VictorJuiz/thesis huggingface dataset:
Spatial Price Integration in Competitive Markets with Capacitated Transportation Networks

In this thesis, we examine the relationship between the equilibrium prices of spatially separated market participants and the transportation network that connects them; we focus in particular on isolating the effect that the transportation network can have on price integration. We first find that certain network structures and link costs can guarantee a bound on price differences between spatially separated participants when there are no capacity constraints. We extend this analysis to the case when there are binding transportation constraints, and generalize the effects of the transportation network on price integration using a time series decomposition. We then develop an empirical methodology, termed the submarket detection method (SDM), which can be used to infer when binding transportation constraints exist by analyzing regional pricing data from a competitive market, and conclude by using the SDM in a case study of the US gasoline market.

Keywords: Gasoline Market
Market Integration
Spatial Price Equilibrium Models
Time Series Analysis
Advisor: Chan, Timothy C.Y.
Associating the Bulbar and Respiratory Dysfunctions in Patients with Amyotrophic Lateral Sclerosis

Motivated by the need to establish clinical measures of bulbar motor dysfunction, this study investigated the associations between bulbar and respiratory measures in patients with amyotrophic lateral sclerosis (ALS). A secondary analysis of 158 participants (female=59) evaluated: (1) group differences in bulbar motor measures between patients with normal respiratory function (ALSnr) and those with impaired respiratory function (ALSir); and (2) correlations between the bulbar motor and respiratory measures. A significantly larger percent pause time during passage reading was revealed in the ALSir (24.4±7.1) as compared to ALSnr (19.6±6.5) group. A significant negative correlation between percent pause time and forced vital capacity (%FVC) was identified; a partial correlation between percent pause time and speaking rate remained significant after controlling for %FVC. The findings suggested that the respiratory deficit minimally affected the selected bulbar motor measures, thus supporting their use in clinical assessment of bulbar ALS.

Keywords: amyotrophic lateral sclersis
bulbar dysfunction
bulbar motor assessment
physiological subsystem measures
respiratory dysfunction
Advisor: Yunusova, Yana
Design, Analysis, and Testing of the NorSat-3 Microsatellite Mission Communications Subsystem

The NorSat-3 microsatellite will use a combination of Automatic Identification System data and civilian navigation radar to track cooperative and non-cooperative maritime targets. NorSat-3 leverages a Space Flight Laboratory designed and built spacecraft bus, and extends the performance provided by the communications subsystem offered on previous missions. A design for the communications subsystem is proposed which maximizes the use of heritage components, consisting of an uplink system, high speed uplink system, and downlink system. Spacecraft antennas are positioned to optimize performance for all payload and bus antennas during the navigation radar detector payload operations. Analyses and testing performed on this design prove that the links meet requirements on link margin, data throughput, gain coverage, and incident power. The implementation of this design on NorSat-3 will demonstrate the capabilities of microsatellites and improve upon the spacecraft bus design.

Keywords: antenna performance
data budget
link budget
NorSat-3
satellite communications
small satellite
Advisor: Zee, Robert E
Syncytins and cell fusion in the placenta: Structural insights into lipid membrane fusion and placental development

Endogenous retroviruses (ERV) are genetic elements found in eukaryotes of retroviral origin. Despite making up a substantial portion of vertebrate genomes, very few ERV genes encode functional proteins. Interestingly, many animal species have evolutionarily converged in the adoption of ERV envelopes for facilitating necessary cell fusions during placental development. These placental ERV envelopes are called syncytins. Structural characterization of syncytins will provide invaluable insight into placental development and evolution as well as contribute to a general understanding of envelope facilitated membrane fusion. Crystallization of and subsequent x-ray crystallographic experiments of human syncytin-2 transmembrane ectodomain in its post-fusion conformation were carried out and the structure was solved at 1.3Å. Comparative analysis between syncytin-2 and other CX6CC type class I viral fusion proteins reveals, despite high structural conservancy, nuanced structural divergences that may reflect functional differences arising by the distinct contexts in which each protein must facilitate membrane fusion.

