VictorJuiz/thesis huggingface dataset:
Identification of Genetic Regulators of Mitochondrial DNA Content during Respiratory Growth

In order to discover novel regulatory pathways of mitochondrial DNA (mtDNA) content, I developed and carried out a high-throughput screen to quantitatively measure mtDNA level across two yeast whole-genome deletion collections with different HAP1 genotype. I inoculated and extracted genomic DNA from over eleven-thousand cultures and quantified mtDNA content by quantitative PCR using Taqman probes. The screen was able to identify the known genes required for respiratory growth and mtDNA maintenance, indicating the accuracy of the screen results. As expected, mutants that increase cell size also showed increased mtDNA. I showed that the mtDNA level but not the mitochondrial volume was affected by the HAP1 genotype in wild-type strains. According to the gene ontology enrichment analysis, mutants lacking ESCRT-I and ESCRT-II components were enriched in the high mtDNA content. Follow-up experiments showed that these mutants also had increased mitochondrial volume. I hypothesized that the ESCRT machinery may play a role in mitochondrial turnover process under active respiratory growth. This work can lead to future studies on mtDNA regulation under diverse conditions.

Advisor: Caudy, Amy
Advanced Applications for Finite Element Analysis in Assessment of Concrete Structures in Nuclear Power Plants

Finite element analysis (FEA) software is widely adopted in the field of structural engineering. Although the capabilities of the existing software packages have been steadily improving, the demand for ever more intricate analyses have also been escalating. The standard tools provided by the FEA software packages are often insufficient for performing the complex analyses. Two case study projects are provided to demonstrate how the existing FEA software functionalities can be extended through programmatic means. The first project discusses the implementation of the numerical hybrid framework, which combine pieces of a model from separate FEA software into a single hybrid model for an integrated analysis. In the second project, FEA is carried out to study the containment structure’s thermal and mechanical strain behavior during the periodic Reactor Building Leak-Rate Tests. Thermal strain results from the FEA are subtracted from the sensor measurements, so the underlying mechanical strain can be independently examined.

Keywords: Abaqus
Reinforcement concrete
Structural engineering
VecTor4
Advisor: Bentz, Evan
Kwon, Oh-Sung
Effect of Alkali-silica Reaction (ASR) on Steel-concrete Bond

While significant effort has been dedicated to studying flexural and shear strength of concrete affected by alkali-silica reaction (ASR), bond behaviour and anchorage strength of steel bars and metal anchors embedded in ASR concrete have frequently been overlooked. Bond stress-slip response was studied by means of pullout specimens, both plain and reinforced, to examine the effects of confinement on bond of ASR concrete subjected to different levels of deterioration. Additionally, bond properties in the beam flexural tension regions were also investigated. Lastly, tensile testing of headed bolts cast in unreinforced ASR concrete was conducted as a pilot series of tests. While effect of ASR on the normalized bond strength of confined concrete was negligible, up to 20% reduction in peak bond stresses was observed in unconfined specimens. For the given amount of free expansion, ASR did not detrimentally affect the breakout concrete capacity of anchor bolts embedded in reactive concrete.

Advisor: Sheikh, Shamim A.
From Forests to Formulas: Contextual Examination of Composers’ Sources, Materials, and Practices Involving Creative Insight

This thesis reports the findings of an exploratory, mixed-methods study of the information phenomena associated with musical composition. It employs a semi-structured interview and a survey among participants of the current musical composition community, the majority of which resided in the greater Toronto area. The guiding question is “What are the information activities and resources of composers as they strive to compose new music?” During research, the concept of creative insight, emerged as a necessary supplement to previous inquiries into composers' inspiration. The findings explore the varied sources of creative insight utilized by composers; differing uses of creative insight, Creative Insight Storage Units (CISUs), composers' record keeping devices; creative insight in embodied form; and the varying information needs of composers at different stages in their profession. The report closes with the introduction of a new model of creative information phenomena in musical composition, and questions for future research.

