VictorJuiz/thesis huggingface dataset:
Responses of Astrocytes Exposed to Elevated Hydrostatic Pressure and Hypoxia
Keywords: Astrocyte
Hypoxia
Elevated Hydrostatic Pressure
Migration
Optic Nerve Head

Several research groups have applied elevated hydrostatic pressure to ONH astrocytes cultured on a rigid substrate as an in vitro model for glaucoma. These studies have shown significant biological effects and this hydrostatic pressure model is now becoming generally accepted in the ophthalmic community. However, since the applied pressures were modest the finding of significant biological effects due to pressure alone is surprising. We hypothesized that the application of hydrostatic pressure as described in these studies also altered gas tensions in the culture media. Our goal was to design equipment and carry out experiments to separate the biologic effects of pressure from those of hypoxia on cultured astrocytes. We designed equipment and carried out experiments to subject cultures of DITNC1 astrocytes to the four combinations of two levels of each parameter. We explored the morphology and migration rates of astrocytes, but observed no significant change in any of these properties.
Mental Workload Measurement Using the Intersaccadic Interval
Keywords: mental workload
saccade
mental effort
eye movements

Mental workload is commonly defined as the proportion of a person's total mental capacity in use at a given moment. A measure of mental workload would have utility in a number of rehabilitation medicine applications, but no method has been adequately examined for these purposes. A candidate measure is the intersaccadic interval (ISI), which is the duration between two successive saccades. Previous studies indicate that ISI length may be linked to mental workload, but this link is poorly understood for tasks that are not primarily visual. Therefore, the current study was an investigation of ISI and workload intensity in three non-visual tasks: mental arithmetic, verbal fluency, and audio perception. Workload was manipulated through changes in task difficulty as well as study participant motivation level. An analysis of eye movements and other experimental workload measures indicated a significant association between audio perceptual workload and ISI length.
Effects of Genistein Following Fractionated Lung Irradiation in Mice
Keywords: genistein
mouse lung
pneumonitis
fibrosis

Radiation therapy for lung cancer and cancers of the upper thorax is limited by side effects to normal tissue of the lung. An understanding of mechanisms leading to radiation induced lung damage is essential to developing protective agents. In this thesis an anti-oxidant and anti-inflammatory agent Genistein was investigated for its potential to affect DNA damage, tissue inflammation, functional deficits and survival. We hypothesized that chronic oxidative stress and the subsequent inflammatory response play a key role in the development of major lung complications, radiation pneumonitis and fibrosis. If side effects of radiation could be reduced, then larger doses could be delivered to the tumor with a better chance of eradicating the disease.
An Investigation of Ethylene Laminar Diffusion Flames at Sub-atmospheric Pressures to Simulate Microgravity
Keywords: Microgravity
Combustion

Ethylene/Air diffusion flames were studied at sub and super-atmospheric pressures to simulate a microgravity environment at fuel flow rates of 0.482 mg/s and 1.16 mg/s. Flame properties including flame dimensions, soot formation, temperature, and attachment mechanisms were investigated. Overall, luminous flame height decreased with decreasing pressure to the point of visible luminosity disappearance, resulting in blue flames. Flame width increased with decreasing pressure until the flame was almost spherical. Soot formation decreased with decreasing pressure to negligible concentrations in a near vacuum. At 0.482 mg/s, the percentage of carbon converted into soot was between 0.01% and 0.12%, whereas at 1.16 mg/s, this percentage was between 0.5% and 11% at sub-atmospheric pressures. Maximum flame temperatures increased with decreasing pressure. Regardless of fuel flow rate, the diffusion flames remained attached to the exterior of the burner. This attachment point moved further down the burner exterior as pressure decreased until a near vacuum.
ICAM-1 as a Novel Binding Partner for LPS to Mediate TLR4-Independent Cell Activation
Keywords: Lipopolysaccharide
ICAM-1
TLR4-Independent

