VictorJuiz/thesis huggingface dataset:
Elucidating the Role of ARKL1 in Regulating Epstein-Barr Virus (EBV) Iinfection

ARKL1 and Arkadia were previously identified as proteins that bind to the CK2Î˛ KSSR motif. Since the Epstein-Barr virus (EBV) protein Epstein-Barr nuclear antigen 1 (EBNA1) is also known to bind to the same sequence, it was hypothesized that ARKL1 and Arkadia might play a role in regulating EBV infection. Silencing experiments demonstrated that both ARKL1 and Arkadia function to suppress EBV reactivation. ARKL1 was subsequently found to colocalize with the PRC1 protein CBX4 in distinct nuclear foci. This localization of ARKL1 to CBX4 foci was dependent upon its SIMs, as mutation of its SIMs resulted in diffused nuclear staining. In order to gain mechanistic insights into how ARKL1 regulates EBV infection, I carried out affinity purification-mass spectrometry (AP-MS) of ARKL1. ARKL1 was found to bind the transcriptional activators Jun and CREB1. This result raises the possibility that ARKL1 may function to recruit PRC1 to sites bound by Jun/CREB1, thereby repressing transcription.

Keywords: Arkadia
ARKL1
EBV
Jun
Polycomb
Reactivation
Advisor: Frappier, Lori
Nishnaabeg Encounters: Living Indigenous Landscapes

This thesis is an exploration of Nishnaabeg geography in what is now known as Southern Ontario that takes into consideration the dominating settler colonial context. Using a mixed method of textual document analysis, and embodied research, I develop a Nishnaabeg geography of a region colonized by a the Trent Severn Waterway (TSW), a large canal composed of several locks and dams that connect natural lakes, and dense settlement in the form of privately owned cottages. The TSW was integral to establishing settlement in the region and is commemorated as a part of Canada’s nation-building project over Indigenous lands. This research considers how the colonization of the water contributed to the creation of a built colonialscape and helped to spatialize Indigenous land relations as belonging “somewhere else.” I argue that in spite of these imagined spatializations, the Indigenous landscape continues to live on beneath the built colonialscape in geographical layers.

Keywords: Indigenous Geography
Land-based Research
Nishnaabeg Methodology
Paddling Methodology
Property
Settler Colonialism
Advisor: Wakefield, Sarah
Successes and Challenges of Implementing the Oak Ridges Moraine Conservation Plan

A common planning response to urbanizing regions is the creation of protected zones or greenbelts at the edge of existing urban development, with the goal of controlling the location of future development while conserving natural features. The Oak Ridges Moraine Conservation Plan (2002) was created by the Ontario Provincial Government to protect the Oak Ridges Moraine, one of the few remaining large greenspace corridors in southern Ontario that is threatened by the expansion of the Greater Toronto Area. This research investigates the effectiveness of the Plan at protecting the Moraine. It explores the successes and challenges of implementing the Plan and the proposed changes by the provincial government. Regional town hall meetings and open houses were attended, and interviews and questionnaires were conducted. The results suggest the Plan has effectively protected the Moraine through changing building practices, although the Plan requires some modifications to better protect the Moraine.

Keywords: environmental conservation
greenbelt
land use
sustainable development
urban containment policy
urban sprawl
Advisor: Conway, Tenley
Predicting Upper Airway Abnormalities by Detecting Inspiratory Flow Limitation with Temporal Features of Nasal Airflow

The purpose of this thesis is to explore the potential of the temporal features extracted from nasal airflow as the source for detecting inspiratory flow limitation non-invasively. This thesis focused on developing and validating algorithms capable of extracting physiologically meaningful features from nasal airflow recording, followed by classification of flow limited breaths, utilizing supervised and un-supervised learning. The feature values and the classification results were compared with the upper airway anatomical measurements such as neck circumference, upperairway cross-sectional area, and neck fluid volume. Three features (deviation index, peak amplitude variability, and peak number) were found to be significantly correlated with the upper airway measurements. Un-supervised classification suggested that participants with more neck fluid volume before sleep are associated with more flow limited breaths. The findings corroborated our understanding that inspiratory flow limitation is associated with upper airway anatomical abnormalities.

