VictorJuiz/thesis huggingface dataset:
The Neurotrophic Actions of TCAP-1 in an Immortalized Neuronal Cell Line Under a Chronic-exposure Model

Teneurin C-terminal associated peptide (TCAP) is a highly conserved ancestral bioactive peptide known to antagonize the cortical stress response. Recently, TCAP-1, along with its receptor, latrophilin, have shown to regulate energy metabolism in muscle cells, exhibited by increased glucose uptake, NADH turnover, and ATP production in vitro. Neurons, however, have historically failed to exhibit robust Ca2+ regulation upon acute TCAP-1 administration, challenging the notion of conserved intracellular signalling mechanisms across excitable cell types. Subsequently, I hypothesized that chronic TCAP-1 treatment would potentiate Ca2+-mediated outcomes, such as mitochondrial activation, morphological alterations, and glutamatergic signalling, in an exposure time-dependent manner. To test this, I examined the effect of a chronic TCAP-1 treatment in modulating neuroprotection, cytoskeletal dynamics, O2 consumption, and glutamate receptor expression in the N38 neuronal cell line. Taken together, findings indicate reversal of the ‘Warburg Effect’ via the differentiation of neurons upon chronic administration of TCAP-1.

Keywords: Neurons
Neuroscience
Peptides
Signalling
Advisor: Lovejoy, David A
Hardware Acceleration of Biophotonic Simulations

The simulation of light propagation through tissue is important for medical applications like diffuse optical tomography (DOT), bioluminescence imaging (BLI) and photodynamic therapy (PDT). These applications involve solving an inverse problem, which works backwards from a light distribution to the parameters that caused it. These inverse problems have no general closed-form solution and therefore are approximated using iterative techniques. Increasing the accuracy of the approximation requires performing many light propagation simulations which is time-consuming and computationally intensive. We describe algorithmic techniques to improve the performance, accuracy and usability of the fastest software simulator for forward light propagation, FullMonteSW. Additionally, we explore two acceleration methods using a GPU and an FPGA. Our results show that the GPU and FPGA accelerator improve the performance by 4-13x and 4x, respectively, over the software baseline. We give insight for improving the performance and usability of the GPU- and FPGA-accelerated simulators for various medical applications.

Keywords: Biophotonics
FPGA
HPC
Monte Carlo
OpenCL
Advisor: Betz, Vaughn
Brown, Stephen
Investigating Escape from Adaptive conflict in the Legume Medicago truncatula

Trade-offs between genetically correlated traits cause significant evolutionary consequences. One example of an agriculturally and ecologically important trade-off exists between the ability for the legume plant Medicago truncatula to attract nitrogen-fixing rhizobia and to repel parasitic root-knot nematodes. In this study, I conducted a greenhouse experiment to examine one Medicago truncatula genotype that appears to have escaped this genetic conflict. I also included 17 closely grouped genotypes (based on phylogenetic distance) to see if I could identify others that behave similarly. While I was not able to replicate a positive correlation between susceptibility to rhizobia and nematodes, I did confirm the phenotype of the previously identified outlier genotype. Finally, I identified one other genotype that formed significantly more interactions with beneficial rhizobia while forming significantly less interactions with parasiti nematodes. My findings provide some very exciting avenues to pursue future research in identifying the genetic underpinnings of this interesting phenotype.

Advisor: Stinchcombe, John
Experimental Implementation of DC Microgrid with Energy Management System

Due to the impacts of climate change, there is a need to reduce emissions from fossil fuel based electricity generation. DC microgrids are effective for integrating solar photovoltaics and battery energy storage together with local loads due to simple power conversion and control systems. This thesis focuses on a decentralized energy management strategy for a DC microgrid operating in islanded mode to ensure long-term health and protection of the battery energy storage systems. The energy management system utilizes variable-intercept droop characteristic adjustments to balance the state-of-charge of multiple storage elements, and a renewable source limiter to avoid overcharging batteries. The functionality of the energy management approach was validated through PSCAD/EMTDC simulations, and an experimental DC microgrid consisting of a PV source, two energy storage systems, and a DC load. The proposed decentralized energy management system achieved the intended objectives and proved its successful application to practical DC microgrids.

