VictorJuiz/thesis huggingface dataset:
Priming Human Mesenchymal Stromal Cells to Enhance their Regenerative Potential
Keywords: 3D
Cardiac
Mesenchymal Stromal Cells
MSC
TLR
Treg

MSCs show promise for cell therapy due to their immune-suppressive and regenerative properties. Consequently, MSCs have been widely used in an increasing number of clinical trials to treat a variety of pathological conditions including cardiovascular diseases and disorders with dysregulated immune function. The outcome of prospective MSC therapy trials however, has shown marginal benefit warranting further investigation to develop strategies to enhance their therapeutic potential. The latter requires better understanding of the mechanisms by which MSCs exert their effects, and studying MSCs under conditions resembling the in vivo microenvironment will help to develop such understanding. The focus of this thesis is to explore the effect of a collagen-based matrix (successfully used in bioengineering approaches for tissue regeneration including for cardiac repair) and Toll-like receptor (TLR) stimulation (providing an in vitro model of an inflammatory environment and widely used for priming MSCs in vitro) on the regenerative properties of MSCs. The first aim of this study (discussed in Chapter 3) involves a comparative analysis of the regenerative properties of MSCs cultivated as a monolayer or on collagen scaffolds, or activated with TLR3 or TL4 agonists. I found that MSCs developed a more cardioprotective phenotype on scaffolds, although no functional changes were detectable when analyzing MSCs in a bioengineered model of heart tissue. The findings of this chapter provide a mechanistic explanation for the potential contribution of MSCs primed with cardiomyogenic cues or TLR agonists. In the second aim (discussed in Chapter 4), signaling through TLR3 was dissected and the effects on MSC phenotype were investigated. The knowledge created in this aim provide some insight into the dynamics of TLR3 signaling, which can be further used to develop preconditioning strategies. In Aim 3 (discussed in Chapter 5), the effects of TLR3 and TLR4 activation on immunomodulatory function of MSCs were further explored. I discovered that activation of either TLR3 or TLR4 enhanced the capacity of MSCs to generate regulatory T lymphocytes. The findings in this aim are applicable to a variety of settings, including tissue regeneration, organ transplantation and autoimmune disorders in which boosting immune suppression can prevent disease development and/or progression.
Insights into the warm interval of the mid-Pliocene from geodynamic and climate modelling
Keywords: Cenozoic
Climate sensitivity
ENSO
Neogene
Pliocene

The mid-Pliocene warm period, roughly 3–3.3 million years ago (Mya), was the most recent time period during which the global temperature was higher than present day for an interval of time longer than any of the Pleistocene interglacials. This thesis reports on an extensive analysis of diverse attributes of the mid-Pliocene based on numerical geodynamic and climate modelling. On the basis of geodynamic modelling we infer that the globally averaged sea level during this time period was 15±7 m higher that present day. In the most likely scenario, ∼7 m originated from the ice contained in the Greenland ice sheet which is known to have been absent at this time, ∼5 m from the West Antarctic ice sheet which is very susceptible to a runaway instability and likely had disintegrated under the warm mid-Pliocene climate and the remaining coming from coastal subglacial basins in East Antarctica. Furthermore, informed by the ESL estimate, we provide a reconstruction of the orography and the bathymetry of the mid-Pliocene. The climate modelling investigation has focused on understanding the characteristics of the ∼40 ppmv climate, the mechanisms and feedback processes supporting the warming, and on the comparison of modelled results with proxy inferences. It is found that with the latest constraints on the boundary conditions for the mid-Pliocene the fidelity of simulated climate to those proxies has been significantly improved. Our analysis suggests the mid-Pliocene warming was strongly enhanced by feedback processes operating over the long interval of relatively stable climate.
Molecular and Synaptic Alterations in the Striatum of GluN1-Deficient Mice
Keywords: Autism Spectrum Disorder
NMDA Receptor
Schizophrenia
Striatum
Synaptic Plasticity
WAVE-1

