VictorJuiz/thesis huggingface dataset:
Promoting Nutrition Security in Diverse Low-Income Communities: Methods to Comprehensively Assess Food Access
Keywords: Nutrition
Food security
Nutrition security
Community-engaged
Geographic information systems
Citizen science
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Thesis

It is well understood that what we eat is intimately connected with our health. Traditional health promotion strategies rely heavily on individual behavioral interventions, but not all individuals have equitable access to the nutritious foods needed to live a healthy and disease-free life. Moreover, quantifying and addressing food access is difficult because of the multitude of complex factors involved. In response to this challenge, this study evaluates how a mixed multi-method approach of characterizing the food environment 1) addresses the conceptual definitions of food access; and 2) identifies assets and areas for community activation to increase access to nutritious foods. In particular, a food environment map using geographic information systems (GIS) will be discussed as a method to assess food access surrounding four independently owned mid-sized grocers and corner stores in San Jose, California. The GIS food environment map in this study is a supplemental piece of a larger project with the Our Voice initiative and The Food Trust which utilizes citizen science to promote nutrition security in the community. The map revealed a high prevalence of food outlets with processed food options as compared to food outlets with fresh produce options. It also revealed there were numerous opportunities to obtain food that were not acknowledged by the USDA Food Access Research Atlas. An accurate understanding of food access in the local environment, inclusive of community member insights, essential for developing and implementing solutions (interventions, policies, programs) to promote nutrition security in a community.
Proteomic Profiling of Purkinje Cell Surface Reveals the Critical Role of Armadillo-like helical domain containing protein 4 in Mammalian Dendrite Morphogenesis
Keywords:  Department of Biology
Biology
Molecular biology
Genetics
Proteomics
Morphogenesis
Developmental biology
Neurodevelopment
Dendrites
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Thesis

Improper dendrite development is exhibited in a range of human neurodevelopmental disorders and neurodegenerative diseases, such as autism spectrum disorder and schizophrenia. Yet, the underlying molecular mechanisms of dendrite morphogenesis are not well characterized. During neuronal development, highly conserved, precisely timed protein interactions at the cell surface mediate dendrite morphogenesis; therefore, cell surface protein identification and characterization may provide key insights to the intricate molecular processes essential to proper dendrite development. Using cell surface proteomic datasets attained by a novel spatiotemporally resolved proteomic profiling technique in situ, we instructed a loss-of-function candidate screen of 13 cell surface proteins to observe their impacts on dendrite morphology. We found that in vivo disruption of the transmembrane protein Armadillo-like helical domain-containing protein 4 (Armh4) engendered a striking dendrite morphological phenotype in transfected cerebellar Purkinje cells. Armh4 disrupted cells exhibited significant height deficiency, decreased total dendrite length and branching, and growth of additional primary dendrites. Here, we present the critical cell-autonomous function and characterization of the signaling mechanisms of the Purkinje cell surface protein Armadillo-like helical domain containing protein 4 (Armh4) during dendrite morphogenesis. We demonstrate that dendrite morphogenesis is sensitive to Armh4 cell surface levels and that endocytosis is required for Armh4 signaling downregulation in proper dendrite development.
The protestant road to state bureaucracy
Keywords: Political Science.

After the seventeenth century, rulers across Europe attempted reforms to replace amateur administrators with professional bureaucrats. The success of administrative reforms hinged on whether rulers could compensate entrenched patrimonial office-holders and recruit talented employees for a wage. I show that the degree to which these two administrative conditions were met at the time of state reforms depended on whether states experienced a Protestant Reformation in the sixteenth century. I argue that the Reformation, which involved the expropriation of the Catholic Church's assets, set in motion two processes. First, to finance their wars, Protestant rulers used confiscated assets instead of selling offices, leading to smaller stocks of venal office-holders who resisted administrative reforms. Second, expropriations made churches poorer and reduced the number of plum jobs in the clergy, and this incentivized a reallocation of educational investments from religious to "secular" skills that were more useful for state administration. This distinctive Protestant developmental path hastened the demise of the patrimonial state, and by 1789 the only major territorial states that were bureaucratic were Protestant, while all Catholic states remained patrimonial
Pursuing Credit: Sovereign Debtors’ Economic and Political Motivations to Oscillate in Creditor Selection
Keywords: Sovereign debt; sovereign debt default; Ecuador
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Thesis

