VictorJuiz/thesis huggingface dataset:
X-ray spectroscopy of dilute metalloproteins with a transition-edge sensor
Keywords: Physics.

Proteins are some of the most complex and finely tuned molecules found in chemistry, responsible for critical tasks such as oxygen delivery, photosynthesis, or nitrogen fixation in cells. Although proteins are mostly composed of hydrogen, carbon, nitrogen, and oxygen, the active site is often a metal. Hemoglobin, responsible for carrying oxygen to the cells, utilizes iron to bond to O2. In order to understand these proteins, it is critical to understand the behavior of the bonding electrons of the metal center. Core-level X-ray spectroscopy is a set of techniques that can yield deep insight into electronic structure. By exciting electrons to the unoccupied orbitals, we can probe the oxidation state, symmetry, and spin of a target element. However, for the most important proteins, the signal of interest is faint, and the samples prone to damage upon exposure to X-rays. New instruments are required that can collect data more quickly and with less noise, so that proteins and other challenging samples can be measured. In this thesis, I present the development of a new instrument for X-ray spectroscopy at the Stanford Synchrotron Radiation Lightsource (SSRL), based on superconducting transition-edge sensors (TES). First, I will describe the capabilities of this detector, and show that it fills a substantial gap in the experimental capabilities of present X-ray instruments. Then I will detail a series of X-ray spectroscopy experiments that I performed with the TES. Using this instrument, I measured both extremely dilute and extremely damage-sensitive samples. This experience allowed us to obtain the first undamaged soft X-ray spectrum of oxyhemoglobin. This spectrum has allowed us to constrain the electronic structure of hemoglobin. Finally, I describe future instruments that will make such measurements more routine
The X-ray transform on asymptotically euclidean spaces
Keywords: Mathematics.

The x-ray problem is a linear inverse problem which asks if a function can be determined from its integral along a class of curves. This thesis goes through a brief history including the x-ray transform's relationship to nonlinear problems such as boundary distance rigidity. It provides an introduction to microlocal analysis and the scattering algebra, before intro- ducing a new algebra similar to the scattering algebra. Using this new algebra, a modified x-ray transform on asymptotically Euclidean spaces is a locally elliptic operator in this new setting. This ellipticity in turn shows that the original x-ray transform has a left inverse up to a finite rank error in a region near infinity on asymptotically Euclidean spaces
"You're not even reading!" : How one first-grade class negotiated identity and belonging in reading partnerships
Keywords: Education.

Learning to read is becoming a reader. As children move through first grade, they are not only learning to read, but they are becoming readers. They are learning what it means to read and what a reader does. They are also figuring out what kind of reader they are and are not. These negotiations of meaning and identity are happening within the context of their classroom community and impact students' trajectories as developing readers. This microethnographic study of a racially, linguistically, and socioeconomically diverse first-grade class used discourse analysis to examine such negotiations between and among reading partners. As they read together, the students creatively employed instructional practices, such as reading levels and sounding out words, as part of their identifying practices. They also recognized the authority of some peers while rejecting the authority of others. For one student in particular, this rejection was part of a trajectory of exclusion, which ultimately led to their removal from class reading time. By focusing on the ways that young students are making sense of each other and their reading practices as they are identifying and being identified as readers in a community of reading practice, we can understand and address the ways that these practices privilege some students while excluding others
2D materials and nonlinear quantum optics
Keywords: Applied Physics.

Nonlinear optics has long been studied as a basis for realizing fast information processing devices and sensors. Nonlinear photonic logic enables the elimination of slow electron-photon transduction processes and supports high signal bandwidth at optical carrier frequencies. Recent breakthroughs in material science have ushered in a new era of research on atomically thin 2D materials with strong and novel properties for nonlinear optics. 2D materials may be incorporated with scalable nanophotonic technologies via post-lithographic integration. This thesis presents fundamentals for nonlinear optical properties of the 2D materials and their application for nonlinear quantum optics. It first describes the electronic band structures of two prominent 2D materials, namely, graphene and monolayer MoS2. Their linear and nonlinear optical properties are analyzed and presented. The analysis of graphene's optical property uses an innovative first-order perturbative S-matrix formalism that systematically identifies various physical mechanisms contributing towards the optical Kerr nonlinearity. On the other hand, the analysis of the optical property of monolayer MoS2 adopts a massive Dirac Hamiltonian that leads to linear and nonlinear optical susceptibilities through a standard perturbative calculation. It turns out that, although its real Kerr nonlinear susceptibility is enormously large compared to bulk materials, graphene has an even larger imaginary Kerr nonlinear susceptibility that degrades coherence via strong two-photon absorption. Hence, graphene is not a suitable material for applications where coherence is essential. In contrast, monolayer MoS2 that has non-zero finite bandgap energy turns out to be a simultaneously suitably coherent and highly nonlinear material as its real-to-imaginary ratio of the Kerr nonlinear susceptibility can be adjusted through detuning the optical carrier frequency. The thesis also presents a metamaterial configuration based on Kerr nonlinearity of the monolayer MoS2 coupled to a local surface plasmon. The unique combination of a strong field enhancement from the plasmonic effect and the atomic thickness of highly nonlinear 2D materials constitutes an optical nonlinear oscillator. This system produces highly quantum behavior, namely, photon antibunching and non-Gaussianity. When built on rapidly developing nanophotonic platforms, 2D materials are promising nonlinear optical materials that have a vast potential for a future large-scale quantum information processing network.
4-membered ring construction in the synthesis of natural products : total synthesis of Ladderane phospholipids and progress toward the synthesis of fomannosin
Keywords: Chemistry.