Keywords: DC
Energy Management
Microgrid
Power Electronics
Renewable Energy
Solar
Advisor: Lehn, Peter W
Hot, then Cold: Predicting Hypothesis Revision Strategies across Development with Rational Process Models

This research explores the hypothesis revision strategies of adults and children, and develops two computational models of Bayesian inference that predict distinct patterns of behaviour observed across development. Data were collected for adults (N = 90) and 4- to 6-year-old children (N = 119) on a causal inference task in which initial evidence supported a naively salient hypothesis, but was followed by evidence which violated this hypothesis. Consistent with prior work, adults showed an “exploitation-biased” strategy, performing better in a condition where the true rule governing the causal outcomes of the task was reachable through a process of iterative hypothesis revision than in a condition where reaching the true rule required abandoning a local optimum. Children, on the other hand, did not display this bias and performed equally in both conditions, perhaps due to a willingness to more broadly explore alternative hypotheses.

Keywords: Bayesian inference
belief revision
causal inference
causal learning
explore-exploit dilemma
process model
Advisor: Buchsbaum, Daphna
A Biomechanical Assessment of Stepping into and out of a Bathtub using a Temporary Rim-mounted Grab Bar

Temporary rim-mounted grab bars are often recommended when installing a permanent grab bar is not feasible; however, their safety and effectiveness is unknown. This thesis explores the effect of using a rim-mounted grab bar for assistance as 10 older adults with bathing difficulty stepped into and out of the bathtub. Compared to the low and high rim- mounted grab bars, the vertical grab was safer and more effective at reducing task demands and preferred by participants. The high rim-mounted grab bar may reduce some task demands compared to low. Further research is required to investigate whether rim-mounted grab bars can withstand forces applied during use. Four participants refused to step into and out of the bathtub using only the wall. A summary of lower limb joint angles across all conditions provides insight into range of motion requirements to complete the task. Findings may inform clinical recommendations, grab bar design, and standards.

Keywords: Bathing
Bathing difficulty
Bathing safety
Grab bars
Rim-mounted grab bars
Temporary grab bars
Advisor: Novak, Alison C
Leveraging Pre-trained Detection Networks for Label Generation on New Datasets

The development of 3D object detection solutions for autonomous driving requires labelled real-world datasets for training and evaluation, which are costly to produce. This thesis presents a 3D click labelling approach to individual scene labelling, in which annotators are provided a specially designed user interface to click on objects in the point cloud of each scene. The click labels are subsequently processed by a pre-trained network to generate a label for each click. The proposed annotation scheme demonstrates a 30x lower human annotation time. This thesis also presents a method for automatic labelling of static objects through the use of full drive sequences. In this work proposals from a pre-trained detection network, over the course of a drive sequence, are transformed into a global reference frame. Overlapping detections are processed to produce high recall label proposals for static vehicles in the sequence, eliminating the need for manual annotation.

Advisor: Waslander, Steven L.
Determining the Role of Gαi3 in Ischemic Cardiac Injury

Gαi3¬ knockout was previously shown to reduce acute murine infarcts following ischemic injury. We assessed long-term effects of Gαi3 knockout on cardiac outcome by performing transthoracic echocardiography in Gαi3 wild-type and knockout mice at 1-, 2- and 4-week timepoints after permanent LAD-ligation. Additionally, we assessed region-specific cardiac fibroblast density and macrophage populations in Gαi3 wild-type and knockout mice at 5- and 28-day timepoints after injury. There were no significant effects of genotype on mouse cardiac function observed by echocardiography nor any effects of genotype on region-specific cardiac fibroblast density and cardiac macrophage populations after injury. Despite lack of statistical significance, Gαi3 knockout appeared to improve left-ventricular fractional shortening, anterior wall thinning cardiac fibroblast density in infarcts after injury. Prospective studies determining validity of these potential phenotypes should be conducted in larger mouse cohorts using transient LAD occlusion as Gαi3’s regulation of cardiac recovery was previously elucidated using an ischemia-reperfusion model.

