VictorJuiz/thesis huggingface dataset:
Effect of De-Watering Wood Derived Pyrolysis Liquid Biofuel on its Properties, Characteristics, and Combustion Behavior in a Diesel Engine
Keywords: Bio-oil water removal upgrdation
Diesel/ Bio-oil emulsification
Diesel engine operation
Pyrolysis liquid combustion
pyrolysis liquid corrosion
Wood pyrolysis liquid

Two different methods were employed to successfully reduce the water content of Wood Derived Pyrolysis Liquid Biofuel (also known as wood pyrolysis liquid or bio-oil). Removing water increased fuel heating value and improved its storage stability. Removing moderate quantities of water from WPL was found to be favorable for its emulsification with diesel. Atlox 4196 produced most stable emulsions. Stainless steel was the only material that displayed no corrosion. Reducing water content significantly reduced the fuel corrosion rates. Surface XPS analysis stipulated chemical nature of the corrosion. Four different emulsions of pure and water removed WPL were tested in caterpillar diesel engine at various loads for emissions and fuel consumption. Injector clogging and fuel pump failure were identified as two key challenges hindering WPL utilization in a diesel engine. Although, diesel fuel showed least fuel consumption and lower emissions in most cases differences between diesel fuel and emulsions tends to reduce considerably at higher loads indicating WPL potential for fueling a diesel engine.
Advancements in the Design and Fabrication of Ultrasound Transducers for Extreme Temperatures
Keywords: brazing
high temperature
lithium niobate
non destructive testing
porous zirconia
ultrasound transducers

An ultrasound transducer for operation from room temperature to 800 째C is developed. The device includes a lithium niobate piezoelectric crystal, a porous zirconia attenuative backing layer, and a quarter wavelength matching layer. The manufacturing procedure for porous zirconia is optimized by adjusting pore size and forming pressure to yield good acoustic performance and mechanical integrity. Several acoustic coupling methods are evaluated. A novel silver-copper braze and an aluminum-based braze are found to be suitable at elevated temperatures. Several materials are evaluated for their performance as a quarter wavelength matching layer in the transducer stack. The use of either a nickel-chromium or stainless steel matching layer is established in place of ceramic components. Equipment limitations prevent evaluation at 800 째C, though ultrasound transmission is theoretically achievable with the devices established by this study. Reliable high-amplitude, wide-bandwidth ultrasound transmission is achieved from room temperature to 600 째C with two transducer variants.
Development of a flexible polarimetric probe for assessment of structural bladder disease
Keywords: biomedical optics
Mueller matrix
partial bladder outlet obstruction
polarimetry
probe
urology

Optical polarimetry uses polarized light to quantitatively characterize the morphology of tissue. It can provide contrast between healthy and pathological tissues otherwise invisible to standard intensity imaging1â 4. In the first half of this thesis a polarimetry study of murine partial bladder outlet obstruction (pBOO) is detailed that assessed a pharmacological muscle response to obstruction-induced myopathy. No significant changes in tissue anisotropy were observed between control and obstructed bladder regions and the pharmaco-treatment enhanced the pathologic response in both control and obstructed bladders. In the second half of this thesis a polarimetric probe is described and validated by accurately measuring 3x3 Mueller matrices of known polarization components. It is later used to probe morphological contrasts between normal and stretched ex vivo tissue. Translating traditional, free-space polarimetry from the optics bench to a flexible, fibre-based probe represents a significant step toward in situ polarization-enhanced endoscopies, such as cystoscopy for pBOO.
Prying of a Large Span Plate Undergoing a Moment Load Applied by a Round Pier
Keywords: base plate
digital image correlation
solid mechanics

Large span base plates with a moment load applied, in any direction, to the centre of the plate by a round pier are commonly used in the design of anchors for faรงade access systems. There is no current method of predicting the behaviour of these large span plates under a moment load. Six anchor base plate configurations are physically tested. The deflection of the plate is analysed using digital image correlation (DIC) to track the change in location of points on the base plates under various applied loads. The shapes are plotted and used to determine at what point the plates transition from linear to nonlinear deformation. A method of predicting the moment resistance of the base plates for each test was proposed and a finite element model for the base plates was analysed and validated using the test data.
Knowledge-Based Automated Planning for Oropharyngeal Cancer
Keywords: Automated planning
Intensity-modulated radiation therapy
Inverse optimization
Knowledge-based planning