Introduction: The mechanism of cell activation by LPS in the absence of surface Toll-like receptor 4 (TLR4) is unclear. We hypothesize that ICAM-1 binds LPS on the cell surface, mediating cell activation independent of TLR4. Methods: The interaction between murine ICAM-1 and LPS was measured in a binding assay. Alveolar macrophages (AMs) isolated from TLR4 deficient mice were stimulated with LPS. Cell activation was measured by flow cytometry and cytokine production. The role of ICAM-1 in cell activation was determined by siRNA transfection. Results: Murine ICAM-1 binds LPS. TLR4 deficient AMs respond to LPS stimulation by upregulation of LPS binding sites, ICAM-1 expression and cytokine release. Cell activation is attenuated by treatment with polymyxin B and ICAM-1 gene silencing. Conclusions: ICAM-1 binds LPS and is important in TLR4-independent cell activation. Strategies devised to target ICAM-1 may have the potential to block the excessive inflammatory response seen in gram-negative sepsis.
A Cost-effectiveness Analysis of Capecitabine and Folfox for the Adjuvant Treatement of Stage III Colon Cancer: Which is the More Cost-Effective Option in Ontario?
Keywords: economic evaluation

Background: There are a number of treatment options for colon cancer. These regimens have different toxicity profiles and the age of the patient may affect outcomes of care and cost-effectiveness. An economic evaluation was conducted to explore treatment options for stage III colon cancer. Methods: A Markov model was developed to compare the cost-effectiveness of capecitabine with oxaliplatin combined with fluorouracil/leucovorin (FOLFOX) for the adjuvant treatment of stage III colon cancer. Results: At age 70, FOLFOX was the preferred option, costing $25,314 per quality-adjusted life-year gained. However, the difference in effect between the regimens ranged by 6 months and the model was sensitive to a number of variables. At age 80, capecitabine became the preferred option. Conclusion: FOLFOX is the most cost-effective treatment option in Ontario, but above age 80, capecitabine becomes the favoured option. Uncertainty remains in determining the most cost-effective treatment option for stage III colon cancer.
Genomic and Transcriptome Profiling of Serous Epithelial Ovarian Cancer
Keywords: ovarian cancer
copy number variation

Epithelial ovarian cancer is the leading cause of death by gynaecological malignancy. Elucidation of the driver genes of ovarian cancer will lead to treatment targets and tailored therapy for this disease. The Affymetrix Genome-Wide SNP Array 6.0 was used to study 100 serous ovarian samples and 10 normal ovarian samples to identify loci and driver genes. The ovarian cancer genome was found to have high overall genomic instability across all chromosomes and key known genes in this disease were identified in the dataset. Aberrant regions of copy number gain were located in “blocks” of constant copy number at 1p, 1q, 8q, 12p, 19q and 20q. The range in copy number for gains was 4.2 to 5.1. The “blocks” of genes were located at 8p and 5p for copy number losses. The range for copy number loss was 0.6 to 0.9.
Hyper-methylation of the SOCS2 Promoter in AML: An Unexpected Association with the FLT3-ITD Mutation
Keywords: Leukemia
Methylation

Haematopoiesis requires strict regulation in order to maintain a balanced production of the various blood cell components. Escape from this regulation contributes to the development of cancers such as leukemia. SOCS2 is a member of the Suppressor of cytokine signalling (SOCS) family, and normally functions as a negative regulator of the JAK/STAT pathway. I examined gene expression and promoter methylation in acute myeloid leukemia (AML) cell lines and patient samples. SOCS2 expression was quite variable in AML patients, and very low in acute promyelocytic leukemia (APL) patients. Promoter hyper-methylation was found in these patients, particularly those with high white blood cell count and a FLT3-ITD. I speculate that SOCS2 interacts with an aspect of the signalling complex to inhibit cell growth in these patients, and silencing SOCS2 is necessary for leukemia progression. Treating these patients with a de-methylating agent, such as decitabine, may show promise in the clinic.
Integrating Transit Pass Ownership into Mode Choice Modelling
Keywords: Logit Model
Transit Pass
Mode Choice