Keywords: Inspiratory flow limitation
Sleep-disordered breathing
Advisor: Popovic, Milos R
Yadollahi, Azadeh
Preliminary Mapping of HopZ1b Resistance-associated Loci in Arabidopsis thaliana via EMS and Ecotype Screens

Pseudomonas syringae is a plant pathogen that infects agriculturally important crops and the model organism Arabidopsis thaliana. P. syringae deploys type III effectors to suppress immunity and enhance bacterial growth. However, plants possess resistance proteins to recognize these effectors. Thus, effectors have diversified to evade recognition. For example, in Arabidopsis Columbia-0, HopZ1a effector triggers robust immunity through ZAR1 resistance protein, but the related HopZ1b elicits a weak resistance-like phenotype. We conducted EMS and ecotype forward genetic screens in A. thaliana to identify variations conferring HopZ1b resistance. We found one EMS mutant and one ecotype Gabelstein-0 with enhanced HopZ1b resistance. Resistance correlated with bacterial growth inhibition, and was enhanced by surface bacterial inoculation rather than direct injection into plant tissue. Resistance required putative HopZ1b catalytic function and localization. We also analyzed Gabelstein-0 ZAR1 and found enriched variations in the NB-ARC activation domain. These variations may facilitate ZAR1 activation and consequent HopZ1b resistance.

Keywords: HopZ1b
plant immunity
pseudomonas syringae
type III effector
Advisor: Desveaux, Darrell
Guttman, David
The Development of a New Experimental Facility for Pyrolysis Liquid Biofuel (Bio-oil) Combustion

Bio-oil is made from pyrolysis of waste biomass, which provides a carbon-neutral combustion energy alternative. This study focuses on developing burners for use with bio-oil. The previous burner using bio-oil/ethanol mixtures had a small combustion chamber with no refractory lining. It was not feasible to stabilize flames of pure bio-oil and the pollutant emissions were relatively high. In this study, the burner is made more comparable to actual bio-oil burners by implementing a refractory-lined combustion chamber and increasing the size of the chamber to investigate the relationship between burner design and combustion performance of bio-oil. After making some modifications in the new burner configuration and adjusting the operating parameters, stable flames of pure bio-oil are achieved with no major nozzle coking problems, and almost no unburned hydrocarbons and low CO emissions (below 10 ppm) in the exhaust gases. The effects of operating conditions on the pollutant emissions are also investigated.

Keywords: Bio-oil
Burner
Carbon-neutral
Combustion
Pollutant emissions
Pyrolysis
Advisor: Thomson, Murray J
NFV and VNF Service Chaining on SAVI SDI

Network Function Virtualization, a flexible networking architecture virtualizing network nodes, allows modular development of network functionalities and quick deployment on cloud infrastructures. Each network module individually deploys a virtualized network function (VNF). A network application might demand a set of inter-connected VNFs to work together. The logic and process of connecting VNFs together are called VNF service chaining. In this thesis, two contributions were presented. First, a framework for VNF service chaining for software dened infrastructure was designed and tested using security attacks. The shortcomings of deploying security as a service with VNFs was examined, and a combined NFV/SDN solution was proposed. A parallelism technique was employed to make the NFV/SDN security solution scalable. Second, the real-time content delivery network of a stadium, equipped with virtualized customer premises Edges (vCPEs), accommodated a higher number of users employing our service chaining algorithm.

Keywords: NFV
SDI
SDN
Security
vCPE
VNF
Advisor: Leon-Garcia, Alberto
Topology Optimization Studies for Light Weight Acoustic Panels

With the growing need to reduce green house gas emissions, increasing flight effciency has been a primary challenge faced by the aviation industry. Designing lighter and more effcient aircraft is becoming a goal shared throughout the global air transportation industry. A light weight acoustic panel is desired to replace heavy and bulky foam panels inside the fuselage for cabin noise control. Currently, there is no consensus on the best panel design. Therefore, this thesis will explore using topology optimization to suggest new panel designs. This thesis contains studies of some acoustic panel designs as well as methodologies used to optimize the core topology of a sandwich panel with a maximized band gap while remaining light and stiff. In this thesis, the sound transmission loss has been related to the existence of band gap, and a band gap is being maximized as a surrogate for sound transmission loss. The main results obtained from this thesis show interesting topologies with a band gap around 300 Hz being maximized under mass and stiffness constraints, and the core topologies have been found to have resemblance to resonators.

