VictorJuiz/thesis huggingface dataset:
The Influence of Dietary Factors on Reproduction in the Fruit Fly, Drosophila melanogaster

Food and nutrition are important for energy balance, reproduction and maintenance of health in all species. Drosophila melanogaster feed on yeast and sugar and food availability affects reproduction. In this thesis, I show that mating frequency and fertility are affected by the composition of food in two D. melanogaster wild-type strains, Canton-S and Oregon-R. Canton-S flies mate multiple times in the presence of yeast and sugar, while Oregon-R only remate in the presence of yeast. However, Oregon-R flies have higher fertility counts on all food types compared to Canton-S. These effects of food do not appear to depend on smell or taste, because both chemosensory mutants and artificial sweeteners tested fail to block the effects of food on reproduction. Moreover, Canton-S, but not Oregon-R flies show an interaction between food and group size. I conclude that genetic differences, social context and nutrition interact to regulate reproduction in flies.

Keywords: drosophila melanogaster
behaviour
food
reproduction
Advisor: Levine, Joel
Analysis of Sequence and Function of Drosophila Microvillus Cadherins, Cad74A, Cad87A, and Cad88C

Microvilli are actin-based protrusions at the apical surface of epithelial cells and have diverse functions. My bioinformatic analysis suggests that human Cadherin 23, which is critical for normal microvillus development, has three paralogous homologues in Drosophila, Cad74A, Cad87A, and Cad88C. All three fly cadherins are present in follicle cell microvilli in late stages of oogenesis. The combined loss of Cad74A, Cad87A, and Cad88C did not produce any obvious defects in follicle cell microvilli or egg morphology. However, in a Cad74A Cad88C double mutant, Cad87A is strongly reduced at the apical surface of follicle cells. Furthermore, females overexpressing Cad74A produced abnormal eggs. This phenotype was rescued by increasing or reducing Cad87A expression. Together, my data suggest genetic interactions between the three cadherins, and that Cad74A and Cad87A may be involved in eggshell formation.

Keywords: Drosophila
Microvillus
Cadherins
Oogenesis
Advisor: Godt, Dorothea
Accurate and Efficient Evaluation of the Second Virial Coefficient Using Practical Intermolecular Potentials for Gases

The virial equation of state p = ρRT[ 1 + B(T) ρ + C(T) ρ2 + · · ·] for high pressure and density gases is used for computing chemical equilibrium properties and mixture compositions of strong shock and detonation waves. The second and third temperature-dependent virial coefficients B(T) and C(T) are included in tabular form in computer codes, and they are evaluated by polynomial interpolation. A very accurate numerical integration method is presented for computing B(T) and its derivatives for tables, and a sophisticated method is introduced for interpolating B(T) more accurately and efficiently than previously possible. Tabulated B(T) values are non-uniformly distributed using an adaptive grid, to minimize the size and storage of the tables and to control the maximum relative error of interpolated values. The methods introduced for evaluating B(T) apply equally well to the intermolecular potentials of Lennard-Jones in 1924, Buckingham and Corner in 1947, and Rice and Hirschfelder in 1954.

Keywords: Second Virial Coefficient
Intermolecular Potential Energy Models
Polynomial Interpolation
Quantum Correction
Advisor: Gottlieb, James J.
Reducing Pain in Four- to Six-month Old Infants Undergoing Immunization using a Multi-modal Approach

Background: Infant immunization pain is not currently well managed despite effective strategies. Objective: To determine the effectiveness of tactile stimulation when added to a combination of pain-reducing interventions in infants undergoing immunization. Methods: Healthy infants aged 4-6 months undergoing immunization in primary care were randomized to tactile stimulation or usual care. All infants also received pain-relieving interventions. A validated measure of acute pain in infants, the Modified Behavioral Pain Scale (MBPS), was the primary outcome. Results: Altogether, 120 infants participated. Characteristics did not differ (p > 0.05) between those allocated to tactile stimulation and usual care groups. Mean MBPS pain scores did not differ between groups: 8.2 (1.1) vs. 8.0 (1.3); p = 0.57, respectively. Conclusions: Parent-led tactile stimulation did not improve pain relief in infants when added to other interventions. Parental attention could have been focused on tactile stimulation, preventing parents from performing appropriate soothing activities. Additional investigation of the effectiveness of clinician-led tactile stimulation is recommended.

