VictorJuiz/thesis huggingface dataset:
The Effects of Biotic Interactions on Ambrosia artemisiifolia L.

Plant invasions can ensue when plants are introduced to regions without their specialist enemies (the Enemy Release Hypothesis). This assumes natural enemies limit survival and fecundity in an invader's native range. I tested this assumption for a native invasive species, Common Ragweed (Ambrosia artemisiifolia), by excluding natural enemies from seeds, seedlings and adults. At the adult stage, I added disturbance and conspecific density treatments. Protection from herbivores slightly improved performance at the seedling stage only, while disturbance greatly increased survival and fecundity. Increasing conspecific density reduced performance only in disturbed plots. I also tested herbivore tolerance using simulated damage. Heavy (75%) damage did not reduce fecundity; light damage even increased seed production. These results suggest enemies do not limit Ambrosia in its native range, especially compared to the effects of habitat disturbance. While enemy release may have occurred during Ambrosia’s invasions, it is not likely to be their principal cause.

Keywords: Invasions
Biotic interactions
Life cycle
Ambrosia artemisiifolia
Advisor: Kotanen, Peter M.
Hybrid Waveguide Theory-based Modeling of Indoor Wireless Propagation

The current options for wireless signal prediction in indoor scenarios generally either lack precision or require immense computational resources. Thus, a new method is proposed that attempts to consolidate the desired accuracy with an easy to implement and time efficient scheme. This work identifies and takes advantage of dominant physical qualities of indoor environments to solve indoor channel problems using a hybrid of numerical and analytical approaches. Specifically, the guiding effect of hallway structures is investigated as they allow electromagnetic fields to propagate with relatively low attenuation. Combining waveguide mode analysis and rigorous numerical techniques, the proposed prediction model computes the hallway fields in a large building floorplan both quickly and with good accuracy in comparison to full finite-difference simulations. Signal measurement data will also be used to verify the applicability of the model.

Keywords: indoor channels
wireless prediction
electromagnetics
propagation
Advisor: Sarris, Costas D.
Characterization of Suppressor and Enhancer Mutants of BREVIPEDICELLUS in Arabidopsis thaliana

The brevipedicellus (bp) mutant, caused by a loss-of-function mutation in the KNAT1 homeobox gene, is known to affect the stem morphogenesis. BP and ERECTA (ER) genes are required to promote internode and pedicel development and delineate nodal boundaries to maintain the radial symmetry of stems and pedicels. My research aims to identify genes acting on the BP pathway by utilizing a forward genetics approach. The suppressor4 mutant, identified from the bp er mutant screen, exhibits moderate length and perpendicularly-oriented pedicels with partially formed distal pedicel bulges, absent in the bp mutant. The kinky mutant, identified from the bp mutant screen, develops severe bends at the floral nodes and enhanced achlorophyllous stripes. These results suggest the SUPPRESSOR4 gene contribution in inhibiting the development of distal pedicel bulge and influencing both pedicel angle and length whereas the KINKY gene might act with BP in regulating proper inflorescence development.

Keywords: Arabidopsis thaliana
BREVIPEDICELLUS
plant molecular biology
Advisor: Riggs, C. Daniel
The Efficacy of Trimethoprim in Wound Healing of Patients with Epidermolysis Bullosa: A Randomized, Double Blinded, Placebo Controlled, Cross-over, Pilot Study

Hypothesis: Trimethoprim promotes wound healing, decreases lesion counts and improves quality of life of recessive dystrophic epidermolysis bullosa (RDEB) patients. Objectives: Assess feasibility of conducting a large randomized clinical trial. Determine efficacy of trimethoprim in healing of chronic wounds, decreasing lesion counts and improving quality of life of RDEB patients. Methods: Prospective, randomized, double-blinded, placebo-controlled, cross-over pilot study. Results: Ten patients enrolled in the trial, 7 completed both study periods. Despite showing that all patients improved on trimethoprim and that there was a 41% difference in affected area percent change favoring trimethoprim, the cross-over analysis did not show a significant difference between the drug and placebo (p=0.08). Secondary outcome measures did not achieve statistical significance. Limitations: Small sample size, large variation in wound size and unaccounted confounders. Conclusions: Although patients experienced improvement while on trimethoprim, no statistical significant change was showed when compared to placebo.