Keywords: Cardiac ischemia
Fibroblast
Gαi3
Macrophage
Advisor: Heximer, Scott
Using Insect Communities from Window-pane Traps to Test the Sustainability of Forest Management in Northern Temperate Hardwood Forests

Conservation of biodiversity is an essential component of single-tree selection (STS) harvesting in Ontario’s hardwood forests. Here, I compare family-level insect communities (Coleoptera, Diptera, and Hymenoptera) between mature STS-managed and unmanaged stands. I also investigate the effects of trap placement on insect communities, including traps located in the lower-canopy and understory of sugar maple and eastern hemlocks and adjacent to early- and late-decay snags and downed woody debris (DWD). Finally, I explore insect community variation as a function of tree community composition and the quality and quantity of DWD and snags. In total, 57,434 insects were collected, and no overall statistical differences were observed between communities in differently managed stands. However, strong effects on insect community composition and larval trophic guilds were observed due to trap placement. I found little evidence that insect communities varied with habitat features, although abundances of several coleopteran and hymenopteran families varied with DWD quantity.

Keywords: DWD
Single-tree selection
Snag
Temperate
Vertical stratification
Advisor: Malcolm, Jay
Design of Pressure Feedback Sensors for Miniaturized Intra-ventricular Neurosurgery Robotic Tools

Remote-controlled minimally invasive neuroendoscopic robotic surgical tools can be miniaturized to less than 2 mm-diameter range while maintaining their dexterity and force required to perform operations without open-skull surgeries. However, these platforms lack haptic information for surgeons, leading to possible loss of control over tissue. This thesis investigates two places on the surgical tool for integration of sensor systems: the bendable tube shaft of recently developed concentric tube robot, and the miniaturized magnetically driven forceps. For the tube shaft, a highly sensitive resistive based sensor is optimized, developed and wrapped around to provide force and location feedback while being adaptable to the tube’s changing curvatures during operation. For the microgipper, a microstrutured capacitive sensor design is proposed and optimized using computer simulations to measure normal and shear stresses. These sensors are then developed using microfabrication techniques before subjecting to bench-top and brain phantom tests for assessments of their performances.

Keywords: Concentric tube robots
Contact mechanics
Flexible pressure sensor
Haptic feedback
Microelectromechanical systems
Minimally invasive surgeries
Advisor: Naguib, Hani E
Alveolar-Like Stem Cell-Derived Macrophages Protect Against RSV Induced Lung Damage

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in young children and infants. There are no approved vaccines or effective antivirals. Alveolar macrophages are known to play an essential role in establishing and resolving the inflammatory response to infection. We have investigated the capacity for alveolar-like macrophages (ALM) generated from stem cells to protect against RSV infection and pathology. We initially established that ALMs are not productively infected by RSV, and co-incubations of ALMs and RSV led to a dose- and time-dependent reduction in viral titer. During in vivo studies, ALM groups were given an intra-tracheal instillation of ALMs prior to infection. Mice given ALMs prior to infection showed reduced weight loss, lower viral titers, and evidence of reduced lung inflammation and injury. These results suggest that ALMs currently being developed for lung disease therapies may be beneficial in protecting against RSV pathology.

Keywords: alveolar like macrophage
alveolar macrophage
macrophage
respiratory syncytial virus
rsv
rsv therapeutic
Advisor: Moraes, Theo
Assessment of Fatigue in Patients with End-stage Kidney Disease: Validation of PROMIS Fatigue Computer Adaptive Test and Identifying Correlates of Fatigue in Patients with End-stage Kdney Disease

Fatigue is a common and debilitating symptom in patients with end-stage kidney disease (ESKD). The routine assessment of fatigue with patient-reported outcome measures can help clinicians identify and manage fatigue efficiently. In this study, the measurement properties of the Patient-Reported Outcomes Measurement Information System Fatigue Computer Adaptive Test (PROMIS Fatigue CAT) were assessed in patients with ESKD. A cross-sectional sample of adult patients on dialysis and kidney transplant recipients completed the PROMIS Fatigue CAT as well as a legacy instrument. PROMIS Fatigue CAT demonstrated excellent reliability and validity. Excellent discrimination was also found for PROMIS Fatigue CAT to discriminate patients with fatigue. In addition, sex, depression, anxiety, social support and self-reported health status were strongly associated with fatigue. Thus, PROMIS Fatigue CAT may be a useful measure of fatigue and psychosocial interventions may be important to consider in the management of fatigue in patients with ESKD.

