VictorJuiz/thesis huggingface dataset:
A Novel Approach to Identify Candidate Imprinted Genes in Humans
Keywords: Allele
Allele-specific DNA Methylation
Allele-specific Gene Expression
Allele-specific Expression
Allele-specific Methylation
AnCHM
Androgenetic
Androgenetic Mole
Mole
Complete Mole
Hydatidiform Mole
Complete Hydatidiform Mole
Androgenetic Hydatidiform Mole
Androgenetic Complete Hydatidiform Mole
Biparental Tissue
Bisulfite
Bisulphite
Blood
Blood DNA
Computational Biology
DNA Methylation
DNA Methylation Profiling
Epigenetic
Epi-genetic
Epigenomic
Epi-genomic
Expression
Expression Regulation
Gene Expression
Gene Expression Regulation
Genetic
Genetic Imprint
Genetic Imprinting
Genomic
Genomic DNA
Genomic Imprint
Genomic Imprinting
Human
Imprint
Imprinting
Teratoma
Ovarian Teratoma
Cystic Teratoma
Mature Teratoma
Mature Cystic Teratoma
Mature Ovarian Teratoma
Cystic Ovarian Teratoma
Mature Cystic Ovarian Teratoma
MCT
Methylation
Cytosine Methylation
Microarray
Neoplasm
Ovarian Neoplasm
Placenta
Profiling
Promoter
Promoter Region
Sodium Bisulfite
Sodium Bisulphite
Uniparental Tissue
WB
WBC
Imprinted Gene
Polymorphic Imprinting
Parent-of-origin
Parent-of-origin-specific DNA Methylation
Parent-of-origin-specific Methylation
Parent-of-origin-specific Gene Expression
Parent-of-origin-specific Expression

Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood.
FormWorks-Plus: Improved Pre-processor for VecTor Analysis Software
Keywords: FormWorks
VecTor
Pre-processor

VecTor© is a suite of computer programs developed for nonlinear finite element analysis of reinforced concrete. A graphics-based pre-processor (FormWorks) was developed for 2D concrete membrane structures, greatly contributing to the software’s utility and success. However, modeling other types of structures is a time consuming process, requiring manual definition of the finite element mesh, loads and analysis parameters in standard text files. A user-friendly pre-processor is required for the entire suite of programs if they are to be of greater use to design engineers. The purpose of this study is to develop an updated version of FormWorks, FormWorks 3.5, which is more user-friendly and compatible with the improvements made in VecTor2 over the past ten years. In addition, an extended version of FormWorks, FormWorks-Plus, will be created for the remaining VecTor programs with a wide range of viewing features, and facilities for specification of node coordinates, elements, loads and material properties.
Trends in Access to Dental Care among Middle-class Canadians
Keywords: access
dental care
middle-class
dental insurance

Objective: To explore the changes in the accessibility of dental services among middle-class Canadians in response to recent changes in the labour market and the increasing costs of dental plans. Methods: Secondary analyses of all Canadian surveys that collected information on dental insurance, utilization and out-of-pocket expenditures were conducted. Descriptive analyses were used to identify and compare trends among middle-class against the Canadian average. Results: Since 1996, the number of insured middle-class grew from 43% to 48%, with the number perceiving cost-barriers to dental care increasing by 2.7 times. In 2009, 30% of middle-class visited a dentist only when emergency happened. Since 1978, fewer middle-income households spent out-of-pocket on dental care, while per capita costs per household spending increased. Compared to national average, middle-class trends implied to poorer access. Conclusions: Access to dental care issues might be ascending from lower income sectors to involve middle-income earners as well.
Real-time Correction By Optical Tracking with Integrated Geometric Distortion Correction for Reducing Motion Artifacts in fMRI
Keywords: Functional MRI
Artifact Correction

