VictorJuiz/thesis huggingface dataset:
Advancing multidimensional chemical mapping of RNA structure through next-generation sequencing [electronic resource]
Keywords: Biochemistry.

RNAs are an essential and versatile category of biopolymers, fulfilling roles from relaying genetic information to catalysis to regulation of gene expression. The formation of and interconversion between conformational states is crucial to the biological functions of RNAs. Chemical mapping methods have proven valuable in providing solution-state, per-nucleotide structural information for RNAs, and computational prediction methods, which can incorporate chemical mapping data, have permitted modeling of both secondary and tertiary RNA structures. However, certain techniques have faced limitations: high-confidence secondary structure prediction through '2D' chemical mapping of systematic mutants (mutate-and-map, M2) is limited by RNA size, and tertiary structure inference through analysis of spatially localized hydroxyl radicals (multiplexed •OH cleavage analysis with gel electrophoresis, MOHCA-gel) is limited by imprecise readouts of proximal residue pairs. Next-generation sequencing (NGS) has greatly enhanced the throughput of chemical mapping, allowing for estimation of chemical reactivities for viral genomes and cellular transcriptomes, but has not yet been leveraged to alleviate the limitations on M2 and MOHCA. In this dissertation, I present the application of NGS readouts to advance a multidimensional chemical mapping (MCM) pipeline for probing and modeling RNA secondary and tertiary structure. First, I demonstrate that a sequencing-based MOHCA-seq method allows for precise detection of tertiary proximities throughout target non-coding RNA (ncRNA) domains. Using constraints from MOHCA-seq data improves Rosetta modeling with experimentally inferred secondary structures to 1-nm accuracy, which allows both visualization of complex ncRNA states, such as the ligand-free states of cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers, and blind structure predictions of a 188-nt lariat capping ribozyme and a Hox internal ribosome entry site domain. Second, I apply MCM to a bioengineered, directionally switchable RNA-protein motor and demonstrate that it is able to detect distinct sets of tertiary proximities in alternative conformations of a multistate RNA system. Finally, I show that the length and throughput limits of M2 can be overcome by deriving 2D data from high-modification mutational profiling experiments, which permit readout of multiple modifications in single RNA molecules, and explore the basis of the 2D signal. These results improve the applicability and usability of the MCM pipeline and enable structural characterization of previously intractable RNAs.
Advertiser Retaliation Against Media: Evidence from South Korea
Keywords:  Department of Economics
Stanford Department of Economics
Thesis

In this paper, I present evidence on financial retaliation by advertisers in the newspaper market in South Korea. Specifically, I study whether the coverage of negative news stories about the advertisers affects their advertising expenditure. I obtained data on daily advertising spending by the top 50 advertisers in South Korea, as of 2007, across seven national newspapers during the period 2007-2011 I also retrieved daily newspaper coverage of negative news about those top 50 advertisers for the same seven national newspapers during that period. I then performed a difference in differences analysis comparing advertising spending before and after the negative news was published, and between media outlets responsible for breaking negative news and the rest to see an average differential effect. I also interacted the difference in differences model with the date variable to observe the acute effect of publishing negative news about advertisers on ads amount. In order to identify each negative story, I manually selected events that attracted nationwide interest. Then, I separated outlets responsible for breaking news from those that did not, based on both quantitative and qualitative measures.
Aggressive terrain following for motion-constrained vehicles in uncertain environments [electronic resource]
Keywords: Aeronautics and Astronautics.

