VictorJuiz/thesis huggingface dataset:
Addressing Limitations of a Spatially Sensitive Large-Area Ion Chamber for Real-Time Verification of Intensity Modulated Radiation Therapy

Lack of light transparency and overall thickness are limitations of a previously described spatially sensitive large-area ionization chamber used for real-time verification of radiation therapy beam delivery. The first limitation was addressed with investigation of a commercially available light transparent conductive glass plates as replacements for aluminum plates in the construction of the chamber. Resulting chamber produced expected spatial sensitivity, allowed the light field to be transmitted with 35% attenuation in intensity, and caused deviation of field position due to refraction up to 0.4 mm. The second limitation was investigated with a novel interleaved comb patterned electrode pairs. The pattern was ablated on a light transparent conductive glass plate and utilized for construction of an experimental prototype ionization chamber that was 35% thinner, light transparent, and produced a spatial sensitivity comparable to the original design. However, further refinement in the design and manufacturing process will be necessary to make a practical comb patterned ionization chamber pair.

Keywords: IMRT
large area ionization chamber
light transparency
online treatment verification
real-time quality assurance
Advisor: Islam, Mohammad K
Heaton, Robert K
Hydrological and Biogeochemical Fluxes of Throughfall and Stemflow in Temperate Swamps

This study quantifies the hydrological and biogeochemical inputs that precipitation (P) provides to temperate swamp ecosystems. The meteorological influences on throughfall and stemflow in two temperate swamps of southern Ontario over two growing seasons separated by a major ice storm is presented. This study also presents the investigation of dissolved organic carbon (DOC) and nitrogen (N) fluxes within throughfall and stemflow for two temperate swamps of southern Ontario during the 2014 growing season. Field-based measurements in two mixed-deciduous temperate swamps over the course of two growing seasons, combined with chemical analyses from extensive laboratory work form the basis of the results presented here. The quantification of P, DOC and N fluxes has rarely been studied in temperate swamp ecosystems and is important to quantify as these inputs have large impacts on the physical and chemical processes occurring at the wetland floor.

Keywords: Ontario
Rainfall Partitioning
Temperate Wetlands
Advisor: Duval, Tim P
MonArch: Scalable Monitoring and Analytics for Visibility and Insights in Virtualized Heterogeneous Cloud Infrastructure

With rapid development of cloud computing technologies, cloud data centers continue to grow in scale and complexity. Monitoring and analytics are the key enablers to provide visibility and insights in a large-scale infrastructure. In this thesis, we present a monitoring and analytics system, called MonArch, designed for monitoring data collection, storage and analytics in a virtualized heterogeneous cloud environment. MonArch provides high scalability and flexibility to enable multi-layer heterogeneous resources monitoring. Scalable anomaly detection, root cause analysis, and graph processing capabilities are offered in MonArch to simplify resource monitoring and support real-time identification of system anomalies. MonArch supports a wide variety of use cases including security detection, system diagnosis, resource allocation, and IoT sensor data storage and processing. MonArch is implemented and deployed in the SAVI Testbed. The evaluation results demonstrate MonArch's scalability and efficiency in data monitoring, as well as its effectiveness in anomaly detection and root cause analysis.

Keywords: Cloud Computing
Data Analysis
Monitoring
Advisor: Leon-Garcia, Alberto
Environmental Requirements Underlying Effector-triggered Immunity in Arabidopsis thaliana

Pseudomonas syringae is a Gram-negative bacterium that infects multiple plant species via injection of type three secreted effectors (T3SEs) into host cells. Nucleotide-binding leucine-rich repeat (NLR) resistance (R) proteins recognize specific T3SEs and trigger an immune response, called effector-triggered immunity (ETI). ETI is often associated with localized programmed cell death (PCD), known as the hypersensitive response (HR), which limits pathogen proliferation. We examined two abiotic factors that differentially affect ETI outputs – humidity and temperature. We observed that high relative humidity or elevated temperature conditions capable of suppressing HR had minimal influence on ETI-associated virulence suppression, thereby uncoupling these two ETI responses. We have identified ecotypes of Arabidopsis that show suppression of ETI-associated virulence suppression at elevated temperature, highlighting the natural variation that exists in coping with elevated temperature. These results reinforce the influence of abiotic factors on plant immunity and emphasize the importance of carefully documented environmental conditions in studies of plant immunity.

