VictorJuiz/thesis huggingface dataset:
An Investigation of Benzene-degrading, Nitrate-reducing Bacterial Cultures: Strategies for Countering Nitrite Buildup and for Assaying Anaerobic Enzymatic Activation of the Benzene Ring

Benzene is a widely used precursor compound in the chemical industry. Benzene could enter the environment in a variety of ways, including oil spills, leakage from underground gasoline storage tanks, and gasoline combustion. Bacterial cultures have demonstrated the ability of degrading benzene under a variety of electron acceptor conditions, including methanogenic, sulfate-reducing, iron-reducing, and nitrate-reducing. Benzene degradation under nitrate-reducing conditions is among the most energetically favorable conditions, but is hampered by the buildup of nitrite, the product of nitrate reduction. In this work, successful strategies for countering nitrite buildup were developed. Such strategies would enable the cultivation of large quantities of benzene-degrading, nitrate-reducing cultures, which could be applied to both bioremediation and for research purposes. This work also began to investigate assay systems to attempt to demonstrate benzene carboxylation as the first step of benzene degradation under nitrate-reducing conditions.

Keywords: Anaerobic benzene degradation
Enzyme assays
Nitrite inhibition
Advisor: Edwards, Elizabeth A
Investigating the Functional Consequence of Pik3c2b Ablation in a Skeletal Muscle Model

Phosphoinositide 3-kinases (PI3Ks) and its three distinct classes are involved in a myriad of cellular processes, including: cell growth, survival and intracellular trafficking. The Class II PI3Ks remain one of the least studied classes of lipid kinases. There are three isoforms of class II kinases, PIK3C2α, PIK3C2β and PIK3C2γ. Our laboratory identified PIK3C2β as a modifier of X-linked myotubular myopathy (XLMTM) caused by mutations in MTM1. However, PIK3C2β’s role in muscle and the consequences PIK3C2β ablation has not been elucidated. To answer this question. I generated a skeletal-muscle specific PIK3C2β KO mouse and found lower fasting glucose levels and increased AKT activation in muscle in an age-dependent manner. Next, I created and characterized PIK3C2β KO C2C12 myoblasts and discovered increased surface GLUT4 levels upon insulin stimulation. These new insights into the consequences of PIK3C2β ablation represent an opportunity to develop novel therapeutic strategies in XLMTM and metabolic disorders.

Keywords: c2c12
glucose metabolism
lipid kinases
PIK3C2B
skeletal muscle
x-linked myotubular myopathy
Advisor: Dowling, James
Validity of the Verbal Intelligence Quotient as a Proxy for Language Ability

Autism Spectrum Disorder (ASD) is characterized by impairments in social communication and restricted interests and repetitive behaviors. Structural language deficits are commonly observed. Studies examining the neurobiology of these structural language deficits have reported conflicting findings. It is suspected that the choice of measure used to evaluate language, and in particular the use of the Verbal Intelligence Quotient (VIQ) from the Wechsler cognitive batteries, may be contributing to these inconsistencies. This thesis explored whether VIQs could be reliably used as a measure of language ability in ASD and typical development. In a large cohort of children and youth with ASD and typically developing peers, we showed that across diagnosis and sex, VIQ scores accounted for a small proportion of variance in language scores from the Oral and Written Language Scales, 2nd Edition. Therefore, VIQ is not a suitable measure of language ability in ASD and typical development.

Keywords: Autism Spectrum Disorder
Language Assessment
Oral and Written Language Scales
Proxy for Language Ability
Verbal Intelligence Quotient
Advisor: Anagnostou, Evdokia
Brian, Jessica
Using a Knowledge Engineering Framework to Develop the Clinical Reasoning of a Hybrid Therapy System for Upper Extremity Rehabilitation after Stroke

This thesis presents preliminary studies in developing clinical reasoning capabilities for an autonomous, intelligent, post-stroke upper-extremity rehabilitation hybrid therapy system. The hybrid system combines functional electrical stimulation (FES) with robotics, which allows the hybrid system to monitor a patient's performance during therapy while using its clinical reasoning capabilities to intelligently decide when to intervene with FES during a therapy session so as to be most beneficial to the patient. A novel approach to develop the hybrid system's clinical reasoning capabilities is taken by applying a systematic Knowledge Engineering (KEG) framework to elicit tacit knowledge of four experienced physical and occupational therapists, and explicate it into a knowledge model. A prototype of the hybrid system is then demonstrated to three occupational therapists via a mock therapy session. The KEG framework generated a sufficient amount of knowledge for implementation in the hybrid system software, while therapists agreed with the FES control decisions.