Keywords: composers
creative insight
information behaviour
information studies
musical composition
Advisor: Hartel, Jenna
Hatzis, Christos
Minority Stress, Positive Sexual Minority Identity and Eudaimonic Well-being Experiences Among Sexual and Gender-diverse Communities

Significant literature has documented the negative mental health experiences of LGBTQ2-identified people. More recently, research has begun to examine LGBTQ2 well-being and resiliency in the context of positive, eudaimonic well-being outcomes. Based in the minority stress model, the current study examines the relationship between minority stressors and eudaimonic well-being, and resiliency factors that may reduce the negative impact of such stressors on these eudaimonic outcomes. Such analyses were conducted through regression and mediation models. 300 participants who self-identified as LGBTQ2 were recruited through online spaces and responded to relevant questionnaires. Regression results indicated that higher scores on internalized homophobia and lower scores on outness were significantly predictive of eudaimonic well-being outcomes. Furthermore, both authenticity and community connectedness were shown to partially reduce the direct relationships between proximal minority stressors and eudaimonic well-being. Relevant implications for the minority stress model, and clinical and practical uses of findings are discussed as well.

Keywords: eudaimonia
LGBTQ2
mental health
minority stress
resiliency
sexual minority health
Advisor: Gillis, Roy
Foul Tip Impacts to Catchers’ Masks American League East: A Study of Head Impacts to Catchers

Purpose: To observe and describe foul tip impacts (FTIs) experienced by MLB catchers and to examine if batting performance was affected by FTIs. Method: Retrospective data analysis was conducted to examine FTIs in games (n= 648) observed using MLB TV. Descriptive statistics, incidence of, and absolute risk for FTIs were calculated. Mixed effects models were used to explore the association between FTIs and catchers’ batting performance. Results: 172 FTIs ranged in speeds (76.7-100.3mph) with 74% reaching 90mph or greater. There were 17.52 FTIs per 10,000 pitches thrown and 17 games with >1 FTI. FTIs varied between catchers (range: 0-32 FTIs). Neither FTI frequency nor speed predicted catchers’ batting performance. Contribution: Described the characteristics and descriptive statistics of FTIs across four MLB teams. Catchers experienced many FTIs at speeds which caused concussion cited in previous research. These findings highlight the need for future research to explore the conditions surrounding FTIs and sports medical management practices.

Keywords: baseball
catcher
foul tip
head impact exposure
head impacts
MLB
Advisor: Mainwaring, Lynda
Functional Study on the GLP-1 Based Drug Liraglutide in High Fat Diet Fed Mice

The incretin effect is essential for glucose homeostasis. Glucagon-like peptide 1 (GLP-1) based drugs, like liraglutide, and GLP-1 C-terminal fragment, GLP-128-36, have garnered attention for their weight lowering effects. However, their “preventative effects” on obesity development have not been explored in animal models. To investigate this, male C57BL/6J mice were given liraglutide or GLP-128-36 after 10 days of HFD or LFD continued for 8 weeks, with injections 6 times per week. The daily body weight and other metabolic parameters were assessed. Liraglutide moderately reduced body weight gain, fasting blood glucose and triglyceride (TG) levels, and improved glucose disposal as well as insulin-stimulated hepatic Akt (Ser473) phosphorylation in HFD fed mice and moderately increased β-catenin (Ser675) phosphorylation in INS-1 cells. Also, the body weight gain lowering effect of liraglutide gradually diminished with continued treatment. Altogether, the findings indicate that liraglutide, but not GLP-128-36, has a moderate preventative effect on obesity development.

Keywords: Diabetes
GLP-1
GLP-1R agonists
Insulin Resistance
Liraglutide
Obesity
Advisor: Jin, Tianru
Evaluating the Proteomic Landscape of Diffuse Intrinsic Pontine Glioma for Therapeutic Targets

Diffuse Intrinsic Pontine Glioma (DIPG) is a devastating brain tumour arising in the brainstem of children. Currently there is no effective cure for this disease and new therapeutic targets are desperately needed. High performance liquid chromatography mass spectrometry was carried out on 15 DIPG tumour and 10 normal brain tissues to identify potential therapeutic targets. The methionine salvage pathway was selected from proteomic analysis and validated in vitro as a potential therapeutic target for DIPG. DIPG cells and H3K27M expressing cells have a differential dependency on methionine and homocysteine compared to control immortalized normal human astrocyte (iNHA) and immortalized oligodendrocyte (MO3.13) cells. K27M and DIPG cells are unable to survive in homocysteine supplemented methionine deprived conditions whereas iNHA and MO3.13 cells can survive, providing a therapeutic window. DIPG4 and SF8268 cell lines are deficient in 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), elucidating one potential mechanism driving the methionine dependent phenotype.

