VictorJuiz/thesis huggingface dataset:
Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits
Keywords: Algorithm
Alzheimer's Disease
DNA words
Expression Quantitative Trait Loci (eQTLs)
Gene-Tissue Expression (GTEx) Project
Genome wide association studies (GWAS)

Genome-wide association studies and expression quantitative trait loci (eQTL) studies have identified thousands of variants associated with complex diseases and gene expression levels. The frequency of DNA words associated with these variants has not been extensively evaluated. These words may help understand the biological role of trait-associated variants and also enable their identification in future studies. An exact word-counting method was developed to investigate the hypothesis that short DNA words have different frequencies near single nucleotide polymorphisms (SNPs) associated with (1) Alzheimer’s disease and (2) thyroid eQTLs, compared to the rest of the genome. No significant DNA words were found near AD associated SNPs. Some words enriched in GC content have significantly higher frequency around thyroid’s eQTLs compared to controls. These DNA words were no longer significant when the controls were matched for nucleotide frequency, but this is likely due to over-matching.
Synthesis, Characterization and Potential Applications of Nanoparticles based on Naturally-occurring Polymers
Keywords: alginic acid
crosslinking
hyaluronic acid
nanoparticles
polyelectrolytes
polymer collapse

Counterion condensation was employed to achieve polyelectrolyte collapse for naturally occurring polymers, hyaluronic acid (HA) and alginic acid (AL). Secondary crosslinking led to the formation of the desired nanoparticles (NPs). HA or AL NPs were stabilized by covalent crosslinker with the help of carbodiimide. Ideal pH ranges for the most extended conformation of HA and AL were pH 5.5-7.5 and 6.5-7.5 respectively. It was found that HA and AL can be condensed with Na+ ions (>0.25 M) and Ag+ ions (>100 mM, HA only). Particle sizes were examined using kinematic viscosity (St), dynamic light scattering (DLS), and atomic force microscopy (AFM). DLS was able to assess the polydispersity of the NPs in the solution, where two main peak distributions for HA, 1-10 nm and 100-1000 nm, and 160-280 nm for AL. AFM results confirmed the presence of multiple particle sizes for HA NPs, with the height between 1-4 nm.
Development of Deployable Antennas for Advanced Maritime Communication and Monitoring with Small Satellites
Keywords: AIS
antenna
deployable
microsatellite
tape spring
VDES

NORSAT-2 is a 16-kilogram microsatellite designed, constructed and tested at the University of Toronto Space Flight Laboratory commissioned by the Norwegian Space Center. The spacecraft supports maritime safety and security using an Automatic Identification System ship tracking payload as well as the first space-based Very High Frequency Data Exchange System, considered to be the next generation of the Automatic Identification System. This thesis describes the author's mechanical design contributions to the development of NORSAT-2. To enable payload operations, two unique deployable antennas - a monopole and a cross-Yagi - leveraging tape spring technology are presented. The designs were elaborated iteratively through deployment, communications, vibration and thermal vacuum test campaigns. A spacecraft structural design capable of accommodating the payloads was achieved. The antennas were successfully deployed following spacecraft launch, as confirmed through on-orbit imagery. Payload operations were conducted, demonstrating on-orbit ship tracking data reception and data transmission to a Norwegian vessel.
Multi-Scale Entropy (MSE) of Eye Movements
Keywords: Memory
Multi-Scale Entropy
Partial Least Squares
Saccadic Eye Movements
Scene viewing
Vision

Conventional eye movement (EM) metrics are static in that they quantify only one particular aspect of vision (e.g. number of gaze fixations made in a trial etc.). Therefore, in the current study we use a metric called Multi-Scale entropy (MSE) to quantify the spatial and temporal changes in EMs as viewing unfolds over time. In particular, we aimed to capture the inherent complexity and information contained in gaze signals produced by EMs when viewing different types of scenes. Our results showed that MSE can be applied on gaze signals and that it does quantify the meaningful information contained therein. It also indexed differences in the information encoded from different scenes beyond what can be deduced from conventional metrics like the number of fixations and saccades. However, we also found that this metric is related to and is comparable with saccade amplitude with respect to indexing scene differences.
Aerobic and Anaerobic Biotransformation of Chloroanilines, Chlorobenzenes, and Dichlonitrobenzenes at a Complex Industrial Site in Brazil and Analysis of Associated Microbial Communities
Keywords: Aniline
Biodegradation
Bioremediation
Biotransformation
Chloroaniline
Dichloronitrobenzene