Keywords: acoustic
bandgap
optimization
panel
sandwich
topology
Advisor: Steeves, Craig A
Life Cycle Emissions and Lifetime Costs of Medium-duty Diesel and Alternative Fuel Trucks. A Case Study for Toronto

This thesis analyzes a Class 6 diesel truck, compressed natural gas truck, hybrid-electric truck and battery-electric truck, in terms of energy consumption, life cycle greenhouse gas (GHG) emissions and cost of ownership. The energy consumption simulation and life cycle emissions for the trucks are based on payload, temperature and two drive cycles in Toronto. The energy consumption simulations are performed using Autonomie, a simulation software. The simulation data are used in GHGenius to calculate the life cycle GHG emissions. The cost of GHG emissions abatement for each alternative fuel truck is determined based on the differences in cost and GHG emissions between the alternative trucks and the diesel (reference) truck. The results of the analyses indicate that there is no dominant technology that reduces both GHG emissions and ownership cost under all driving conditions, a conclusion that can inform transportation climate change policies.

Advisor: MacLean, Heather L
Roorda, Matthew J
Motion Control of a Gymnastics Robot Using Virtual Holonomic Constraints

In this thesis the motion control problem of a gymnastics robot performing a bar routine is analysed, and a comprehensive solution is developed using the framework of virtual holonomic constraints. The routine is a combination of swinging manoeuvres on the bar and a back-ďŹ ipping dismount in the air. Virtual holonomic constraints are used extensively to parametrize the motions, for which stabilizing controllers are developed. Using tools such as high-gain observers, PoincarÂ´e analysis, and linearization about a trajectory, the virtual constraints are dynamically reshaped so as to meet the control objectives for each motion. A physical gymnastics robot was built in the lab, and experiments were conducted to verify the theoretical predictions. Results show that the solutions developed were robust to real-world imperfections.

Keywords: gymnastics robot
motion control
robot locomotion
virtual holonomic constraint
Advisor: Maggiore, Manfredi
Effects of the Lyme Disease Pathogen Borrelia burgdorferi on Murine Bone Biology

This thesis reports the effects of infection by the Lyme disease pathogen Borrelia burgdorferi on bone biology in mice. Bone mineral density, microarchitecture, and cellular morphology were analyzed. B. burgdorferi was found to directly invade bone. Infection induced osteopenia in long bones but not vertebraes. Trabecular bone was deteriorated by infection, but cortical bone was unaffected. Bone loss was not due to increases in osteoclastogenesis or bone resorption. Instead, it was associated with reduction in osteoblast numbers. Osteoid-producing and mineralization activities of existing osteoblasts were unaffected by infection. This suggested that osteopenia and disruption of trabecular bone in response to B. burgdorferi infection was likely caused by mechanisms which impaired osteoblastogenesis and/or induced osteoblast cell death. Together, these data represent the first evidence that B. burgdorferi infection can induce bone loss, and suggest that this phenotype is due to the effects of infection on osteoblastogenesis and/or osteoblast survival.

Keywords: Bone biology
Lyme disease
Mouse models
Osteopenia
Advisor: Moriarty, Tara
Gaming to Safety: The Design and Evaluation of Feedback Gamification for Mitigating Driver Distraction

This thesis examined the gamification of feedback systems for potential benefits in mitigating driver distraction and enhancing driving performance. Distraction is detrimental to traffic safety. Integrating driver feedback with elements of game design could effectively reduce distraction and motivate lasting behavioral changes. A simulator study was conducted with younger drivers (n = 42) comparing no feedback, a real-time feedback system, a post-drive feedback system (real-time feedback + post-drive feedback), and a gamification feedback system (real-time feedback + post-drive feedback + game design elements). No differences were observed between no feedback and the real-time feedback system. Comparing the gamification and post-drive feedback systems, the gamification system provided more benefits in the rate of manual interactions with an in-vehicle display and the post-drive system provided more benefits in the 95th percentile glance duration to the in-vehicle display. Despite these differences, both gamification and post-drive feedback systems were effective, short term countermeasures of distracted driving.

