VictorJuiz/thesis huggingface dataset:
Travel Time Prediction Model for Regional Bus Transit

Over the past decade, the popularity of regional bus services has grown in large North American cities owing to more people living in suburban areas and commuting to the Central Business District to work every day. Estimating journey time for regional buses is challenging because of the low frequencies and long commuting distances that typically characterize such services. This research project developed a mathematical model to estimate regional bus travel time using artificial neural networks (ANN). ANN outperformed other forecasting methods, namely historical average and linear regression, by an average of 35 and 26 seconds respectively. The ANN results showed, however, overestimation by 40% to 60%, which can lead to travellers missing the bus. An operational strategy is integrated into the model to minimize stakeholders’ costs when the model’s forecast time is later than the scheduled bus departure time. This operational strategy should be varied as the commuting distance decreases.

Keywords: regional bus
travel time prediction
ITS
GPS
loop detector
operational strategy
artificial neural network
Advisor: Shalaby, Amer Saïd
Abdulhai, Baher
Mechanisms of Hypothalamic and Small Intestinal Nutrient Sensing

Nutrient sensing pathways in both the brain and gut decrease hepatic glucose production. Hypothalamic activation of lactate metabolism decreases glucose production, but it is unknown whether the hypothalamus detects circulating lactate to maintain glucose homeostasis. In the gut, lipids decrease glucose production via a neuronal network but the downstream signaling mechanisms are unknown. We tested whether circulating lactate activates central lactate metabolism to decrease glucose production and postulated that duodenal protein kinase C (PKC) acts downstream of lipids to decrease glucose production through a neuronal network. We report that central lactate metabolism is required for the maintenance of glucose homeostasis in the presence of circulating lactate and that activation of duodenal PKC is required for lipids to decrease glucose production. This shows the importance of the brain and gut in the regulation of glucose production, and could pave the way for restoration of glucose homeostasis in disease.

Keywords: metabolism
diabetes
Advisor: Lam, Tony K. T.
Use of Lanthanide Ions for Encoding One-bead-one-compound Combinatorial Libraries

The advantage of one-bead-one-compound combinatorial libraries is that hundreds of thousands to millions of compounds can be rapidly synthesized and screened simultaneously. The beads supporting the compounds of interest are then isolated and analyzed to decipher the structure of the desired compound. Many methods are currently used to allow deconvolution of the compound on the individual beads. Herein is described a novel method to encode TentaGel beads using absorption of different ratios of lanthanide ions. The encoding process is completed in parallel with the synthesis of the library of compounds. Once the desired beads are identified, the lanthanide ions can be released from the bead and analyzed using Inductively Coupled Plasma-Mass Spectrometry (ICP-MS).

Keywords: Lanthanide
combinatorial chemistry
ICP-MS
TentaGel
Advisor: Nitz, Mark
Access via a Multiple Camera Tongue Switch for Children with Severe Spastic Quadriplegic Cerebral Palsy

Access technologies facilitate novel and alternative methods for individuals with disabilities to interact with their environment. Finding suitable access solutions for children with severe spastic quadriplegic cerebral palsy can be difficult because of their poor motor control and targeting abilities due to spasticity at the limbs, neck, and head. In this research a multiple camera tongue switch was developed for a 7 year-old case study participant with severe spastic quadriplegia. Remotely via video, this system reacts to tongue protrusions as cues for single-switch access. Having multiple cameras mitigates targeting problems with the head that conventional single camera systems would present. Results of a usability experiment with the participant show that good sensitivity (82%) and specificity (80%) can be achieved with a non-contact tongue protrusion access modality for a user with spastic quadriplegia. Moreover, the experiment verified that the extra cameras improve utility of video-based access technologies for the target population.