Keywords: Functional Electrical Stimulation
Knowledge Engineering
Rehabilitation
Robotics
Stroke
Advisor: Mihailidis, Alex
Wang, Rosalie
Machine Learning for Topic Classification and Prediction on Twitter

The rise of social media networks such as Twitter presents us with a massively distributed portal of information covering every topic from social and political news to entertainment. However, this coverage of different topics coupled with the high rate of content generation on Twitter results in an overwhelming volume of content that makes it difficult to detect and retrieve information relevant to a specific topic. Access to efficient methods for retrieval and analysis of this topical content can be of great value in a lot of different domains from social sciences to marketing analysis. Hence, the concept of learning topical classifiers and predictors for Twitter has become an important area of research. This thesis aims to address the challenges of topical content retrieval and analysis via efficient ways that will allow users to have real-time access to insights on their desired topics.

Keywords: Information Retrieval
Machine Learning
Popularity Prediction
Social Media Analysis
Time Series Analysis
Topic Classification
Advisor: Sanner, Scott
3D Dental Subsurface Imaging Using Enhanced Truncated Correlation-Photothermal Coherence Tomography

With dental caries being the most common disease in human, development of accurate and sensitive dental imaging technologies for early caries detection and routine monitoring are crucial for preventive dentistry. However, radiographic technologies fall short of these objectives due to low sensitivity for small lesions and use of ionizing radiation. Here, dental enhanced Truncated Correlation-Photothermal Coherence Tomography (eTC-PCT) is presented as the first 3D tomographic thermophotonic dental imaging modality capable of monitoring and characterizing tooth demineralization with high sensitivity and without ionizing radiation. To this end, eTC-PCT is applied to teeth with natural defects, and artificially generated controlled early caries and surface erosion. Additionally, eTC-PCT performance for dental imaging is compared with other thermophotonic technologies. The results demonstrate that, eTC-PCT is capable of detecting and monitoring early demineralization in teeth at clinically applicable laser power levels, and visualizing the relative progression and extent of lesions through 3D reconstruction.

Keywords: 3D Imaging
Dental Imaging
Non-Destructive Testing
Optical Imaging
Photothermal Effect
Preventive Dentistry
Advisor: Mandelis, Andreas
Clogging and Maintenance of Permeable Interlocking Concrete Pavement

This research evaluates five of the different maintenance techniques to restore surface infiltration rate for permeable interlocking concrete pavements: (1) specialized maintenance equipment for permeable pavement; (2) pressure washing followed by manual vacuuming, (3) a regenerative air streetsweeper, (4) a vacuum streetsweeper and (5) a mechanical streetsweeper. A synthetic accelerated clogging method was developed to prepare the pavement for maintenance. Surface infiltration rates were measured throughout the clogging process and after the application of maintenance. Following the application of maintenance, joint penetration depths were also measured. The specialized equipment had the best performance, completely restoring of the pavement permeability. The vacuum sweeper had the best performance among the sweepers by restoring 80% of the pavement permeability. Results of this work will be used to develop best management practices for maintenance of permeable interlocking concrete pavements.

Keywords: clogging
maintenance
permeable pavement
PICP
Advisor: Drake, Jennifer
Political Documents and Political Dissonance: An Analysis of the Meaning Created through Student Engagement in the Revision of Sexual Violence Policies at Universities in Ontario

This thesis investigates student engagement in the revision of sexual violence policies at universities in Ontario. Through case studies, this research analyzes the social and political meaning created through the requirement of Bill 132 for universities and colleges to consider student feedback when the policies are reviewed or amended. Document analyses were completed on the publically available documents pertaining to student engagement and consultations that Brock University, Lakehead University, and Carleton University had available on their institutional websites. By interrogating the power dynamics present in policy consultations, this research problematizes how students and sexual violence are understood within policy frameworks. This thesis calls for universities to challenge the hierarchy inherent to consultation processes and to engage with communities beyond their campuses to work against sexual violence in a comprehensive manner.

