VictorJuiz/thesis huggingface dataset:
Evaluation of a Novel Recombinant Human Bone Morphogenetic Protein-2 Bioimplant for Alveolar Ridge Augmentation in Dogs

Autografts (ABG) are the gold standard for alveolar ridge augmentation (ARA), but involve second-site surgical morbidity. The novel BMP bioimplant URIST™ has been designed to be an effective alternative to autografts. The efficacy of URIST™ with 0.5(D1) or 1(D2) mg BMP/unit was compared to ABG or Bio-Oss®. A split mouth design was employed in Beagle dogs. Caliper and Cone Beam CT analyses were utilized to compare dimensional changes in the alveolus. After 12 weeks, dental implant were placed and bone cores analyzed by histology. Dogs that did not have dental implant placement were analyzed for the effect of prolonged healing time on dimensional bony changes. URIST™ had comparable dimensional changes in ARA to the gold standard autograft, with some statistically significant increases in width. All grafted sites had successful primary stability of dental implant placement. Histology showed no clear differences in the character of new trabecular bone deposited among grafted sites.

Keywords: Bioimplants
BMP
Bone grafting
rhBMP
Advisor: Peel, Sean
Effects of Automation Explanations on Operator Reliance on a Context-Aware Recommendation System

This thesis explores the design, requirements definition and development of an Adaptive User Interface (AUI) that provides context-aware action recommendations to operators performing a cybersecurity network monitoring task. This AUI was used to conduct an experiment that investigated whether providing meta-information about how the automation calculated recommendations would impact trust and reliance on those recommendations. Twenty-four participants performed a cybersecurity task under three different interface conditions, once each with real, random and no explanations of how recommendations were calculated. Results did not show any significant effect of the explanations on operators trust of the system, nor on their reliance on the system recommendations. A significant correlation was found between a participant’s propensity to trust (PTT) automation and their trust ratings, and between PTT and their reliance on recommendations. Results appear to indicate that explanations provided on the AUI were not useful enough to impact participants trust as hypothesized.

Advisor: Jamieson, Greg
Towards Clinical Translation of the Porphysome: Establishment of Endometrial Cancer Applications and Investigation of Metabolic Differences in Pyrolipid Isomers

Treatment of endometrial cancer consists of surgery ± adjuvant therapy depending on lymph node involvement determined by lymphadenectomy. Targeting lymphadenectomy to patients with known metastases would provide diagnostic and therapeutic benefits while reducing morbidity. Porphysomes are self-assembling nanoparticles made from a multifunctional porphyrin-lipid monomer (pyrolipid) which accumulate preferentially in malignant tissue. Pyrolipid is created through an acylation reaction during which isomerization can occur. A VX2 model of endometrial cancer with retroperitoneal metastases was used to investigate the accuracy of pre-operative 64Cu-Porphysome-enabled PET imaging of lymph nodes and the sensitivity / specificity of in-vivo porphyrin-fluorescence image-guided lymphadenectomy. Pharmacokinetic, biodistribution and biodegradation studies were used to determine differences in Sn1 and Sn2 isomeric Porphysomes. This study demonstrated that Porphysomes are a highly sensitive imaging tool to diagnose primary tumour, metastatic lymph nodes and intra-abdominal metastases and that Sn2 pyrolipid is the optimal isomer for clinical translation due to the preferential biodegradation profile.

Keywords: Endometrial Cancer
Fluorescence Imaging
Lymphadenectomy
Metastasis
Molecular Imaging
Nanoparticle
Advisor: Bernardini, Marcus Q
The Financial Production of Bankruptcy: Denaturalizing Fiscal Crisis in the City of Detroit

Accounts of urban crisis in the United States focus largely on issues of deindustrialization, depopulation, property abandonment, and racial conflict. In the aftermath of the 2008 financial crisis, however, another issue has come to light: the role of financial shocks and volatile debt arrangements in shaping urban outcomes. Through a case study of the City of Detroit’s 2013 bankruptcy, this thesis questions the seeming inevitability of fiscal crises in declining cities. Instead, it analyzes the ways in which fiscal crises can be understood as products of risky financial relationships and debt structures. Drawing on archival data, policy analysis, and quantitative financial data, the thesis focuses on the City of Detroit’s use of one risk-laden financial instrument—the interest rate swap—and follows this instrument through the city’s fiscal crisis. In so doing, I map out how this volatile financial instrument shaped both the economic and political dynamics of Detroit’s bankruptcy.

