VictorJuiz/thesis huggingface dataset:
Validating Intrinsic Spectral Broadening models via Doppler Ultrasound Simulations

Doppler ultrasound (DUS) is one of the most widely used medical imaging modalities for measuring blood flow velocities to aid in diagnosing patients and analyzing cardiovascular disease. One of the more common artifacts in DUS is intrinsic spectral broadening (ISB), which smears out the measured velocities owing to the finite size of the ultrasound transducer and its focal region, known as the sample volume (SV). Analytic models of ISB have been developed under assumptions that include an axisymmetric SV, and simple, Gaussian-shaped Doppler frequency spectra. The validity of a particular model was tested using the numerical simulator, Field II, by measuring the change in ISB from varying its governing variables including the Lateral focus, using a measurement technique called the Occupied Bandwidth. In conclusion, the model was able to predict the effects of ISB from examining the behavior of a single scatterer, but failed when looking at a velocity profile.

Keywords: Actual focal spot
Doppler ultrasound
Intrinsic Spectral Broadening
Occupied Bandwidth
Advisor: Steiman, David A
Understanding the Effects of Nozzle Design and Spray Characteristics for Optimizing Pyrolysis Liquid Biofuel Ignition and Combustion

This thesis examines how nozzle design and spray characteristics influence the combustion and emissions of a pure pyrolysis liquid biofuel (PLB) flame in a 10kW, insulated, swirl burner using an internally mixed air-blast nozzle. PLB is a carbon-neutral fuel made from waste wood, but its properties make efficient combustion challenging. First, atomization trends were examined with distilled water to elucidate the important parameters and design aspects and to determine the nozzle's primary atomization mechanism(s). With this information, combustion experiments studied how carbon monoxide, nitric oxide, carbonaceous residue, flame stability and coking were influenced by the nozzle's mixing chamber diameter and outlet number/diameter, angle and total area in order to optimize the design of the nozzle. Ultimately, an optimized nozzle was designed that achieved a self-sustaining PLB flame with good stability, low emissions and low coking. In addition, it allowed for "cold-starting" and pilot flame extinguishment at steady-state while maintaining stability.

Keywords: Biofuel Spray Combustion
Flame Stability
Internally Mixed Twin-Fluid Nozzle
Nozzle Design
Pyrolysis Liquid Biofuel
Sustainable ENergy
Advisor: Thomson, Murray
Design and Modelling of a Miniature Instrument for Robotic Surgery

The da VinciÂŽ Surgical System, the worldâ s most prominent form of robotic surgery, provides significant advantages over conventional surgery yet currently it cannot be used for surgical applications involving small operating volumes due to the existing instrument sizes (5-8mm shaft diameter). This research explores the feasibility of creating and accurately controlling a robotic instrument with a 2mm diameter and a three degree-of-freedom wrist. A unique wrist joint composing of a two degree-of-freedom bending notched-nitinol tube pattern is developed along with a proposed kinematic model. A base mechanism for controlling the wrist is designed for integration with the da Vinci Research Kit. A basic teleoperation task is successfully performed using two of the miniature instruments. The performance and accuracy of the instrument suggests that creating and accurately controlling a 2mm diameter instrument is feasible and the design and modelling proposed in this work provides a basis for future miniature instrument development.

Keywords: Miniature Instrumentation
Notched nitinol tube joint
Surgical Robotics
Wrist joint design
Advisor: Drake, James
Designing an Effective Millirobot for Swarm Behaviour Studies with Human-Swarm Interaction

This thesis presents a novel design of an open-source millirobot utilized for swarm behaviour studies and a novel swarm localization algorithm to enable human-swarm interaction (HSI). Millirobots have increasingly become popular over the past years in swarm robotics research. However, currently existing millirobots for swarm robotics research are typically custom made, with few off-the-shelf components, and exhibit integral design. Furthermore, as these robots have become smaller in size, their sensory capabilities and battery capacities have been reduced. This thesis proposes a new millirobot design that addresses the abovementioned limitations. For swarm robots to be successfully integrated into real world applications, HSI must be enabled; a human supervisor monitors and provides meaningful commands to the robots. One method of enabling HSI is through localization. This thesis proposes a novel localization method to estimate the swarm topology without the use of any external sensors such as overhead cameras monitoring the robots.