In a decade and a half, three Presidential administrations in the Republic of Ecuador have led the country to oscillate three times in its selection of sovereign and private creditors. Beginning in 2007 with the election of President Rafael Correa, Ecuador foreclosed any possibility of borrowing from Western multilaterals and bond markets following a puzzling decision to default on bonds. Over the next ten years, Ecuador became one of the 30-most indebted countries to the People’s Republic of China. Then, when Correa’s successor President Lenín Moreno was elected in 2017, a process many described as a parricide marked a re-embrace of multilaterals, though the administration also continued to borrow heavily from China. Finally, in 2021, President Guillermo Lasso aligned himself, and therefore, the country, closer once more with multilaterals, and finally qualified Chinese lending to Ecuador as detrimental to the country’s growth. In this thesis, I seek to determine what a country’s guiding and principal motivations are when choosing with which creditor to engage. I examine each of these three Presidential administrations as distinct time periods in Ecuador’s history of sovereign borrowing, and seek to answer the aforementioned question through interviews with seven high-ranking officials in the Ecuadorian government or regional and international multilaterals. I also leverage qualitative analysis of public declarations, government decrees, and contracts. I find that, broadly, incentives to oscillate between creditors can be split into economic and political motivations. Each of these in turn can be subdivided further into considerations. These are availability of capital, cost of capital, ideological affinity, geopolitical considerations, and political and electoral benefits. I concluded that while these considerations vary in importance from one administration to the next, availability of capital and ideological affinity were central across all three administrations. I also highlight how creditor selection can be used to garner political and electoral benefits, particularly through the use of signaling mechanisms for voters. This is an element that escapes the literature and is a new contribution to the field.
Putting Things in the Right Perspective: liberating the mind through the performative Zhuangzi
Keywords:  Stanford Global Studies
East Asian Studies
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Thesis

This thesis offers an English translation and interpretive analysis of the Inner Chapters of the Zhuangzi. I examine how the text resets the reader's firmly established beliefs and behaviors to transport the mind and free the spirit from the shackles of culture and language frameworks, prejudices, and distinctions through the narrative force of language. I present my own interpretation of what the text accomplishes, showing how crucial the presentation of Zhuangzi’s dialogues, stories and poems is to the text’s very substance and how the Zhuangzi effectively leads its audience toward positive change by the process of interacting with it.
Quantifying hydrologic change in tropical peatlands
Keywords: Earth System Science.

Tropical peatlands are a globally significant carbon sink that store over 100 Gt of carbon. In pristine peatlands, this sink is enabled by unique hydrologic characteristics that keep peat soils waterlogged year-round, in turn slowing down the decomposition of organic matter and protecting peat soil from burning. But Southeast Asian peatlands, which store about half of all tropical peatland carbon, have experienced extensive deforestation, drainage, and conversion to agricultural use in recent decades. Already, this degradation has resulted in devastating impacts. Deadly fires during drought years release massive amounts of carbon dioxide and smoke, and there is also evidence of increased decomposition rates throughout the region. Climate change threatens to further disrupt the hydrologic and carbon balance in peatlands. In this dissertation, I quantified changes in Southeast Asian peatland hydrology by developing the first datasets for two key hydrologic variables: surface soil moisture and drainage canals. This was made possible with new satellite-based sensors and advances in retrieval algorithms and computer vision. In Chapter 2, I showed that soil moisture can be measured with sufficient accuracy using data from NASA's Soil Moisture Active Passive satellite (counter to previous understanding), and found it can be used for predicting peat fire risk up to a month later. In Chapter 3, I created the first regional map of drainage canals. I found that drainage density correlates with higher carbon emissions rates, and counter to previous assumptions, does not correlate one-to-one with land use. In Chapter 4, I built a model to predict future soil moisture regimes under climate change, and found that drier climatic conditions may cause significant decreases in soil moisture, implying more severe fire regimes in the future. Thus, this dissertation provides new tools for studying and modeling changes in peatland hydrology, and the implications that these changes have for earth's carbon cycle
Quantifying the diversity of sulfate-reducing microbes in the human gut
Keywords:  Department of Biology
sulfate-reducing microbes
biology
microbiology
human gut
phylogeny
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Thesis