Chapter 1 introduces anaerobic ammonium oxidizing (anammox) bacteria and the ladderane lipids, unusual membrane lipids consisting of linearly concatenated cyclobutane motifs. The distinctive biological features and global applications of anammox bacteria are covered, with a focus on anammox catabolism and the possible function of ladderane lipids. The isolation and structural determination of ladderane lipids are outlined, as well as previous and concurrent synthetic efforts. Chapter 2 details our extensive synthetic efforts toward the synthesis of ladderane lipids. Key features of our synthesis of a [5]-ladderane include a scalable synthesis of key building block bicyclo[2.2.0]hex-2-ene, copper(I)-mediated dimerization of this building block, and C--H functionalization of the ladderane core. We also present a synthesis of [3]-ladderane utilizing a [2+2] photocycloaddition with a chiral dihalide, stereospecific alkylzinc addition, and unusual bis-hydrazone oxidative decomposition. Our efforts to determine for the first time the absolute stereochemical configuration of ladderane lipids are also detailed. Finally, the synthesis of two natural and one unnatural ladderane phospholipid as well as biophysical interrogation of synthetic ladderane phospholipids is presented. Chapter 3 describes an ongoing synthetic campaign toward the phytotoxic sesquiterpene fomannosin. Our synthesis requires a challenging quaternary carbon-forming epoxide opening reaction, as well as a cascade cyclization-Ramberg--Bäcklund ring contraction sequence. Efforts toward the completion of the natural product are presented.
626: The Rise of an Asian American Suburb and the Future of Housing and Place in America
Keywords: gentrification
San Gabriel Valley
Asian Americans
Los Angeles
demographic change
mansionization
Program on Urban Studies
Thesis

This project explores the physical and social changes caused by demographic transition in western San Gabriel Valley — a suburban region east of Downtown Los Angeles — since the late 1970’s. During that time, what was once a string of overwhelmingly white suburbs transformed into one of the largest Asian American enclaves in the continental US. This dramatic transformation has had profound effects on the area’s built environment, including significant increases in density, reconstruction of the existing housing stock, and the proliferation of Asian American businesses and growth of commercial development. Much of the existing literature on the area has focused on the racial aspect of the San Gabriel Valley’s transformation, and used racial conflict as the lens of understanding the tensions between existing and new residents during this period. Using a combination of census and property tax data, archival research of local newspapers, and examination of the built environment, I seek to augment that narrative with a focus on issues of development and growth. Much of the changes that occurred in the region — and consequent backlash — often mirror patterns of increased density and tear-downs of older single-family homes found in other metropolitan areas in America that have experienced influxes of new residents in the late 20th and early 21st centuries. To this end, I posit that conflicts around the built environment is a primary cause of tensions in the area, which has significant implications for similar ongoing trends of development elsewhere in the United States.
A Bayesian Model of Attention Allocation: Applications in Gaokao School-Choice Reform
Keywords:  Department of Economics
Department of Economics
school-choice
matching
Bayesian
information acquisition
cost-effectiveness
college admissions
gaokao
China
Zhejiang
Thesis