Keywords: Dermatology
Paediatrics
Epidermolysis bullosa
Wound healing
Advisor: Parkin, Patricia C
Physicians Practicing in Ontario Long-term Care Homes: Characteristics and Variation in Antipsychotic Prescribing Rates

Antipsychotic use is an important issue in long-term care (LTC) homes due to their widespread use, the potential for serious adverse events and limited evidence about their efficacy in treating behavioural and psychological symptoms of dementia. Rates of antipsychotic use vary across LTC homes, but little is known about the contribution of physicians to this variation. This study documented the characteristics of physicians who regularly treated residents in Ontario LTC homes and examined variation in antipsychotic prescribing across physicians. In a population-based retrospective cohort of LTC residents, 637 (52.8%) of 1,207 LTC physicians cared for 46,365 (90.4%) of all residents. Overall, 27.3% of residents received antipsychotic therapy, but extremely high prescribers prescribed antipsychotics to 42.8% of their patients. Variation in physician antipsychotic prescribing persisted after controlling for clinical and behavioural resident characteristics. This variation was reduced by 47.1% when LTC homes were accounted for in multilevel cross-classification logistic regression models.

Keywords: long-term care
antipsychotic
administrative data
physician characteristics
Advisor: Bronskill, Susan Elizabeth
Population Structure and Genetic Diversity of Lake Sturgeon (Acipenser fulvescens) in Canada: Evaluation of Designatable Units for Conservation

The lake sturgeon (Acipenser fulvescens), is a species with considerable ecological, social and economic value. Unfortunately, over-exploitation and habitat alteration have led to the collapse of lake sturgeon fisheries across North America. Based on conservation concerns, the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) identified eight designatable units (DUs) among Canadian populations of lake sturgeon using the limited information available. These DUs are intended to represent taxonomically, genetically, geographically, or biogeographically distinct units below the species level. In this study, the genetic structuring among 20 lake sturgeon localities was examined using nine microsatellite loci. Lake sturgeon localities conformed to hierarchical partitioning of genetic diversity, with the greatest genetic divergence between localities in the Great Lakes and Hudson Bay drainages. Finally, minimal divergences among the current DUs warrant adjustment of lake sturgeon DU boundaries, to more appropriately reflect the distribution of genetic differentiation among lake sturgeon localities.

Keywords: microsatellite DNA
conservation
lake sturgeon
COSEWIC
Advisor: Lovejoy, Nathan
WIlson, Chris
50,000 Tiny Videos: A Large Dataset for Non-parametric Content-based Retrieval and Recognition

This work extends the tiny image data-mining techniques developed by Torralba et al. to videos. A large dataset of over 50,000 videos was collected from YouTube. This is the largest user-labeled research database of videos available to date. We demonstrate that a large dataset of tiny videos achieves high classification precision in a variety of content-based retrieval and recognition tasks using very simple similarity metrics. Content-based copy detection (CBCD) is evaluated on a standardized dataset, and the results are applied to related video retrieval within tiny videos. We use our similarity metrics to improve text-only video retrieval results. Finally, we apply our large labeled video dataset to various classification tasks. We show that tiny videos are better suited for classifying activities than tiny images. Furthermore, we demonstrate that classification can be improved by combining the tiny images and tiny videos datasets.

Keywords: computer vision
video retrieval
image recognition
Advisor: Aarabi, Parham
Uric Acid as a Growth Factor for Activated B Cells

Cancer vaccines targeted against tumour cells seek to mimic immune responses against viral infections. Given the unique properties of B cells that allow them to present antigens proficiently, activated B cells can be used in a vaccine setting to launch effective anti-tumour T cell responses. Activation induced cell death, however, presents a major hurdle in the generation of large numbers of B cells. Since apoptosis is mediated by oxidative stress, uric acid was used as an antioxidant, enabling increased growth of normal B cells. Further investigation in TK6 cells revealed that uric acid was mediating its effects extracellularly and initiating signaling pathways that culminated in the activation of ERK and JNK proteins and production of IL10, which was necessary, but not sufficient, in mediating the growth effects of uric acid. The results outlined in this study implicate uric acid as a novel growth factor for activated B cells.