Keywords: Arabidopsis thaliana
Effector-Triggered Immunity
Elevated Temperature
High Relative Humidity
Plant Immunity
Pseudomonas syringae
Advisor: Desveaux, Darrell
Guttman, David
Rank Metric Convolutional Codes with Applications in Network Streaming

We consider end-to-end error correction codes for real-time streaming over a network, where the source and destination are nodes in a graph. Links between nodes are erasure channels and the source-destination relationship a rank-deficient channel matrix. In an isolated rank loss model, the channel matrix arbitrarily decreases to a minimum rank within each sliding window of network uses. We prove the column sum rank metric determines the effectiveness of a code and construct a family of codes that achieve the maximum column sum rank. In a burst rank loss model, a fraction of links are simultaneously erased for consecutive network uses. We derive the capacity and prove achievability with a layered construction using the previously introduced codes. Simulations over statistical models reveal our construction to be superior over baseline codes.

Keywords: error correction codes
rank metric
real-time streaming
super-regular matrices
Advisor: Khisti, Ashish
An Emulator-based Prediction of Dynamic Stiffness for Redundant Parallel Mechanisms

For Parallel Kinematic Mechanisms (PKMs) with kinematic redundancy, mechanism configurations with higher stiffness can be chosen during motion-trajectory planning. However, substantial computational resources would be required for this optimization problem, specifically, for the solution of the two intertwined sub-problems: (i) calculation of the dynamic stiffness of any considered PKM configuration, at a given task-space location, and (ii) searching for the PKM configuration with the highest stiffness at this location. Herein, the former sub-problem is addressed via a novel effective emulator to provide a computationally efficient approximation of the dynamic-stiffness function suitable for optimization. The proposed method for emulator development identifies the mechanism’s structural modes in order to break down the high-dimensional stiffness function into multiple functions of lower dimension. Via extensive simulations, some of which are described herein, it is demonstrated that the proposed emulator can predict the dynamic stiffness of a PKM at any given configuration with high accuracy and at a low computational expense.

Keywords: Dynamic Stiffness
Emulator
MLS
Parallel Kinematic Mechanism
Redundancy
Advisor: Benhabib, Beno
Mills, James K
Data Driven, Force Based Interaction for Quadrotors

Quadrotors are small and agile, and are becoming more capable for their compact size. They are expected perform a wide variety of tasks including inspection, physical interaction, and formation flight. In all of these tasks, the quadrotors can come into close proximity with infrastructure or other quadrotors, and may experience significant external forces and torques. Reacting properly in each case is essential to completing the task safely and effectively. In this thesis, we develop an algorithm, based on the Unscented Kalman Filter, to estimate such forces and torques without making assumptions about the source of the forces and torques. We then show in experiment how the proposed estimation algorithm can be used in conjunction with controls and machine learning to choose the appropriate actions in a wide variety of tasks including detecting downwash, tracking the wind induced by a fan, and detecting proximity to the wall.

Keywords: Force Estimation
Learning
Quadrotor
Advisor: Schoellig, Angela P
The Runahead Network-on-chip

With more cores per chip multiprocessor and higher memory demands from applications, it is imperative that networks-on-chip (NoC) provides low-latency, power-efficient communication. Conventional NoCs tend to be over-provisioned for worst-case bandwidth demands. This results in ineffective use of network resources and power inefficiency. In terms of performance, low-latency techniques often introduce overheads and incur complexity in the router microarchitecture. We find that both low latency and power efficiency is possible by relaxing the constraint of lossless communication. We propose the Runahead NoC, a lightweight, lossy network that provides single-cycle hops. Allowing for lossy delivery makes it possible to design an extremely simple bufferless router microarchitecture. The Runahead NoC operates either as a power-saver to improve power-efficiency, or as an accelerator to provide ultra-low latency communication for selected packets. The Runahead NoC reduces network power consumption by 1.80x as a power-saver and improves latency by 1.66x as an accelerator.

