VictorJuiz/thesis huggingface dataset:
Integrative Preoteomic Analysis of Cell Line Conditioned Media and Pancreatic Juice for the Identification of Candidate Pancreatic Cancer Biomarkers

Novel serological biomarkers to aid in the detection and clinical management of pancreatic cancer patients are urgently needed. In the present study, we performed in-depth proteomic analysis of conditioned media from six pancreatic cancer cell lines (MIA-PaCa2, PANC1, BxPc3, CAPAN1, CFPAC1 and SU.86.86), the normal pancreatic ductal epithelial cell line HPDE, and pancreatic juice samples from cancer patients for identification of novel biomarker candidates. Using 2D-LC-MS/MS, a total of 3479 non-redundant proteins were identified with ≥2 peptides. Subsequent label-free protein quantification and integrative analysis of the biological fluids resulted in the generation of candidate biomarkers, of which five proteins were shown to be significantly elevated in plasma from pancreatic cancer patients in a preliminary assessment. Further verification of two of the proteins in ~200 serum samples demonstrated the ability of these proteins to significantly improve the area under the receiver operating characteristic curve of CA19.9 from 0.84 to 0.91.

Keywords: Pancreatic Cancer
Proteomics
Serum Biomarkers
Mass Spectrometry
Cell Line Conditioned Media
Pancreatic Juice
Bioinformatics
Advisor: Diamandis, Eleftherios P.
The Effects of Maternal Folic Acid Supplementation Provided in Utero and during Lactation on Genomic DNA Methylation and Global Gene Expression in the Offspring

The effects of high maternal folate status on the offspring are unknown; however, early life exposure to environmental stimuli, including dietary factors, is thought to influence the risk of developing chronic disease. An animal study was performed to determine the effect of maternal folic acid supplementation during pregnancy and lactation on DNA methylation and global gene expression patterns in the offspring. Supplementation of the maternal diet with folic acid (5, 8, and 25 mg/kg diet) induced global DNA hypomethylation in the liver of juvenile and adult offspring, and altered the expression of the imprinted H19 gene and genes involved in lipid metabolism, coagulation, and iron transport and homeostasis. Our data suggest that intrauterine and early postnatal periods are susceptible to changes in DNA methylation and gene expression in response to high levels of folic acid, which may be associated with health status and disease later in life.

Keywords: folic acid
maternal
Advisor: Kim, Young-In
A Randomized Double Blind Sham-controlled Comparison of Bilateral and Unilateral Repetitive Transcranial Magnetic Stimulation for Treatment-resistant Major Depression

Objectives: High frequency left-sided (HFL) and low frequency right-sided (LFR) unilateral repetitive transcranial magnetic stimulation (rTMS) are efficacious in treatment-resistant major depression (TRD). Similar benefit has been suggested for sequential bilateral rTMS (LFR then HFL). Therefore, this study evaluated the efficacy of HFL and sequential bilateral rTMS compared to sham in TRD. Methods: Seventy-four subjects between the ages of 18 and 85 with TRD and a 17-item Hamilton Depression Rating Scale (HDRS) greater than 21 were randomized to receive unilateral, bilateral, or sham rTMS. Remission rates were compared among the three groups. Results: Remission rates differed significantly among the three groups. The remission rate was significantly higher in the bilateral group (34.6%) than the unilateral (4.5%) and sham (5.0%) groups. The remission rate in the unilateral group did not differ from sham group. Conclusion: These findings warrant larger controlled studies that compare the efficacy of sequential bilateral rTMS and HFL rTMS in TRD.

Keywords: Depression
TMS
Treatment-Resistance
Advisor: Daskalakis, Zafiris Jeff
Description of the Dynamic Responses to Hypoxia:Ventilation, Cerebral Blood Flow (CBF), Blood Pressure (BP), and Heart Rate (HR)

This thesis describes experiments to measure the ventilatory response to hypoxia at a constant (isocapnic) level of CO2 (HVR) in 18 subjects. So as to provide a complete picture of the autonomic responses, middle cerebral artery velocity, a surrogate for cerebral blood flow (CBF), as well as finger plethysmography blood pressure (BP) were also measured. Ventilatory responses have been previously described only in terms of an acute peak followed by a decline. However, rather than a single type of response, I found four types categorized as: Decline, Double, Plateau, or No response. The Double pattern, characterized by a second peak of response was the most common, yet is described here for the first time. These patterns are also characteristic of the CBF and BP responses. Furthermore the temporal correlations between these brainstem-controlled responses are also reported here for the first time.