Keywords: Bill 132
Education
Policy Revision
Sexual Violence
Student Engagement
University
Advisor: Todorova, Miglena
Archiving Afghan-Canadian Long-time Settlement Experiences: Emergent Methods Digital Design

Skewed, damage-centered narratives based on war and violence have shaped Canadian views of the Afghan-Canadian diaspora despite almost four decades in Canada. This study uses critical ethnography and iterative digital design methodologies to conduct oral histories of a slice of the long-time settled Afghan-Canadian diaspora in order to understand their digital archival needs and identity-formation processes. The result is a proof-of-concept digital archive called the Afghan-Canadian Digital Archives (ACDA). The findings demonstrate that the Afghan diaspora in Canada, more specifically the intersection of the diaspora represented in this thesis, agree that digital archives could provide answers to problems that they identified in their community: working against symbolic annihilation of minority identities within the community, the lack of a pedagogical resource on the community’s history and stories, and the desire for a platform to present their successful integration to all Canadians.

Keywords: afghan
archives
diaspora
digital archives
ethnography
identity
Advisor: Cowan, TL
Predictors of Locus of Care in Adolescents and Young Adults with Cancer

Introduction: Adolescents and young adults (AYAs) with cancer represent a unique and underserviced population. Methods: Administrative databases were used to identify adolescents diagnosed with cancer between 1994 and 2004, in Ontario. Associations between demographic, disease, and health-care system factors and adolescents’ initial treatment centre (pediatric/adult) were examined. In addition, a Triple-I policy analysis was used to compare Canadian, Australian and English AYA cancer-care delivery policies. Results: Adolescents’ age, cancer diagnosis, time period of diagnosis, distance of residence from pediatric centre, residing in a LHIN with a pediatric centre and PCP speciality were significantly associated with their initial treatment centre. Although Canadian AYA oncology policies were similar those from Australia and England, they were not as well developed. Conclusion: Adolescents’ initial treatment location is be influenced by patient, diagnostic and health-care system factors as well as health-care policy. Future AYA cancer care policies must consider these variables during their development.

Keywords: Adolescents and Young Adult
Health Policy
Health Service
Oncology
Advisor: Nathan, Paul
Polycyclic Aromatic Compounds (PACs) in Alberta’s Oil Sands Tailing Ponds: Levels and Reassessment of Emissions

Polycyclic aromatic compounds (PACs) are semi volatile organic compounds emitted from Alberta’s oil sands tailing ponds (OSTPs). They have been classified as priority compounds for monitoring because of their toxicity and environmental ubiquity. Alberta’s open-air OSTPs have large surface areas from which PACs can volatize. Water analysis from four different OSTPs taken at different times were analyzed for targeted PACs, where magnitude differences in concentrations between ponds showed spatial heterogeneity. An equilibrium chamber study was devised to determine the air-OSTP water partition coefficients for PACs. Air-OSTP water partition coefficients were found to be 10-59% lower than literature values depending on the compound. With these newly determined partition coefficient values, this research also estimated point-in-time fluxes of PACs from four different ponds. Flux estimates can vary as much as 5 orders of magnitudes between ponds.

Keywords: Air-water partition coefficient
Net fluxes
Oil sands
Polycyclic aromatic compounds
Polycyclic aromatic hydrocarbons
Tailings ponds
Advisor: Diamond, Miriam
Jantunen, Liisa
The Brain Disease Model of Addiction and Implications for Public Stigma: A Cross-national Study

The definition of addiction impacts stigma levels attributed to the addictive population. Researchers in the United States (US) believe a brain disease model of addiction (BDMA) reduces stigma, though other researchers worldwide disagree. Via MTurk, data was collected from Canada, the US and Australia. Participants were randomized to one of four vignette manipulations describing an individual with the following condition(s): addiction, mental health, co-occurring addiction and mental health, or non-psychiatric medical. Participants’ beliefs in five models of addiction and stigma attributed to the individual was measured. Addiction was the most stigmatized condition though greater beliefs in the nature and psychological MOA predicted lower stigma. Beliefs in the psychological, nature, and sociological MOA moderated the vignette condition and stigma relationship and the moral MOA mediated the geographical region and public stigma relationship. US accepted the BDMA more than Canada, although greater beliefs in the BDMA did not predict lower public stigma.

