VictorJuiz/thesis huggingface dataset:
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
Keywords: End-stage Kidney Disease
Fatigue
PROMIS CAT
Validation

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.
Ridesharing and Social Inclusion: The Role of Ridesharing in Improving Job Access for Disadvantaged Populations
Keywords: Access
Accessibility
Equity
Job Access
Ride Hailing
Ridesharing

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.
Understanding Venular Amyloid in Alzheimer's Disease
Keywords: Alzheimer's disease
Cerebral amyloid angiopathy
Glympathic clearance
Periarterial drainage
TgF344-AD
Venular amyloid

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.
Quantitative Functional Imaging and Dosimetry of Photodynamic Therapy: Clinical Feasibility of Performing Dosimetric Measurements in Non-melanoma Skin Cancer Patients
Keywords: Dosimetry
Fluorescence
Non-melanoma Skin Cancer
Photodynamic Therapy
Spatial Domain Frequency Imaging
Speckle Variance

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.
Architecture and Automation for Efficient Convolutional Neural Network Acceleration on Field Programmable Gate Arrays
Keywords: Accelerator
Computer Architecture
Convolutional Neural Networks
FPGA

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.
A Lower-body Exoskeleton Simulation and Control Framework based on Deep Reinforcement Learning
Keywords: Biomechanics
Deep Reinforcement Learning
Lower-body Exoskeletons
Post-stroke gait rehabilitation

Stroke is a leading cause of disability, and post-stroke individuals often experience hemiparesis, which can result in compensatory movements that affect their overall gait pattern. Lower-body exoskeletons allow for repetitive, intense, and task-based practice of movement patterns that can promote gait recovery. Validating exoskeleton gait patterns in simulation is vital for ensuring patient safety and comfort; however, current simulation tools possess challenges in controlling exoskeleton hardware. Additionally, present model-based adaptive controllers rely on complex dynamics models for the user and exoskeleton that are difficult to accurately define. In this thesis, a centralized exoskeleton simulation and control framework is presented, where desired gait patterns can be validated and customized on-the-fly in physiotherapy sessions. A model-free, end-to-end deep reinforcement learning controller is also presented, to allow for exoskeleton control that is robust to desired gait patterns and a user's interaction with the device. Several experiments were conducted to validate these approaches.
Characterizing Head and Eye Movements used to Compensate for Impaired Biaural Hearing through Unilateral Plugging
Keywords: Binaural Hearing
Compensatory Movements
Eye Movements
Head Movements
Sound Localization
Spatial Hearing

The primary objective of this thesis was to characterize the magnitude and time course of natural head and eye movements during auditory localization in the azimuthal plane when binaural hearing is impaired. Towards this aim, thirty-three youth and adults with typical hearing were testing using a novel moving speaker arm set-up which presented stationary and moving sounds within an arc of 120. Testing was completed under normal conditions and was subsequently repeated in an acute unilateral ear plugging scenario. Primary findings were as follows: localization accuracy and precision were found to be excellent under normal conditions but declined during ear plugging, head and eye movements revealed that under normal conditions, movements were biased towards the target location and eye movements led head movements, whereas during plugging head movements were biased towards the side of the plugged ear suggesting an adaptation to reduce the head shadow.
PKCδ Regulates Actomyosin Organization in Leading Cellular Protrusions during Drosophila Border Cell Migration
Keywords: Actomyosin dynamics
Border cell cluster
Cellular protrusions
Collective cell migration
Confocal microscopy
PKCδ