We automatically generate intensity-modulated radiation therapy plans for oropharyngeal cancer by combining knowledge-based planning (KBP) predictions with an inverse optimization (IO) pipeline into a single automated treatment planning pipeline. We extended two existing KBP methods, which use patients' anatomical geometry to predict achievable dose volume histograms (DVHs), and developed the first IO method that takes DVHs as direct inputs. The DVH predictions from KBP are put into the IO pipeline to automatically generate treatment plans via an intermediate step using objective function weights and an inverse planning problem. This step enables our automated planning pipeline to seamlessly fuse with the current treatment planning paradigm to increase its efficiency. Our automated pipeline can replicate, and often improve upon the clinical treatment plans by reducing the dose to healthy tissue and increasing primary target coverage. These results have been validated using a large cohort of 217 oropharyngeal cancer patients.
Examining the Fundamental Biology of Primitive Neural Stem Cells
Keywords: Developmental Biology
Neural Stem Cells
Pluripotency vs Multipotency
Primitive Neural Stem Cells
Stem Cell Biology

Definitive (d) neural stem cells (dNSCs) are multipotent, self-renewing, neurally committed stem cells. More recently, a novel primitive (p)NSC was identified in the early postnatal brain that persists into adulthood. pNSCs are upstream of dNSCs in the neural lineage and are self-renewing with the capacity to generate neural cells. pNSCs, unlike dNSCs, express the pluripotency genes Oct4, and Nanog and are able to incorporate into the developing blastocyst. Based on these findings we hypothesized that pNSCs are pluripotent cells able to generate cells outside the neuroectodermal lineage. To test this hypothesis, we utilized well established pluripotency assays in vitro embryoid body assay and the in vivo teratoma formation assay. When placed in these assays pNSCs revealed no pluripotentiality, demonstrating consistent neural commitment and no differentiation into mesoderm or endoderm lineages. In addition, pNSCs expressed the epithelial marker Krt18 indicating that their origin may be from an embryonic time before neurulation.
Transcriptome-wide Measurements of mRNA Stability
Keywords: 4-thiouridine
DRUID
introns
metabolic labeling
RNA degradation
transcription inhibition

Numerous regulatory processes work at the level of RNA to ensure proper control of gene expression. Of these, transcription and decay are particularly important as together they determine the abundance of a given transcript. Several methods have been developed over the last two decades to interrogate the stability of transcripts genome-wide. Despite inherent limitations, methods based on transcription inhibition remain popular. I have developed two redundant normalization methods for in vivo metabolic labeling time course data generated by high-throughput RNA sequencing (RNA-seq) that will make such experiments more accessible. I demonstrate that the use of exogenous whole organism spike-ins can help overcome transcript specific biases by averaging the behavior of thousands of exogenous transcripts. Additionally, I demonstrate that internal short-lived RNA species, e.g. introns, can be used to normalize the same time course data, often yielding more reproducible results than those obtained by normalizing to exogenous spike-ins.
Evolution and epigenetic control of acute inflammation in mammalian endothelial cells
Keywords: cis-regulatory elements
CRISPR/Cas9
endothelial cells
evolution
inflammation
NF-kB

Vascular endothelial cells (ECs) line the interior of blood vessels and respond to inflammation through a series of well-characterized chemokines and receptors. Less is known about the cis-regulatory elements (CREs) that control the endothelial inflammatory response in humans and other mammals. The NF-κB complex, in particular its subunit RELA (p65), is an essential inflammatory mediator in ECs. To study the evolution and function of endothelial acute inflammatory response, we characterized RELA binding sites and epigenetic changes that occur after TNF-α treatment in primary aortic ECs isolated from human, mouse, and cow. We discovered ~5000 RELA binding sites at orthologous regions in all three species near genes involved in vascular development and pro-inflammatory responses. The conserved RELA binding sites were enriched for known regulatory disease mutations. We established a CRISPR/Cas9 gene editing approach in an immortalized human aortic EC line and used this platform to study the function of TNF-α-induced CREs.
The Role of an Autoimmune Disease-Associated Phosphatase in Dendritic Cell Biology
Keywords: Autoimmune Disease
Dendritic Cells
Genetics
Mouse model
Phosphatase