Keywords: Computer Architecture
Interconnection Architectures
Network On Chip
NoC
Advisor: Enright Jerger, Natalie
Steffan, J. Gregory
Preclinical Modeling of Habitual Nicotine Seeking

Current theories of substance dependence suggest that contributions to compulsive drug use may include the aberrant recruitment of cognitive processes normally responsible for automatizing repeated behaviors, or “forming habits”. While evidence has shown that both ethanol and cocaine can abnormally accelerate the formation of drug-seeking habits, whether this could be the case for nicotine has received little attention. In the current work, subjects acquired self-administration of both intravenous nicotine and orally consumed saccharin in two separate daily operant sessions, receiving 10 sessions of FR1 training for each reinforcer. Behavioral assays of “aversion-pairing” and “contingency degradation” were respectively utilized in Experiments 1 and 2 to determine if responding for each reward was goal-directed or habitual. Both tests were consistent in suggesting the training parameters employed produced goal-directed saccharin responding, but habitual nicotine responding. Particularly noteworthy is the exceptionally rapid rate at which nicotine-seeking habits appear to have developed.

Keywords: Degradation
Devaluation
Habit
LiCl
Nicotine
Saccharin
Advisor: Lê, Anh D
What Kind of Poland? Exploring the Role of the National Education Reforms (1999-2015) in the Neo-colonialist Expunging of Polishness and the Production of a New European-Unionized Subject.

This thesis examines the role of Poland’s post-communist national education reforms (1999-2015) in the reproduction of (neo)colonial relations within Polish society. By focusing on Polish literature education in public high schools in Poland, this study investigates how literary curriculum reform contributes to Poland’s neo-colonial subjugation through Western, European-Union-centered postmodern hegemonic constructions of nationality/citizenship, fracturing Polish society into an Enlightened colonial elite, and Poland’s backward internal Orient, demystifying the post-communist transformation as neo-colonial oppression versus independence, and the current III Republic as a neo-communist construct, rupturing continuity with the self-governing I and II Republics. In proposing a colonial view of Polish education and society, past and present, from the 19th century partitions, 20th century Nazism and communism, to present-day EU liberalism, this study inducts Poland/Central Eastern Europe into colonial discourse. In its call for decolonization, both educational and social, it propounds modernization based on indigenous Polish traditions versus imported Western models.

Keywords: Central Eastern Europe
education reform
literature/civic education
Poland
post-communism
post/neo-colonialism
Advisor: Feuerverger, Grace
Real-world Effectiveness of Bupropion versus Varenicline for Smoking Cessation: Exploring the Role of Metabolic and Personality Variables

Varenicline and bupropion are efficacious, prescription-only pharmacotherapies for smoking cessation; however, their real-world impact is limited by affordability and accessibility. Using a randomized design, we evaluated the real-world effectiveness of mailed bupropion and varenicline, as well as the roles of nicotine metabolism (NMR) and personality traits, in a sample of interested smokers, utilizing web-based recruitment and follow-up. Quit rates at the end-of-treatment were significantly higher for varenicline (28.3%) compared to bupropion (16.8%). Medication compliance was a significant predictor of quit outcome. NMR was not associated with nicotine dependence, or with quit success with either bupropion or varenicline. Neuroticism (positively) and extraversion (negatively) were significantly correlated with nicotine dependence in men only. Furthermore, in males, conscientiousness and neuroticism were significant predictors of smoking abstinence. Given the low real-world quit rates, improving medication compliance and implementing personalized pharmacological and behavioral interventions are promising approaches to increase effectiveness of tobacco cessation treatments.