Environmental contamination is a widespread problem and many industrial sites need significant attention. The potential for using bioremediation as a low cost environmentally-friendly restoration approach was evaluated at a contaminated site in Brazil. Aerobic and anaerobic biotransformation of chloroanilines, chlorobenzenes, and dichloronitrobenzenes were studied in long-term microcosm experiment, where novel reactions were observed, such as anaerobic biotransformation of dichloronitrobenzenes. Further microbial community analysis was performed based on multiple samples with the objective to recommend a course of action at the site. To evaluate the identity and distribution of microorganisms in microcosms and field samples, amplicon sequencing of the 16S rRNA gene was performed. Cupriavidus was found to degrade dichlorobenzenes, Diaphorobacter degrades dichloronitrobenzenes aerobically, among others. Statistical analysis was done to interpret the data and identify significant factors that drive a microbial community. The conclusion is that this site has a high potential for being bioremediated, by promoting aerobic biodegradation processes.
The Multiscale Essence of Multimediated Reality
Keywords: Human Computer Interaction
Humanistic Intelligence
Multimediated Reality
Smart System
Sousveillance
Wearable Computing

Virtual Reality (VR), Augmented Reality (AR), eXtended or MiXed Reality (XR), and Mediated Reality (MR or XYR) are examples of the new multi-axis "Multimediated (All) Reality" (XYZR or ZR) that exist at multiple scales: "wearables", "smart cars", "smart cities", etc.. ZR forms a tight feedback loop with users through Humanistic Intelligence (HI). This thesis explores Multimediated (All) Reality through HI across all physical scales: (1)the human body, exemplified by Integral Kinesiology that brings about corporeal integrity through the combination of dexterity and strength; (2)clothing, exemplified by the Open EyeTap, an affordable smart-glass design that is modular and 3D printable; (3)bicycles, exemplified by rear-view vision that helps cyclists see better; (4)vehicle mobility, exemplified by an HDR vision system that enables cars to see under a wide variety of lighting conditions; and (5)the "vironment" (invironment + environment) through sousveillant technologies (metaveillogrammetry and metaveillography).
Defining the Role of SOX17 in Human Hematopoietic Development
Keywords: Cell differentiation
Hematopoiesis
Hematopoietic stem cells
Stem cells
Transcription factors

The transcriptional regulators that govern the generation of hematopoietic stem cells (HSCs) from hemogenic endothelial cells (HECs) during human definitive hematopoiesis have not been identified. Based on findings from studies in the mouse, we hypothesized that the transcription factor SOX17 plays a pivotal role in the establishment of the definitive, but not the primitive hematopoietic program generated from human pluripotent stem cells (hPSCs) differentiated in culture. We observed that SOX17 was expressed within definitive CD34+ ‘HECs’ and emerging definitive, but not primitive, CD43+ hematopoietic cells. Detailed analyses showed that expression of SOX17 was downregulated as CD34+ HECs differentiate and undergo an endothelial-to-hematopoietic transition (EHT) to acquire a hematopoietic fate. This transition from a SOX17+ to a SOX17– population was blocked using a NOTCH signaling inhibitor. Despite the expression of SOX17 in definitive progenitors, the loss of SOX17 had no effect on definitive or primitive hematopoiesis in the hPSC differentiation cultures.
Interplay between phagocytosis and pro-inflammatory cytokine production in macrophages
Keywords: Inflammation
Macrophages
Phagocytosis

Macrophages are able to recognize, bind and internalize pathogens through two types of phagocytic receptors; the Fc receptors (FcγR) and the complement receptors (CR). FcγRs have prevailed to be more pro-inflammatory than CRs in the literature. Our lab wanted to revisit this paradigm and elucidate the signalling mechanism responsible for upregulating cytokine production when opsonic receptors are activated. In this thesis, we show that CR-mediated phagocytosis leads to higher mRNA levels of TNF, IL-1β, IL-6, MMP9 and iNOS than FcγRmediated phagocytosis. Further investigation into the signaling mechanism showed that there is higher NF-κB activation in CR-mediated phagocytosis than FcγR-mediated phagocytosis. We investigated the role of calpain during phagocytosis and our qPCR data shows that the addition of PD 150606, a calpain inhibitor, reduces cytokine expression levels in CR-mediated phagocytosis. Our findings suggests that the upregulation of pro-inflammatory mediators during CR-mediated phagocytosis, in macrophages, maybe dependent upon calpain-mediated activation of NF-κB.
Exploring the Role of HOP2 in the Double Strand Break Repair Pathway beyond Meiosis in Arabidopsis thaliana
Keywords: Arabidopsis thaliana
DSB repair
Homologous Recombination
HOP2
Meiosis
Mitosis

