VictorJuiz/thesis huggingface dataset:
The role of Arp5 and Ies6 in the INO80 chromatin remodeling complex
Keywords:  Department of Biology
Biology
Arp5
Ies6
INO80
chromatin remodeling
Saccharomyces cerevisiae
Thesis

Within the nucleus of the eukaryotic cell, DNA is packaged into chromatin, a compact yet dynamic structure consisting of DNA wrapped around histones to form nucleosomes. Chromatin remodelers are the protein complexes responsible for the repositioning and restructuring of nucleosomes, an essential process for regulating access to the genome. Previous research on INO80, a chromatin remodeler conserved from Saccharomyces cerevisiae to humans, has shown that one module of the complex (consisting of two protein subunits, Arp5 and Ies6) can exist as a separate subcomplex in the cell, capable of binding to chromatin independently. This Arp5 subcomplex appears to be essential for regulation of several key metabolic genes in yeast. This study examines how Arp5 and Ies6 bind to each other and to the full INO80 remodeling complex, as well as how the subcomplex is loaded onto chromatin by the full complex, the mechanism of which has yet to be determined. Through immunoprecipitation experiments in yeast, it was determined that the C-terminus of Ies6 is critical for complex assembly. Through chromatin fractionation experiments, we show that the deposition of the subcomplex is dependent upon the Nhp10 module of INO80, but independent of the catalytic activity of the Arp8 module. Chromatin remodeling is an important means of epigenetic regulation, and the discovery of the Arp5 subcomplex presents a novel method of chromatin regulation by remodeling complexes. Further research aims to reveal the presence of other subcomplexes and elucidate their distinct chromatin remodeling functions.
THE ROLE OF SHALE KEROGEN – HYDRAULIC FRACTURING FLUID INTERACTIONS IN HYDROCARBON TRANSPORT AND CONTAMINANT RELEASE
Keywords:  Department of Geological Sciences
School of Earth Energy &amp; Environmental Sciences
kerogen
hydraulic fracturing
Thesis

The recent increase in unconventional oil and gas exploration and production has
stimulated significant research on hydraulic fracturing, but the many possible chemical
reactions between the fracturing fluids and the minerals and organic matter comprising the
shale host rocks are not well understood. In particular, there is a lack of information
concerning the evolution of organic matter in shale reservoirs during hydraulic fracturing
operations. Organic matter, primarily in the form of kerogen, is the dominant source of
hydrocarbons in shale plays and is therefore critical to productivity. In addition, kerogen is
enriched in metals, making it a potential source of contaminants to produced waters. In the
present study, two different kerogens of contrasting types and maturities (Green River and
Marcellus) were reacted with a variety of fluids, including a commonly used synthetic
hydraulic fracturing fluid, in order to determine the effect of these fluids on shale minerals
and organic matter before and after exposure and solid-fluid partitioning. No trends in the
concentrations or speciation of carbon, hydrogen, or oxygen were quantifiable, due to
either the absence of reactions or difficulties in detecting such trends because of significant
natural heterogeneity in the kerogen samples. However, solubilization of organic
compounds occurred in the more immature Green River kerogen when it was exposed to
fracturing fluid. The same effect was not observed in experiments involving Marcellus
kerogen. The organic compounds released from the Green River kerogen to solution
impacted Fe speciation in particular. Additionally, experiments with Green River and
Marcellus kerogens and either fracturing fluid or pH 2 water mobilized metal contaminants.
The source of contaminants varies between the two kerogens, with metals in the Marcellus
largely sourced from associated pyrite, and with metals within the Green River sourced
from a combination of accessory mineral dissolution and desorption from kerogen. These
results suggest that chemical reactions between fracturing fluid and more immature
kerogens can impact reservoir geochemistry, potentially affecting production. However,
the apparent stability of kerogenic pores based on the lack of observable changes in
functional group chemistry of either kerogen studied suggests that important transport and
storage parameters such as wettability and gas sorption capacity should remain constant
throughout the lifetime of a well.
The Sharon Formula: The U.S.-Israel Relationship and the Age of Israeli Unilateralism
Keywords: Ariel Sharon
Israeli disengagement
unilateral
Gaza
Palestinian
Israel
Ehud Olmert
George W. Bush
minor power
great power
convergence
Thesis