Artifacts caused by head motion are a substantial source of error in fMRI that limits its use in neuroscience research and clinical settings. Real-time scan-plane correction by optical tracking has been shown to correct slice misalignment and non-linear spin-history artifacts, however residual artifacts due to dynamic magnetic field non-uniformity may remain in the data. A recently developed correction technique, PLACE, can correct for absolute geometric distortion using the complex image data from two EPI images, with slightly shifted k-space trajectories. We present a correction approach that integrates PLACE into a real-time scan-plane update system by optical tracking, applied to a tissue-equivalent phantom undergoing complex motion and an fMRI finger tapping experiment with overt head motion to induce dynamic field non-uniformity. Experiments suggest that including volume by volume geometric distortion correction by PLACE can suppress dynamic geometric distortion artifacts in a phantom and in vivo and provide more robust activation maps.
Angiopoietin-1 and -2 in Infectious Diseases associated with Endothelial Cell Dysfunction
Keywords: angiopoietin-1
angiopoietin-2
endothelial cell
streptococcal toxic shock
hemolytic-uremic syndrome
sepsis

Normal endothelial cell function is controlled in part by a tightly regulated balance between angiopoietin-1 and -2 (Ang-1 and Ang-2). Angiopoietin dysregulation (decreased Ang-1 and increased Ang-2) leads to an activated endothelium that is contractile, adhesive, and prothrombotic. Since an activated endothelial phenotype is seen in invasive group A streptococcal infection, E. coli O157:H7-induced hemolytic-uremic syndrome (HUS), and sepsis, we hypothesized that angiopoietin dysregulation might also be present in these syndromes, and to that end, measured angiopoietin levels in several well-characterized patient cohorts. Decreased Ang-1 and/or increased Ang-2 were found in all three syndromes, and were predictive of clinical outcome in HUS and sepsis. The prognostic utility of Ang-2 in sepsis was further enhanced by combination with biomarkers of inflammation. Angiopoietin dysregulation may therefore represent a shared final common pathway to endothelial activation as well as a clinically useful prognostic biomarker in streptococcal toxic shock, HUS, and sepsis.
Modeling Damage and Damage Evolution in Periodic Cellular Sandwich Panels
Keywords: multifuctinal structures, truss core, macroscopic strength, failure surface, damaged state

Among the light bending structures currently available, truss core panels are one of the most efficient when properly designed. The proper selection of the truss core lattice allows the incorporation of additional functionality. To exploit the multi-functional advantages of truss core sandwich structures, it is crucial to understand how the materials survive in challenging environments. In this research, the strengths of truss core panels have been predicted. Numerical calculations and experiments were carried out to validate the predictions. The effects of damage and damage propagation on the overall strength of the panel were also addressed. The strength and failure surfaces of arrays of partially damaged truss core unit cells were calculated under shear and axial loading. The results highlight the modes and trends of damage propagation in truss core panel, and the estimated damaged strength. Experiments were also performed to validate the damaged strength.
Endothelial Progenitor Cells (EPCs) for Fracture Healing and Angiogenesis: A Comparison with Mesenchymal Stem Cells (MSCs)
Keywords: Fracture Healing
Stem Cell Therapy

The purpose of this study was to compare the effects of two types of stem/progenitor cells on the healing of critical sized bone defects in a rat model. Endothelial progenitor cells (EPCs), a novel cell type with previously demonstrated effects on both osteogenesis and angiogenesis, were compared to both a control group (no cells), and a treatment group of mesenchymal stem cells (MSCs). The hypothesis was that EPCs would demonstrate both superior bone healing and angiogenesis, when compared to MSCs and controls. EPCs, MSCs, or a control carrier were placed in surgically stabilized bone defects in a rat femur and both bone formation and angiogenesis were assessed. EPC treated defects demonstrated significantly more bone formation and angiogenesis at the bone defect site than MSC or control treated defects. These results strongly suggest that EPCs are more effective than MSCs for therapeutic osteogenesis and angiogenesis in a bone defect model.
Role of Oxidative Stress in Mediating Elevated Atrial Fibrillation by Tumor Necrosis Factor-alpha
Keywords: Atrial Fibrillation
Oxidative Stress
Reactive Oxygen Species (ROS)
Inflammation
TNF-alpha
Calcium Sparks
Triggered Activity
Mitochondria
NADPH Oxidase