Keywords: paediatric rehabilitation
cerebral palsy
access technology
image processing
assistive technology
Advisor: Chau, Tom
Effect of Activity on Appetite, Food Intake and Net Energy Balance After a Glucose Drink in Normal Weight, Overweight and Obese Boys

The effect of exercise (EXR) on food intake (FI), subjective appetite and net energy balance was investigated in normal weight (NW), overweight (OW) and obese (OB) boys. Each boy received in random order either a non-caloric sweetened control (CON) or glucose (GLU) drink after either EXR or sedentary activity. Normal weight and OW/OB boys exercised at their ventilation threshold (VeT) in experiment 1 and NW boys exercised at 25% above their VeT in experiment 2. Overweight/OB boys ate significantly more total food than NW boys but not when adjusted for body weight. Food intake was lower after the GLU drink. Although EXR increased average appetite it did not affect FI. However, net energy balance was reduced by EXR in OW/OB boys, but not in NW boys. Thus, while EXR increases subjective appetite, apparent intake compensation occurred only in NW, but not in OW/OB boys, resulting in reduced net energy balance in OW/OB boys.

Keywords: food intake
exercise
appetite
net energy balance
activity
children
adolescents
Advisor: Anderson, G. Harvey
Resveratrol Increases Mitochondrial Protein Import in Differentiated PC12 Cells

Mitochondrial function is dependent upon mitochondrial protein import (MPI), a complex process that transports nuclear-encoded proteins into mitochondria. Little is known about MPI in neurons. We examined the effects of Resveratrol (RSV), a polyphenolic antioxidant compound from grapes, on MPI in a neuronal cell model, differentiated PC12 cells. RSV (50µM, 24h) increased levels of mtGFP, a nuclear encoded mitochondrially targeted green fluorescent protein, and mtHsp70, a physiological mitochondrial heat shock protein, in mitochondria. In addition RSV also increased levels of Tom20, a key translocase of the outer mitochondrial membrane. The RSV mediated increases in mitochondrial proteins were independent of increases in mitochondrial mass or changes in intramitochondrial degradation. RSV also reduced mitochondria membrane potential and decreased basal levels of reactive oxygen species. Taken together, these findings show that RSV increases MPI and that this effect may be an important mechanism in the reported neuroprotective effects of RSV.

Keywords: Reseveratrol
Mitochondrial protein import
PC12 cells
Advisor: Mills, Linda
When do Systematic Gains Uniquely Determine the Number of Marriages between Different Types in the Choo-Siow matching model? Sufficient Conditions for a Unique Equilibrium

In a transferable utility context, Choo and Siow (2006) introduced a competitive model of the marriage market with gumbel distributed stochastic part, and derived its equilibrium output, a marriage match- ing function. The marriage matching function defines the gains generated by a marriage between agents of prescribed types in terms of the observed frequency of such marriages within the population, relative to the number of unmarried individuals of the same types. Left open in their work is the issue of existence and uniqueness of equilibrium. We resolve this question in the affirmative, assuming the norm of the gains matrix (viewed as an operator) to be less than two. Our method adapts a strategy called the continuity method,more commonly used to solve elliptic partial differen- tial equations, to the new setting of isolating positive roots of polynomial systems. Finally, the data estimated in [4] falls within the scope of our results.

Keywords: Matching
Gumbel
Choo-Siow
Equilibrium
Uniqueness
Existence
Advisor: McCann, Robert
Engineering Polymers for Organic Photovoltaics

In this thesis, I have produced low polydispersity polymers of poly(chloromethylstyrene) and polyvinylphenol. Modification reactions for both polymers were attempted and were successful for only poly(chloromethylstyrene) as conditions in our experiments produced insoluble polymer salts using polyvinylphenol. A set of modified polymers were produced using a low polydisperse poly(chloromethylstyrene) as we believe that polymers with PDIs < 1.4 will be preferable for use in an eventual solar cell device. Finally a set of experiments were completed to determine the conditions to minimize the PDI of poly(chloromethylstyrene) and found that the main variable was maximizing the amount of 3-chloromethylstyrene with respect to 4-chloromethylstyrene in a polymerization. This result has lead us to believe that 3-chloromethylstyrene is less prone to transfer reactions, which in turn leads to smaller PDI values.