Why did Israel disengage from Gaza in 2005? By analyzing my interviews with American and Israeli officials, studying memoirs by high-level officials in the United States, Israeli, and Palestinian governments, and examining government documents and the relevant academic literature, I show that contrary to the literature, the Israeli government did not decide to disengage from Gaza in response to domestic or foreign pressure. Rather, Israeli Prime Minister Ariel Sharon disengaged in order to initiate negotiations with America through which Israel could consolidate favorable shifts in American foreign policy that occurred between 2001 and 2003. In these negotiations, Israel gained American support for its positions on final-status issues, including ownership of major settlements in the West Bank and the status of Palestinian refugees. These negotiations culminated in an exchange of letters between President Bush and Prime Minister Sharon on April 14, 2004 at the White House. This thesis shows that the current literature on the topic fails to fully appreciate the significance of the April 14 Letter and the fact that Israel treated the Roadmap for Peace, created in 2003, as a major diplomatic victory. Additionally, Prime Minister Sharon and Prime Minister Olmert rejected the idea of negotiating with the Palestinians and intended to take further unilateral actions in the West Bank after the disengagement from Gaza. By analyzing this negotiation process, this thesis sheds light on the complex and calculating nature of the American-Israeli relationship. This thesis reveals that Ariel Sharon developed a formula to prevent negotiations with the Palestinians, while gaining American support for unilateral action. Finally, this thesis’ study of the American-Israeli diplomatic relationship also reveals how Israel and America’s democratic makeup prevents certainty in negotiations. Neither country can be sure of the outcome of the other country’s elections or legislative votes, which creates challenges and openings in negotiations.
The Significance of Sleep and Circadian Rhythms in Learning and Memory
Keywords:  Department of Biology
Biology
Neurobiology
Circadian Rhythms
Learning
Memory
Sleep
Sleep Deprivation
Novel Object Recognition
Thesis

Previous studies have demonstrated that sleep plays an important role in learning and memory, and that lack of sleep impairs memory consolidation. Starting with the observation that rodents performed poorly on hippocampal-dependent memory tests at certain times of the day, we sought to determine: 1) how the circadian system modulates learning, and 2) how sleep deprivation (SD) impairs learning and memory as a function of circadian phase. The present study evaluated the cognitive function of animals with intact circadian rhythms using variations of the Novel Object Recognition (NOR) test at four different time points of a 12-hour light/dark cycle – light onset (9:00am), mid-light (3:00pm), dark onset (9:00pm), and mid-dark (3:00am) – with or without SD. Although the tests on the effects of SD were inconclusive, animals tested with the simple NOR test demonstrated equivalent learning at all daily time points, while animals tested with the complex NOR test demonstrated greater performance at the mid-light and mid-dark time points. These results suggest that time of day effects modulate learning and memory, and that the degree to which time influences cognitive performance is dependent on the complexity of the cognitive task.
The Three Warfares: China's Political Warfare Doctrine
Keywords:  Stanford Global Studies
Stanford Global Studies
East Asian Studies
Three Warfares
Political Warfare
CCP
PLA
Taiwan
Democracy
Thesis

China’s growing military might and regional assertiveness have further exacerbated tensions in the Asia-Pacific. While the specter of China’s military capability is indeed worthy of concern, it is also the case that the employment of this capability to pursue strategic objectives through conventional war is extremely unlikely. Increasing its military capability has an obviously positive affect on China’s ability to negotiate for, deter, defend and secure its national interests in the region and potentially beyond. As China continues to gain international influence, it will also continue to shape the international order to its benefit. Even if the CCP, as it has in the past, uses existing institutions in the international system to compete for its advantage, the result will likely be a system more tolerant of behaviors that are counter to or degrading of the foundations underpinning the liberal international order. However, the ways and means that China will use to change the status quo, increase its international standing, and pursue the reunification of the Chinese nation are primarily political, not military.
In late 2003, the CCP Central Committee and the Central Military Commission (CMC) issued new regulations on political work in the Chinese People’s Liberation Army (PLA). These guidelines updated multiple aspects of PLA party building, ideological education and liaison work. Within the updated guidelines, the General Political Department (GPD), or zǒngzhèngzhìbù (总政治部), was tasked with three new offensive aspects of wartime political work: public opinion (or media) warfare (舆论战), psychological warfare (心理战), and legal warfare (法律战). Collectively known as the “Three Warfares,” sānzhǒngzhànfǎ or simply sānzhàn (三种战法／三战), this aspect of Chinese strategy has become increasingly visible as the CCP pursues its interests in the region. Understanding what the Three Warfares are, how they have evolved with China’s military strategy, and how they are employed in the pursuit of China’s strategic interests is essential to addressing the geopolitical frictions that will arise as the CCP attempts to re-shape its strategic environment
The Use of Designed Learning Spaces
Keywords: learning space
design
high school students
teachers
principal
designer
perspectives
use of space
classroom experience
field observations
Stanford Graduate School of Education
Thesis