The purpose of this study was to investigate the role of HOP2 protein in non-meiotic cells in Arabidopsis. HOP2 is known to be important to meiotic chromosome pairing and homologous recombination, yet the role of HOP2 outside of meiosis is far from being fully elucidated. My study focused on the mitotic chromosome events with and without the application of radiation. In the absence of radiation, no fragments and chromatin bridges were found in hop2-1 plants, but they did seem to experience a modest chromosome separation delay. When irradiated, both genotypes had significant decreases of mitotic indices and increases of bridges. The decrease in mitotic indices were comparable for the two genotypes, suggesting they accomplish repair at similar rates. Irradiated hop2-1 had significantly more incorrectly repaired breaks, as determined by the bridges. My findings suggest that HOP2 is also important for the fidelity of the exchange process in non-meiotic HR repair.
Efficacy Of Artemether In Attenuating Spontaneous Intracerebral Hemorrhage
Keywords: Animal research
Brain
Endothelial biology
inflammation
Pharmacology
Stroke

Spontaneous Intracerebral Hemorrhage (ICH) is a debilitating form of stroke that most commonly emerges from dysfunction of brain interendothelial junction proteins. Previous studies by our laboratory generated brain vascular instability in zebrafish by perturbing CDC42-Cadherin pathway and found the drug artemether effective for the reduction of ICH. The current study investigates the efficacy of artemether against spontaneous ICH in mice. Our data indicate that treatment with artemether significantly inhibits ICH and cerebral microhemorrhage as assessed by histology and magnetic resonance imaging. By immunostaining microglia and astrocytes, we demonstrate a marked attenuation of inflammation. Artemether might confer vascular stability by protecting endothelial barrier function as indicated by the in vitro assay on cultured endothelial cells. Gene expression analysis demonstrated a down-regulation of inflammatory genes by artemether. In conclusion, our data collectively suggest that artemether therapy may serve as a novel approach in preventing spontaneous ICH in the at-risk human population.
Analysis of Long Noncoding RNAs in the Drosophila melanogaster Male Reproductive System
Keywords: Drosophila melanogaster
Long noncoding RNA
RNA localization
spermatogenesis

Long noncoding (lnc) RNAs are transcripts that are at least 200 nucleotides long and are not translated into proteins. lncRNAs have been associated with wide-ranging aspects of disease and development in numerous organisms, including Drosophila melanogaster and humans. This project analyzed the subcellular localization of ~500 lncRNAs in the Drosophila male reproductive system. ~90% of lncRNAs were found to be expressed in at least one male reproductive tissue, and ~80% of these were clearly subcellularly localized in at least one tissue. lncRNAs were expressed in a variety of cell types and stages of spermatogenesis. These findings suggest that higher numbers of lncRNAs are expressed and posttranscriptionally regulated than previously hypothesized. As well, lncRNA subcellular localization may give insight into the potential functions of these transcripts. The generation of deletion fly lines for three lncRNAs, CR43282, CR44889 and CR46216, was also attempted using the CRISPR-Cas9 system.
Middle School Teachers' Successes and Challenges in Supporting Students' Mathematical Communication Using Manipulatives and Technology in a Professional Development Study
Keywords: Elementary Education
Inner-City Education
Mathematics Education
Professional Development

The case studies of four inner-city Grade 6 educators involved in a year-long Professional Development (PD) study were examined to determine: a) successes and challenges teachers face supporting students' mathematical communication, b) teachers' manipulatives and technology use to support communication, and c) the study's effects on teachers' attitudes and beliefs. The Ten Dimensions of Mathematics Education Framework (McDougall, 2004) was used to examine the findings. Teachers had success with learning environment, student tasks and teachers’ comfort with mathematics. Teachers faced many challenges, primarily in learning environment, communicating with parents, and teacher’s comfort with mathematics. Teachers provided varied integration of manipulative use, and need to continue to integrate technology, to support mathematics communication. It was determined that, while the PD study was greatly successful in providing support towards aligning teachers' attitudes and beliefs with current mathematical practices, PD alone is insufficient for improving teachers' attitudes.
Radiographic Progression in Ankylosing Spondylitis
Keywords: Ankylosing spondylitis
Disease progression
HLA-B27
Radiography
Sacroiliitis
Tumor Necrosis Factor-alpha

