VictorJuiz/thesis huggingface dataset:
Central and Peripheral Neuroimaging in Magnetic Resonance-guided Focused Ultrasound
Keywords: diffusion tensor imaging
diffusion weighted imaging
focused ultrasound
neuroimaging
therapeutic ultrasound
tractography

Magnetic resonance-guided focused ultrasound (MRgFUS) is a non-invasive treatment modality which uses acoustic waves to generate precise thermal lesions. There is growing interest in its application to the treatment of neurological conditions. Conventional MR contrasts can provide anatomical references for targeting and lesion identification but do not impart information about the cellular environment or neural microstructure. Diffusion weighted imaging (DWI) is a technique sensitive to the motion of water within tissue that can be used to visualize fiber bundles and quantitatively assess treatment changes to nerve architecture in vivo. The main aims of this thesis are to: 1) develop an imaging and acoustic sonication procedure using DWI and tractography; and 2) incorporate DWI in the thermal lesioning of intracranial white matter and peripheral nerves to enhance targeting and understand the treatment effect on tissue microstructure. Specific aims of this thesis are to: 1) investigate the DWI characteristics of ex vivo animal brain tissue as a model for neurosurgical treatment development; 2) generate thermal lesions on brain white matter in an in vivo animal model and determine the treatment effect via diffusion tensor imaging (DTI) metrics, tractography, and histological validation; 3) reconstruct the sciatic nerves via tractography to enhance target determination; and 4) produce focal ablations on the sciatic nerve and measure the microstructural changes via DTI metrics. Imaging results from Study I reveal that non-fixed ex vivo brain tissue does not differ from in vivo tissue in terms of diffusion anisotropy, demonstrating its potential use in neurosurgical technique characterization. In Study II, lesion size and location were automatically determined in vivo using Mean DWI and confirmed by histology. DTI metrics in the lesion revealed a pattern of treatment-related anisotropy and diffusivity alterations. Affected fiber pathways were visualized via tractography. In Study III, higher order tractography methods permitted consistent reconstruction of sciatic nerves and precise MRgFUS target placement. Significant microstructural changes in the nerve were observed due to lesioning. Taken together, this thesis demonstrates significant advancements in the visualization of MRgFUS treatment targets and the assessment of microstructural changes that occur following thermal ablation within the central and peripheral nervous systems.
Cytoplasmic Mislocalization of CTCF by Leukemic Oncogene NPM1c in Acute Myeloid Leukemia
Keywords: Acute Myeloid Leukemia
alternative splicing
CTCF
cytoplasmic mislocalization
DNA methylation
NPM1c

Acute myeloid leukemia (AML) cells with normal cytogenetics frequently harbor a TCTG insertion in exon 12 of Nucleophosmin 1 (NPM1), resulting in a frameshift creating a nuclear export signal and cytoplasmic localization of the mutant protein NPM1c. Although the mutation directs NPM1c to the cytoplasm, the underlying mechanism of how NPM1c causes AML remains incompletely understood. NPM1 participates in multiple protein-protein interactions; among those interacting proteins is the CCCTC binding factor (CTCF), the master weaver of the genome. CTCF is involved in several important nuclear functions including DNA looping, regulation of gene expression, and RNA splicing through binding to CTCF DNA binding sites. I hypothesized that NPM1c could mislocalize CTCF into the cytoplasm, thereby reducing the functional level of nuclear CTCF and so alter its regulatory roles regarding gene expression and epigenetic functions in the nucleus. Our studies verified the interaction of CTCF with NPM1. Furthermore I demonstrated that CTCF interacts with NPM1c, partially redistributing CTCF into the cytoplasm. The interaction of CTCF and NPM1c involves the amino terminus of CTCF and the last 50 amino acids on the C-terminus of NPM1. Moreover, cytoplasmic CTCF can be relocalized to the nucleus by interfering with the interaction of CTCF and NPM1c.
Neural Synchrony in Neuromagnetic Signals and the Role of Alpha Oscillations for Working Memory
Keywords: Brain oscillations
Magnetoencephalography
Neuroimaging
Working memory

Brain functions for perception, cognition, and action involve coordination between distributed neural networks across extended brain regions. Findings from invasive intra-cranial recordings in animals suggest that brain networks interact through precise timing of neural activity. Such timing mechanism plays an important role for communication between brain areas and can be measured as synchrony in neuroelectric oscillations. Extra-cranial measurement of synchrony can be obtained from magnetoencephalographic (MEG) recordings in humans. However, measurement of synchrony in brain oscillations with MEG is more challenging than using direct electrode recordings because the small MEG signals are embedded in noise, and propagation of the electromagnetic signal across the brain volume may result in false interpretation of synchrony. I combined simulation studies and analysis of MEG data in a working memory (WM) study to improve the methods of detecting synchrony as an indicator of functional connectivity in the MEG. I analyzed the functional roles of alpha frequencies during working memory encoding and maintenance. I provided findings of the functional relevance of alpha oscillations in the memory retrieval process. These results will improve the feasibility of connectivity analysis using MEG in basic research and clinical applications.
“Caught in the Middle”: Investigating Middle School Teachers’ Pedagogical Approaches in Instrumental Music Class
Keywords: Curriculum
Education
Instruction
Middle School
Music
Pedagogy