Advisor: Benhabib, Beno
Nejat, Goldie
MODELLING PRDM14 EXPRESSION IN HUMAN ACUTE MYELOID LEUKEMIA

PRDM14 is an embryonic stem cell pluripotency regulator that is ectopically expressed in human malignancies. The aim of my thesis is to gain insight into the role of PRDM14 in human leukemia and its effects on the proliferation and differentiation of the hematopoietic system. Our lab has previously shown that Prdm14 expression in mouse bone marrow cells results in lymphoblastic leukemia. To test if it has the same effect on the human hematopoietic system, I expressed PRDM14 in human hematopoietic stem and progenitor cells. Here, I show that PRDM14 arrests myelopoiesis at an early CD34+CD38+ stage, resulting in the expansion of a relatively immature hematopoietic progenitor population. Taken together, these experiments advance our understanding of the role of PRDM14 in human leukemia.

Advisor: Justice, Monica
FINITE ELEMENT VIBRATION MODELLING AND EXPERIMENTAL VALIDATION FOR AN AIRCRAFT ENGINE CASING

This thesis presents a procedure for the development and validation of a theoretical vibration model, applies this procedure to a pair of aircraft engine casings, and compares select parameters from experimental testing of those casings to those from a theoretical model using the Modal Assurance Criterion (MAC) and linear regression coefficients. A novel method of determining the optimal MAC between axisymmetric results is developed and employed. It is concluded that the dynamic finite element models developed as part of this research are fully capable of modelling the modal parameters within the frequency range of interest. Confidence intervals calculated in this research for correlation coefficients provide important information regarding the reliability of predictions, and it is recommended that these intervals be calculated for all comparable coefficients. The procedure outlined for aligning mode shapes around an axis of symmetry proved useful, and the results are promising for the development of further optimization techniques.

Keywords: Modal testing
Model validation
Vibration analysis
Advisor: Behdinan, Kamran
Energy Level Alignment at Donor-Acceptor Interfaces and Its Correlation with Open-Circuit Voltage

Organic photovoltaic (OPV) cell has attracted great interests due to its low cost manufacturing method and its flexible form factor. In this thesis, we utilize physical vapor deposition to fabricate different donor-acceptor interfaces and devices. First, we study the effect of substrate work function on the energy level alignment at these interfaces by ultra-violet photoemission spectroscopy (UPS). Second, OPV cells are fabricated based on the same sets of materials used in the UPS study. Third, a theory is proposed in order to explain the observed relationship between open-circuit voltage VOC and the donor-acceptor energy offset EDA. The main findings of this thesis are: (a) the substrate work function has negligible impact on energy level alignment between donor and acceptor; (b) VOC is closely related to EDA; and (c) a new proposed theoretical model predicts that VOC reaches a maximum if EDA is equal to the difference between singlet energy and a constant which relates charge transfer state energy to EDA.

Keywords: Donor-acceptor interface
Energy level alignment
Open-circuit voltage
Organic photovoltaic cell
Advisor: Lu, Zheng-Hong
Investigating the Immune Microenvironment in Osteosarcomas

Osteosarcoma (OS) is a mesenchymal tumor that is the most common malignant bone tumor in children and young adults. Our objective was to identify novel pathways in OS that may be related to the expression of an immunosuppressive protein ‘programmed cell death ligand 1 (PD-L1)’. Using RT-qPCR, varying levels of relative PD-L1 gene expression was shown in 69 primary OS tumors. Ingenuity pathway analysis was utilized to analyze 400 significantly differentially expressed genes between the high and low PD-L1 expressing OS tumors and the elongation initiation factor 2 (EIF2) pathway was illustrated to be significantly down-regulated (p=3E-07; z-score=-2.5) and the ‘cell death of OS cells’ was predicted to be significantly activated in OS tumors with high PD-L1 expression (p=1E-04; z-score=2.53). Both IFN- and thapsigargin were utilized to observe the effects of attenuating the EIF2 pathway on PD-L1 expression. Overall, the down-regulation of the EIF2 pathway did not influence PD-L1 expression.