Keywords: Fusion Proteins
Placental Development
Structural Biology
Syncytin
Viral Fusion
X-Ray Crystallography
Advisor: Lee, Jeffrey E
Effect of Anodal Transcranial Direct Current Stimulation on Motor Learning in Healthy Individuals

Practice is required to improve your shot in basketball or play a musical instrument. Learning these motor skills can be further enhanced by non-invasive brain-stimulation. Prior studies have shown that transcranial direct current stimulation (tDCS) applied concurrently with practice of a motor task, results in better skill performance, than practice alone with sham-tDCS. This thesis sought to investigate how many additional days of practice it will take for individuals receiving sham-tDCS to reach the same performance level as individuals who receive anodal-tDCS for 1 day. Skill, composed of movement time and error-rate, was the primary dependent measure. A trend towards a greater proportion of individuals in the anodal-tDCS group (n=11) obtained the pre-determined skill level earlier than individuals in the sham-tDCS group (n=11), however skill level at 24-hour retention was comparable between groups. These findings suggest anodal-tDCS does not have additional benefits on motor learning after a period of rest.

Keywords: Motor Learning
Non-Invasive Brain Stimulation
Rehabilitation
Stroke
Trancranial Direct Current Stimulation (tDCS)
Transcranial Magnetic Stimulation
Advisor: Chen, Joyce L
Understanding Teacher Perceptions of Assistive Technology

This research examined grade 6-10 Ontario Certified Teachers’ (n = 24) perceptions of assistive technology (AT), and the factors correlated with perceived usefulness of AT. A mixed-methods design, which included a survey consisting of open- and closed-ended items elicited information about teachers’ AT knowledge and training, their basic computer literacy, their perception of administrative support for access to and implementation of AT, the usefulness of AT, and the factors that encourage or discourage AT use in the classroom. Results of correlational analysis suggested that computer literacy and AT knowledge were significantly positively correlated with perceived usefulness of AT and a thematic analysis further identified that training and student factors may influence AT use. Implications for pre-service and professional development teacher training are discussed given the consistency of teacher-reported need for greater training opportunities for both students and teachers.

Keywords: assistive technology
education
learning disabilities
teacher training
Advisor: Cunningham, Todd
Structural Variant Discovery Using Long Read Sequencing in Group 4 Medulloblastoma

Improper repair of double stranded breaks in the genome can cause structural variants. As technology continues to advance, these events are identified with increasing resolution. Indeed the introduction of long read sequencing identified new structural variants not previously seen in a variety of cancers. Long read sequencing was performed on two cancer types: nine Group 4 medulloblastoma samples and two PF-A ependymoma samples. This has led to the identification of numerous somatic and germline structural variants in both types of cancer. A germline insertion near the amyloid beta precursor protein (APP) gene was seen across all samples of Group 4 medulloblastoma, with the event not called by short read sequencing. Long reads aided in an improved assembly of the tumour and normal genomes, which were used to validate certain structural variants. Genome doubling events also seemed to be enriched in Group 4 medulloblastoma.

Keywords: Ependymoma
Long Reads
Medulloblastoma
PacBio
Structural Variants
Advisor: Taylor, Michael D
The Role of Polarity Protein Angiomotin (AMOT) in the Human Placenta

Angiomotin (AMOT) is a scaffolding protein involved in cell polarity regulation, cell migration and early embryo lineage differentiation, yet its biological significance in the human placenta remains unknown. I hypothesized that AMOT controls trophoblast cell polarity and migration, and is further regulated by transforming growth factor beta (TGF) signalling and upstream oxygen tension. AMOT localization to extravillous trophoblast (EVT) cells, corroborated by AMOT 80 overexpression increasing JEG3 cell migration rate, supports a role for AMOT in EVT migration. TGF1/3 treatment decreased AMOT protein levels and redistributed AMOT from the tight-junction to cytoplasmic F-actin in JEG3 cells. TGF1/3 also prompted a novel association between AMOT 80 and Partitioning Defective Protein-6. Similarly, low oxygen exposure negatively regulated AMOT levels and localization. Furthermore, Jumonji C Domain Containing Protein-6 (JMJD6), an oxygen sensor, was discovered to positively regulate AMOT via lysyl hydroxylation. Finally, AMOT levels were found markedly reduced in preeclampsia, a disease characterized by aberrant TGF signalling and chronic hypoxia. In conclusion, this study reveals AMOT is a mediator of TGF and oxygen signalling to regulate trophoblast migration in the human placenta.

