VictorJuiz/thesis huggingface dataset:
The Role of ER-localized HSP90 in Modulating the WUSCHEL-CLAVATA pathway and ER Stress Resistance in Arabidopsis thaliana

Arabidopsis HSP90.7 is the ER-localized isoform of molecular chaperone HSP90 and has been implicated to play a role in the WUSCHEL-CLAVATA (WUS-CLV) pathway. A short and highly charged region is identified specifically in the middle domain of plant-derived ER-localized HSP90s. To understand the role of this charged region, we analyzed the function of HSP90.7 and a mutant form HSP90.7∆22, which has the charged region deleted. HSP90.7∆22 has higher ATP hydrolysis efficiency compared to HSP90.7, and seedlings expressing HSP90.7∆22 display enhanced sensitivity to ER stresses. Expression of HSP90.7∆22 was also found to partially rescue the phenotype of clv3-2 mutants in the Landsberg erecta ecotype. Furthermore, HSP90.7 directly interacts with CLV2 and deleting the charged region increases the interaction strength. We propose that the charged region in the middle domain of HSP90.7 is involved in regulating its own ATP hydrolysis and may play a specific role in modulating the WUS-CLV pathway.

Advisor: Zhao, Rongmin
Optimization of Hybrid Renewable Energy Systems

Use of diesel generators in remote communities is economically and environmentally unsustainable. Consequently, researchers have focussed on designing hybrid renewable energy systems (HRES) for distributed electricity generation in remote communities. However, the cost-effectiveness of interconnecting multiple remote communities (microgrids) has not been explored. The main objective of this thesis is to develop a methodology for optimal design of HRES and microgrids for remote communities. A set of case studies was developed to test this methodology and it was determined that a combination of stand-alone decentralized HRES and microgrids is the most cost-effectiveness power generation scheme when studying a group of remote communities.

Keywords: Distributed Generation
Hybrid Renewable Energy Systems
Optimization
Remote Communities
Sustainable Energy
Advisor: Amon, Cristina
Wavelength-modulated Differential Photoacoustic Spectroscopy for Early Detection of Breast Cancer and Hypoxia Monitoring

In the field of medical diagnostics, biomedical photoacoustic (PA) imaging is a non-invasive hybrid optical-ultrasonic imaging modality. Due to the unique hybrid capability of optical and acoustic imaging, PA imaging has risen to the frontiers of medical diagnostic procedures such as human breast cancer detection. The current study introduces a novel PA spectroscopic modality for ultra-sensitive characterization of functional information for breast cancer imaging. Wavelength-modulated differential Photoacoustic spectroscopy (WM-DPAS) detection has been developed to address angiogenesis and hypoxia monitoring, two well-known benchmarks of breast tumor formation. Based on the WM-DPAS theory, this modality efficiently suppresses background absorptions while amplifying the small PA signal, thereby optically identifying pre-malignant tumors before they are anatomically apparent. The potential of the WM-DPAS to sensitively detect human breast pre-malignancy and quantify the corresponding breast carcinogenesis benchmarks was studied using an in-vitro blood circulation system. The experimental results were compared to the developed theoretical formalism.

Keywords: breast cancer
Differential-modulated
hypoxia monitoring
Photoacoustics
Advisor: Mandelis, Andreas
SORTAH: System Optimal Re-routing Transit Assignment Heuristic

Traditionally, transit networks are modelled to follow the user equilibrium principle where passengers take a path that would benefit them the most. This does not directly address the system perspective and results in inferior performance compared to the pure system optimal model for congested networks. This research presents a new framework for the transit assignment problem to address the system perspective of an overcrowded transit network while integrating individual travel needs. It proposes a novel approach called System Optimal Re-Routing Transit Assignment Heuristic (SORTAH) that minimizes the overall congestion effects on a transit network. SORTAH leads to a better performing solution than that of a user equilibrium model, while simultaneously guaranteeing superior fairness compared to the pure system optimal model. A proof-of-concept prototype is implemented to compare network performance of the user equilibrium solution and the SORTAH solution. A large-scale real-world application is conducted on the Toronto Transit Commission (TTC) network.