Keywords: Cancer
Glioma
Metabolism
Proteomics
Advisor: Hawkins, Cynthia
Development of a New Experimental Model for Investigating Osseointegration of Titanium Mini-screws Placed Intraorally

A novel in-vivo pilot study was developed using the rabbit mandibular diastema to evaluate the effect of implant micro- and nano-surface topography on the rate of osseointegration. Six rabbits received one titanium mini-screw from both topographies in each diastema. Two rabbits were euthanized at 6, 22 and 85d post-implantation. Harvested mandibles were measured and processed for reverse torque, microCT, SEM and histological analyses. At 22 days, the nano- surface screws had higher mean torque values but both topographies reached nearly identical mean values after 85 days. Localized areas of crestal bone resorption were seen around all screw heads at 22 days. Sub-periosteal bone formation lateral to the screw heads led to complete coverage of the screws at 85 days. The epithelium of the overlying mucosa was parakeratinized stratified squamous. This intra-oral animal model is suitable to study osseointegration.

Keywords: Implants
Osseointegration
Advisor: Davies, John E
Mendes, Vanessa
Diversity and Drug Resistance in Plasmodium falciparum Malaria Infections

Plasmodium falciparum malaria infections often consist of multiple co-infecting strains with different phenotypic traits and responses to drug treatment. Traditional techniques used to study malaria infections do not account for co-infections and are unable to reveal the presence of rare drug resistant phenotypes within diverse infections. However, high-throughput sequencing can uncover parasite genotypes (or haplotypes) at low relative abundances within individual hosts. We detect 29 infections with signatures of drug resistance by quantifying haplotype-specific clearance curves, and five infections using a novel approach inspired by Fisher’s fundamental theorem. A second set of analyses reveal that parasite density and initial haplotype richness have a positive and negative relationship with the probability of an infection persisting after 72 hours of treatment, respectively. Overall, this study shows the utility of high-throughput sequencing for detecting variation in drug sensitivity and provides insight on the within-host dynamics of diverse infections.

Keywords: Antimicrobial resistance
Community ecology
Drug resistance
High-throughput sequencing
Malaria
Plasmodium falciparum
Advisor: Mideo, Nicole
A Portable and Low-cost Frequency-scanned Traffic Radar with Metasurface Collimation

Highway traffic monitoring is important for obstacle detection and collision mitigation. In this work, a portable millimeter-wave frequency-scanned radar is developed to provide a low-cost, low maintenance alternative to mechanically scanned radar sensors. For this purpose, small components and software were utilized to recreate the functionality of a function generator and oscilloscope. This allowed the radar to shrink in overall size to allow better portability while exploring opportunities in component selection toward chip-level components for use in a printed circuit board radar, which would further reduce the implementation cost significantly. The radar was tested both indoors and outdoors to operate at 33.5 to 35 GHz and allow up to a target range of 150 m with an electronic scanning ability from +5 to -20 degrees. Future development would be expected to increase the range close to 1 km with more refined components and better amplifiers.

Keywords: frequency-scanning
metasurface
radar
Advisor: Eleftheriades, George V
Ultrafast Dynamics of Zinc Tetraphenylporphyrin and [FeII(bpy)3](PF6)2

In this work, femtosecond transient absorption (TA) spectroscopy is applied for the first time to solid state, single-crystal ZnTPP. Absence of the solvent environment leads to a monoexponential decay of the S2 excited state, as opposed to the biexponential decay in the solution state. The results provide insight for the first time into the structural dynamics of this molecule on the femtosecond and picosecond timescale. Ultrafast electron diffraction (UED) does not reveal a significant structural change for ZnTPP, as is expected for a full d-shell metalloporphyrin. A decrease in Bragg peak intensity is noted on a timescale of tens of picoseconds; this is explained by the Debye-Waller effect. UED was also used to probe the SCO dynamics of [FeII(bpy)3](PF6)2 (BPY), a prototypical SCO compound. Results from these experiments revealed ultrafast structural dynamics consisting of four key modes: Fe-N bond elongation, Fe-ligand motion, Fe-N rotation, and Fe-ligand rotation.