Keywords: pain
infants
immunization
vaccine
procedural pain
tactile stimulation
sucrose
distraction
randomized controlled trial
blinded
injection pain
immunization pain
Advisor: Taddio, Anna
Riddell, Rebecca Pillai
Katz, Joel
Becoming a Muslim Woman: Conversations on Conversions

This thesis deals with the conversion stories of five female converts to Islam; considering the expectations my interlocutors have faced, the pressures to tell a certain type of narrative, the formation of their practice and the stories they choose to narrate. The concept of an ‘epiphany’ narrative, a story of inspiration and divine intervention, will be discussed and placed into tension with ‘rupture’ narratives; the stories my interlocutors tell in order to ‘make sense’ of their conversions.

Keywords: conversion
Muslim
Advisor: Mittermaier, Amira
O'Neill, Kevin
Climate-induced Tree Migration in Southern Ontario: Pathways and Source Populations

Under the current rapid climate change, trees are of critical interest because of diverse ecosystem services that they provide. Although increasing landscape connectivity is though to be crucial in order to maximize their migration capabilities, there are few studies indicating where exactly such increases might best take place. To understand the impact of fragmentation on species climate-change induced migrations and source populations, I calculated migration pathways and source populations under six climate change scenarios in southern Ontario where >70% of forest has been lost through human-use. The results showed that although forest fragmentation increased species required migration rates, the most important migration corridors and source populations were quite similar across all migration models and were concentrated in exiting forest corridors and extensively forested areas, including northeast of Lake Ontario, the Niagara Escarpment, and the Oak Ridges Moraine.

Keywords: Climate change
Tree migration
GIS
Advisor: Malcolm, Jay R.
Fabrication of Photonic Crystal Optofluidic Devices for Electrochromatography and Spectroscopy on a Chip

Femtosecond laser processes were optimized for nonlinear interactions with optical materials to develop a novel biophotonic lab-on-a-chip device that integrates laser-formed waveguides, microfluidic channels and photonic crystals (PCs). Such integration seeks the novel demonstration of dual PC functionalities: (1) efficient chromatographic separation and filtration of analytes through a porous PC embedded inside a microfluidic channel and (2) optofluidic spectroscopy through embedded waveguides that probe PC stop band shifts as varying analyte concentrations flow and separate. The building blocks for such integration were demonstrated through the accelerated analyte flow rates measured through the embedded porous PC and the optical characterization of a PC’s stop band via integrated waveguides. Together, these laboratory results give promise for achieving simultaneous chromatographic and spectroscopic capabilities in a single PC optofluidic device. Future improvements in the laser process and possible new research directions are also offered.

Keywords: Microfluidics
Photonic Crystals
Laser Processing
Advisor: Herman, Peter R.
Implementation of Electronic Medical Records and Preventive Services: A Mixed Methods Study

The implementation of Electronic Medical Records (EMRs) may lead to improved quality of primary health care. To investigate this, we conducted a mixed methods study of eighteen Toronto family physicians who implemented EMRs in 2006 and nine comparison family physicians who continued to use paper records. We used a controlled before-after design and two focus groups. We examined five preventive services with Pay for Performance incentives: Pap smears, screening mammograms, fecal occult blood testing, influenza vaccinations and childhood vaccinations. There was no difference between the two groups: after adjustment, combined preventive services for the EMR group increased by 0.7% less than for the non-EMR group (p=0.55, 95% CI -2.8, 3.9). Physicians felt that EMR implementation was challenging.

Keywords: Electronic health records
Preventive health services
Quality of health care
Primary health care
Advisor: Barnsley, Janet
A Detailed Genomic and Transcriptomic Analysis of Paediatric Undifferentiate Sarcomas

Paediatric undifferentiated soft tissue sarcomas (USTSs) are a diagnostically challenging group of neoplasms. We hypothesized that USTSs contain distinct subgroups that can be identified based on their morphology, genomic aberrations and expression profiles. We sought to characterize genomic aberrations within primitive round cell (PRC) sarcomas which may underlie aberrant expression patterns. Using molecular and cytogenetic analyses, we identified 5 of 18 CIC-DUX4-positive PRC sarcomas. The consistent involvement of the CIC-DUX4 fusion in a subset of PRC sarcomas suggests a central role for the fusion transcript in such tumours. These analyses also identified a cohort of CIC-DUX4-negative USTSs with no established genetic markers. We performed integrative copy number and expression profiling, and identified significant genomic and transcriptomic changes. We propose that these genes are involved in biological pathways that are important to the initiation and progression of undifferentiated sarcoma, and may provide novel insights into the biological events responsible for sarcomagenesis.