Keywords: Heuristic
System Optimal
System Optimum
Transit Assignment
Advisor: Shalaby, Amer S
Performance-centric Bandwidth Allocation for Data Parallel Applications in Private Datacenters

In the context of private datacenters that are operated by Web service providers such as Google, multiple applications using data parallel frameworks, such as MapReduce, coexist and share a limited supply of link bandwidth capacities. In this thesis, we propose the notion of performance-centric fairness to guide bandwidth allocation among data parallel applications in private datacenters. With a tunable degree of relaxation on fairness, we design a distributed bandwidth allocation algorithm to arbitrate the tradeoff between fairness and utilization. We then conduct a deeper investigation of performance-centric bandwidth allocation with the presence of failures, and the flexibility of path selection, respectively. To minimize the adversing effect of failures, we propose an algorithm to jointly optimize bandwidth allocation and task placement. Also, by designing an application-level scheduling algorithm that jointly optimize bandwidth allocation and path selection, we are able to improve application performance as well as bandwidth utilization.

Keywords: bandwidth allocation
datacenter
data parallel application
fairness
Advisor: Li, Baochun
Central Set and Motor Preparation: Neural Correlates of Movement Optimization

The ability to respond to task demands with goal-directed movement is essential in many daily activities. Movement efficiency depends on the processing of environmental stimuli within a given context. Two such processing mechanisms are central set and motor preparation. This study evaluated the neural correlates of central set and motor preparation and how these processes allow humans to process contextual cues to optimize movements. It was hypothesized that cTBS would decrease movement efficiency in conditions that suppress central set, but not for conditions that facilitate it. Twelve healthy participants completed a response-time task involving Go/NoGo conditions. The contribution of PMd to movement optimization was assessed by examining changes in response time, EMG activity, and pre-movement-EEG. Results showed that differences in preparatory EEG between both conditions pre- and post-cTBS may depend on individual strategy. Improvements in movement efficiency during the NoGo condition suggest central set properties even during situations of task uncertainty.

Keywords: Contingent negative variation
Electroencephalography
Motor preparation
Transcranial magnetic stimulation
Advisor: Mochizuki, George
Carnahan, Heather
In Relationship: Expressive Writing as a Decolonizing Adult Learning Praxis

The central argument is that the traditional academic essay format, coerced into cognitivist conventions by the fear of appearing uncritical, preserves the hegemonic colonial mindset when it suppresses the clear, direct, and relatable voice of the student or scholar. Inspired by Dr. Marie Battiste's use of four directions in First Nations Education in Canada: The Circle Unfolds (1995), the thesis is organized into 4 sections, East, South, West, North, representing research directions into the expressive potential of a decolonizing adult learning praxis and offering possible approaches to writing that can be allied with Indigenous scholars. I focus on praxis, the reflexive prompts of non-verbal image communication, historical origins of the cognitivist essay, and existing Indigenous viewpoints on the changing dimension of words used in academic contexts. Decolonized writing forms critical pathways by acknowledging the dialectics of colonialism and honouring the community surrounding the scholar that informs and buoys the research process.

Keywords: Aboriginal education
adult education
decolonization
ethnography
Indigenous studies
writing
Advisor: Restoule, Jean-Paul
A Qualitative Study of Ontario Cancer System Leaders' Views on the "Promises of Accountabiltiy"

How governments compel compliance is a central issue of public policy. The move towards contracting specialized services to agencies is characteristic of a movement that emphasizes a certain set of tools intended to enhance accountability. Critics identify a lack of clarity regarding what accountability is and how it works within and across contexts. Using Dubnick’s “promises of accountability” framework, this study aimed to understand how healthcare leaders’ in Government and a specialized agency make sense of accountability in the context of Ontario’s cancer services system. This study was designed using qualitative description and incorporated key informant interviews, document review of historically relevant texts, and informal observation of advisory council meetings. Findings highlight the need to apply both instrumental and intrinsic tools to foster meaningful inter-personal and inter- organizational relationships. Additionally, while instrumental tools seem to operate sequentially, there is less of a distinction between intrinsic tools.