Keywords: Immunology
Cell and molecular biology
Advisor: Spaner, David
Learning, Participation and Power: The Community Training Plan at the Toronto Community Housing Corporation

Workplace learning and training is often explicitly or implicitly planned to serve the economic interests of the organization. Furthermore, training planning and processes are generally determined by managers, instead of those who will be engaging in the learning. What happens to learning in the workplace when workers themselves determine its content and methods? As seen in the Community Training Plan (CTP), implemented at the Toronto Community Housing Corporation in 2003, control over workplace training by frontline staff has resulted in profound changes in many facets of working and community life. Using testimonials from a recent participatory evaluation of the CTP as well as a series of promotional videos, all of which were created by participants in the CTP, I demonstrate that the CTP has created new forms of engagement and participation; new learning foci; new spaces in the workplace; and finally a sense of staff ownership over learning.

Keywords: participation
power
informal learning
Toronto Community Housing
workplace learning
community
Advisor: Sawchuk, Peter H.
Understanding Receptor Adaptation And Co-receptor Use For Feline Leukemia Viruses

Feline leukemia viruses (FeLVs) are pathogenic retroviruses of the domestic cat. FeLV transmission and emergence of pathogenic variants show striking similarity to HIV pathogenesis. The emergence of pathogenic subgroup-C FeLV from the transmitted subgroup-A FeLV coincides with a switch in host receptor used for infection as a result of mutations in the viral envelope protein (Env). I have characterized a novel FeLV Env that may represent an evolutionary intermediate between FeLV-A and FeLV-C. I have also reported evidence suggesting that FeLVs may use co-factors/co-receptors for infection. I have found that FeLVs inefficiently infect murine NIH3T3 cells overexpressing FeLV receptors (NIH3T3/Receptor). I have provided evidence that the low infection is caused by a block at a post-binding but pre-entry stage of FeLV infection. Furthermore, fusion of NIH3T3/Receptor cells with highly susceptible cells rescues inhibition to infection suggesting that FeLVs, like HIV, may also use co-receptors for infection.

Keywords: Feline Leukemia Virus
Co-receptor
Evolution
Advisor: Tailor, Chetankumar
Characterization of Friable1-like Homologues in Arabidopsis using Bioinformatics and Reverse Genetics

The FRIABLE1 (FRB1) gene is identified to be a novel glycosyltransferase involved in cell adhesion, based on reverse genetics and immunocytochemistry studies. A total of 31 FRB1 paralogues were found in Arabidopsis thaliana using a bioinformatics approach. The following expression analysis has revealed 6 FRB1 paralogues to be pollen-specific. One pollen-specific FRB1 paralogue, At1g14970, exhibits longer silique lengths when exposed to higher than normal temperature at 28oC in its T-DNA insertional knockout when compared to Columbia wildtype plants. This may be due to the loss of temperature sensing and the continuous stimulated pollen tube cell wall growth or the up-regulation of genes that encode other glycosyltransferases. Thus, the identification of FRB1 paralogues and homologues in both rice and poplar may have tremendous potential to increase their yield in global warming for agricultural and industrial benefits.

Keywords: FRIABLE1
Pectin
Glycosyltransferase
Pollen
Cell adhesion
Advisor: Provart, Nicholas
Measuring Highway Work Zone Throughput

The focus of this project is highway construction zones and the impact of lane closures on traffic. By measuring throughput (the number of vehicles that can flow through a work zone in a given amount of time), analysis was performed to determine the factors that affect this value. Successful data collection uncovered a paradox. Often work zones would see no queuing, indicating the lane could have been closed for longer hours. Alternatively sites with forced flow allowed fewer vehicles through the site than expected, indicating that the design value is too high, requiring shorter lane closure hours. A generic model for throughput was developed as well as a better functioning highway specific model. In addition to these models, this project developed a spreadsheet-based form of analysis named SZUDA (Simplified work Zone User Delay Analysis) that determines queue length and approximate costs associated with road user delay.

