VictorJuiz/thesis huggingface dataset:
Exploring Different Approaches for Constructing Temperature Sensitive Alleles of Yeast Essential Genes

Exploring the phenotypes associated with conditional alleles of essential genes has been widely used to study gene function in multiple model systems. In the budding yeast, Saccharomyces cerevisiae, geneticists have long made use of temperature-sensitive (TS) alleles, which support cell growth at permissive but not at non-permissive temperatures, to study essential gene function. Over the years, TS mutants have been isolated in most yeast essential genes, but a subset has been refractory to standard methods for isolating TS mutants. In my thesis project, I aimed to explore new and existing methods for systematic gene mutagenesis, with the goal of completing the TS collection of yeast essential gene mutants. I also aimed to use the TS collection as a resource to explore mechanisms that underly the phenomenon of temperature sensitivity.To approach my goals, I explored two different methods, deactivated Cas9 linked to Cytidine Deaminase and the CRISPEY mutagenesis system, in both a low and high throughput manner, to determine which method may be most suitable for construction of new TS alleles of yeast essential genes. I also analyzed existing TS mutations to better understand what mutations give rise to temperature sensitivity, which may guide construction of TS alleles in other genes.

Advisor: Andrews, Brenda
Boone, Charles
Quantitative Magnetic Resonance Imaging Differentiating Pediatric Neuroblastic Tumours

The main objectives of this thesis work were to answer the following questions:1. Are magnetic resonance imaging (MRI) features able to accurately distinguish malignant from benign neuroblastic tumours? 2. Are quantitative Diffusion Weighted Imaging (DWI)-MRI features able to accurately differentiate malignant from benign neuroblastic tumours? The thesis is presented as two manuscripts resulting from the two primary research studies: 1. Diagnostic Accuracy of MRI for Pediatric Neuroblastic Tumour Differentiation: Systematic Review and Meta-Analysis. 2. Quantitative MRI Features Characterizing Pediatric Neuroblastic Tumours at Diagnosis. The results of both studies confirm that Apparent Diffusion Coefficient (ADC), a quantitative feature derived from DWI measuring the motion of free water molecules, has high accuracy for differentiating between malignant and benign pediatric neuroblastic tumours. Therefore, use of this quantitative feature as a non-invasive tool could contribute to the diagnostic armamentarium and help guide management decisions of this highly heterogenous solid tumour in children.

Keywords: Diffusion Weighted Imaging
Ganglioneuroma
Magnetic Resonance Imaging
Neuroblastic Tumours
Neuroblastoma
Pediatric Oncology
Advisor: Doria, Andrea S
Fixed Beliefs, Low Control, and Well-being: Can Believing Something Cannot Change Be Good?

Believing that attributes are fixed – “fixed beliefs” – is often associated with negative outcomes, but emerging evidence suggests that fixed beliefs can be beneficial. I suggest that for populations who have low control, fixed beliefs may be positively related to well-being through greater goal disengagement and lesser goal engagement. I investigated how fixed beliefs relate to control efforts and well-being in low-SES individuals (Study 1; n = 321) and older adults (Study 2; n = 418). Results suggest that fixed beliefs negatively relate to goal engagement, goal engagement positively relates with well-being, and fixed beliefs negatively impact well-being through decreased control efforts. In addition, goal disengagement positively relates with well-being for low-SES-individuals. Overall, the results suggest that even in low-control populations, fixed beliefs may negatively impact well-being and that control efforts are one mechanism through which this can occur.

Keywords: Malleability Beliefs
Advisor: Neel, Rebecca
Educator Perspectives on Indigenous Child Suicide in Canada

Indigenous children are disproportionately impacted by suicide in Canada. Despite the severity of the crisis, limited research has been conducted on the phenomenon. The purpose of this research was to: (1) initiate some of the first conversations related to the factors contributing to this crisis and (2) discuss support that is needed within the classroom to better support both Indigenous children and educators. Since children spend a majority of their day within the classroom, educators were interviewed for the purpose of this study. Thematic analysis of the interviews revealed three main themes and several subthemes related to Indigenous child suicide theory, and four main themes and several subthemes related to supports needed within in the classroom. The findings detail applied implications for suicide prevention and life promotion services within the classroom and education system for Indigenous children, as well as some research related and community-based recommendations.