Axial spondyloarthritis (axSpA) is a chronic inflammatory disease of the spine and sacroiliac joints (SIJs) with an unknown etiology. The spectrum of axSpA is thought to start from a pre-radiographic stage and may progress to radiographic sacroiliitis over time. Some axSpA patients may develop structural damage because of new bone formation in the spine which are known as syndesmophytes. These structures may limit spinal mobility and can contribute to the functional impairment, which is a well-known complication of axSpA. In this thesis, through three manuscripts, we studied different aspects of radiographic progression in axSpA. The first study focused on the characteristics of axSpA patients who had non-diagnostic SIJs at baseline and progressed to radiographic axSpA. The second study aimed to address progression rates and factors predictive of spinal progression in ankylosing spondylitis (AS). In the third study we investigated the effect of spinal structural damage on spinal mobility in AS.
Behaviour of Welded Steel Wire Mesh as Surface Support
Keywords: discrete element method
ground support
welded wire mesh

An effective ground support is a requirement for the design of underground excavations in rock. In order to design a ground support system, it is necessary to understand the mechanical behaviour of each ground support system component. The focus of this thesis is the behaviour of welded steel wire mesh as surface support. A critical review of the results obtained from various testing rig configurations has been undertaken. This provided the basis for a series of numerical experiments to reproduce the mechanical behaviour of welded steel wire mesh as observed in the laboratory tests. The mechanical behaviour of welded wire mesh was captured using the 3D-Distinct Element Method (3D DEM). Finally, a series of parametric investigation demonstrated the influence of testing rig configuration on the performance of the mesh. This has significant implications in the design of testing rigs to quantify the performance of mesh.
Colour Variation in Automotive Paint Films
Keywords: automotive
Color
Colour
electrostatic bell applicator
Paint
Surface tension

A modeled paint, developed at the University of Toronto, and the amount of pigments added to it, were varied, and uniformly coated at different thicknesses onto a stainless steel reflective substrate. These samples were place in a natural convection oven, observed with a high-speed camera with a field of view of 5.6mm, and mass was recorded every 60 seconds. The surface tension driven flows due to concentration gradients were observed, velocity magnitudes were calculated using Particle Image Velocimetry (PIV), and paint’s colour was measured. An analytical model was used to calculate the mass evaporation and compare it with experimental results, and the Marangoni number was calculated and compared to the velocity. This experiment was conducted with automotive paint, to observe if the Marangoni effect occurs during the curing process. Automotive paint’s contents were also changed, against various parameters of an electrostatic bell applicator, to identify how it changes the colour.
Deep Sequencing and Annotation of the Trichoplax adhaerens mRNA Transcriptome Identifies Novel Genes and a Rich Repertoire of Neural Signaling Machinery, Providing Insight into Nervous System Evolution
Keywords: Evolution
Nervous System
Rab3-interacting molecule
RIM
Transcriptome
Trichoplax adhaerens

Trichoplax adhaerens is an early-diverging animal capable of motile behavior such as feeding, chemotaxis, and phototaxis, despite lacking synaptically-connected neurons and muscles. Our lab has produced a high-quality T. adhaerens transcriptome in which ~85% of the assembled genes are complete protein-coding sequences, with 2,483 newly-identified genes missed in the genome sequencing effort. One objective of this research was to identify genes involved in neural signaling. Using in silico prediction algorithms we identified an array of neuropeptide genes, GPCRs, ion channels, and synaptic scaffolding and signaling proteins. We also discovered a previously unknown group of presynaptic Rab3-Interacting Molecule (RIM) homologues in the animal phylogeny, absent in humans but present in many invertebrates. Our work sets the stage for future studies aimed at understanding the concurrent evolution of metazoan cell types, and their ability to communicate with each other through various forms of cell signaling including electrochemical signaling in the nervous system.
Early Retinal Changes Following Paediatric Optic Neuritis
Keywords: Demyelination
Multiple Sclerosis
Optical Coherence Tomography
Optic Neuritis
Retina