Keywords: Polymer
Engineering
Advisor: Bender, Timothy
Characterization of Active Joint Count Trajectories in Juvenile Idiopathic Arthritis

Aim: To describe the longitudinal active joint count (AJC) trajectories in juvenile idiopathic arthritis (JIA). Methods: A retrospective cohort study at two Canadian centres was performed. The longitudinal trajectories of AJC were described using latent growth curve modeling. The association of baseline characteristics stratified by trajectory group was examined by univariate methods. Results: Data were analyzed for 659 children diagnosed with JIA between 1990/03-2009/09. A maximum of 10 years of follow-up data were included in the analysis. Participants were classified into 5 statistically and clinically distinct AJC trajectories by latent GCM. Conclusions: Using a novel longitudinal statistical method we were able to classify patients with JIA based on their pattern of AJC over time. The trajectory classes need to be examined for their relationship to important genetic and biological predictors. Identification of patterns of disease course is important in working towards the development of a clinically relevant outcome-based classification system in JIA.

Keywords: Group Based Trajectoryc Modeling
Juvenile Idiopathic Arthritis
Advisor: Bombardier, Claire
Identification of Ryanodine Receptor 1 (RyR1) Interacting Protein Partners Using Liquid Chromatography and Mass Spectrometry

Ryanodine receptor 1 (RyR1) is a homotetrameric calcium channel located in the sarcoplasmic reticulum (SR) of skeletal muscle. We employed metal affinity chromatography followed by liquid chromatography mass spectrometry from HEK-293 cells to purify affinity tagged cytosolic RyR1, with interacting proteins. In total, we identified 703 proteins with high confidence (>99%). Of the putative RyR1 interacting proteins, five candidates [calcium homeostasis endoplasmic reticulum protein (CHERP), ER-golgi intermediate compartment 53kDa protein (LMAN1), T-complex protein (TCP), phosphorylase b kinase (PHBK) and four and half LIM domains protein 1 (FHL1)], were selected for interaction studies. Immunofluorescence analysis showed that CHERP co-localizes with RyR1 in the SR of rat soleus muscle. Calcium transient assays in HEK293 cells over-expressing RyR1 with siRNA suppressed CHERP or FHL1, showed reduced calcium release via RyR1. In conclusion, we have identified RyR1 interacting proteins in CHERP and FHL1 which may represent novel regulatory mechanisms involved in excitation-contraction coupling.

Keywords: Ryanodine Receptor 1
Metal affinity chromatography
Mass Spectrometry
Protein-protein interactions
Advisor: Gramolini, Anthony
Seasonal Abundance of Different Chlorella Viruses in Two Contrasting Freshwater Environments in Ontario, Canada

The aims of this study were to identify Chloroviruses in two different Ontario freshwaters and to determine if the seasonal abundance patterns of Chloroviruses in different environments are similar. Gene fragments nearly identical to cultivated Chloroviruses were obtained from Lake Ontario and a nearby pond at the University of Toronto Mississauga (UTM) and novel Chlorovirus gene fragments were obtained from Lake Ontario. Quantification of these two Chlorovirus genes over several seasons revealed the presence of persistent viruses with different seasonal dynamics suggesting that different Chloroviruses replicate by infecting different hosts. Additionally, patterns of seasonal abundance and timings of peak abundances for individual viruses differed between Lake Ontario and the UTM pond, demonstrating the critical role of the environment in Chlorovirus dynamics. The observation of different Chloroviruses with different seasonal dynamics allows speculation that these viruses and their hosts stably coexist in Ontario freshwater environments.

Keywords: Algal viruses
Phycodnaviruses
DNA polymerase
Quantitative PCR
freshwater
Lake Ontario
pond
Chlorella viruses
Chlorovirus
abundance
seasonal dynamics
Chlorophyll a
persistent
Advisor: Short, Steven
The Impact of Climate Change on Late Medieval English Culture

This MA thesis scrutinizes metaphors used by the late medieval English in order to explore the cultural response to climate anomalies of varying severity prefacing the Little Ice Age. The thesis indicates that changes in these cultural expressions marked a transformation in late medieval English writers' conceptions of the natural world and their relationship to it. The central hypothesis is that repeated, long-term unreliable and uncertain weather conditions, and the resulting material insecurities and losses, stimulated a fundamental cultural response which reconfigured the metaphors used for the natural world. Although the representation of nature is inescapably an act of imagination, metaphors and metonymies for nature will be identified in the medieval creative literature, as well as the proto-scientific study of weather, and, in the context of the socioeconomic metabolism model, be brought under the light of conceptual metaphor analysis for elucidation.

