VictorJuiz/thesis huggingface dataset:
The Effects of Aging on Mesenchymal Stem Cell Extracellular Vesicle Treatment following Myocardial Ischemia/Reperfusion

Extracellular vesicles (EV) have recently emerged as a key factor secreted by stem cells which improve infarct healing post-myocardial infarction (MI). However, the cellular processes which regulate EV function are largely unknown. Here we investigate young and old mouse bone marrow mesenchymal stem cells (MSCs) to determine whether aging impacts the beneficial effects of secreted EVs. Cells and EVs were studied in-vitro to determine the effect of aging on cell function as well as EV secretion. Using a mouse model of myocardial ischemia/reperfusion (I/R) we show that young, but not old, MSC-EVs preserve left ventricular function at four weeks post-I/R by echocardiography. Mechanistically, we found that young MSC-EVs modulate the inflammatory response more effectively than old MSC-EVs in-vitro and in-vivo. Understanding how aging affects EV secretion and function will lead to a better understanding of the cellular processes which regulate the beneficial effects of EVs on cardiac repair.

Keywords: Aging
Cardiac
Extracellular Vesicles
Stem Cells
Advisor: Li, Ren Ke
Is Being Worse than You Worse for Us? The Effect of Social Comparisons to Friends

Friendship is an important source of well-being, but remarkably little research has investigated the processes that can undermine these connections. One such process is the tendency to compare oneself to others, especially to close others. Across three studies, I examined how the frequency and direction of social comparisons influence the evaluations of the self and of a new friend. In Studies 1 and 2, frequent upward comparisons were positively associated with global markers of closeness. In Study 2, I found that individuals reported lower self-evaluations after an upward comparison, and that this comparison negatively impacted immediate evaluations of their friendship. In Study 3, the valence (positive or neutral) of a message from a friend had no effect on one’s self- or friendship evaluations. These studies may suggest that social comparisons do have an impact not only on how one thinks about the self, but also on how friendships are perceived.

Keywords: Friendship
Friendship Outcomes
Social Comparison
Advisor: Lockwood, Penelope
Classification of Neural Tissue Types for an Endoscopic Full-field Optical Coherence Tomography Imaging System

Optical coherence tomography is a volumetric imaging technique that can differentiate brain regions with micron-scale resolution. Our group has previously developed an endoscopic full-field swept-source OCT system with the aim to provide real-time surgical guidance for the implantation of electrodes for deep brain stimulation. This thesis builds on our prior work. Due to the limitations in the resolution and contrast due to scattering from the tissue, to identify different types of neural tissues, we developed an image classification algorithm that uses texture features and optical attenuation. The algorithm could classify three different brain regions in the ex vivo data set with a test accuracy of 70%. Also, we performed a comparative analysis on the optical properties of the ex vivo and in vivo data sets to provide directions on how to achieve high accuracy for in vivo data.

Keywords: Image Processing
Optical Coherence Tomography
Optical Devices
Surgical Instruments
Advisor: Poon, Joyce K.S.
Organ-on-a-chip Applications using Collagen Tubular Constructs

Collagen is the most abundant protein found in the human extracellular matrix. Tubular structures are also found in abundance in various human tissues. This thesis demonstrates two applications using extruded collagen-I tubular structures for organ-on-a-chip models. The first application is to use a collagen tubes as the foundation of a tubular-based organ-on-a-chip device to model the human airway. With this device, we showed the ability to culture a confluent monolayer of human bronchial epithelial cells that showed functional responses to various stimuli. Next, we recreated the Quake-style valve and pump using these collagen tubular constructs. Quake-style valves and pumps are predominantly fabricated with the elastomer, polydimethylsiloxane. This material is not the best choice for use with organ-on-a-chip platforms, which we rectify with our collagen-based devices.