Keywords: Angiomotin
Cell Polarity
Placenta Development
Preeclampsia
TGF-beta signalling
Trophoblast Migration
Advisor: Caniggia, Isabella
Two-Tier Networks: Beamforming at Secondary Node, applied to LTE

This thesis explores the gains and limitations associated with Two-Tier cellular communication systems comprising classical base stations, User Equipment (UE) and Secondary Nodes facilitating the connection of UE to base stations using beamforming antenna arrays. To investigate the merit of the proposed connectivity structure, data was collected from a live Long-Term Evolution (LTE) cellular network around the University of Toronto downtown campus. To facilitate data collection, a detailed framework was developed, implemented and refined using commercial hardware and software for collecting live data from cellular communication systems. By determining the Direction of Arrival (DoA) of received signals, the utilized antenna arrays were shown to provide substantial performance gains. Specifically, utilization of a 16-element antenna array was shown to increase the spectral efficiency range by 2.48 to 15.8 times or improving the coverage radius range by 1.11 to 1.85 times.

Keywords: Beamforming
Software Defined Radio
Two Tired Network
Advisor: Sousa, Elvino
Automated image based registration of endoscopy to CT views for improved target delineation in image guided radiation therapy

One of the largest uncertainties in radiotherapy treatment planning for squamous cell carcinomas of the head and neck is contouring the gross tumour volume (GTV). The treatment planning CT is used to contour the GTV, but under-contouring of the mucosal extent of the disease is common. Endoscopy exams can be used to reduce GTV errors by registering endoscopy images to the CT to project contours of the mucosal extent of the disease viewed under endoscopy. To register endoscopy and CT images, a rigid registration pipeline was developed using electromagnetic tracking and image based registration with a target of achieving a contouring error of less than or equal to 2mm between the two image sets. On phantom data, a contouring error of less than or equal to 2mm was achieved in 14 of 18 images. On four images of glottal tumours from two clinical cases, the contouring error ranged between 2.4-6.1mm.

Keywords: CT
endoscopy
image guided interventions
image processing
radiation therapy
registration
Advisor: Weersink, Robert
Primary Care Provider’s Perspectives on Physical Activity Counseling

Physical activity counseling in primary care has been a key health sector response to the health risks of physical inactivity. This thesis examined how providers in a clinic group understood physical activity counseling, perceived their experiences in practice, and to what extent their perspectives differed based by discipline. Two focus groups were conducted, one each for physicians and nurses/nurse practitioners, with short surveys at the start. Physical activity was understood as a health issue, and physical activity counseling was generally accepted as a routine part of care. Though it was an accepted practice, providers noted several areas of challenges, including how to apply recommendations to particular patient contexts, how to address barriers patients face, and different challenges between disciplines in incorporating counseling into practice. These results inform how providers are understood to perceive physical activity and counseling for it, and the challenges providers face integrating physical activity counseling in practice.

Advisor: Silver, Michelle P
Generic Policy Evaluation Model In a Multi-Facility Diagnostic Imaging Setting

When evaluating regional health performance in a multi-facility setting, patient behaviour must be accounted for with services where facility choice is available. This paper describes the development of an agent-based simulation model designed to evaluate policy scenarios which incorporates facility choice, patient behaviour and operational constraints in the diagnostic imaging setting, specifically in MRI. The model is validated by retrospectively simulating the performance of the region for a year and comparing the results with actual performance. Using the model, theoretical results are confirmed where additional facility choice leads to more equitable but higher waiting times. We demonstrate how the model can be used by policy makers to evaluate various planning scenarios by expanding capacity at selected sites and show that the benefits of additional capacity is not limited to the expanding sites.