PTPN22 encodes the human lymphoid tyrosine phosphatase, Lyp, a protein exclusively expressed in hematopoietic cells and involved in numerous signaling pathways. Lyp has been of great interest since the discovery of a variant affiliated with multiple autoimmune diseases. The variant, PTPN22-C1858T, has been investigated in human and animal models with conflicting results. Some groups claim the variant causes a gain-of-function effect while others claim a loss- of-function effect. This study sheds light on how the variant influences the dendritic cell (DC) network, a network comprised of multiple subpopulations, each with specific and overlapping functions. Here we show mice expressing the orthologous variant have abnormal splenic DC frequencies and distribution, with an increase in the CD4+ conventional type 2 DC population. Furthermore, all DC subpopulations investigated consistently displayed increased expression of CD40, indicating a hyperactive phenotype. Additionally, bone marrow-derived DCs produced more IL-12 after TLR9 stimulation and collectively these factors may contribute to autoimmune disease.
Sequencing Effects in Memories of Online Video Technical Quality
Keywords: Customer loyalty
Peak-end effect
Quality of Experience
Sequencing
Technical quality
Video streaming

While researchers have shown that memories of experience diverge from actual experience, little is known about how variations in online video service quality impact overall ratings of Technical Quality (TQ), satisfaction, and frustration after a sequence of videos is viewed. Additionally, it is yet to be determined how accumulated experiences of TQ may impact customer loyalty measures like Likelihood-to-Recommend (L2R) and Likelihood-to-Churn (L2C). This thesis addresses these gaps in the literature by conducting two experiments that vary the sequencing of videos with good, mediocre, and bad TQ. In the first experiment, a negative end effect was found. The second experiment found the negative end effect as well as an effect of linear trend (both increasing and decreasing). Overall ratings of L2R and L2C at the end of a one-hour viewing session suggest that satisfaction is the closest predictor to significance of L2R while frustration is the best predictor of L2C.
Measuring Cerebrovascular Pulsatility Using Cardiac Cycle Fluctuations of fMRI BOLD Data
Keywords: aerobic exercise
BOLD fMRI
cardiac cycle
cerebrovascular pulsatility
physiological fluctuations

Arterial pulsatility is linked to cerebral small vessel damage and neurodegeneration, but measuring cerebrovascular pulsatility in humans has largely been impeded by the skull. This thesis describes a method that generates cerebrovascular pulsatility maps based on resorting blood-oxygenation level dependent (BOLD) volumes according to their cardiac cycle position. Sensitivity of this method was tested using 20 minutes of moderate-intensity exercise as an acute physiological stressor in 45 healthy adolescents. Further examinations evaluated the influence of repetition time (TR) and echo time (TE) via simulation and multi-echo data, respectively. There were global, tissue-specific, and region-specific decreases in cerebrovascular pulsatility 20 minutes following exercise cessation. Cardiac-related pulsatility detection was comparable over a range of TR and TE values, with highest detection during rapid TRs (â ¤300ms) or shorter TE (~14ms). These results suggest that cardiac-related fMRI may represent a potent and easily adoptable method of mapping cerebrovascular pulsatility influences with voxel-wise specificity.
Investigating the Role of the Vascular Endothelium in Insulin Delivery
Keywords: diabetes
endothelium
insulin
macrovasculature
microvasculature

