VictorJuiz/thesis huggingface dataset:
The risks of nuclear states' signals of resolve

This dissertation presents three studies on the risks of nuclear states' signals of resolve. I examine how nuclear states manage the dual nuclear foreign policy goals of 1) reassuring allies that nuclear proliferation is not necessary for their security and 2) deterring adversaries from using or acquiring nuclear weapons. Traditionally, these aims are accomplished through demonstrations of states' resolve to use their nuclear arsenals to defend allies or attack adversaries. Existing literature posits that the main challenge for nuclear states lies in making these demonstrations sufficiently credible. I examine the conditions under which these demonstrations work. I argue that, while insufficiently credible demonstrations of resolve can fail to reassure allies and deter adversaries, overly credible demonstrations of resolve can also backfire. I examine this phenomenon in the context of nuclear security on the Korean Peninsula. Backfire occurs in two critical, but underappreciated, ways. First, while nuclear states' demonstrations of resolve are designed to reassure their allies of defense commitments, I use survey experiments among the South Korean public to show that highly credible U.S. nuclear security guarantees can backfire. These guarantees create public fears of entrapment in precipitous nuclear conflicts. In this way, a guarantor's demonstrations of resolve can drive citizens in the allied state to support more independent security policies, including the acquisition of nuclear weapons. Second, I show that demonstrations of resolve can create and escalate crises by posing threats that cause adversaries to respond aggressively. I demonstrate that US-South Korean joint military exercises do not deter North Korea. Instead, North Korea systematically responds to exercises with rhetorical and military belligerence. In addition, I show that North Korean threats are not ``cheap talk" but meaningful demonstrations of resolve. Aggregate patterns in these threats reveal information about North Korea's threat perceptions and predict subsequent, provocative behaviors. In this way, even low-level demonstrations of resolve can contribute to escalation. In sum, these studies suggest nuclear states' signals of resolve--rather than reassuring and deterring--can worsen the security environment

Keywords: Political Science.
Advisor: Sagan Scott Douglas
Schultz Kenneth A.
Tomz Michael
Robust learning and evaluation in sequential decision making

Reinforcement learning (RL), as a branch of artificial intelligence, is concerned with making a good sequence of decisions given experience and rewards in a stochastic environment. RL algorithms, propelled by the rise of deep learning and neural networks, have shown an impressive performance in achieving human-level performance in games like Go, Chess, and Atari. However, when applied to high-stakes real-world applications, these impressive performances are not matched. This dissertation tackles some important challenges around robustness that hinder our ability to unleash the potential of RL to real-world applications. We look at the robustness of RL algorithms in both online and offline settings. In an online setting, we develop an algorithm for sample efficient safe policy learning. In an offline setting, we tackle issues of unobserved confounders and heterogeneity in off-policy policy evaluation

Advisor: Brunskill Emma
Pavone Marco
Van Roy Benjamin
Robust variation of the infant gut microbiome around the world

In the first two years of life, the human gastrointestinal tract goes from a blank slate to a diverse ecosystem of trillions of microorganisms. Throughout infancy, assembly of this microbial ecosystem plays important roles in many aspects of host health, from immune development to metabolism and the central nervous system. Features of lifestyle industrialization, such as hygiene, are linked with a distinct gut microbiota and "missing" indigineous bacteria, whose absence are linked to the onset of chronic inflammatory disease. Relatively little is known about the global variation of the infant microbiome and how lifestyle shapes distinct microbial assemblies. Limitations in our knowledge are due to a lack of deep sequencing data characterizing infants from traditional lifestyles and a paucity of analyses across large cohorts of geographically diverse infants. An introduction to the infant gut microbiota and the key studies that I built my thesis upon are discussed in Chapter 1. The work in Chapter 2 fills gaps in metagenomic reference databases by assembling and curating genomes from gut microbiota of Hadza, a group of modern day hunter-gatherers in Tanzania. In Chapter 3, I use this new database and curate a selection of 2,582 infant samples from around the world to report statistically robust associations between the infant gut microbiota with age and lifestyle. In Chapter 4, databases built and methods established in previous chapters are applied to identify features that associate with healthy infant gut microbiota outcomes in a cohort of infants from an ongoing nutritional intervention trial to treat malnutrition in Pakistan. Finally, Chapter 5 summarises the findings of this study in a proposed model of lifestyle-dependent infant gut microbiota and concludes with a statement of future directions