Advisor: Miller, Dwayne
“Grounded in the Interconnectedness of Life, Guided by love and Growing in Wisdom”: Exploring Wisdom and Moral Virtue Through the Lens of a Canadian Atheist Exemplar

The present study explored a highly influential exemplar of moral virtue and wisdom, Gretta Vosper, using a mixed-method person-centered case study analysis. Vosper is an Atheist Christian minister at West Hill United, a Christian church within the United Church of Canada. We interviewed her in 2017, during the time she was under review by the church to see if she was deemed fit to still be a minister as well as being outspokenly Atheist. A semi-structured interview, as well as scales such as the Three-Dimensional Wisdom Scale, were administered during a three-hour session. Analysis revealed that her own theory of wisdom and virtue cultivation is a four-step process: community, empathy, moral virtue development through interconnectedness, and lastly the development of wisdom. Commentary across all scales administered is also discussed in relation to her place as an exemplar of moral virtue and wisdom.

Keywords: Atheism
Christianity
Moral Virtue
Religion
Wisdom
Advisor: Ferrari, Michel
Prehabilitation for Women Undergoing Breast Cancer Surgery: A Mixed Methods Study

Research examining prehabilitation prior to cancer surgery has grown rapidly in recent years, but data in the breast cancer setting are scant. This study examined the feasibility of an exercise-centred prehabilitation intervention prior to breast cancer surgery using a mixed methods design. Participants (n=22) received an individualized exercise prescription including aerobic and upper quadrant-specific resistance and mobility training for the duration of their surgical waiting period. Primary outcomes included feasibility and acceptability. Exploratory outcomes included measures of physical and psychosocial wellbeing. Semi-structured interviews with a sub-set of participants (n=5) and health care providers (HCPs; n=2) provided further insights into acceptability. The study demonstrated feasibility based on pre-determined thresholds. Inductive thematic analysis demonstrated that prehabilitation was perceived as highly favourable by both participants and HCPs, including suggestions that it be offered to all surgical candidates. Randomized controlled trials to examine prehabilitation efficacy in people with breast cancer are warranted.

Keywords: Breast cancer
Prehabilitation
Surgery
Survivorship
Advisor: Santa Mina, Daniel
Co-packaged 100+ Gbps Optical Communication Receiver Front-ends in FinFET CMOS

Approaches for co-packaged optical receiver front-ends are presented with a 16nm FinFET CMOS prototype for over 100 Gb/s communication. A co-packaging solution for the optical receiver front-end is sought with the discrete photodetector, and CMOS dice flip-chip attached to a shared package substrate and interconnected by an on-package microstrip. The microstrip interconnect provides an opportunity to improve the passive front-end bandwidth over what is achieved with no interconnect by making an appropriate choice for characteristics impedance of the microstrip line. Furthermore, an inverter-based transimpedance amplifier consisting of a variable-gain-amplifier and programmable equalizers is proposed. Post-layout simulations predict 60 dBΩ gain, 39 GHz bandwidth and output noise of 4.3 mVrms. Simulations of -5 dBm 4-PAM input at 100 Gb/s exhibit an output eye opening of 50 mV, assuming photodetector responsivity of 0.8 A/W. Finally, a custom package substrate is prepared for co-packaged integration of the CMOS prototype alongside commercial photodetectors.

