VictorJuiz/thesis huggingface dataset:
After Intracerebral Hemorrhage, Oligodendrocyte Precursors Proliferate and Differentiate Inside White-matter Tracts in the Rat Striatum

Using a rat model of ICH, I quantified survival, proliferation and differentiation of oligodendrocyte-lineage cells (Olig2+) in the peri-hematoma region, surrounding striatum and contralateral striatum from 1â 28 days. In the peri-hematoma, their density increased dramatically and peaked at 7 days, coinciding with disorganization of myelinated axon bundles. By 3 days, many were proliferating locally. By 14 days, their density declined, and by 28 days, it was the same as the contralateral striatum. At 14 and 28 days, many surviving axons were aligned into white-matter bundles, which appeared less swollen or fragmented. Oligodendrocyte maturation was prevalent over the 28-day period. Densities of immature OPCs (NG2+Olig2+) and mature (CC-1+Olig2+) oligodendrocytes increased dramatically over the first week. Regardless of the maturation state, they increased preferentially inside the white-matter bundles. Thus, endogenous oligodendrocyte precursors proliferate and differentiate in the peri-hematoma region and have the potential to re-myelinate axons tracts after hemorrhagic stroke.

Keywords: hemorrhagic stroke
myelinated axon tracts
oligodendrocyte maturation
peri-hematoma recovery
post-stroke recovery
Advisor: Schlichter, Lyanne C
An Inter-vascular Bed and Inter-species Investigation of Epigenetic Regulatory Elements in Endothelial Cells

A major challenge in human genetics is to understand the mechanisms that control gene expression. To identify gene regulatory regions required for vascular homeostasis, we performed chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) for a variety of histone modifications and the JUN transcription factor in primary aortic endothelial cells (ECs) isolated from human, rat (Rattus norvegicus) and bovine (Bos taurus). We generated a chromatin state map for human aortic ECs and found that the vast majority of regulatory regions in aortic ECs were also active in venous ECs. By comparing the genomic occupancy of JUN and a histone modification indicative of active enhancers (H3K27ac) between species, we identified a set of conserved regulatory regions that were enriched for EC-specific pathways and human regulatory disease variants. Overall, we demonstrate that comparative epigenomics is a viable strategy to identify functionally important vascular gene regulatory elements.

Advisor: Wilson, Michael D
Effect of Surface Treatments on Zirconia Roughness and Wear of Opposing Artificial Enamel

Abstract: Yttria-tetragonal zirconia polycrystal Y-TZP is used in dental restorations. Although occlusal adjustments are often necessary, their effect on Y-TZP surface roughness and tooth wear is unknown. This study investigated the effect of surface condition (Control polished–CPZ; ground–GRZ; repolished–RPZ; Glazed–GZ; Porcelain-veneered–PVZ) on zirconia roughness and wear of opposing enamel (steatite indenters) after chewing simulation (500,000cycles, 80N, artificial saliva). A surface profilometer was used to evaluate zirconia roughness (μm) and steatite volume loss (mm3). Representative specimens from each group were characterized by scanning electron microscopy (SEM). Three-way Analysis Variance (ANOVA) and Tukey HSD (p≤0.05) showed that there was a significant interaction effect (p

Advisor: DE SOUZA, GRACE M
Investigating the Differences between the Self-heating of Bark and Wood Piles during Storage through the Use of Computer Modeling

Due to the problems associated with self-heating in large piles of woody materials and the requirement of Nova Scotia Power to use bark to power a large biomass boiler, modeling was conducted to determine whether wood self-heating models could be used for softwood bark piles. During an approximately 100 day storage trial of 2 large bark dominated biomass piles, the piles peaked at average temperatures of 40째 C and 50째 C. Modeling in Comsol Multiphysics with bark parameters obtained from physical characterization tests of material from trial site yielded accurate predictions of pile temperature, with pile 2 being simulated closely by the model. Pile heating differed between sections of the piles, with the bottoms of the pile heating much slower than the rest. A sensitivity analysis yielded several parameters, which affected the model, such as bulk density, thermal conductivity, pile height and microbial death and growth rates.

