VictorJuiz/thesis huggingface dataset:
Magnetic Resonance Imaging Detected Intraplaque Hemorrhage in Non-stenotic Carotid Artery Atherosclerotic Disease of Asymptomatic Diabetic Patients
Keywords: Atherosclerosis
Carotid artery disease
Diabetes
Image processing
Intraplaque Hemorrhage
Magnetic Resonance Imaging

Cerebrovascular disease represents a major cause of death globally. It is directly related to atherosclerotic development in the carotid arteries where risk is mainly assessed by measurement of stenosis. Diabetic patients are predisposed to cerebrovascular event occurrence and atherosclerotic development. An advanced feature of atherosclerotic disease is intraplaque hemorrhage (IPH), which increases the risk of such events. In this study, magnetic resonance imaging techniques were used to define an optimal method for measuring IPH. This method was applied to a cohort of diabetic patients without carotid artery stenosis, to find the prevalence of IPH, which was compared with carotid artery wall measurements to determine its related effects. This thesis provides evidence that advanced features of atherosclerosis, in the form of IPH, can be found even when no carotid stenosis is present and may provide insight into the added risk borne by diabetic patients.
Long Non-coding RNA Fingerprint Regulated by Cyclic Mechanical Stress in Vascular Smooth Muscle Cells: Implications for Hypertension and Aortic Aneurysms
Keywords: aortic aneurysm
hypertension
mechanical stretch
vascular smooth muscle cell

Long noncoding RNAs (lncRNAs) are a new class of noncoding RNA and emerging evidence suggests that they represent a cellular hub for coordination of various cellular processes involved in health and disease. We hypothesized that lncRNAs may be involved in mechanical stretch-induced alterations in human aortic smooth muscle cells (HASMCs), which play a critical role in the pathophysiology of aneurysms and hypertension. Transcriptome analysis was performed on HASMCs that had been subjected to mechanical stretch. Human long intergenic non-coding RNA-p21 (hLincRNA-p21) was found to be significantly up-regulated in stretched HASMCs as well as in aneurysmal samples from patients undergoing aortic valve replacement (both P
Wearable Gait Analysis Using Vision-aided Inertial Sensor Fusion: WearGait
Keywords: Gait analysis
Inertial sensors
Instrumented shoes
Position estimation
Sensor fusion

Gait analysis is useful in characterizing impaired gait in patients with various neuromusculoskeletal disorders. Contemporary gait analysis is conducted using numerous motion capture cameras and force plates. However, this setup is restricted to a constrained and artificial testing environment, which may lead patients to make unnatural movements that poorly represent real-world human gait. We proposed a shoe-mounted gait analysis system composed of two 9-axis Inertial Measurement Units (IMUs), an IR sensor, and a pair of instrumented shoes. The system was validated against a state-of-the-art gait lab in a study with ten subjects. The results showed that the system was able to estimate the 3D kinematics, the global Centre of Pressure (COP), and gait parameters such as step length and gait phases acceptably well. This work provides a portable and unobtrusive method of performing lower-limb gait analysis in unconstrained and ambulatory environments.
Applications of Gluco-oligosaccharide Oxidase
Keywords: Biorefinery
Carbohydrate-active enzymes
Click chemistry
Hemicellulose
Lignocellulose

The nascent study of carbohydrate-active enzymes is now influencing a variety of industries at the commercial scale, particularly in processing lignocellulosic biomass for the production of fuels, materials, and other commodities. These enzymes are highly specific and can modify sugars with selectivity unmatched by chemical processes. Our group has worked extensively with gluco-oligosaccharide oxidase (GOOX), and feel the enzymeâ s oxidative activity would prove desirable in many new and existing applications where other commercialized carbohydrate oxidases are employed. The work presented here has demonstrated the improved characteristics of an immobilized fusion enzyme, CtCBM22A_GOOX-Y300A, on insoluble polysaccharide fibre, with potential applications in food additives, protein purification, and aldonic acid production. A second study has successfully employed GOOX oxidation as part of a synthetic pathway to generate a clickable monomer from glucuronoxylan capable of forming a carbohydrate-based polytriazole polymer; a process which could be extended to include neutral hemicelluloses such as galactoglucomannan.
The Chemical Composition of High Arctic Snow: Deposition Mechanisms and Sources
Keywords: Arctic snow
Black carbon
Deposition and scavenging
Snow albedo
Source apportionment