Keywords: Analog Circuit Design
FinFET CMOS
High-Speed Circuit Design
Integrated Circuits
Optical Communications
Transimpedance Amplifier
Advisor: Chan Carusone, Anthony
Exploring the "Home" in Home-based Exercise for People with Cancer: The Influence of Environmental Characteristics on Exercise Participation

Home-based exercise interventions have demonstrated the ability to improve a variety of outcomes for people with cancer. However, the environments that constitute “home-based” exercise and the different benefits and barriers of various home-based settings are poorly and inconsistently described in the exercise-oncology literature. The purpose of this exploratory qualitative study was to develop an improved understanding for what constitutes the “home” for home-based exercise in oncology and how factors of the “home” environment impact exercise participation. Data collection consisted of photo elicitation semi-structured interviews with sixteen cancer survivors enrolled in a home-based exercise program. The findings of this study contribute to a foundational understanding of the diversity of environmental resources that influence home-based exercise participation, and the complexity of participant experiences regarding the implementation of a home-based exercise prescription. Specific recommendations are made to facilitate the prescription of home-based exercise according to the environmental resources available to people with cancer.

Keywords: cancer survivors
exercise
home-based
qualitative
Advisor: Santa Mina, Daniel
Differential Expression of PD-1 and PD-L1 in Oral Potentially Malignant Disorders and Oral Squamous Cell Carcinoma

Background: The immune checkpoint system is frequently activated in cancer to suppress anti-tumor immune responses. Interaction of programmed cell death protein 1 (PD-1) with its ligands PD-L1/ PD-L2 suppresses anti-tumor immunity. In this project, we investigated the expression of PD-1/PD-L1 in oral potentially malignant disorders (OPMD) and oral squamous cell carcinoma (OSCC). Methods: 37 Oral biopsies samples were analyzed which contained 18 transforming and 19 non- transforming cases. FFPE sections were stained with monoclonal antibodies for PD-1 and PD-L1, followed by conventional peroxidase reaction (IHC) and fluorescent immunohistochemistry (FIHC) after which analysis was performed. Results: Using conventional IHC, we showed a progressive increase in expression of PD-1/PD-L1 from dysplasia to OSCC. Using FIHC, we found a significant increase in PD-L1 expression with no difference in expression for PD-1. Conclusion: We developed a new FIHC-based quantitative method to study PD-1/PD-L1 expression and showed that PD-L1 is highly expressed in progressing dysplasia.

Advisor: Magalhaes, Marco
Exploring Current Nutritional Recommendation Practices by Physicians and Dietary Changes in Patients Following Sport-Related Concussion

Sport-related concussion is a concern for athletes. Currently, recommendations of initial rest followed by a gradual re-introduction of cognitive and physical activities is common practice among physicians following concussion. However, there is no standard rehabilitation strategy to manage a sport-related concussion. Additionally, the literature maintains gaps addressing nutritional recommendations in the current concussion paradigm. Therefore, this thesis was two-fold: (1) To characterize current recommendation practices of physicians managing SRC, with interest examining frequency of nutritional interventions, and (2) to characterize and identify changes in nutrition status and food behaviours. Collectively, these studies found an undeniable gap between the recommendation practices of physicians regarding nutrition and the observed nutritional changes occurring post-injury in patients with concussive injury. Future research should evaluate physicians’ nutrition knowledge in greater depth and continue to characterize nutritional changes in patients.

Keywords: nutraceuticals
nutrition
sport-related concussion
traumatic brain injury
Advisor: Hutchison, Michael G
Attitudes and Barriers Design Professionals Face in Creating Inclusive Digital Products for Older Adults

When websites or apps are not designed with the age-related needs of the older population in mind, they create barriers by limiting the content available to seniors. This is particularly aggravating when such content could be beneficial for their health or wellness, for their financial security, or for maintaining social connections. This research focuses on investigating the attitudes and perceptions of design professionals in the context of designing digital products for seniors. The study was conducted using an online survey with the participation of 45 design professionals. Findings reveal that very few design professionals consider senior-friendliness in their design projects, primarily due to a lack of awareness of the needs of senior users and a lack of familiarity with senior-friendly design guidelines. The study also identified several challenges design professionals faced when designing for seniors and provided recommendations to improve their design practices.

Keywords: Human-Computer Interaction
Inclusive Design
Older Adults
Usability for Seniors
User Experience Design
Web Accessibility
Advisor: Munteanu, Cosmin