VictorJuiz/thesis huggingface dataset:
Delving into “Dark Matter” and an Anti-Phage Defense Encoded by Pseudomonas aeruginosa Phage LES4

The evolutionary arms race between bacteria and phages has given rise to myriad bacterial anti-phage defenses and phage-encoded counters to those defenses. Phages themselves also encode anti-phage systems to inhibit the replication of competing phages. This multifaceted nature of phage-host interactions makes the mass of uncharacterized phage genes an enticing subject of study. Herein I discuss a functional screen of uncharacterized genes from the Pseudomonas aeruginosa phage LES4. I identified a phage gene termed Gp15 that induces anti-phage defense in Pseudomonas aeruginosa. Affinity purification demonstrated that Gp15 binds a hitherto-uncharacterized serine kinase termed PA0588. This kinase is linked to the Gac/Rsm signaling pathway, and I subsequently determined that the master regulator of this pathway, the sensor kinase RetS, also interacts with Gp15 in vitro and is essential for Gp15-induced anti-phage defense.

Advisor: Maxwell, Karen
Fragile-X Mental Retardation Autosomal Homolog 1 and Glycogen Synthase Kinase 3 Regulation by Antipsychotics

Schizophrenia is defined by varying symptoms between patients that all lead to impaired quality of life. An underlying cause of schizophrenia is thought to be a dysregulated dopamine system, with dopamine related antipsychotics being the first form of care. Current treatment options for patients are limited to chronic antipsychotic use which all target dopamine receptor D2. Part of D2 signalling involves downstream proteins, like Akt and GSK3β. GWAS studies have recently implicated FXR1, a protein downstream of GSK3β, as a risk factor for schizophrenia. This thesis looks at the changes in downstream effectors of D2 due to chronic antipsychotic treatment to elucidate the role of FXR1 in schizophrenia management. Using qPCR and western blot techniques, no significant changes were seen in downstream protein or gene levels due to chronic antipsychotics. However, these results do show promise as this study was underpowered and future research should be done to confirm these findings.

Keywords: Antipsychotics
D2R
Fxr1
GSK3
Schizophrenia
Advisor: Beaulieu, Jean Martin
The Role of Transforming-growth Factor Beta 1 and Platelet-derived Growth Factor in Right Ventricular Remodeling in Response to Right Ventricular Pressure and Volume-loading

Residual lesions in repaired Tetralogy of Fallot (rTOF) induce chronic right ventricular (RV) pressure- and volume-loading which can lead to maladaptive RV remodeling and dysfunction. Recent work has found that pro-fibrotic, transforming-growth factor β1 (TGFβ1) and platelet-derived growth factor (PDGF) are upregulated in RV hemodynamic overloading models. However, the functional impact and underlying mechanisms of RV fibrosis are poorly defined. Therefore, we hypothesize that TGFβ1 and PDGF induce RV fibrosis which drives RV dysfunction in RV pressure and volume-loading conditions. Utilizing a pulmonary artery band and pulmonary regurgitation in vivo model, to mimic residual lesions found in rTOF, we administered a potent dual inhibitor of TGFβ1 and PDGF, Tranilast (TRN). Our study shows that TRN reduced RV fibrosis and/or hypertrophy in PAB and PR models, which were associated with improved RV function. These results form a basis that TGFβ and PDGF signaling are key drivers of RV dysfunction.

Keywords: Cardiology
Congenital heart disease
Fibrosis
Hypertrophy
Right ventricle
Tetralogy of Fallot
Advisor: Friedberg, Mark K
Integration Experiences of Kenyans in North America: A Case Study on Canada and the USA

This thesis examines the integration experiences of Kenyan immigrants in North America, with a primary focus on Canada and the US. The study employs a qualitative methodology and integration and transnational theory to investigate the different experiences of Kenyan immigrants in both nations, as well as the factors affecting their integration. Findings indicate that although Kenyan immigrants to North America encounter language, cultural and social capital obstacles, they are also able to find a sense of community and belonging. Despite these challenges, the study shows that Kenyans have used a variety of tactics to disrupt the obstacles and seize the chances that North America has to offer. This thesis offers significant insights into the ways in which immigrants from Kenya manage their life in their new cultures and helps our knowledge of the integration experience of those immigrants in North America. Additionally, through this study, both the positive and negative impacts of transnationalism are determined and examined.