Actin-based membrane protrusions are essential for cell migration, including the collective migration of the border cell cluster (BCC) during Drosophila oogenesis. Our lab previously showed that the serine/threonine kinase Protein Kinase C δ (PKCδ) regulates the structure and behavior of the leading protrusion of the BCC. Here, I investigated the influence of PKCδ on the actomyosin network of BCC protrusions. Examination of PKCδ loss-of-function mutants revealed that PKCδ is required for normal F-actin organization and Myosin II (MyoII) distribution in protrusions. Overexpression of PKCδ caused a severe reduction in actomyosin in protrusions. Moreover, PKCδ prevents simultaneous formation of multiple leading protrusions. Rho1, a positive upstream regulator of MyoII, appears to be activated in the leading protrusion precociously when PKCδ function is lost. In summary, my analysis contributes to our understanding of the function of PKCδ as a regulator of the actomyosin network in leading cellular protrusions during collective cell migration.
Finite Element Modelling of Ultra-high Performance Fibre Reinforced Concrete
Keywords: Fibre Reinforced Concrete
Finite Element Modelling
Ultra-High Performance Concrete
VecTor2

Ultra-high performance fibre reinforced concrete (UHPFRC) is a relatively new material showing increased use for practical engineering problems. Although significant research has been undertaken in the development of constitutive models for the finite element modelling of steel fibre reinforced concrete (SFRC), the reliability of these models in analyzing UHPFRC remains unassessed. This thesis outlines the investigation of these models in finite element software VecTor2 for their applicability in analyzing UHPFRC. Localized behaviour at cracks was investigated, leading to improvements in current crack spacing formulations through the inclusion of an effective aggregate size for UHPFRC. An embedded steel reinforcement rupture formulation for specimens subjected to tension was also implemented to predict reinforcement rupture strains of reinforced concrete specimens. Finally, studies were conducted to validate these models for structures subjected to various loading effects by comparing the finite element simulations with experimental results found in the literature.
Exploring Ecologies of the Heart: a Pedagogy for Healing
Keywords: ancient knowledge
educating the soul
emotions
holism
human-nature
re-indigenization

Throughout this work I outline the crucial role education plays in developing students’ capacities to lead a good life. Without an awareness of the nature of life as interdependent, the mind as self-deceptive and spirit as all encompassing, students are shielded from their capacity to emancipate from cognitive distortions and attune to the healing potential of nature. Without the engagement of contemplative practice from which ecologies of the heart can emerge to cultivate meaning and significance in life, education remains confined to recreating relationships of disconnect and contributing to a colonialist cycle of trauma and self-destruction. The entangled relationship between declining ecological diversity and student mental health and well-being reveals a problem with education. This problem is argued to be grounded in the narrative of human-nature duality (Orr, 2013; Louv, 2011; Zylstra et al., 2014).
Outcomes in Pulmonary Hypertension Among Adults Undergoing Percutaneous Atrial Septal Defect Closure
Keywords: Atrial Septal Defects
Health Service Research
Interventional Cardiology
Outcomes and Evaluation
Pulmonary Hypertension

Atrial septal defects (ASDs) are one of the most common forms of congenital cardiac lesions diagnosed during adulthood. If left untreated, ASDs can lead to right ventricular failure and pulmonary hypertension (PH). Patients with PH and ASD suffer from worse prognoses than patients without PH. The role of ASD closure and its effects on PH remain unclear and information regarding the relationship between ASD closure and PH is limited. The first objective of this thesis was to synthesize the current body of ASD with PH literature through a systematic review and meta-analyses. Our second objective was to produce a high-quality cohort study assessing long-term outcomes of ASD closure between patients with and without PH. We found that PH prevalence and mean pulmonary arterial pressure decrease after ASD closure. Our analyses found that ASD patients with PH undergoing closure experience more comorbidities and worse long-term outcomes, compared to patients without PH.
Maintenance and Reliability Models for a Public Transit Bus
Keywords: Maintenance
Opportunistic
Reliability
Semi-Markov Decision Process
Simulation
Transit Bus

