VictorJuiz/thesis huggingface dataset:
The rheology of polydisperse colloidal suspensions in spherical confinement
Keywords: Chemical Engineering.

In this work, we present a computational study of the rheology and dynamics of spherically-confined polydisperse suspensions of hydrodynamically interacting colloids, a simple model system that provides an important framework for studying the behavior of living and non-living confined colloidal suspensions. Colloids are microscopically small particles suspended in a solvent. Examples include the cytoplasm of biological cells, micro-reactor vesicles, and particle-laden droplets ubiquitous in additive manufacturing and industrial coatings. Here we present an extension of the Confined Stokesian Dynamics algorithm (CSD) capable of modeling the bulk rheology of confined colloidal suspensions of arbitrary particle-size distribution, at and away from equilibrium. We will present novel hydrodynamic functions we developed that couple particle dynamics to suspension properties and, after a brief overview of the CSD algorithm, the results of a systematic study of the impact of changes in confinement and size polydispersity on equilibrium structure and dynamics. We showed that an interplay between polydispersity and confinement reveals demixing and localized dynamics that help explain our previous discovery that such dynamics control the speedup of protein synthesis in faster-growing bacteria. Next, we will present a new theoretical framework we developed for measuring the intrinsic viscosity and osmotic pressure in confined suspensions. The first significant outcome of this work was that tighter confinement and crowding significantly increase equilibrium viscous dissipation and osmotic pressure compared to unconfined suspensions. This result is important for the rational design of biochemical tests, where up to now, only the effect of passive crowders was taken into account. The second significant outcome of this work was the modeling of strong departures from equilibrium, including a representation of biomolecules localized at one pole of the cavity that subsequently diffuse - mimicking the Min cycle in E. coli our work shows that concentration gradients inside cells increase the residence time of proteins close to the membrane, which is beneficial for Min-protein membrane reaction kinetics that promotes correct cell division. Finally, we will present three other significant theoretical developments in the field of microhydrodynamics done in service of the underlying theoretical framework of our model
Ribonucleic acids in the microbiome
Keywords: Genetics.

Much remains to be characterized and identified in the human microbiome, ranging from small proteins to RNAs that form secondary structures. Recent innovations in sequencing technologies and informatics approaches have enabled us to study the microbiome at many new levels of regulation. In this dissertation, I develop new methods and informatics pipelines to study protein synthesis and predict functional elements in the microbiome. Chapter 2 describes the development of MetaRibo-Seq, a technology that enables high-throughput study of translation in microbiomes and applies it to discover new small proteins. Chapter 3 addresses limitations of Ribo-Seq, the prevalence of contaminant Ribo-Seq signal across structured RNAs, and the likely source of such contamination. Chapter 4 describes a large-scale comparative genomics approach to reveal thousands of novel candidate structured RNAs. Overall, these chapters bring new technologies and resources to study small proteins and RNAs in the human microbiome
Rights and Resistance: A Comparative Analysis of the Post-Partition Civil Rights Movements in Indian Occupied Kashmir
Keywords: Kashmir
Civil rights movements
Text
Thesis

Muskan Shafat’s capstone project explores the history and politics surrounding the post-colonial Kashmir civil rights movement and how this has been influenced by continued military occupation. Muskan specifically contrasts the civil rights movement in the 1990s with that in the 2010s, highlight the unique role of digital advocacy in raising awareness of Kashmir globally, eventually leading to increasing global pressure on India and raising awareness about human rights violations in Kashmir. She examines various ways the diaspora can aid this political movement by organizing global protests and holding political representatives accountable to speak up for Kashmir, all the while encouraging activists in Kashmir to document their struggle while relying on media outputs to the wider world. With this analysis, Muskan hopes to highlights the Kashmiri struggle, bringing together voices and narratives of Kashmiri artists, to better understand the role of the international community.
Ripple Effects Mapping in Community-Engaged Research: Capturing the “Ripples” of the Steps for Change Physical Activity Intervention Trial
Keywords: ripple effects mapping
community-engaged research
participatory action research
citizen science
community-engaged evaluation
social ecological model
Science > Citizen participation
COVID-19 (Disease) > Social aspects
COVID-19 Pandemic (2020-)
physical activity
Text
Thesis

An emergent evaluation tool known as ripple effects mapping (REM) is a participatory qualitative method that engages program participants and other stakeholders in exploring intended and unintended intervention impacts. REM was used to explore the intervention impacts of the Steps for Change intervention programs. Steps for Change is a group-randomized controlled physical activity intervention trial targeting lower-income midlife and older adults who live in or near 10 senior affordable public housing sites in two San Francisco Bay area counties. The two intervention arms consisted of an evidence-based behavioral intervention targeting individual-level factors influencing regular physical activity vs. the same behavioral intervention in combination with a citizen science intervention, called Our Voice, which targeted local physical and social environmental factors affecting physical activity. Thematic analysis of the intervention impacts obtained during the REM sessions was used to identify major themes, such as COVID-19, physical activity, and social connectedness. The purpose of the present study was to begin to explore the 12-month intervention-derived impacts under the COVID-19 major theme in a housing site (Site A) randomized to the multi-level intervention and its comparison site (Site B) randomized to the individual-level intervention only. The reported impacts under the COVID-19 theme were examined and quantified based on the different organizational levels of the social ecological model. A quantitative comparison of the two sites revealed a statistically significant difference in the relative frequency distribution of impacts based on the levels of the social ecological model (p < 0.01). Using thematic analysis, four subthemes under COVID-19 were identified: (1) meeting physical activity goals, (2) maintaining social connections, (3) balancing health and wellbeing, and (4) learning the Zoom online meeting platform. The content in these subthemes related to challenges and individual adaptations associated with the COVID-19 pandemic and its influence on participant engagement in the intervention programs. Striving to identify the full complement of intervention impacts through novel qualitative approaches such as REM can provide insights related to both expected and unexpected impacts of a community-based health promotion program. REM in community-engaged research can be a valuable evaluation tool to capture broader intervention effects and potentially enhance program implementation and sustainability in a more comprehensive manner.
The risks of nuclear states' signals of resolve
Keywords: Political Science.

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
Robust variation of the infant gut microbiome around the world
Keywords: Microbiology and Immunology.

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
A role for a mechanosensitive ion channel in long-distance electrical signaling in Arabidopsis
Keywords: Biology.

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
The role of differential carcinogen susceptibility in melanoma mutagenesis
Keywords: Biology.

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
Role of evaluation and market feedback in innovation and search
Keywords: Business.

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
The role of turbulence in the aggregation of ash particles in volcanic plumes
Keywords: Mechanical Engineering.

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
The rooted world beneath our feet : a global analysis of the size, shape, and allometry of plant root systems
Keywords: Environmental Earth System Science.

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
Rural-Urban Distinction in the Late Ming Huaben
Keywords:  Stanford Global Studies
rural-urban distinction
huaben
Thesis

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.