Keywords: Sarcoma
Molecular Biology
Advisor: Somers, Gino
Zielenska, Maria
Modeling of an Underground Mine Backfill Barricade

In this thesis finite element analyses were performed to investigate the behavior of fill fences installed in underground mines to retain Cemented Paste Backfill (CPB) pressure. For this purpose, two fill fences installed and tested in the Cayeli mine in Turkey were modeled using a 2-D nonlinear finite element analysis program, Augustus-2, and a 3-D nonlinear finite element analysis program VecTor4, and the results were compared with measured field data. Different models were employed representing the material properties, boundary conditions, reinforcement ratio, and geometric properties, and it was found that boundary conditions (stiffness of surrounding rocks) has the highest influence on the pressure capacity of the fence among the other factors. The accuracy of the Augustus-2 program was investigated by modeling and comparing the analytical response with test results of 12 axially restrained beams tested by Su et al. (2009).

Keywords: Underground fill fence
backfill
Augustus-2
VecTor4
Advisor: Grabinsky, Murray
Evan, Bentz
Oxidation of Organic Species in Ice

Oxidation of organic species, in particular dicarboxylic and humic acids, was investigated in ice. Products were analyzed by Proton Transfer Reaction Mass Spectrometry, ion and gas chromatography, and a Total Organic Carbon analyzer. Photolysis of succinic acid with H2O2, an OH precursor, produced malonic acid and malic acid, illustrating that diacids are subject to photochemical degradation in ice. First-order decay rate constants were an order of magnitude higher at room temperature (~23 °C) than in ice (-20 °C). A smaller difference was observed for malonic acid, a more soluble diacid, suggesting that partial segregation of H2O2 and succinic acid during freezing played an important role in the kinetics. VOCs, likely to be aldehydes and ketones, were produced from ice containing humic acid through heterogeneous ozonolysis and photooxidation which was enhanced by NO3-, an OH precursor. VOCs also formed from ice made from deionized water, likely through oxidation of organic contaminants.

Keywords: ice chemisty
dicarboxylic acids
humic acids
snow photochemistry
OH radical
Arctic chemistry
photochemistry
organic films
Advisor: Abbatt, Jonathan P. D.
111In-labeled Nimotuzumab Modified with Nuclear Localization Sequences (NLS): An Auger Electron-emitting Radiotherapeutic Agent for EGFR-overexpressing and Trastuzumab-resistant Breast Cancer

Objective: The cytotoxic property of anti-EGFR-1 monoclonal-antibody nimotuzumab modified with nuclear localization sequence and radiolabeled with 111In was evaluated in trastuzumab-resistant breast cancer cells. Methods: 111In-nimotuzumab-NLS was constructed and its immunoreactivity was determined. Cellular and nuclear uptake was evaluated by cell fractionation. Finally, the cytotoxicity of conjugates (111In-nimotuzumab/111In-nimotuzumab-NLS) was studied by clonogenic assays. Results: The immunoreactivity of 111In-nimotuzumab-NLS was conserved. 111In-nimotuzumab-NLS exhibited 2-fold higher nuclear translocation as compared to 111In-nimotuzumab in MDA-MB-468 cells. Nuclear importation of 111In-nimotuzumab-NLS in MDA-MB-468 cells was 4-fold and 6-fold higher than moderate and low EGFR expressing cell lines, respectively. Clonogenic survival (CS) for MDA-MB-468 cells showed 111In-nimotuzumab-NLS to be 10-folds and 60-folds more potent than 111In-nimotuzumab and nimotuzumab, respectively. Moderate killing for TrR1 and MDA-MB-231 was observed. 111In-hEGF showed significantly higher cytotoxicity and 2-fold higher γ-H2AX foci integrated density/nuclear-area as compared to 111In-nimotuzumab-NLS. Preserved selectivity of 111In-nimotuzumab-NLS makes it an excellent drug for treating cancers.