Advisor: Ansloos, Jeffrey
Impacts of Test Variables on The Electrical Resistivity Measurements of Hardened Concrete

Evaluating concrete quality and performance, especially determining the resistance of concrete to fluid and ion ingress is fundamental to estimating concrete’s durability and predicting the service life of concrete structures. As a simple and rapid indicator of concrete’s resistance to any fluid and ion ingress, the bulk electrical resistivity test has gained increasing interest. However, the bulk resistivity measurement can be affected by many factors. This study aims to analyze the impacts of different factors on bulk resistivity measurement, including curing condition and storage solution, degree of saturation, temperature, AC frequency, different test devices, specimen shape and thickness, and mixture compositions. The correlations between each test variable and bulk resistivity are discussed. The bulk and surface resistivity measurements are compared as well. The results show that different factors affected resistivity measurements differently, the clear understanding of their impacts could result in more accurate resistivity measurements for assessing the durability of concrete.

Keywords: Concrete bulk resistivity
Concrete durability
Concrete quality control
Electrical resistivity
Advisor: Hooton, R. Douglas
Detection of Non-coding RNAs and Assessment of their Predictive Value for Monotherapies

The introduction of high-throughput sequencing technologies has allowed for RNA species detection, both coding and non-coding. This led to the discovery of predictive and prognostic biomarkers, however their validity can be questioned by the RNA selection protocol used by RNA-sequencing for their detection. This project investigates the consistency of mRNA and circRNA expression across inter-lab cell lines from pharmacogenomic datasets and patient lung adenocarcinoma tumors utilizing poly-A selection and rRNA depletion RNA-seq protocols. The results identify features that influence the prediction of instability in mRNA abundance through supervised learning, along with a potential circRNA prognostic biomarker. The intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community. To overcome these issues, we created ORCESTRA (orcestra.ca), a cloud-based platform providing a flexible framework for the reproducible processing of multimodal biomedical data into shareable data objects, allowing for mRNA and circRNA exploration.

Advisor: Haibe-Kains, Benjamin
Characterization of Compounds with Novel Bioactivity Against the Fungal Pathogens Candida albicans and Cryptococcus neoformans

Systemic fungal diseases represent an overlooked global health burden, whose treatment is challenged by a limited antifungal armamentarium and the emergence of drug resistance. This research encompasses two complementary strategies to bolster the antifungal drug pipeline: rational optimization of existing antifungal scaffolds, and phenotype-forward screening with subsequent mode of action identification to discover novel antifungal targets. First, I evaluated in vitro target engagement, bioactivity against the fungal pathogen Cryptococcus neoformans, and mammalian cytotoxicity for over 70 analogs of a previously validated Hsp90 inhibitor scaffold. Through these structure-activity relationship (SAR) analyses, I identified several lead molecules with improved whole-cell activity and fungal target selectivity. Then, I also performed preliminary characterization of nine molecules with novel antifungal bioactivity identified from prior large- scale chemical screening. I outlined their spectrum of activity, mammalian cytotoxicity, and putative molecular target(s) via chemogenomic profiling, identifying NP-BTA as a potent and selective inhibitor of Candida albicans glutaminyl-tRNA synthetase.

Advisor: Cowen, Leah
Developing Indium Arsenide Nanowire Field Effect Transistor Sensors for Biological Applications

Nanowire field effect transistors have emerged as a promising platform for rapid and direct electrical sensing. The present work characterizes indium arsenide multiwire devices for liquid and gas phase sensing applications. Studies evaluating the pH response of the devices demonstrated the importance of the careful selection of an appropriate figure-of-merit to relate potential response to ion concentration that is free from the effects of electrostatic history. Furthermore, measurement parameters were tuned to optimize the sensitivity of the sensor response. In the gas phase, the sensing responses to ethanol and dimethyl methylphosphonate were compared and found to exhibit a differing response based on the respective dipole moments and adsorption properties of these analytes. Finally, a preliminary bio-sensing response of biotin-functionalized devices to streptavidin is presented. While the devices demonstrate versatility in different sensing media, they should be tailored appropriately to the specific sensing application.