Keywords: Collagen
Microfluidics
Organ on a chip
Pumps
Soft Materials
Valves
Advisor: Guenther, Axel
Provincial Funding of Faith-based Schools in Ontario: Contemporary Framing Contests

Ontario is the only province in Canada that continues to exclusively provide government funding to Catholic schools while not providing any funding to schools of other faiths. The research question asks; how do stakeholders, advocates for funding, and proponents of one public school system make their perspective persuasive? The project explores perspectives on how arguments about funding for faith-based schools have shifted over the past sixty years. Frame analysis is used as both a theoretical framework and a method to explore how participants frame their argument in today’s sociocultural climate. All participants were found to frame their arguments using social justice rhetoric - its themes, terms, imagery, and priorities - in some form. The use of social justice language represents a shift in framing of this topic from older styles that focused on multiculturalism (1990’s) and even older ones that saw religious instruction as a moral duty (pre 1980’s). The findings highlight that there are many tensions between advocates of social justice who are concerned with how faith groups will treat women and members of the LGBTQ+ community and advocates for funding faith-based schools who believe they face discrimination by their lack of funding.

Keywords: Education Policy
Faith-Based Schools
Frame Analysis
Framing Methodology
Religion
Religious Schools
Advisor: Davies, Scott
On the Elementary Symmetric Polynomials, Inverse Vandermonde Matrix, and its Application in Signals and Images

The Vandermonde matrix naturally appears in systems of equations for applications of polynomial approximation. Solving the system, which requires inverting the Vandermonde matrix, may be preferred because researchers can utilize efficient matrix computation methods. However, the Vandermonde is ill-conditioned and prevents standard methods from calculating accurate entries to the inverse. Many of the derived algorithmic solutions to the Vandermonde inverse contain a mathematical expression called the Elementary Symmetric Polynomial (ESP). The ESP is computationally inefficient to solve directly, so there are also algorithms to solve them. The state-of-the-art ESP and inverse methods are fully recursive and may be more susceptible to noise perturbations in the Vandermonde matrix than a closed-form inverse method. In addition, the performances of the methods in a variety of applications in polynomial approximation are unexplored. This thesis investigates the utility of the state-of-the-art methods against a novel ESP and closed-form Vandermonde inverse method in applications of polynomial interpolation and Fourier reconstruction in the presence of Gaussian noise.

Keywords: Elementary Symmetric Polynomial
Magnetic Resonance Imaging
Vandermonde Inverse
Vandermonde Matrix
Advisor: Plataniotis, Konstantinos N
Investigation of Superior Mechanical Properties of PP Homopolymer and PP Elastomer Self-reinforced Blends

Self-reinforced blend (SRB) of PP homopolymer and Poly(propylene-co-ethylene) copolymer (= PP elastomer) were prepared with 15 different ratios ranging from 100:0 to 0:100. PVDF and PP elastomer non-self-reinforced blend (n-SRB) with the same ratios were prepared to examine the self-reinforcement effects. Unlike n-SRB, SEM images revealed that the Polypropylene SRB showed perfect interface with no evident phase boundaries between two components. Further DSC characterization confirmed that PP homopolymer and PP elastomer exist as separate phases. Tensile test on SRB and n-SRB taught us that although PP homopolymer has inferior young’s modulus, tensile toughness, and ultimate strength than PVDF, all the properties got better in SRB than n-SRB. Superiority of SRB over n-SRB was especially prominent in co-continuous phase. Good interface let SRB took advantage of PP elastomer component, allowing the blend to have strain-hardening behavior. The strain-hardening effect contributed SRB to have better strength and tensile toughness compared to n-SRB.

Advisor: Park, Chul B
Lee, Patrick C
SMX Recruitment to Repetitive Regions of the Genome

Chromosomal translocations and rearrangements are hallmarks of cancer and have been directly implicated in many cancers. It is generally accepted that DNA double-strand breaks are a precursor for many rearrangements, and that nucleases are involved in the formation/repair of these breaks. One such nuclease is the SMX tri-nuclease complex is comprised of the SLX1-SLX4, MUS81-EME1, and XPF-ERCC1 endonucleases, where SLX4 provides the scaffold. The goal of this project is to determine if SMX is recruited to genomic loci that form DNA secondary structures. I show that fluorescently-tagged SLX4, SLX1, MUS81 and XPF assemble SMX and localize to sites of replication stress and the nucleolus. I also show that SLX4 is recruited to nucleolar caps in response to rDNA damage and localizes to common fragile site 3B in cells experiencing replication stress. These results indicate that SMX is recruited to repetitive regions of the genome, including common fragile sites and rDNA.