Recent observations of Arctic temperature increases and ice/snow loss have highlighted the importance of defining pollutant pathways to the Arctic. Fresh snow samples collected at Alert, Nunavut, from September 2014 to June 2015 were analyzed for carbon species, major ions, and metals, and their concentrations and fluxes reported. Comparison with simultaneous atmospheric monitoring found dry deposition to be a dominant removal mechanism for several compounds over the winter while wet deposition increased in importance in the fall/spring, possibly due to enhanced scavenging by mixed-phase clouds. This unprecedented dataset provided an opportunity for a temporally-refined source apportionment of key snow impurities. The majority (73%) of the black carbon in snow, a light-absorbing compound critical to the Arctic radiative balance, was identified as the product of fossil fuel burning with limited biomass burning influence. Both depositional and sourcing analyses suggested the external mixing of black carbon, sea salt, crustal, and sulphate aerosols.
Silicon Integrated Transmitter for Quantum Key Distribution
Keywords: integrated photonics
quantum key distribution
silicon photonics

Silicon (Si) photonics is reaching maturity and has the potential of offering low-cost, reliable, chip-scale systems for quantum key distribution (QKD). On the other hand, QKD is also maturing with the bridging of theory and practice. This work presents a Si integrated photonic transmitter for polarization-encoded QKD. The chip was fabricated in a standard Si photonic foundry process and integrates a pulse generator, intensity modulator, variable optical attenuator, and polarization modulator in a 1.3 mm x 3 mm die area. The devices in the photonic circuit meet the requirements for QKD. The transmitter was used in a proof-of-concept demonstration of the BB84 QKD protocol over a 5 km long fiber link. A quantum bit error rate of 5.4% and an asymptotic secure key rate of 0.95 kbps is obtained. This work shows the feasibility of foundry based Si photonics for quantum information applications.
Field Extensions Generated by Kernels of Isogenies
Keywords: class number
elliptic curve
field extension
isogeny

Given an odd prime p, A technique due to Jean-Francois Mestre allows one to construct infinitely many quadratic fields for which the ideal class group has p-rank at least 2, using a degree p isogeny between elliptic curves such that the kernel has a rational point. This technique only works for primes p ? 7; we attempt to generalize the construction for larger primes. One line of approach uses higher degree isogenies (which have no rational point in the kernel), from which we obtain higher-degree number fields with p-rank at least two. In the process, we collect data on the number fields generated by the points in the kernel of an isogeny, and make a series of conjectures based on the data. We also discuss the possibilities and limitations of replacing the elliptic curves in Mestre's technique with more general abelian varieties.
The Axial Spray Mode I as a Solution for Miniaturized Ion Mobility Spectrometry
Keywords: axial spray mode I
chemical detection
electrospray
ion gating
ion mobility spectrometry
pulsating regime

Miniaturized ion mobility spectrometers present several advantages as portable chemical detection tools. They are fast, simple and inexpensive. However, they still suffer from low resolving power and hard implementation of ion gates in micro scale designs. Even in examples where they are successfully combined, ion gates cause dispersion, compression, and depletion effects that result in ion packets than are wider than desired. This thesis describes an alternative gating method that is free of ion gates and that can be used in liquid phase ion mobility spectrometry (LPIMS), a technique where conventional ion gates are currently unsuitable. A parametric study shows that the method proposed has the potential to achieve resolving powers comparable to macro scale designs if successfully coupled to LPIMS. Observations relating the maximum meniscus height to current measurements are presented and are of particular interest to E-jet printing and similar techniques.
Psycho-socio-economic and Health Outcomes of Patients with Work-Related Asthma and Relationships to Different Models of Clinic Organization
Keywords: Clinic Structure
Occupational asthma
Outcomes
Work-exacerbated asthma
Work-related asthma