Keywords: Bark
Canada
Modeling
Pile
Self-Heating
Woodchip
Advisor: Krigstin, Sally
Enhancement of Hydride-terminated Silicon Nanocrystals for Gas-phase Heterogeneous Carbon Dioxide Reduction

Utilization of solar energy for the conversion of carbon dioxide into fuels and chemical feedstocks serves as a promising solution to mitigate anthropogenic greenhouse gas emissions while providing global energy security and environmental protection. Silicon nanocrystals (ncSi) are attractive materials for the photoreduction of CO2 due to their favorable earth-abundance, non-toxicity, optical properties, and high surface area. Herein, through rational modification of ncSi by introducing boron and phosphorus dopants utilizing a novel, facile sol-gel synthesis, it was demonstrated that dopants successfully enhanced the gas-phase CO2 adsorption capacity and solar fuel production rate. Remarkably, it was found that phosphorus-doped ncSi was the best performer among the various ncSi samples due to the combination of the number of surface hydrides and the addition of electronegative surface atoms. Preliminary results of the optimization of reaction conditions in a batch photoreactor enabled an enhancement of the solar fuel production rate.

Keywords: carbon dioxide conversion
doping
silicon nanocrystals
solar fuels
Advisor: Ozin, Geoffrey A
Femtosecond Laser Direct-write of Optofluidic Lab in Fiber through Polymer-coated Optical Fibers

Three-dimensional femtosecond laser processing of lab in fiber, the combination of integrated photonics and microfluidics inside optical fiber, was demonstrated in silica glass fibers coated with polymer buffer. This enables the laser fabrication of lab-on-chip functionalities onto optical fiber without the time-consuming and mechanically-compromising process of buffer removal. In this thesis, an assessment of laser-induced damage in buffer-coated fiber is reported, along with methods to avoid and mitigate this damage. Further, selective buffer machining is studied enabling in-tandem processing of the glass fiber core and cladding with the polymer buffer. Structuring of the fiber core, cladding photonic circuits, and microfluidics were demonstrated in buffer-coated fiber without removal of or damage to the polymer buffer. The methods and processes here make the lab in fiber platform to be more industry viable and opens new opportunities for device architectures spanning across the fiber core, cladding, and buffer, representing a significant technological advancement.

Keywords: Femtosecond laser
Lab in fiber
Lab on chip
Micromachining
Optical sensing
Optofluidics
Advisor: Herman, Peter R
Aitchison, James S
Characterization of the Solvus Transformation in Ternary and Quaternary Bismuth Containing Lead-free Solder Alloys

Compliance with RoHS requirements has necessitated the development of high reliability alternatives to SAC305 lead-free solder. Bismuth containing ternary and quaternary alloys are emerging as an attractive lead-free high reliability solder. A particular point of interest is the solvus temperature â the point above which Bi will form a solid solution, and below which Bi will precipitate out of the matrix. The solvus temperature of these solders was determined using a novel differential scanning calorimetry (DSC) method. A study was conducted to characterize the effects of aging above- and below-solvus on microstructure and mechanical properties. Metallographic analysis showed that above-solvus aging improved bismuth distribution as well as reduced grain size. It was concluded that above-solvus aging could be used as a restorative treatment for in service electronics. Nano-indentation was used to collect creep and hardness data, and it was found that above-solvus aging had a positive effect on mechanical properties.

Keywords: Bismuth
Lead-free
Quaternary
Solvus
Ternary
Advisor: Perovic, Doug D
Intraoperative Pulmonary Nodule Localization with Cone-beam Computed Tomography and Deformable Image Registration

Localization of small pulmonary nodules is challenging during video-assisted thoracic surgery. Current localization methods complicate surgical workflow, increase radiation exposure and introduce additional complication risks. This study evaluates the use of cone-beam computed tomography (CBCT) and deformable image registration to help predict the final location of lung nodules in the intraoperative deflated lung. Porcine and phantom models were developed to simulate the CBCT image acquisition process. To improve the lung registration accuracy, two additions to the Demons registration method were tested, including correcting for lung tissue density differences, and estimating whole lung deflation motion with sampled airway tree landmarks (LDE). CBCT image acquisition during VATS was found to be feasible. The target registration error (TRE) for the unmodified Demons method ranged 13.363-33.974 mm. Only LDE helped significantly reduce TRE by an estimated 7.8 Âą 2.3 mm. The developed registration methods lay the groundwork for future CBCT-based intraoperative nodule localization methods.