Keywords: hypoxic ventilatory response
cerebral blood flow
Advisor: Fisher, Joseph A.
An Investigation of the Role of Sodium Carbonate and Silica in the Neutral/Alkaline Pressure Oxidation of Pyrite

Pressure oxidation of refractory gold ores containing carbonate minerals is conducted under neutral/alkaline conditions in order to promote fast kinetics, reduced reagent consumption and suppressing the formation of elemental sulphur and CO2 (which reduces the effectiveness of the process). In this work, both the addition of sodium carbonate and the presence of silica were investigated during the pressure oxidation of pyrite in the presence of calcium carbonate. It was found that the shift to an alkaline leaching environment favours the formation of soluble sulphate products over anhydrite (an industrial scale), but that the increase in kinetics is likely due to an increase in pH and carbonate/bicarbonate concentrations. The presence of silica in the autoclave induces the formation of an in situ iron oxyhydroxide silicate coating and a significant reduction in pyrite oxidation, which was minimized by addition of sodium carbonate.

Keywords: pyrite oxidation
pressure oxidation
pressure oxidation of pyrite
alkaline pressure oxidation
sulphide leaching
silica coating
autoclave
refractory gold
hydrometallurgy
Advisor: Papangelakis, Vladimiros G.
Chinese Enough For Ya? Disrupting and Transforming Notions of Chineseness through Chinesenough Tattoos

Using interpretive methods of social inquiry, this thesis explores the socio-political significance of body tattoos made of Chinese-like text, which have recently become popular Western phenomena. It theorizes how contemporary Western tattooing complicates bodily and social boundaries, providing context to interrogate ideas of authenticity. Coining the term "Chinesenough" (from “Chinese” and “enough”), I describe how many such tattoos do not reflect in Chinese what many wearers and viewers assume they do. I contrast how Chinesenough tattoos (re)produce whiteness to the multiple and contradictory Chinesenesses that are also (re)produced. Reading Chinesenough flash art on tattoo studio walls as objects constituting social space, I consider the social meaning of their English subtitles and manner of organization. I theorize the body’s absence from Chinesenough flash art while articulating my body’s sense experience of encountering the same. Finally, I produce and theorize five illustrations that carnivalize Chinesenough iconography to disrupt and transform the phenomenon.

Keywords: Authenticity
Hybridity
Chineseness
Chinese
Chinese Tattoos
Tattooing
Body Modification
Flash Art
Arts Informed Inquiry
Arts Informed Research
Whiteness
Hanzi
Kanji
Diasporic Studies
Interpretive Social Inquiry
Carnivlesque
Cultural Appropriation
Chinese Canadian
Social space
Subtitling
Sense Experience
Absent Body
Third Space
Anti-fashion
Asian Studies
Asian American Studies
Asian Canadian Studies
Cultural Studies
Visual Culture
Phenomenology
Advisor: Titchkosky, Tanya
Paddling as Place Arts-informed Inquiry into Experiential Learning of Place and Ecological Identity

I explore how recreational canoeists develop sense of place developed and ecological identity through experience. The intersection between artefact and narrative is the entry-point of exploration of understandings of how recreational canoeists learn through experiences. There are three structural elements. A factional narrative arc of a canoe trip frames the work. Fragments of collective narratives: weave into this story and add richness and depth of experience. Participants’ interwoven narratives form the second element of this work. Finally, footnotes underpin this text to explain and support the research. They emerge to reflect the complexity of telling, and understanding, experience. This is a story of stories. This is a story of a trip that never happened. It holds real participants’ narratives based in lived experiences that shape this story. Narratives emerge between artefact and experience, between experience and ecological identity, between ecological identity and place, and between place and story.