Scientific missions requiring underwater imagery or sample collection have often used highly maneuverable, remotely operated vehicles in order to operate close to the terrain. However, these vehicles come with limited operational range and high cost of operation. Long-range autonomous underwater vehicles (AUVs) can provide access to remote, potentially dangerous sites at a greatly reduced operational cost, but come with the added challenges of limited maneuverability and onboard computation. Recent advances in Terrain-Relative Navigation allow for high-precision map-relative localization. This in turn enables the use of prior map information for path planning purposes. This thesis presents a new approach for planning aggressive terrain-following trajectories that can provide improved imaging coverage while keeping the vehicle safe in an uncertain environment. Two methods are implemented for planning trajectories, incorporating constraints to both satisfy the dynamics of the vehicle and to maintain a safe minimum standoff distance in an uncertain environment. The first, using Model Predictive Control, allows for direct application of known vehicle dynamics, but does not provide real-time performance. The second, using geometric spline-based trajectories, must approximate the dynamics of the vehicle, but can provide trajectories to the vehicle in real time. This allows current measurements of the terrain to be combined with prior map information to provide the most up-to-date terrain information. This thesis also introduces a design tool utilizing the trajectory planning approach that can be used by vehicle designers to understand the terrain imaging capabilities of a particular vehicle configuration. Results of trajectories planned over regions of Monterey Bay are presented, and preliminary field trial results are shown for the vehicle tracking commanded trajectories. The design tool is demonstrated for challenging terrain in Monterey Bay evaluating the performance of the current vehicle and providing direction for the work required to perform imaging missions using the current vehicle.
Air entrainment and micro-bubble generation by turbulent breaking waves [electronic resource]
Keywords: Mechanical Engineering.

Bubble generation and air entrainment on ocean surfaces and behind ships are complex phenomena which usually accompany turbulent flows. Non-linear wave-breaking events entrain air and generate turbulence. Turbulence consequently fragments the entrained air into smaller bubbles. This process drastically increases the flux of air into the oceans and rivers, which is important for both aerating the water bodies and reducing greenhouse gases from the atmosphere. Wave breaking and bubble generation behind ships also have important effects on the hydrodynamics of ships and on their performance. The bubbly flow as a result of ship passage generates ship trails which remain for several minutes thereafter. Although turbulence is responsible for the fragmentation of larger bubbles into smaller ones, it cannot be the cause of the generation of micron-size bubbles. These bubbles are observed in ship wakes and natural waves and are associated with liquid-liquid impact events. These phenomena, due to their complexity, are far from being completely understood. In addition, there is missing quantitative connection between the large-scale non-linear wave-breaking events and the micron-size bubble generation as a result of impact events. There is a large-scale separation between these two phenomena which makes elucidation of the problem very challenging. The aim of this study is to use direct numerical simulations of turbulent hydraulic jumps as canonical representation of non-linear breaking waves, to study the air entrainment and large bubble generation. Furthermore, this study provides statistics of liquid-liquid impact events, which are precursors to micro-bubble generation in these flows. As far as we know, the present work is the first direct numerical simulation of turbulent hydraulic jumps, as well as the first attempt to obtain interface impact statistics in a stationary turbulent breaking wave. In addition to bubble generation, we investigate turbulence statistics such as mean and turbulent velocity fluctuations, Reynolds stress tensors, turbulence production terms, energy spectra and one-dimensional energy budget of the flow. Finally, we present investigation of the effect of relevant non-dimensional parameters such as Weber number and Reynolds number on both large bubbles and impact statistics in these flows.
Algorithms for accurate and sensitive interpretation of mass spectra against arbitrarily large peptide search spaces [electronic resource]
Keywords: Chemical and Systems Biology.

Tandem mass spectrometry (MS/MS) enables the high-throughput identification and characterization of complex protein mixtures, and depends critically on bioinformatics tools to interpret mass spectra as peptide sequences. There exist two general techniques for the interpretation of mass spectra: de novo sequencing and database search. In de novo sequencing, a mass spectrum is directly interpreted as a protein sequence. In database search, a mass spectrum is identified from its best match in an existing sequence or spectrum database. Though more unbiased and less restrictive than database search algorithms, de novo sequencing algorithms are less popular due to their relatively lower accuracy and lack of automated statistical validation tools. However, database search algorithms suffer greatly in both speed and sensitivity as database search spaces increase through the addition of protein sequences and post-translational modifications. To able to apply MS/MS to more diverse systems, I developed the de novo sequencing algorithm Label Assisted De novo Sequencing (LADS). LADS utilizes chemical strategies to bolster introduce signatures into mass spectra which improve sequencing accuracy, and employs a support vector machine-based model to discriminate true from false identifications. I also developed a method by which to empirically estimate false discovery rates (FDRs) from any de novo sequencing algorithm. In the last stage of my PhD, I developed TagGraph, an unrestricted database search tool able to match peptides to mass spectra from sequence databases without assuming any protease specificity or requiring a user-specified set of modifications. I demonstrate the utility of TagGraph on the recently published human proteome dataset, matching over four million spectra to modified peptides, and identifying new functional roles and disease associations for protein hydroxylation. Both TagGraph and the de novo FDR calibration technology described herein have the potential to greatly extend the scope and depth of tandem MS analyses.
Algorithms for analyzing third generation sequencing data [electronic resource]
Keywords: Electrical Engineering.