Keywords: Microbiology and Immunology.
Advisor: Sonnenburg Justin
Holmes Susan
Huang Kerwyn Casey
Relman David A.
A role for a mechanosensitive ion channel in long-distance electrical signaling in Arabidopsis

Plants contend with a myriad of environmental stressors, including insect herbivory. To defend against insect herbivory, plants employ defense responses to mitigate damage. Insects are mobile organisms, therefore, wounded tissues in plants send systemic signals to engage defense mechanisms in unwounded tissues to attenuate further herbivory. These defense signals are mechanistically complex. Long-distance electrical signals are speculated to convey the wound signal to distal tissues. Ionotropic glutamate receptors have previously been identified as key components of the electrical defense signal, but additional molecular components are expected to play a role as well. To uncover new molecular players, I performed a genetic screen which revealed that the mechanosensitive ion channel, MSL10, is important for wound induced long distance signaling. In Chapter 1, I review wound signaling in plants and explore the various mechanisms proposed to drive long-distance signals. Chapter 2 describes the discovery of the MSL10 phenotype and characterization of its role in electrical wound signaling. In Chapter 3, I explore the cell biology of MSL10 and how localization in the vasculature is important for signaling. I employed genetically encoded biosensors to study signaling events in plants to better understand their spatial patterning in Chapter 4. Finally, Chapter 5 summarizes the key findings of the thesis project and proposes new avenues of research to answer new open questions. Taken together, this work within the thesis provides a new foundation of knowledge for long-distance plant signaling and opens exciting new areas of study

Keywords: Biology.
Advisor: Frommer Wolf B.
Mudgett Mary Beth
Ehrhardt David (David Walter)
Lin Michael Z.
Shen Kang
The role of differential carcinogen susceptibility in melanoma mutagenesis

Cancer cells evolve through the acquisition of mutations that confer selective advantages associated with malignant transformation. Mutagenesis is preceded by DNA damaging events that occur during exposure to environmental carcinogens or from sporadic cell-intrinsic processes. The acquisition of DNA damage in the presence of genotoxic stressors is determined by the underlying DNA sequence and the surrounding chromatin, a highly dynamic environment involved in the coordination of all DNA-templated processes (such as transcription and replication). If unrepaired, or repaired with poor fidelity, DNA damage causes mutations that increase the probability of sporadic acquisition of malignant characteristics. This work investigates the precise molecular determinants that initiate carcinogenesis. Specifically, we introduce a new DNA sequencing technology to map and quantify various types of DNA damage at ultra-high resolution across the genome. We demonstrate the ability to map DNA lesions induced by UV exposure, heat, oxidative stress, and other conditions at single-base resolution from low input samples. We utilize this technology to provide a detailed atlas of photoproduct acquisition after acute UV exposure in model human cells, and then leverage extensive epigenomic characterizations of these cells to infer novel mechanisms of carcinogenesis. We next introduce genetic alterations that mimic early stages of tumorigenesis and reveal the previously unreported phenomenon of differential susceptibility, whereby tumor-promoting genetic and epigenetic changes alter genome susceptibility to carcinogen exposure and bias subsequent mutagenic potential. We observe unique mutational signatures in melanoma associated with these differentially susceptible regions and suggest that altered carcinogen susceptibility is a generalized principle of human cancer. In summary we have uncovered previously unreported aspects of genome stability and the associated epigenetic mechanisms that underlie them. This work provides the foundation for the development of new therapeutic approaches that interrupt the earliest stages of tumorigenesis. Excitingly, as this novel phenomenon is regulated by reversible epigenetic alterations, the next generation of "epi-drugs" may be thoughtfully designed to override differential susceptibility and prevent cancer