Keywords: Agent based simulation
Diagnostic imaging
Patient behaviour
Advisor: Carter, Michael
Development of Specifically Ablatable Neural Precursor Cells to Investigate the Cell-Based Mechanism of Exogenous Cell Transplants

Stroke is a leading cause of long-term disability, and new therapies are needed to improve quality of life for those affected. Stem cell transplantation produces functional recovery in rodent stroke models, but therapeutic mechanisms remain unclear. Transplanted neural precursor cells (NPCs) lead to functional recovery in rodents following stroke and differentiate into neural cell types; whether they need to integrate into host tissue long-term to be therapeutic remains to be elucidated. To study this, I have engineered specifically ablatable cortical neuroepithelial cells (cNEPs), allowing transplant ablation to determine whether cells are required for long-term functional recovery. Engineered cNEPs express nitroreductase, allowing conversion of metronidazole (MTZ) into toxic metabolites, and respond to MTZ in a dose response manner, allowing ablation in vitro/in vivo with no bystander effect between 100μg/ml - 400μg/ml of MTZ. Transplanted into rodents, these cells enable study of mechanisms of functional recovery mediated by NPC transplants.

Advisor: Morshead, Cindi M
Genetic Screen to Characterize Shank Interactors at the Drosophila Neuromuscular Junction

Mutations in Shank family genes are highly implicated in idiopathic autism spectrum disorders (ASD) and therefore have been repeatedly studied using rodent models, however, study results have been varied possibly due to redundancy from multiple Shank family genes. Drosophila models offer a clearer approach as they possess only one Shank gene, allowing in-depth study of Shank and its interactions with other factors. Using the Drosophila neuromuscular junction as a model of glutamatergic brain synapses, a genetic screen was performed to identify novel interactors of Drosophila Shank and characterize new molecular pathways to understand how Shank functions at synapses. Results from this screen indicated that Ca-1d may share a relationship with Shank. Further characterization in a Shank overexpression background confirmed an interaction that is not apparent in a Shank loss-of-function background. Studying genes linked to ASDs in a simple model may reveal unappreciated signalling pathways providing new directions in autism research.

Keywords: Ca-alpha1d
Drosophila
Neuromuscular junction
Shank
Advisor: Stewart, Bryan A
The Future of the Past: Third-Party Heritage Preservation Interventions and 3D Printing

This thesis investigates the role of the international community and 3D technologies in heritage interventions. This research seeks to ascertain how interventions initiated by the international community that seek to re-create cultural property destroyed by ISIS/ISIL/Daesh since the beginning of the Syrian Conflict in 2011 may both resist and support Daesh’s aims. Daesh’s destruction of cultural property is understood as a form of violence against cultural identity that seeks to erase and impose cultural narratives. Through an examination of three case studies that re-created cultural property destroyed by Daesh through 3D printing technologies, this research considers how such heritage reconstruction projects resist or support Daesh’s aims of erasure and imposition of cultural narrative and encourages critically-aware reconstruction and restoration efforts.

Keywords: 3D Printing
Cultural Property
Heritage
ISIS
Syria
Advisor: Krmpotich, Cara
Cerebellar Characterization in Mouse Models of 7q11.23 Copy Number Variation Disorders

Williams-Beuren Syndrome (WS) and 7q11.23 Duplication Syndrome (Dup7) are neurodevelopmental disorders caused by the deletion and duplication of ~26 genes in region 7q11.23 on chromosome 7, respectively. Despite cerebellar-associated neurological symptoms and altered cerebellar volume in WS and Dup7, very little is known about the role of the cerebellum in explaining these phenotypes. This study aimed at characterizing the cerebellum and cerebellar Purkinje cells in mice with varying copy numbers of two candidate genes, Gtf2i and Gtf2ird1. Our findings show that Gtf2i and Gtf2ird1 cause dose-dependent changes to the thickness of the cerebellar molecular layer. The cause of this change has yet to be determined, however the change appears to be driven by a smaller sample size and by differences in wildtype mice rather than mutant mice. We conclude that the genes, GTF2I and GTF2IRD1, are unlikely to be major drivers of the cerebellar-related deficits seen in WS and Dup7.

