VictorJuiz/thesis huggingface dataset:
Computational Simulation of Copper (Cu) and Nickel-Copper (Ni-Cu) Alloy Electrodeposition

A study on the electrodeposition of Cu and Ni-Cu alloys in a Hull cell was conducted using both experimental and simulation approaches. For the simulation study a commercial software package, COMSOL Multiphysics, was chosen to explore the predictive power of electrodeposition process simulation. For the relatively simple Hull cell electrodeposition configuration, the agreement between the experimental results and the simulation results were excellent. In addition to Hull cell electrodeposition, the simulation was completed for a much more challenging and industrially highly relevant inner diameter (ID) tube plating configuration without considering bubble flow inside the tube. Different parameters, for instance, tube diameter, the Ni/Cu ion ratio in the plating bath, current density, volumetric flow rate, and cathode length were analyzed regarding their sensitivities. A relative high influence was observed for certain electrodeposition parameters.

Keywords: computational simulation
copper
electrodeposition
nickel-copper alloy
Advisor: Erb, Uwe
Transdermal Optical Imaging Reveal Basal Stress via Heart Rate Variability Analysis: A Novel Methodology Comparable to Electrocardiography

The present study examined the validity of a novel physiological measurement technology called transdermal optical imaging (TOI) technology at assessing basal stress. This technology conveniently, contactlessly, and remotely measures facial blood flow changes using a conventional digital video camera. We compared data from TOI against the pulse data collected from the FDA approved BIOPAC system. One hundred thirty-six healthy adults participated in the study. We found that TOI measurements of heart rate and heart rate variability, which reflects basal stress, corresponded strongly to those obtained from BIOPAC. These findings indicate that transdermal optical imaging technology is a viable method to monitor heart rate and heart rate variability not only accurately but also conveniently, contactlessly, and remotely. Further, measures of heart rate variability obtained via transdermal optical imaging serves as a valid index of basal stress. Potential applications of this technology in psychological research and other fields are discussed.

Keywords: autonomic nervous system
heart rate variability
hemoglobin concentration
respiratory sinus arrhythmia
stress
transdermal optical imaging
Advisor: Lee, Kang
Insights into Fracture Repair using a Murine Model of Osteofibrous Dysplasia

Osteofibrous dysplasia (OFD) is a rare disease characterized by the development of radiolucent lesions at the tibial periosteal surface, where it causes non-healing fractures. We previously identified gain-of-function mutations in the MET gene as a cause for OFD. Fracture tissue samples from OFD patients exhibit aberrant MET activity and delays in osteoblast differentiation. We hypothesized gain-of-function MET mutations result in delayed bone repair ability due to reduced osteoblast differentiation. MetΔ15-HET mice exhibit aberrant and prolonged upregulation of MET signaling and total β-catenin levels similar to OFD patients. MetΔ15-HET osteoblasts demonstrate a differentiation defect in vitro though no gross skeletal defects were identified. Fracture repair is delayed in MetΔ15-HET mice, with decreased bone formation 2-weeks post fracture-inducing surgery. Our data is consistent with a novel role for MET-mediated signaling regulating osteogenesis and open up the possibility of modulating the MET pathway to augment fracture healing.

Keywords: fracture repair
osteofibrous dysplasia
Advisor: Kannu, Peter
Mitochondrial Function and Inflammation in Individuals at Clinical High Risk for Psychosis and Patients with Early Stage Schizophrenia

Schizophrenia (SCZ) is a chronic brain disease. Early detection and treatment are associated with improved disease outcome; and while there are interview-based methods of identifying clinical high risk for psychosis (CHR) individuals, there are yet to be reliable biomarkers to identify at- risk population. Several lines of evidence implicate mitochondrial function and inflammation in the etiology and pathology of SCZ. Here, we examine changes in peripheral mitochondrial function, measured by mitochondrial electron transport chain expression and levels of lactate and pyruvate, and changes in levels of inflammatory cytokines in CHR and early stage SCZ individuals; and compare these to clinical symptoms. We did not detect differences in peripheral mitochondrial function and levels of inflammatory cytokines between our non-psychiatric control, CHR, and early stage SCZ groups; however mitochondrial function may be associated with prodromal symptom severity. Additional studies are warranted to further elucidate mitochondrial changes during the start of disease development.