Advisor: Wyatt, Haley
Telling Stories in Order to Live: An Inquiry into Applied Theatre and Critical Media Education in an Urban Middle School

As youth media programs proliferate in an age of “algorhythmic governance” (Boler Davis, 2018), critical questions emerge about the process and direction of the content being created, particularly, how to develop stories “without necessarily recirculating dominant relations” (Gaztambide-Fernandez, 2013, p. 227). Grounded in critical race theory, this arts-based inquiry highlights the way that applied theatre approaches and a lens of cultural production offer a promising paradigm for bringing greater depth and nuance to student counter-storytelling (Solorzano Yosso, 2002). This thesis describes the strengths of key practices that were carried out in two urban middle school classrooms. Drawing on student interviews, group discussions and creative work, three stories by youth that I am calling propositional stories, are offered as examples that illustrate important implications for the way in which educators and practitioners might approach media production and storytelling with youth.

Keywords: applied theatre
counter-storytelling
critical race theory
cultural production
media literacy education
middle school
Advisor: Gallagher, Kathleen
Gaztambide-Fernandez, Rubén
Hybrid Silicon-Organic Augmented Low Index Guiding Waveguides for Nonlinear Optics

Silicon-on-insulator (SOI) has emerged as a versatile and economical platform for a va- riety of nano-photonic devices and applications. However, it has many intrinsic limi- tations. Within nonlinear optics, two-photon absorption and the resultant free carrier effects severely limit the power and speed of Kerr-effect processes. These problems can be circumvented by designing hybrid structures which integrate organic materials with more favorable properties. These strategies rely on the waveguide’s ability to guide light in the low refractive index region of index high contrast silicon waveguides. While several structures such as slot and hybrid plasmonic waveguides have been explored for this pur- pose, these approaches suffer from high loss, high fabrication complexity or poor optical confinement. In this thesis we design, fabricate and test hybrid silicon-organic waveguides based on the augmented low index guiding (ALIG) principle introduced by Alam et al [1]. In the ALIG structure the transverse magnetic (TM) mode is mostly confined to the low-index organic region while the transverse electric (TE) mode is primarily confined to the high index silicon core. Compared to the slot structure, we find that the ALIG design can achieve higher confinement to the organic material and lower loss. Beyond χ 3 nonlinear optics, this approach can be extended to other materials which add other functionality such as biosensing, electro and magneto-optics, and gain on chip.

Keywords: nonlinear optics
optical materials
silicon photonics
waveguides
Advisor: Aitchison, J. Stewart
Analysis and Development of a Halbach Array Motor for Application into a Novel Delivery Drone Driving Cycle for Powertrain Optimization and Maximization of Delivery Radius

Large companies such as Amazon and Google are currently testing deliveries using unmanned drones, with the intent of using these drones on the market. Topics tackled in this field of research include delivery routing optimization, object collision routing optimization, battery management optimization, and the addition of solar panels on the drones. Little publicly available research has been found to have been conducted on the developing methods to optimize the powertrain of the drones to maximize their delivery radii. To achieve this end, this work puts forth a delivery drone driving cycle simulation written in MATLAB with which to monitor their performance and fine-tune their properties. A halbach array motor is designed and analyzed in ANSYS Maxwell, and a data processing tool is written in MATLAB to manipulate the halbach array motor and propeller data into useable states for the simulation. The driving cycle simulation is tested on fifty-four drone configurations.