Keywords: EIF2
microenvironment
osteosarcoma
PD-L1
Advisor: Andrulis, Irene L
Wunder, Jay S
Role of HDAC6 in Transcription Factor EB Mediated Clearance of Misfolded Proteins in Chronic Kidney Disease

The autophagy-lysosomal pathway is a homeostatic mechanism to prevent the accumulation of misfolded proteins. Here, we observed a downregulation in a master regulator of autophagy, transcription factor EB (TFEB) and an increase in misfolded protein accumulation in kidneys from humans with diabetic kidney disease and in subtotally nephrectomized (SNx) rats, pointing to dysregulated autophagy as a common occurrence in chronic kidney disease (CKD). In assessing methods to induce autophagy, we found that inhibition of histone deacetylase 6 (HDAC6) caused hyperacetylation and nuclear translocation of TFEB, and reduced cell death in cultured proximal tubule cells. Similarly, in SNx rats, HDAC6 inhibition decreased misfolded protein accumulation in tubule epithelial cells, attenuated tubule cell death, diminished fibrosis and blunted proteinuria. These findings point to the occurrence of dysregulated autophagy in CKD and identify HDAC6 inhibitors as a novel method to activate TFEB mediated upregulation of the autophagy-lysosomal pathway that may confer renoprotective benefits.

Keywords: Chronic kidney disease
Diabetic nephropathy
Histone deacetylase 6
Misfolded protein
Transcription factor EB
Tubastatin A
Advisor: Advani, Andrew
Progressive Slowing of the Cerebrovascular Response in the Temporal and Parietal Cortex of Patients with Alzheimer's Disease and Mild Cognitive Impairment

There is accumulating evidence that neurovascular dysfunction plays a major role in Alzheimerâ s disease (AD). Recent investigations now suggest that cerebrovascular reactivity (CVR) is impaired in AD and may underpin part of the neurovascular contribution. However, our understanding of the relationship between the magnitude of CVR, the speed of cerebrovascular response, and the progression of AD is still limited. This is especially true in patients with mild cognitive impairment (MCI), which is recognized as the prodromal stage of AD. The purpose of this thesis was to investigate AD and MCI patients using new repeatable and accurate measures of cerebrovascular function, namely the magnitude and speed of vascular response to a vasoactive stimulus. The findings of this thesis demonstrate that AD is associated with a progressive slowing of the cerebrovascular response in proportion to the progression of the disease.

Keywords: Alzheimer's Disease
Cerebrovascular Reactivity
MRI
Advisor: Mikulis, David J
Effects of Decompressive Craniectomy on Functional Outcomes and Mortality in Poor-Grade Aneurysmal Subarachnoid Hemorrhage

Background: Decompressive craniectomy (DC) is often considered as a life-saving measure for trauma and ischemic stroke. Selected patients with poor-grade aneurysmal subarachnoid hemorrhage (aSAH) have been subjected to DC, but its benefits remain unknown. The aim of this meta-analytic review is to surmise the overall effects of DC on poor-grade aSAH outcomes. Methods: Data were acquired from previous publications on DC and the Subarachnoid Hemorrhage International Trialists (SAHIT) Repository. We performed both study-level and individual participant analysis. Results: Fifteen published studies and one dataset from SAHIT met our inclusion criteria. DC was associated with high event rate of unfavorable outcomes and mortality, however, the overall quality of evidence was poor due to high risks of bias and significant heterogeneity in most outcome measures. Conclusion: The currently available evidence suggests that the impact of DC on poor-grade aSAH outcomes is trending toward a harmful effect. High-quality prospective studies are urgently needed.

Keywords: decompressive craniectomy
hemicraniectomy
ICP
intracranial pressure
subarachnoid hemorrhage
Advisor: Macdonald, R. Loch
The Effect of T1 Signal Decay on Ventilation Mapping using Hyperpolarized Gas MRI during Multiple Breath Wash-out

Cystic fibrosis (CF) is a hereditary disease that can severely hinder lung function and cause death at a young age. Sensitive diagnostic tools are necessary to treat CF early. Hyperpolarized xenon-129 magnetic resonance imaging (HP 129Xe MRI) provides a novel technique to assess regional changes in lung function by measuring signal loss through a multiple breath gas wash-out maneuver. This thesis explores how multiple breath wash-out (MBW) imaging is confounded by T1 signal decay. A model of T1 as a function of wash-out breath was developed and investigated in a cohort of healthy mechanically-ventilated rats. By incorporating this model into analysis, measurements of ventilation were corrected by up to 19.3% relative to a published method that utilized a simplified approximation of T1. Significant improvements in the accuracy of MBW imaging were observed, particularly at long time-scales and at reduced lung function. Applying this model to MBW imaging is therefore an important step towards clinical translation of the technique.