Keywords: Immigration
intergration
Trans migration
Advisor: Madibbo, Amal A.M
Assessing Astrocyte Function in Bipolar Depression

Bipolar Disorder (BD) is a chronic mental disorder characterised by episodes of hypomanic/manic, depressed, or mixed mood. Monoamine oxidase B (MAO-B) is an enzyme that is associated with oxidative stress in the brain and is found in astrocytes, a type of glial cell. Reports suggest neuroinflammation in BD may be associated with astrocyte dysfunction. The aim of this pilot positron emission tomography (PET) study was to evaluate MAO-B volume distribution (VT) as an index of astrocyte activity in the prefrontal cortex, and anterior cingulate cortex of adults with BD depression using the radiotracer, [11C]SL2511.88. Recruitment was conducted at the Centre for Addiction and Mental Health (CAMH), Toronto from January 2021 and is ongoing. Findings indicated reduced MAO-B VT in participants with BD depression (n=4) compared to healthy controls (n=20), suggesting astrocyte loss/dysfunction. Further investigations are required to confirm whether reduced MAO-B VT is associated with the neuropathology of BD depression.

Keywords: Astrocytes
Bipolar Depression
Bipolar Disorder
MAO-B
PET imaging
Advisor: Husain, Dr. Muhammed Ishrat
Modeling and Comparison of Parallel Heuristic Algorithms for Trade Optimization

This thesis proposes a mathematical optimization model for the trade optimization (TO) problem, considering various general features and key performance indicators (KPIs) from both commodity suppliers and retailers' perspectives. It also introduces parallel models for genetic algorithm (GA), simulated annealing (SA), and large-scale neighborhood search (LNS) to solve the TO problem. The study aims to evaluate and compare the performance of these heuristic optimization algorithms in terms of convergence behavior, solution quality, and robustness. The contributions include a novel optimization model, a parallel framework implemented using Python, and a comprehensive evaluation of different heuristic optimization algorithms in the TO context. Experimental results indicate that the suggested parallel framework greatly improves both the convergence rate and the quality of the solution. Overall, among the three algorithms, SA exhibits the most superior performance. The study provides insights and guidelines for solving complex optimization problems in the context of trade optimization.

Keywords: Genetic Algorithm
neighborhood search
Optimization
promotion
Simulated Annealing
trade
Advisor: Kwon, Roy
Osteochondral Allograft Transplantation: Tissue Storage and Surgical Factors Using an Ovine Model

An effective surgical treatment for large cartilage lesions is Osteochondral Allograft Transplantation (OCAT). The method and duration of cadaveric donor tissue storage prior to transplantation can reduce chondrocyte viability, which is directly correlated to negative clinical outcomes. Active research aims to increase chondrocyte viability at extended durations of storage. Effects of long-term storage were investigated by quantifying changes in ovine cartilage explants after storage in a proprietary, DMEM-based media known as MOPS. OCAT surgical techniques can also negatively impact cartilage quality. This thesis investigated the relationship between increased graft press-fit and insertion forces and resulting cell viability, using both human and ovine tissues. Finally, 3D-printed drill guides were developed for placement of osteochondral grafts in a pre-clinical ovine model. This thesis highlights interdependent factors that influence donor cartilage quality in OCAT, as well as identifying species differences that are important to consider when interpreting results from the pre-clinical ovine model.

Keywords: Allograft
Osteochondral
Tissue Storage
Transplant
Advisor: Changoor, Adele
Grynpas, Marc D
Characterization of the Wildland Fire Environment and Situational Factors associated with Historical Wildfire Evacuations in the Province of Ontario, Canada

Evacuations in Ontario are used to ensure public safety from either the direct threat of wildfire or from the health impacts of smoke. The recommendation to evacuate is based on several factors, one being forecasted fire weather and fire danger from the Canadian Fire Weather Index (FWI) System. We examined fire danger and evacuation occurrence at both an annual scale and an individual community scale for Ontario. Annually, in Ontario smoke evacuation occurrence was associated with extreme Build Up Index (BUI), while direct threat evacuations were associated with extreme Fire Weather Index (FWI). When a fire occurred in the area around communities, fire size, distance from the community and maximum BUI had the strongest associations with evacuation occurrence. When differentiating evacuation cause, fires closer to communities were more strongly associated with direct threat evacuations. These results can inform Ontarians of the conditions associated with evacuations from wildland fires.