Keywords: Delivery Drone
Driving Cycle
Efficiency
Electric Motor
Halbach Array
Powertrain Optimization
Advisor: Behdinan, Kamran
Evaluation of Accuracy of Teeth Surface Registration of NaviDent, a Dynamic Computer-guided Navigation System for Placing Dental Implants

Objectives: To compare the accuracy achieved between trace and fiducial registration used by Navident, a dynamic navigation system for placing dental implants. Materials and Methods: Metal spheres were placed in partially edentulous casts. CbCT scans were taken and used to localize the centre of the spheres. The experimental trace and conventional fiducial registration protocols were performed to localize the sphere centres, and the results compared to the findings from the CbCT scans. Each protocol was completed three times for each sphere, for a total of 756 data points. The average difference found between the registration methods was compared. Results: The trace and fiducial registration protocols were comparable, localizing the centre of each sphere to an average difference of 0.33 mm, though trace registration measurements showed greater variability. Conclusions: With appropriate case selection, trace registration may be a practical and comparably accurate alternative to fiducial registration with the Navident system.

Advisor: Somogyi-Ganss, Eszter
Machine Learning Applications for Clinical Data in Otolaryngology-Head Neck Surgery

Applying novel analytic techniques -- such as machine learning -- may be fruitful in identifying possibilities for resource optimization and novel methods of care delivery. In this thesis, the current state of machine learning in Otolaryngology-Head Neck Surgery and the specific application of machine learning to a full range of challenges is reviewed. Novel analyses using computer vision for automatic audiogram interpretation, predicting post-operative cochlear implant performance using diverse pre-operative patient variables, and natural language processing for detecting patterns in adverse event reports related to cochlear implant devices are presented. We observe that conventional machine learning techniques generate high performance in these prediction tasks. Thinking more broadly, uncertainty in medicine and subsequent wasteful care is one of the key drivers of runaway health care spending in today's health care ecosystem. Machine learning is poised to help reduce uncertainty in clinical decision making to serve the value-based health care mandate.

Keywords: cochlear implants
deep learning
hearing loss
machine learning
natural language processing
neural networks
Advisor: Chan, Timothy CY
SHIP: A Storage System for Hybrid Interconnected Processors

Drivers for accessing storage are complex. In addition to the complexity involved in using the solid-state drive protocols, navigating filesystems is a process requiring multiple storage accesses and data processing between each access. As a result, efforts to create storage drivers for non-CPU processors (FPGAs and GPUs) have either failed, require too many resources/time, or remove some of the functionality expected by storage users (such as removing the filesystem). In this thesis, we explore the creation of a wrapper encapsulating a solid-state drive that performs all of the filesystem operations, and presents a much simpler network-based interface, simple enough for FPGAs and GPUs to use efficiently. Data transfers are performed via the network-based RDMA protocol, for which drivers exist for CPUs, GPUs, and FPGAs. ASIC accelerators for RDMA are also available. This system can sustain a throughput of 294 MBps, offers better scalability and is better adapted for cloud architectures, compared to current storage solutions

Keywords: FPGA
NVMe
NVMe-OF
RDMA
RoCE
Storage
Advisor: Chow, Paul
Latent Critiquing for Conversational Recommender Systems

Critiquing is a method for conversational recommendation that iteratively adapts recommendations in response to user feedback regarding item attributes. This thesis addresses four problems: (1) how can user preferences and feedback be represented and manipulated in the same latent space to provide updated recommendations after critiquing? (2) how can recommender systems be equipped with language-based interaction? (3) how can item critiques be co-embedded with user preference so as to properly take critiques into account for subsequent recommendations? Finally, (4) how can the strength of multi-step critiquing feedback be weighted. Empirical results show that our approach not only provides a strong baseline recommender and high-quality personalized item keyphrase suggestions, but that it also properly suppresses items predicted to have one-step critique. Furthermore, the proposed model reduces the number of interactions required to find a satisfactory item and increases the overall success rate compared to a standard approach of averaging critique feedback.