The prevailing assumption implicit in the seminal works of school-choice matching is that students have fully informed preferences. As a contribution to the literature, we consider how the information acquisition costs that students incur while learning
about their preferences factor into the welfare calculus. Specifically, we adopt cost-effectiveness as a desideratum of mechanism selection and introduce a novel approach that leverages sequential Bayesian updating to help students better allocate their attention to a subset of schools at which they have a higher probability of admission. Using China's gaokao market as a case study, we compare the performance of this Bayesian recommendation mechanism against that of the Chinese Parallel Binning mechanism as deployed in Zhejiang in 2017. Without sacrificing outcome stability, we find that our Bayesian approach generates significant welfare gains, across all levels of preference correlation, by drastically reducing the number of schools to which students must apply.
A Computational Study of Conduction in Dielectrics, with Implications for Neuromorphic Computing
Keywords:  Department of Materials Science and Engineering
Materials Science and Engineering
Electrical Engineering
Neuromorphic Computing
RRAM
MIM
MIS
device physics
Text
Thesis

Dielectrics are vital for a wide range of important devices, from MOSFETs and FinFETs to emerging nonvolatile memory devices such as Resistive Random Access Memories (RRAMs), and metal-insulator-semiconductor (MIS) contacts for photovoltaics and nanoelectronics. Developing an understanding and intuition for the underlying physical mechanisms that result in conduction in dielectrics is a challenging task to undertake experimentally, since the electron transport mechanisms are stochastic and unpredictable. In this work, we use Ginestra, a commercial tool developed by MDLSoft (acquired by Applied Materials in March 2019) to simulate and provide explanations for anomalies that were observed in experimental data. This work has three focus areas: (1) Using Ginestra to explain endurance issues observed in a Hf-based RRAM device, (2) Using Ginestra to verify Fermi Level pinning factor for ZnO, that had been extracted experimentally, and (3) studying the use of nonfilamentary RRAMs for Neuromorphic Computing applications.
We find that Ginestra is well-suited for studying metal-insulator-metal (MIM) device structures, providing key insights into how the endurance and reliability of RRAM cells can be optimized. However, Ginestra’s simulations suggested a trend opposite to the one observed experimentally for our ZnO pinning factor experiments, suggesting that its model set may need to be enhanced to account for effects specific to MIS structures. Our analysis of nonfilamentary RRAMs for Neuromorphic Computing suggests that a hybrid pulsing scheme, comprised of a stepped pulsing scheme for potentiation (LTP), and a standard uniform pulsing scheme for depression (LTD) produces a synaptic signature that has the linearity and symmetry that is desired for neuromorphic computing applications.
A Critique of How Television Represents Race Through Humor
Keywords:  Department of Communication
black
black culture
blackness
blackvoice
humor
race
racial humor
ethnic humor
sitcom
Thesis

The racial identity of an ethnic minority character is often portrayed through their reinforcement of stereotypes, or frequently expressed/mentioned with humor as an aid. The humor driven characterizing of minority characters is in stark contrast to characters who tend to have a more accurate and full range of character identity building/expression that is not limited to what humor can convey. This led me to analyze the history of race in television as well as the tactics of more recent shows with the hope of determining how using humor as a crutch consistently impacts the perpetuation of stereotypes, the development of diverse characters, and the representation of authentic racial experiences.
A Finite Element Analysis of a Radio for Probing the Dark Sector
Keywords:  Department of Physics
dark matter
hidden photons
axions
DM Radio
superconductivity
Thesis

We report on the modeling of the electromagnetic properties of a dark matter detector designed to look for field-like dark matter. Hidden photons are massive U(1) vectors, and are attractive cold dark matter candidates. They exhibit a weak coupling to photons through kinetic mixing, allowing them to interact with Standard Model particles. This allows the presence of a background hidden photon field to be detected by using an electromagnetic resonator. This is the motivation behind Dark Matter Radio (DM Radio), an experiment that uses such a resonator to search for these particles. We present the results of modeling this resonator using finite element methods (FEM). These are techniques to numerically solve PDEs in systems that do not exhibit high degrees of symmetry. These techniques are implemented in COMSOL, which is a software that is industry standard in performing finite element analyses. We present the results of modeling the background hidden photon field as an effective current density, and measuring the observable electromagnetic fields sourced by this current density. We also study the screening current that develops in the superconducting resonator due to these fields, which is the signal that is measured. Finally, we present various measurements of the electromagnetic properties of the resonator
A Green Light at the End of Kim's Dock? North Korea and International Cooperation on the Environment
Keywords: North Korea
Satellite Imagery
Environment
International Cooperation
Thesis

