VictorJuiz/thesis huggingface dataset:
Contribution of Rare Copy Number Variants to the Development of Autism Spectrum Disorder in High-risk Siblings
Keywords: Autism
Copy Number Variation
High-Risk Siblings
Microarray

As microarrays are commonly used to identify the causes of autism spectrum disorder (ASD) we are investigating whether genetic testing in young children can predict ASD status prior to the typical age of onset of symptoms. A total of 441 individuals (190 probands, 88 siblings with ASD, 163 unaffected siblings) from the Infant Siblings Research Consortium were genotyped on the high-resolution Affymetrix CytoScan HD platform. De novo and inherited presumed pathogenic CNVs were identified in 23/199 families (11.4%). In 6 of these families, the index case and one or more siblings carried the presumed pathogenic CNV; in every such case the carrier individual either had ASD (4) or had a subclinical form of ASD (2). There were 6 additional families in which CNV data would have been informative for early ASD diagnosis or detection of developmental delay. Our results suggest CNVs may serve as biological markers for ASD.
Hippocampal Subfield Volumes and Relations to Associative Memory in Children and Adolescent Survivors of Pediatric Brain Tumors
Keywords: associative memory
cranial radiation
hippocampal subfields
neurodevelopmental abnormalities
pediatric brain tumor survivors

Pediatric brain tumor survivors (PBTS) treated with cranial radiation therapy (CRT) experience debilitating cognitive deficits, including impaired learning and memory. These impairments may be linked to volume abnormalities in the hippocampus. Animal studies suggest that radiation induces memory impairments in part, by disrupting neurogenesis in the hippocampal dentate gyrus. However, the effects of CRT on hippocampal subfields and relations to impaired memory in humans remain unknown. We used MRI and segmented hippocampal subfields (CA1, CA2/3, dentate gyrus/CA4, stratum radiatum, lacunosum, moleculare (SR/SL/SM) and subiculum) in PBTS and typically developing children using an automated segmentation tool. Hippocampal subfield volumes in PBTS were assessed in relation to memory performance. We observed that PBTS displayed smaller dentate gyrus/CA4, CA1, and SR/SL/SM volumes compared to typically developing children. Moreover, smaller dentate gyrus/CA4 and SR/SL/SM volumes correlated with lower memory performance. These findings suggest that damage to hippocampal subfields may in part underlie memory deficits in PBTS.
Auto-tuned Near Minimum-deviation Digital Controller for Hard Switching DC-DC Converters
Keywords: controller
Converters
dc-dc
deviation
digital
mixed-signal

This thesis presents a practical auto-tuned digital controller applicable to various kinds of hard switching dc-dc converters. Controller consists of three main functional blocks: i) an output current estimator which can obtain the instantaneous load current value for both direct and indirect energy transfer converters, ii) a conventional digital compensator for steady state regulation and, iii) a nonlinear digital module for fast transient response to minimize voltage deviation.
The Effects of Matrix Metalloproteinases on Fetuin's Role as an Inhibitor of Transforming Growth Factor-beta1
Keywords: BMP
Cardiovascular
Fetuin
Periodontitis
TGF-beta

Periodontitis may increase the risk of developing cardiovascular diseases, yet mechanisms of this association are undefined. Transforming growth factor beta-1 (TGF-β1) has both atheroprotective and atherogenic roles. Fetuin, a serum glycoprotein, binds and inhibits TGF-β1, which may affect atheroma formation. Some matrix metalloproteinases (MMP) elevated in periodontitis are known to cleave fetuin. We hypothesized that fetuin cleavage by MMPs may reduce fetuin’s ability to inhibit TGF-β1. SDS-PAGE, densitometry and mass spectrometry confirmed bovine fetuin was degraded by MMP-2, 3, 7, and 9 (MMP:fetuin=1:60), identifying unique cleavages. TGF-β1 activity at 2ng/mL was assessed with intact or MMP-cleaved fetuin utilizing a cell growth assay. TGF-β1 inhibited cell growth by 28.6%. Intact fetuin, at 1mg/mL and higher, reduced TGF-β1 inhibition of cell growth to 19.8%. MMP-7-cleaved fetuin, at 0.2mg/mL, significantly reduced the TGF-β1 inhibition to 8.6%. Thus, MMP-7 cleavage of fetuin enhances fetuin’s ability to inhibit TGF-β1.
Proton Conducting Ionic Liquid-polymer Electrolytes for Solid Electrochemical Capacitors
Keywords: electrochemical capacitor
energy storage
ionic liquid
polymer electrolyte
pseudocapacitor
supercapacitor