This study has investigated the extent to which the behavior and perceptions of students and
teachers of an innovative learning space aligned with its intended functions as described the
designer and principal of the school. Additionally, the research aimed to identify which design
features appeared to be most utilized and salient to student activities associated with learning.
Qualitative observations and notes were conducted in two classrooms at an innovative high school
in Silicon Valley. Following observations, interviews were conducted with eight students, the two
teachers of the observed classrooms, the school’s principal, and the designer of the school. A
significant discrepancy between design intent and use of space was identified by both designer and
principal. Although the spaces of the school were designed for a rotating classroom model, where
teachers schedule different classrooms for use, the school currently adopts a more traditional
teacher-to-classroom model. Despite this, there was a significant alignment of institutional mission
in the behavior of teachers and students. Results suggest that the design of classrooms influenced
teacher pedagogy towards certain activities. Tools such as wheeled chairs gave students actual and
perceived mobility, which likely fostered student autonomy and sociability that traditional
classrooms do not afford. The results of this study speak to the need for adaptable learning spaces.
Ultimately, the learning space is an important tool that administrators and teachers can use to
influence student learning and experience.
Theory of few-photon quantum scattering in nanophotonic structures [electronic resource]
Keywords: Physics.

The capability to create strong photon-photon interaction at a few-photon level in integrated photonic systems is of central importance for quantum information processing. To achieve such a capability, an important approach is to confine photons in a one-dimensional waveguide coupled to a local quantum system with strong nonlinearity. At a fundamental level, photon-photon interaction in such system is described by multi-photon scattering matrix (S matrix). In this thesis, we discuss both computational and conceptual aspects of multi-photon S matrix. For the computational aspect, we provide a systematical way to compute N-photon S matrix using the input-output formalism. The main result is a general connection between the N-photon S matrix and the Green functions of the local quantum system. Such computation can be generalized straightforwardly to the case of multiple waveguide channels to study the Fano interference in the presence of photon-photon interactions. For the conceptual aspect, we discuss the general structure of two-photon S matrix without explicit computation. Using techniques that are closely related to cluster decomposition principles in quantum field theory, we provide a general constraint on the analytic properties of the two-photon S matrix. Furthermore, we present a generalized form of the cluster decomposition principle. The two-photon S matrix, when the local quantum region supports multiple ground states, has an analytic structure that differs significantly from what is commonly anticipated.
Thermodynamic studies of semiflexible copolymers using field theory and molecular simulations [electronic resource]
Keywords: Chemical Engineering.

Polymers are big molecules consisting of repeating chemical units. Polymeric self assembly is critical in many biological processes and materials applications. Biomolecules such as protein, lipid, and DNA all require structural organizations to accomplish biological functions. Performances of polymer materials also rely on their microscale structures. These microstructures form due to the interactions between the different chemical units. Most of our knowledge of macromolecular phase behavior is based on a Gaussian chain model which models polymer configurations as random walks. However, such model is challenged in many biological and experimental systems. When working with low-molecular-weight polymers, stiff polymers (such as DNA, and conjugated polymers), or random copolymers which phase segregate on monomer length scales, chain semiflexibility plays a critical role in determining the polymeric microstructures. Towards this goal, we develop theories and simulations that study the phase behavior of semiflexible copolymers. We will discuss the impact of finite chain rigidity on phase transition temperatures, domain sizes, and microstructures of diblock copolymers and random copolymers. We show that polymer semiflexibility has strong impacts on the collective equilibrium behaviors of copolymers.
Threat and polarization [electronic resource] : social identity and bias among American partisans
Keywords: Communication.

Recent research in political communication has defined polarization in affective terms (how partisans feel toward their opponents), as opposed to ideological terms (position on a left-right spectrum). This progression has enabled researchers to demonstrate that contempt between Democrats and Republicans has increased over the past half-century, as well as to document extant levels of attitudinal and behavioral biases between party opponents. The original research in this dissertation relies on this definition to examine how the psychological mechanisms of threat and affirmation affect interparty bias. Studies 1 and 2 give evidence of self and group-threat's ability to exacerbate partisan bias, while no support was found for affirmation's hypothesized attenuating effect. Study 3 was unable to provide evidence of a threat response among Democrats following the 2016 presidential election.
Three essays in development and environmental economics [electronic resource]
Keywords: Economics.