Keywords: medieval history
environmental history
cultural history
English history
human ecology
conceptual metaphor theory
nature and culture
cultural evolution
late medieval England
Advisor: Hoffmann, Richard
Navigation and Control Design for the CanX-4/-5 Satellite Formation Flying Mission

CanX-4/-5 is a formation flying technology demonstration mission that shall demonstrate sub-meter formation tracking control. The key to this precision control is carrier phase differential GPS state estimation, which enables centimeter-level relative state estimation. In this thesis, the formation flying controller design is reviewed in detail, and an innovative closed-loop formation reconfiguration strategy is presented. In addition, the designs of both coarse- and fine-mode relative state estimators are presented. Formation flying simulations demonstrate the efficacy of the proposed control and coarse estimation. Furthermore, hardware tests are performed to test the computational efficiency of the control algorithms and to validate the fine-mode relative navigation filter.

Keywords: Satellite Formation Flying
Control
Estimation
Advisor: Damaren, Christopher John
Mass-independent Fractionation of Mercury Isotopes in Freshwater Systems

Mass-independent fractionation (MIF) of Hg isotopes has the potential to track the environmental transport and fate of Hg. Herein we demonstrate that reducing both the frequency and intensity of light have a large effect on the expression and magnitude of MIF. This strongly supports the magnetic isotope effect as the mechanism behind MIF observed during aqueous photo-reduction of Hg(II) and MeHg. The ratios of MIF, KapDelta199Hg/KapDelta201Hg, were 1.00 ± 0.04 (2SE) for Hg(II) and 1.35 ± 0.16 (2SE) for MeHg respectively and did not change as incident radiation energy and magnitude of MIF diminished, suggesting the respective MIF pathways remained constant regardless of experimental conditions. Comparable amounts of total photo-reduction were shown to coincide with different magnitudes of MIF depending the wavelength light available for photo-reduction. This confirms there are multiple pathways for photo-reduction in freshwater reservoirs and indicates that quantitatively relating photo-reduction and MIF will be challenging.

Keywords: mercury isotopes
methylmercury
Advisor: Bridget, Bergquist
The Role of ps20 in Two Respiratory Virus Infections: MHV-1 and Influenza A/WSN/33 H1N1

The objective of this thesis was to examine the role of ps20 in virus infections. We provide evidence that MHV-1 infection resulted in increased lung viral titers in ps20-/- mice. These data highlight an antiviral role for ps20 in MHV-1 infection. We also observed an increase in the percentage of GR1+ neutrophils infiltrating the BAL and in the lung draining lymph node of ps20-/- mice, on day 2 post-infection. In vitro, gene expression analysis identified an increase in expression of CXCL1 and CXCL2 in MHV-1 infected ps20-/- fibroblasts. These data suggest a role for ps20 in regulating neutrophil chemotactic factors, and migration. Next, we examined influenza A/WSN/33, and provide evidence that ps20 functions as a proviral factor. In vivo, ps20-/- mice infected with influenza A/WSN/33 exhibited decreased lung viral titers. These data suggest that ps20 functions as either a proviral or antiviral agent, dependent on the infecting virus.

Keywords: whey acidic protein
ps20
influenza
MHV-1
neutrophil
Advisor: Fish, Eleanor N.
Development and Validation of an Assessment Model for Open Surgical Procedures

In surgical education, two of the current primary assessment tools for technical skills are the OSATS checklist and electromagnetic (EM) hand tracking. There are few bench models available for open procedures. The first two chapters of this thesis introduce these concepts further and provide detailed background knowledge. Chapter 3 explores interference that may from the concurrent use of EM tracking and cautery, finding that monopolar cautery interferes, while bipolar cautery does not. Chapter 4 discusses the validation of an assessment tool for open cholecystectomies (OCs) consisting of a porcine bench model and a Wii remote based infrared (IR) hand tracking system. The assessment tool is found to have construct validity and the face validity of the OC model is established. Chapter 5 concludes the thesis and presents several avenues of future research for the improvement of both the OC model and Wii remote based hand tracking system.