Keywords: accountability
chronic disease management
qualitative
Advisor: Dobrow, Mark
The Role of Concrete Maturity in Resistivity-based Performance Specifications

This research aims to develop a standard method for estimating concrete bulk resistivity via the maturity method. Eight different concrete mixtures were cured in different environments and monitored for resistivity development with relation to specimen maturity. Additionally, various factors and their effects on bulk resistivity readings are discussed, such as: degree of sample saturation and the saturating fluid. Furthermore, three commercially available resistivity meters are compared: the RCON by Giatec Inc., the Merlin by Germann Instruments and the Resipod by Proceq. Due to the sensitivity of bulk resistivity development to curing temperature, a log-linear equation relating bulk resistivity and maturity of a particular concrete mixture could not be developed. Calibration between the three commercially available resistivity meters continues to pose a challenge for the standardization of resistivity-based performance specifications due to the difference in results produced by each meter, an average of +/- 9.0%.

Keywords: Bulk Resistivity
Concrete Maturity
Concrete Resistivity
Advisor: Hooton, Douglas
A Person-search System for an Assistive Robot

This thesis presents the design of an assistive robotic system, developed to aid a growing elderly population in maintaining quality of life and age in place independently. The robot is designed to operate in a home environment and aid a person with the performance of independent activities of daily living, primarily focusing on guided meal preparation. This work begins with the development of a novel person-search approach using a time-discretized Hidden Markov Model (HMM). Subsequently the prototyping and development of the robotic system is discussed, followed by a benchmarking of the person-search system and an information gathering experiment evaluating the robot's interactive capabilities. Experiments show that the HMM-based person-search system is effective at locating a target person considerably faster than an uninformed baseline approach.

Keywords: Assistive Robotics
HMM
Person Search
Advisor: Nejat, Goldie
Health Human Resource Planning of Physiotherapists and Occupational Therapists in Newfoundland and Labrador

This research seeks to substantiate the gap between demand and supply of physiotherapists (PTs) and occupational therapists (OTs) in Newfoundland and Labrador through the development of a system dynamics (SD) model. The model was used to test "what-if" scenarios by exploring various school sizes at Memorial University of Newfoundland (MUN). A needs-based modeling approach was used to define the population's requirement for PTs and OTs. Data obtained from Newfoundland Centre for Health Information was used to populate the demand model, and the workforce data obtained through Canadian Institute for Health Information was used to populate the SD supply model; both demand and supply were projected to the year 2055. The results show a shortage of PTs and OTs, with this gap expected to increase over time. It is recommended that schools with eventual sizes of 90 PT and 34 OT students be opened at MUN to gradually close the gap.

Keywords: occupational therapy
physiotherapy
Advisor: Carter, Michael W
The Effect of Red Blood Cell-derived Lipids on Epithelial and Endothelial Injury

Transfusion-related acute lung injury (TRALI) is a major complication resulting from transfusion and the leading cause of transfusion-related fatalities. In recent years, focus has shifted from the antibody-mediated pathogenesis narrative to the role played by stored red blood cell (RBC)-derived breakdown components on acute lung injury. Existing evidence on the harms of RBC-derived oxidized lipids encouraged closer investigation into their role in TRALI. Herein we designed an in-vitro model to test epithelial and endothelial injury caused by RBC-derived lipid 5(S)-hydroxy-6,8,11,14-eicosatetraenoic acid (5-HETE) and its metabolite 5-oxo-6,8,11,14-eicosatetraenoic acid (5-oxoETE) by assessing cytotoxicity, apoptosis, and inflammation with and without treatment with oxoeicosanoid receptor 1 (OXE) antagonist, Gue1654. Our results showed that 0.5 µM 5-oxoETE and 5-HETE have cytotoxic, apoptotic, and pro-inflammatory effects on lung epithelial and endothelial cells following 8-hour stimulation mediated via lipid-OXE receptor complex. We reported herein that Gue1654 can inhibit the RBC-derived lipid-induced epithelial and endothelial cell injury.