Advisor: Andreazza, Ana C
The Formation Mechanism of Induced Draft Booster Fan Scale in a Sulfite Pulp Mill

Pulp mills burn the spent pulping liquor in a boiler to recover pulping chemicals and to generate electricity. At the sulfite mill in this study, an induced draft booster fan is between the ammonia and caustic scrubbers. There is significant scale formation on the ID booster fan blades. This results in fan vibration that is severe enough that the boiler needs to be shut down to remove the scale. This leads to both maintenance costs and lost revenue. The objective of this project is to understand the scaling mechanism. This work includes mill sample analysis, field tests at the mill, laboratory studies and mill operating data analysis. The ID booster fan scale mainly contains (NH4)2Mn2(SO4)3, CaSO4 and (NH4)2SO4. The work shows that the key to scale formation is the formation and precipitation of (NH4)2Mn2(SO4)3 that is formed from the reaction of ammonia scrubber carryover droplets and the particulate matters.

Keywords: ID fan
Inorganics
Pulp and paper
Recovery boiler
Scaling
Sulfite process
Advisor: DeMartini, Nikolai
Tran, Honghi
Investigating Lentiviral based Gene Therapy for Purine Nucleoside Phosphorylase Deficiency

The purine metabolic disorder Purine Nucleoside Phosphorylase deficiency leads to Severe Combined Immunodeficiency and there is no current cure other than bone marrow transplants. Given the recent advances and the promising clinical trials seen in the field of lentiviral gene therapy, it is an appealing alternative treatment for PNP deficiency. My project investigated lentiviral based gene therapy in-vitro by transducing a lentiviral vector containing the PNP gene into various PNP-deficient cells including lymphoblastoid cell lines, induced pluripotent stem cells, and lineage depleted mouse bone marrow cells. Transduced cells showed statistically higher PNP expression and activity than non-transduced cells, and were comparable with PNP-proficient cells. Enzyme replacement therapy was also investigated as it compliments gene therapy. Lentiviral based gene therapy showed promising effects in various types of PNP-deficient cells, and should be further investigated together with enzyme replacement therapy to become a standard treatment for PNP deficiency.

Keywords: gene therapy
hematopoietic stem cell manipulation
lentivirus
PNP deficiency
Severe Combined Immunodeficiency
Advisor: Grunebaum, Eyal
Characterization of ATM-mediated Phosphorylation of PTEN

Phosphatase and tensin homolog (PTEN) is a tumour suppressor gene that is commonly lost in many human cancers, such as glioblastoma, prostate, and breast. PTEN’s functions as a lipid phosphatase opposing the oncogenic phosphatidylinositol 3-kinase (PI3K) signaling pathway. However, many cancer-associated PTEN mutations have no effect on its lipid phosphatase activity, indicating that additional PTEN function(s) may contribute to cancer development. Work from my laboratory has shown that PTEN has lipid-phosphatase-independent functions in the nucleus in the maintenance of genome integrity, partially under the control of another tumour suppressor, ATM. Here, I characterize the significance of ATM-mediated phosphorylation at PTEN S398 in the control of its subcellular localization. I demonstrate that DNA-PKcs alternatively phosphorylates PTEN at S398 and identify PTEN S170 as a vital site for maintaining PTEN tertiary structure and ATM-mediated phosphorylation. Further understanding of PTEN regulation is essential in developing new therapeutic strategies against PTEN-deficient tumours.

Keywords: ATM
phosphorylation
PTEN
radiation
subcellular localization
Advisor: Stambolic, Vuk
Metabolomic Profiling of the DASH Diet: Novel Insights for the Nutritional Epidemiology of Type 2 Diabetes Mellitus

Metabolic changes arising from DASH adherence and their relationships with incident T2DM have not been described. We aimed to determine metabolite clusters associated with adherence to a DASH-type diet in the Insulin Resistance Atherosclerosis Study (IRAS) cohort and explore if they predicted 5-year T2DM incidence. DASH adherence for 570 non-diabetic participants was determined using two scoring indices. Metabolite clusters associated with adherence to each of the indices were identified using partial least squares (PLS). Multivariable-adjusted logistic regression was used to explore associations between metabolite clusters and incident T2DM. Results indicated that acylcarnitines and fatty acids loaded strongly on the PLS components. Component 2 was inversely associated with incident T2DM after adjustment for covariates for the first index (odds ratio (OR):0.89; 95%CI:0.80-1.00), and prior to adjustments for the second index (OR:0.88; 95%CI:0.81-0.96). In conclusion, DASH adherence may contribute to reduced T2DM risk through modulations in acylcarnitine and fatty acid physiology.