Public transit buses are an essential part of modern society and are prone to frequent breakdowns. The goal of this research is to develop an opportunistic maintenance policy that maximizes bus availability. A transit bus is composed of over 10 000 components which can be classified into modules based on their location and function in the bus. A reliability model considering imperfect repair is developed using real transit bus failure data to identify the components that have the largest impact on bus availability. A method to find the maintenance policy that maximizes the availability of a bus module is developed using the semi-Markov decision process framework. Discrete event simulation is used to find an opportunistic maintenance policy that maximizes the availability for an entire transit bus. The developed maintenance policies are compared with the conventional maintenance practice of repairing only on failure.
The Effects of Exercise and Osteocalcin on Metabolism, Behaviour and Cognition of Female Mice Fed Either a Low-fat or High-fat Diet
Keywords: Behaviour
Cognition
Osteocalcin
Type 2 Diabetes Mellitus

Osteoblast-derived osteocalcin (Ocn) is implicated in the endocrine actions of the skeleton in modulating cognition, mood and energy homeostasis. Here we compared the effects of daily treadmill exercise, 30 ng/g/day Ocn administration, or the combination of both in female C57Bl/6J mice fed either a low-fat or high-fat diet. Weight gain from high-fat diet was decreased and glucose tolerance improved by exercise with or without Ocn but not by Ocn alone. Exercise, osteocalcin and their combination alleviated the depressive-like but not anxiety-like behaviours induced by a high-fat diet. Cognitive deficits induced by high-fat diet were reversed by exercise or Ocn, with combined treatment having the greatest effect. Under normal metabolic conditions, neither exercise nor Ocn altered behavioural responses. Together, these results suggest that exercise is more effective in improving metabolism while osteocalcin or exercise are effective in treating cognitive deficits and depressive-like behaviours caused by high-fat diet.
Investigating the Role of the Ventral Hippocampal CA1 and CA3 in Approach-avoidance Conflict using Fiber Photometry
Keywords: Anxiety
Approach-avoidance conflict
Decision making
Fiber photometry
Rat
Ventral hippocampus

Approach-avoidance conflict occurs when an organism encounters a stimulus that is imbued with both positive and negative valences and must choose to either approach or avoid this scenario. Converging evidence supports the role of the ventral hippocampus (vHPC) in the resolution of such forms of conflict. This thesis aimed to further elucidate the contributions of the vCA1 and vCA3 subregions of the vHPC in conflict resolution processes using fiber photometry. To achieve this, genetically encoded calcium indicators (GECIs) were virally introduced into the vCA1 or vCA3 and calcium activity was subsequently recorded through an optic fiber. Using a Y-maze paradigm, animals were trained to associate three distinct visuo-tactile cues with either an appetitive, aversive, or neutral outcome. Post-acquisition, animals underwent a cued conflict task in which a neutral and conflict arm (appetitive and aversive cues superimposed) were presented. Neuronal recordings revealed dissociable activation of the vCA1 and vCA3 during approach and avoidance of the conflict arm, respectively.
Body Representation of Bodies with Absent Limbs
Keywords: Body Representation
Body Schema
Body-Part Compatibility
Hidden limbs
Missing limbs
Self-other matching

Self-other interactions are facilitated through the activation of the body schema – a representation of one’s body is used as a reference to map others’ bodies. Here, the body-part compatibility effect was used as an index of self-other matching. The body-part compatibility effect describes the finding that there are shorter response times to targets presented on an observed limb that is homologous to the responding limb than when the observed and responding limbs are non-homologous. This compatibility effect was investigated as participants viewed bodies with hidden or visible limbs (Experiment 1) and missing or intact limbs (Experiment 2). Compatibility effects were present when viewing hidden and visible limbs (Experiment 1), whereas the compatibility effect was only present for both responding limbs when viewing the missing legs (Experiment 2 preliminary). Overall, the results indicate that self-other matching may be reduced when the limbs of the model are hidden behind an object.
Saturation Transfer Neuroimaging Features of Sickle Cell Anemia
Keywords: CEST
Magnetization Transfer
MRI
Saturation Transfer
Sickle Cell Anemia
Sickle Cell Disease