This thesis explored the impact of clinic structure on psychological, socioeconomic, workplace and quality of life (QoL) outcomes among work-related asthma patients between two tertiary clinics (Toronto Western Hospital [TWH] and St. Michael’s Hospital [SMH]). A cross-sectional comparison was carried out between the two clinics and data was collected through administration of five questionnaires: Beck Anxiety and Depression Inventories, Marks’ Asthma QoL Questionnaire, Work Limitations Questionnaire and Survey of Work and Non-work Related Respiratory Symptoms and their Impact. Forty-seven subjects participated from TWH and 30 from SMH. This study reported a better psychological status for SMH patients compared to TWH patients. SMH patients had better QoL for the ‘mood’ domain, and less workplace limitation for the ‘mental-demands’ domain. However, SMH included a greater number of patients with reduced income compared to TWH. Future research should explore the impact of clinic structure on a more homogenous group with larger sample sizes.
Measuring Gas Composition And Temperature In Highly Particle Laden Flow Using Terahertz Spectroscopy
Keywords: Gas Composition
Gas Temperature
Particle Laden Flow
Terahertz
Water Sensor

This work veriďŹ es that THz radiation has the potential to be used as gas sensors in industrial furnaces. Testing proved that THz signals do not attenuate due to particle scattering, of particle sizes common in furnace ducts. High-temperature (773 K) H2O vapor and room temperature CO can be measured quantitatively with terahertz (THz) spectroscopy in the frequency range of 0.5-0.9 THz. THz spectroscopy is also used with two diďŹ erent methods to perform gas temperature measurement: using the area ratio of two H2O vapor absorbance peaks, and using the relative time delay of the THz signal. The absorbance peak ratios were tested in the frequency range of 0.5 - 0.8 THz at temperatures of 523 - 773 K. The time delay was tested at a frequency of 0.5 THz and temperatures of 293 - 773 K, and is used to determine temperature by calculating the index of refraction of the gas.
A 4x, 3-level Blind ADC-based CDR in 65nm CMOS
Keywords: ADC-based
CDR
DFE
Equalizer
High-speed signalling
Receiver

This thesis presents the design, implementation, and measurement of a 4 times oversampled, 3-level blind ADC-based CDR. The goal of this work was to provide a blind ADC-based design that reduced the overall power consumption. This was achieved by reducing the ADC resolution to 3 levels, while increasing the oversampling ratio to 4. Also, by non-uniformly distributing the threshold levels of the ADC, the design incorporated a speculative DFE. The speculative DFE is implemented with comparator pairs whose symmetric offsets correspond to the first post cursor ISI. The samples from the comparator pairs are then passed to the digital CDR which uses them to recover the clock phase and data. The digital power was measured to be 18mW, while an estimate for the ADC and CLK Divider measured power was found to be 35.5mW. The estimate of the total measured power for the chip was 53.5mW.
Design and Evaluation of a Mobile Marker-based Motion Capture System Using the Kinect Sensor for Biomechanical Assessments of Caregivers in the Home
Keywords: Biomechanical Assessments
Confined Spaces
Home Caregivers
Kinect V2 Sensor
Motion Capture Systems
Trunk Movements

Care in the home is desirable but puts the home caregivers at high risk of injury. This problem has been ignored from a physical ergonomics perspective since lab-based motion capture (MoCap) systems to understand biomechanical challenges of providing care are too bulky and costly to be used in homes. This work describes the design and usability testing of a mobile Kinect-based MoCap system for the home environment. When compared to a lab-based system, the Kinect-based system was found to be accurate overall. RMS error in flexion angle of the spine relative to gravity was as low as 4.25째, 2.52째 flexion angle between upper back and lower back, 2.17째 for lateral bending angle and 1.51째 for twisting angle of the trunk relative to the pelvis. The percentage of data captured by the system is 82%. The Kinect-based system is also more efficient than a lab-based system. Users rated the hardware and software aspects as high as 5 on a five point scale. A second prototype was developed and tested, leading to modal usability score improvements from 2 to 5 and 3 to 5 on a five point scale for certain aspects of the system.
Non-genetic Resistant Mechanism to EGFR Tyrosine Kinase Inhibitory Therapy
Keywords: drug resistance
lung cancer
non-small cell lung cancer
tyrosine kinase inhibitor

Despite initial high response rate to tyrosine kinase inhibitor (TKI) treatment, non-small cell lung cancer (NSCLC) patients whose tumors harbour activating mutation in their epidermal growth factor receptors (EGFR) gene invariably develop TKI resistance. Secondary mutation T790M in EGFR and MET amplification were found in over 50% tumors. However, there are up to 30% of cases, whose mechanisms underlying the acquired resistance remains unknown. In this study, we used whole-genome loss-of-function shRNA library screen and mRNA expression microarray to identify LAYN, EPDR1 and DNMT1 that could potentially confer TKI resistance in NSCLC cell lines. Unfortunately, knockdown of them using shRNA hairpins did not restore drug sensitivity in drug resistant models. Further studies are needed to investigate the resistance mechanism of TKI resistant NSCLC cell lines.
The Development of Quantitative Filter Forensics for Indoor Air Quality Sampling and a Pre-retrofit Indoor Environmental Quality Assessment of Pre-war Multi-Unit Residential Buildings
Keywords: Dust
Filtration
HVAC
Indoor Concentration
Literature Review
Particle Composition