Atrial fibrillation (AF), the most common arrhythmia encountered in clinical practice, is a major source of morbidity and mortality, and is highly associated with inflammation and oxidative stress. In the present study, we show that acute exposure of mice atrial tissue to tumor necrosis factor-α (TNF-α) increases susceptibility to AF. We further show that acute exposure to TNF-α led to increased spontaneous sarcoplasmic reticulum (SR) calcium release and generated triggered activities in isolated mice atrial myocytes. This increase in spontaneous SR calcium activity was found to be due to elevated reactive oxygen species production from mitochondria and NADPH oxidase sources triggered by TNF-α. Hence we concluded that acute exposure to TNF-α leads to elevated oxidative stress that increases spontaneous SR Ca2+ release and triggered activity through which it can lead to AF induction and maintenance
The Influence of Thermal Barrier Coating Surface Roughness on Spark Ignition Engine Performance and Emissions
Keywords: Thermal Barrier Coating
Surface Roughness
Emissions
Performance
SI Engine
Heat Transfer

The effects on heat transfer of piston crown surface finish and use of a metal based thermal barrier coating (TBC) on the piston crown were studied in an SI engine. Measured engine parameters such as power, fuel consumption, emissions and cylinder pressure were used to identify the effects of the coating and its surface finish. Two piston coatings were tested: a baseline copper coating and a metal TBC. Reducing surface roughness of both coatings increased in-cylinder temperature and pressure as a result of reduced heat transfer through the piston crown. These increases resulted in small improvements in both power and fuel consumption, while also having measurable effect on emissions. Oxides of nitrogen emissions were increased while total hydrocarbon emissions were decreased. Improvements attributed to the TBC were found to be small, but statistically significant. At an equivalent surface finish, the TBC performed better than the baseline copper finish.
Utility of Lorenz Curves in Examining Physician Prescribing Practices: Example of Ontario Neurologist Prescribing of Multiple Sclerosis Disease-modifying Therapies in 2009
Keywords: multiple sclerosis
Lorenz curve

BACKGROUND: Differences in disease-modifying therapy (DMT) prescribing patterns between different groups of neurologists have not been explored. HYPOTHESIS: MS-specialist neurologists use a broader range of DMTs in contrast to generalist neurologists who preferentially prescribe Avonex. METHODS: Ontario neurologist demographic and geographical characteristics were linked to 2009 DMT prescription data. Lorenz curves and Gini coefficients were constructed to examine prescribing patterns; separating neurologist characteristics dichotomously and separating Avonex from the other DMTs. Gini Coefficients were compared using jack-knife statistical techniques to derive 95% confidence intervals. RESULTS: Prescriptions are highly concentrated with 12% of Ontario neurologists prescribing 80% of DMTs. High-volume prescribers show a broader range of DMT use while low-volume prescribers tend to use a particular DMT. CONCLUSIONS: The majority of DMTs are prescribed by a small subset of neurologists. High-volume prescribers show more variability in DMT use while low-volume prescribers tend to individually focus on a narrower range of DMTs.
Investigation of the Effects of Aging and Small Vessel Disease on Cardiac Frequency Signal in Cerebral White Matter as Imaged by Echo Planar Imaging using Magnetic Resonance
Keywords: magnetic resonance imaging
small vessel disease
MRI
SVD
physiological noise
echo planar imaging

Cerebral small vessel disease (SVD) is highly prevalent in older adults and is a predictor of stroke, dementia, and death. SVD is also associated with cognitive dysfunction, gait problems, and urinary incontinence. SVD is diagnosed based on white matter hyperintensities on T2 weighted scans. This thesis investigates the cardiac frequency component of resting state functional magnetic resonance imaging data in young healthy adults, older healthy adults, and older adults with pronounced SVD. A cardiac pulsatility metric is defined, and a tissue type contrast is observed between white matter, grey matter, and cerebrospinal fluid. Aging and disease effects are observed on cardiac pulsatility in white matter. The increased pulsatility may reflect the pathology of venous collagenosis and draining vein stenosis. Developing a better understanding of the etiology of SVD is an important step towards treating the disease.
Trapping and Removal of Bubbles in a Microfluidic Format
Keywords: microfluidic
bubble trap
bubbles
trap