Keywords: Computed Tomography
Deformable Image Registration
Image Processing
Lung Cancer
Minimally Invasive Surgery
Thoracic Surgery
Advisor: Yasufuku, Kazuhiro
Fabrication of Lipid-Stabilized Oil-in-Water Nanoemulsions as Dual-Modal CT, Fluorescence Contrast Agents

The staggered use of CT and near-infrared fluorescence imaging enables mapping of patient vasculature in surgeries involving free tissue transplantation. Visualization of tissue perfusion by CT determines surgical margins of donor site during pre-operative planning. Subsequent to this vascular mapping, fluorescence imaging with the dye indocyanine green (ICG) is used to intra-operatively assess blood flow during donor tissue implantation and later post-operatively evaluate the transplanted tissueâ s circulatory health in recipient sites. Considering the individual shortcomings of CT contrast media and ICG, the design of a CT, fluorescence a dual-modal agent would eliminate the need for separate contrast and imaging agent administration and combine pre-operative vascular architecture mapping by CT with the standard method of evaluating tissue circulatory health intra- and post-operatively by fluorescence. In this work, the fluorescent and X-ray attenuating properties of a CT, fluorescent active lipid nanoemulsion (LNE) formulation, have been characterized in vitro and in vivo.

Keywords: computed tomography
fluorescence
free flap tissue transfer
lipid monolayers
nanoemulsions
porphyrins
Advisor: Zheng, Gang
Determining the Effect of Small Doses of Fructose and its Epimers on Glycemic Control

Given that sugars have emerged as the dominant nutrient of concern in diabetes, there is a need for the development of alternative sweeteners. To assess the role of small doses (5g, 10g) of fructose and allulose on postprandial glucose metabolism, we conducted an acute randomized controlled trial in individuals with type 2 diabetes. We found that small doses of allulose, but not fructose, modestly reduced the postprandial glycemic response to a 75g oral glucose load. To assess whether low-dose (

Advisor: Sievenpiper, John L
Using Functional Electrical Stimulation to Improve Upper Limb Function: Determining Feasibility and Effectiveness in Children with Hemiplegic Cerebral Palsy

Children with hemiplegic cerebral palsy (HCP) often have impaired reaching and grasping. Multichannel-functional electrical stimulation (mFES) therapy has been used for upper limb rehabilitation after adult stroke, but treatment response in HCP has seldom been studied. Furthermore, most of the previous investigations on the use of FES in cerebral palsy have employed systems that only stimulate one to two muscles at a time. The purpose of this study is to evaluate the feasibility and effectiveness of upper limb mFES in children HCP. Feasibility indicators for recruitment, adherence, safety, and pain/discomfort were assessed, and clinical effectiveness outcomes were collected before, immediately after, and six-month post-intervention for three children with HCP (6 – 13 years; MACS: I–II). Criteria were met for all feasibility indicators, except recruitment. Grasping ability as measured by the Quality of Upper Extremity Skills Test (QUEST) grasp domain improved in two out of three children post-test, while another child’s ability deteriorated. Performance changes on remaining outcomes were low and evidence for positive response was inconclusive.

Keywords: cerebral palsy
electric stimulation therapy
hemiplegia
motor disorders
stroke
upper extremity
Advisor: Fehlings, Darcy
BIO-INSPIRED, DYNAMIC MICROTOPOGRAPHY SURFACES FOR WETTING CONTROL

Controlling the wettability of solid surfaces has been a fundamental topic in the realm of surface engineering. Although previous research in this field has examined the connection between wetting properties and static solid surfaces for various surface structures and chemical compositions, few studies have examined how wetting behaviour is affected by dynamic changes in surface structures. In this study, we can dynamically control the wetting properties of superhydrophobic surfaces via microfluidic channels and digitally-controlled pneumatic pressure. We have designed a bio-inspired, multi-layer microfluidic polydimethylsiloxane device with micropillar array surfaces (7.5-10 Âľm diameter) that can be mechanically deformed to dynamically change the pillar spacing (pitch) and orientation. We show that the static contact angle, the adhesion force of droplet, roll-off angle, dynamic control of surface wetting (catch-and-release, direction control, merge-and-mix) and selective transition of wetting state (from Cassie-Baxter to Wenzel) can reliably be influenced by the topographic deformation.