Keywords: Financialization
Municipal bankruptcy
Urban decline
Urban governance
Advisor: Hackworth, Jason
The Effect of Bone Marrow-Derived Progenitor Cell Therapy to Improve Fracture Healing in a Diabetic Rat Critical Size Defect Model

Our study aimed to explore the efficacy of locally implanted endothelial progenitor cells (EPCs) from healthy and diabetic animals on bone defect healing in healthy and diabetic recipients. EPCs seeded on gelatin scaffolds were implanted in surgically created 5mm femoral defects to create six randomized treatment groups. The animals underwent biweekly radiographic assessment until the 10-week endpoint. Post-mortem specimens were analyzed by micro-computed tomography and biomechanics. Most cell-treated healthy animals achieved union by 8 weeks. EPC-treated diabetic animals achieved higher radiographic scores than the diabetic controls. Healthy animals that received diabetic cells demonstrated greater bone volume, fractional bone volume, bone mineral density and biomechanical stiffness to diabetic animals that received diabetic cells but did not significantly differ from healthy animals that received healthy cells. Thus, EPC therapy promotes fracture healing in diabetic animals irrespective of the cell source, though diabetes may decrease their healing capacities compared to treatment-matched healthy animals.

Keywords: Cell Therapy
Diabetes
EPC
Regenerative Medicine
Advisor: Nauth, Aaron
Effects of Anxiety and Daytime Clenching on Orthodontic Pain Perception

Objectives: This study assessed the relationship between anxiety and oral parafunctional behaviours in individuals with and without orofacial pain; and whether the relationship between anxiety and orthodontic tooth pain is dependent upon wake-time tooth clenching. Methods: The State-Trait Anxiety Inventory (STAI), Oral Behaviour Checklist (OBC) and TMD-Pain Screener were completed by 255 students with (n=47, 24.8±4.2 years) and without (n=208; 26.0±4.8 years) TMD pain. STAI score distribution was examined and 45 volunteers (26.0±3.4 years) with low-, intermediate-, and high-anxiety were recruited and submitted to experimental orthodontic-tooth-movement. Results: A significant effect of the interaction group*trait anxiety on OBC scores was found (p=0.028). A significant effect of the interaction clenching*study group*day on tooth-pain was found (p

Keywords: anxiety
orthodontic pain
wake-time clenching
Advisor: Cioffi, Iacopo
Examining Causes and Consequences of Mental Health Disorders in Chronic Traumatic Brain Injury

Traumatic brain injury (TBI) is characterized by a host of persisting mental health (cognitive and psychiatric), motor and neurological sequelae, including progressive, degenerative change in the hippocampi. This thesis postulates that hippocampal volume loss may contribute to the increased risk of psychotic disorder that is observed in this population, through dysregulation of dopaminergic networks. The thesis also posits that TBI is implicated in the substantial mental health deficits observed in persons experiencing homelessness. This thesis specifically investigated (1) The relationship between increased psychotic symptom severity and hippocampal volume loss from 5 to 12 months post-injury and (2) The relationship between TBI and cognitive/psychiatric dysfunction among persons experiencing homelessness. A significant association between increasing hippocampal degeneration and increasing psychotic symptom severity was demonstrated. TBI was also demonstrated to bear strong associations with mental health dysfunction among homeless populations.

