VictorJuiz/thesis huggingface dataset:
The War Needed Women: Gender and Militarization in Angola, 1961-2002

This dissertation reconceptualizes war and conflict by exploring Angolan women’s complex and contradictory entanglement with war and peace. Given the gendered ways that Angolan women were mobilized to enter national war projects, this dissertation examines the experiences and pivotal roles women played in the “People’s War” (1961-1975) and the civil war and conflict following the proclamation of independence (1976-2002). How Angolan women participated in national liberation struggles as well as how they respond to violence, gets at the intersection of theories of memory and embodiment and disrupts the popular narrative that all women are inclined toward peacemaking. Taking a feminist theoretical approach and utilizing feminist ethnography as a pertinent tool for making visible the experiences and voices of African women in wartime, this dissertation argues that women are often rendered invisible in the big narrative of nationalism because of the highly masculinist nature of national politics. Nevertheless, their presence as historical agents and patriots is made possible through the symbolic trope of women as mothers of the nation. Paying attention to the centrality of the Angolan female body in the politics of the nation also reveals that despite women’s participation in national freedom struggles, peace and security for them remained elusive, limited, and always precarious. Lastly, this dissertation interrogates gender-specific forms of wartime violence against women in order to demonstrate how the Angolan female body functioned as a screen onto which both Portuguese colonialists and Angolan men could project their patriarchal desires and anxieties around power and masculinity.

Advisor: Taylor, Ula Y
Quantum Simulation of Triangular, Honeycomb and Kagome Crystal Structures using Ultracold Atoms in Lattices of Laser Light

Ultracold atomic gases trapped at the interference of coherent beams of light constitute an artificial material. This optical lattice material may be used for controlled quantum simulations of condensed matter theories. The bulk of this dissertation concerns the construction and calibration of an optical superlattice that can form the triangular, honeycomb and kagome crystal structures. The properties and geometry of this artificial material may be dynamically changed, allowing for the experiments discussed in this thesis that would be impossible with real materials./nThe use of ultracold atoms in optical lattices for quantitative tests is challenging because of the novelty of many of the techniques in the field, and because of the myriad experimental differences between these artificial materials and true materials. This thesis reports the development of a method to characterize optical lattice potentials using matter-wave diffraction. We observe an enhancement of inversion asymmetry in matter-wave diffraction from a honeycomb lattice, which we explain using a time-independent perturbative treatment of the single-particle band structure of the lattice. Our experiment also provides new insight into a commonly used detection technique./nThis thesis culminates in the development and experimental realization of a quantitative test of a condensed-matter theory. The test is insensitive to the experimental differences between artificial materials and real materials. We focus on a prediction from a mean-field treatment of the Bose-Hubbard model that concerns the difference in behavior of itinerant particles on lattices that are identical but for their geometry. Using the tunable geometry of our quantum simulator, we measure the properties of ultracold atomic gases trapped in the triangular and kagome lattices under otherwise identical conditions and find that they are consistent with the mean-field scaling prediction.

Advisor: Stamper-Kurn, Dan M.
Development of a Targeted Chromatin Associated Protein Purification Method Identifies Novel Histone Gene Regulators

Regulation of gene expression is fundamental to many biological processes such as lineage specification during embryonic development or metabolic responses to environmental cues. Classic in vitro biochemical experiments have been successful at identifying various components that are necessary for controlling gene expression, such as transcription factors, and co-activators as well as components of the machinery that regulate RNA processing, stability and degradation. However, detailed mechanistic understanding of gene regulatory mechanisms for many specific genes and gene networks remains unknown. Recently, many labs have attempted to couple mass spectrometry with purification methods that enrich for a specific genomic locus to identify potential novel regulators associated with specific chromosomal targets of interest. Here, I describe the development of a novel dCAS9 mediated purification method for proteins associated with specific cis-regulatory chromatin elements. First, I established the proof of principle by identifying specific human telomere associated proteins. I then further advanced this “reverse-ChIP” strategy by applying it to the de novo identification of novel regulators linked to the Drosophila histone gene locus./nChapter 1 provides an overview of what is currently known and unknown about gene regulation at the Drosophila histone cluster as well as a summary of recent advances in the field of “reverse-ChIP” techniques. Chapter 2 describes my development of the dCAS9 mediated purification method for proteins specifically associated with targeted chromatin elements, including the purification and identification of proteins bound to human telomeres. Chapter 3 details how I’ve adapted the dCAS9 mediated purification method to identify novel regulators of the Drosophila histone cluster.

