VictorJuiz/thesis huggingface dataset:
Estimating a Toronto Pedestrian Route Choice Model using Smartphone GPS Data: It's Not the Destination, but the Journey, that Matters
Keywords: Path Size Logit
Pedestrian
Route Choice
Smartphone Data
Stochastic

City planning has an emphasis on working towards creating walkable cities with boulevards, wide sidewalks, and social spaces. This study uses revealed preference GPS data collected through a smartphone-based travel survey and discrete choice modelling techniques to determine pedestriansâ preferences towards street infrastructure, built environment, and land use. A path size logit model with stochastic route choice generation choice set was used for this model. The results of the model showed that distance, the number of turns, the number of signalized intersections, and distance along links with sidewalks on both sides of the street were significant variables in the route choice model. Turns are found to be equivalent to an additional 32m, signalized intersections are equivalent to a reduction of 34m, and travel along streets with sidewalks on both sides of the road is perceived as 33% shorter than streets with other sidewalk conditions.
Objective Vision-based Assessment of Parkinsonism and Levodopa-induced Dyskinesia in Persons with Parkinsonâ s Disease
Keywords: Computer vision
Deep learning
Disease management
Health monitoring
Parkinson's disease

Parkinsonâ s disease (PD) is the second most common neurodegenerative disease, with the incidence rate climbing rapidly as the global population ages. While levodopa is effective at treating PD symptoms, prolonged usage can introduce additional motor complications called levodopa-induced dyskinesias (LID). Assessment of PD/LID requires regular visits to a clinic; however, the intermittent nature of assessments can fail to capture changes in a personâ s condition. With computational power becoming increasingly more affordable, computer vision is an accessible means of performing more frequent and objective PD assessments. A study of deep learning for human pose estimation was conducted to examine the feasibility of extracting body movements from videos of PD assessments. Machine learning was applied to detect and estimate the severity of PD/LID using movement features. Results indicate computer vision is a promising candidate for objective PD assessment, thus laying the foundation for an automated system for evaluation of PD motor symptoms.
Exploration of Essential Biological Processes by Construction of Conditional Alleles of Non-essential Genes in S. cerevisiae
Keywords: Budding yeast
Dosage suppression
Genetic interactions
Mutagenesis
Synthetic lethality

Conditional mutants in S. cerevisiae have been useful tools in studying essential gene functions. In this study, I describe a new method that makes use of yeast deletion collections with a marker swap system to generate conditional temperature sensitive (TS) mutations in non-essential genes. I created TS mutants of BNI1, a non-essential formin gene, in various genetic backgrounds that BNI1 is essential for viability. I also constructed reciprocal TS alleles in five genes that are synthetic lethal with bni1 deletion. I screened for dosage suppressors in various synthetic lethal backgrounds of BNI1, covering different biological processes. I identified process-specific as well as common suppressors for each synthetic lethal pair. I also constructed morphological marker strains that are compatible with my system. My studies demonstrate the feasibility of construction TS mutant alleles of non-essential genes, and their utility for exploring synthetic lethal phenotypes.
Genetic Adaptation Contributing to Increased Gonococcal Fitness during Vaginal Infection of CEACAM-humanized Mice
Keywords: bacterial fitness
carcinoembryonic antigen-related cell adhesion molecule
Neisseria gonorrhoeae
transgenic mice
vaginal infection
whole genome sequencing

Neisseria gonorrhoeae (Gc), the obligate human pathogen responsible for gonorrhea, has drastic consequences on reproductive health, if left untreated. Although, vaginal infection in wild-type mice can simulate asymptomatic colonization, important host-specific factors essential for human infection are overlooked. I utilize mice expressing human CEACAM3, CEACAM5, and CEACAM6, to reveal factors promoting mucosal colonization. By serial passaging Gc in the lower genital tract of these mice, I demonstrate a higher proportion of mice colonized in subsequent infections, suggesting selection for bacteria better capable of colonization. No changes in susceptibility of bacteria to low pH, complement-mediated killing or antimicrobial peptides, mCRAMP and mBD-1, were observed. Finally, a genome-wide analysis identified mutations acquired by in vivo adapted isolates. One mutation has previously been investigated as a promising vaccine target, validating the infection model and screening process. Further examination of other identified changes may provide insight into the Gc lifestyle within the genital mucosa.
Balance and Knee Joint Kinematics after Total Knee Arthroplasty: Comparing Cruciate-retaining and Posterior-stabilized Designs
Keywords: Balance
Biomechanics
Knee
Posterior Cruciate Ligament
Total Knee Arthroplasty