Unwanted gas bubbles are a challenge for microfluidic-based systems, as adherence to channel networks can disrupt fluid delivery. This is especially true for devices with biological applications, as the presence of a single bubble creates thin fluid films with extremely high shear stresses, which can damage biological samples. Current strategies to remove bubbles require complicated fabrication or off-chip components. This thesis describes an on-chip microfluidic strategy utilizing permeation for in-plane trapping and removal of occasional gas bubbles. The trap was demonstrated with nitrogen bubbles, which were consistently removed at a rate of 0.14 µL/min for a single trap, and shown to have long-term operation capability by removing approximately 4,000 bubbles during one day without failure. The trap was integrated with a microfluidic system for the study of small blood vessels. Experiments were complemented with analytical and numerical models to characterize the bubble removal process.
Surface Plasmon Polariton Based Polarization Modulators Using Metal-polymer Waveguides
Keywords: polarization modulator
surface plasmon polariton

A tunable polarization modulator based on the periodic metal strips embedded in a polymer waveguide is presented. The periodic metallic structure is analyzed by Finite Element simulation (COMSOL). The calculation results show that the giant birefringence is formed by the selective cut-off of TE polarization over TM polarization, which makes it possible to design an efficient polarization modulator with a short conversion length. The metallic strips are made by using four-layer lift-off fabrication technology. The transmission and group indices of TE and TM modes are measured. However, it is observed that TE and TM modes cut off at same time, which does not agree with our predictions. The reason for failure is that the change in refractive indices is different from what we expected, which makes the device perform in opposite way. Finally, further suggestions are provided to modify the design so that the device can achieve its expected function.
Miniaturized Electrochemical Immunosensors for the Detection of Growth Hormone
Keywords: Immunosensor
Growth hormone

The first part of this research involves the development of a gold-nanoparticle based sandwich type immunosensor to identify trace amounts of human chorionic gonadotropin hormone based on the direct electrochemical detection of Au nanoparticles. The second part of this research is to design a biosensor that can be easily handled, has higher specificity, sensitivity, low-cost, and rapid response and has a better detection of growth hormone (GH). Current bioanalytical techniques have reported the difficulty to detect GH doping. This research aims to address the issue of measuring GH in small volumes, which has been challenging the limits of analytical detection systems. The electrochemical measurements utilize the redox activity of ferro/ferricyanide in cyclic voltammetry and impedance spectroscopy. The detection limit 10 pg/mL was observed for GH in 20 μL sample volume, which indicated that this versatile platform can be easily adapted for decentralized electrochemical immunosensing of clinically important proteins.
Stress-constrained Structural Topology Optimization with Design-dependent Loads
Keywords: topology optimization
design dependent loads
pressure loads
self-weight
stress constraints
block aggregated constraints

Topology optimization is commonly used to distribute a given amount of material to obtain the stiffest structure, with predefined fixed loads. The present work investigates the result of applying stress constraints to topology optimization, for problems with design-depending loading, such as self-weight and pressure. In order to apply pressure loading, a material boundary identification scheme is proposed, iteratively connecting points of equal density. In previous research, design-dependent loading problems have been limited to compliance minimization. The present study employs a more practical approach by minimizing mass subject to failure constraints, and uses a stress relaxation technique to avoid stress constraint singularities. The results show that these design dependent loading problems may converge to a local minimum when stress constraints are enforced. Comparisons between compliance minimization solutions and stress-constrained solutions are also given. The resulting topologies of these two solutions are usually vastly different, demonstrating the need for stress-constrained topology optimization.
The Thermal Grill Illusion of Pain: Effects of Altering Placements of Warm and Cool Grill Elements
Keywords: Thermal Grill Illusion
Psychophysics
Pain
Thermoreception