Keywords: Hippocampus
Homelessness
Psychosis
Rehabilitation
Schizophrenia
Traumatic brain injury
Advisor: Green, Robin EA
Bayley, Mark
Empirical Estimation of Bias in Randomized and Nonrandomized Study Designs: A Meta-Epidemiological Case Study using TAVI vs. SAVR

Objective: To quantify the bias associated with nonrandomized study (NRS) design attributes in literature comparing Transcatheter Aortic Valve Implantation (TAVI) vs. Surgical Aortic Valve Replacement (SAVR). Methods: 1) Conducted meta-analysis; 2) Compared estimates of treatment effects (ETE) between study designs; 3) Identified associations between 41 NRS attributes and pooled ETE. Results: We included 87 NRSs and 6 randomized controlled trials (RCTs). Lower quality studies underestimated the benefit for TAVI. Randomization in low quality RCTs and risk adjustments in NRSs did not always bring estimates closer to high quality RCT compared to NRSs without adjustment. NRSs that described lost to follow-up reported ETE significantly closer to high quality RCTs than NRSs that did not. Conclusion: ETEs in NRSs are often biased compared to RCTs. Simply categorizing a study as an RCT or NRS fails to reflect the range of bias in each category. Factors related to follow-up may explain important bias.

Keywords: aortic valve replacement
bias in study design
health technology assessment
meta-epidemiological study
surgical trials
Advisor: Urbach, David
Investigating the Role of Phosphoinositides in Skeletal Muscle Development and Substructure Formation

The triad, formed by the close apposition of the T-tubule and terminal sarcoplasmic reticulum, is an important skeletal muscle substructure that regulates excitation-contraction coupling and calcium homeostasis. Recently, defects in triad structure and function have emerged as important underlying contributors to a wide range of human muscle diseases. I hypothesized that dysregulation of phosphoinositide (PIP) activity is a major contributing factor to the irregular triad formation seen in congenital myopathies. To address this, I generated a phosphatidylinositol synthase (CDIPT) mutant zebrafish using CRISPR/Cas9 to determine the overall requirement for PIPs at the triad. In parallel, I also used confocal microscopy to investigate the live dynamics of PIP activity upon overexpression of both wildtype and mutant membrane modelling proteins. The work herein sets the stage further exploration of PIP pathway dynamics and demonstrates that loss of PI(4,5)P2 localization may contribute to disease pathology.

Keywords: muscle
phosphoinositide
triad
zebrafish
Advisor: Dowling, James J
Instrument, Analysis, and Coaching Considerations with Velocity-Based Training

The purpose of this thesis was to assess: 1) The validity of commercial instruments to quantify barbell velocity, 2) The influence of an instruction to attain a specific target velocity in comparison to “move as fast as possible” on barbell velocity and subsequent repetition maximum test performance, and 3) The variability in load-velocity profiles and maximum velocity capabilities between athletes, and if the variability in training intensity is dependent on the absolute velocity target. GymAware was found to be valid across the widest range of velocities, followed by Tendo. PUSH was not valid. Participants moved faster when provided with a specific target velocity (p

Keywords: GymAware
Instruction
Push
Tendo
Validity
Velocity-Based Training
Advisor: Frost, David M
Distributed Linear Quadratic Control with an Attack Detectability Constraint

Cyber physical systems such as power network are vulnerable to various attacks in everyday life. Due to the critical role of cyber physical system, the development of advanced methods to protect cyber physical system against attacks is very important. In this thesis, we adopt the linear time invariant (LTI) system model of such systems. An optimization problem based on the LTI model framework is formulated to study the trade-off between system performance and state feedback communication overhead, subject to attack detectability constraints. We use network flow to model the attack detectability constraints. To demonstrate the effectiveness of our method, we design an attack detection filter based on the Luenberger observer. We validate our result using a six-state system and two power network models.

Keywords: attack detectability
distributed control
network flow
optimization
Advisor: Taylor, Josh
Liang, Ben
Affective Metadata for Object Experiences in the Art Museum

Affective metadata for object experiences in the art museum explores the notion of affect as related to visitor experiences of artworks in a museum gallery setting, resulting in the specification of a data structure and knowledge organization system capable of methodically documenting these experiences. This proposed system presents an interdisciplinary view of museum object documentation that pushes the boundaries of what is conceptualized as object information worthy of documentation in order to adequately account for affective knowledge. Through an analysis of the literature – including affect and affect modeling, art museum information systems, and empirical aesthetics – and a visitor research study at the Art Gallery of Ontario, this thesis argues that affect needs to be considered as a salient dimension of art museum information infrastructures and metadata standards. One possible model for developing such a structure and corresponding standard is presented and validated using the results of this visitor research study.