Keywords: Bupropion
Nicotine Metabolism
Personality
Pharmacotherapy
Smoking
Varenicline
Advisor: Zawertailo, Laurie
Zack, Martin
The Impact of the Common European Framework of Reference on Foreign Language Instruction: The Case of Sociolinguistic and Pragmatic Competence

This qualitative study investigates the role of the Common European Framework of Reference (CEFR) in Sociolinguistics and Pragmatics (SP) instruction in an Italian secondary school where English and Spanish are taught as foreign languages. While research points to the considerable influence of the CEFR on language policies, little is known about its pedagogical impact on language teaching. In addition, despite the positive findings on the benefits of SP teaching for learners’ development of communicative competence, SP seems to be usually neglected in language classrooms. This study sheds light on the presence of the CEFR and SP in foreign language teaching by focusing on teachers’ cognition and instructional practices. In-depth analysis of documents, interviews and classroom observation shows that the CEFR and SP play marginal roles in the participant school, which were found to be largely related to the external language exams implemented and to practitioners’ knowledge and beliefs regarding these concepts.

Keywords: Common European Framework of Reference
English as a foreign language
Pragmatics
Pragmatics instruction
Spanish as a foreign language
Advisor: Piccardo, Enrica
Electrolytic Hydrogen Charging of Zr-2.5Nb Alloy in Molten NaOH-KOH Eutectic Mixture at Low Overpotential

The major contributions of this thesis include: first, it proved the effectiveness for the method of electrolytic charging Zr-2.5Nb alloy with hydrogen in moist NaOH-KOH melt at low overpotential; second, it employed a Hg/HgO RE in YSZ membrane and investigated its performance; last, it found an optimized voltage range for the potentiostatic charging process. The equilibrium potential of hydrogen evolution reaction in the melt is estimated to be slightly higher than -0.85V, measured by the Hg/HgO RE. The optimized voltage range is -0.85 V to -0.875 V. Within this range, scattered hydride distribution in the internal metal bulk is observed, and hydrides precipitate at controllable rates, avoiding the intensive accumulation in a thin subsurface layer. The Hg/HgO RE provides a stable and reproducible OCP reading around -0.785 V for nickel plated zirconium samples in the melt. The potential difference between the three Hg/HgO RE for this project is ±10 mV.

Keywords: Hydride
low overpotential
Molten alkali
Pressure tube
YSZ
Advisor: Newman, Roger C
Foraging Theory as a Model to Examine Parasitism by the Tachinid parasitoid fly Ormia ochracea on the cricket Gryllus rubens

This paper tests the effects of auditory and chemical sensory input on the foraging and larviposition behaviour of an eavesdropping parasitoid fly. Ormia ochracea (Diptera: Tachinidae) use the dominant calling field cricket in their habitat as hosts for their larvae; females locate hosts by eavesdropping on the acoustic calls produced by male crickets. By manipulating directional cues in the auditory stimulus experienced by foraging females their ability to locate hosts and their ability to switch to a novel host following a switch in the location of the stimulus were examined. Success was dependent upon walking behaviour and proximity at stimulus change. After locating potential hosts females must deposit larva and differences in larviposition rates of females, after they had located an attractive sound source (cricket call), in the absence and presence of chemical cues associated with crickets indicate that females may use additional sensory modalities in host-foraging decisions.

Advisor: Mason, Andrew C
Advanced Microfluidic Platform for Epithelial and Endothelial Cell Dimorphic Coculture

Biological cells cultured in a 3D microenvironment are more realistic and exhibit characteristics found in vivo when compared to 2D cell cultures. However, culturing 3D cellular structures such as epithelial mammary spheroids and endothelial cells simultaneously is tedious using conventional cell cultureware. To address this issue, we have developed a CNC-milled microfluidic system that enables simultaneous culturing of 3D tumor spheroids and endothelial-lined lumens. We employed an accessible polishing techniques to make optical quality concave features in milled microfluidic platforms. This system can be used to potentially study the complex and dynamic cellular interactions of cancer development, angiogenesis and other malignancies involving the interactions between different cell types of different morphologies.

