aerial systems (UAS) have been found across industries from construction to environmental monitoring. In particular, the payload transport function for autonomous water sampling has garnered notable research interest in recent years. This paper investigates an uncertainty disturbance estimator-based (UDE) nonlinear model predictive control (NMPC) framework to navigate a slung-load UAS around an obstacle in highly limited workspaces. Scenarios arise where the allowable flight space for the vehicle body is less than that of the payload. The use of NMPC allows for the manipulation of the payload motion to avoid incoming obstacles while respecting workspace boundaries for all components of the slung-load UAS. The addition of UDE enhances controller performance in the presence of parametric uncertainties. Three solutions facilitating collision-free flights for a pair of slung-load UAS in a similar workspace are then compared. The advantages of the proposed method are demonstrated through simulations. High-fidelity simulations with PX4 software-in-the-loop (SITL) and Gazebo are used to validate the proposed approaches.
Distance Correlation Market Graph
Keywords: complex networks
Distance correlation
Index Tracking
Investment science
market graphs
stock network

Financial markets, with their complex interconnections, demand refined tools for understanding. This thesis delves into market graph construction, transitioning from Pearson correlation to the nuanced distance correlation, focusing on the S\&P 500 index. Empirical findings reveal that distance correlation excels during market turbulence, offering superior insights compared to Pearson correlation. When constructing portfolios using distant stock pairs based on distance correlation, the study evidences enhanced risk management. Additionally, by integrating Quadratic Programming with K-Medoid clustering, traditional index tracking challenges are addressed. Evaluations across equity indices demonstrate the combined approach's marginal advantage in precisely capturing market intricacies. This research underscores the potential of distance correlation in advancing market graph construction and optimizing index tracking paradigms.
Experimental Analysis of Partially Premixed Combustion in a Direct Injected Spark Ignited Natural Gas Engine
Keywords: combustion
engine
natural gas
partially premixed
stratified

Partially premixed combustion using early direct injection of natural gas was explored in a spark ignited single cylinder research engine. An overall equivalence ratio of 0.70 was used, with intake pressures of 5 and 10psig. Varied injection timings were employed to investigate different degrees of premixing, from full premixing with injection near BDC, to stratified combustion with injection near TDC. The effects on engine performance and combustion behaviour were assessed, along with NO, CO, unburnt hydrocarbon, and particulate matter emissions levels. Two injector nozzle designs were employed to evaluate the effects of confining the fuel to the piston bowl. Substantial increases in efficiency were seen in partially premixed operation, along with decreases in unburnt hydrocarbon emissions, resulting in significantly lowered greenhouse gas emissions. This came with the consequence of increased CO and particulate matter emissions at later injection timings.