Keywords: Hyperpolarized
Lung
Multiple breath wash-out
Ventilation
Xenon
Advisor: Santyr, Giles E
THE DYNAMIC BEHAVIOR OF SLAG BASED GEOPOLYMER MORTAR UNDER VARIOUS CURING TIMES

Currently, geopolymers (e.g. fly ash and slag) are excellent replacements of the traditional ordinary Portland cement (OPC) concrete due to the less production of carbon dioxide into the environment. In this thesis, a split Hopkinson pressure bar (SHPB) system is used to study the dynamic mechanical properties (i.e. dynamic compressive strength, dynamic tensile strength and dynamic fracture toughness) of slag based geopolymer mortars with two pastes and curing times (7 days, 28 days and 56 days). The results indicate that the dynamic mechanical properties of geopolymer mortars increase with the loading rates. In addition, the dynamic compressive strength, tensile strength, and fracture toughness increase with the increase of curing time and decrease with the increase of water content. Some formulas are proposed to describe the trend of the dynamic compressive strength, tensile strength, and fracture toughness.

Keywords: DYNAMIC BEHAVIOR
GEOPOLYMER MORTAR
Advisor: Xia, Kaiwen
Imaging of FTLD-tau Using [18F]AV-1451

Frontotemporal lobar degeneration is a family of heterogenous syndromes with underlying protein pathology including tau, TDP-43, and FUS. There is considerable overlap in the different clinical phenotypes of frontotemporal lobar degeneration and pathological diagnosis of the causative protein is not possible in vivo. The positron emission tomography radioligand [18F]AV-1451 demonstrates specificity to tau protein in Alzheimerâ s disease. The aim of this study was to investigate whether frontotemporal lobar degeneration due to tau protein accumulation could be distinguished from frontotemporal lobar degeneration caused by TDP-43 and controls using [18F]AV-1451. There were no brain regions where [18F]AV-1451 retention was elevated compared to the other groups. In addition, [18F]AV-1451 retention did not correlate to tau localization in autopsy-confirmed progressive supranuclear palsy. [18F]AV-1451 may not have suitable characteristics necessary for detecting tau deposition in frontotemporal lobar degeneration. Ongoing studies will help understand the relationship between [18F]AV-1451 retention and tau deposition in frontotemporal lobar degeneration.

Keywords: frontotemporal lobar degeneration
neurodegenerative
neuroimaging
positron emission tomography
tau
tauopathy
Advisor: Tartaglia, Maria Carmela
Feasibility of Phase-Contrast Cine MRI for Measuring Blood Flow in the Sheep Fetus

Phase-contrast cine magnetic resonance imaging (PC-MRI) is the gold-standard non-invasive technique for measuring vessel blood flow and has been applied in the human fetal circulation. We aimed to examine the feasibility of using PC-MRI to define the distribution of the fetal circulation in late gestation sheep. 13 fetuses underwent MRI at ~123 days gestation under isoflurane sedation, with the mother ventilated at an FiO2 of 1. PC-MRI was performed with blood pressure triggers from fetal arterial catheters. Blood flows were measured in major fetal vessels and indexed to estimated fetal weight. The mean flows were successfully obtained in 82% of the vessels targeted. Failed measurements resulted from poor visualization of target vessels. There was good interobserver agreement (R2=0.993, P

Keywords: Fetal Blood Flow
Fetal Circulation
Phase Contrast MRI
Advisor: Seed, Mike
Development of an In-vitro Organoid Assay to Study Engraftment of Photoreceptor Precursors

Labeled cells in the host retina following transplantation of reporter-labeled donor cells were thought to arise from donor cell migration and engraftment into the tissue, but more recently this interpretation has been challenged with new findings that material transfer occurs between host and donor photoreceptors. In-vivo studies are laborious and impractical to investigate the mechanisms of cell engraftment. As such, we have developed a simpler in-vitro assay that uses retinal organoids to monitor photoreceptor precursor engraftment. Dissociated retinal cells have the propensity to self-organize and form spherical laminated structures or organoids that have features in common with normal retinal organization. Here, we characterize the cellular composition and the cell type requirement for efficient organoid formation. We have further developed an engraftment assay, established a cell integration baseline and shown the application of this assay to models of retinal degeneration.