Electrochemical capacitors (ECs) are energy storage devices with high power density and high efficiency, but their liquid electrolytes can contain environmentally unfriendly compounds and are vulnerable to leakage. Ionic liquids (ILs) provide non-volatile ionic conductivity in flexible polymer electrolytes, which can alleviate these issues. The ILs 1-ethyl-3-methylimidazolium hydrogen sulfate (EMIHSO4) and 1-methylimidazolium hydrogen sulfate (MIHSO4) were combined into a binary mixture with a deeply depressed melting point, and a phase diagram was constructed after thermal analysis. On ruthenium dioxide electrodes, 70-30 wt% EMI-MIHSO4 showed an increase in capacitance of about 75% over that of neat EMIHSO4, demonstrating its proton activity. The binary IL mixture was incorporated into a polyvinyl pyrrolidone polymer matrix to form polymer electrolytes that showed good electrochemical performance and rate capability under electrochemical impedance spectroscopy and cyclic voltammetry. On ruthenium dioxide electrodes, the PVP-EMI-MIHSO4 electrolyte showed a 30% improvement in capacitance over PVP-EMIHSO4.
Not all in one Rhythm: A Critical Analysis of the Media Discourse against the Indigenous Re-existence of the Maraká’nà Village in Kûánãpará
Keywords: Discourse Analysis
Indigenous Education
Kรปรกnรฃparรก
Pindorama
Re-existence

Indigenous people created the re-existence known as Maraká’nà village, by re-occupying the sacred territory of a building in Kûánãpará (Rio de Janeiro) located next to the popular Maracanã stadium. The village became a meeting place for re-existences that encompass issues of Indigenous sovereignty, sacred land right, spirituality practices, decolonizing education, and the creation of the first Intercultural Indigenous University in Pindorama. It challenged the economic and social impacts of the neoliberal sports mega-events, which raised tensions during the organization of sports mega-events. These tensions were amplified through media discourse, by perpetuating violent treatment of Indigenous peoples, and naturalizing the dominant elite. Employing a transdisciplinary methodology that combines Critical Discourse Analysis and Critical Political Economy, this study examines the media discourse that obstructs the Indigenous re-existence of Maraká’nà by favoring capitalist structures. Despite demonstrating unbalanced power relations, the findings show unbalanced power relations Maraká'nà and media discourses.
Development of a Universal Rubric Bank for Curriculum-embedded Assessment of Engineering Design Learning Outcomes
Keywords: Engineering design
Engineering education
Learning outcomes
Learning outcomes assessment
Rubric development
Rubrics

This thesis report focuses on the process of constructing, testing, and refining a bank of universal analytic rubric rows. The objective was to produce a valid and reliable instrument that could be implemented in any engineering design course to measure program-level learning outcomes. A draft rubric was constructed by formulating descriptors of performance quality for each indicator row and validating the outcomes, indicators (criteria), and descriptors with experts. Indicator rows were then tested in focus groups with teaching assistants. The universal rubric bank was refined based on analysis and interpretation of testing results. The outcome of this process is a bank of 23 rubric rows that can be deployed in courses and/or developed further. The universal design provides a common measure for comparing student cohorts in different courses, disciplines, and year-levels. Refinement activities improved reliability, and the rigorous development process is evidence for the validity of the assessment tool.
Cellular Response to Diesel Engine Exhaust Particulate Exposures: Impact of Extraction Method and Reactive Oxygen Species as a Biomarker
Keywords: Cell death
Diesel engine exhaust particulate
Human lung epithelial cells
Oxidative stress
Particulate filter extraction
Reactive oxygen species