Keywords: Injury
Lung
RBC
TRALI
Advisor: Zhang, Haibo
Hare, Gregory M.T.
"Known to the Police": A Black Male Reflection on Police Violence in Toronto

In response to the increased prevalence of gun violence in Toronto, local politicians and media have focused on how to more efficiently police the city's most violent neighborhoods. Because of the racialized nature of this violence, much attention has been given to the role of structural and institutional effects of systemic racism and marginalization on the manifestation of violence in the City of Toronto. Obscured from these discussions however are the ways in which narratives of criminality are internalized by Black and Brown bodies and their communities. In light of this, this research will highlight the lack of attention given to the discursive remapping, and the reimaging of the Black male body in urban spaces. Ultimately, what I propose is a radical decentering of this institutional paradigm in favour of one that takes the subjectivity of the Black male as its point of entry.

Keywords: Crime
Police
Race
Space
Urban
Violence
Advisor: Ruddick, Susan
Semantic Priming Study Suggests Concrete and Abstract Words have Qualitatively Similar Representational Systems

Despite the important role abstract concepts play in human life, the representational framework of abstract concepts has remained largely unexplored. The present study examined and compared abstract and concrete concept representation by way of a priming study. Specifically, this study tested the claim by Crutch and Warrington (2005) that concrete concepts are organized by a principle of similarity whereas abstract concepts are organized by a principle of association. A semantic priming task using semantically-similar but unassociated primes and associated but semantically-dissimilar primes for each target (e.g. mallet -> hammer; nail -> hammer) was used to test this claim. Analysis of variance and pairwise comparisons reveal no interaction between the main effect of priming and the concreteness of the target, suggesting that there is no qualitative difference in the representational systems of abstract and concrete words.

Keywords: Abstract
Concept Representation
Semantic Memory
Advisor: Cree, George
Joordens, Steeve
Simulated Geophysical Monitoring of Radioactive Waste Repository Barriers

Estimation of attenuation of the elastic waves in clays and high clay-content rocks is important for the quality of geophysical methods relying on processing the recorded waveforms. Time-lapse imaging is planned to be employed for monitoring of the condition of high-radioactive waste repositories. Engineers can analyze and optimize configuration of the monitoring system using numerical modelling tools. The reliability of modeling requires proper calibration. The purpose of this thesis is threefold: (i) propose a calibration methodology for the wave propagation tools based on the experimental data, (ii) estimate the attenuation in bentonite as a function of temperature and water content, and (iii) investigate the feasibility of active sonic monitoring of the engineered barriers. The results suggest that pronounced inelastic behavior of bentonite has to be taken into account in geophysical modeling and analysis. The repository--scale models confirm that active sonic monitoring is capable of depicting physical changes in the bentonite barrier.

Keywords: attenuation
bentonite
HLRW repository
numerical modelling
Advisor: Grasselli, Giovanni
Tisato, Nicola
Pharmacogenetic Inhibition of the Ventral Medial Medulla Influences REM Sleep in Mice

During REM sleep, the body's muscles are forced into a state of paralysis. Hence, understanding how the brain controls muscle paralysis during REM sleep is important since its dysfunction can lead to REM sleep behavior disorder (RBD). The neural circuitry underlying the generation of muscle paralysis during REM sleep is hypothesized to be mediated by the GABA/Gly neurons of the ventral medial medulla (VMM). To test this hypothesis, I used a pharmacogenetic technique called Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) to inhibit presumed GABA/Gly neurons of the VMM. I found that inactivation of these neurons significantly increased muscle activity during REM sleep. An additional unexpected finding of this study was that inactivation of VMM neurons also decreased the frequency of REM sleep episodes. This sheds a light on the role that the VMM plays in controlling REM sleep paralysis as well as controlling REM sleep itself.