This dissertation explores various topics in development and environmental economics. The first chapter is coauthored Mauricio Romero. In it we investigate how illegal mining, a very common phenomenon in Colombia, changed with a mining tax reform that reduced the share of revenue transferred back to mining municipalities. To overcome the challenge of measuring illegal activity, we construct a novel dataset using machine learning predictions on satellite imagery features. Theoretically we expect illegal mining to increase because the amount required to bribe the local authority is smaller after the reform. Using a difference-in-differences strategy, with Peru as the control, we find that illegal mining increased by 4.47 percentage points as share of the mining area. In addition, we provide suggestive evidence that illegal mines have more harmful health effects on the surrounding population than legal mines. These results illustrate unintended effects of tax revenue redistribution. The second chapter is also co-authored with Mauricio Romero. The motivation is that mining can propel economic growth, but its pollution could negatively impact human health. Using a difference-in-differences strategy we estimate the effect of gold mining on the health of newborns in Colombia. We find heterogeneous effects depending on where mothers are located with respect to a mine. Specifically, mothers living in the vicinity of a mine are positively affected experiencing a reduction of 0.51 percentage points in the probability of having a child with a low APGAR score at birth (from a basis of 4.5\%). However, for mothers living downstream from a mine the gains are reverted due to pollution. We provide suggestive evidence that contaminated fish consumption in the first weeks of gestation is the mechanism behind these results using an exogenous increase in fish consumption caused by a religious celebration. The final chapter is co-authored with Pascaline Dupas and Jon Robinson. In it we use detailed observational data constructed from daily passenger-level logbooks and weekly surveys to study the intertemporal labor supply decisions of Kenyan bicycle taxi drivers, while generating variation in cash on hand through randomized cash payouts. We document three key facts: (1) drivers work more in response to both unexpected and expected cash needs; (2) drivers increase the probability of quitting once they have reached their day's cash need; but (3) randomized cash payouts have no effect on labor supply. These results are consistent with models in which workers have reference-dependent preferences over earned income targets. A calibration exercise suggests that workers with such preferences earn about 5\% more than they would with neoclassical preferences. We propose a model and interpretation of earned income targeting as morphine: it partially numbs the effort cost until the target is reached.
Three essays in public financial economics [electronic resource]
Keywords: Economics.

This dissertation explores three issues of public finance. The first chapter presents evidence that the rise in house prices in California caused an expansion of local governments' debt in the early 2000s. Using a novel dataset on all local government debt in California dating back to the 1960s, the main empirical findings suggests that a percentage point rise in house prices in a given county beyond the long-term trend is associated with a 0.44 percentage point rise in debt of local governments within the county. The second chapter documents, using data of all municipal bonds issued in California and New York between 1996 and 2014, a significant decline in the benefits of using municipal bond insurance from approximately 5.1% of the overall deal value at 1996-2002 to 0.5% by 2011-2014. The main reason for the decline is associated to the decline in insurer's credit strength. The final chapter identifies a large class of cases where claiming Social Security early is a mistake regardless of any liquidity constraints, mortality concerns, bequest motives, time discount rates, or a variety of other preference related factors. The magnitude of the mistake can reach up to $250,000.
To Bomb or Stab? The Impact of Ideology and Territorial Control on Rebel Tactics
Keywords: Center for International Security and Cooperation
Insurgency
Ideology
Territorial Control
Philippines
Tactics
Thesis

This thesis explores how ideology and territorial control can affect the types of violent attacks and tactics insurgent groups choose to employ. Building on existing literature regarding target selection in civil war and insurgency, I develop a model to explain when insurgent groups choose to use violent attacks that are indiscriminate (such as bombings and improvised explosive devices), as opposed to discriminate attacks (such as assassinations and abductions). The claim is tested both qualitatively and quantitatively, focusing on four case studies in the Philippines. Fine-grained data compiled from incident level field reports maintained by the Armed Forces of the Philippines across a 36-year time span provides evidence in support of this model's claim: indiscriminate attacks are more common across groups with weaker ideological commitment and less territorial control of the population. Furthermore, a qualitative examination of changes to the case studies’ ideology and/or territorial control provides support for this model’s mechanistic claims. The results of my analysis can help policymakers link ideology and territorial control – variables that can be associated with a rebel group’s objectives – to tactics used, which helps predict the type of violence expected from a group based on their stated objectives. These findings help government forces employed to combat insurgency prepare for the type of violence predicted, and can potentially aid in the understanding and anticipation of future violent attacks used by different groups.
Topics in high-dimensional asymptotics [electronic resource]
Keywords: Statistics.

Many multivariate statistics problems of current interest involve data with a large sample size and a large dimension. In this thesis we study several problems in this area. We work in the framework of high-dimensional asymptotics, where both the sample size and the dimension grow to infinity, such that their aspect ratio converges to a constant. In this setting, we leverage and further develop results from random matrix theory for the analysis of correlated multivariate data. Our first problem develops a fundamental new computational tool to numerically find the limiting empirical eigenvalue spectrum of sample covariance matrices. Our second problem uses this to develop new tests in PCA under local alternatives. Our third problem studies the problem of PCA from linearly modulated data, arising in missing data and deconvolution problems.