VictorJuiz/thesis huggingface dataset:
Personal Disability Identity Measurement: Self-Worth and Personal Meaning

In this study, I examined validity evidence for a new disability identity scale, Personal Disability Identity Scale–Self-Worth and Meaning, in a sample of 525 adults with visual impairment (VI) or blindness. Personal disability identity (PDI) refers to feelings about having a disability as well as incorporation of disability status into overall self-concept (Dunn & Burcaw, 2013). Pre-existing measures of PDI (Darling & Heckert, 2010; Hahn & Belt, 2004) operationalize three factors of the PDI concept (i.e., Affirmation, Denial, Pride), which has been theorized to encompass more domains (Dunn & Burcaw, 2013; Forber-Pratt, Lyew, Samples, & Mueller, 2017). The Self-Worth and Meaning subscales were intended to capture previously unexplored PDI domains, including self-worth as a person with a disability (Putnam, 2005) and personal meaning found in the experience of disability (Dunn & Burcaw, 2013). Exploratory and confirmatory factor analyses supported the structural validity of Self-Worth and Meaning scores as well as an overarching four-factor structure of PDI scores composed of Pride/Affirmation, Acceptance (versus Denial), Self-Worth, and Positive Personal Meaning (i.e., Meaning). Correlational analyses between Self-Worth, Meaning, and existing PDI measures supported the convergent and divergent validity of Self-Worth and Meaning scores. Further correlational analyses between Self-Worth and Meaning subscales and indicators of well-being (i.e., satisfaction with life, anxiety/depression) offered support for the external validity of Self-Worth and Meaning. This dissertation contributes to the literature on disability identity by offering an expanded empirical model of PDI as well as a new PDI measure that is derived from models of disability identity that had not been explored empirically (Dunn & Burcaw, 2013; Putnam, 2005).

Advisor: Worrell, Frank
Modeling Vascular Homeostasis and Improving Data Filtering Methods for Model Calibration

Vascular homeostasis is the preferred state that blood vessels try to maintain against external mechanical and chemical stimuli. The vascular adaptive behavior around the homeostatic state is closely related to cardiovascular disease progressions such as arterial aneurysms. In this work, we develop a multi-physics computational framework that couples vascular growth & remodeling (G&R), wall mechanics and hemodynamics to describe the overall vascular adaptive behavior. The coupled simulation is implemented in patient-specific geometries to predict aneurysm progression. Lyapunov stability analysis of the governing equations for vascular adaptation is conducted to obtain a stabilizing criterion for aneurysm rupture. Also, to facilitate patient-specific computations, an algorithm is proposed to generate vascular homeostatic states by incorporating non-uniform residual stress and specifying optimal collagen fiber deposition angles. Since the accuracy and effectiveness of the computational models relies on properly estimating the unknown/hidden model parameters, we also demonstrate recent progress on improving data filtering techniques for inverse problems derived from model calibration. First, iterative ensemble Kalman filter (IEnKF) is applied to solve the inverse problems. The convergence of standard IEnKF is discussed and we show that the poor convergence of IEnKF is caused by the covariance shrinkage effect of the standard Kalman updates. An ensemble resampling based method is proposed to resolve this issue by perturbing the covariance shrinking via ensemble resampling and ensuring "correct" update directions by keeping the first and second moments of the resampling distribution unchanged. In the case of ill-posed inverse problems, we demonstrate that solution non-uniqueness can be overcome by incorporating additional constraints in a Bayesian inference framework. Constraints are imposed by defining a constraint likelihood function, and the method is demonstrated in both exact Bayesian and approximate Bayesian inference scenarios.

Advisor: Shadden, Shawn C
Death Ritual in the Tang Dynasty (618–907): A Study of Cultural Standardization and Variation in Medieval China

By exploiting a vast trove of underutilized original sources, including thousands of epitaphs, archaeological reports, ritual manuals, and anecdotes, and by using digital humanities tools to analyze this large pool of data from a multiregional perspective, this dissertation reconstructs funerary practices in Tang-era China, and thereby explores cultural standardization and the effect of sociocultural changes on death rituals. My research demonstrates that certain death ritual practices prevailed among Tang elites of various regions and social strata and remained stable throughout the entire Tang dynasty, suggesting the existence of a standardized way of commemorating death in medieval China. Furthermore, my research reveals significant regional variations and temporal changes, which I use to examine the mechanisms behind uniformity and variety./nThis dissertation also makes an original contribution to the understanding of actual mortuary practices among Tang elites of various strata and regional backgrounds. My core research material, the many thousands of Tang-era epitaphs, allows me to get closer to the actual practices of “ordinary” elites rather than rely on descriptions of rites by the ritual specialists in charge of compiling prescriptive ritual manuals. Moreover, as each tomb epitaph text usually provides a glimpse of a person’s life, tomb epitaphs are often the most direct and personal accounts of individuals, and they offer a perspective on a greater range of elite society than do either dynastic-history biographies or the eulogies preserved in the literary collections of famous writers.