Keywords: affect
documentation
information systems
knowledge management
metadata
ontologies
Advisor: Dallas, Costis
Identification of Novel miRNA that Regulate Skeletal Muscle Regeneration in Intensive Care Unit-Acquired Weakness

Intensive care unit-acquired weakness (ICUAW) is a common complication of critical illness that may cause long term muscle atrophy and weakness, resulting in permanent physical disability. Our understanding of the mechanisms underlying sustained ICUAW is limited. Survivors of critical illness with sustained atrophy exhibit reduced muscle satellite cell content, suggesting their muscles suffer from an impaired regenerative capacity. Our integrated miRNA/mRNA analysis of quadriceps biopsies from patients with early and sustained ICUAW identified dysregulated expression of miRNAs (miR-206, miR-424-5p, miR-487b, miR-23a-3p, miR-29b-3p) and their gene targets that regulate skeletal myogenesis, supporting the notion that prolonged weakness is explained by an inability to repair muscle. Importantly, we identify miR-490-3p and miR-744-5p as novel miRNA in skeletal muscle that are upregulated in patients with sustained ICUAW, and that regulate skeletal myoblast proliferation and differentiation in vitro. miR-490-3p overexpression significantly downregulates CDK1 expression and inhibits myoblast proliferation, while miR-744-5p overexpression prevents myogenic differentiation.

Keywords: Critical Illness
Intensive Care Unit-Acquired Weakness
miRNA
Muscle Atrophy
Myogenesis
Skeletal Muscle
Advisor: Batt, Jane
Exploring the Role of Resilience in the Experiences of Family Caregivers of a Patient Requiring an Alternate Level of Care

Patients requiring an Alternate Level of Care (ALC) wait in the hospital for an appropriate discharge setting despite being cleared for discharge. The increasing ALC rates have negative implications for health system performance and patient and caregiver health and wellbeing. To date, there are few studies focusing on caregiver perspectives during the ALC period and no research has been conducted on caregiver resilience during this period. This thesis describes the development of a conceptual framework on resilience and family caregiving. Using this conceptual framework, a secondary analysis of qualitative data was undertaken to explore how resilience was impacted and reflected in family caregivers who are caring for a patient who requires an ALC. Three themes were identified: becoming an advocate, variable communication with the healthcare team and searching for balance. Findings from this study shed light on how the health system can support caregivers during this stressful time.

Keywords: ALC
alternate level of care
caregivers
qualitative
resilience
secondary analysis
Advisor: Kuluski, Kerry
Boolean Modeling of Developmental Gene Networks in T Cell Progenitor Differentiation

T cell lineage differentiation of hematopoietic progenitors is controlled via gene regulatory networks. We apply computational Boolean network (BN) modeling to simulate systems-level dynamics of this developmental program. Asynchronous Boolean simulations mapped the transcriptional space that is accessible to T cell progenitors under combinations of Notch, interleukin-7 and pre-T cell receptor signaling. Simulations also predict steady states that correspond to known T cell progenitor types and multiple distinct trajectories that can lead to these steady states. Heterogeneous transcriptional dynamics and trajectories were explored further by single-cell transcriptomics to elucidate differences between in vivo thymopoiesis and novel in vitro differentiation platforms. Finally, our BN modeling framework was integrated into a systems biology software platform to facilitate future extensions to the model. Overall, BN modeling presents a powerful advancement over existing static models for predicting heterogeneous transcriptional responses of T cell progenitors to extrinsic signals during development and in vitro differentiation.

Keywords: Boolean networks
Gene regulatory networks
T cell
Thymopoiesis
Advisor: Zandstra, Peter W
Close to Home: The Evolving Engagement Strategies of Alberta's Local Museums in Canada's Cultural Landscape

In February 2016, the Canadian Government announced for the first time in thirty years it would undertake a study on the state of Canadian museums, yet there was no mention of small local museums. Despite the prolific nature of local museums in Canadian communities, little scholarly work has been done with or on them to understand their specific obstacles and locally-focused engagement strategies. Local museums, then, develop distinct forms of museological practice but receive little attention when it comes to policy, strategic planning, or reliable public funding. To address this gap, my thesis contributes a comparative analysis based on three local museums in rural and suburban Alberta. Through an analysis of policy, funding, programming, and community contexts, I seek to explore how community well-being, museum-community relationships, and museum sustainability can be identified and understood though local museums.