This dissertation explores how middle school instrumental music teachers describe their pedagogical approaches in order to navigate challenges encountered with their teaching assignments. This comparative case study investigates five middle school music teachers’ perceptions of their pedagogical approaches in the classroom. It uses the framework of Pedagogical Content Knowledge to understand their instructional strategies in the context of middle school, including the environmental, social-relational, and psychological aspects that influence their choices. The data was collected through three semi-structured interviews over the course of the school year and was analyzed using a constructivist approach. The author argues that middle school music teachers can address the challenges of working with their instrumental music classes by incorporating different pedagogical approaches into their daily teaching. The results of this study have implications for practicing music educators and teacher candidates through recommendations focused on further developing their Pedagogical Content Knowledge.
Quantitative Measurement of Parliamentary Accountability using Text as Data: the Canadian House of Commons, 1945-2015
Keywords: accountability
Canadian politics
debate
text analysis
text as data

How accountable is Canada’s Westminster-style parliamentary system? Are minority parliaments more accountable than majorities, as contemporary critics assert? This dissertation develops a quantitative measurement approach to investigate parliamentary accountability using the text of speeches in Hansard, the historical record of proceedings in the Canadian House of Commons, from 1945-2015. The analysis makes a theoretical and methodological contribution to the comparative literature on legislative debate, as well as an empirical contribution to the Canadian literature on Parliament. I propose a trade-off model in which parties balance communication about goals of office-seeking (accountability) or policy-seeking (ideology) in their speeches. Assuming a constant context of speech, I argue that lexical similarity between government and opposition speeches is a valid measure of parliamentary accountability, while semantic similarity is an appropriate measure of ideological polarization. I develop a computational approach for measuring lexical and semantic similarity using word vectors and the doc2vec algorithm for word embeddings. To validate my measurement approach, I perform a qualitative case study of the 38th and 39th Parliaments, two successive minority governments with alternating governing parties. I find that similarity scores are positively related with the substantive quality of opposition questions and government responses. In the quantitative analysis phase, I study Question Periods from 1975-2010 and daily debates from 1945-2015 using the lexical similarity measurement. I find that minority parliaments are more account- able than majority governments since the 30th Parliament, but find no significant relationship between government seat percentage and parliamentary accountability. I show that Parliament becomes more accountable as a government’s popularity decreases. However, the data more strongly support a non-linear model. A structural break analysis yields one significant break at 33%: below this critical value, polling popularity and parliamentary accountability are positively related, and above, are negatively related. Finally, I confirm that the correlation between measures of lexical and semantic similarity varies in strength and direction across parliamentary sessions, suggesting two distinct generative processes are indeed at work.
Flow Field and Soot Formation Characteristics in Swirl-stabilized Non-premixed Turbulent Flames
Keywords: Laser diagnostics
Soot
Swirl-stabilized flames
Turbulent combustion

Soot formation and evolution in relation with the flow fields were investigated experimentally in turbulent swirl-stabilized non-premixed flames using three different fuels: methane, ethanol and aviation Jet A-1. The studied flames were confined and stabilized in a model gas turbine combustor with a swirl number of ~0.55. Soot volume fraction, fv, and primary soot particle size, dp, were measured using auto-compensating laser-induced incandescence, and planar three-component velocity fields were measured using stereoscopic particle image velocimetry. Measurements of planar laser-induced fluorescence of OH and OH* chemiluminescence were also made for methane and ethanol flames. The OH* field was further Abel-inverted to qualitatively locate the heat release zone. The flow field for all flames featured pronounced inner and outer recirculation zones (IRZ, ORZ), each bounded by their corresponding inner and outer shear layers (ISL, OSL). Abel-inverted OH* intensity maps showed that primary reaction zones occurred in the vicinity of ISL. The central fuel jet penetrating into the IRZ accompanied by a stagnation zone was observed in all methane flames. Soot measurements showed that the overall dp for methane and Jet A-1 flames ranged between 30 nm and 60 nm without discernible trends. In methane flames, peak time-averaged fv occurred between the central jet penetration and the ISL. The decrease and the final disappearance of time-averaged fv were strongly correlated with elevated OH, demonstrating a dominant oxidative attack of OH on soot. With a ~7% increase in air flow rate, the level of soot volume fraction dropped by nearly threefold due to enhanced turbulence intermittency. The appearance of ethanol spray flames, which lacked a bright yellow color, largely differed from others. The absence of soot was confirmed in the laser-induced incandescence measurements. The isothermal flow field of ethanol flames exhibited a large-scale structure of precessing vortex core which was then suppressed under reacting conditions. In Jet A-1 flames, spray pattern changed from V-shaped hollow cone to semi-solid cone when air flow rate increased by 20%, resulting in a 60% reduction in peak time-averaged fv. In contrast to results obtained from the methane flame, soot was found primarily outside the ISL where fuel existed in abundance.
Investigation of the Antibody Response and the Role of IgM Immunoglobulin in Experimental Cervical Spinal Cord Injury
Keywords: Autoantibodies
Autoimmunity
IgG immunoglobulin
IgM immunoglobulin
Inflammation
Spinal cord injury