Keywords: Herceptin resistant breast cancer
Auger eletron radiotherapy
Nimotuzumab (mAb of EGFR)
Indium-111
Advisor: Reilly, Raymond Matthew
Neuroanatomical Correlates of Depressive Symptoms Following Acute Ischemic Stroke

This study investigated the hypothesis that severity of depressive symptoms following acute ischemic stroke is associated with degree of tissue infarction and severity of white matter changes (WMCs). It employed a novel quantitative region-based approach considering both infarction and WMCs. Of 54 ischemic stroke patients recruited, 50 (72.3 ± 12.8 years, 52.0% male) had useable CT scans. The typical patient was recruited within 3 weeks of their stroke (19.7 ± 31.0 days), exhibited minor cognitive impairment (MMSE score 25.8 ± 4.6), and had mild to moderate stroke severity (NIHSS score 6.5 ± 5.4). 28.0% of patients screened positive for clinical depression with a CES-D score ≥16. While neither degree of infarction nor severity of WMCs (ARWMC score) in the 12 brain regions correlated with depressive symptoms (CES-D score), stroke severity was a significant predictor of depressive symptoms. This stressor, related to physical disability, was a predominant predictor over lesion characteristics.

Keywords: stroke
depression
neuroimaging
CT
Advisor: Lanctôt, Krista
Attitude Determination and Control Hardware Development for Small Satellites

The development of a small spacecraft attitude determination and control subsystem is described. This subsystem is part of The Space Flight Laboratory's Generic Nanosatellite Bus. With a 20cm3 body, the bus has an attitude determination and control subsystem capable of full three-axis stabilization and control enabling more advanced missions previously only possible with bulkier and more power-consuming attitude control hardware. Specific contributions to the Space Flight Lab's attitude control hardware are emphasised. Particularly, the full development of a 32g three-axis nanosatellite rate sensing unit is described. This includes embedded software development, skew calibration, hardware modeling and qualification testing for the unit. Development work on a three-axis boom-mounted magnetometer is also detailed. A full hardware design is also described for a new microsatellite-sized rate sensor. Larger and more powerful than the nanosatellite rate sensors, the design ensures a low noise, low drift architecture to improve attitude determination on future microsatellite missions.

Keywords: Attitude Determination and Control Hardware Development for Small Satellites
Advisor: Zee, Robert E.
A Phenomic Assessment of Yeast DNA Damage Foci using Synthetic Genetic Array Analysis and High-content Screening

Aberrant DNA synthesis and maintenance have been implicated in numerous human diseases. I describe here a novel strategy for systematically identifying budding yeast mutants with elevated levels of DNA damage foci, which represent hubs of DNA damage and repair. A previous study manually scored foci in single mutants but was limited in its ability to survey many conditions in large populations. I developed an automated and statistically robust method for identifying aberrant foci phenotypes by combining synthetic genetic array (SGA) and high-content screening (HCS) methodology. Using this approach, I scored thousands of essential and non-essential gene mutants subjected to environmental and genetic perturbations, including the DNA damaging agent, phleomycin, and deletions of DNA repair genes, SGS1 and YKU80. Collectively, I identified a functionally enriched set of 367 mutants that had increased frequencies of DNA damage foci and established SGA-HCS as a powerful tool for investigating the yeast DNA damage response.

Keywords: Budding yeast
Genomics
Synthetic genetic array analysis
High-content screening
DNA damage foci
DNA repair
Rad52
Advisor: Andrews, Brenda
Boone, Charles
On the Use of Double Auctions in Resource Allocation Problems in Large-scale Distributed Systems

In this thesis, we explore the use of double auction markets as a general approach to tackle resource allocation problems in large-scale distributed systems, which are traditionally solved using optimization techniques. Prevalently adopted in real-world markets, double auctions have the power of arbitrating mappings between participating players and trading commodities in a decentralized fashion, with every player trying to maximize her own utility selfishly. Through the design of prefetching strategies in peer-assisted video-on-demand systems, we show how the problem of minimizing server bandwidth costs by reallocating media contents can be solved by double auction markets gracefully. However, not every resource allocation problem satisfies requirements of double auctions. We illustrate the limitation of double auctions with an example of virtual machine migration in container-based datacenters, which is then modeled into a Nash bargaining game and solved by a Nash bargaining solution.