Keywords: evacuation
forest fire
FWI system
Ontario
wildfire
wildlandfire
Advisor: Wotton, Mike
Inhibiting Thioredoxin Reductase for Dual Molecular Targeted and Photodynamic Cancer Therapy

Conventional cancer treatment is limited by lack of selectivity, limited efficacy towards metastatic cancer and resistive mechanisms acquired by cancer cells. Thus, alternative cancer treatments such as molecular targeted therapy and photodynamic therapy have emerged as promising therapies to combat these issues, although these therapies also present their own limitations. Alternatively, these two types of therapies can be combined for enhanced potency, selectivity and to combat limitations presented by each type of therapy individually. This thesis describes a novel dual therapeutic approach whereby a single small molecule drug, DG-EryB, can irreversibly and covalently inhibit thioredoxin reductase 1 (TrxR1) for molecular targeted therapy, while simultaneously acting as a photosensitizer for photodynamic therapy. This thesis also describes how a photocleavable group can be attached to DG-EryB in a prodrug design for improved pharmacokinetic properties.

Keywords: Inhibition
Photocage
Photodynamic Therapy
Photosensitizer
Targeted Therapy
Thioredoxin Reductase
Advisor: Beharry, Andrew A
Nitz, Mark
Accessible Localized, Trauma-focused Support for Refugee Students in K-6 Canadian Classrooms: A Codified Workbook for Educators

Canadian educators play an important role as first responders for the increasing number of refugee students in classrooms. Refugee students enter the classroom with prior experiences of trauma from premigration, migration, and resettlement; educators must be trained and equipped to support the needs of these students. The present research explores a fusion of Narrative Exposure Therapy (NET) and Art Therapy (AT) methodologies to design an accessible workbook format to be utilised by educators. NET and AT are effective strategies for trauma support with refugee communities and can efficiently translate into the localized and cooperative format of a workbook. An in-class workbook is a multi-modal trauma focused intervention strategy to incorporate family, peer, and community networks at the local level to accommodate the diversity and individuality of each refugee student. A biopsychosocial methodology works to emphasize the psychological, educational, and social realities of individual refugee students to develop resiliency skills and trauma support networks.

Keywords: Curriculum
Educator
Refugee
Resettlement
Trauma
Advisor: Oladi Ghadikolaei, Soudeh
Kipkosgei, Evelyn
Mechanical Properties of Outcropped Montney Formation

This thesis presents experimental and image-processing studies on outcropped Montney Formation. The mechanical properties of the rock were obtained from a series of laboratory testing that was conducted following the International Society of Rock Mechanics Suggested Methods. From the results, the studied Montney Formation was classified as relatively strong compared to previous studies on other rocks from Montney Formation. Additionally, size effect was observed, and a positive correlation between acoustic emission and fracture toughness was discovered. In the second part of this thesis, the fracture network generated in a Montney Formation cube during a companion laboratory hydraulic fracturing experiment was three-dimensionally reconstructed using the serial section images method to understand the rock behaviour and fracture propagation. The serial section images and three-dimensional visualization showed that bedding planes and rock anisotropy have a significant influence on the generated fracture network geometry. These observations have important implications on the evaluation of the stimulated rock volume, as well as on completion strategies, as preferential opening of bedding planes might result in horizontal intra-well connectivity and increase parent-child interactions.

Keywords: 3D Reconstruction
Fracture Propagation
Hydraulic Fracturing
Montney Formation
Serial Sectioning
Advisor: Grasselli, Giovanni
Challenges and Possibilities for the Creation of Knowledge Building Dashboards

In this paper, I discuss challenges and possibilities for design of a Knowledge Building dashboard. Knowledge Building aims to foster knowledge creation in education and requires high levels of agency in planning, monitoring, evaluating, and pursuing promising ideas to create new knowledge. Students must take collective responsibility for advancing community knowledge, working as an expert team to take ideas to increasingly high levels. Typically, education and learning dashboards focus on individual achievement; in contrast, Knowledge Building focuses on collective responsibility for advancing public knowledge. I review the literature on limitations in learning dashboards; for example, data misinterpretation, failure to accommodate personal preferences, irrelevant metrics, and lack of pedagogical focus, followed by designs that aim to moderate these limitations and provide bases for Knowledge Building dashboards to be added to Knowledge Forum, a technology specially built to support Knowledge Building.