Total knee arthroplasty (TKA) is a common surgical procedure for osteoarthritis and other degenerative conditions of the knee. Posterior stabilization may be achieved using a cam and post mechanism (PS), or by retention of the posterior cruciate ligament (CR). Little evidence exists to indicate superiority of either PS or CR designs. Further, few studies have examined balance in TKA patients, despite an established link to falls risk. Patients with PS- and CR-TKA were compared to healthy, age-matched controls. A methodology was established for assessment of balance and knee kinematics in TKA patients. Data collection included demographics, participant-reported outcomes, objective functional measures, and balance and kinematic assessment during postural perturbations. While all groups displayed similar balance performance, we identified important functional and kinematic differences between TKA groups. Further study is required to identify the mechanisms by which TKA impacts falls risk, and to further define biomechanical differences between these implants.
Examining Civil Society Participation in the Health Sector: The Case of Brazil's Health Councils
Keywords: Brazil
civil society participation
good governance
health councils
health policy

This thesis focuses on Brazil's Health Councils (Conselhos de Saude) to explore challenges in institutionalizing civil society participation. By conducting interviews with Health Council members at the municipal, state and national levels, this thesis examines how Health Councils operate and identifies some of the challenges evident in institutionalizing civil society participation. The thesis reports that Health Councils lack autonomy from the government to fulfill their mandate, membership guidelines limit the level of inclusion of civil society members, government representatives manipulate other members and provide limited support for Health Councils. In addition, it also reports that there is a lack of resources necessary to run Health Councils, there is an inadequate level of training of Health Council members, and there is a reported strong sense of individualism amongst members. These issues appear to have an impact on Health Councilsâ ability to successfully fulfill their mandate.
Investigating Molecular Differences related to T-bet-Positive Tumor-infiltrating Lymphocytes in Axillary Node-negative Breast Cancer
Keywords: BRD4
Breast Cancer
miRNA
PD-L1
T-bet
TIL

The clinical outcomes of axillary node-negative (ANN) breast cancer (BC) patients were previously shown to be positively associated with T-bet+ tumor-infiltrating lymphocytes (TILs). This study identified differences in miRNA and gene expression, and in PD-L1 expression between T-bet+/high and T-bet-/low tumors that provided insights into how T-bet+ TIL- mediated immunesurveillance may relate to tumor characteristics and disease outcome in ANN BC. The differentially expressed (DE) miRNAs were associated with intrinsic cancer-related pathways and immune-modulatory activities. miR-135a, in particular, was downregulated in T- bet+/high tumors, and was shown to be a direct suppressor of CXCL10, a T lymphocyte-recruiting chemokine. Among the DE genes, BRD4, a co-activator of NF-kB, was upregulated in T-bet+/high tumors at both mRNA and protein levels, suggesting a link between BRD4 expression and T-bet+-TIL-mediated inflammatory activities. The mRNA expression of PD-L1, a T-cell inhibitory marker, was associated with T-bet+ TILs, and basal subtype.
Transit User Mode Choice Behaviour in Response to TTC Rapid Transit Service Disruption
Keywords: Mode Choice
Public Transit
RP-SP survey
Subway Service Disruption
Toronto Transit Commission
Travel Behaviour

Disruption of transit service is a common occurrence in many cities around the world, and these incidents may have serious impacts on the transit userâ s journey. The purpose of this study is to investigate transit user commuting mode choice in response to rapid transit service disruption in the City of Toronto. A joint Revealed Preference and Stated Preference survey is designed to gather information on the respondentâ s actual response to the most recent service disruption and also responses under a set of hypothetical service disruption scenarios. A transit trip planner tool is developed to generate alternative transit options to avoid the disrupted segment. Econometric models are presented, including a joint RP-SP model, showing that the following factors, in addition to travel time and cost, are significant at 95% confidence: frequency of subway trip, trip purpose, subway delay, shuttle bus delay, weather, age, and income. Policy implications are also discussed.
Modelling H3.3-G34R mutation in vitro and in vivo
Keywords: Cancer
H3.3-G34R
H3K36me3
High Grade Glioma
Histone Mutation
Pediatric