Keywords: double auction
resource allocation
large-scale distributed systems
Advisor: Li, Baochun
Physical Activity Participation in Children with Autism Spectrum Disorders: An Exploratory Study

Introduction: Little is known about the physical activity [PA] habits of children with Autism Spectrum Disorders [ASD]. ASD specific PA barriers and facilitators have not been investigated. Purpose: To describe the PA habits of children with ASD and the barriers and facilitators to optimal PA participation. Methods: Twenty-three parents of children with ASD reported on their child’s PA habits, perceived barriers to PA participation, and functioning. A rating scale was applied to score responses and children were classified into functional level groups and PA level groups. Results: On average, children were reported to meet or exceeded national PA frequency guidelines, belonged to active families and participated in a variety of physical activities. Parents identified several barriers to optimal PA for their children. Conclusions: Children with ASD can attain optimal PA. Exposure to a variety of PA opportunities and experiences aids in identifying the ideal activity for each individual child.

Keywords: Autism Spectrum Disorders
Physical Activity
Barriers
Advisor: Berg, Katherine
Using Tele-rehabilitation to Address Executive Dysfunction and to Promote Community Integration after Traumatic Brain Injury: A Pilot Study

Executive dysfunction can affect community integration in adults with traumatic brain injury (TBI). The Cognitive Orientation to daily Occupational Performance (CO-OP) approach has shown some promise in promoting functional improvements in adults with executive dysfunctions post TBI. However, access to rehabilitation is often limited especially in rural communities. This study aimed to (1) investigate the feasibility of administering the CO-OP approach in a tele-rehabilitation format and (2) examine its impact on community integration and executive dysfunction. A pilot series of 3 case studies was conducted. Participants identified 5 goals; 3 were trained and 2 were untrained to allow examination of transfer. Outcome measures included the Canadian Occupational Performance Measure, the Mayo-Portland Adaptability Inventory-4 Participation Index, and the Dysexecutive Questionnaire. Descriptive analyses demonstrated goal achievement and transfer, suggesting it is feasible to implement the CO-OP approach in a tele-rehabilitation format. Community integration and executive dysfunction behaviours also showed trends towards improvement.

Keywords: brain injury
executive function
tele-rehabilitation
community integration
Advisor: Dawson, Deirdre R.
Infertility and Women’s Age

In the first part of study, our objective was to determine the effect of CoQ10 supplementation of culture media on preimplantation mouse and human embryo development. CoQ10 supplementation of culture media did not improve mouse or human embryo development in vitro. Since the results appeared to be negative, we decided to move on to research the effect of age on female infertility. In the second part, we investigated the effect of female age and ovarian stimulation protocols on IUI outcome in 411 infertile women. We found that the ongoing/live birth rate per cycle in women ≤ 37 years was significantly higher than in older patients. In the third section, we determined if very young age (≤25 yrs) has an impact on pregnancy outcome in women undergoing IVF-ET. Our results demonstrating lower pregnancy rates in very young patients and egg donors compared to the patients in their early thirties were surprising.

Keywords: Infertility
age
Advisor: Casper, Robert
Elevated Intracellular Ca2+ Alters Mitochondrial Protein Import and the Accumulation of Intramitochondrial Proteins in Neurons

Most (99%) mitochondrial proteins are nuclear-encoded and must be imported into mitochondria. Deficits in mitochondrial protein import (MPI) affect mitochondrial function and can cause neurodegenerative diseases. I hypothesized that MPI was regulated by iCa2+. In differentiated PC12 cells, treatment with the Ca2+ ionophore (A23187; 24h, 0.15uM) increased iCa2+, ROS generation and promoted neurite outgrowth. Western blot and flow cytometry in live cells showed that A23187 increased levels of mitochondrial proteins; mtHSP70 and mtGFP in mitochondria and autoradiography confirmed that A23187 increased the import of mtGFP. A23187 also slowed intramitochondrial mtGFP degradation. Increased MPI was not associated with mitochondrial biogenesis, but appeared partially dependent on cAMP. In rat cortical neurons, mtHSP70 also increased after A23187 treatment. These results show that, in neurons, increased iCa2+ can regulate MPI. Further, increased iCa2+ can slow intramitochondrial protein degradation. These results indicate that MPI is labile and may be altered in response to neuronal activity.

Keywords: mitochondria
calcium
neuron
calcium
ionophore
calcium
A23187
degradation
Advisor: Mills, Linda