Sulfate-reducing microbes (SRM) are a diverse group of bacteria and archaea that utilize sulfate as the terminal electron acceptor in anaerobic respiration and are hypothesized to contribute to gut inflammation in humans. The presence of common SRM have been correlated to chronic gastrointestinal inflammatory diseases such as Crohn’s Disease, Ulcerative Colitis, Inflammatory Bowel Disease, and Irritable Bowel Syndrome in geographically homogeneous, adult, Western populations. However, little is understood of the full diversity of the SRMs within the human gut, especially outside of adult, Western populations. This study aims to characterize the full diversity of the SRMs in the human gut by comprehensively identifying SRM species from a wide set of metagenomic data. This study utilizes a computational approach to search publicly available metagenomes from human gut samples for dsrAB, an SRM-specific gene encoding for dissimilatory sulfite reductase. Using dsrAB genes from a manually curated database, we constructed a profile hidden Markov model (HMM) and applied a commonly used bioinformatics tool, HMMER, to identify homologous sequences from 14,286 gut metagenomes. The returned sequences were then phylogenetically classified using Random Axelerated Maximum Likelihood Evolutionary Placement Algorithm (RAxML-EPA) on a reference dsrAB tree. Phylogenetic analyses of collected dsrAB sequences suggests the presence of diverse SRM in the gut from various taxa, including the Desulfovibrionaceae family, the Firmicutes group sensu lato, and the Archaeoglobus cluster. The analysis showed that most common SRM were Desulfovibrio piger, Bilophila wadsworthia, and an uncultured relative of Desulfovibrio desulfuricans, confirming the widely accepted presumption that Desulfovibrionaceae is the most common family of gut-SRM. Many dsrAB sequences from SRM not previously catalogued in the gut environment were found at lower frequencies. These results indicate the SRMs in the human gut are more diverse than previously hypothesized. The results of this study comprehensively characterize an understudied microbial group with implications in gut health, determine the prevalence of different SRM taxa within the human gut, and inform future studies in assessing causality between SRM and gut inflammation.
Quantifying the effects of polar lipid proportions on the stability of model tear films
Keywords: Huang, Yogi
Dry eye syndromes
Tear film
Interfacial science
Rheology (Biology)
Interfacial lipid layer
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Thesis

Dry eye Disease (DED) is one of the most widespread ocular surface disorders across the world and is thought to affect hundreds of millions of people worldwide, including costs of over $50 billion annually to the United States alone. However, despite DED’s widespread prevalence, there are very few effective clinical treatments for the syndrome, in part due to the complexity of the thin liquid coating – i.e. tear film – over the surface of the eye.
One hallmark of DED is premature destabilization of the tear film, which can be caused by many different mechanisms. Although we have an extensive knowledge of the various underlying biological causes for DED, we know relatively little about the resulting physical processes that lead to DED, which makes it difficult to design targeted treatment options.
Particularly little is known about tear film lipids – which are thought to sit on the surface of the tear film. Deficiencies in certain types of polar lipids are thought to be linked to an increased risk of DED, but we do not yet understand why this is the case. Finally, despite a wide array of literature on lipid chemistry, structure, and rheology, no clear link has been made yet between lipid composition on the surface of the eye and the severity of DED.
To address these deficiencies in knowledge, this thesis aims to improve our understanding of the role of polar lipids in the stability of the tear film. We test the stability of model tear films supplemented with varying amounts of the phospholipid “dipalmitoyl phosphatidylcholine” (DPPC) and the wax ester “stearyl stearate,” both of which are comparable to common lipids found natively in the eye. We find that model tear films can be stabilized by both DPPC and SS, likely through a combination of lipid-specific physical mechanisms. When model tear films are created with combined DPPC and SS lipid layers, we find that large increases in the DPPC composition can increase the stability of the model films. Finally, we find that mixed lipid layers have physical properties that differ from the pure lipid components, implying that a more nuanced understanding of lipid interactions is required.
Altogether, this data indicates that large changes to lipid compositions in the tear film could play a role in reducing tear film stability, as is thought to occur in patients with DED. However, a more advanced understanding of multi-component lipid layers is necessary before well-targeted therapeutics can be developed. DED remains a pressing health and societal problem, but this work improves our understanding of the lipid layer of the tear film and provides a basis for future research on the role of lipids in dry eye disease.
Quantitative phase contrast imaging with a nonlocal angle-selective metasurface
Keywords: Electrical Engineering.

Phase contrast microscopy has played a central role in the development of modern biology, geology, and nanotechnology. It can visualize the structure of translucent objects that remains hidden in regular optical microscopes. The optical layout of a phase contrast microscope is based on a 4f image processing setup and has essentially remained unchanged since its invention by Zernike in the early 1930s. Here, we propose a conceptually new approach to phase contrast imaging that harnesses the non-local optical response of a guided-mode-resonator metasurface. We highlight its benefits and demonstrate the imaging of various phase objects, including biological cells, polymeric nanostructures, and transparent metasurfaces. Our results showcase that the addition of this non-local metasurface to a conventional microscope enables quantitative phase contrast imaging with a 0.02π phase accuracy. At a high level, this work adds to the growing body of research aimed at the use of metasurfaces for analog optical computing
Quantum control and entanglement of nanomechanical oscillators
Keywords: Physics.