Keywords: 7q11.23 Duplication Syndrome
Cerebellum
GTF2I
GTF2IRD1
Purkinje Cell
Williams-Beuren Syndrome
Advisor: Osborne, Lucy R
Mental Health, Sleep, Physical Activity and Family Functioning in Adolescents with Narcolepsy

Background: Pediatric narcolepsy is a lifelong sleep disorder that is associated with depressive symptoms. The factors associated with depressive symptoms are unclear. Research on family functioning in pediatric narcolepsy is also limited. The primary objective of this study was to evaluate sleep and physical activity (PA) as factors associated with depression scores in adolescents with narcolepsy and controls. The secondary objective was to assess family functioning in pediatric narcolepsy Methods: Adolescents with narcolepsy and controls were recruited from the Hospital for Sick Children and Toronto area respectively. Participants wore an actigraph and pedometer to measure sleep and PA respectively. Depression scores were evaluated with the Children’s Depression Inventory-2. Family Functioning was assessed using the PedsQL Family Impact Module Results: Sixty adolescents (30 narcolepsy; 30 controls) participated. Poor sleep quality, excessive daytime sleepiness, and low PA levels were associated with greater depression scores. Family functioning was impaired in pediatric narcolepsy patients.

Advisor: Narang, Indra
Understanding Physiotherapists’ Use of Motor Learning Strategies in Gait-Based Physiotherapy Interventions for Children with Cerebral Palsy

This thesis aims to understand motor learning strategies (MLS) use in physiotherapy interventions for children with cerebral palsy by measuring MLS application and exploring physiotherapists’ perspectives. The Motor Learning Strategies Rating Instrument (MLSRI-20) measures the extent MLS are used within an intervention, but does not necessarily reflect the therapist’s intention to use them. The inter- and intra-rater reliability of the MLSRI-20 were evaluated in traditional and Lokomat-based physiotherapy interventions. Semi-structured interviews explored PTs’ intentions during these interventions. Results indicate the MLSRI-20 reliably measures MLS in physiotherapy interventions and most MLS were used intentionally. These studies provide a preliminary indication that while the independent observation of MLS use captures some of therapists’ intentions and clinical decisions, greater awareness of the range of MLS available is required. The MLSRI-20 can be used as the framework for therapist training, and should be used to measure MLS implementation in clinical and research settings.

Keywords: cerebral palsy
children
motor learning
motor learning strategies
pediatrics
physical therapy
Advisor: Wright, F Virginia
Effect of rest seat on the in vitro mechanical performance of monolithic zirconia crowns supporting bilateral free-end removable partial dental prostheses: a pilot study

Objectives: To compare the load-to-fracture of surveyed and conventional monolithic zirconia crowns for cast removable partial dental prosthesis’ (RPDP) abutments. Methods: Premolar typodont teeth were prepared and received milled zirconia crowns (n=5) designed without (control) or with rest seats with different rest seat thicknesses (0.5 versus 0.75 mm) and timing of rest seat preparation (prior to versus after sintering). Restorations were subjected to artificial aging with free-end cast RPDPs in place, and then loaded until fracture. Statistical analyses included two-way analysis of variance and Tukey tests. Results: Surveyed crowns supporting cast RPDPs demonstrated significantly greater load-to-fracture when compared to control crowns (p

Keywords: bilateral free-end cast removable partial dental prostheses
load-to-fracture
mechanical performance
monolithic zirconia
rest seat
surveyed crowns
Advisor: Shokati, Babak
Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits

Genome-wide association studies and expression quantitative trait loci (eQTL) studies have identified thousands of variants associated with complex diseases and gene expression levels. The frequency of DNA words associated with these variants has not been extensively evaluated. These words may help understand the biological role of trait-associated variants and also enable their identification in future studies. An exact word-counting method was developed to investigate the hypothesis that short DNA words have different frequencies near single nucleotide polymorphisms (SNPs) associated with (1) Alzheimer’s disease and (2) thyroid eQTLs, compared to the rest of the genome. No significant DNA words were found near AD associated SNPs. Some words enriched in GC content have significantly higher frequency around thyroid’s eQTLs compared to controls. These DNA words were no longer significant when the controls were matched for nucleotide frequency, but this is likely due to over-matching.

Keywords: Algorithm
Alzheimer's Disease
DNA words
Expression Quantitative Trait Loci (eQTLs)
Gene-Tissue Expression (GTEx) Project
Genome wide association studies (GWAS)
Advisor: Knight, Jo
Paterson, Andrew D