Keywords: Biosensing
Indium Arsenide
Nanowires
pH Sensing
Semiconductors
Streptavidin
Advisor: Ruda, Harry
Developing a Generative Design Framework for Optimising Public Transit Network Planning

Despite the plethora of tools and data available to transit planners, transit network design has remained mostly a manual task. There have been many attempts to algorithmically optimise algorithms transit network design based on geography, travel demand, and operating resources. However, the Transit Network Design Problem (TNDP) and Transit Network Design and Frequency Setting Problem (TNDFSP) remain challenging due to their NP-hard nature and the volume of data and computation required to produce good and realistic solutions. Generative Design is an emerging design methodology that takes advantage of computational power and efficient solution generation methods to develop high-quality solutions for complex, multi-objective optimisation problems. This thesis presents a framework that adopts the Generative Design methodology towards optimising transit network design and examines ways to improve adaptability and applicability of the framework in real-world scenarios.

Keywords: Generative Design
Public Transport
Transit Frequency
Transit Network
Transit Planning
Advisor: Miller, Eric
Correcting Deficient Papillae and Gingival Recession using a Conservative Surgical Approach utilizing a Dermal Filler (Juvéderm) and Enamel Matrix Derivative (Emdogain); A Pilot Study

Gingival recession, and “black triangle” (BT) defects are a common complaint for patients. While gingival recession seems to be more amenable to treatment this is not the case for BTs. We have developed a minimally invasive approach with the use of dermal filler and concurrent enamel matrix derivative (EMD). A total of 8 patient with 34 sites needing treatment were involved in this pilot study. Mean gain in attachment was 0.82mm ± 1.47mm (p = 0.002). Mean root coverage was 70.37%. Papilla fill was improved by an average of 1.5mm (mean fill 44.58%) from baseline. Patient satisfaction at 6-month post-operative VAS data shows satisfaction improvement of 92.9% ± 7.0% (p

Keywords: Black triangles
Papilla
Recession
Regeneration
Advisor: Tenenbaum, Howard
Masjid Ball: The Influence of Mosque-based Physical Activity Programs on the Physical Cultural Practices of Young Muslim Women

The values mediating exclusionary practices in Western sporting environments posit religiosity and physical activity as opposite principles, forcing many Muslim women to choose between faith or play (Knez et al., 2012). Religious institutions like mosques are essential structures that link Muslims to their communities, making them valuable when designing lifestyle interventions (Banerjee et al., 2017). The study used a space-based racial analysis to explore how six young Muslim women experienced mosque-based women’s-only sports programs, the relationships that form in such settings, and the physical cultures being practiced. The results demonstrate the significance of studying faith as a racializing identity within sport science, and gendered Islamophobia’s role in influencing Muslim women’s sporting participation. The findings also highlight how sporting exclusion is mediated through agentic processes of creating and negotiating safe sporting spaces by transforming faith spaces, and the relationships Muslim women develop with themselves, and their communities through faith-focused physical activity.

Keywords: Basketball
Belonging
Faith-focused
Safe spaces
Sporting cultures
Young Muslim women
Advisor: MacNeill, Margaret
Phase Aware Approximation

Modern computing needs have led to the emergence of eccentric new computing paradigms, including approximate computing. However, the widespread adoption of approximate computing necessitates techniques to control and minimize output error. As a step towards resolving this, our work leverages the domain of adaptive computing – architectures that dynamically adapt to the evolving behavior of a workload over its execution. We propose Phase Aware Approximation, a novel technique that conditionally applies approximation only in periods of execution where it ascertains the workload would see a performance benefit. Specifically, we explore the efficacy of our technique in conjunction with Load Value Approximation (LVA) – an approximate computing technique that mitigates the effects of L1 misses. Using the PERFECT benchmark suite, we conduct a thorough evaluation of different metrics that can be used as indicators of LVA being beneficial in an execution period. Our analysis concludes that the dynamics of Load Value Approximation are too complicated to accurately predict which periods of execution are likely to see benefits and which ones are not.