The broad symptomatology of sickle cell anemia (SCA) includes severe neurologic complications, such as stroke and cognitive impairment, from a young age in many patients. Evidence suggests that chronic oxygen deprivation leads to alterations in cerebral blood flow, metabolism, and tissue microstructure which contribute to neurologic morbidity. We have proposed that saturation transfer MRI, an imaging modality sensitive to the microstructure and biochemical environment of tissues, could improve our understanding of neurologic pathology in SCA and have potential clinical utility for assessing disease severity. This thesis reports on a preclinical study to characterize saturation transfer neuroimaging features in a mouse model of SCA. The results of this study demonstrate that saturation transfer MRI is sensitive to microstructural and metabolic alterations in the normal-appearing grey matter of SCA mice. These findings warrant further investigation into saturation transfer neuroimaging as a research tool and a clinical biomarker of brain injury in SCA.
Modular UHPFRC Waffle Deck Slabs For Highway Bridges
Keywords: Bridges
UHPFRC
Waffle Deck Slabs

This thesis examines the design of an Ultra High Performance Fibre Reinforced Concrete (UHPFRC) bridge deck for use in slab on girder highway bridges. The deck will be assembled from prefabricated panels and on-site closure pours. Each panel will consist of a thin, unreinforced slab cast monolithically with an orthogonal gird of reinforced ribs – a system sometimes called a waffle slab. Using a linear elastic grillage model of the system, a preliminary design of rib sizing, reinforcing and post-tensioning was developed. This was followed by physical tests on unreinforced slabs to determine the optimal combination of slab thickness and rib spacing. Results were analyzed using the yield line analysis method and novel developments for applying yield line analysis to UHPFRC specimens were explored. The thesis concludes with a discussion about the next test – a test of full scale, small size specimens with final candidate dimensions with and without post-tensioning.
G-protein Signaling Regulating Opioid-induced Respiratory Rate Depression
Keywords: Opioid
PreBotzinger Complex
Respiratory Depression
RGS

Opioids are pain treatment mainstays, but present with potentially lethal respiratory depression. To develop safer opioid therapies, mechanisms underlying opioid-induced respiratory depression must be better understood. Opioids mainly bind to µ-opioid receptors (MORs), Gprotein-coupled receptors that activate heterotrimeric G-proteins, including Gβγ. There is significant debate around whether G-proteins or β-arrestins, proteins involved in receptor internalization/desensitization, directly regulate respiratory circuit inhibition. While Gβγ activates G-protein inwardly rectifying potassium (GIRK) channels, which are key mediators of respiratory rate depression, its direct role in opioid-induced respiratory depression is unknown. We investigated the contribution of Gβγ in opioid-induced respiratory rate depression and found Gβγ inhibition in respiratory circuits reversed opioid-induced respiratory rate depression, regulators of G-protein signaling 4 (RGS4) are co-expressed with MORs in respiratory circuits, and RGS4 inhibition in vivo potentiates opioid-induced respiratory rate depression. Our data suggest G-protein signaling is key in opioid-induced respiratory depression and is not limited to β-arrestin recruitment.
Development of a Core Outcome Set for Studies on the Prevention and Management of Pregnancy-associated Venous Thromboembolism
Keywords: Delphi survey
Interviews
Outcomes
Patient-reported outcomes
Pregnancy
Venous Thromboembolism

Background: The objective of this thesis was to identify a list of outcomes to consider in the development of a core outcome set (COS) to inform future studies on pregnancy-associated venous thromboembolism (VTE), with aim of standardizing outcome reporting. Methods: We conducted a systematic review (Study-1) of 70 studies and 18 interviews (Study-2) with health service users and healthcare professionals, to generate a list of outcomes and inform a two-part online Delphi survey (Study-3). Results: Studies-1 and 2 identified 35 and 57 outcomes, respectively, which were condensed to 45 unique outcomes. The Delphi survey included 81 participants in round-1 and 66 in round-2 including health service users, clinicians and academics, representing 21 countries. Conclusion: We have attained consensus on outcomes that should be considered in the COS for future studies on pregnancy-associated VTE.