Advisor: Tjian, Robert
Teacher Educators: Addressing the Needs of All Learners

This qualitative dissertation examines how teacher preparation programs take up policy messages from two state agencies. These questions guided the study: 1) What are the messages about RTI and MTSS from the California Department of Education and the California Commission on Teacher Credentialing; and, 2) How are RTI and MTSS taken up by preparation programs and understood by teacher educators? The research sites were two large public universities in urban areas in California with general and special education teacher preparation programs. Data was obtained from the websites of the CDE and CCTC, interviews with teacher educators, and preparation program materials./nFindings support that the CDE is the major proponent of RtI and MTSS but lacks the regulatory power to impact teacher preparation. While the CCTC did have regulatory authority over teacher preparation its guidelines were written in broad language and did not require that programs include specific practices necessary to implement RtI and MTSS. Without this regulatory press incorporation of RtI and MTSS was at the discretion of faculty. Special education was the source of knowledge about RtI and MTSS despite the fact that the CDE clearly situates these practices in general education. General education teacher educators were ambivalent about RtI and MTSS and were unwilling to sacrifice precious time during initial preparation to these topics./nThese findings have implications for policy makers, teacher educators, and research on policy implementation.

Advisor: Little, Judith W
Melatonin Synthesis and Signaling for Seasonal Reproductive Timing

This dissertation critically investigates research in melatonin across species and disciplines. It offers a broader perspective within the field of reproductive neuroendocrinology by integrating research in pharmacology, genetics, and evolution. The first chapter of this dissertation reviews melatonin administration techniques across fields. The timing, dose, and mode of administration is compared across species. This juxtaposition of previous protocols using melatonin administration illustrates the importance of context to help inform future experimental designs. Furthermore, details of the experiment that affect the findings are emphasized to improve replicability of melatonin administration studies. The second chapter focuses on melatonin synthesizing enzymes in two different songbirds. The zebra finch (Taeniopygia guttata) is an opportunistic breeder in the wild and uses primarily food and water availability to time reproduction (Perfito et al., 2007). The European starling (Sturnus vulgaris) is a photoperiodic breeder whose reproductive state relies on changes in day length (Gwinner, 1977). Melatonin-synthesizing enzymes were expressed in photoreceptive sites of the brain. Key melatonin-synthesizing enzymes were differentially expressed in the hypothalamus of the photoperiodic breeder at certain times of the year, and this expression was not analogously observed in the opportunistic breeder. Melatonin may be a distinguishing physiological factor in reproductive timing between these two breeding types. The last chapter determines the physiological relevance of melatonin binding at the level of the gonad, specifically measuring how melatonin affects testosterone output from cultured testes from Syrian hamsters (Mesocricetus auratus), a photoperiodically-breeding mammal.

Advisor: Bentley, George E
Flesh Redeemed: Religious Materialism in Early Enlightenment Britain, 1640-1715

This dissertation examines how early modern Britons came to deem the material world as worthy of attention, care, and redemption. It traces a broad current of philosophical and theological speculation regarding material bodies that began in the 1640s. In a series of case studies, I chart how a range of formulations regarding the nature of corporeal bodies and matter increasingly served as a resource for theological discourse, philosophical debate, and popular belief in the late seventeenth century. I argue that heterodox religious ideas in the mid-seventeenth century served as an engine of change, driving early modern Britons to rethink how divinity, the soul, and the material world interacted. By focusing on the relationship between divinity and earthbound corporeality, this dissertation reframes heterodox religious ideas, often relegated to the historical margins, as in fact generative of modern conceptions of the human body and the material world./nIn the following study, I trace the material linkages that connected religious belief and early modern philosophies of embodied substance. The project follows changing early modern interest in the material world as a range of thinkers reconfigured the perceived interaction and interpellation of spiritual, corporeal, and divine substances. Redeeming the flesh—discovering the nature of the body and the means to God’s sanctifying grace—continually motivated a variety of investigations into the nature of body, soul, and spirit. But the Christian project of corporeal redemption drove early modern interests beyond the specific human body to engage with questions of cosmology, vitalism, and the nature of knowledge. This was part of a new willingness of early moderns to probe into scriptural mysteries to better understand the human body, but also to extend these questions to wider material processes and entities.

Advisor: Shagan, Ethan
Sheehan, Jonathan
Disproportionate Discipline and Racial Differences in Educational Attainment: The Effect of Suspension on College Matriculation

In this study, I use multilevel modeling and multivariate matching to estimate the effect of suspension on college attendance. I build upon existing research that has suggested a negative relationship between school suspension and educational outcomes but that has mostly not been able to control for pre-existing differences in academic achievement between suspended and non-suspended students. I also extend my analysis to college attendance, which is currently an under-studied outcome related to high school suspension and thought to be important for many life outcomes. After controlling for baseline academic achievement, socioeconomic status, and other potential confounders, the college attendance rate of students who were suspended once or twice in the first semester of tenth grade was approximately 10 percentage points lower than that of non-suspended students. These results suggest that racial differences in educational attainment are in part due to the disproportionate discipline of African American students.