Keywords: Bio-inspired
microtopography
superhydrophobic
surface wetting
wetting control
Advisor: Hatton, Benjamin D
Pathways to Eating in Children and Adolescents with Obesity

Objective: To determine whether treatment-seeking children and adolescents with obesity cluster into phenotypes based on known eating drivers and whether phenotypes can be distinguished based on clinical characteristics. Methods: Latent Profile Analysis was used to cluster participants based on seven eating driver scores obtained from questionnaires. Analysis of variance was used to determine phenotype differences on clinical variables. Results: Seven eating drivers clustered into three distinct phenotypes, namely: 1) loss of control eating, impulsivity, inattention (named LOCE-ADHD), 2) No elevated drivers (named No-ED), and 3) loss of control eating, emotional eating, external eating, restrained eating, hyperphagia (named Restrained-Triggered). LOCE-ADHD was younger, non-White, ate out or ordered in meals less frequently, and had lower BMI, decreased social functioning, and fewer diagnoses of depression than the other groups. Restrained-Triggered had the lowest body esteem. Conclusions: Distinct eating phenotypes are found in youth with obesity that should be considered in treatment approaches.

Advisor: Hamilton, Jill
Pharmacokinetics of Vancomycin in Paediatric Patients Receiving Haemodialysis and Haemodiafiltration

Optimal vancomycin dosing in paediatric patients requiring haemodialysis (HD) or haemodiafiltration (HDF) remains unknown. The current study aimed to characterize vancomycin pharmacokinetics in this population. The pharmacokinetic parameters were estimated using a single compartment model and least-squares algorithm. The mean drug removal was 56.38% immediately post-dialysis, rebound was 23% post-redistribution, and net drug removal was 43% for patients on vancomycin undergoing HD/HDF. While on HD/HDF, the median elimination constant (ke) was 0.32h-1, and clearance was 0.18L/kg/h. When off dialysis, the median ke was 0.013h-1, clearance was 0.0066L/kg/h and volume of distribution was 0.64L/kg. All patients who received vancomycin 10 mg/kg/dose post-dialysis for proven infections were successfully treated. No adverse effects were reported except for one case of Redman syndrome. Monte Carlo simulations demonstrated that the current regimen is optimal to reach therapeutic range for 4-hour post-dialysis vancomycin concentrations and 24-h area under the curve over minimum inhibitory concentration â Ľ400.

Keywords: Dialysis
Nephrology
Paediatrics
Pharmacokinetics
Vancomycin
Advisor: Seto, Winnie
Probing the Molecular Interactions of ATRX

Alpha thalassemia/mental retardation syndrome X-linked (ATRX) is linked to both developmental disease and cancer. ATRX functions in coordination with Death Domain Associated Protein 6 (DAXX) in a histone deposition pathway of a histone 3 variant at heterochromatin. While ATRX has recently been implicated in many alternative functions, mechanistic information is lacking. We performed proximity dependent biotinylation and protein identification to determine an unbiased list of labile ATRX interactors. As expected, we found transcriptional repressors and DAXX. Surprisingly, we also found many proteins involved in homologous recombination and nucleotide excision repair to be interacting with ATRX in the absence of DNA damaging events. Additional interactions include proteins involved in centromere maintenance and one nucleolar protein involved in RNA processing. These results suggest ATRX has a dynamic role in DNA damage repair and provide further support for its role as a nuclear protein involved in H3.3 deposition at endogenous retroviral elements.