Keywords: experiential learning
sense of place
ecological identity
arts-informed research
narrative inquiry
canoe trips
canoeists
artefact
writing inquiry
Advisor: Knowles, J. Gary
Investigation of the Feasibility of Manufacturing Solid Oxide Fuel Cell Graded Electrolytes by Suspension Plasma Spraying

Solid oxide fuel cell compositionally graded electrolytes could offer the advantage of improving electrical performance and efficiency compared to single-layered or bi-layered yttria stabilized zirconia and samaria doped ceria electrolytes and improving mechanical performance by reducing thermal expansion mismatch stresses compared to bi-layered electrolytes with sharp interfaces. Manufacturing of these graded structures is difficult if implementing conventional wet ceramic techniques. Suspension plasma spraying is an emerging technology that has the potential to rapidly produce thin, dense ceramic layers with no requirement for post deposition heat treatments. However, SPS requires a careful examination of the stability of the feedstock suspensions in order to produce high quality coatings. Optimum suspension formulations with excellent particle dispersion were designed based on rheological and electrostatic stability measurements. These optimized suspensions were used as feedstocks for the fabrication of suspension plasma sprayed compositionally graded YSZ/SDC layers. The feasibility of fabricating graded electrolyte structures was thus demonstrated.

Keywords: Graded YSZ/SDC electrolyte
Electrostatic stability
Isoelectric point
Suspension plasma spraying
Advisor: Kesler, Olivera
Sand and Soil: Ecological Management and the Framing of Mildred Lake

This paper explores representations of nature that emerge through the ecological management of Mildred Lake, Syncrude’s Alberta-based oil sands extraction facility. Examining the ways Mildred Lake’s ecology has been re-presented by site eco-management teams, I argue that technologically produced visions help reproduce the regime of power infusing a state-sanctioned scientific practice of eco-management. ‘Using governmentality theory, Chapter 1 contextualizes activities at Mildred Lake: I show how the Alberta government, tethering the growth of the oil sands to technological innovation, submits eco-management questions to a capital-driven state-developmental framework. Chapter 2 examines how state-sanctioned science is discursively performed through eco-management acts. Chapter 3 uses a case study approach to consider three Mildred Lake eco-management projects: Beaver Creek, the Tailings Pond, and reclamation. While Mildred Lake’s eco-management practices cannot withstand critical scrutiny, they reveal the culturally and ecologically significant transformations of nature required to sustain authority amid the destructive effects of bitumen extraction.

Keywords: oil sands
science studies
political ecology
geography
Canada;
Advisor: Prudham, W. Scott
Ruddick, Susan M.
Effect of Nitrous Oxide Exposure during Surgery on the Homocysteine Concentrations of Children

In this study we determined the effect of nitrous oxide (N2O) on homocysteine concentrations in children and whether blood levels of folate, vitamin B12, B6, methylmalonic acid (MMA) and methylenetetrahydrofolate reductase C6777T genotype affected this relationship. Homocysteine was measured before and after N2O. Vitamin levels, MMA and genotype were determined preoperatively. Median age of the 32 participants was 11 months (3-126 months). All children had folate and B6 levels above deficiency values (7.4, 20nmol/L respectively). Five children had MMA levels indicating deficiency (≥0.21µmol/L). Post-exposure homocysteine concentrations increased by 25% (P= <0.001). Duration of exposure and initial homocysteine concentrations were predictors of the increase (r2= 0.821, P= <0.001). Vitamin B12 and initial homocysteine concentrations were inversely associated (r2 = 0.277, P= 0.004). Folate, vitamin B6 and genotype showed no effect. In conclusion, N2O exposure leads to increased homocysteine in children. Studies investigating benefit of pre-surgical vitamin B12 supplementation may prove worthwhile.

Keywords: homocysteine
children
nitrous oxide
Advisor: O'Connor, Deborah Louise
Which Siblings of Children with Cancer are Best Helped by Participating in a Specialized Intervention Program?