Keywords: Driver distraction
Driver feedback
Gamification
Intrinsic motivation
Advisor: Donmez, Birsen
Mechanistic Modelling in Support of Human Biomonitoring

Lifetime exposures to polychlorinated biphenyls (PCBs) were calculated using a combined mechanistic model of environmental fate (BETR-Global) and human food chain bioaccumulation (ACC-Human) for 6128 participants of the United States National Health and Nutrition Examination Survey (NHANES) 1999-2004. Important questionnaire information from NHANES (year of birth, diet, body mass index (BMI), sex, reproductive behaviour) were used as model input. The model performed well on a popula- tion level, where the geometric mean modelled concentration of 13.3 ng/g lipid is close to the geometric mean measured concentration of 22.0 ng/g lipid. While the model successfully reproduced measured trends with age, sex, BMI, a failure was observed with diet. Furthermore, the model was used to explore the relationship between PCB levels and BMI, and it was found that these relationships depend on i) age, ii) the time of sampling, and iii) the range of body mass index sampled.

Keywords: Bioaccumulation
Biomonitoring
Exposure Modelling
Persistent organic pollutants
Polychlorinated Biphenyls
Advisor: Wania, Frank
Driving Performance and Underlying Brain Activation Patterns in Chronic Stroke Patients

Resuming driving is an important priority for many stroke patients, yet persistent deficits may result in impaired driving performance. The present study used driving simulation and functional magnetic resonance imaging to examine whether stroke patients exhibit behavioural impairments and differences in brain activation patterns during driving tasks of varying complexity. Stroke patients committed more hazardous errors and errors at intersections, specifically when making complex left turns at intersections with oncoming traffic. Patients exhibited deviations from expected neural activation patterns during the most complex driving maneuver. The results of the present study suggest that stroke patients exhibit impairment during complex aspects of driving, specifically during intersections, and display altered patterns of neural activation as the perceptual and cognitive demands of the driving task increase. Further research is required to develop and validate existing screening measures and rehabilitation programs that target these specific driving impairments observed in functionally independent, chronic stroke patients.

Keywords: Driving
fMRI
Ischemic Stroke
Stroke
Subarachnoid Hemorrhage
Advisor: Schweizer, Tom A
Sex in Space! Does Sexual Selection Accelerate or Hinder Adaptation?

Theory suggests sexual selection should accelerate adaptation in novel environments. A number of past studies used Drosophila species to test this prediction, and yielded inconsistent result. However, these experiments were all conducted in settings where the test populations are being housed in spatially restricted, simple mating environments. The use of high-density, small and physically simple arenas can exacerbate the effect of male harassment, which reduces both selection on high condition females, and selection against low condition males. Adult fly interaction in large and complex mating environment is predicted to alter selection by alleviate the intensity of male harassment, and increase selection on males. As a necessary extension to past studies, we give evidence suggesting that sexually selected populations evolving under complex ecological environment yields fitness measure more consistent with the alignment of natural and sexual selection.

Keywords: Adaptation
Drosophila
Evolutionary Ecology
Good Genes
Sexual Conflict
Sexual Selection
Advisor: Agrawal, Aneil F
Rundle, Howard D
Role of Notch Signaling in Human Pluripotent Stem Cell-derived Hematopoiesis

Hematopoietic development of pluripotent stem cells (PSCs) begins with the emergence of hemogenic endothelial (HE) precursors, followed by endothelial-to-hematopoietic transition (EHT). To test the effect of Notch signaling on HE specification, PSCs were differentiated on OP9-control or OP9-DL1 cells expressing the Notch ligand Delta-like 1 (Dll1), and then induced to become T-cells. There was high variability in T-cell generation from many experimental repeats. As a result, we tested different serum lots and also administered anti-TGF-Î˛ treatments during co-culture. However, the inconsistency of T-cell generation using this protocol remained unaffected. Next, we engineered OP9 cells to ectopically express human JAG1 (OP9-JAG1), and evaluated their ability to promote EHT by culturing HE cells on OP9-JAG1 or OP9-DL4 cells. Of note, cells undergoing EHT in the presence of JAG1 showed better hematopoietic conversion than those on OP9-DL4. Collectively, these data suggest a preferential role for JAG1 during human EHT in vitro.