Traumatic spinal cord injury (SCI) results in motor, autonomic and sensory impairment, and is a condition for which there are no established therapies that promote repair or regeneration. Antibody responses are dysregulated in traumatic SCI, leading to increased infections and autoimmunity. However, the status of antibody responses in cervical SCI (cSCI), the most common injury level seen in patients is unknown. In this thesis, I characterized the antibody responses in a clinically relevant rodent model of cSCI. There was an autoantibody response against the spinal cord in the subacute phase (2 weeks post-injury), which did not persist in the chronic phases (10 and 20 weeks post-injury) of the condition. I observed localization of IgG and IgM antibodies in the injured spinal cord, which appeared to target perilesional astrocytes and ventral horn neurons. In parallel, I found that peripheral T- and B-cell frequencies and total serum immunoglobulins were decreased 2 weeks after injury, suggesting that peripheral immune suppression and spinal cord-targeted autoreactivity co-exist in cSCI. Additionally, I found increased serum IgM immunoglobulin at 10 weeks post-injury. As IgM immunoglobulin is important in homeostasis against autoimmunity, I investigated the role of IgM immunoglobulin in IgG-mediated autoimmunity after cSCI. Mice that lacked secreted IgM were found to have impaired neurobehavioral recovery, increased lesion size and less spared white matter in their spinal cords after cCSI, as compared to wild-type controls. Moreover, IgM-deficient mice had higher complement-fixing IgG antibody deposition in the spinal cord, coupled by increased T-lymphocyte and microglia/macrophages. Taken together, these data suggest that IgM immunoglobulin serves to regulate detrimental IgG deposition during the recovery phase after SCI. In conclusion, I demonstrated that cSCI provokes an autoantibody response against the spinal cord, in conjunction with peripheral immune suppression, during the subacute phase of injury. I have also shown that IgM immunoglobulin is necessary for spontaneous recovery in cSCI, by limiting detrimental IgG deposition in the lesioned spinal cord. These novel findings advance our knowledge of the immune-mediated pathology after cSCI and warrant the further investigation of the therapeutic potential of IgM immunoglobulin during the subacute phase of SCI.
Essays in Financial Economics
Keywords: Corporate
Financial Markets
Information Economics

This thesis consists of three essays on financial markets, product markets, information markets, and their interaction. Chapter 1 offers an introduction of the essays and summarizes the main findings. Chapter 2 studies how product markets shape managerial short-termism (myopia). It shows that under market competition, managerial short-termism may arise endogenously as a means for firms to commit to competing aggressively. Such managerial short-termism is facilitated by financial markets as firms tie their managers' pay to the short-term stock prices. The following two chapters focus on the interaction between financial markets and information markets; both chapters demonstrate that information markets are crucial in determining asset prices and market quality in financial markets. Chapter 3 develops an information-sales model in which investors acquire uncertain skills to interpret purchased data, thereby changing the behavior of data sellers. It leads to several novel results (e.g., price informativeness increases with skill-acquisition costs), which help clarify certain empirical regularities. Chapter 4 examines sales of financial market information in an economy with two information sellers. In equilibrium, the two sellers form either orthogonal or overlapping clientele, depending on the similarity of the information to be sold. When the two sellers' information is very distinct and the sellers have relatively large bargaining power in sharing trading profits, investors' information purchase behavior exhibits complementarity, leading to the possibility of multiple equilibria.
Quantitative Models and Methods for Risk-informed Physical Asset Management
Keywords: Asset Management
Bayesian Inference
Decision Analysis
Monte Carlo Simulation
Quantitative Risk
Risk Management