Keywords: Biology.
Advisor: Morrison Ashby J.
Cyert Martha S.
Gozani Or Pinchas
Snyder Michael
Role of evaluation and market feedback in innovation and search

A slow but powerful revolution in organizational decision-making has been unfolding in the last decades. The stereotypical charismatic executive who generates brilliant ideas out of thin air and sees the exact value in every idea in a heartbeat is a rare sight nowadays. This is especially true in Silicon Valley, where, ironically, many still worship the epitome of that stereotype, Steve Jobs. The sheer brilliance of the charismatic executive is replaced by a variety of rigorous techniques such as A/B testing or crowdsourcing that are designed and optimized to extract information from people outside of the organization's boundaries. This revolution is perhaps best reflected in the contemporary primacy of the concept of product-market fit, which imagines organizations as machines for understanding their environments, first and foremost. In this three-part dissertation, I accomplish two goals. First, I examine how the diffusion of randomized business experiments (A/B testing) and crowdsourcing have moved the idea evaluation and selection out of organizations' boundaries. Second, I study how idea generation is endogenous to the selection method in organizations. Drawing on models of bounded rationality and learning in organizational theory, my dissertation investigates the effects of different evaluation processes and how the anticipated feedback from those processes determines the search for innovation. In the first chapter, I ask how the adoption of experimentation as a selection method shapes the direction of innovation. The second chapter examines the interaction between the variation and selection stages of organizational innovation by investigating individuals' idea generation patterns under internal and external evaluation systems. The final chapter examines the effect of success and failure on experimentation-based iterative search behavior

Keywords: Business.
Advisor: Sorensen Jesper B.
Barnett William P.
Clement Julien (Julien Alexandre Romain)
The role of turbulence in the aggregation of ash particles in volcanic plumes

Explosive volcanic eruptions eject large quantities of ash particles into the atmosphere. Fine ash can remain airborne for days following the eruption and travel for hundreds of kilometers before settling to the ground. Field observations indicate that much of the fine ash is stripped from the plume early on through the process of ash aggregation, which greatly reduces the residence time of ash in the atmosphere. Predicting the transport of ash requires better understanding of the aggregation process and is important for minimizing the societal impact of future eruptions. We present a new experimental apparatus, the turbulence tower, which replicates the conditions in the core of a water-rich buoyant plume at the lab-scale. The influence of turbulent mixing on aggregation of wetted particles is studied using a variety of optical techniques. In particular, high-speed imaging is used to detect individual collision events. The outcome of each collision is classified as either rebound, aggregation, or disaggregation, depending on the relative collision velocity and effective film thickness of water coating the particles. The experimental data are used to fit a semi-empirical sticking efficiency function. A 1D volcanic plume model that incorporates the effects of aggregation and turbulent mixing is also developed. The model is applied to the 2009 eruption of Redoubt Volcano, Alaska, predicting the plume rise height, concentration of hydrous phases, and ash aggregate grain size from a set of eruption source parameters

Keywords: Mechanical Engineering.
Advisor: Eaton John K.
Elkins Christopher J. 
Ouellette Nicholas (Nicholas Testroet)
The rooted world beneath our feet : a global analysis of the size, shape, and allometry of plant root systems