Keywords: Addiction
Brain Disease
Stigma
Advisor: Hendershot, Christian S
Survival of Single Implant-supported Restorations Placed Distal to Residual Dentitions and Followed up for at Least One Year

The purpose of this retrospective study utilising a chart review was to determine the survival of single implant-supported restorations in distal end partially edentulous arches and identify factors associated with biological and mechanical complications of those restorations. A total of 132 participants (M = 66.8 years) from the University of Toronto Faculty of Dentistry clinics were included. Follow-up ranged from 7 to 119 months (M = 58.2 month). Out of 149 implants, seven (4.7%) failed during the follow-up period. No predictors of biological complications were statistically significant. However, light occlusion was associated with significantly fewer mechanical complications compared to evenly distributed occlusion. In this study, light occlusion associated with fewer chipped restorations, fewer loosened screws/crowns, and fewer fractured crowns. These findings suggest that implant-supported single restorations have high survival rates over a mean follow-up for five years.

Keywords: distal edentulous
distal implant
distal single unit implant
implant
single unit
survival rate
Advisor: Somogyi-Ganss, Eszter
Goldberg, Michael
Neutrophil Extracellular Trap Formation in Cystic Fibrosis

Genetic defects in CFTR is associated with mucus dehydration, opportunistic bacterial infection, and inflammation in CF lung disease. Neutrophil extracellular traps (NETs) contribute to the extracellular DNA in CF airway mucus, and increase the risk for mucus obstruction. Although adult CF females are reported to be at a disadvantage for CF lung disease, the role of NETosis in the CF sex-difference is not clear. I hypothesized that CF neutrophils will display sex-difference. I isolated CF and healthy peripheral blood neutrophils, and measured levels of NETosis, and reactive oxygen species (ROS) in response to various stimuli. CF neutrophils formed more NETs and less ROS at baseline than healthy neutrophils. Female CF neutrophils formed more NETs than CF males. Female sex-hormones had varying effects on NETosis in CF but not healthy neutrophils. The sex-based discrepancy in NETosis observed in CF may put females at a higher risk for worse lung related outcomes.

Advisor: Palaniyar, Nades
Sweezey, Neil
Utilizing Machine Learning and Virtual Reality to Facilitate Brain-computer Interface Control

Brain-computer interface (BCI) users must first participate in many training sessions to obtain adequate data for optimizing the classification algorithm and subsequently acquiring brain-based control. Such traditional training paradigms are neither motivating nor engaging. In recent years, it has been shown that the synergy of virtual reality (VR) and a BCI can lead to increased user engagement. This study created a 3-class BCI that initially presented sham feedback but was eventually driven by EEG associated with motor imagery to navigate a single-path maze in VR. Ten of the eleven recruited participants achieved online performance superior to chance (p

Keywords: Artificial Intelligence
Brain Computer Interface
Machine Learning
Pattern Recognition
Signal Processing
Virtual Reality
Advisor: Chau, Tom
Physical Separation of Thermally Upgraded Pyrrhotite

Over the past 40 years, the depression of pyrrhotite during the flotation of nickel sulphide ores has led to a significant build-up of pyrrhotite tailings. These tailings are stored in tailings ponds, where they have the potential to generate acid rock drainage. These tailings contain up to 1% nickel, are easily accessible, and do not require grinding. A pyrometallurgical method of nickel extraction is being developed which involves converting pyrrhotite (Fe1-xS) to a ferronickel alloy (FeNi) and troilite (FeS). This thesis focuses on physically separating the FeNi and FeS phases, by either froth flotation or magnetic separation. The variables studied for froth flotation are pH, particle size, and additive concentrations. Moreover, magnetic separation characteristics studied are magnetic field intensity, particle size, and the production temperature of FeNi and FeS. Results showed that magnetic separation produced concentrates of higher Ni grade and Ni recovery compared to froth flotation.