Keywords: DASH diet
Epidemiology
Metabolomics
Type 2 diabetes
Advisor: Hanley, Anthony J
The Utility of MRI for Measuring Hematocrit in Fetal Anemia

Doppler ultrasound measurements of the peak systolic velocity of the middle cerebral artery (MCA) can be used to non-invasively diagnose fetal anemia but are less precise following fetal blood transfusion and in late gestation. We have previously demonstrated the feasibility of estimating fetal hematocrit in vitro using MRI relaxation times. The objective of this thesis is to report the use of MRI as a non-invasive tool to accurately detect fetal anemia in vivo. MRI- estimated hematocrit of the umbilical vein of fetuses undergoing fetal blood sampling or transfusion was compared against MCA Doppler and fetal blood sampling measurements. Excellent correlation and low systematic bias were found between MRI and laboratory measurements. MRI had higher specificity than MCA Doppler for detecting fetal anemia. Our results suggest there may be a role for fetal MRI as an adjunct to ultrasound in fetuses with suspected anemia, particularly following previous transfusion and in late gestation.

Keywords: Fetal hematocrit
Fetal MRI
MRI relaxometry
T1 mapping
T2 mapping
Advisor: Seed, Mike
Maximal Information Leakage based Data-driven Models for Privacy in Data Disclosure Applications

We consider the problem of privacy preservation in disclosure of data sets, and use maximal information leakage as a privacy measure. This research problem is motivated by recent data breaches and an increasing concern for data privacy for individuals and entities who wish to publish data. We show that it achieves the same result as minimizing an adversary’s accuracy in a theoretical data setting with a Bernoulli-Gaussian data model, and the same result is shown with a numerical approximation of Sibson mutual information. We validate this theoretical result with machine learning models on synthetically generated data following our theoretical model, and show it is a suitable privacy measure. Our data-driven models use a numerical proxy of maximal information leakage, and it out-performs conventional mutual information in experiments for several data sets.

Advisor: Khisti, Ashish
Exploring Gaze Behaviours toward Videos of Physically Active Individuals with a Physical or Intellectual Disability

Having a disability can elicit negative behaviours from others, such as staring. This behaviour often causes discomfort among persons with disabilities. Research grounded in the stereotype content model suggests that depicting somebody with a physical disability (PD) as physically active can improve how they are treated. For example, people gazed less at images of individuals with physical disabilities (PD) who were active versus sedentary. This research, however, did not evaluate gaze toward other stigmatized individuals, including people with intellectual disabilities (ID). The current study examined gaze behaviour toward videos of people with ID, PD, and without disabilities who were depicted as active or sedentary. Participants gazed most at individuals with ID and least at individuals without a disability, with greater gaze directed toward those who were active versus sedentary. Additional research is needed to investigate mechanisms underlying gaze behaviour in order to understand why people gaze at individuals with disabilities.

Keywords: disability
eye tracking
gaze behaviour
physical activity
stereotype content model
Advisor: Arbour-Nicitopoulos, Kelly P
Ultra-wideband Multi-phase Clock Generation for 200+GS/s Time Interleaved ADCs

This thesis investigated multi-phase clock generation circuits for next generation fiber-optic receivers that employ high-speed, 200+GS/s, time-interleaved ADCs. A DC-to-62GHz 4-phase quadrature generator for clock signals with 25% duty cycle was fabricated in a production 55nm SiGe BiCMOS technology and consumed only 178mW. The measured output signals remained in quadrature up to 62 GHz they maintained a duty cycle of 25-26% up to 30GHz and increased up to 33% at 50GHz, beyond which measurements were impacted by the test equipment bandwidth. To the best of the author's knowledge, this is the highest frequency 4-phase 25% duty cycle clock generator in silicon. The use of said clock generator to drive the analog front-end of a DC-to-200+GS/s time-interleaved ADC was investigated. The circuit demonstrated a simulated multi-tone SNDR of over 31.6dB with 54GHz input bandwidth and consumed a total of 442mW.