Keywords: Engraftment
In-vitro model
Photoreceptor transplantation
Retinal organoids
Stem cells
Advisor: Wallace, Valerie A
Burn-Derived Stem Cells - A Promising New Cell Source For Skin Regeneration

Introduction: Burns affect millions of people worldwide. Available wound coverage materials are insufficient due to a lack of cells. Mesenchymal stem cells (MSCs) promote wound healing but are limited by lack of availability. We hypothesise that burned skin contains functioning MSCs (burn derived MSCs; BD-MSCs) that promote wound healing. Methods: BD-MSCs were compared to umbilical cord MSCs in terms of key biological characteristics. Then, skin-scaffolds were cellularized with BD-MSCs, applied onto excisional porcine wounds and observed over 30d. Results: We found no difference between BD- and UC-MSCs in mitochondrial function, proliferation, colony formation, cell cycle stage distribution, reactive oxygen species, and MHC I/II expression. BD-MSCs are safe and improved wound healing in mice and pigs. Conclusion: Burned skin contains healthy MSCs that promote wound healing. Key biological functions are not altered by burn trauma. Further studies are needed to evaluate the role of BD-MSCs in wound healing.

Keywords: Burns
Regenerative Medicine
Skin regeneration
Stem Cells
Wounds
Advisor: Jeschke, Marc G
Impact of Protein Intake on Protein Metabolism and Exercise Performance in Endurance-Trained Males

Background: Current recommendations for athletes consider dietary protein requirements that maintain nitrogen (i.e. protein) balance rather than an optimal dosage to enhance metabolism and exercise performance. Purpose: The primary objective of this study was to determine how differing protein intakes alter protein metabolism and exercise performance. Methods: Using a double blind randomized crossover design, 10 male runners completed 3 trials involving 4 days of controlled training and ingestion of either 0.94 (LOW), 1.20 (MOD) or 1.83 g protein/kg body weight/d (HIGH). Whole body protein metabolism and exercise performance were assessed. Results: Whole body net protein balance displayed a relative dose-response (HIGH > MOD > LOW, P

Keywords: endurance
exercise
metabolism
muscle
protein
Advisor: Moore, Dan
Molding Makers: An ethnography of an academic makerspace

As an exploratory ethnography, this work provides a rich description and analysis of studentsâ experiences in an academic makerspace. Its findings are intended to inform the design and administration of this space and others like it with the voices and perspectives of the people who enliven them. Topics covered are how students first discovered the space, their motivations, needs and wants once there, views of the space, and how they worked together within it.

Keywords: academic
design
ethnography
library
makerspace
student
Advisor: Hartel, Jenna
MOBILITY IN THE CITY: Dalian's Streetcar System from 1890s to 1940s

The electric streetcar is both a product of electric modernity and a form of social technology that shapes the experience of modernity. Using the city of Dalian in northern China from 1890s to 1940s as the site of investigation, this study seeks to provide a deeper understanding of the formation of modern urban landscapes in terms of the movement and division of people engendered by the streetcar in general, and the system’s role in Japan’s colonial project in East Asia in particular. I seek to provide a detailed analysis of the historical roots of the formation of Dalian as a colonial city vis-à-vis its streetcar system to examine the structuring of urban space. I also explore the streetcar both as an engineering and social technology to shed light on theoretical issues such as the notion of mobility and rhythms of everyday life.

Keywords: china
colonialism
japan
streetcar
transportation
urban history
Advisor: Han, Ju Hui Judy
Making HLS a Bit Wiser: From Standard High-Level Datatypes to Arbitrary Low-Level Bitwidths

High-level synthesis provides an easy-to-use abstraction for designing hardware circuits. However, standard datatypes available in high-level languages are over provisioned for typical applications, incurring unnecessary area overhead since the underlying FPGA hardware can support arbitrary bitwidths. We provide a bitwidth minimization (BWM) framework that analyzes and eliminates unused bits in the circuit's datapath and allows for the use of arbitrary width datatypes in the high-level source code. We then propose Sensei, an advisor that predicts the post-synthesis area savings brought about by reducing bitwidth and presents users with a ranking of program variables based on area impact. Together, these two contributions aim to bridge the gap between the over-provisioned datapaths of high-level languages and the arbitrary-width datapaths of low-level circuits.

Advisor: Anderson, Jason H