Keywords: Work Zone
Throughput
Capacity
Road Construction
Advisor: McCabe, Brenda
Functional Hydration and Conformational Gating in the D-channel of Cytochrome c Oxidase

Cytochrome c oxidase couples the reduction of dioxygen to proton pumping against an electrochemical gradient. The D-channel provides the principal uptake pathway for protons. A water chain is thought to mediate the relay of protons through the D-channel, but it is interrupted at N139 in all crystallographic structures. Here, free energy simulations are used to examine the proton uptake pathway in the wild type and in single-point mutants N139V and N139A, where reduction and pumping is compromised. A general approach for the calculation of water occupancy in protein cavities is presented and demonstrates that combining efficient sampling algorithms with long simulation times is required to achieve statistical convergence of equilibrium properties in the protein interior. The relative population of conformational and hydration states of the D-channel is characterized. Results shed light onto the role of N139 in the mechanism of proton uptake and clarify the physical basis for inactive phenotypes.

Keywords: water-mediated proton transport
free energy simulations
protein hydration
Advisor: Pomès, Régis
The Influence of Age and Sector on the Occupational Therapists Labour Market in Ontario

The purpose of this thesis was to analyze factors related to labour market survival and withdrawal behaviour in the profession of Occupational Therapy in Ontario from 1997 to 2006. To provide a portrait of the OT labour market in Ontario overall, and in relation to sector and age, three types of analysis were used: descriptive statistics (including “stay, switch, and leave” analysis), “Stickiness” and “Inflow” analysis, and survival analysis. The largest proportion of OTs worked in the Hospital sector, which had a great ability to retain OTs according to the “Stickiness” analysis. However, when controlling for other variables using survival analysis, none of the sector variables had a significant effect on survival. The youngest and oldest age groups had the highest propensity of leave, due to mobility, family commitments, and retiring (oldest group only). Overall, the profession in Ontario had a strong ability to retain OTs working in the profession during the study period.

Keywords: Health Care Management
Rehabilitation and Therapy
Labor
Advisor: Deber, Raisa Berlin
Using Repositories for Ontology Design and Semantic Mapping

There are two significant impedances to the realization of the potential of ontologies. First, many ontology designers lack the necessary background in formal logics to express their intuitions clearly and precisely, resulting in the proliferation of ontologies with low expressivity. Concurrently, developing semantic mappings between existing ontologies is difficult, because much of the semantics is external to the representation. This thesis uses the idea of metaphor to develop architectures for ontology repositories to serve as bottom-up reusable resources. Moreover, an ontology design algorithm has been developed that allows designers to communicate their ideas at the semantic level, simply by generating and vetting models. Finally, a semantic mapping algorithm has been developed that uses an ontology repository to determine the similarities and differences between any number of target ontologies. An ontology for partial orders has been elaborated to demonstrate the proof of concept and populate the first iteration of the repository.

Keywords: ontologies
ontology repository
semantic mapping
ontology reuse
ontology design
knowledge engineering
Advisor: Gruninger, Michael John
Soluble Globotriaosylceramide as a Potential Systemic and Local Inhibitor of HIV Infection

Previously we have identified the glycosphingolipid globotriaosylceramide (Gb3/Pk) as an inhibitor and resistance factor against HIV-1 infection in vitro. Here we show that a novel, soluble, completely synthetic Gb3 analogue, FSLGb3, inhibits infection of X4 strains of HIV-1 in the Jurkat T-cell line and both R5 and X4 strains in PBMCs. FSLGb3 absorbs into cellular plasma membranes and membrane adsorbed FSLGb3 was able to inhibit subsequent HIV-1 infection. We have also developed a mouse model to test in vivo the efficacy of soluble Gb3 analogs in the prevention of mucosal viral infection. Soluble Gb3 was incorporated into gel or alone and applied directly to the vaginal and rectal mucosal tissue of mice. We have not yet shown a statistically significant reduction in infection, although a trend towards inhibition is evident. Our studies show synthetic Gb3 to be an inhibitor of HIV-1 infection and further exploration of therapeutic strategies are warranted.