The relationship between monthly transit pass ownership and home-work trip mode choice in the Greater Toronto Area was explored using a logit formulation. A Nested Logit model was specified with the primary mode (non-motorised, auto, transit, or auto access to transit) in the upper level and the pass ownership in the lower transit nests. Inclusive value parameters confirm the chosen structure, and a range of policy sensitive, statistically significant parameters having expected signs and magnitudes reveal differences between socio-economic characteristics of pass holders and non-pass holders. In particular, pass holders are less likely to possess a driver’s license or automobile than non-pass holders, implying that passes can be thought of as complementary mobility tools. Cost parameters, which include differentiated pricing for pass and non-pass holders, result in plausible in-vehicle values of time of approximately $31/hour, $33/hour and $8/hour for auto, auto access to transit, and transit all way, respectively.
Role of Distal Airway Epithelial Glucocorticoid-Glucocorticoid Receptor Signalling in Mouse Lung in Late Gestation
Keywords: Lung
Development
Glucocorticoid Receptor

Glucocorticoid (GC) signalling via the GC receptor (GR) regulates many aspects of lung development. To determine the need for epithelial GC-GR signalling, triple transgenic (TT) mice with doxycycline (dox) – inducible suppression of GR exclusively in the distal lung epithelium (DLE) were created. Following exposure to dox, E18.5 TT fetuses showed a reduction in GR mRNA levels and elimination of GR protein expression exclusively in the DLE. Newborn TT pups had decreased viability and TT fetal lungs had increased tissue to airspace ratios, decreased levels of proximal epithelial protein CC10, of all surfactant proteins (ATII cell proteins), of ion conductance channels β and γENaC, of water channel AQP5, and of ATI cell protein T1α. Thus DLE GC-GR signalling is important for neonatal viability and increased mortality of TT pups could be due to impaired epithelial differentiation, leading to decreased surfactant protein expression, delayed fluid clearance and/or increased lung cellularity.
The Effects of Biotic Interactions on Ambrosia artemisiifolia L.
Keywords: Invasions
Biotic interactions
Life cycle
Ambrosia artemisiifolia

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.
Hybrid Waveguide Theory-based Modeling of Indoor Wireless Propagation
Keywords: indoor channels
wireless prediction
electromagnetics
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.
Characterization of Suppressor and Enhancer Mutants of BREVIPEDICELLUS in Arabidopsis thaliana
Keywords: Arabidopsis thaliana
BREVIPEDICELLUS
plant molecular biology

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.
The Efficacy of Trimethoprim in Wound Healing of Patients with Epidermolysis Bullosa: A Randomized, Double Blinded, Placebo Controlled, Cross-over, Pilot Study
Keywords: Dermatology
Paediatrics
Epidermolysis bullosa
Wound healing

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.
Physicians Practicing in Ontario Long-term Care Homes: Characteristics and Variation in Antipsychotic Prescribing Rates
Keywords: long-term care
antipsychotic
administrative data
physician characteristics

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.
Population Structure and Genetic Diversity of Lake Sturgeon (Acipenser fulvescens) in Canada: Evaluation of Designatable Units for Conservation
Keywords: microsatellite DNA
conservation
lake sturgeon
COSEWIC

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.
50,000 Tiny Videos: A Large Dataset for Non-parametric Content-based Retrieval and Recognition
Keywords: computer vision
video retrieval
image 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.
Uric Acid as a Growth Factor for Activated B Cells
Keywords: Immunology
Cell and molecular biology

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.
Learning, Participation and Power: The Community Training Plan at the Toronto Community Housing Corporation
Keywords: participation
power
informal learning
Toronto Community Housing
workplace learning
community

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.
Understanding Receptor Adaptation And Co-receptor Use For Feline Leukemia Viruses
Keywords: Feline Leukemia Virus
Co-receptor
Evolution

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.
Characterization of Friable1-like Homologues in Arabidopsis using Bioinformatics and Reverse Genetics
Keywords: FRIABLE1
Pectin
Glycosyltransferase
Pollen
Cell adhesion

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.