The roots of woody plants, trees and shrubs, account for 39% of woody plant biomass, and herbaceous plants have greater than 50% of their biomass belowground on average, making plant roots a major component of the terrestrial carbon pool. Roots also act as a terrestrial plumbing network, moving water, carbon, and nutrients throughout the environment. Given the important role roots play in our earth system, there is still much we do not know about the belowground organs of plants. This dissertation focuses on understanding the size and shape of plant root systems using a variety of tools and techniques in order to study a system that is immensely difficult to directly observe and measure. Specifically, I 1) created a new version of the Root Systems of Individual Plants (RSIP) database to understand the maximum depth and width of root systems across the globe, 2) developed an image analysis pipeline to investigate the above- to belowground allometry of woody plant volume and biomass, and 3) used a forested drought manipulation experiment to unearth the vertical root niche partitioning of co-dominant trees undergoing drought stress. Through my graduate work I found that roots show considerable variation in their depth and spread, with deeper-narrower root systems in arid climates and wider-shallower root systems in humid climates. I also found that plants can often be much larger belowground compared to aboveground, with the width of plants belowground being 2.25 times wider than the width of plants aboveground. Furthermore, 86% of the volume taken-up by plants is belowground. I also found that co-dominant trees in a northeastern forest portray different rooting strategies when facing drought-stress. However, when facing drought stress, many of the root profiles had an increase in roots at deeper depths, shifting their average rooting depth distribution by 80% towards deeper soil layers. Beyond the creation of new plant size and shape data, the analyses contained within this dissertation greatly expands on our understanding of the form and function of plant root systems

Keywords: Environmental Earth System Science.
Advisor: Fendorf Scott
Jackson Rob
Schenk H. J. (H. Jochen)
Rural-Urban Distinction in the Late Ming Huaben

This paper delves into the rural and urban representations in the late Ming huaben texts. While cities are portrayed as rich and prosperous places, rural areas are depicted in an opposite way. The literary construction of rural people and spaces reveals that urban people, represented by huaben writers and audiences, are very conscious of the rural-urban distinction.
I hope this interdisciplinary study will cast new light on the rural-urban issues.

Keywords:  Stanford Global Studies
rural-urban distinction
huaben
Thesis
Advisor: Zhou Yiqun
Safer practices and novel modalities for clinical CRISPR applications

CRISPR technologies have revolutionized the field of medicine and granted us the power to precisely diagnose or edit the human genome to treat disease and to elucidate the potential causes and solutions to disorders. In my thesis, I aim to tackle two main projects to help move CRISPR-based therapeutics into clinical use and many other projects that I contributed to that helped push the boundaries on current CRISPR technologies. First, I explored the potential del- eterious side effects from gene editing. I assess whether CRISPR editing can lead to the formation and display of neoantigens, or antigens that have not been previously encountered by the immune system and which may be potentially immunogenic. I found that CRISPR editing can indeed lead to neoantigen formation and I also computationally predict that this phenome- non can occur with relative frequency, underscoring the need for safer clinical gene editing practices. To help circumvent this issue and reduce the potential for neoantigen-induced host- versus-graft disease, I develop a tool, SAFE-EDIT, which can computationally predict when this phenomenon may occur and better inform guide RNA design for best therapeutic practices. Second, I explore utilizing CRISPR as an antiviral to treat influenza, SARS-CoV-2, and other coronaviruses. I use CRISPR to interfere with both host genes essential for viral replication and with the viral genome itself, finding that both can strongly reduce viral burden in cells and together lead to an increased antiviral effect. Furthermore, treatment with small-molecule in- hibitors and CRISPR antivirals shows a strong synergistic effect at reducing the viral load, highlighting that CRISPR can be used to augment existing therapies. The high efficiency, spec- ificity, and simplicity of CRISPR opens the potential for a bevy of new applications clinically. In sum, my thesis work greatly expands CRISPR as a clinically relevant tool by further deline- ating best practices for safe therapeutic use and establishing new modalities for the treatment of infectious disease

Keywords: Bioengineering.
Advisor: Qi Lei (Professor of Bioengineering)
Bryant Zev David
Li Jin (Billy)
Safety critical bounds for precise positioning for aviation and autonomy