Keywords: Knowledge Building
Learning Dashboard
Advisor: Scardamalia, Marlene
Resequencing Identity: African Americans and Direct-to-Consumer Genetic Testing

This thesis examines the integration of direct-to-consumer genetic testing technologies into personal and group identity formation practices among African Americans. In framing race and identity as performative, I applied digital ethnographic and situational analyses frameworks to examine ‘ancestry reveals’ shared by African Americans mobilizing test results on YouTube. To do so, I examined 10 ancestry reveals highlighting collaborative meaning-making processes mediated through information infrastructures, both direct-to-consumer genetic testing (DTC GT) technologies and YouTube. Exploring ancestry reveals among African American consumers offers insight into an emerging practice merging technology, and the performativity of race and identity online.

Keywords: African Diaspora
Direct-to-Consumer Genetic Testing
Human Computer Interaction
Identity
Race
Technological Appropriation
Advisor: Ratto, Matt
Development and Optimization of Multi-Motif Ionizable Lipid Nanoparticles for the Delivery of Ribonucleic Acids

Lipid nanoparticles and the emergence of RNA technology has come forth as a key player in the medical field in recent years. With the development of mRNA vaccines to treat SARS-COV2 the potential applications for RNA and lipid nanoparticles have expanded. Lipid nanoparticles comprised of an ionizable lipid encapsulating RNA payloads in its core, provide the delivery vehicle required for RNA to effectively enter cells. Using engineering design criteria and a rational approach, we discuss the synthesis of a novel ionizable lipid and its formulation into RNA nanoparticles. Lipid nanoparticle formulation optimization is an intricate process which can be engineered many ways to meet design criteria. In this body of work the process from conception to lead formulation is described, as well as in vitro and in vivo validation studies.

Keywords: Delivery System
Lipid Nanoparticles
Ribonucleic Acid
Advisor: Khan, Omar F
Concentric Tube Robot Optimization and Path Planning for Epilepsy with 3D Slicer

Robot-assisted minimally invasive surgery (MIS) has been widely studied in recent years, as they reduce pain and recovery time in patients compared to open surgery. However, one major concern of conventional MIS is safely accessing the diseased sites with straight instruments. Concentric tube robots (CTR) have the potential to address this problem with their shape flexibility. One of the applications of CTR is the treatment of epilepsy. Epilepsy effects about 1% of the pediatric population, and surgeries can make considerably improved seizure outcomes in 90% of patients. An integrated software platform is proposed in this thesis, which allows surgeons to find optimal patient-specific and procedure-specific CTR design and surgical plans, as well as to validate the plans in simulation. It is believed that this platform would demonstrate feasibility of using CTR in epilepsy surgeries, and lead to increased adoption rate of CTR in those surgeries in the future.

Keywords: 3D Slicer
Concentric Tube Robots
Continuum Robots
Epilepsy Surgeries
Optimization
Advisor: Drake, James
Burgner-Kahrs, Jessica
Development and Optimization of Multi-motif Ionizable Lipid Nanoparticles for the Delivery of Ribonucleic Acid

Lipid nanoparticles and the emergence of RNA technology has come forth as a key player in the medical field in recent years. With the development of mRNA vaccines to treat SARS-COV2 the potential applications for RNA and lipid nanoparticles have expanded. Lipid nanoparticles comprised of an ionizable lipid encapsulating RNA payloads in its core, provide the delivery vehicle required for RNA to effectively enter cells. Using engineering design criteria and a rational approach, we discuss the synthesis of a novel ionizable lipid and its formulation into RNA nanoparticles. Lipid nanoparticle formulation optimization is an intricate process which can be engineered many ways to meet design criteria. In this body of work the process from conception to lead formulation is described, as well as in vitro and in vivo validation studies.