Advisor: Tackett, Nicolas
Molecular and Stochastic Biophysical Modeling of mRNA Export and Quality Control

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Export and quality control of messenger ribonucleic acids (mRNAs) feature a prominent example of such an intricate molecular system. Export of mRNAs into the cytoplasm is a fundamental step in gene regulation processes, which is meticulously quality controlled by highly efficient mechanisms in eukaryotic cells. Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how aberrant mRNAs are recognized and retained inside the nucleus. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. In this dissertation, I present my research on mRNA quality control using different computational techniques./nUsing the agent-based modeling (ABM) approach, which is an emerging molecular systems biology technique for exploring the dynamics of molecular systems/pathways in health and disease, we first developed a minimal model of the mRNA quality control (QC) mechanism. Our results suggested that regulation of the affinity of RNA-binding proteins (RBPs) to export receptors along with the weak interaction between the RBPs and nuclear basket proteins, namely myosin-like protein-1 (Mlp1) or translocated promoter region (Tpr) protein, are the minimum requirements to distinguish and retain aberrant mRNAs. In addition, we demonstrated how the length of mRNA may affect the QC process./nThe interaction between Mlp1 with one of the Saccharomyces cerevisiae RBPs, namely the nuclear polyadenylated RNA-binding protein (Nab2), was then investigated. Mlp1 plays a substantial role in mRNA quality control by interacting with other proteins involved in this process, specifically the RBPs. Yet, the mechanism of the interaction between Mlp1 and RBPs is still elusive. Using an array of integrated computational approaches including protein structure prediction, protein-protein docking, and molecular dynamics simulations, we dissected Mlp1-Nab2 interaction. Our results were consistent with experimental observations, which suggested that Nab2 residue F73 is essential for Mlp1 binding and further uncovered an indirect role of Nab2-F73 in this interaction.

Advisor: Mofrad, Mohammad R.K.
Two-Dimensional Boron Nitride and Related Materials: Synthesis, Vacancy Formation, and Applications for Nanopores and Nanomachines

Without changing a material’s chemical composition, lattice geometry, or orbital structure, the physical properties of a material can be drastically modified by changes to its dimensionality. Two-dimensional materials are therefore an ideal platform for exploring the role of reduction in material geometry because they can be stacked to form three-dimensional structures or etched to form one- and zero-dimensional features./nIn this dissertation, I explore the methods for isolating two-dimensional hexagonal boron nitride (h-BN) and related materials, for controlling their three-dimensional structural properties synthetically, and for using irradiation to locally reduce their dimensionalities through vacancy formation. After discussing these techniques and their underlying physics, I investigate the applications of etched two-dimensional materials for nanopore sequencing and nanomachines./nIn Chapter 2, I outline the techniques for isolation of two-dimensional materials by both exfoliation from bulk crystals and by synthetic deposition. I delve into the mechanics of chemical vapor deposition synthesis of h-BN graphene and establish methods for controlling their three-dimensional stacking./nIn Chapter 3, I investigate the effects of electron irradiation on h-BN. I show that accelerated electrons induce specific vacancy geometries in h-BN depending on its stacking sequence and develop a method for creating atomically precise nanopores. I explore the application of these nanopores for DNA sequencing./nIn Chapter 4, I similarly characterize the effects helium ion irradiation on two-dimensional materials. I explore the damaging effects on the lattice of h-BN and MoS2 while assessing the controlled use of these helium ions to etch one- and zero-dimensional nanostructures./nIn Chapter 5, I study the use of patterned graphene for softened mechanical actuators. I show that micron scale graphene can be used as an acoustic transducer and demonstrate a novel electron beam driven rotational actuator.