Advisor: Branch, Donald R.
Lingwood, Clifford A.
Role of Simulation in Rehabilitation: The Effectiveness of Model Hands When Learning to Make Othoses

Simulation has not been extensively studied for teaching rehabilitation practitioners technical skills. The purpose of this study is to test the efficacy of an artificial hand as a teaching tool for orthosis-making. Thirty-four participants were randomized into three groups. The first group made five orthoses on a human hand, the second made five orthoses on a model hand, and the third made one orthosis on a human hand. A one-week transfer test consisted of all participants making one orthosis on a human hand. Their performance and orthoses were evaluated using a validated checklist and global rating scale. No differences were found between groups for process-related measures. The model hand group did better on final product measures and had a larger movement time than the other two groups. Practicing on artificial hands is a useful way of learning to make orthoses. Additionally, higher practice volume did not lead to better performance.

Keywords: Simulation
Education
Rehabilitation
Orthoses
Motor learning
Advisor: Carnahan, Heather
An 8-bit, 12.5GS/s Folding-interpolating Analog-to-digital Converter

The motivation behind this work is to target the demand for high-speed medium-resolution ADCs for satellite communication systems. An 8-bit, 12.5GS/s folding-interpolating ADC was designed in 0.25µm, 190GHz SiGe BiCMOS technology from IHP. The ADC consists of a THA, a reference resistor ladder, folding amplifiers, an interpolating resistor string, a comparator array, a digital encoder, a coarse quantizer and a bit synchronizer. Post-layout simulation results of the ADC verify that its performance meets all the required specifications. By comparison to other high-speed ADCs, implemented in SiGe technologies, the present design features the highest sampling rate for 8-bit resolution ADCs to date with a good FOM (12.9pJ/conversion). The THA and the comparator were implemented experimentally and characterized to verify their performance and to ascertain the possibility of implementing the complete ADC. The experimental results meet the expected specifications and indicate that both circuits are suitable for the implementation of the ADC.

Keywords: An 8-bit, 12.5GS/s Folding-Interpolating Analog-to-Digital Converter
high speed ADC
shoreh ghetmiri
Shohreh Ghetmiri
C.A.T Salama
Folding interpolating ADC
8 bit SiGe ADC
IHP ADC
Advisor: Salama, C. A. T.
The Effect of Speaking Rate on Velopharyngeal Function in Healthy Speakers

This study investigated the effect of speaking rate on aerodynamic and acoustic measures of velopharyngeal (VP) function in 27 adult speakers (14 M, 13 F). The pressure-flow method (Warren & Dubois, 1964) was used to collect aerodynamic data of /m/ and /p/ segments in the word “hamper” and the utterances “Mama made some lemon jam” (MMJ) and “Buy Bobby a puppy” (BBP). A Nasometer was used to collect nasalance scores and nasalance distance for MMJ and BBP. Measures were collected under 4 speaking rate conditions (normal, fast, slow, and slowest). Results indicated that nasal airflow and VP orifice area were unaffected by speaking rate whereas intraoral pressure decreased as speaking rate slowed. Nasalance was greater for BBP at slow speaking rates and nasalance distance (MMJ – BBP) decreased at slow rates. The data was interpreted with respect to expectations set forward in the literature on normal and disordered speech motor control.

Keywords: speaking rate
velopharynx
velum
velopharyngeal function
soft palate
VP
Advisor: Yunusova, Yana
Comparisons between MATSim and EMME/2 on the Greater Toronto and Hamilton Area Network

The agent-based micro-simulation modelling technique for transportation planning is rapidly developing and is being applied to practice in recent years. In contrast to conventional four-step modelling with static assignment theory, this emerging technique employs a dynamic assignment principle. Based on summary of various types of traffic assignment models and algorithms, the thesis elucidates in detail the theories of two models, MATSim and EMME/2, which represent two genres of traffic assignment, i.e., dynamic stochastic stationary state assignment and static deterministic user equilibrium assignment. In the study, the two models are compared and validated to reflect both spatial and temporal variation of the traffic flow pattern. The comparison results indicate that numerical outputs produced by MATSim are not only compatible to those by EMME/2 but more realistic from a temporal point of view. Therefore, agent-based micro-simulation models reflect a promising direction of next generation of transportation planning models.

Keywords: agent-based micro-simulation modelling
MATSim
EMME
traffic assignment
Advisor: Miller, Eric