Keywords: Alberta
Albertan museums
Canada
Canadian museums
Local museums
small museums
Advisor: Krmpotich, Cara
Workplace Learning in Non-Profit Organizations – Three Essays

This three-essay thesis uses the systematic review of literature as the method to examine workplace learning in non-profit organizations. The first essay studies how human resource development practitioners conceptualised workplace learning and the factors informing their decisions on workplace learning in organizations. The second essay explores human resource management in non-profit organizations and the third essay analyzes scholarly literature to explore the management of workplace learning in non-profit organizations. The essays reveal a still contested and fuzzy understanding of workplace learning being deployed by non-profit organizations to function in an increasingly competitive and marketized landscape. As the sector adapts to operating in competitive markets, formal learning of professional and managerial programs is privileged over informal learning.

Keywords: Change management
Employee engagement
Isomorphism
Nonprofit
Organizational development
Workplace learning
Advisor: Vieta, Marcelo A
Simulation Model to Assess the Impact of a Centralized Scheduling Policy for Imaging Procedures in Ontario

Due to constrained capacity, wait times for imaging procedures in Ontario hospitals are frequently higher than the provincial target. A new approach that centrally schedules outpatients and assigns them between different locations is expected to be more efficient. Discrete event computer simulation was used to evaluate the impact of this approach by comparing individual hospital models versus a centralized model with imaging demand data from two Ontario hospitals. Results show that the proposed policy can lead to shorter wait times in the system. We also analyzed the different variables that drive better system performance. Final recommendations are given on the real-life application of this policy.

Keywords: MRI
Optimization
Scheduling
Simulation
Advisor: Carter, Michael
Craniofacial Morphology in Children With Obesity or Down Syndrome With and Without Obstructive Sleep Apnea

Introduction: Obstructive Sleep Apnea (OSA) is common in children. Risk factors include adenotonsillar hypertrophy, obesity, and craniofacial abnormalities (e.g. Down Syndrome, DS). The aim was to describe the craniofacial morphology in children with suspected OSA referred for polysomnography (PSG) in 2 cohorts: DS and obesity. Methods: Cross-sectional study of children with DS or obesity referred for PSG at SickKids, Toronto. Orthodontic examinations, PSG, lateral cephalograms, and sleep questionnaires were completed. Results: 42 children (20 DS, 22 obese) aged 5-18 (11.9 +3.6) were included. DS with OSA (Obstructive-Apnea-Hypopnea-Index (OAHI) >1) had increased palatal depth (p=0.04); OAHI was correlated with intercanine distance (r=0.48, p=0.03). ANB angle was increased in Obesity with OSA (p=0.03); OAHI was correlated with ANB (r=0.58, p

Keywords: Craniofacial
Dentofacial
Down Syndrome
Obesity
Obstructive Sleep Apnea
Orthodontics
Advisor: Amin, Reshma
Tompson, Bryan
TALEN-mediated site-specific integration of human CFTR gene by a helper-dependent adenoviral vector

Approximately 2,000 different mutations in CFTR gene have been identified to cause cystic fibrosis (CF). Gene therapies are being developed to target all types of CFTR mutations and to reduce drug burdens in long term. Major challenges of CFTR gene transfer to the lung are the efficient delivery to relevant cells and the safe integration for long-lasting expression. Exploiting the maximized packing capacity of helper-dependent adenoviral vectors (HD-Ad), we are able to deliver a donor CFTR expression cassette together with site-specific TALEN gene editing system in one single vector for accurate transgene integration. We show an approximately 5-7% integration efficiency at the AAVS1 locus in IB3-1 cells by delivering a LacZ reporter with the HD-Ad-TALEN system. Furthermore, we show expression of CFTR mRNA and functional protein by delivering a CFTR expression cassette. Overall, these results demonstrate great potential of the HD-Ad-TALEN system as a novel strategy for CF lung disease.

Keywords: cystic fibrosis
gene therapy
helper-dependent adenoviral vector
Advisor: Hu, Jim