Advisor: Holloway, Susan D
Biophysical Characterization of Ribosome Nascent Chain Energy Landscapes

Protein folding is necessary for proper cellular and organismal function. The disruption of accurate protein folding is highly detrimental to numerous cellular processes and can lead to cell death and disease. A major protein homeostasis node in the cell is the ribosome, which interacts with a number of quality control factors that help guarantee protein folding fidelity. For many years, co-translational folding has been investigated mainly within the context of cellular proteostasis and quality control. Unfortunately, how the ribosome and translational machinery modulates the nascent chain itself has, for the most part, remained a mystery. It is essential to understand how translation changes a protein’s energy landscape during translation in order to understand how folding fidelity can be guaranteed in vivo. Here, I introduce new methods for studying the folding thermodynamics and kinetics of stalled nascent chains and pioneer a new assay for studying folding kinetics during translation in real-time. In addition, I characterize the folding landscape of the protein HaloTag and determine that the process of translation itself increases HaloTag’s folding efficiency by modulating its folding trajectory. The methods developed herein, as well as novel observations about the biophysical properties of nascent chains reported here, pave the way for understanding protein folding in vivo.

Advisor: Marqusee, Susan
Efficient Abstraction and Refinement for Word-level Model Checking

Model Checking (MC) on a word-level circuit has important applications in the IC design industry, where MC is used to prove that a word-level circuit always satisfies a set of given properties./nMC is challenging at the word level, when complex arithmetic operators like multipliers are involved./nAbstraction and refinement are commonly used to address challenging MC problems./nIf an abstraction is proved, so is the original problem./nOtherwise, spurious counterexamples are analyzed to refine abstractions./nAlthough many abstraction refinement algorithms for word-level MC have been developed, few take full advantage of state-of-the-art bit-level MC algorithms, like Property Directed Reachability (PDR), which is considered the most efficient method for deriving unbounded proofs./nTherefore, this thesis presents several techniques that enable efficient word-level MC by performing abstraction refinement at the word-level while verifying abstractions at the bit-level./nTo compute good abstractions and refinements at the word-level, novel refinement strategies were proposed to take advantage of both structural and proof-based analysis./nThe proposed strategies are shown to achieve a good balance between the sizes of the abstractions and the number of refinement iterations needed for convergence./nTo achieve efficient integration of abstraction refinement and bit-level MC algorithms,/na bit-level algorithm, PDRA, was created, that minimally modifies the original PDR algorithm to perform on-the-fly abstraction refinement./nInspired by this, a word-level algorithm, PDR-WLA, was developed that efficiently integrates bit-level PDR implementations with word-level abstraction refinement. An important feature is the re-use of reachability information learned in previous refinement iterations./nMotivated by real industrial benchmarks characterized by having many related arithmetic operators,/na word-level MC algorithm, UFAR, was proposed that uses uninterpreted functions (UF) constraints as a method of refinement./nA UF constraint, between a pair of word-level operators, requires that if their inputs are equal then their outputs are equal./nTo enhance the applicability of UF constraints, a procedure for normalizing operators was devised. This allows UF constraints to be applied to a pair of same-type operators with different operator sizes and signedness./nUFAR explicitly encodes UF constraints into word-level circuits. This allows any bit-level or word-level MC algorithm to be used, including both PDRA and PDR-WLA./nAll these developments were implemented in a publically available model checking system, ABC./nExperiments were done which show that UFAR successfully solves most cases in a large set of challenging benchmarks provided by an industrial collaborator.

Advisor: Brayton, Robert K.
Combinatorics and Computations in Tropical Mathematics