Advisor: Voinigescu, Sorin P
Characterizing the Longitudinal Course of Depression after Moderate-Severe Traumatic Brain Injury: Trajectory Analysis at 2, 5, 12 30+ Months Post-TBI

Depression can compound the already devastating effects of moderate-severe traumatic brain injury (TBI). Depression after TBI has been correlated with decreased quality of life, poorer community re-integration, and lowered rates of return to productivity. While the persistence and impact of depressive symptoms have been well-documented in patients with moderate-severe TBI, less is known about the course of depression from the sub-acute to chronic stages of injury. The aim of this thesis was to investigate the trajectories of depressive symptoms from the sub-acute to the chronic stages of moderate to severe TBI and factors that may play a role in the onset and persistence of depression post-injury. Trajectory analysis revealed 4 distinct trajectory classes of depressive symptoms post-injury and multinomial logistic regression did not identify any significant predictive demographic or medical factors of class membership. Establishing factors underlying trajectory membership can help to target patients for early prophylactic treatment.

Keywords: Brain Injury
Depression
Trajectory Analysis
Advisor: Green, Robin
Trends in Repeat General Anesthesia for Treatment of Dental Caries at a Children's Hospital: A 10-year Retrospective Review

Abstract Objective: To determine the rate of repeat treatment of caries under general anesthesia (GA) over a ten-year period at a children’s hospital and to assess the frequency of repeat dental treatment under GA by comorbidity. Methods: The health records of children who required repeat GA for dental treatment at The Hospital for Sick Children from January 1, 2006, to December 31, 2015, inclusive were reviewed. Results: The rate of repeat dental treatment under GA for dental treatment over a ten-year period was 10.8%. The yearly repeat rate and simple moving five-year rate of repeat dental treatment under GA increased over the study period. Repeat GA for dental caries was not associated with any particular medical comorbidity. Conclusions: The rate of repeat dental treatment under GA was consistent with the rates reported in the dental literature. The rate of repeat GA for treatment of dental caries increased over the period investigated.

Keywords: anesthesia
caries
medically compromised
repeat
Advisor: Casas, Michael
Investigating the Limits of Psychophysical Differential Thresholds in Audition

The differential threshold is the minimum difference in physical intensity needed for an observer to distinguish one signal from another. For example, two tones applied sequentially can be distinguished in loudness if their respective intensities equal or exceed the differential threshold. In this thesis, the entropy theory of sensation (a model of sensory processing) is used to further the understanding of differential thresholds. Three hypotheses governing information processing are introduced as a means of understanding differential thresholds mathematically. These hypotheses incorporated both the intensity and the duration of applied auditory signals, extending previous research in this area. Experiments were conducted to evaluate the relative merits of the three hypotheses. The differential thresholds of intensity of pure tones were studied in three young adults with respect to both magnitude and duration. Psychometric functions were also collected for future work with the entropy model. A better understanding of differential thresholds can help improve clinical measures of hearing function.

Advisor: Wong, Willy
Connectivity-based Mapping for Diverse Coarse-grained Reconfigurable Architectures

Coarse-Grained Reconfigurable Architectures (CGRAs) are programmable logic devices with large coarse-grained Arithmetic Logic Unit-like logic blocks, and multi-bit datapath-style routing. CGRAs often have relatively restricted data routing networks, so they attract CAD mapping tools that use exact methods, such as Integer Linear Programs (ILPs). However, tools that target general architectures must use large constraint systems to fully describe an architecture’s flexibility, resulting in lengthy run-times. In this thesis, we present a method to derive connectivity information from an otherwise generic device model, and use this to create simpler ILPs, which we combine in an iterative schedule and retain most of the exactness of a fully-generic ILP approach and significantly improve runtime. We then extend this approach to architectures that have arbitrary latency characteristics. The proposed mapping techniques are integrated into, and evaluated using the open-source CGRA Modelling and Exploration (CGRA-ME) framework [1].

