VictorJuiz/thesis huggingface dataset:
Cell-autonomous mechanisms that suspend PVD dendrite outgrowth during dauer diapause
Keywords:  Department of Biology
dma-1
mec-3
mbl-1
rig-1
PVD neuron
dauer diapause
forward genetic screen
Thesis

Development in animals is not merely an intrinsically programmed event. Response to environmental conditions plays a large role in an organism’s development. The nematode species C. elegans develop from egg to adulthood through a life cycle known as reproductive development, but in environments of stress, such as starvation, overcrowding, or high temperatures typically found in nature, the worms will enter a dormant larval stage called dauer diapause. Recent work has shown that during the dauer diapause, dendrite outgrowth of the mechanosensory neuron PVD in C. elegans is suspended. Yet, the molecular mechanisms governing the arrest of the development of this neuron remain unknown. To identify the factors involved in pausing PVD dendrite outgrowth during dauer, we tested whether overexpression of four genes that are required for dendrite outgrowth of the PVD neuron during reproductive development (dma-1, mec-3, mbl-1, and rig-1) could bypass the dauer-induced dendrite growth suspension. Additionally, we conducted a forward genetic screen to isolate mutants that fail to suspend PVD development during dauer. The two methods, though, were unsuccessful in identifying the factors governing this phenomenon. Over-expression of the four genes did not cause complete development of PVD’s dendritic arbor, suggesting these genes, individually, do not control the suspension of PVD’s dendritic outgrowth. Also, a mutant of interest with complete development of dendritic outgrowth was not found in the forward genetic screen. However, a mutant with a peculiar phenotype was identified; the PVD neuron of the worm looks like wild-type in reproductive development, but in dauer, the PVD neuron develops abnormally. The mutant is still being studied to understand which gene is affected, but it seems there are multiple genetic events governing the phenotype.
Characterization of NF90 as a transcriptional activator with histone acetyl transferase activity
Keywords:  Department of Biology
Biology
NF90
ILF3
histone acetyl transferase
transcription factor
chromatin remodeling
epigenetics
Thesis

Eukaryotic gene expression is tightly controlled on multiple levels. Proteins that bind both DNA and RNA are involved in multilevel gene expression by regulating both transcriptional and posttranscriptional processes. Nuclear Factor 90 (NF90) is a DNA- and RNA-binding protein encoded by the Interleukin enhancer-binding factor 3 (Ilf3) gene first cloned based on inducible binding to the Nuclear Factor of Activated T cell (NF-AT) target DNA sequence in the IL-2 promoter. NF90 has been widely studied as a double-stranded RNA-binding protein that participates in stabilization of transcript, splicing, and export of mRNA. The role of NF90 in regulating gene expression as a DNA-binding transcription factor has not been systematically studied. In Jurkat T cells, chromatin immunoprecipitation (ChIP) demonstrated inducible binding of NF90 and NF45 at the IL2 and Pdcd1 promoters in vivo upon T cell activation. In K562 cells, ChIP followed by deep sequencing (ChIP-seq) was used to characterize genome-wide binding patterns of NF90. Proteomic analysis elucidated stimulation-dependent post-translational modifications in Jurkat T cells. NF90 showed a sequence-specific DNA binding activity to a highly-conserved purine-rich motif in its genome-wide binding sites. NF90 colocalizes with histone marks H3K9ac at active promoters and H3K27ac at enhancers, closely associates with core histones in the nucleus, and exhibits a novel histone acetyl transferase activity. Taken together, these results characterize NF90 as a transcriptional activator with histone acetyl transferase activity.
Characterizing Infrared Filters for Large Aperture Millimeter Wave Telescopes
Keywords:  Department of Physics
Infrared Filtering
BICEP3
Millimeter Waves
Thesis

Ground based telescopes operating in the millimeter wave regime are attempting to image the sky with increasing sensitivity and depth by employing larger arrays of cryogenically cooled detectors. However, the increase in aperture is accompanied by a corresponding increase in the infrared (IR) loading. This poses a significant challenge for the cryogenic system. BICEP3 met this challenge by developing laser etching as a fabrication technique for producing large aperture metal-mesh infrared filters. Because metal-mesh filters are crucial to the heat load balance of the cryogenic system, we conducted a systematic investigation into the quality, repeatability of production and improvement in the yield of filters.
Characterizing the interaction between cell identity and cell-cycle regulation in the stomatal lineage of Arabidopsis
Keywords:  Department of Biology
Biology
Cell Biology
Molecular Biology
Developmental Biology
Genetics
Plant Biology
Thesis