Keywords: Computer Architecture
Hardware
Microarchitecture
Advisor: Enright Jerger, Natalie
A Retrospective Study on Endodontic Treatment Outcomes in Patients with Special Needs

Outcomes following endodontic treatment of teeth in patients with special needs are not fully understood and have not been meaningfully quantified. Consequently, this study aimed to evaluate the outcomes of endodontic treatment and determine prognostic factors of periapical healing in patients with special needs.This retrospective cohort study included patients who had permanent teeth endodontically treated at the Dental Clinic for Persons with Special Needs, Mount Sinai Hospital, Toronto, Canada between 1998 to 2019. Periapical healing and tooth survival were evaluated. 62 patients (108 teeth) met the inclusion criteria. Most common treatment modality was initial therapy with 73.1% of cases being managed solely with local anaesthesia. Healing rate was 89.9%. Survival rate was 73%. With most cases being adequately managed using local anaesthesia administration, if treatment condition permits, therapy can be administered by any community dentists rather than waiting for a patient to be seen in a hospital setting.

Keywords: Endontic Outcome
Endontic Success
Patients with Special Needs
Periapical Healing
Survival
Advisor: Azarpahooh, Amir
Multidisciplinary Design Optimization of Coaxial Drone Propellers

With the growing popularity of autonomous drones for commercial uses, there is a need to optimize the performance of propellers to increase the flight time and carry capacity. Coaxial propellers are of particular interest as they can generate greater lift with only a small increase in weight and space. The challenge with optimizing coaxial propellers lie in the varying downwash effects generated when modifying propeller designs though an optimization process. A Multidisciplinary Design Optimization framework with 3D Computational Fluid Dynamics and Finite Element software was implemented to resolve the difficulties of analyzing coaxial propellers. This work will attempt to maximize the figure of merit of a coaxial propeller by modifying both its geometry and other environmental factors. To demonstrate the effectiveness of the Multidisciplinary Design Optimization framework, a case study was applied to an aircraft wingbox. Experimental testing was performed to validate the optimized designs and show significant performance increases.

Keywords: Coaxial Propeller
Multidisciplinary Design Optimization
Optimization
Advisor: Behdinan, Kamran
Additive Manufacturing of Polyphenylene Sulfide and their Carbon Compositions through Fused Filament Fabrication

This study explored the interlayer bonding strength enhancement through process parameters (print temperature chamber temperature and layer height) optimization of polyphenylene sulfide (PPS) parts printed with fused filament fabrication (FFF) by the response surface method (RSM). Using DSC, rheometer, and optical microscopy, it was revealed that interlayer bonding was significantly enhanced with parameters’ optimization showing tensile strength and Young’s modulus of 93% and 96% of compression molded specimen, respectively. Optimized parts showed excellent chemical resistance, suggesting potential for under-the-hood application.Moreover, recycled carbon fiber (rCF) reinforced PPS filaments with fiber percentages up to 10% were developed. The superior performance of parts containing 10% fiber (10%CF) was proved using mechanical (tensile, flexural, and impact) and thermal (DSC, TGA, and DMA) tests. Excellent chemical resistance and high print quality of an actual industrial part using 10%CF was verified. Mentioned results suggested a desirable performance of 10%CF for lightweight high-temperature applications in the automotive industry.