Filter forensics is a promising indoor air investigation technique involving the analysis of dust which has collected on filters. In this thesis, past filter forensics research is synthesized and an approach to quantitatively link filter forensics to average indoor air concentrations is developed. A significant advantage of FF is a large increase in the limit of detection when compared to alternative sampling techniques. In the next chapter, I discuss pre-retrofit comfort and moisture results from an ongoing indoor environmental quality study of post-war multi-unit residential buildings undergoing energy retrofits. A major finding of this study was a high level of discomfort due to overheating and the lack of observed correlations between comfort, moisture and building parameters. I present an application of filter forensics to portable air cleaners deployed in the same study. Preliminary data suggests no significant relationship between particle counts and gravimetric filter results.
Pre-clinical MR-based Volumetric Dosimetry: Dosimetric Characterization and the Effects of Time and Temperature
Keywords: 3D Fricke dosimetry
Correction algorithm
Improved accuracy
MRI readout
Time and temperature dependencies

Previously developed MR-based three-dimensional Fricke-xylenol orange gel (FXG) dosimeters can provide end-to-end quality assurance and validation protocols for pre-clinical radiation platforms. Variable TR spin-echo imaging of FXG dosimeters characterize changes in spin-lattice relaxation rates (R1 = T1-1) caused by irradiation induced oxidation of Fe2+ ions to Fe3+ ions. FXG dosimeters are water and tissue equivalent over the pre-clinical energy range, 30-225 keV, and exhibit a linear dose response up to 22 Gy. However, chemical instabilities in FXG dosimeters cause time and temperature dependencies that manifest themselves as baseline R1 shifts between initiation of pre- and post-irradiation R1 mapping. By characterizing and modeling R1-temperature and R1-time dependencies, a novel correction algorithm was developed that could be applied to FXG dosimeter R1 maps. This algorithm corrected baseline R1 shift from -2.8x10-2 s-1 to 1.5x10-3 s-1, and improved the reported dose accuracy to the 1% level when compared to standardized ion chamber measurements.
Regulation of Gnrh mRNA Expression by the ω-3 Polyunsaturated Fatty Acid Docosahexaenoic acid and the Saturated Fatty Acid Palmitate in a GnRH-synthesizing Neuronal Cell Model
Keywords: DHA
Free fatty acid
Gonadotropin-releasing hormone (GnRH)
GPR120
palmitate
reproductive neuroendocrinology

Gonadotropin-releasing hormone (GnRH) neurons coordinate reproduction. Whether GnRH neurons directly sense free fatty acids (FFAs) is unknown. We investigated the individual effects of the FFAs palmitate, palmitoleate, oleate, and docosahexaenoic acid (DHA) (100 μM each) on Gnrh mRNA expression in the mHypoA-GnRH/GFP neuronal cell model. We report that 2 h exposure to palmitate or DHA increases Gnrh transcription. Using the inhibitors AH7614, K252c, U0126, wortmannin, and LY294002, we demonstrate that the effect of DHA is mediated through G protein-coupled receptor 120 to downstream PKC/MAPK and PI3K signaling. Moreover, we propose that the effect of palmitate may depend on palmitoyl-coA synthesis and PI3K signaling. Finally, we explored the effects of FFA combinations, and we report that oleate abolishes the effect of 2 h palmitate treatment on Gnrh. Overall, these studies advance our understanding of the cellular mechanisms underlying FFA sensing in a GnRH neuronal model and may relate to reproductive function.
Development of a Population-based Pharmacokinetic-pharmacodynamic Model to Simulate Treatment Efficacy in Metastatic non-small-cell Lung Cancer Patients on Erlotinib
Keywords: epidermal growth factor receptor
erlotinib
model
non-small-cell lung cancer
pharmacokinetic-pharmacodynamic
progression free survival