The simultaneous application of interlaced innocuous warm and cool stimuli can elicit sensations of burning heat (the Thermal Grill Illusion, TGI). The TGI is thought to reflect changes in the central interactions between somatosensory sub-modalities (i.e. cold-inhibition of pain). Previous studies used multiple alternating warm and cool bars to elicit a TGI. The primary objective of this study was to evaluate the effects of altering the placements of warm and cool grill elements on the intensities of perceived pain and unpleasantness in 26 male subjects. Arranging the thermal grill elements in a warm flanking cool (WCW) pattern evoked significantly higher intensities of pain and unpleasantness than a cool flanking warm (CWC) pattern and a uniform warm stimulus. Conversely, CWC did not elicit significantly different intensities of perceived pain and unpleasantness than a uniform cool stimulus. This finding may reflect differences in the level of activation of central neurons.
In Vitro Examination of Secondary Caries Using Infrared Photothermal Radiometry and Modulated Luminescence
Keywords: Photothermal Radiometry and Luminescence
Secondary Caries

Dental secondary caries is the carious lesion developed around existing restoration margins. Many new technologies have been developed for caries detection purposes, but their performance is unsatisfactory for the specific purpose of secondary caries diagnosis. Therefore, the development of a novel technology to detect secondary caries has been highly necessary. The objective of this research was to investigate the ability of photothermal radiometry and modulated luminescence to detect secondary caries: wall lesions and outer lesions. Changes in experimental PTR-LUM signals due to sequential demineralization on vertical walls of sectioned tooth samples were investigated. Another study was conducted to investigate how two different types of secondary caries, wall lesions and outer lesions, affect the PTR-LUM signals. The studies demonstrated that PTR-LUM is sensitive to progressive demineralization and remineralization on vertical walls of sectioned tooth samples, as well as to the presence of wall lesions and outer lesions developed around composite restorations.
The Effects of Green Tea on Salivary Production and Viscosity, and on Quality of Life in Patients with Sjögren’s Syndrome: A Pilot Study
Keywords: Sjögren’s syndrome
Green tea

Several beneficial effects of green tea polyphenols (GTPs) have been shown in both in vitro and animal studies. This pilot study tested their effects on relief of dry mouth and quality of life (QoL) in Sjögren’s syndrome (SS) patients. After one month of green tea consumption in 18 SS patients, and three months in 7 patients, there was an improvement in the patients’ oral health and QoL. In addition there was an increase in the unstimulated salivary flow rate and a decrease in the viscosity of stimulated saliva, although not statistically significant. Furthermore, 83% of the patients reported that they would continue to drink green tea. Although the mechanism of action of the GTPs is unknown in this patient population, we have shown that regular green tea consumption by SS patients is a simple yet effective and enjoyable means of dry mouth relief.
Investigation of the Oncogenic Role of Sox2 in the Pathogenesis of Lung Squamous Cell Carcinoma using Normal Human Lung Basal Progenitors
Keywords: lung squamous cell carcinoma
Sox2
basal cells
lung progenitor

Sox2 is the most frequently amplified oncogene in lung squamous cell carcinoma (SCC). Lung SCC arises in the proximal to central airways and is thought to originate from the p63-positive basal progenitor cells. Since Sox2 amplification occurs early in SCC pathogenesis, we investigated the oncogenic role of Sox2 using normal primary human lung basal progenitor cells. Although Sox2 is highly expressed in normal basal progenitors in a quiescent tracheal epithelium in vivo, we found that Sox2 expression decreases substantially during in vitro proliferation. When Sox2 expression is elevated in the proliferating basal cells in vitro to a level clinically observed in lung SCCs, Sox2 causes hyperplasia and promotes both squamous and Mucin16-positive glandular lineages at the expense of ciliated cell differentiation. Furthermore, our data suggest that the squamous and glandular-differentiating activity of Sox2 is differentially modulated by Receptor tyrosine kinase (RTK) and/or PI3-kinase signaling to promote squamous metaplasia of basal progenitor cells during SCC development.