N-methyl-D-aspartate receptors (NMDARs) are essential for proper neurodevelopment and cognitive function. NMDAR dysfunction contributes to many neurological disorders, with striatal changes linked to psychosis and cognitive impairment. GluN1 knockdown (GluN1KD) mice have low NMDAR expression, striatal synaptic deficits, and cognitive behavioural abnormalities. How these phenotypes functionally relate to one another is unclear. We studied molecular and synaptic changes in the GluN1KD striatum to understand the molecular underpinnings of GluN1KD behaviours. From a screen of Rho GTPase pathway proteins, which regulate synapses and cognition, Ras-related C3 botulinum toxin substrate 1 (Rac1) signaling proteins were specifically identified. GluN1KD mice at 6 and 12 weeks of age consistently had less Rac1 and its downstream effector Wiskott-Aldrich syndrome protein-family verprolin homologous protein 1 (WAVE-1). These deficits were developmentally aligned with medium spiny neuron (MSN) spine density deficits and previously published behavioural abnormalities. To assess the biological and behavioural significance of these findings, we restored WAVE-1 levels by intercross-breeding GluN1KD mice and WAVE-1 overexpressing (WAVE-Tg) mice. GluN1KD-WAVE-Tg F1 hybrids had improved WAVE-1 levels and spine density at the striatum, as well as better Y-maze and 8-arm radial maze performance. These phenotypic recoveries were not mirrored by WAVE-1 levels in the hippocampus nor by neuronal dendritic spines in cornu ammonis 1. From a broader RNAseq analysis of the GluN1KD striatal transcriptome, both neurodegeneration-related and cell-growth signaling pathways were distinguished as affected by NMDAR knockdown. These transcript changes were greatly sex-dependent, potentially mediated by aberrations of estrogen receptor α signaling. Our data suggest that different molecular changes in male and female GluN1KD mice contribute to similar behavioural abnormalities. Restoring WAVE-1 at the striatum improved some of these phenotypes, pointing to a nuanced relationship between its function, striatal synaptic plasticity, and cognition. Specifically, striatal WAVE-1 and MSN spine density may be important for goal-directed maze exploration in mice.
Three Essays in Industrial Organization
Keywords: consumer learning
dynamic structural models
entry dynamics
social learning

My thesis includes three chapters that examine the dynamics of competition in the retail industry. Chapter One of the thesis demonstrates that online review platforms help consumers learn faster about product quality and improve consumer welfare as a result. To examine this, I use a novel dataset containing the universe of full-service restaurants in Texas, consumer search interest on major online review platforms and their online review information. I illustrate that online review platforms' effects on learning show up in restaurant revenues and survival probabilities. Specifically, doubling consumers' exposure to Yelp, the dominant platform, increases the revenue of a high-quality new independent restaurant by 8-20% and decreases that of a low-quality restaurant by about the same amount. Doubling Yelp exposure also raises the survival rate of a new high-quality independent restaurant by 7-19 basis points and reduces that of a low-quality restaurant by a similar level. Other platforms, especially Google, have similar effects but in smaller magnitude. In contrast, online platforms do not affect the revenues or survival rates of chains and old independent restaurants. Counterfactual analysis based on a structural demand model with consumer learning shows that online review platforms speed up the learning process by 0.5 to 2.5 years, increase consumer welfare by 5.4% and the total industry revenue by 5.9% during the period of 2005-2015. Chapters Two and Three deal with the entry and exit dynamics of the retail industry, in particular, how chain retailers can pre-empt the entry of competitors by densely packing a geographic area with their outlets. Chapter Two develops a measure for preemptive motives in dynamic oligopoly games with entry and exit, and applies the measure in both theoretical and empirical studies. Chapter Three uses this measure in the fast casual dining industry in Texas to investigate if there is a trade-off between preemptive entry and survival of firms. The results show that under some conditions, preemption in fact helps the incumbent firm survive, while in other cases, preemption harms survival.
THE FORMATION OF CLASSICAL IMĀMĪ EXEGESIS: Rawḍ al-jinān wa-rawḥ al-janān fī tafsīr al-Qurʾān of Abū al-Futūḥ Rāzī (d. in or after 552/1157)
Keywords: Abu al-Futuh Razi
Hermeneutics
Persian
Qur'an
Rawd al-jinan
Shi'i school of thought