Retinal nerve fiber layer (RNFL) and ganglion cell/inner plexiform layer (GCIPL) thinning occurs in the chronic phase following optic neuritis (ON) in children, but early changes have not been reported. This cross-sectional study evaluates children with ON as part of a first demyelinating event (n=33) using spectral-domain optical coherence tomography (OCT) performed within 30 days of onset. Comparison was made to healthy controls (n=33). GCIPL thickness was reduced in both ON-affected (-5.71um; p = 0.0013) and fellow eyes (-6.00um; p = 0.0013) compared to controls. Fewer ON-affected eyes in children with MS (3/10 eyes; 30%) demonstrated RNFL swelling above the 95th percentile of controls compared to those of other demyelinating disorders (29/37 eyes; 78.4%; p = 0.007). This suggests that early retinal injury occurs in paediatric ON, which may reflect pre-existing subclinical injury not directly related to clinical ON. Patterns of injury may differ in youth with MS.
Cardiac Outcomes in Long-Term Survivors of Childhood Cancer
Keywords: Cardiovascular Disease
Clinical Epidemiology
Health Services Research
Pediatric Oncology
Survivorship

Childhood cancer survivors (CCS) experience elevated risks for cardiac morbidities and mortality due to cancer treatments such as anthracyclines and chest radiation. Morbidities include heart failure, arrhythmias, valve abnormalities, pericardial disease, and coronary artery disease. However, previous studies have focused primarily on heart failure. We used health administrative data to determine the incidence among 7,289 survivors and 36,205 matched cancer-free individuals. Overall, CCS experienced a higher risk for cardiac events (Hazard Ratio 3.2 95% CI 2.7-3.8), with the risk ranging 2- to 10-fold depending on the specific outcome. Predictors included high doses of anthracyclines (>250 mg/ m2), diabetes, and hypertension. Subsequent childhood cancer was also associated with cardiac risk; however, this was mediated through exposure to chest radiation and hematopoietic stem cell transplantation. This study suggests that survivors are at risk for several cardiac late effects, and highlights the need for directed and continuous follow-up of CCS over their lifetime.
Aerostructural Analysis of Aircraft Wings using High-Fidelity Aerodynamics and Medium-Fidelity Structural Analyses
Keywords: aeroelastic
aerostructural
aerostructure
aircraft
airplane
wing

Aerostructural optimization has the potential to provide valuable information to aircraft designers conducting new concept exploratory analyses. An aerostructural analysis tool for wings has been incorporated into the high-fidelity three-dimensional Reynolds-averaged Navier-Stokes aerodynamic shape optimization framework Jetstream for future development of aerostructural optimization capability. Investigations were conducted using this tool, which uses medium-fidelity structural analyses and models, to evaluate the accuracy of the models with respect to wing weight and deflection estimates. Weight estimates using two medium-fidelity simplified structural models were found to have errors of 9.7% to 91.1% relative to weight estimates of high-fidelity aerostructural optimization test case results. Wing tip twist deflection estimates were found to have errors of 3% to 157% relative to the same baseline results. Both sets of results are deemed insufficiently accurate for the medium-fidelity structural models that were investigated; however recommendations for future development and improvements to an aerostructural analysis tool are presented.
Assessing the role of PTEN in cholinergic neurons in glucose and energy homeostasis
Keywords: ChAT
Cholinergic
Dorsal Vagal Complex
Insulin
PI3K
PTEN

Insulin resistance and insulin deficiency are key determinants of type 2 diabetes. Insulin resistance is manifested by attenuation of insulin signaling. A major insulin signaling pathway is mediated by phosphatidyl inositol kinase (PI3K), which is negatively regulated by phosphatase and tensin homologue (PTEN). Neuronal PI3K-mediated insulin action plays a critical role in the regulation of systemic insulin resistance. The dorsal ventral complex (DVC) is the control centre of vagal activity and utilizes acetylcholine, a neurotransmitter, which is synthesized by the enzyme choline acetyl transferase (ChAT). To assess the role of PTEN in cholinergic neurons, we generated mice deficient of PTEN in these neurons using the cre-loxP system. These mice were protected against high fat diet-induced weight gain and glucose intolerance. They also had less inflammatory adipose tissue. Overall, PTEN deletion in the cholinergic neurons provides protection against diet-induced obesity and diabetes.