In recent decades, tropical mathematics gradually evolved as a field of study in mathematics and it has more and more interactions with other fields and applications. In this thesis we solve combinatorial and computational problems concerning implicitization, linear systems and phylogenetic trees using tools and results from tropical mathematics./n/nIn Chapter 1 we briefly introduce basic aspects of tropical mathematics, including tropical arithmetic, tropical polynomials and varieties, and the relationship between tropical geometry and phylogenetic trees./n/nIn Chapter 2 we solve the implicitization problem for almost-toric hypersurfaces using results from tropical geometry. With results about the tropicalization of varieties, we present and prove a formula for the Newton polytopes of almost-toric hypersurfaces. This leads to a linear algebra approach for solving the implicitization problem. We implement our algorithm and show that it has better solving ability than some existing methods./n/nIn Chapter 3 we compute linear systems on metric graphs. In algebraic geometry, linear systems on curves have been well-studied in the literature. In comparison, linear systems on metric graphs are their counterparts in tropical mathematics. We introduce the anchor divisors and anchor cells in order to compute the polyhedral cell complex structure of the linear system |D| and the tropical semi-module R(D). We develop algorithms, discuss their efficiency and present computational results for canonical linear systems on metric graphs./n/nIn Chapter 4 we extend the previous chapter by introducing the tropical Hodge bundle, which is the counterpart of the Hodge bundle in tropical geometry. We study properties of tropical Hodge bundles and present computational results for some examples./n/nIn Chapter 5 we study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all ultrametrics. The CAT(0)-metric of Billera-Holmes-Vogtman arises from the theory of orthant spaces. While its geodesics can be computed by the Owen-Provan algorithm, geodesic triangles are complicated. We show that the dimension of such a triangle can be arbitrarily high. Tropical convexity and the tropical metric exhibit properties that are desirable for geometric statistics, such as geodesics of small depth./n/nIn Chapter 6 we study the Fermat-Weber points under the tropical metric. This is motivated by its application to the space of equidistant phylogenetic trees, here realized as the tropical linear space of all ultrametrics. While the Fréchet mean with the CAT(0)-metric of Billera-Holmes-Vogtman has been studied by many authors, the Fermat-Weber point under the tropical metric in tree spaces is not well understood. We investigate Fermat-Weber points under the tropical metric and we show that the set of tropical Fermat-Weber points for a given configuration is a classical convex polytope. We identify conditions under which this polytope is a point.

Advisor: Sturmfels, Bernd
Integrating community phylogenetics and phylogenetic beta diversity to understand Amazonian trees community assembly: a biogeographical and conservation approach

Understanding the tree species composition and turnover in Amazon forests has fascinated ecologists and evolutionary biologists since the first botanical expeditions from the 19th century. More recently, the advent of community phylogenetics and phylogenetic beta diversity methods has been demonstrated to be powerful tools to investigate the patterns and causes of Amazonian tree species assemblies./nHowever, the lack of a comprehensive sampling of tree species communities using well-standardized taxonomy across gradients of soils, geology and climate has precluded making conclusions about the relative importance of these environmental filters on the patterns of species and lineage composition and turnover. In addition, due to current threats that Amazon forests are experiencing an ecologically informed delineation of floristic boundaries is urgently needed to guide conservation decisions./nIn this dissertation, I present the results of intensive floristic sampling at two spatial scales continental and regional, and show that the complementary implementation of phylogenetic beta diversity and community phylogenetics can help us to better describe and analyze floristic patterns of Amazon tree communities. Additionally, I used this combination of methods to determine high priority conservation areas that are currently experiencing severe threats in Ecuador Amazon.

Advisor: Fine, Paul V.A.
Symmetry-Allowed Spin-Orbit Coupling in Quantum Materials

Strong interaction between the spin and orbital angular momentum of electrons in a material can give that material unusual quantum properties beyond what can be described by textbook band theory. It can lift the spin degeneracy of electronic bands and create a spin-momentum locking that can be a lever for electrical control of a material's magnetism. It creates a new state of matter: topological insulators, by twisting the energy ordering of electronic states. It adds complexity to how light interacts with the material, enabling some/nmeans for pointing photoelectron spins in a chosen direction./nHowever, the way spin-orbit coupling is manifested in a material is shaped by the symmetries of the crystal. In presenting findings from topological insulators, this dissertation demonstrates how those symmetries can force a material to have multiple spin textures in momentum space, each coupled to a distinct atomic orbital. Further, it shows how changes to those symmetries can eliminate those orbital-dependent spin textures and leave a single overall spin texture. Lastly, it shows how symmetries can allow crystals to harbor hidden spin textures in certain parts of their real space unit cells even when the overall band structure is spin degenerate. This last point is demonstrated in a cuprate high temperature superconductor, in which the newly discovered spin structure could have profound implications for the nature of superconductivity./nThe results presented in this dissertation come from spin- and angle-resolved photoemission measurements of several quantum materials using a uniquely efficient and high resolution spectrometer. The details of how the spectrometer works when coupled with a laboratory-based laser and how that enables new experiments that were otherwise infeasible are given./nThis dissertation is organized into six chapters. Chapter 1 reviews atomic spin-orbit coupling and ways it can influence the properties of materials. Chapter 2 explains spin- and angle-resolved photoemission and the unique instrumentation used for experiments in this work. Chapter 3 details experiments that show how spin textures in materials can couple to different orbitals. Chapter 4 shows how that coupling can break down when symmetry no longer requires it. Chapter 5 presents surprising findings of a spin texture hidden in a cuprate superconductor. Chapter 6 presents discussion of future research directions on the study and manipulation of the spin-orbit interaction in materials.

Advisor: Lanzara, Alessandra