Brain tumours are the most common solid tumours in children, with pediatric high-grade gliomas (PHGG) displaying clinically aggressive behaviour and dire survival outcomes. Previous evidence points toward a histone 3 variant H3F3A mutation (H3.3-G34R) in pediatric glioblastomas, which results in redistribution of the histone mark H3K36me3. It has been shown that H3K36me3 is necessary for recruitment of the mismatch repair (MMR) protein complex hMutSalpha (hMSH2-hMSH6). In vitro, Western blot and immunofluorescence analysis was performed on immortalized normal human astrocytes (iNHAs) to establish decreased H3K36me3 levels in S phase synchronized H3.3-G34R mutant cells. MSH6 foci formation was unaffected in the absence of a DNA damage inducing agent. In vivo, immunohistochemical analysis on H3.3-G34R xenograft tumour showed decreased levels of H3K36me3. Therefore, the H3.3-G34R mutation leads to loss of H3K36me3 levels, highlighting another impact of epigenetic disruption in PHGG.
Functional Analysis of Short Linear Motifs in Intrinsically Disordered Regions
Keywords: coevolution
comparative phylogenetics
computational biology
intrinsically disordered regions
short linear motifs
SLiM combinations

Short linear motifs (SLiMs) are regulatory binding sites that are involved in signalling and protein regulation. SLiMs are often found in intrinsically disordered regions (IDRs) which are rapidly evolving and lack stable tertiary conformations. Despite their prevalence throughout the proteome, many SLiMs still remain unknown and understanding how they cooperate and evolved are ongoing endeavours. The goal of this thesis is to address the properties of SLiMs and how they evolved, using bioinformatics methods and evolutionary models. To further examine the role of SLiMs in signal transduction, I show that deletion of predicted SLiMs (pSLiMs) has a broad range of quantitative effects on signalling pathway output. Next, to explore what properties are important in substrate recognition, I show that the combination and order of motifs can predict target specificity. Lastly, using a comparative phylogenetic approach to investigate the evolution of motifs, I provide evidence that phosphorylation and docking sites coevolved.
Characterizing Novel Interactions of Transcriptional Repressor Proteins BCL6 and BCL6B
Keywords: BCL6
BCL6B
BioID
BTB-ZF
Proteomics
TLE

B-cell Lymphoma 6 (BCL6) and its close homolog BCL6B encode proteins that are members of the BTB-Zinc Finger family of transcription factors. BCL6 plays an important role in regulating the differentiation and proliferation of B-cells during the adaptive immune response, and is also involved in T cell development and inflammation. BCL6 acts by repressing genes involved in DNA damage response during the affinity maturation of immunoglobulins, and the mis-expression of BCL6 can lead to diffuse large B-cell lymphoma. Although BCL6B shares high sequence similarity with BCL6, the functions of BCL6B are not well-characterized. I used BioID, an in vivo proximity-dependent labeling method, to identify novel BCL6 and BCL6B protein interactors and validated a number of these interactions with co-purification experiments. I also examined the evolutionary relationship between BCL6 and BCL6B and identified conserved residues in an important interaction interface that mediates corepressor binding and gene repression.
In-situ visualization of Steam Assisted Gravity Drainage with Chemical and Solvent Additives
Keywords: condensation
Enhanced oil recovery
Microfluidics
Petroleum
solvents
Steam asssisted gravity drainage(SAGD)

The introduction of steam-assisted-gravity drainage (SAGD) brought a significant improvement in the recovery of extra heavy oil, bitumen. The viscosity of bitumen being heavily dependent on temperature, makes the steam injection in SAGD highly effective in mobilizing the oil. The porous geometry of the reservoir structure plays an important role in the oil recovery process, along with the multiphase flow that takes place during the oil recovery process. Visualization of SAGD and the addition of chemical and solvents additives were conducted in this thesis at reservoir matching temperature and pressures (0.7-1.3 MPa, 170-210째C). Results of the experiments showed that alkaline additives brought improvement in oil recovery through wettability alteration, and solvents improve oil recovery through combination of mass transport and heat transfer effects. For the hexane-SAGD run, compositional separation of bitumen based on polarity difference was observed.
Applying Machine Learning with Spatio Temporal Analysis to Classify Crowdsourced Data from the 2010 Haiti Earthquake Relief Efforts
Keywords: classfication
Crowdmap
Crowdsource
Machine learning
spatio
temporal