To understand why some SCC experience psychological distress while others do not, researchers have turned their attention to potential protective factors that may influence the ability of SCC to cope with the cancer experience. Provision of protective/buffering factors specifically to less-resilient siblings (defined as those with higher initial depression and anxiety symptom scores) in the form of a structured program has not been previously attempted. The objective of this study was to explore outcomes of a specialized 8 week, intervention program for SCC. SCC and one parent completed standardized questionnaires exploring symptoms of depression and anxiety pre and post intervention. Results showed that the gender of the SCC, and the specific diagnosis of the child with cancer were factors significantly associated with the degree of reported symptoms of anxiety and depression respectively. Looking at significant interactions, we found that girls whose siblings had brain tumours improved less than other subgroups

Keywords: siblings
intervention
Advisor: Barrera, Maru
High Efficiency Organic Light Emitting Diodes with MoO3 Doped Hole Transport Layer

Organic Light Emitting Diodes (OLEDs) are widely viewed as next generation platform for flat panel displays and solid state lighting. Currently, OLED efficiency is not high due to high driving voltage. Molybdenum trioxide (MoO3) is ideal for p-type doping of the wide bandgap organic semiconductor 4,4’-bis-9-carbozyl biphenyl (CBP). With p-type doped CBP layer as Hole Transport Layer (HTL), driving voltage can be significantly reduced. Effective design for doped OLED structure consists of a HTL with doped layer from 20nm to 40nm and MoO3 concentration above 5%, the optimized OLED with doped CBP HTL present an 18% improvement over a standard device with CBP HTL at 100mA/cm2. Injection is found to be the principle cause of the reduction of driving voltage and shows close relations to doped layer thickness. Also charge balance is an important factor for high current efficiency, doped layer can be used as tools to promote charge balance.

Keywords: OLED
Dopant
Hole Injection
High Efficiency
Advisor: Lu, Zhenghong
Performance Evaluation of Pattern Reconfigurable Antennas in MIMO Systems

With the fast adoption of LTE and IEEE 802.11N, more devices are employing multiple antennas to boost the data rate and reliability of the communication link. Traditionally, fixed antennas are used in such devices. In recent years, reconfigurable antennas have been sought out to further boost the performance, which can adaptor to the changing wireless channel by altering their radiation characteristics, and maintain or exceed the performance of fixed antennas. This thesis studies the possibility of performance increase using pattern reconfigurable antennas as receivers. Their performance potential was first estimated using simulations, and then demonstrated using two electrically steerable passive array radiator (ESPAR) antennas against a pair of monopole antennas on a hardware bit error rate (BER) testbed. The former produces equal performance in BER with certain pattern combinations and excels in theoretical capacity with substantial lead making pattern reconfigurable antenna a potent option as receiver in MIMO-related applications.

Keywords: MIMO
reconfigurable antenna
channel capacity
bit error rate
ESPAR
bit error rate testbed
Advisor: Hum, Sean Victor
Control of Emerging Contaminants by Granular Activated Carbon and the Impact of Natural Organic Matter

This research ranked the adsorbability of 115 emerging contaminants by granular activated carbon (GAC) from drinking water, mainly the organic chemicals identified on the Contaminant Candidate List 3 (CCL3), using classical and quantum quantitative structure activity relationships (QSAR). 80% of the investigated contaminants were classified as cost effectively treatable by GAC based on the models. A rapid small-scale column test (RSSCT) conducted with Lake Ontario water spiked with 8 selected emerging contaminants showed the modeling results were accurate. This research also tested the hypothesis that GAC exhaustion for geosmin and 2-methylisoborneol would be due entirely to natural organic matter, and would occur independently of the presence of these two compounds. RSSCT results confirmed this hypothesis. Mathematical modeling supported this observation by demonstrating that the ratio of the effluent concentration to the influent concentration of a trace organic contaminant is only dependent on the NOM loading state at any bed depth.

Keywords: activated carbon
QSAR
emerging contaminant
NOM
RSSCT
Advisor: Hofmann, Ronald
RGS4 Expression is Associated with Spontaneously Beating Cardiomyocytes during Sinoatrial Node Development

RGS4 is highly expressed in the SAN and is an important regulator of parasympathetic signaling in those cells. Our study set out to determine the utility of RGS4 expression as a marker of SAN myocyte progenitors during cardiac development. In the intact RGS4-LacZ mouse, RGS4 expression was observed in the SAN region starting at E11.5 and its expression remains strong in the SAN throughout cardiac maturation. In mESC-derived cardiomyocytes, RGS4 expression was observed to be associated in the contractile regions of the monolayer. When a RGS4-GFP transgenic mESC line was used to select for differentiated cardiomyocytes with high RGS4 expression, this cell population showed many similarities to SAN myocytes. Specifically, they expressed the pacemaker channel, HCN4, and showed spontaneous action potentials that were characteristic of SAN myocytes. Taken together these data suggest that RGS4 reporter expression may be used to select for SAN myocyte-like cells during cardiomyocyte differentiation from mESCs.