Keywords: Coarse Grained Reconfigurable Architectures
Coarse Grained Reconfigurable Arrays
Computer Aided Design
Connectivity
Integer Linear Programming
Advisor: Anderson, Jason H
Algal Analysis through a Chip-based Flow Cytometer

Flow cytometry has been used to analyze cells suspended in fluids and is also widely used as an analyzing tool for marine and aquatic microorganisms. Combining flow cytometry with a microfluidic chip, we show the feasibility of using a chip-based flow cytometer to analyze algae species. As algae tend to live in colonies, we investigated the possibility of differentiating alga in a non-monoculture system through the algae’s autofluorescence. We ran Scenedesmus obliquus and Chlorella vulgaris through a benchtop flow-cytometer to see the differences in their autofluorescent signals. Afterwards the same samples were analyzed using our chip-based flow cytometer system to replicate the previous results. Lastly, we used image analysis to gather the parameters from the autofluorescent signals. We successfully show that chip-based flow cytometers can be an alternative tool to gather algae parameters, and even showed feasibility of using only autofluorescent signals to distinguish two algae species from one another.

Keywords: Algae Analysis
Chip-based flow cytometry
Flow cytometry
Photonics
Advisor: Aitchison, Stewart J
Effect of Imperfect Direct Simple Shear Test Boundary Conditions on Monotonic and Cyclic Measurements

The direct simple shear (DSS) test is commonly used to assess shear strength of soil, estimate liquefaction resistance, or calibrate constitutive models. However, constitutive models are calibrated assuming ideal simple shear stress conditions even though this is not achieved in the DSS test. Near frictionless vertical boundaries cannot develop the complementary shear stresses necessary for ideal simple shear conditions. Difficulties in maintaining constant height during undrained tests violates the constant volume assumption. The top cap holding the top of the specimen can rock (rotate) during shear also violating the assumed perfect simple shear conditions. Parametric studies were conducted to investigate the effect of contact friction between the soil and vertical boundaries, vertical compliance and top cap rocking on the results of undrained DSS tests. The study simulates an industry-standard SGI type simple shear device using a 3-D finite element model and an advanced plasticity model to capture soil behaviour.

Keywords: Constitutive Model
Finite Element Analysis
Friction
Simple Shear
Top Cap Rocking
Vertical Compliance
Advisor: Ghafghazi, Mason
Knowing Beyond the Head - Insights from the Body

What is the connection between mindfulness to insight and is the body involved? Are insights gained through mindfulness transformative in nature? What differences emerge in ‘knowing’ when one practices meditation vs mindful movement? The following heuristic inquiry will explore the experience of 5 practitioners with Theravada meditation (i.e. Vipassana) and mindful dance (i.e. 5 Rhythms) practice. Through personal reflections, interviews, and the researcher’s firsthand experience, the connection between mindfulness, insight and the body are explored. Several findings were revealed as a part of this research. The data highlights the body as a powerful site for understanding, learning, and guidance. Themes such as awareness (of: sensations, mind, emotion, multilayered self), body knowing (expression, understanding, trust), practice (making time, type) and perspective shed greater light on this inquiry. This research whets the appetite of future researchers who are interested in exploring ideas around embodiment, body wisdom, somatic and mindfulness practices.

Keywords: Awareness
Dance
Embodiment
Meditation
Mindfulness
Somatics
Advisor: Ryan, Sherida
Miller, John J
Compensatory Afforestation in Odisha, India: A Political Ecology of Forest Restoration

To mitigate climate change and protect biodiversity, states across the globe have ambitious plans to restore degraded lands (globally, 350 million hectares by 2030, as per the latest Bonn Challenge commitment). Seeking to understand the potential unintended consequences of these vast state-led restoration efforts, in this thesis I explore India's seven-billion-dollar compensatory afforestation program through a political ecology lens. I find that in practice this policy contradicts India’s broader attempts to democratize forest governance by failing to foreground local communities and institutions, affirm customary rights, and safeguard livelihoods. Instead, compensatory afforestation contributes to dispossession and precarity, while relying heavily on industrial tree plantations. With ground-truthed geospatial data, I explore how this policy impacts Adivasi shifting cultivators on their tenure-insecure territories in Odisha, east India. In so doing, I support calls from the field of Forest Landscape Restoration (FLR) to ensure restoration is tenure-sensitive and rights-based.

Keywords: Afforestation
Climate change mitigation
Compensatory afforestation
Forest landscape restoration
Forest rights
Odisha
Advisor: Singh, Neera