Keywords: DREADDs
GABA
Mice
Muscle atonia
REM sleep
Ventral medial medulla
Advisor: Peever, John H
Thirty to Fifty Years of Change in Forests of the Western Lake Ontario Region

The woody and herbaceous vegetation in forests of the increasingly urbanised western Lake Ontario region, first sampled 30 to 50 years ago, were resurveyed for an inter-decadal comparison with current forest vegetation. Using multivariate ordination techniques, this research aimed to: 1) explore change to two forest layers', overstory and understory, composition and structure with time; 2) determine the extent to which any changes can be interpreted in terms of progressive urbanisation. In the overstory, nearly half of forested stands are progressing through forest development but rural selective cutting has also strongly influenced forest structure. Significant losses to native understory species in protected areas, and the ubiquitous increase of an exotic species, garlic mustard (Alliaria petiolata), indicate that the understory layer has experienced a wave of damage over the 30 to 50 years. Much of this was linked to forest fragmentation and heavy browsing by deer.

Keywords: Composition
Forest structure
Fragmentation
Monitoring
Temporal change
Understory
Advisor: Careton, Terry J
Multidisciplinary Design Optimization of Turbomachinery Blade

This thesis presents an approach for designing a more-efficient and reliable turbomachinery blade. A High-Cycle Fatigue testing is conducted to evaluate fatigue behavior of the design and determine the fatigue limit. The sine-dwell approach is employed to accelerate fatigue failure by applying a base excitation at the resonance frequency of the design. A multidisciplinary design optimization architecture integrated into a stochastic and population-based optimization algorithm is developed in order to improve efficiency and maintain strain level of the blade below the maximum allowable strain determined from the fatigue testing. The NURBS surface is employed to parameterize the shape of the blade and enable the optimizer to alter the design. The design optimization process involves fluid flow analysis coupled with structural analysis to evaluate the isentropic efficiency and the maximum strain level of the blade. The optimized design is compared with the baseline design and validated by other studies.

Keywords: CFD analysis
Design Optimization
High-Cycle Fatigue Testing
Particle Swarm Optimization
Sine-Dwell Test
Turbomachinery Design
Advisor: Behdinan, Kamran
Surface Functionalization of Piezoelectric Aluminum Nitride with Selected Amino Acid and Peptides

In the present contribution, we elaborate on the covalent attachment of the amino acid cysteine and selected cysteine-bearing peptides, in aqueous buffered media, onto AlN surfaces modified with adlayers of one of our homemade bifunctional alkyltrichlorosilane cross-linking molecules bearing the benzenethiosulfonate head group. Surface characterizations confirmed the successful covalent immobilization of cysteine in buffered media, whereas the attachment of the peptides proved to be difficult as the undesired partial destruction of the adlayer on AlN by hydrolysis in aqueous/buffered solvent systems, which was confirmed in a separate study, appeared to have interfered with the covalent attachment and resulted in one of the peptides failing to immobilize. Future directions from this will focus on optimizing the solvent conditions for the cysteine/peptide immobilizations and the implementation of the surface chemistry to the covalent functionalization of AlN with biologically significant protein fragments, among them the antigen-binding fragment of antibodies.

Advisor: Thompson, Michael
The Importance of Invasive Earthworms as Seed Predators of Common Forest Flora of Ontario

Soil seed banks are vital to forest plant community regeneration, having long been viewed as a refuge for seeds vulnerable to granivory. Here evidence is provided suggesting many seeds entering the seed bank are subject to previously underestimated rates of granivory via the commonly found invasive earthworm, Lumbricus terrestris. Results from an earthworm-addition microcosm experiment suggest nearly 70% of seeds are removed from the soil surface when exposed one earthworm. Results from a separate granivore-exclusion field experiment indicate granivory by rodents eclipses that of earthworms under more natural conditions. When analyzed individually it is clear that different granivores target certain species of seed over others. This suggests that although rodents are the main driver of seed predation, earthworms may have the potential to act as an ecological filter, potentially further influencing the species composition of future forest plant communities by selectively targeting certain seeds, or seed traits, over others.

Keywords: Earthworm
Granivory
Lumbricus terrestris
Seed predation
Advisor: Kotanen, Peter M