Keywords: Delivery System
Lipid Nanoparticles
Ribonucleic Acid
Advisor: Khan, Omar F
Portraying the Urban Food Environment of the City of Toronto before and during the COVID-19 Pandemic through Yelp Reviews

The obesity epidemic encompassing diet-related health outcomes, such as obesity and overweight, has risen as a public health crisis. The urban food environment, within which we make our daily food choices, is essential in influencing eating behaviours. Recent impacts of the COVID-19 pandemic on urban dwellers have signaled changes in the urban environment that ultimately affected food consumption habits. This study utilizes Yelp reviews to capture changes in the environment, and improve our understanding of the consumers’ perceived urban food environment in the City of Toronto. The list of food words that can be used to identify content in social media data is expanded, then a comparison of the environment before and during the pandemic in relation to neighbourhood characteristics is performed. Results reveal that the food environment is disproportionately affected, and consumers’ favourableness towards healthy foods varied with neighbourhood characteristics. These findings should be considered for policy interventions catering to consumers’ characteristics.

Keywords: COVID-19
Food choices
Food environment
Urban food environment
Yelp Reviews
Advisor: Wang, Jue JW
Staying Hydrated: An Automated Fluid Intake Monitoring System using a Vision-based Approach

Staying hydrated is important at any stage of life and even more so as we age, as there are increased risks. There is a need for an accurate, automated system that tracks the amount of liquid consumed to prompt the user to drink. The objective of this thesis is to determine whether using cameras and depth cameras can accurately detect drinking events and determine the amount consumed when using deep learning models. We collected data with subjects performing household tasks, eating and drinking in a simulated home environment. We compared the use of both static images and videos as inputs to train the models, and the videos yielded a higher detection performance. Notably, using video inputs also allowed us to estimate the amount consumed throughout a sip with an error comparable to previous literature. If hydration can be tracked at home remotely to encourage intake, hospitalizations from dehydration can decrease.

Keywords: artificial intelligence
computer vision
dehydration
home monitoring
Advisor: Roshan Fekr, Atena
Fernie, Geoff
Adsorption of Per- and Polyfluoroalkyl Substances and Microcystins by Virgin and Weathered Microplastics in Freshwater Matrices

Microplastics and per- and polyfluoroalkyl substances (PFAS) both represent persistent environmental contaminants that have been associated with human health risks. Microcystins are naturally occurring cyanobacterial toxins that may be present in drinking water sources. Recent concerns have emerged regarding the ability of microplastics to adsorb various types of organic contaminants, including PFAS and microcystins. This study examined the adsorption of two long-chain and two short-chain PFAS by virgin microplastics, as well as two common microcystins by both virgin and weathered microplastics in freshwater. Results indicate adsorption to be driven by specific types of polymers and dominated by hydrophobic interactions. Weathering may decrease adsorption of microcystins by introducing hydrophilic oxygen-containing groups to microplastic surfaces. This is the first known study to determine if PFAS and microcystins may be concentrated by microplastics in freshwater when considering environmentally relevant concentrations while also addressing questions regarding weathered microplastics.

Keywords: adsorption
microcystins
microplastics
PFAS
Advisor: Andrews, Robert C.
Evaluation of Peracetic Acid Treatment for Reducing Disinfection By-product Formation in Drinking Water

Prechlorination is a widely adopted mussel control strategy by water treatment utilities. Although prechlorination is effective and inexpensive, it leads to disinfection by-product (DBP) formation. Peracetic acid (PAA), which exists in equilibrium with hydrogen peroxide (H₂O₂), is a promising alternative to prechlorination for mussel control. At the same time, PAA may also destroy DBP precursors, thereby serving two concurrent roles in drinking water treatment. This research explored the ability of PAA pre-oxidation to reduce subsequent chlorination DBPs (THMs, HAAs, and AOX). The results showed that a 5 mg/L PAA dose (containing about 10% H₂O₂ by mass) decreased DBP formation potential by up to 40% in raw water (pH:7.8-8.2, temperature:22-24 °C) collected from three Ontario utilities. The findings also indicate that H₂O₂ is more effective than PAA for reducing DBPs on a per mass basis. However, the poorer reactivity of PAA is compensated by its higher concentration in the PAA/H₂O₂ mixture.

Keywords: Adsorbable Organic Halides
Disinfection By-products
Haloacetic Acids
Hydrogen Peroxide
Peracetic Acid
Trihalomethanes
Advisor: Hofmann, Ronald