Advisor: Zuniga-Pflucker, Juan Carlos
Completing the Feedback Loop: An Assessment of the Implementation of an Early Stage Audit and Feedback Intervention in Primary Care

Audit and Feedback (A) is a common quality improvement strategy characterized as an feedback loop enabling an iterative, self-regulating progress. The objective of this thesis was to evaluate the implementation of a specific A program in team-based primary care practices. Eighteen semi-structured interviews were conducted to explore its implementation and factors influencing participation. Interview transcripts were analyzed deductively with the support of the Consolidated Framework for Implementation Research. Findings revealed that implementation was not representative of a complete feedback loop. Participation was primarily associated with a perception that the program would develop into a best-in-class A initiative for primary care. The relationship between physicians and organizational administrators was identified as a key factor which may support or deter implementation. The study also identified factors related to the design and delivery of A that may explain why and how an A intervention in primary care can achieve its objectives.

Keywords: Audit and Feedback
Primary Care
Advisor: Ivers, Noah M
Exploring the Feasibility of Prompting Daily Task Execution using the NAO Humanoid Robot with Children with Autism Spectrum Disorder

This thesis seeks to improve the state of the art prompting system, COACH, for the children with ASD population. It investigates the feasibility of using a humanoid robot, NAO, as its prompting agent through a Wizard of Oz (WoZ) pilot study. The WoZ study showed promising results of the robot potentially being used as an assistance to a child with ASD through hand-washing tasks. The study also suggested parent robot joint prompting sessions as a valid method for improving child's compliance to the robot. The important challenges faced are summarized and possible recommendations for overcoming these challenges are suggested.

Keywords: asd
assistive technology
autism
hand washing
prompt
robotics
Advisor: Mihailidis, Alex
Multicast Routing for Virtual Network Functions on SDN

Many multicast services such as live multimedia distribution and real-time event monitoring require constructing a multicast mechanism to chain network functions (e.g. rewall, video transcoding). Network Function Virtualization (NFV) is a concept that proposes using virtual-ization to implement network functions on infrastructure building blocks (such as high volume servers, virtual machines), where software replaces the functionality of existing purpose-built network equipment. We present an approach for building the multicast mechanism whereby multicast ows are processed by NFV before reaching end users. We propose a routing algorithm and a method for building an appropriate multicast topology. First we proposed a approximation algorithm to give an oine solution of the problem, then we further extend this problem to consider the eect of the NFV on bandwidth consumption. Finally, we consider the online version of this problem and present an online algorithm to adjust the multicast topology based on the dynamic cost of resources.

Advisor: Leon-Garcia, Alberto
Inflammatory Cell Responses to Vascular Regenerative Methacrylic Acid-containing Materials

Poly(methacrylic acid-co-methyl methacrylate) (MAA) beads improve vascularization when applied to cutaneously-wounded diabetic mice. The aim of this thesis is to understand the vascular regenerative properties of MAA at the cellular and molecular level. Subcutaneous injection of MAA beads promoted the formation of a denser and perfusable network of blood vessels at days 3 and 7 relative to poly(methyl methacrylate) (MM) control beads. MAA beads modulated the host response; promoting more neutrophils at day 1 and more macrophages at day 7, relative to MM beads. A M2 macrophage polarization bias was observed in MAA-treated animals but not in MM-treated animals. Additionally, complement was involved in the mechanism of MAA; complement inhibition (at the C1 or C3 levels) diminished the M2 polarization bias at day 3, although no changes in vascularity were noted. These findings deepen our understanding of MAA and benefit the development of MAA-based biomaterials for applications in regenerative medicine.

Keywords: complement activation
host response
macrophage polarization
methacrylic acid
Advisor: Sefton, Michael V.