Advisor: Zettl, Alexander K
Scalable Manufacturing of Superhydrophobic Micro- and Nanostructured Condensation Accelerating and Droplet Shedding Surfaces for Air Conditioning Performance Enhancement

One solution currently being explored for reducing the condensation effects of water inside the evaporator coil of an air conditioning system is the use of textured surface morphologies on the evaporator fins that may enable water droplets to both condense and shed more quickly. While multiple pattern scales and geometries have been characterized on metal substrates, including posts, pillars, post arrays, reentrant structures, micro/nano hierarchical patterns, and microchannels, there is a dearth of research associated with microdome patterns, the significance being that nature’s most famous superhydrophobic, water-shedding surface, the lotus leaf, utilizes these features. Here, aluminum surfaces have been fabricated with varying micropillar and microdome structures and a hydrothermally grown nanoporous layer of zinc oxide to create a hierarchical morphology that is reminiscent of the lotus leaf geometry. Micropillar and microdome array structures with comparable feature sizes and areal densities were fabricated, and their static and dynamic water contact angles were characterized in order to understand the influence of microstructural geometry on water-shedding performance. These hierarchical surfaces were further characterized in dynamic condensing conditions using a custom-designed wind tunnel setup to simulate an air conditioning inlet environment. Video footage was recorded, and an image analysis algorithm was developed and applied in order to compare surface performance. The entire zinc oxide nanostructure synthesis process was then scaled and applied to a full-scale cooling coil for later evaluation in a simulated building testbed. The results of all surface characterization methods and condensation tests, the wind tunnel test bed design, the image analysis algorithm development, and the scaling process are reported.

Advisor: Taylor, Hayden K
Allegory and the Art of Memory

Scholars of early modern literature often consider allegory inherently idealist, particularly in its exploitation of visual description, which, they argue, produces a spurious vividness that tries to pass off the schematic and the ideal as natural. Critics who subscribe to this view often celebrate Edmund Spenser's Faerie Queene (1590/96) as both a pinnacle of the genre and a skeptical anatomy of it—a great allegory that is great because it exposes allegory's illusions. As the argument goes, Spenser reveals the false visuality at the heart of allegory by complicating his imagery with naturalistic description. By turning allegorical images against themselves, the poem prevents allegory from subordinating the world of matter and appearances to a timeless conceptual order./nThis dissertation, Allegory and the Art of Memory, offers an alternative framework for understanding allegory's visuality and Spenser's use of it: the mental visualization techniques of the classical and medieval memory arts. Because these mnemonic methods draw mental imagery into the service of memorizing words and ideas, they too have been accused of visual bad faith, but recent scholarship has excavated the practical and philosophical contexts in which these methods were used, and this visual regime gives us a new way to think about allegorical imagery as well. I argue that in adapting the memory arts to narrative poetry, medieval allegorists did not aspire to impress an idealist image of cosmic harmony upon the empirical world but to lead readers through a voluntary and collaborative process of composing meditative imagery./nIn the following pages, I analyze three pre-Spenserian allegorical poems particularly engaged with the theory and practice of memory: Guillaume de Deguileville's Le Pèlerinage de la Vie Humaine (1330-32), Olivier de la Marche's Le Chevalier Délibéré (1483), and Stephan Batman's loose adaptation of Le Chevalier Délibéré into The Trauayled Pylgrime (1569). I use these analyses to illuminate crucial episodes of The Faerie Queene to show that, rather than revealing the fissures in the earlier poems' methods, The Faerie Queene continues their project by adapting allegory to the transformed media environment of sixteenth-century England, where the visual mnemonics of the memory arts had mostly been discarded. The pre-Spenserian poems I analyze borrow formal elements from mnemonic techniques while critically evaluating the practices and the role of memory in human life. The Faerie Queene, I argue, follows their trajectory into the age of print. Whereas the older poems treat their imagery as a script for composing mental images, Spenser uses the formal tropes of the memory arts—image (imago), place (locus), and order (ordo)—to represent memory-processes, not just of the individual but of an entire culture, a collective record that is both analogous to memory and radically unaccommodating to the human mind.

Advisor: Landreth, David
Synthesis of Multiscale Transient Analytical, Experimental, and Numerical Modeling of Latent Energy Storage for Asynchronous Cooling