In the last decade, the management of physical assets has emerged as a crucial business function for companies operating in asset intensive industries. Risk, defined as the likelihood and consequence(s) of undesired events, is an integral part of asset management. In this work, we set out to develop quantitative models and methods to facilitate risk-informed decision-making for the management of physical assets in the natural gas industry. We develop a novel practical approach that can be used in reliability analysis of physical assets. A Bayesian framework is implemented to cohesively integrate objective data with expert opinion and tacit knowledge with the aim toward deriving predictive models for time to failure for physical assets. The methodology presented provides an elegant and powerful way of addressing uncertainty by allowing the analyst to take into consideration all types of available information. To quantitatively analyse potential production losses due to critical asset failures, we develop a physics-based system performance and reliability model for an underground gas storage facility. The model combines a thermo-hydraulic performance model for a gas storage facility consisting of a gathering system, compression system and transmission system with a Monte Carlo simulation of potential disruption events. The model captures interdependence of assets within the system and facilitates quantitative analysis of operational reliability risk for a gas storage system. Additionally, a framework and methodology for decision-making under risk and uncertainty is developed for prioritization of a portfolio of capital investment decisions. The methodology uses quantitative risk measures to prioritize projects based on a combination of risk tolerance criteria, cost-benefit analysis and uncertainty reduction metrics. We use multi-criteria decision analysis methods to integrate subjective decision-maker preferences with objective project performance measures to prioritize potential capital investments. The methodology provides a practical and transparent way of making decisions for the management of physical assets.
Scaling the Huaca: Constructing Space, Time, and Identity at the Late Moche Ceremonial Centre of Huaca Colorada, Jequetepeque Valley, Peru
Keywords: Architecture
Jequetepeque
Moche
Peru
Ritual
Spatial Analysis

This dissertation examines how the ritual architecture of the Moche site of Huaca Colorada served as a form of symbolic technology that unified communities across the Jequetepeque Valley of Peru during the Late Moche (650-800) and Transitional Periods (ca AD 750-950). An investigation of the construction history of the ceremonial precinct at Huaca Colorada has identified ritualized acts of renovation that encoded a particular cosmology that materialized sociopolitical transformations through time. The analysis provides an opportunity to interpret shifts in Moche traditions as a reaction to increasing influence from distant highland communities associated with the foundation of Tecapa. An objective of the dissertation is to present a detailed diachronic study of an expression of Late Moche politico-religious ideology through the analysis of the construction and occupation sequence of a single ceremonial monument. I thus present the architectonic history of the site of Huaca Colorada in the form of two dialectically interrelated biographies, the biography of the architecture itself, and the biography of a larger political community materialized and emplaced in the landscape through rituals of architectural renovation. These two biographies reveal how the powerful ideology responsible for the creation and maintenance of this structure was grounded in explicit strategies of place-making that changed over time. Ultimately, my research at Huaca Colorada provides an empirically rich case study of how architecture and representations of place were variably wielded to “construct” and contest an imagined Moche community. Across the ancient Andes, acts of place-making relied upon the conflation of social actors, ancestors, and the built environment through cycles of renovation of sacred architecture. I argue that the creation of the Huaca Colorada religious community was realized through cyclical acts of architectural construction and renewal within the ceremonial precinct. My interpretations are based on a comparison of three-dimensional models and spatial analysis of this uniquely preserved ritual setting in relation to the material residues of practice associated with each phase of renovation. In the end, my dissertation combines phenomenological, semiotic and quantitative approaches in order to shed original light on Moche ontology, conceptions of time, and constructions of home, memory, and identity.
Cicero’s Incomplete Orator: The Transmission and Reception of the Mutilus Text
Keywords: Cicero
De oratore
Gasparino Barzizza
Manuscript Tradition
Orator
Textual Criticism

This dissertation traces the tradition of Orator, Cicero’s late work on oratorical style, through the Middle Ages. During that time and due to mechanical losses, the text circulated in a reduced or mutilus form consisting of only the middle half and tail-end of the treatise. An early chapter (1) covers the tradition of the text as fragmentary quotations in other Classical and Late Antique authors. The core of my project, however, is a full codicological examination and catalogue (Appendix C) of the fifty-four surviving manuscript witnesses to this mutilus text. Proceeding from that research, I present the stemmatic relationships of the manuscripts, the geographic and chronological spread of the text, and the creation of two separate vulgate versions by early Italian humanists (Chapters 2 and 3). I present an edition of and commentary on a version of the text created by the early 15th c. schoolmaster Gasparino Barzizza, whose conjectures have long been praised by editors (Appendix A). I edit and classify the marginal and paratextual additions made by medieval readers to show how and why they read the text (Appendix B). Beyond the obvious contributions to textual criticism and the history of rhetoric, my dissertation demonstrates, through the lens of a single text, many of the various Ciceronianisms and Ciceros that existed in Latin intellectual history in the over a millennium and a half following his death.