Insulin delivery is an integrated process that first requires perfusion of the capillary bed supplying the tissue, followed by the transit of insulin across the endothelium that lines each vessel. Methodological limitations have hindered the ability to study transendothelial insulin transfer in isolation of hemodynamic forces that also promote the delivery of the hormone. We aimed to determine whether or not the aortic endothelium represented a rate-limiting barrier to insulin transit towards the underlying smooth muscle. Using an ex vivo approach, we determined that the aortic endothelium may not be rate-limiting to insulin action. Two permeability-inducing agents (histamine or platelet activating factor) induced inter-endothelial gap formation, but had no effect on insulin action in the aorta. Together, these data demonstrated that the aortic endothelium may not be a rate-limiting barrier to insulin delivery.
A Population-Based Study of the Impact of Pregnancy on Breast Cancer Mortality in Women in Ontario.
Keywords: Breast cancer
Pregnancy
Survival
Women's Health

Population-based, retrospective cohort study, linking health administrative databases of Ontario, Canada, comprising 7,553 women aged 20 to 45 years with invasive breast cancer, from January 1, 2003, to December 31, 2014. Women were classified into four exposure groups: no pregnancy (n = 5,832; the referent), pregnancy before breast cancer (n = 1,108), pregnancy-associated breast cancer (n = 501), and pregnancy following breast cancer (n = 112). The 5-year overall survival rate was 87.5% for women with no pregnancy (the referent); 85.3% (age-adjusted HR, 1.03; 95%CI, 0.85-1.27; P = .73) for women with pregnancy before breast cancer; 82.1% (age-adjusted HR, 1.18; 95%CI, 0.91-1.53; P = .20) for women with pregnancy-associated breast cancer; and 96.7% (age-adjusted HR, 0.22; 95%CI, 0.10-0.49; P
Development of Site-Specific CFTR Gene Integration Tools for Testing Gene Editing in Pig Cells
Keywords: CFTR
CRISPR/Cas9
Cystic Fibrosis
Gene therapy
Helper-Dependent Adenoviral vector

Development of Site-Specific CFTR Gene Integration Tools for Testing Gene Editing in Pig Cells Liang Yang Master of Science Department of Laboratory Medicine and Pathobiology University of Toronto 2017 Abstract Cystic Fibrosis (CF) is a genetic disorder caused by autosomal recessive mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. In this study, we proposed a novel gene therapy strategy to integrate a transgene expression cassette into GGTA1 locus utilizing the precise genome cleavage capability of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated protein (Cas) and the large packaging capacity of Helper Dependent Adenoviral vector (HD-Ad). Using a LacZ reporter gene expression cassette, we determined this novel strategy can achieve stable and sufficient integration in the pig IPEC-J2 cell line. In addition, the CFTR transgene mRNA and protein can be successfully detected post HD-Ad delivery. Future experiments include investigating the CFTR functional correction and the impact of enhancing homology directed repair (HDR), which is the major pathway we rely on for transgene integration, on integration efficiency and assess CFTR transgene functional corrections.
A Starvation-Induced Heritable Stress-Resistant State in Saccharomyces cerevisiae
Keywords: Heritable
Starvation
Stress Resistance

Transient exposures to diverse stimuli induce altered physiological properties in exposed cells that persist after the stimulus has been removed. This state, referred to as cellular memory, can be passed on to daughter cells. In the budding yeast Saccharomyces cerevisiae, I found that meiotically produced yeast spores possess a state of heightened stress resistance that, following their germination, is propagated through their descendants. As yeast meiotic development is essentially a starvation response that diploid cells engage, I modelled this phenomenon by subjecting haploid cells to starvation conditions. Haploid cells exposed to glucose withdrawal acquire elevated hydrogen peroxide resistance following the reintroduction of the cells to glucose-replete-media. In both haploid starved cells and diploid produced meiotic spores I show that their cellular memories are not attributable to trehalose, a proposed stress protectant. My findings identify nutritionally induced states of cellular memory in yeast that exhibit striking degrees of persistence and inheritance.
Thompson Sampling for the Control of a Queue with Demand Uncertainty
Keywords: admission control
Bayesian inference
parameter uncertainty
queueing
Regret bounds
Thompson sampling