Keywords: Angiogenesis
Microfabrication
Microfluidics
Tumor Spheroids
Advisor: Young, Edmond WK
Effect of local delivery of HEBP and inorganic pyrophosphate on bone healing

We sought to investigate the effects of local delivery of Etidronate or inorganic pyrophosphate (PPi) on bone healing. These compounds were loaded onto PLGA-CaP scaffolds at five different concentrations. A drug release study was conducted with scaffolds immersed in solutions at different pHs from 1h to 45d. In addition, 165 rats received bilateral femoral implants of drug-loaded or control scaffolds and were euthanized at 7d, 15d, 30d, 3mo and 6mo. Harvested femora were processed for histological and microCT analyses. Partially mineralized woven bone formed adjacent to drug-loaded scaffolds at early time-points, indicating some effect of the drugs. At the highest dose, PPi-loaded scaffolds resulted in greater bone volume, trabecular number and connectivity density at the 3mo time-point. Despite challenges faced with the scaffold manufacturing and animal model, our findings suggest that local delivery of PPi at high concentrations enhanced bone healing. However, further studies are necessary to validate these observations.

Advisor: Davies, John E
Tenenbaum, Howard
Novel Directions in Debug Automation for Sequential Digital Designs in a Modern Verification Environment

Digital systems are growing in complexity, introducing significant verification challenges in the design cycle. Verification has grown to take 70% of the design time with debugging being responsible for half of this effort. Automation has mitigated part of the resource-intensive nature of rectifying erroneous designs. Nevertheless, these tools have scalability difficulties and thus, verifying large designs requires further innovation. This thesis introduces three novel methodologies that address this issue. First, a framework to verify designs with multiple clocks using Quantified Boolean Formula satisfiability is presented. It models an iterative logic array representation with universal quantification to achieve synchronization. Next, a framework that ranks revisions based on their likelihood of being responsible for a particular failure is developed. Finally, an automated correction algorithm is discussed. It takes an erroneous design, and corrects failures caused by typical source code mistakes. Experiments demonstrate the benefits of augmenting the verification cycle with these methodologies.

Keywords: Multiple Clock Domains
Online Verification
Regression Verification
Re-Synthesis
Revision Debug
Syntax-Guided RTL Correction
Advisor: Veneris, Andreas
Optimizing Key-value Stores For Hybrid Storage Environments

Modern write-intensive key-value stores have emerged as the prevailing data storage system for many big applications. However, these systems often sacrifice their read performance to cope with high data ingestion rates. Solid-state drives (SSD) can lend their help, but the volume of data and the peculiar characteristics of SSDs make their exclusive use uneconomical. Hence, hybrid storage environments with both SSDs and hard-disk drives (HDD) present interesting research opportunities for optimization. This thesis investigates how to design and optimize key-value stores for hybrid storage environments. We first modify and extend an existing key-value store to leverage the SSD as a cache. We next formulate an analytical cost model to predict the performance of a generic log-structured hybrid system. Finally, we use insights from our model to design and implement a new hybrid-optimized key-value store, LogStore. We demonstrate that LogStore is up to 7x faster than LevelDB, a state-of-the-art key-value store.

Keywords: databases
flash
hybrid storage
key-value stores
log-structured
ssd
Advisor: Jacobsen, Hans-Arno
Validation and Refinement of the Susceptibility to Driver Distraction Questionnaire (SDDQ): A Measure of Voluntary, Involuntary, and Habitual Components of Driver Distraction

Driver distraction is a major contributor to vehicle crashes, and as such, it has become a major concern for road safety. The current work presents the findings of various studies examining the validity and reliability of the newly developed Susceptibility to Driver Distraction Questionnaire (SDDQ). In general, SDDQ demonstrated good concurrent validity and internal consistency. In addition, these studies provided valuable insights for improving SDDQ. An exploratory revision incorporated a new component of habitual distraction in addition to the already existing voluntary and involuntary distraction components. Responses to the revised SDDQ were correlated to performance on various measures of executive function to understand the role of individual differences in cognition on drivers’ susceptibility to voluntary, involuntary, and habitual distractions. Overall, findings of this research suggest SDDQ to be a promising self- report measure for driver distraction. The implications of these findings for the development of distraction mitigation strategies are discussed.

Keywords: Driver distraction
Human factors
Reliability
Survey
Validity
Advisor: Donmez, Birsen