Oxidative stress induction by diesel engine particulate was investigated. The objectives were: to determine the temporal profile of cell oxidant generation, elucidate engine condition effects on particulate toxicity, and assess filter extraction impact on potency. Calu-3 cells were exposed to particulate from a tier 1 diesel engine, an off-road diesel generator, and a soot generator. Particulate filters were extracted into different solvents, using multiple sonication methods; with reactive oxygen species and cell death biomarkers measured upon exposure. Dose-dependent effects and an effective dose of > 35 Âľg/mL were observed for all particulate types. Greater oxidative potential was positively associated with engine load in the tier 1 system, but tier 3 diesel generator particulate was most potent (> 18 Âľg/mL effective dose). Additionally, phosphate buffer extracted particulate, and sonicator probe use enhanced the oxidative stress response. The methods validated can be applied to larger matrices of diesel particulate exposures, incorporating various emission control technologies, testing cycles, and fuel types.
Fabrication and Machining of Bulk Metallic Glass for Airborne Gravity Gradiometry
Keywords: Bulk metallic glass
Glass forming ability
Machining
Minor alloying
Zr-based

Bulk metallic glass is an intriguing material ideally suited for use as a flexure in an airborne gravity gradiometry. Successful fabrication of Zr56Ni20Al15Cu5Nb4 was achieved using arc melting and suction casting. The effect of oxygen and microalloying Nb into this alloy composition was investigated. It was determined that oxygen in solute form is much more detrimental than as an oxide with respect to glass forming ability. Through microalloying Nb, a high glass forming region was observed between 2 â 4 at.% Nb. Studies on crystallization kinetics revealed that upon heating these amorphous samples, a multi-step phase transformation pathway can be observed. Lastly, electrochemical micromachining (ECMM) and abrasive water jet machining (AWJM) were shown to be effective techniques which can be used to shape BMGs after casting without inducing crystallization. ECMM parameters were investigated to optimize the micron-machining process. AWJM demonstrated that fast cutting could be achieved with smooth surface finishes and good dimensional tolerance.
Optimization Models for Energy-efficient Railway Timetables
Keywords: Energy efficiency
Linear Programming
Railway networks
Regenerative braking
Train scheduling

This thesis presents two novel optimization models to calculate energy-efficient railway timetables in a railway network. The first optimization model is a mixed integer programming one, which saves energy by maximizing the total overlapping time between the braking and accelerating phases of suitable train pairs. However, it suffers from some limitations associated with NP-hard computational complexity and modeling of energy saving strategy. To overcome the limitations of the first model, we propose a second optimization model consisting of two stages. The first stage of this model minimizes the total energy consumed by all trains and the second stage maximizes the transfer of regenerative braking energy between suitable train pairs. Both of these stages are solvable in polynomial time, compared to other existing models, which are NP-hard. The two-stage model has proven to be very effective in practice and has been incorporated into an industrial railway timetable compiler.
Shade Tree Effects on Intraspecific Leaf Trait Plasticity and Decomposition in a Willow Agroforestry System
Keywords: Agroforestry
Decomposition
Leaf plasticity
Nutrient cycling
Resource acquisition
Salix dasyclados

Agroforestry systems enhance nutrient cycling, in part, through modifications to leaf quality and quantity, and subsequently, decomposition rates. However, leaf traits are plastic and thus variable across both temporal and spatial scales in agroforestry systems. Using a temperate tree- based intercropping system with willow, this study examined effects of shade tree functional group (N2-fixer, Non N2-fixer, or monoculture) and distance from shade tree on i) willow leaf traits (leaf area, leaf weight, specific-leaf area (SLA), leaf nitrogen concentration (LNC), and subsequently ii) trait variability influence on decomposition rates in a lab incubation. Willow leaves within agroforestry treatments exhibited greater leaf area, SLA, and LNC than within the monoculture treatment. Willow leaf decomposition followed a two-pooled kinetic model with k1 values ranging from 0.20 to 0.29 d-1 and k2 values ranging from 0.0019 to 0.0023 d-1. Willow litter in agroforestry systems presumably provides soils with additional N, potentially reducing required fertilizer inputs.
Purifying and Positive Selection Influence Patterns of Gene Loss and Gene Expression in the Evolution of a Plant Sex Chromosome System
Keywords: dosage compensation
genetic degeneration
Rumex
sex chromosomes