Conventional wisdom suggests that North Korea is an isolated state, with Pyongyang typically disengaged or excluded from various forms of international cooperation. North Korea, however, has ratified a significant quantity of multilateral environmental agreements (MEAs) since the country’s inception in 1948. Motivated by this apparent contradiction, this thesis asks: does North Korea actually comply with the MEAs it ratifies? If so, why? If not, why not? Prior scholarship on the relationship between North Korea and MEAs has been limited due to the lack of data on North Korea’s environment. This thesis, therefore, employs a special type of satellite imagery---namely, multi-spectral satellite imagery---to cover the gaps in the understanding of the evolution of North Korea’s environment. Specifically, this thesis utilizes spectral indices, which are proxies for on-the-ground environmental indicators that can be derived from multi-spectral satellite imagery, to chart the progress (or lack thereof) of different facets of North Korea’s environment between 1985 and 2011. This thesis examines North Korea’s compliance with MEAs by comparing the pre and post-convention trends for customized sets of spectral indices assigned to each MEA, across several sites in North Korea. This thesis finds support for the notion that North Korea complies with MEAs when doing so is consistent with buttressing the stability of the Kim regime, which offers important implications for future cooperative endeavors with North Korea within the international environmental domain.
A Literature Review and Case Study of Teledermatology
Keywords: Community Health and Prevention Research
Stanford School of Medicine
Stanford Prevention Research Center
Thesis

I conducted a literature review on telemedicine, and more specifically, teledermatology. This covered everything from teledermatology's history and modalities, to the reliability, and accuracy across all skin types.
Our group then conducted a retrospective, descriptive analysis of the teledermatology program at the Zuckerberg San Francisco General Hospital and Trauma Center (ZSFG) in San Francisco, California. We assessed patient access to dermatology services at ZSFG as well as the difference in costs to ZSFG’s dermatology department for dermatology services at ZSFG before and after the implementation of the teledermatology referral system.
Our study suggests that implementation of teledermatology in capitated healthcare systems may improve patient access and clinical efficiency at a reasonable cost. Our findings may be generalizable to both academic and non-academic settings, as well as to healthcare settings that are strained in providing specialty services to their patients, such as safety-net hospitals and rural areas with low provider-to-patient ratios. Areas of future investigation include studying the absolute financial costs of teledermatology implementation and sustainment, as well as patient and primary care provider satisfaction and quality of care when dermatology is provided through a virtual system.
‘A little more insight’: How California’s new transparency law is helping the families of those killed by police
Keywords:  Department of Communication
Department of Communication
Journalism
police shootings
use of force
SB 1421
Senate Bill 1421
transparency
police accountability
Thesis

This story examines how Senate Bill 1421, a California transparency law that went into effect in January 2019 that made public police use-of-force and misconduct records, has helped the families of police shooting victims by giving them access to internal investigation reports and body camera footage. Additionally, it looks at other pushes from activists and legislators in the state to increase police transparency and accountability. This story focuses on the shootings and family members of Oscar Grant, Antonio Guzman-Lopez, Jacob Dominguez and Richard “Pedie” Perez.
A Noncanonical Role for Troponin I In Cardiac Reperfusion Injury Following Delta Protein Kinase C (δPKC) Phosphorylation
Keywords:  Department of Bioengineering
Chemical and Systems Biology
Bioengineering
drug discovery
kinase inhibitors
reperfusion injury
Thesis

Ischemia reperfusion (IR) injury, which is characterized by the paradoxical acceleration of damage associated with reoxygenation following ischemia, is a hallmark of myocardial infarction (MI) and is responsible for many post-MI complications, such as heart failure. IR injury is primarily mediated through signaling cascades that converge at mitochondria. However, developing therapeutics that target the specific mitochondrial factors that mediate IR damage has been challenging. Previous work in the Mochly- Rosen Lab has shown that inhibition of cTnI phosphorylation by delta PKC (δPKC) using a rationally designed peptide inhibitor protects against IR injury, suggesting that phosphorylated cTnI, a canonically cytoskeletal protein, plays a damaging role at the level of mitochondria. However, the underlying mechanism that precipitates the inhibitor’s protection is not well understood.
To further investigate, the rational design methodology of this inhibitor we called ѰTnI was validated using computational tools. Then live microscopy and high throughput image analysis was performed to investigated the localization of cTnI following IR. The C-terminal domain of cTnI co-localized with mitochondria in response to IR. Parameters such as mitochondrial morphology, mitochondrial membrane potential, mitochondrial ROS production all improved in the presence of ѰTnI. Lastly, in silico modeling demonstrated plausible mechanisms behind cTnI-mediated mitochondrial dysfunction.
Further work will attempt to identify the order of IR cellular events induced by δPKC phosphorylation of cTnI, including where the phosphorylation takes place and how ѰTnI prevents this phosphorylation. Additionally, investigation into cTnI’s mitochondrial interaction partners may reveal how cTnI-mediated mitochondrial dysfunction takes place, potentially leading to new rational design targets for more specific therapeutics.