Unmanned aerial vehicle (UAV) and autonomous platforms can greatly benefit from an assured position solution with high integrity error bounds. The global navigation satellite system (GNSS) offers nearly ubiquitous positioning, and the expected high degree of connectivity in these vehicles will allow users to receive real time precise clock and ephemeris corrections to the GNSS navigation messages. Such corrections enable the use of precise point positioning (PPP) techniques. Up to now, these techniques have mostly been used to provide high accuracy, rather than focusing on high integrity applications. In this thesis, I apply the methodology and algorithms used in aviation to determine position error bounds with high integrity (or protection levels) for a PPP position solution. A navigation system that incorporates measurements from GNSS, an inertial measurement unit (IMU), and an odometer, and is tolerant to faulted measurements was developed and demonstrated with static, automobile, and flight data. Methods are developed and discussed that reduce the complexity and computational load of the system. In order to stress the error detection capabilities, faults are injected into the measurements. The overall position error bounds produced, which are often under two meters, offer a significant improvement over the state of the art in high integrity navigation, which is driven by the aviation industry and are on the order of tens of meters. Another contribution relaxes the requirements on the use of precise orbit and clock corrections by the navigation filter while still producing tighter error bounds through the use of precision navigation techniques. A final topic discussed involves techniques developed for measuring the errors affecting the GNSS satellites as they relate to GNSS constellation monitoring, which is required to support advanced receiver autonomous integrity monitoring (ARAIM). ARAIM is a high integrity navigation technique in development for aviation and that was adapted here to provide the protection levels for PPP. Significant temporal variations in the satellite performance are observed in ways that are undetectable to other constellation monitoring techniques

Keywords: Aeronautics and Astronautics.
Advisor: Walter Todd
Gao Grace X. (Grace Xingxin) 
Powell J. David
'Saving the mind' : an etymological inquiry into the cognitive-behavioral function of the Ancient Greek value ΣΩΦΡΟΣΥΝΗ (sōphrosynē)

Sōphrosynē is a word with deep cultural significance. Genres as diverse as epic, tragedy, history, and philosophy speak about it as an ideal of human behavior. Yet, the traditional etymology ('soundness of mind') overemphasizes its cognitive or intellectual aspects, at the expense of its behavioral or emotional aspects. Drawing on linguistic, anthropological, and psychological studies of archaic Greek culture, I here propose a new etymological understanding of sōphrosynē that also accounts for its ancient association with emotions and behavior. I find support in the language of Homer and hitherto neglected evidence from personal names beginning in Sō-. I conclude that sōphrosynē is best explained not as a normal cognitive state ('sanity'), but as a cognitive-behavioral achievement: namely, the verbal action of 'saving the mind'. This prototype accounts for both the word's meanings 'sanity' and 'self-control': the self-controlled person 'saves her mind' (action), whereas the sane person 'has a safe mind' (state). Each meaning represents, so to speak, different sides of the same linguistic coin. The results of this investigation are far-reaching. By abandoning an intellectualist account of the Greek word sōphrosynē, we are in a better position to understand the idea or value denoted by it. The interpretation 'soundness of mind' is quite symptomatic of our own cultural distance: it seems to be dictated by a culture that gives preference to the cognitive or intellectual ('mind') and sees it as susceptible of health ('soundness'). In other words, our common sense has freely assumed that the archaic Greeks shared the same model of the mind as we do. On closer inspection, however, it becomes clear that they located mental activity not in the head but in the chest: more specifically, in the lungs and the heart. This pulmo-cardiac theory of the mind is based on the observation that a variation in mental activity corresponds to a variation in respiration. Since breath moves briskly within those organs in moments of emotional unrest or cognitive indecision, it was identified with the thought-impulse of the thinking and feeling person. If so, the word sōphrosynē testifies to a holistic conception of human and animal consciousness, where body and mind are regarded as such an interdependent unity that 'self-control' entails a real psychosomatic achievement

Keywords: Classics.
Advisor: Martin Richard P.
Bobonich Christopher
Netz Reviel