Novel energy technologies have the potential to address climate change by efficiently using natural resources and reducing greenhouse gas emissions into our shared global atmosphere. In preparation for a future society powered by renewables, engineering solutions must include environmentally conscious and cost-effective methods to store, transport, and convert energy./nI have numerically investigated the use of latent thermal energy storage (TES) technology, with solid to liquid phase change material (PCM), to shift cooling loads to off-peak hours. I first non-dimensionalized differential equations describing sensible and latent heat transfer in the PCM, and their finite difference counterparts, in order to facilitate scaling for the wide array of asynchronous cooling applications that could benefit from this technology. Next, I compared closed form analytical solutions and experimental testing of a TES prototype with the numerical prediction of its melting and freezing processes. Both the analytical solutions and the experimental tests matched the predicted results within 10% agreement, validating the computational model’s capacity to capture the physics governing the transient behavior of the device with high precision and accuracy. As no adjustable parameters were tuned to maximize agreement, the numerical model can be effectively employed to determine the performance of different designs without the need to fabricate, charge, and test them./nUsing this model, I explored potential improvements to power and refrigeration cycles for power plants and commercial buildings integrated with thermal storage. I accomplished this task by taking simple representations of these systems in MATLAB and transforming them into declared relationships between complex components using the dynamic programming language of Modelica. Simulations in integrated development environments of both languages demonstrate improvements of up to a 1.4% increase in power plant energy output and a 2.4% decrease in building chiller energy consumption with thermal storage. With thoughtful selection of the phase change material and better charging and discharging control strategies for the thermal energy storage, further performance enhancement of such systems can be achieved.

Advisor: Carey, Van P
Comparative genomics and chromosome evolution

Viewed through the lens of comparative genomics, how have chromosomes and karyotypes evolved, particularly under extreme scenarios of rapid or torpid evolution? To examine this question, I produced and analyzed new high-quality, chromosome-scale genome assemblies, representing cases of extreme chromosome evolution. The interplay between convergent and divergent genomic architectures can further our understanding into the maintenance of chromosome structure and organization as well as the underlying biological mechanisms./nDespite their recent divergence, muntjac deer show striking karyotype differences. In Chapter 2, I produced new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyzed their evolution and architecture. I identified six fusion events shared by both species relative to the cervid ancestor and, therefore, present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and 26 fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Although comparative Hi-C analysis uncovered differences in long-range genome contacts and A/B compartment structures, I discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. Analysis of the muntjac genomes revealed new insights into this unique case of rapid karyotype evolution and the resulting biological variation./nIn contrast to muntjacs, frogs are a more phylogenetically ancient order, with two prominent species, Xenopus laevis and Xenopus tropicalis, being utilized as vertebrate cell and developmental model systems. In Chapter 3, I reported new chromosome-scale genome assemblies for three distantly related frogs: the common coquí (Eleutherodactylus coqui), the túngara frog (Engystomops pustulosus), and the Zaire dwarf clawed frog (Hymenochirus boettgeri). Through comparative sequence analysis of these and other frog genomes, I identified long-range and even chromosome-scale synteny, denoting the stability and pervasiveness of this type of genomic conservation across the frog phylogeny. These chromosome-scale comparisons also revealed the 13 ancestral chromosomes, with limited Robertsonian translocations and end-to-end fusions explaining the observed chromosome variations. These assemblies, encompassing over a billion years of evolutionary divergence, unmasked insights into torpid karyotype evolution in frogs.

Advisor: Rokhsar, Daniel
Quantitative assessment of nascent chain energy landscapes

In the cell, the first time a protein has the opportunity to fold is co-translationally. In addition to the non-equilibrium nature of co-translational folding, the ribosome presents a unique environment for protein folding. Attachment to the P-site tRNA, interactions with the ribosome surface, and the large mass of the ribosome may all modulate nascent chain folding and stability. Co-translational folding has been shown to improve protein folding efficiency compared to refolding in an idealized solution, but quantitative assessment of nascent chain stability and kinetics has been a longstanding challenge. Usually, these parameters are determined by spectroscopic methods; however, the ribosome contains over 50 proteins and would obscure the spectroscopic signal from the nascent chain. Here, we use a simple, gel-based method – pulse proteolysis – to quantify nascent chain stability and kinetics while stalled on the ribosome. We show that the ribosome destabilizes three different model nascent chains and that, for an RNase H I53D nascent chain, this destabilization is rooted in an increase in the unfolding rate rather than an effect on the folding rate. This increased unfolding rate and destabilization suggest a mechanism by which the ribosome may aid in disrupting non-native structures that form during translation, decreasing the time a protein spends in a misfolded state until enough of the polypeptide chain is exposed to allow for correct native structure formation. Developing pulse proteolysis for experiments on ribosome-stalled nascent chains opens a wealth of possibilities for quantitative studies of nascent chains in the context of not only the ribosome, but also various chaperones and co-factors. Within this dissertation, I also explore the folding of RNase H I53D on the ribosome by arrest peptide-based force-profile analysis and describe my work toward a method to fluorescently label ribosome-stalled nascent chains for single-molecule experiments. Together, this work advances our understanding of the mechanisms by which the ribosome modulates nascent chain folding and adds to the techniques that can be applied to investigate ribosome-stalled nascent chains.

Advisor: Marqusee, Susan