Keywords: froth flotation
magnetic separation
pyrometallurgy
pyrrhotite
troilite
Advisor: Bobicki, Erin
Barati, Mansoor
Phosphorus in the Lime Cycle of Kraft Pulp Mills

The accumulation of non-process elements in the recovery cycle of kraft pulp mills is a current and growing problem. Phosphorus is one of these elements and there is limited information about its behavior in the recovery cycle. Phosphorous reacts with lime, reducing the amount of lime available for recausticizing. The first part of this project, through laboratory work, identified rhenanite (NaCaPO4) as the form of phosphorous in the lime cycle and showed the negative effect of phosphorus on lime availability. Now that rhenanite has been identified, it can be used in future work to build an equilibrium database for equilibrium modeling of phosphorous in the lime cycle. The second part of this project involved field studies and performing a mass balance for phosphorus at a Canadian kraft pulp mill to better understand the flows of phosphorus in the pulp mill and its distribution between the solid and soluble forms.

Advisor: DeMartini, Nikolai
Transcriptomic Profiling of VHL-dependent Long Noncoding RNAs in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC), the most common form of kidney cancer, has a five-year survival rate of only 65%. Currently, there are no reliable diagnostic tools or curative therapies for ccRCC, but there lies hope in a relatively unexplored field: the noncoding genome, particularly long noncoding RNAs (lncRNAs). LncRNAs are known to be dysregulated in ccRCC, but no study has yet assessed the expression of lncRNAs relative to VHL status. VHL is the most commonly inactivated gene. In this project, we conducted a microarray-based transcriptomic analysis, uncovering numerous VHL-dependent candidate lncRNAs. To gain mechanistic insight into these lncRNAs, the hypoxic-responsiveness and HIF-dependency of the top dysregulated lncRNAs was examined. One lncRNA, which we named MARVEL, has emerged as an exciting molecule for further study, being upregulated in ccRCC cells and paired kidney tissue, functioning in a hypoxia and HIF-responsive manner, and having clinical value as a predictor of overall survival.

Keywords: cancer
kidney
lncRNA
Advisor: Marsden, Philip A
Novel Classification Method Development for Microbiome Data

The microbiome data is a popular research topic used in recent medical science. However, the microbiome data has its own features, such as high skewness, sparsity, and abundant outliers, which pose huge challenge towards the classification. The classification method is a supervised learning method which builds a classifier to predict the grouping for unknown observations. In this project, we come up with a novel medoids-based classification method targeting toward microbiome data. The medoids-based classification method is constructed by locating the medoids for each group based on L2 pairwise distance measure. Next, we compare our method with the existing classification methods, such as logistic regression, LDA/MDA, CART, and KNN. The performance of these classification methods is evaluated based on the diagnostic test on simulation studies and the two real microbiome data. The sensitivity test will also be conducted to test on the outlier effect on the stability of the classification method.

Keywords: Classification methods
diagnostic test
Microbiome Data
Advisor: Xu, Wei
A Prototype of a Machine Learning Workflow to Classify Land use from Housing Market Dynamics. Part of a Longitudinal Analysis of Housing Sales in the Greater Toronto-Hamilton Area

There is ample evidence of the role of land use and transportation interactions in determining urban spatial structure. The new data sources introduced by increased digitization of human activity, such as Teranet’s dataset of real estate sales, offer opportunities for development of integrated urban models or studies conducting longitudinal analysis of changes in land value distributions. To facilitate this, data from various sources (Census, TTS, etc.) needs to be merged at the land parcel level to enhance datasets with additional attributes, while maintaining the ease of data storage and retrieval. In addition, accurate land use information needs to be added to Teranet records to allow separating sales data by major property types. This thesis proposes a prototype of a workflow to augment Teranet’s dataset with data from multiple sources and use machine learning to classify land use of each Teranet record based on the housing market dynamics.

Keywords: Land-use/transport interactions
Machine Learning
Advisor: Miller, Eric J