We study an admission control problem in which the customer arrival rate is unknown and needs to be learned from data using Bayesian inference. Two key defining features of this model are that: (1) when the arrival rate is known, the DP equations can be solved explicitly to obtain the optimal policy over the infinite horizon, and (2) uninformative actions are unavoidable and occur infinitely often. We extend the standard proof techniques for Thompson sampling to admission control, in which uninformative actions occur infinitely often, and show that asymptotically optimal convergence rates of the posterior error and worst-case average regret are achieved. Finally, we show that under simple assumptions, our techniques generalize to a broader class of policies, which we call Generalized Thompson sampling. We show that this class of policies achieves asymptotically optimal convergence rates and can outperform standard Thompson sampling in numerical simulation.
The Impact of Catalytically Inactive Sirt1 on Age-Associated Cardio-Renal Dysfunction
Keywords: Aging
Cardio-renal function
Glomerular number
Kidney disease
Sirt1

Aging is one key risk factor that leads to kidney and cardiovascular disease; however, little is known about the pathogenesis of these age-related disorders. One potential target is the Sirtuin 1 (Sirt1) enzyme, which has been shown to mediate health span extension. While Sirt1 activation may attenuate the aging process, we hypothesized that a reduction in Sirt1 activity will accelerate age-related cardio-renal disease. Wild type mice were compared with Sirt1Y/Y mice, known to have undetectable Sirt1 catalytic activity, at 4 weeks and 14 months of age. Compared to their wild type counterparts, Sirt1Y/Y mice had lower glomerular filtration rates, fewer glomeruli, and abnormal measures of cardiac contractility. Interestingly, diminished Sirt1 activity during development plays a role in glomerular endowment. These catalytically inactive Sirt1 mice also provide a model of cardiac aging. Therefore, strategies that increase Sirt1 activity may provide a new approach to treating cardio-renal disease.
INTERACTOME REWIRING THROUGH CANCER-ASSOCIATED MUTATION IN GROWTH FACTOR SIGNALING PATHWAYS
Keywords: AP-MS
BioID
Growth factor signaling
Protein phosphatase 6
Proteomics
Raf

Many somatic mutations acquired in cancer have been identified in upstream regulators that normally relay growth factor signals to downstream effectors, notably kinases (PI3 kinase, AKT, RAF), phosphatases (PTEN) and G-proteins (K-Ras). This work seeks to apply both affinity purification coupled to MS (AP-MS) and BioID to quantitatively characterize changes in protein interactions between wild-type (wt) and cancer-associated mutations. In this study, 26 wt proteins and 27 cancer-associated mutants were profiled using both AP-MS and BioID. Several novel interactions and multiple differential associations were revealed. I validated that mutant Raf-1 and A-Raf display increased interactions with subunits of protein phosphatase 6, which may impact the activation of the classical Raf-ERK pathway and the Hippo pathway. The results presented in this thesis show that interaction profiles are often altered in cancer-associated mutants in growth factor pathways, identifying many routes of potential crosstalk with the Hippo pathway, HER2 signaling, and translation initiation.
ME31B globally represses maternal mRNAs by two distinct mechanisms during the Drosophila maternal-tozygotic transition
Keywords: Development
Drosophila
Maternal-to-zygotic transition
mRNPs
Post-transcriptional regulation
RNA-sequencing

In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryoâ s own genome in a process referred to as the maternal-to-zygotic transition (MZT). Here, I show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B undergoes a switch in its regulatory role throughout the MZT mediated by its protein binding partners. In the early embryo, ME31B represses translation, while after MZT, it promotes mRNA decay. In a process dependent on the PNG kinase, levels of ME31B and its partners, Cup and Trailer Hitch (TRAL), decrease by over 10-fold during the MZT, leading to a global change in mRNP composition and, thus, the mode of repression. I propose that these changes in the ME31B mRNP complex provide an explanation for the shift in post-transcriptional regulatory environment in the early embryo.
Validating Intrinsic Spectral Broadening models via Doppler Ultrasound Simulations
Keywords: Actual focal spot
Doppler ultrasound
Intrinsic Spectral Broadening
Occupied Bandwidth

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.