Keywords: Conversational Recommendation
Critiquing
Deep Learning
Recommender Systems
Sequential Recommendation
Advisor: Sanner, Scott P
Impact of Residential HVAC Filters on Particle Concentration and Exposure

Filters in heating, ventilating, and air conditioning (HVAC) systems can improve indoor air quality. In North America, residential air cleaning is usually done by recirculating indoor air through a filter. In this work, I explored two methods of assessing the impacts of HVAC filters in residences. The first method was through examining year-long PM measurements in 20 Toronto homes where different types of filters were installed. I found no evidence that higher efficiency filters reduced long-term exposure to PM. The second method was by studying the particle size distribution of filter dust. I explored the possibility of size separating filter dust to gain more information on smaller particles. One major challenge is the sticky nature of filter dust makes both the separation and mixing (with water for size analysis) processes difficult. Despite the caveats, these findings suggest that both methods are promising and can provide useful information for future studies.

Keywords: filtration
indoor sources
low-cost monitors
particulate matter
Advisor: Siegel, Jeffrey A.
Determination of Exercise Capacity Indices Using Acoustic Signal Analysis

Cardiovascular and respiratory diseases are the leading causes of deaths. The gold standard diagnosis tool is the cardiopulmonary exercise test (CPET). The equipment has low accessibility and we propose acoustic analysis to measure the exercise capacity as an alternative. Thirty healthy participants were recruited. Measurement from the CPET system was the reference and tracheal breathing sounds were recorded using a microphone for acoustic analysis. We compared wavelet thresholding, empirical mode decomposition, and Synchrosqueezing filtering for cardio-respiratory signal retrieval. Cardio-respiratory features were then extracted from the sound signal.VO2 max was estimated using random forest and the breakpoints of sound features were inspected to determine AT. We showed that Synchrosqueezing had the highest signal to noise ratio (p

Keywords: Acoustic analysis
Cardiopulmonary exercise test
Exercise capacity
Advisor: Yadollahi, Azadeh
Behaviour of Ultra High Performance Fibre Reinforced Concrete Subjected to Pure Shear

Recent years have shown Ultra High-Performance Fibre-Reinforced Concrete (UHPFRC) to be applicable to practical design problems, including 100-metre length bridges being built without conventional shear reinforcement. Although UHPFRC is promising, its shear response is an area that requires more research. An experimental program consisting of five large-scale UHPFRC panel elements was completed to better understand the behaviour of UHPFRC under pure shear. The panels had varying amounts of conventional reinforcement and a constant 2% volume fraction of steel fibres. The panels cracked at lower stresses than their companion prisms. However, the panels demonstrated a strain-hardening response with a linear post-cracking stiffness and reached a peak shear stress of 8-10 MPa. At peak shear stress, fibres began to pull out along a single crack where strains localized, causing gradual degradation in strength. Finite element predictions captured the strength of the panels well but identified areas in which modelling could be improved.

Keywords: Fibre Reinforced
Finite Element Models
Reinforced Concrete
Shear
Structural Design
Ultra High Performance
Advisor: Bentz, Evan C
Physical Activity and Sleep in Gynecological Cancer Survivors

Sleep disturbances can lead to numerous negatives health outcomes among gynecological cancer survivors (GCS). Sleep disturbances are a common and impactful adverse effect of treatment in GCS and may potentially be ameliorated by increased PA; however, the relationship between PA levels and sleep is poorly understood in this population. This study examined within- and between-individual associations between objectively measured PA and sleep quality. Sixteen women wore an accelerometer for three separate seven-day periods; 24-hour sleep/wake data were obtained to assess PA and various metrics of sleep quality. Multilevel modeling was used to assess if within- and between-individual variability in PA is associated with fluctuations in sleep patterns. Statistical analyses revealed no significant relationship between PA levels and sleep outcomes. While these findings suggest no relationship between daily PA and sleep, further research with larger sample groups is needed to ascertain if increased PA could improve sleep outcomes among GCS.

Advisor: Santa Mina, Daniel