The degeneration of the Y chromosome is a hallmark of sex chromosome evolution. However, it is not known whether degeneration occurs as a direct result of selective interference due to lack of recombination, or whether adaptive gene silencing on the Y results in neutral degeneration. I used comparative transcriptome data from two related plant species with heteromorphic sex chromosomes, Rumex rothschildianus and R. hastatulus, to investigate processes underlying Y chromosome degeneration. The rate of degeneration varied greatly between the two species. In R. rothschildianus, I infer widespread gene loss. Genes showing lower constraint and those not expressed during the haploid phase were more likely to be lost. There was evidence of adaptive evolution on the Y from over-expression of Y alleles in certain genes. Targeted dosage compensation was occurring in more constrained genes. These results are consistent with selective interference playing a crucial role in the degeneration of the Y.
A Composite System using Ultra High-performance Fibre-reinforced Concrete and Cross-laminated Timber
Keywords: cross-laminated timber
ductile shear connector
ultra high-performance fibre-reinforced concrete
wood-concrete composite

The application of cross-laminated timber (CLT) as floor panels is limited by excessive deflection and vibration. A composite system combining CLT and ultra high-performance fibre-reinforced concrete (UHPFRC) was developed to extend span limits. Push-off tests were conducted on different connectors, and a glued-in rod connector was chosen and further refined for the proposed system. Static bending tests and free vibration tests were conducted on bare CLT panels and two composite specimens. By comparing the results, it is concluded that the proposed system considerably extend the span limits of CLT panels.
Hybrid Lead-acid/Lithium-ion Energy Storage System with Power-mix Control for Light Electric Vehicles
Keywords: Batteries
DC-DC Converters
Electric Vehicles
Hybrid Energy Storage System
Power Electronics
Power-Mix Control

This work presents a hybrid energy storage system (HESS), using lithium-ion (LI) and lead-acid (PbA) batteries, for light electric vehicles (LEV) that is both cost and performance competitive with single energy storage system (SESS) configurations. A modular HESS architecture with a dc-dc converter and controller is proposed. The power-mix algorithm that minimizes the Peukert effect, and increases the usable energy of the lead-acid battery is presented and verified experimentally. A novel DLL and PLL based off-time control scheme is demonstrated for inductor ripple current interleaving in the multi-phase dc-dc converter. The cost and performance of the HESS are assessed side-by-side with PbA and LI SESS configurations of comparable total energy. The experimental HESS has a total projected cost midway between the SESS PbA cost and the SESS Li cost, while providing 17% range and 23% efficiency increase over the SESS PbA vehicle.
A Comparison between GaN and Silicon Based Class D Audio Power Amplifiers with Pulse Density Modulation
Keywords: Class D Amplifier
GaN power device

GaN power devices have lower specific on-resistance and faster switching speeds when compared to silicon power devices. These attributes make the GaN devices attractive for switching power converters. However, the application of GaN power devices in Class D audio power amplifier have not been widely studied. This thesis studies the performance of two 25 W open-loop GaN and silicon based Class D audio amplifiers using Pulse Density Modulation. The distortion, efficiency and thermal characteristics of a GaN based and a silicon based Class D amplifiers performances are compared under matching operating conditions. The GaN based amplifier shows a 0.15 % reduction in distortion and a 15 % increase in efficiency at output power levels of less than 20 W. However, the GaN based amplifier exhibits a 0.1% increase in distortion with 5 Ë C rise in temperature.
Towards Construction of a Biosensor for the Detection of Early-stage Ovarian Cancer: Evaluation of Novel DNA Aptamers for the Capture of Biomarker HSP10
Keywords: aptamer
biosensor
heat shock protein
ovarian cancer
silanes
surface chemistry

The current test for ovarian cancer is associated with many false positives and false negatives. With ovarian cancer being the deadliest gynaecological cancer, the diagnostic inadequacy of the current test creates an imperative need for a method that can detect for early-stage ovarian cancer. Fortunately, HSP10 has recently emerged as a potential biomarker for early-stage ovarian cancer. Four DNA aptamers were evaluated for their binding affinity towards HSP10 using two methods. The first method employed use of gel electrophoresis, a common method to study interactions, mainly bind-and-release, between biomolecules. The second employed novel surface chemistry with the EMPAS. With the combination of both methods, a candidate DNA aptamer was selected for surface chemistry immobilization, moving towards building a crude biosensor. This is the first steps towards creating a novel biosensor which can provide women with a screening test that has the ability to mitigate deaths associated with ovarian cancer.
Ontario's Grade 6 Learners' Mathematics Achievement Profiles Underlying the EQAO Junior Division Assessment
Keywords: EQAO
Exploratory Factor Analysis
Large-scale assessment
Latent Class Analysis
Mathematics
Ontario