Keywords: ATRX
BioID
Advisor: Campos, Eric I
ISGylation and EGFR Signaling is Modulated by BRCA1 Expression and Follicular Fluid Exposure in Human Fallopian Tube Epithelium

Germline BRCA1 or BRCA2 mutation carriers (mtBRCA1 and mtBRCA2) are at increased risk for high-grade serous ovarian cancer (HGSOC), which is thought to originate in the fallopian tube epithelium (FTE). Other risk factors suggest an impact of ovulation, where FTE is exposed to follicular fluid (FF). Comparisons of the gene expression response of primary FTE cells from mtBRCA1/2 and control women to FF revealed BRCA1/2 impacted gene expression even in the absence of FF exposure, with increased NFκB and EGFR signaling observed in mtBRCA1. Following FF exposure, an increase in interferon-responsive genes was observed, including members of the ISGylation protein modification pathway. A role for increased NFκB signaling in enhancing EGFR signaling and ISGylation was indicated using an immortalized FTE cell line stably transfected with BRCA1. This study demonstrates increased ISGylation from elevated NFκB signaling is associated with decreased BRCA1 expression, representing potential targets for chemoprevention for HGSOC in mtBRCA1.

Keywords: BRCA1
Cancer
Fallopian
Inflammation
Ovarian
Tube
Advisor: Brown, Theodore J
Construct Validity of the Family Impact of Assistive Technology Scale for Augmentative and Alternative Communication: A Parent-Report Measure for Children with Complex Communication Needs

Background: Valid and reliable parent-report outcome measures that detect the functional performance of children who use augmentative and alternative communication (AAC) systems are unavailable. The Family Impact of Assistive Technology Scale for AAC (FIATS-AAC) was developed to fill this measurement need. Objective: To evaluate the construct validity of the FIATS-AAC as a measure of the functional status of children with AAC needs and their families. Methods: Phase 1: Forty-seven parents of children, 6 to 12 years, with AAC needs, completed a mail-out survey that included the FIATS-AAC and two measures of quality of life and child participation in the community. Phase 2: Six parents also participated in a face-to-face interview. Results: Low-to-moderate correlations between the FIATS-AAC and the standardized measures were found. Interviews suggest some consistency between measurement scores and analyzed narratives. Conclusion: The FIATS-AAC has the potential to assess functional status as it relates to community participation and quality of life of children with AAC needs.

Keywords: augmentative and alternative communication
complex communication needs
disabled children
outcome assessment
rehabilitation
validity
Advisor: Ryan, Steve
Evaluation and Design of Interventions to Improve Developmental and Nutritional Outcomes in Children with Severe Acute Malnutrition

The WHO guidelines recommend the provision of psychosocial stimulation for children hospitalized with severe acute malnutrition (SAM) based on expert advice. The first objective of this thesis was to synthesize evidence around this recommendation. Specifically, it was to answer the question, â In children with SAM, does psychosocial stimulation improve developmental, nutritional, or other outcomes?â A systematic review was completed by searching MEDLINE, Embase, CINAHL, and PsycINFO with terms related to SAM and psychosocial stimulation. Results showed that the evidence supporting the recommendation of psychosocial stimulation for children with SAM is sparse and different approaches to psychosocial stimulation interventions should be further explored. Therefore, the second objective of this thesis was to develop a four-day hospital-based intervention program combining psychosocial stimulation with nutrition and water, sanitation and hygiene for primary caregivers of children with SAM. A cluster-randomized controlled trial was designed to evaluate the effectiveness of this intervention program.

Keywords: child development
psychosocial stimulation
severe acute malnutrition
Advisor: Bandsma, Robert H
Development and Validation of a Multifunctional Embolic Platform

Tumor embolization, the occlusion of vasculature, may be performed prior to surgery or when surgical contraindications arise. The use of magnetic resonance (MR) and computed tomography (CT) determine tumor location and margin for the radiotherapy delivery. Clinically available embolic systems provide no contrast enhancement and prevent the delivery of conventional contrast agents, hindering post-treatment imaging and image-guided planning. Thus, a novel solution for post-embolization imaging is needed to enable target localization and delineation for planning and treatment delivery. This thesis describes a proof of principle study to engineer a multifunctional embolic system for embolization and multimodal imaging through CT and MR. In vitro and in vivo methodologies were developed and optimized to assess physical properties, imaging performance, and potential radiosensitizing effects. This preliminary work demonstrated that a multifunctional embolic platform has the potential to positively impact tumor visualization and radiosensitization on embolized tumor, ultimately improving disease monitoring and treatment delivery.

Keywords: Embolization
Imaging
Radiosensitization
Advisor: Zheng, Jinzi