My dissertation charts the development of classical Imāmī exegesis from its origins up to the emergence of the earliest surviving Persian tafsīr of the Imāmī Shīʿī Islam entitled Rawḍ al-jinān wa-rawḥ al-janān fī tafsīr al-Qurʾān. The study shows that Imāmī exegesis was essentially a Kūfan phenomenon for the first two Islamic centuries and exegetical authority was vested in the Shīʿī Imams. This early phase was replete with original esoteric tendencies. This center gradually moved to Qumm in the 3 rd/9th century when a dispute arose over the acceptance of esoteric exegesis as the normative Imami interpretive approach. Eventually, intellectual esoterism was overcome and the earliest surviving Imāmī commentaries were compiled. However, at the beginning of the 5th/11th century a paradigm shift from intellectual esoterism to rational exoterism in Imāmī exegesis occurred. This paradigm shift began with al-Maṣābīḥ of al-Wazīr al-Maghribī (d. 418/1028) and fully developed later in al-Ṭibyān of al-Ṭūsī (d. 460/1067). My dissertation also attempts to situate Rawḍ al-jinān of Abū al-Futūḥ Rāzī in the history of the Islamic tafsīr literature. In his great commentary which was originally written in twenty volumes, Abū al-Futūḥ combined both exoteric and esoteric interpretive approaches. For the exoteric approach his main source was the Imami commentary of al-Ṭibyān, although, for esoteric material he used the most important medieval Sunni commentary al-Kashf wa-al-bayān ʿan tafsīr al-Qurʾān of al-Thaʿlabī (d. 427/1035). At least fifty five percent of Rawḍ al-jinān is a translation of al-Kashf which was written during the transition of power from the Samanids to the Seljuqs in Nishapur. In addition to early Imami ḥadīths, Abū al-Futūḥ also employed proShīʿī traditions of al-Kashf in order to defend his Imami identity in Rayy during the rule of Sunnī Seljuqs which had replaced the Shīʿī Buyids in 447/1055. Finally, a close reading of Abū al-Futūḥ’s hermeneutical approach to the Qurʾān shows that although he was a strong adherent of the new Imāmī theological-jurisprudential-exegetical school of Baghdād, in his preaching style he employed more of the pro-Shīʿī traditions quoted from al-Kashf. He also inclined toward mysticism and for the first time he incorporated Sufi statements into Imami exegesis.
Synchronous small-group collaborative writing via web-based word processing: What facilitates or constrains learners to achieve their goals in summary reports?
Keywords: Activity theory
Interaction patterns
L2 collaborative writing
Synchronous web-based collaborative writing

Collaborative writing has become a common pedagogical activity in second language (L2) classes, informed by sociocultural theory and supported by studies highlighting the importance of peer interaction in learners’ language development (e.g., Storch, 2002). With the emergence of Web 2.0, web-based writing applications such as wikis, blogs, and Google Docs have been implemented into L2 writing activities. The few previous studies that have investigated interaction patterns in peer writing have found variations in these patterns and suggested that collaborative patterns might benefit students’ language learning (Storch, 2002). Informed by sociocultural theory and motivated by the need to understand learners’ experiences in order to make online collaborative writing more beneficial to their learning, this study examined factors that mediate small-group interaction in synchronous web-based collaborative writing using Google Docs and text/voice-chat in the context of a debate club. Adult ESL learners from a voluntary debate club met weekly to practice English communication skills through debating. Four groups of three debate teams participated in this study (N=12). Data were collected from multiple sources including a survey questionnaire, debate summaries, screen recordings, and stimulated-recalls. The survey questionnaire elicited the learners’ background information and individual goals for the writing tasks. Debate summaries, transcripts of screen recordings, and stimulated recall interviews were analyzed to investigate interaction patterns of the groups and mediating factors in their collaborations. Interaction patterns of groups were identified by employing Storch’s (2002) dyadic interaction model, revealing four patterns: facilitator/participants, collaborative, leader/participants, and cooperative. Guided by activity theory (Engeström, 1999) mediating factors of group interaction were identified. The primary mediating factors influencing the quality of collaboration included participants’ goals and goal-directed actions, matches/mismatches between self-perceived and other-perceived goals, task representations, and modes of communication. In addition, participants’ goals were found to be reciprocally influenced by the group interactions. These findings help to explain why interaction patterns vary in collaborative writing groups and provide insights into how web-based collaborative writing activities can be designed and utilized in L2 writing classes.
Parental involvement of Eastern European immigrant parents of elementary school students in Ontario
Keywords: cultural capital
immigration
parental involvement