Erlotinib improves progression-free survival (PFS) in metastatic non-small-cell lung cancer (mNSCLC) patients, but cause toxicities leading to dose reductions. The survival impact of dose reductions is unknown. We constructed a population-based pharmacokinetic-pharmacodynamic (PK-PD) erlotinib model predicting PFS of mNSCLC patients, consisting of an erlotinib population PK component, a PD component describing the concentration-kill-constant relationship, and a tumour growth component tracking tumour size over time. This model was fit against clinical trial data to simulate population-based PFS estimates in mNSCLC patients and externally validated using other trial data. The model simulated population-based PFS estimates of placebo and erlotinib arms with 0.74-9.14% and 0.26-19.83% error, respectively. The model was externally validated with population-based PFS estimate errors of 11.3% and 16.7% in epidermal growth factor receptor (EGFR)-mutant and EGFR-wild-type mNSCLC, respectively. It predicted significant PFS decreases with dose reductions. This is the first population-based PK-PD erlotinib model that predicts PFS in mNSCLC patients.
The Effects of Saturated Fatty Acid Palmitate on Neuropeptide Gene Expression, Signal Transduction, and Insulin Signaling in an Immortalized Hypothalamic Neuronal Cell Model, mHypoA-NPY/GFP
Keywords: Agouti-related peptide
Hypothalamus
Inflammation
Insulin
Neuropeptide
Palmitate

Recent evidence suggests a role for hypothalamic insulin resistance in obesity pathogenesis, and that obesity-associated hypothalamic inflammation underlies this resistance. However, few studies have examined the direct effects of saturated fatty acids on specific hypothalamic neurons. Therefore, an immortalized hypothalamic neuronal cell model expressing NPY and AgRP was used to determine the effects of palmitate on neuropeptide gene expression, signal transduction events and insulin signaling. In the mHypoA-NPY/GFP neuronal cell model, palmitate was found to upregulate the expression of NF-κB and IκBα within 4 hours of treatment, and upregulate expression of AgRP after 24 hours of treatment. Regulation of AgRP gene expression appeared to be palmitate metabolism-dependent. Palmitate also induced p38 MAPK phosphorylation, and prolonged palmitate pre-treatment decreased levels of phosphorylated Akt following insulin re-challenge. This is the first evidence of palmitate-mediated changes in AgRP gene expression and its signaling through p38 MAPK in a representative NPY/AgRP neuronal cell model.
Investigation of PIN1 as a Genetic Modifier in Li-Fraumeni Syndrome
Keywords: Li-Fraumeni Syndrome
modifier
p53
PIN1

Li-Fraumeni syndrome (LFS) is a heterogeneous cancer predisposition syndrome caused by germline mutations in TP53. Some of this phenotypic variability can be explained by presence of oncogenic mutant p53 proteins in patients with missense TP53 mutations. Recent data suggest that the prolyl-isomerase, PIN1, serves a fundamental role in mutant TP53 oncogenic gain-of-function (GOF). We hypothesized that alterations in expression of PIN1, mediated by the promoter SNP(-)842G>C (rs2233678), modify the cancer phenotype of LFS patients. We demonstrate that the PIN1(-)842 GG genotype is associated with increased PIN1 expression at the transcript and protein level. Overexpression of PIN1 selectively enhances the clonogenicity and chemotherapy resistance of LFS fibroblasts harbouring R248Q mutant p53. Concordantly, LFS patients with the PIN1(-)842 GG genotype develop cancer earlier than those with GC/CC genotypes, with a prominent effect in pediatric patients. The GG genotype may also be associated with some predilection for the development of carcinomas.
Centralized Portfolio Optimization in the Presence of Decentralized Decision Making
Keywords: Centralized
Decentralized
Portfolio optimization

We study an asset allocation problem for a multi-asset fund where multiple decentralized managers implement investment strategies in separate asset classes. To control for portfolio measures at the fund, it is a common practice to follow a traditional asset allocation methodology to obtain optimal target weights and force the investment managers to stay close to the target. However, the sophistication and high level of specialization involved in alternative investment strategies create uncertainty in investment managers achieving the target weight; hence causing misallocations. Therefore, we develop two asset allocation models that provide a range of portfolio allocations (i.e. bounds) for individual investment managers to operate in order to maintain desirable firm wise portfolio measures while accounting for potential misallocations. Also, the proposed optimization problems have potentially large number of constraints, so we suggest a procedure to reduce the number of constraints before the optimization.