Keywords: End-stage Kidney Disease
Fatigue
PROMIS CAT
Validation
Advisor: Mucsi, Istvan
Saturation Transfer Properties of Tumour Xenografts Derived from Prostate Cancer Cell Lines 22Rv1 and DU145

Histopathology is currently the most reliable tool in assessing the aggressiveness and prognosis of solid tumours. However, developing non-invasive modalities for tumour evaluation remains crucial due to the side effects and complications caused by biopsy procedures. In this study, saturation transfer MRI was used to investigate the microstructural and metabolic properties of tumour xenografts in mice derived from the prostate cancer (PCa) cell lines 22Rv1 and DU145, which express different aggressiveness. The magnetization transfer (MT) and chemical exchange saturation transfer (CEST) effects, which are associated with the microstructural and metabolic properties in biological tissue, respectively, were analyzed quantitatively and compared amongst different tumour types and regions. Histopathological staining was performed as a reference. Higher cellular density and metabolism expressed in more aggressive tumours (22Rv1) were associated with larger MT and CEST effects. High collagen content in the necrotic regions might explain their higher MT effects compared to tumour regions.

Advisor: Stanisz, Greg J
Ridesharing and Social Inclusion: The Role of Ridesharing in Improving Job Access for Disadvantaged Populations

Research has shown a lot of promise that ridesharing services could be contributing to more- equitable transportation systems by improving job access to groups at high risk of social exclusion. Since the main purpose of transportation is giving individuals access to the destinations that they value, it is most appropriate to evaluate ridesharing through the lens of accessibility. This study investigates how ridesharing contributes to job access in the city of Toronto through a multimodal accessibility assessment. Specifically, the study uses the generalized cost to construct contours of the cumulative opportunities and evaluates the benefit of ridesharing in terms of the accessibility improvement that this mode provides – as seen by socially disadvantaged groups. The findings suggest that ridesharing offers the most benefit in areas with lower transit service levels and with higher job concentrations. Also, using ridesharing as an ingress mode to higher-order transportation lines offers very little benefit.

Keywords: Access
Accessibility
Equity
Job Access
Ride Hailing
Ridesharing
Advisor: Shalaby, Amer
Farber, Steven
Understanding Venular Amyloid in Alzheimer's Disease

In Alzheimer’s disease (AD), Aβ is deposited along the brain parenchyma as well as the cerebral blood vessels, a pathology named cerebral amyloid angiopathy (CAA). Currently, research has expanded on arteriolar CAA, while venular amyloid deposition have yet to be fully explained. My objective is to understand venular amyloid by identifying the Aβ peptide and studying the interplay between venular amyloid and CAA deposition. Mass spectrometry (MS) analysis of amyloid deposits isolated from TgF344-AD rat brains using laser capture microdissection (LCM) identified low abundance Aβ in venular amyloid. In addition, histopathological analysis demonstrated severe arteriolar amyloid accumulation preceding venular amyloid deposition. Immunofluorescent imaging confirmed localization of vascular Aβ along the perivascular spaces of arteries and veins, suggesting perivascular drainage impairments leading to CAA and venular amyloid. Gaining a comprehensive understanding of the mechanisms involved in venular Aβ deposition and associated pathologies provides insight to the connection between CAA and AD.

Keywords: Alzheimer's disease
Cerebral amyloid angiopathy
Glympathic clearance
Periarterial drainage
TgF344-AD
Venular amyloid
Advisor: McLaurin, JoAnne
Does Cold-water Immersion Alter Pro-and Anti-inflammatory Transcription Factors in Rat Skeletal Muscle Following Lengthening Contractions?