This study focuses on the parental involvement among Eastern European immigrant parents of elementary school students in Ontario. Immigrant parents are shaped by their own educational experiences in home countries and face particular challenges to be involved in the education of their children who attend schools in the immigrant-receiving nations due to language barriers and low familiarity with the new school system. I collected my data through interviews with parents and the analysis of parental involvement documents in Ontario. The analysis was informed by the concepts of social and cultural capital developed by Pierre Bourdieu. I found that Eastern European immigrant parents see their role supporting children mainly in the home by emphasizing academic achievement and extracurricular activities. Interviewed parents grew up in countries with strict boundaries between school and family, as a result they often do not see volunteering and taking part in decision making in Ontario schools as meaningful for them. Although most parents possess high levels of cultural capital there was a variation in the amount of social capital available to immigrant parents. Those who managed to recreate rich social networks in the new country communicated with teachers more successfully and were satisfied with school. The critical analysis of policy documents showed that despite the shift towards acknowledging different types of involvement more value is still given to school-based activities, which makes the immigrant parental involvement less visible. The results of the study will enable educators and policy makers to pay more nuanced attention to the involvement among immigrant parents for better achievement and well-being of all children in Ontario classrooms.
CFD-based Methodology for Wind Farm Layout Optimization
Keywords: Adjoint Method
Computational Fluid Dynamics
Reynolds-averaged Navier–Stokes
Turbulence Modeling
Wind Direction Uncertainty
Wind Farm Layout Optimization

Driven by concerns on climate change and global warming, increasing oil prices, government support and public receptiveness, wind energy harvesting is emerging as one of the fastest growing renewable energy technologies. Most wind energy is nowadays produced by wind farms, which consist of hundreds of turbines to take advantage of economies of scale. Wind farm performance is however affected by the wakes generated by the turbines which can significantly diminish their annual energy production. Accurate wake effect predictions and reliable wind farm layout design become therefore critical aspects to the economic success of a wind farm project. The present research project aims therefore to define an innovative design framework that integrates accurate wake effect predictions for the development of the next generation wind farms as part of the strategy for promoting the transition to a renewable energy generation. Computational fluid dynamics (CFD) provides a unique tool to simulate wind turbine wakes because of its capability to provide a complete solution for the flow field in complex configurations. Nevertheless, CFD simulations are strongly influenced by the choice of the turbulence model used to close the Reynolds-averaged Navier-Stokes (RANS) equations. We therefore conducted an analysis of different turbulence models and their influence on the results of CFD wind turbine simulations to suggest the most suitable for such applications. Even though proper turbulence modeling is adopted, several studies showed however that the effectiveness of RANS models in wind farm simulations has not always been consistent. We therefore hypothesized this limitation to arise from uncertainties generated by the wind direction variability and proposed a modeling framework that, by accounting for such uncertainties, consistently improved the agreement of the CFD predictions with the experimental observations. To integrate the CFD models in a design methodology, we developed an innovative continuous adjoint formulation for gradient calculations within the framework of a gradient-based wind farm layout optimization. By testing this optimization methodology under different wind farm configurations, wind resource distributions and terrain topography, we showed that this unique CFD-based design framework effectively improved the annual energy production of a proposed wind farm by optimally siting its turbines.
Solid-State Diffusion of Bismuth in Tin-Rich, Lead-Free Solder Alloys
Keywords: aging
bismuth
diffusion
EBSD
EPMA
solder