Asymmetric cell division is an important process that can link stem cell development to the cell cycle. Arabidopsis stomatal guard cell development, a model for plant stem cell lineages, requires asymmetric divisions and has been well characterized in terms of the distinct developmental stages and the transcription factors involved with each transition. To date, the effects or linkages of these developmental transitions on the cell cycle have not been defined in this system. Further, the existence and effects on the cell cycle of the putative plant DREAM complex, whose homologues regulate the cell cycle in animals, has not yet been demonstrated. In this thesis, I implemented two different methods of visualizing cell cycle stages in Arabidopsis leaves: a method that monitors nucleotide incorporation during DNA synthesis (EdU staining) and the CDT1A reporter line that marks the S and G2 stages of the cell cycle for live cell visualization. The latter method was used to begin to characterize how cell cycle timing is affected by differentiation or by members of the DREAM complex. Here, I present evidence that the critical transcription factors for stomatal development appear beginning in G1 and persist, likely with activity, through G2, as well as evidence that the DREAM complex is active from G1 through G2. To facilitate quantitative measurements of cell behaviors, I developed tutorials for MorphoGraphX, a software program that can segment and measure cell size, shape, and growth over time and that will be essential for continued studies of cell cycle and fate.
Chemical sensing with capacitive micromachined ultrasonic transducers [electronic resource]
Keywords: Applied Physics.

There is a wide array of potential applications for chemical sensors that are sensitive, but also small and inexpensive. Such sensors could be used for detection of dangerous chemicals, air quality monitoring, or even health monitoring. Gravimetric chemical sensors based on capacitive micromachined ultrasonic transducers (CMUTs) are a good candidate technology for such sensors, given their high sensitivity and low cost due to batch fabrication. In this work, we demonstrate an electronic nose using CMUT chemical sensors. We show that this electronic nose, in conjunction with machine learning algorithms, is able to distinguish between several chemicals, recognize ammonia in a background of water vapor, and distinguish coffee beans of different origin. We discuss the design and fabrication of the chemical sensor chip, the electronic circuits used to operate it, and efforts to reduce the drift of the sensor.
China enchanted [electronic resource] : transformations of knowledge in the enlightenment world
Keywords: History.

This study shows that European scholars gave up on China as a rational model for civilization and came to see it instead as an esoteric alternative, through genuine engagement with indigenous Chinese traditions of history and natural philosophy. Toward the end of the Enlightenment, the philosophes began to criticize the civilization of China because it seemed stuck in the past; other savants came to praise it for the very same reason. For those who challenged the emerging view of progress, China still had much to offer. Like gunpowder, printing, and the compass, other Western knowledge might have also had ancient Chinese antecedents: Had the sage-king Yu the Great known the secrets of modern astronomy? Was the theory of animal magnetism prefigured by yin-yang cosmology? French Scholars looked to Beijing to investigate. There, the ex-Jesuit missionary Joseph-Marie Amiot fostered a global conversation between a French statesman, a Swiss Freemason, a Chinese barber, and a Manchu prince. Together, they searched for Atlantis, discovered kung fu, and invented tarot card fortune-telling. In the process, they cemented the idea of China as a land enchanted. Where early-modern missionaries and scholars had once seen a model of Confucian reason, modern sinologists and philosophers instead saw an alternative of Daoist magic, establishing a new intellectual relationship between China and the West.
Choreographic legacies [electronic resource] : (dis)embodied assemblages of queer and colonial histories
Keywords: Theater and Performance Studies.

As many of the pioneers of American modern dance have passed away in recent years, the dance field has become intensely preoccupied with the issues surrounding the role of choreography in artistic afterlives. While contemporary concern with Legacy plans points to the desire to curate the history of the choreographer through the afterlife of the choreography, popular attention to the marginalization of women and people of color from artistic institutions also points to a contemporary effect of historical assertions of control over dancing bodies. This project focuses on the lowercase legacies; the legacies that have persisted invisibly, subtly shaping the landscape of possibility within performance. Shifting the popular orientation of our contemporary preoccupation with Legacy to include the assemblage of racist, sexist, and homophobic legacies that have contoured the Western canon, I focus on the violent imperial legacies that have become choreographically embedded within dance history. By the very nature of their embeddedness, these legacies circulate prolifically throughout dance history, across the genres of ballet and modern dance, to impact dance production across the globe. My focus on the transmission of these embedded legacies over more than a century of dance history and across three continents also attends to the persistent issue of dance's temporality. The debate surrounding dance's ontological relationship with ephemerality compels a necessary characterization dance not as a performance of disappearance, but of endurance. The shift from Legacies with a capital "L" to the embedded legacies on which this dissertation focuses invites a new consideration of legacy that is dependent on the medium of performance itself. These legacies prove dance's temporal endurance and influence within sociopolitical constructs that uphold the power of the dominant. This analysis of the temporalities of dance performance and afterlife points towards new considerations of dance's transmission and durability.
Chromatin accessibility dynamics during C. elegans development reveal regulatory complexity and identify novel enhancers [electronic resource]
Keywords: Genetics.

Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogenous and simple systems, such as isolated cell populations or early development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, I use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism C. elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. Further, chromatin accessibility measurements near transcription start sites are predictive of steady-state gene expression, and ATAC-seq dynamics are correlated with gene expression changes. Importantly, my analysis of dynamic changes in chromatin accessibility within whole organisms sensitively identified novel cell-type- and temporal-specific enhancers, which I functionally validate in vivo. Furthermore, by integrating transcription factor binding motifs into a machine learning framework, I identify EOR-1 as a potential early regulator of chromatin accessibility changes. My study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.
Circle Tracking Game: Testing Coordination
Keywords:  Department of Communication
Coordination Game
Circle Tracking Game
VRPT
VHIL
Stanford
Communication
Media Studies
Thesis

In an effort to study perspective taking in VR (VRPT) as part of the Virtual Human Interaction Lab, a post treatment questionnaire was conducted which examined Selfishness, Distrust and Coordination in negotiation in the from of games. In the scope of this, we created the Circle Tracking Game, a new game designed to test coordination.
Citizenship Contestation and Reprisal Violence in sub-Saharan Africa
Keywords: International Relations Program
Banyarwanda
citizenship
Zaire
Uganda
Dioula
Côte d'Ivoire
Bamileke
Cameroon
Mauritania
Thesis

Why do governments choose to challenge the citizenship of ethnic minority groups? Why do some of these cases result in violence, but not others? My research shows that governments choose to challenge the citizenship when the exclusion of the group benefits the government's political project regardless of a democratic transition, and that affected groups will react with violence when there is an intersection of a political opening and a lack of credible exit options. I examined multiple case studies of ethnic minority groups bisected by international borders in sub-Saharan Africa: the Banyarwanda in Congo/Zaire, the Banyarwanda in Uganda, the Dioula in Côte d’Ivoire, the Bamileke in Cameroon, and black Africans in Mauritania. I analyzed key historical points of citizenship contestation and extension to understand the variation of event outcomes within these countries.
City of Facebook: How East Palo Alto community leaders struck unprecedented $20 million deal with Facebook
Keywords:  Department of Communication
Stanford University
Journalism
Communication
Thesis

In December 2016, Facebook announced an unprecedented agreement to commit $20 million toward affordable housing in the Bay Area. The work by the community coalition, Envision Transform Build EPA, and Facebook’s decision to bargain with a motley group of activists, reflects a new dynamic among residents, city councils, and Facebook – one in which community members are increasingly demanding services from local companies that city governments fail to provide. Members of ETB say the agreement, the single largest contribution that Facebook has made directly towards housing, marks a shift in how the company regards its role in the Bay Area’s affordability crisis. It also highlights the impressive capacity of this grassroots movement to strike a deal with one of Silicon Valley’s most powerful companies.
Civic Education and Political Empowerment Among South Korean Youth
Keywords: democracy
South Korea
youth
political empowerment
political efficacy
civic education
secondary school
textbooks
close reading
Thesis

South Korea’s democratic consolidation over the past half-century has been accompanied by the proliferation of information related to democratic practices and democracy itself. Scholars of democracy agree that a robust democracy requires well-informed and active citizen participation, and young South Koreans between the ages of 18 and 29 have access to historically unprecedented amounts of information about politics. Yet recent survey has revealed that youth reporting feeling that politics and governance are difficult to understand. Given the sprawling extent of South Korea’s democratic development, why do feelings of being able to understand politics among the nation’s youth remain so low? This investigation turns to civic education in South Korea to answer this question—to understand not only whether students are learning about democracy, but also how democracy is taught in schools. This investigation proceeds in five parts: An introduction to the research question, a discussion of methods employed, a brief history of democratic education on the peninsula, close readings of history and society textbooks at the secondary school level and a discussion of the results emerged from close reading and their implications for the future of South Korean democracy.
Collaborative learning at scale [electronic resource]
Keywords: Management Science and Engineering.