Advisor: Heximer, Scott P.
Practical Issues in Quantum Cryptography

Quantum key distribution (QKD) can provide unconditional security based on the fundamental laws of quantum physics. Unfortunately, real-life implementations of a QKD system may contain overlooked imperfections and thus violate the practical security of QKD. It is vital to explore these imperfections. In this thesis, I study two practical imperfections in QKD: i) Discovering security loophole in a commercial QKD system: I perform a proof-of-principle experiment to demonstrate a technically feasible quantum attack on top of a commercial QKD system. The attack I utilize is called phase-remapping attack. ii) Generating high-speed truly random numbers: I propose and experimentally demonstrate an ultrafast QRNG at a rate over 6 Gb/s, which is based on the quantum phase fluctuations of a laser. Moreover, I consider a potential adversary who has partial knowledge of the raw data and discuss how one can rigorously remove such partial knowledge with post-processing.

Keywords: Quantum Hacking
Quantum random number generator
Advisor: Lo, Hoi-Kwong
Data Envelopment Analysis of Corporate Failure for Non-manufacturing Firms using a Slacks-based Model

The purpose of this work was to study the ability of the Slacks-Based Model of Data Envelopment Analysis in the prediction of corporate failure of non-manufacturing companies as compared to Altman’s Z’’ score model. This research looks at non-manufacturing firms specifically and attempts to classify companies without looking at the asset size of the firm. A DEA model based on the Altman’s Z’’ score financial ratios was created as well as a revised DEA model. The overall accuracy of the models showed the revised DEA model to be more accurate than the original DEA model as well as the Altman Z’’ score. This indicated that bankruptcy could be predicted without the use of total assets or liabilities as variables. This also showed the ability of an SBM DEA model to predict bankruptcy.

Keywords: DEA
Altman
Data Envelopment Analysis
Z Score
bankruptcy
non-manufacturing
SBM
Slacks Based Model
Advisor: Paradi, Joseph C.
The Psychometric Properties of the Nonrestorative Sleep Scale and a Prospective Observational Study of the Physiological Correlates of Nonrestorative Sleep

Nonrestorative sleep refers to the experience of sleep as insufficiently refreshing, often despite the appearance of normal sleep according to objective parameters. As a result, a valid and reliable measure of the subjective experience of NRS is required in order to allow for standardization and comparability in its assessment. This thesis reports the results of a study involving the development and validation of a scale to assess NRS, the Nonrestorative Sleep Scale (NRSS). The psychometric properties of the NRSS were assessed in a group of 256 participants recruited from a sleep clinic population. Principal component analysis revealed four domains. The scale demonstrated good internal and test-retest reliability and reasonable validity compared to other measures. Overnight polysomnographic variables were also compared to scores on the scale and a few were found to be weakly correlated with scale scores. These included alpha EEG, sleep efficiency, and REM latency.

Keywords: sleep
nonrestorative sleep
alpha EEG
polysomnography
unrefreshing
Advisor: Shapiro, Colin M.
Development of Conductive Polymer Membranes for Energy Applications

In this thesis, three types of conductive membranes were fabricated and characterized for potential energy applications such as fuel cells and solar photovoltaics. First, a single layer conductive polypyrrole (PPy) membrane was synthesized and activated. Through image analysis, surface pore geometry changes were analyzed. The single layer PPy membrane was proposed as a possible additional layer or coating in polymer electrolyte membrane fuel cells. Next, a novel adaptive trilayer PPy membrane was fabricated. The membranes were activated, and characterized through changes in surface wrinkle, roughness and contact angle. A dynamic range of surface properties were observed. Lastly, conductive fibrous membranes were fabricated with electrospinning. Two methods were utilized to spin conductive fibers including the incorporation of multi-walled carbon nanotubes (MWCNT) in polystyrene (PS) and the utilization of vapor phase polymerization (VPP) to chemically synthesize PPy on electrospun FeCl3/PS oxidant fibers. Properties including fiber morphology, thermal stability and conductivity were characterized.

Keywords: conductive
polymers
activation
surface property
Advisor: Bazylak, Aimy
Naguib, Hani E.