Text categorization of incidental data crowdsourced from a crisis scenario is time-sensitive and requires knowledgeable human input. Instead, this study runs data collected from the 2010 Haiti earthquake relief efforts through a machine learning model. Linear supervised classification with Support Vector Machines, in combination with feature selection using Term Frequency-Inverse Document Frequency, was identified to achieve good performance in comparable literature. The feature sets were extended by spatio-temporal attributes for exploratory analysis and evaluating changes to the modelâ s performance. All phases of the experiments report consistent accuracy rates (87th percentile), with no statistically significant variance in precision, recall and F1 performance measures. Results demonstrate that using class labels alone is sufficient for such classification. Given the absence of known studies utilizing this data-driven approach, this study provides a benchmark analysis, laying the groundwork for further studies on adapting text classification models to similar crowdsourced, emergency relief data.
Insights into the Mechanism of Idiosyncratic Drug-induced Agranulocytosis
Keywords: Adverse Drug Reactions
Agranulocytosis
Animal Model
Clozapine
Idiosyncratic Drug Reactions
Myeloperoxidase

Many drugs are known to cause idiosyncratic drug-induced agranulocytosis, although the mechanism is not well understood. This adverse event is suspected to be the result of the drugâ s reactive metabolite binding to endogenous proteins and creating a foreign body capable of eliciting an immune response. In particular, clozapine has been shown to form reactive metabolites by neutrophil myeloperoxidase (MPO). These studies set out to further characterize MPOâ s role in bioactivating drugs that cause idiosyncratic drug-induced agranulocytosis and to characterize the immune response seen due to clozapine. Overall this work further characterized the early immune response seen due to clozapine treatment using in vitro and in vivo methods. Through this work we have a better understanding of the immune response that may lead to clozapine-induced agranulocytosis. Understanding the clozapine-induced immune response may provide avenues for early detection of clozapine-induced agranulocytosis and ultimately limit the magnitude of this adverse event.
Risk Factors for Death or Heart Transplant for Patients with Right Ventricular Dysfunction after the Norwood Procedure: A Secondary Analysis of the Single Ventricle Reconstruction Trial
Keywords: heart transplant
Hypoplastic left heart syndrome
Parametric hazard modeling
survival
ventricular dysfunction

We investigated patient and procedural factors associated with failure of staged palliation after the Norwood procedure in patients with right ventricular dysfunction (RVDfx). Patients from the Pediatric Heart Network Single Ventricle Reconstruction (SVR) Trial dataset were selected if RVDfx was present, defined as an ejection fraction of less than 44% and a fractional area of change of less than 35% on the post-Norwood echocardiogram. Transplant-free survival after the Norwood procedure was analyzed using multiphase parametric hazard analysis and factors associated with death or transplant were identified. In the SVR cohort, 123 (34%) infants had RVDfx. The six-month transplant-free survival was 87% (70%CI 82-91%). The independent factors associated with increased risk of death or transplant were BT shunt, increased RV size, infectious disease complications and low surgeon volume. Patient factors can help identify which patient with RVDfx is at higher risk of death and help decision making around early transplant listing.
Vision-based Flap Planning Software Tool for Reconstructive Facial Plastic Surgery
Keywords: fea
fem
flap
plastic
surgery
vision

The success of reconstructive facial plastic surgery is determined not only by the treatment of the given pathology but also the restoration or maintenance of normal morphological features and the reduction of scarring. Failure to consider these aesthetic components can have significant negative psychological effects for the patient. A vision-based approach to automatic lesion segmentation and incision planning is proposed. Optical camera images of the face will be analyzed for lesions and estimated lines of relaxed skin tension using feature-based registration. Simulation of stresses within wound closures will consider skin mechanical properties and craniofacial structures to implement a constitutive model for finite element stress analysis. The objective of this research is to develop a consistent and effective approach to flap planning for reconstructive facial plastic surgery. This system has applications for surgical training, surgical automation and control, and the improvement of patient care through the reduction of treatment variation.
Molecular Pathways Responsible for NMDA Receptor-mediated Behavioural Plasticity
Keywords: Behavioural Plasticity
Fear Conditioning
Hippocampus
Immediate Early Genes
Learning and Memory
NMDA receptor