A significant reliability concern with traditional lead-free solder alloys is the degradation of mechanical properties after aging, due to microstructure coarsening. The inclusion of bismuth (Bi) in these alloys stabilizes properties over time and improves reliability. An examination of the microstructure reveals that homogenization of Bi in the tin (Sn) matrix occurs via solid-state diffusion. The goal of this thesis is twofold – to ascertain whether these trends hold over a wide range of aging conditions, and to characterize the previously unknown diffusional mechanisms behind these effects. Several Bi-containing alloys were aged at one of several temperatures/times. The microstructures were evaluated using Scanning Electron Microscopy (SEM), and Rockwell Superficial hardness (15X) was used to measure the mechanical response. Bismuth precipitates became more uniformly distributed over time. Alloy hardness did not change, except for that of Sn-5Bi, which was slightly reduced after 252 days of aging at 25°C. Sn-Bi diffusion couples were prepared and annealed at several temperatures. After a microstructure examination using SEM, diffusion profiles were collected using Electron Probe Microanalysis and analyzed using traditional methods or a forward simulation technique. At all temperatures, the diffusivity of Bi in Sn demonstrated a low anisotropy ratio - samples oriented perpendicular to the Sn ‘c’ axis yielded slightly higher diffusivities than those parallel. Subsequently, low angle grain boundaries in Sn can convolute the orientation relationship. The Arrhenius parameters for lattice diffusivity are greater parallel to the ‘c’ axis than perpendicular. An analysis of concentration-dependent diffusivity was then conducted, and it was found the ratio between lattice and effective impurity diffusivity decreases with temperature, due to grain growth and the active nature of Sn-based systems. Harrison ‘Type B’ kinetics were lastly considered to study the effects of grain boundaries on diffusivity in polycrystalline Sn; further work is necessary to determine grain boundary diffusivity.
The Study and Characterization of Monolithic Wood-Biocarbon Supercapacitor Electrodes
Keywords: Biocarbon
Characterization
Electrochemisitry
Monolithic
Pyrolysis
Supercapacitor

Supercapacitors are fast charging devices that have the potential to store energy at industrial-scales. The biggest barrier to their implementation is cost. At the time of publication, commercial supercapacitors costs 40 000 USD/kWh as compared to 460 USD/kWh for a Li-ion solution. Biocarbons that are derived from porous materials, such as wood, are a promising electrode material in supercapacitors, but require improved energy density. Most efforts focus on improving the energy density of the electrodes which is limited by the reliance on powdered carbon materials. This is because powders can only be made into thin films (
The Influence of Prehospital Times on Trauma Mortality
Keywords: Emergency medical service
Motor vehicle crash
Prehospital time
Response time
Trauma

Emergency medical services (EMS) are a crucial component of high performing systems. The impact of EMS and prehospital trauma system factors on trauma mortality is understudied. This thesis seeks to clarify the role of EMS prehospital times, one important system-level factor, on trauma mortality at the hospital and population-levels. In the first part of the thesis, the influence of prehospital times on trauma center mortality is investigated. Because differences in prehospital times might influence the likelihood that patients with negligible chance of survival (so-called “unsalvageable” patients) will arrive at the emergency department (ED), a case definition for such patients is established. A PROXY definition for the unsalvageable patient based on objective ED metrics (SBP=0, HR=0, GCS=3) is tested. Construct validity and relevance to trauma center benchmarking is demonstrated. Applying the PROXY definition, the influence of prehospital times on trauma center performance is examined. Using novel linkage of the National EMS Information System (NEMSIS) database to trauma centers participating in the Trauma Quality Improvement Program, shorter prehospital times are found to be strongly associated with ED mortality. However, no association between prehospital time and overall trauma center mortality is observed after risk-adjustment. In the second part of the thesis, influence of EMS response times on mortality from motor vehicle crashes (MVCs) is investigated. Using data derived from the Fatality Analysis Reporting System (FARS) of the National Highway Traffic Safety Administration, the role of EMS response times on regional differences in prehospital death from MVCs is examined. After adjusting for potential confounders at the occupant, vehicle, and crash-levels, EMS response times are found to be significantly associated with risk of prehospital death. Finally, using novel linkage of NEMSIS and FARS data, the relationship between EMS response time and MVC mortality is examined at the population-level within 2,268 United States counties. After adjusting for age, gender, on-scene and transport times, access to trauma resources, state traffic safety laws, and rurality, longer EMS response times are found to be strongly associated with greater rates of MVC-related death.