The quantum behavior of macroscopic objects is not readily apparent in our everyday experience, although the governing equations are present nevertheless. Towards studying this regime, solid-state mechanical objects provide a promising testbed, but quantum control of acoustic devices has been a significant experimental challenge to date. Here, we describe efforts to build a hybrid quantum device composed of nanomechanical resonators coupled to a superconducting qubit. In this device, the mechanical resonators consist of phononic crystals made from thin-film lithium niobate, enabling both acoustic confinement and strong piezoelectric coupling. By using the qubit to control and measure these resonators, we can access nonclassical states of motion, find new ways to process quantum information, and study the quantum nature of sound. In this thesis, we present a series of experiments illustrating the capabilities of this quantum acoustics platform. First, we successfully demonstrate strong dispersive coupling between the qubit and nanomechanical resonator, allowing resolution of phonon number states. This result represents the first direct observation of the quantization of sound in a mechanical oscillator's energy levels. Next, we characterize superconducting, acoustic, and two-level system loss channels in the phononic crystal devices, with the goal of achieving coherence times that exceed conventional planar superconducting circuits. Finally, we build a small-scale quantum acoustic processor that not only achieves control at the single-phonon level, but also performs non-demolition measurements to probe the quantum states of motion. By extending these techniques to two nanomechanical resonators simultaneously, we deterministically synthesize mechanical Bell-states and characterize the resulting quantum entanglement between macroscopic objects. Ultimately, this demonstration provides a hardware-efficient approach towards scaling today's quantum computers
Quantum phases on ladders and cylinders
Keywords: Physics.

This thesis is primarily concerned with theoretical approaches to quantum condensed matter systems on ladders and cylinders - i.e. geometries that are infinitely long in one direction but finite in another. Ladders and cylinders are extremely interesting systems in their own right, but the theoretical studies carried out here were designed with a very practical goal in mind: to complement density matrix renormalization group (DMRG), a numerical method. We start off in Chapter 1 by motivating the importance of DMRG in treating paradigmatic problems in strongly correlated electron physics, and explaining why DMRG calculations are most naturally carried out on ladder and cylinder geometries. Chapter 2 explores the use of weak-coupling analyses to identify phases at small interaction strengths, where DMRG simulation is most challenging. One of the prob- lems we treat is the half-filled triangular lattice Hubbard cylinder. We explain how our results relate to recent DMRG studies on the same system that apparently detect spin liquid physics. Chapter 3 presents a systematic finite-circumference scaling theory for supercon- ducting cylinders. We explain how our findings can be used to help extrapolate DMRG results to the infinite-circumference limit. Finally, Chapter 4 discusses a different topic in condensed matter physics -- quan- tum oscillations in the cuprate high temperature superconductors. We develop a theory of quantum oscillations in the presence of phase-disordered charge density waves, and use it to interpret key experiments on the material YBCO
Quantum photonics with the tin-vacancy center in diamond
Keywords: Applied Physics.

Quantum information processing promises to revolutionize computation and communication. Quantum networks, which consist of interconnected quantum nodes, are expected to play an important role in providing secure communication and bolstering the power of quantum computation. Quantum networks have two basic requirements: uniform, long-lived, optically accessible qubits and efficient photonic interfaces. Because of the potential for photonic integration, solid-state quantum emitters have emerged as promising qubit candidates. In particular, atomic-scale defects in diamond known as color centers have garnered much interest for their bright, spin-dependent emission and long spin coherence times. The tin-vacancy (SnV) center in diamond possesses a unique combination of excellent optical properties, inversion-symmetric crystallographic structure, and potential for long spin coherence times at temperatures above 1~K. In this dissertation, I present my work on the SnV center in diamond, from basic optical characterization to photonic integration. We start with a study of the optical and spin properties of single SnV centers isolated in diamond nanopillars. We then demonstrate electrical tuning of the optical transitions of the SnV center via the DC Stark effect, a useful tool for future multi-emitter experiments. We also explore a new approach to generating SnV centers which at once enables site-controlled generation of emitters with a thin, high-resolution implantation mask, mitigates the presence of non-SnV emission, and can be performed without a potentially damaging annealing step. After developing this new color center generation method and a strong understanding of the properties of the SnV center, we proceed to incorporate the SnV center into photonic devices to develop efficient photonic interfaces. We first demonstrate narrow-linewidth emission from SnV centers in nanobeam waveguides, which indicates that we can create photonic structures containing high-quality SnV centers. We then transition from waveguides to cavities. Incorporating SnV centers into photonic crystal cavities, we achieve a 40-fold enhancement in emission intensity, corresponding to a Purcell factor of 25 and a channeling of 90% of the SnV center emission into the cavity mode, a promising result for future SnV center photonic integration. The works presented in this dissertation constitute key developments that have advanced the SnV center from a nascent color center to a competitive optically interfaced qubit candidate