Neurodevelopmental disorders occur from genetic and environmental risk factors that impair the formation of networks involved in learning and memory. Impaired NMDA receptor signaling has been implicated in the pathobiology of schizophrenia and autism. A mouse model of NMDA receptor knockdown and inducible rescue was used to determine the reversibility of neurodevelopmental insults on hippocampal function. Mice were studied for their ability to learn and remember using the fear-conditioning paradigm, which engages the hippocampus in the formation and recall of contextual memory. In addition, studies were performed to determine whether immediate-early genes were induced in the hippocampus of NMDA receptor deficient mice. The findings of this study show that NMDA receptor deficient mice lack the ability to form fear memories, and that this can be partially rescued by increasing the levels of NMDA receptors in adult mice. Furthermore, several immediate early genes are induced without a resulting formation of fear memory.
Predicting Short-term Hospital Inpatient Bed Needs for Up to Four Days in Advance
Keywords: EDD
Forecasting
Hospital
Inpatient Beds
Prediction

The Scarborough Hospital embarked a corporate initiative called Bed Mapping, which maps a better path for inpatient care and has patients in the right bed. A tool is needed to perform short-term predictions of inpatient bed needs. This thesis provides an inpatient demand predictive tool that uses historical, scheduled surgery, and current occupancy data to predict inpatient bed needs for up to four days in advance. It uses staff generated Estimated Discharge Date (EDD), Length of Stay (LOS) distributions, and a Monte Carlo simulation model by Liu [36] to make predictions. First, the tool was tested using retrospective CIHI expected patient LOS data to calculate EDD, and showed that the tool’s error is within 12 beds (5.52%) on day-1 and increases as we go further from day-1. The tool was further tested and showed that if EDD’s were accurate then the tool’s error is within two beds (0.88%) on day-1.
Transport and Development of Microemulsion- and Surfactant-Stabilized Iron Nanoparticles for In Situ Remediation
Keywords: Column Study
Groundwater Remediation
Iron Oxide Nanoparticles
Microemulsion
Mobility
NZVI

This work describes the mobility assessments of microemulsion-stabilized iron oxide nanoparticles and anionic surfactant sodium diethyl hexyl phosphate (SDEHP)-stabilized nanoscale zero valent iron (NZVI) particles in laboratory porous media. The two formulations tested in this work achieved stable iron nanoparticle suspensions for months and prepared via a simple â one-potâ synthesis method developed by Wang et al. Both formulations were tested under field scale velocity of 5 m/day with no mechanical aid during the injection. A three-compartment model, involving colloid diffusion theory, diffusion theory and tailing was applied to describe the breakthrough curves of the studies. The obtained breakthrough curves of both formulations implied excellent transport in porous media with steady plateau C/Co at 0.8-0.9 and recovery of up to 0.95 for SDEHP stabilized NZVI. Post analysis on the retention of iron on the porous media implied ideal transport with consistent data to the breakthrough curves.
FDEMTunnel Modelling in Georgian Bay Shale
Keywords: FDEM
georgian bay
modelling
shale
tunnel

This work describes the experimental and numerical study undertaken to understand potential failure mechanisms associated with the excavation of a tunnel in Georgian Bay shale. The Georgian Bay Formation consists of interbedded shale and limestone layers and was characterized through a laboratory testing program. From the results, shale is classified as relatively weak, soft, not very abrasive, easily weathered and is governed by anisotropic properties; whereas the behaviour of limestone is the exact opposite. Based on laboratory data and specimen photographs, the shale and limestone numerical input parameters were calibrated to match the experimental elastic and strength properties, within Âą 11%, and the observed fracture patterns. Numerical simulations were then used to investigate the failure around a circular excavation. Field-scale modelling suggested tunnel stability is sensitive to increased principal in situ stress ratios, rotation and the presence of limestone layers.