Keywords: Fused Filament Fabrication
Interlayer Bonding
PPS
Recycled Carbon Fiber
Advisor: Sain, Mohini
Violence, Sectarianism, and Decolonization: Re-Framing the Syrian Revolution

This paper examines the colonial legacy, from the late Ottoman period through the French Mandate and into the post-independence era, of Syria in an attempt to re-frame the Syrian Revolution of 2011 onward as an attempt at further decolonization. By engaging with the works of Frantz Fanon, this paper puts contemporary Syrian writers, most notably Yassin al-Haj Saleh, in conversation with ideas of decolonization. Viewed in this framework, the Syrian Revolution can be understood as part of a colonial lineage, and seeking to address social and political ills -particularly sectarianism - exacerbated and manipulated by the French colonial administration and the post/neo-colonial regime of the Assad family.

Keywords: Decolonization
Revolution
Syria
Violence
Advisor: Hanssen, Jens
Electrical Conductivity of Wood-derived Nanoporous Monolithic Biochar

The electrical conductivity was exploited to establish monolithic biochar as a low-cost, high-performance material for electrochemical applications like supercapacitors. With a focus on the structure-property relationship, the effects of precursors and pyrolysis conditions were investigated, with four hardwoods, three softwoods, and one grass. The electrical conductivity of biochar monolith increased with temperature due to simultaneous increases in the degrees of carbonization and graphitization. X-ray diffraction and Raman spectroscopy revealed the growth of graphite nano-crystallites in an amorphous carbon matrix of biochar. Monolithic biochar conductivity is anisotropic; axial is more conductive than radial orientation. Moreover, the conductivity is uniquely dimension-dependent. A 2-D resistor network model was developed where the biochar is represented by a matrix of resistors in axial and radial directions. Model simulations and experiments reveal that anisotropic morphology, preferred orientation of graphite nano-crystallites and broken electron paths in the monolithic biochar are all responsible for its unique conductivity

Keywords: Biocarbon
Characterization
Electrical Conductivity
Monolithic
Pyrolysis
Advisor: Jia, Charles Q
Evaluation of an Online Physician Education Module for the Assessment and Management of Non-traumatic Dental Pain and Infection

Background: Tooth pain and infections encountered by physicians in Ontario, Canada are a common occurrence, where definitive treatment is often unfeasible. This often leads to the prescription of unwarranted antibiotic and opioid analgesics for initial management. Objective: To evaluate the effectiveness of an online educational module on Ontario physicians’ knowledge and confidence when assessing and managing non-traumatic dental emergencies. Methods: 39 participants completed a 1-hour online on-demand educational workshop featuring a cognitive aid, as well as pre- and post-module self-evaluations and clinical case scenario tests. Results: Confidence in all areas pertaining to the initial management of non-traumatic tooth pain and infection was improved and knowledge was gained, with adjusted scores for the total group, specifically in theoretical antibiotic stewardship and local anesthesia application. Conclusion: The online educational module is an effective education tool to enhance the confidence and knowledge of physician participants on the management of tooth pain and infection.

Keywords: antibiotic guidelines
local anesthesia
management
physician
tooth infection
tooth pain
Advisor: Azarpahzooh, Amir
Genome Size and Repeat Abundance Variation in Amaranthus tuberculatus

Genome size and repeat abundances have been shown to vary within species; however, our knowledge of the roles of population structure, selection and mutation in maintaining this variation is limited. In this study, I annotated the Transposable Elements (TEs), rRNA genes, simple repeats, and low complexity regions in the A. tuberculatus genome and estimated their abundances across 182 A. tuberculatus individuals. I used multiple regression analyses to test whether sex, longitude, latitude, ancestry, and local environment are important predictors of each repeat abundance and genome size. I found a lack of evidence for repeat abundance differentiation between agricultural and natural environments. Furthermore, longitudinal clines across genome size and many repeats were shown to be partially explained by population structure. Finally, I found latitudinal clines, with lower repeat abundances in northern individuals, even after controlling for population structure, suggesting this differentiation may be driven by selection or differential TE insertion rates.

Keywords: Agricultural adaptation
Genome size
Geographic clines
Repeat abundance
Transposable Elements
Advisor: Wright, Stephen I