We introduce an online learning platform that scales collaborative learning. We study the impact of team formation and the team formation process in massive open online classes. We observe that learners prefers team members with similar location, age range and education level. We also observe that team members in more successful teams have diverse skill sets. We model the team formation process as a cooperative game and prove the existence of stable team allocations. We propose a polynomial-time algorithm that finds a stable team allocation for a certain class of utility functions. We use this algorithm to recommend teams to learners. We show that team recommendations increase the percentage of learners who finish the class.
Colorful: A Modern Day Epistolary
Keywords: Feminist Gender and Sexuality Studies
Stanford
Black
Gay
Trauma
Queer
Narrative
Thesis

This creative thesis though the Stanford FGSS department is my way of presenting my findings on trauma in the psyche of black-gay males in contemporary America. The novel is a dark-comedy that follows the life of a black-gay teenager during his senior year of high school. The companion essay shows how I imbued my research into the novel.
Combinatorial methods in Markov chain mixing [electronic resource]
Keywords: Mathematics.

This thesis is concerned with various aspects of Markov chain mixing. The general problem is to examine the number of steps of a Markov chain required for the chain to be close to its stationary distribution. Chapter 2 discusses the problem of shuffling a large deck of cards, describing how to implement riffle shuffles using only operations which affect fewer cards at a time. It also gives upper bounds on the mixing times of several related shuffling schemes. Riffle shuffles are usually modelled by the GSR shuffle. Chapter 3 presents the results of several hundred physical riffle shuffles, and compares this data to the predictions of the GSR model. Similar analysis is done for mash shuffles. Chapter 4 describes how the convergence of a Markov chain may be affected by interweaving other operations. It gives examples where these modifications can drastically slow down or speed up convergence, and a conjecture regarding the efficient generation of random partitions. The random transposition walk on the symmetric group is well-understood. Chapter 5 extends the known strong stationary time results regarding this walk to a more general walk where at each step, a larger number of cards are chosen at random and shuffled amongst themselves. Chapter 6 introduces mutation times, a new combinatorial technique similar to the method of strong stationary times. Mutation times can give upper bounds on the mixing times of some Markov chains where strong stationary times may be difficult to construct. This chapter uses mutation times to analyse several models of wash shuffles, as well as some classical random walks on the symmetric group. Chapters 7 and 8 examine the convergence of statistics on Markov chains, rather than the convergence of the chains themselves. Chapter 7 describes how coupling may be used to obtain results about the convergence of statistics, and Chapter 8 uses strong stationary times. Both chapters contain a large number of examples. Finally, Chapter 9 presents a likelihood order for simple random walks on Coxeter groups, showing that the weak Bruhat order describes which elements are more or less likely than others after any number of steps.
Combinatorial signal processing [electronic resource]
Keywords: Electrical Engineering.

We study the problem of interpolating all values of a discrete signal f of length N when d< N values are known, especially in the case when the Fourier transform of the signal is zero outside some prescribed index set J; these comprise the (generalized) bandlimited spaces B^J. The sampling pattern for f is specified by an index set I, and is said to be a universal sampling set if samples in the locations I can be used to interpolate signals from B^J for any J. When N is a prime power we give several characterizations of universal sampling sets, some structure theorems for such sets, an algorithm for their construction, and a formula that counts them. There are also natural applications to additive uncertainty principles. Universal sets are related to the invertible, but possibly poorly conditioned submatrices of a discrete Fourier transform matrix. At the other extreme, we study the problem of finding unitary submatrices of the discrete Fourier transform matrix. This problem is related to a diverse set of questions on idempotents on Z_N, tiling Z_N, difference graphs and maximal cliques. Each of these is related to the problem of interpolating a discrete bandlimited signal using an orthogonal basis.
Communication and computation [electronic resource] : new questions about compositionality
Keywords: Philosophy.

The topic of this dissertation is the famous principle of compositionality, stating that the meanings of complex expressions are determined by the meanings of their parts and how the parts are put together. The title belies its intent: rather than advanc- ing a central thesis, it instead asks and provides answers to new questions about compositionality. In particular, these questions arise by shifting from viewing com- positionality as a property of symbolic systems -- where what I call 'status questions' are naturally discussed -- to viewing it from a procedural perspective, as operative in processes of production and interpretation. The questions the dissertation asks arise at successively narrower levels of scale. At the level of our species, I ask: why are natural languages compositional in the first place? At the level of small conversations: what role does compositionality play in the broader theory of communication? And at the level of an individual language speaker: what is the algorithmic interpretation of compositionality and what demands on complexity does it impose? In the pursuit of answers to these questions, a wide variety of methods are employed, from simulations of signaling games, to logic and formal semantics, to theoretical computer science, as appropriately called for.