Cold-water immersion (CWI) is a common exercise recovery treatment. To determine the effects of CWI on recovery following lengthening contractions (LCs), we compared the responses of activator protein-1 (AP-1), and heat shock factor 1 (HSF-1) transcription factors and Heat shock proteins (HSPs) in tibialis anterior (TA) muscles of male rats (n =24). TA muscles were electrically stimulated with 40LCs and half of them received 10 minutes of 10°C CWI immediately following 40LCs (LCs+ CWI). AP-1 activation was detected at 3-and 8- hours post-exercise with no difference between groups. HSF-1 activation was detected at 0 and 3 hours while HSP72 content was increased at 3-and 8-hours post-exercise in both groups (p

Advisor: Locke, Marius
Fabrication of Lightweight Polymer Composite Materials using Electric Wire-arc Spraying Process

Wire-arc spraying of zinc and aluminium onto polyethylene (PE) and polytetrafluoroethylene (PTFE) was conducted. The impact of surface roughness and substrate temperature on the adhesion strength of the coatings was investigated. Continuous coatings of zinc on PE and PTFE and aluminium on PTFE were fabricated. It was not possible to form continuous aluminum coatings on PE. Individual metal splats were observed using scanning electron microscope (SEM) to provide insights into the adhesion mechanisms. The challenge of metallizing PE was overcome by using porous PE as substrate materials. Copper, aluminum and zinc were successfully deposited on the porous PE to form coatings with thickness of about 400 µm. The coating surfaces and cross-sectional areas were characterized using a SEM, while the coating adhesion strength and electrical resistivity was examined using pull testing and four-wire sensing respectively. The use of polymer composite materials as lightweight heatsinks for LEDs was then investigated.

Advisor: Chandra, Sanjeev
McDonald, Andre
Quantitative Functional Imaging and Dosimetry of Photodynamic Therapy: Clinical Feasibility of Performing Dosimetric Measurements in Non-melanoma Skin Cancer Patients

Photodynamic therapy (PDT) has emerged as a viable alternative to traditional treatment regimes in the treatment of non-melanoma skin cancer. However, approximately 20-25% of patients receiving PDT exhibit heterogeneous response or tumour recurrence. This inconsistency can be attributed to generic treatment protocols and lack of planning, monitoring, and assessment of treatment response. A personalized approach is required to increase treatment efficacy and reduce response variability. To this effect, the work presented in this thesis outlines the development and characterization of: (a) fluorescence- enabled spatial frequency domain imaging system for monitoring the photobleaching response of PpIX; and (b) statistical variance method for monitoring the vascular response in high-frequency ultrasound imaging. Preliminary results from the clinical implementation of this quantitative functional imaging system are also presented. With time, this system can be integrated into the clinical workflow to enable the creation of a personalized treatment plan – improving treatment efficacy and clinical outcomes.

Keywords: Dosimetry
Fluorescence
Non-melanoma Skin Cancer
Photodynamic Therapy
Spatial Domain Frequency Imaging
Speckle Variance
Advisor: Yang, Victor
Yee, Albert
Architecture and Automation for Efficient Convolutional Neural Network Acceleration on Field Programmable Gate Arrays

This thesis explores Convolutional Neural Network (CNN) inference accelerator architecture for FPGAs. We compare and contrast three high-level architectures, and elect to build a layer-pipelined design that leverages custom hardware for every layer in a CNN, and can skip zero-valued weights. While this increases the algorithmic execution efficiency, we find it makes it challenging to achieve a high operating frequency. To address this, we designed latency insensitive hardware templates that build a model of signal fanout and span and instantiate different structures within each compute unit to ensure a high operating frequency regardless of CNN topology. Together these optimizations enable throughput on a sparse Resnet-50 model at a batch size of 1 of 4550 images/s, which is nearly 4x the throughput of NVIDIA's fastest machine learning targeted GPU, the V100, and outperforms all prior work on FPGAs.

Keywords: Accelerator
Computer Architecture
Convolutional Neural Networks
FPGA
Advisor: Betz, Vaughn