The popular approach of using overly simplistic total scores as the sole indicator of learner performances in the complex discipline of mathematics, restricts the recognition of remedial needs (Nichols, 1994). This study analyzed a random sample of 5,000 Grade 6 learner responses, out of 127,302 to the 2013-2014 EQAO assessment, to better understand mathematical performances. Firstly, an Exploratory Factor Analysis was performed to investigate the dimensionality of the test, followed by an investigation of strengths and weaknesses in these dimensions using a Latent Class Analysis (Collins Lanza, 2010). Results revealed that the majority of learners were strong in their ability to apply mathematical knowledge to solve problems, but weak in applying process or thinking skills to do the same. This pattern was consistent regardless of linguistic background. These results highlight the urgent need to not only remediate learnersâ mathematical thinking abilities, but also future research into this skill dilemma.
Inflammatory Responses that Drive Survival and Vascularization of Tissue Engineered Grafts
Keywords: Angiogenesis
Diabetes
Inflammatory Response
Islet Transplantation
Tissue Engineering
Vascularization

Tissue modules containing endothelial cells, vascular support cells, therapeutic cells and collagen self organize upon implantation, producing a vascularized tissue. Hypoxia and inflammatory cells are important aspects of tissue regeneration. First, the effects of a 10x increase in mesenchymal stromal cells (MSC) density on the host response was investigated. Increased MSC densities led to augmented host (CD31+) vessel formation but fewer graft-derived (UEA-1+) vessels compared to standard density controls, with no difference in inflammatory cell recruitment. Next, the host response to transplanted islets using the modular system was investigated. Interestingly, sustained inflammation was found at day 7; more neutrophils and macrophages were found in implants containing islets relative to no islet controls. The presence of endothelial cells led to increased vessel formation and maintained modular integrity. This work demonstrated both the importance of hypoxia on driving vessel formation and the opportunity for modular tissue engineering to enhance subcutaneous islet transplantation.
Design, Synthesis, and Evaluation of Antiepileptic Compounds Based on β-Alanine and Isatin
Keywords: Chemistry
Epilepsy
Isatin
Kindling
Medicinal
Synthesis

Epilepsy is the fourth-most common neurological disorder in the world. Approximately 70% of cases can be controlled with therapeutics, however 30% remain pharmacoresistant. There is no cure for the disorder, and patients affected are subsequently medicated for life. Thus, there is a need to develop compounds that can treat not only the symptoms, but also delay/prevent progression. Previous work resulted in the discovery of NC-2505, a substituted β-alanine with activity against chemically induced seizures. Several N- and α-substituted derivatives of this compound were synthesized and evaluated in the kindling model and 4-AP model of epilepsy. In the kindling model, RC1-080 and RC1-102 were able to decrease the mean seizure score from 5 to 3 in aged mice. RC1-085 decreased the interevent interval by a factor of 2 in the 4-AP model. Future studies are focused on the synthesis of further compounds to gain insight on structure necessary for activity.
Characterization of VPS33B and VPS16B in Megakaryocyte and Platelet α-granule Biogenesis
Keywords: alpha granule
ARC syndrome
BioID
Platelets
VPS16B
VPS33B

Platelets play a key role in vascular homeostasis by triggering platelet adhesion, aggregation, and release of cargo from secretory granules. Inherited defects in α-granule cargo sorting and packaging in platelet precursor megakaryocytes (MKs) include arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome, which is characterized by mutations in VPS33B or VPS16B. In this study, components of the multisubunit tethering complex, GARP/EARP, and an endosomal transport complex, CCC, were identified as potential interacting partners for VPS33B/VPS16B using a BioID screen and mass spectrometry. These interactions were confirmed and characterized via immunoprecipitation experiments, and immunofluorescence microscopy studies of megakaryocytic cell lines (Dami, imMKCL) revealed that subunits of the GARP/EARP and CCC complexes co-localize with markers of the trans-Golgi Network, late endosomes and α-granules. These findings suggest a role for previously unsuspected interactions of GARP/EARP, CCC and VPS33B/VPS16B complexes in α-granule biogenesis by regulating intracellular membrane fusion in a coordinated nature.