Keywords: Wii remote
3D Tracking
surgical education
open cholecystectomy
surgical assessment
Advisor: Grantcharov, Teodor
The Characterization of Fine Particulate Matter in Toronto Using Single Particle Mass Spectrometry

An Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) was used to obtain mass spectra of individual aerosol particles in the 0.5 – 2 µm size range in downtown Toronto, Canada for one to two month periods during each season of 2007. A modified version of the Adaptive Resonance Theory (ART-2a) clustering algorithm, which clusters particles based on the similarity of their mass spectra, was shown to be more accurate than the existing algorithm and was used to cluster the ambient data. A total of 21 unique particle types were identified and were characterized based on their chemical composition, their size, and their temporal trends and seasonal variations. Potential sources are also discussed. Particles containing trimethylamine (TMA) were also observed and a more detailed investigation of ambient trends in conjunction with a laboratory experiment was performed in order to elucidate conditions for which TMA will be observed in the particle phase in Southern Ontario.

Keywords: atmospheric aerosol
single particle mass spectrometry
particulate matter
amine
particle characterization
source apportionment
cluster analysis
aerosol time-of-flight mass spectrometer
Advisor: Evans, Greg J.
Microgels as Artificial Cells in Modeling the Flow of Neutrophils in the Pulmonary Microcirculation

In this study the role of passive mechanism for deformation of neutrophils, namely the effect of mechanical properties, was studied using microgels as model system. Both alginate-poly(N-isopropylacrylamide) interpenetrating polymer network (IPN) microgels and agarose microgels were synthesized in microfluidic device. The Young’s modulus and relaxation time of the IPN microgels were studied using atomic force microscopy equipped with a tipless cantilever. The lower limits of the elasticity found in this study were within the range of the elasticity reported for neutrophils. Agarose microgels were also prepared with a range of elastic shear modulus similar to neutrophils, and their flow under constrained geometries was studied. The flow profiles of four agarose microgel samples in a microchannel containing a constriction were analyzed. It was found that the stiffness of the microgels affected their velocity before, in and after the constriction.

Keywords: microgels
artificial cells
pulmonary microcirculation
mechanical properties
Advisor: Kumacheva, Eugenia
Methylation of Wnt Antagonist Genes and Wnt5a as Prognostic Markers in Colorectal Cancer

DKK1, SFRP1, WIF-1, and Wnt5a encode Wnt pathway genes that are frequently silenced by promoter hypermethylation in colorectal cancer. Despite attractive biological consequences of these events, it is unclear whether they contribute to patient prognostication or may influence tumour cell biology within distinct patient subsets. I sought to determine the prognostic roles of these methylation events in a large cohort of colorectal carcinomas from Ontario and Newfoundland. Methylation was quantified and associated with patient clinicopathlogical features. Methylation was present in cancer tissue. DKK1, Wnt5a, and SFRP1 were strongly and independently associated with tumour subtype in a manner that suggested subtype-specific activity of Wnt signaling. Methylation of DKK1 was a borderline prognosticator of favourable outcome. These results offer intriguing insight into subtype-specific biology and lead to a proposed model whereby methylation-induced Wnt bias may contribute to patient outcome.

Keywords: Wnt
Colorectal
Prognosis
Methylation
Advisor: Bapat, Bharati
Assessment of the Functional Role of the NTR Domain of Complement Component C3 using a Homologous Dmain Exchange Approach

The complement system plays an important role in innate and adaptive immunity. Central to all complement activities is the function of complement component 3 (C3). C3 contains a C-terminal extension of ~150 residues known as the NTR (or C345C) domain. To address the role of the NTR domain in binding and functional activities of C3, a C3/C5 chimera was engineered, in which the NTR domain of C3 was replaced by the homologous domain of the closely related protein C5. Functionally, the C3(C5NTR) was devoid of classical pathway-dependent hemolytic activity and deficient in factor H- and CR1-dependent factor I cleavability. Direct binding SPR assays, using chip bound methylamine treated His6-tagged C3(C5NTR), showed a complete loss of C5 binding while retaining wild type binding with CR1, factor H and factor B. These results present the first evidence for a major C5 binding site within C3 NTR.

Keywords: Complement
NTR
C345C
C3
C5
Complement Receptor 1
factor H
factor B
Advisor: Isenman, David