Sequencing technologies have been evolved since the first human genome was released in 2003. First generation sequencing emerged in the mid-1970s, generating reads with high accuracy. In the mid-2000s, second generation sequencing was commercially available with higher throughput and lower cost per base. In recent years, the third generation sequencing technologies can generate reads of multi-ten kilobases long, though with a relatively lower accuracy. These current unique characteristics of third generation sequencing data, longer sequences and higher error rate, have required development of new algorithms and tools to efficiently process data. In this thesis, we present two methods in analyzing third generation sequencing reads. The first method (COSINE) is a conceptually novel technique for mapping long DNA sequences with high error rates. As a proof-of-concept, COSINE is applied to both simulated and real datasets where it achieves high sensitivity and specificity in wide range of read accuracies with minimal tuning. The second method (IDP-fusion) is a new approach to accurately characterize fusion genes using hybrid RNA sequencing. As a proof-of-concept, IDP-fusion is applied to PacBio and Illumina real datasets from the MCF-7 cell line, where it achieves higher sensitivity and specificity compared to existing tools. The results also show that IDP-fusion could resolve multiple fusion splices and fusion isoforms within tumorigenesis-relevant fusion genes.
"Alle Wege der Welt" [electronic resource] : wandering in early 20th century German/Jewish opera
Keywords: German Studies.

This project traces the 20th century operatic afterlife of two intertwined 19th century wandering figures—the heroic, Romantic, German Wanderer and the cursed, undying Wandering Jew. After World War I, the subsequent depression, and the rise of the Nazi party made anti-Semitism increasingly prevalent, the previously intertwined figures of Romantic Wanderer and Wandering Jew separated in terms of their cultural representation. The four operas I consider, created by German-speaking Jewish artists in 1912, 1920, 1933, and 1937 respectively, chart this process of anti-assimilation and encompass a wide variety of themes: prostitution as a feminized form of wandering, Freudian-inflected undead walkers in the aftermath of the first world war, the wanderer as political poet whose movement inscribes the state of Israel, and wartime exiles attempting to defer the inevitability of death by wandering eternally. A complementary goal is to consider the nature of wandering forms, delving deeply into the meaning of wandering as an aesthetic metaphor in a variety of genres: in theater, music, or literature, what does it mean to be a wandering text? How do theatrical works engaging with the theme of wandering reimagine the nature of the wandering subject? How does wandering create theatrical, political, or musical spaces? In my examination of Franz Schreker's Der Ferne Klang, Erich Wolfgang Korngold's Die Tote Stadt, Arnold Schoenberg's Moses und Aron and Kurt Weill's The Eternal Road, I develop the following claims about the relationship between wandering, space, and form: 1) Operatic wandering is about traversing space and non-space. 2) The proliferation, superfluity, and superimposition of spaces in these texts makes possible a theorization of movement in which spaces wander around characters rather than vice versa. 3) These spatial formations and deformations point towards a definition of wandering that is discursively multiple. 4) Wandering in these operas is not a digression away from the point; wandering is the point.
Alleviating the variability and communication overheads of irregular parallelism for many-core chips [electronic resource]
Keywords: Electrical Engineering.

Technology trends and architectural developments continue to enable an increase in the number of cores available on multicore chips. Certain types of applications easily take advantage of increased concurrency; but there are important application domains that struggle to do so. Such irregular applications, often related to sparse datasets or graph processing, have time-variable, hard-to-predict parallelism. They tend to resist static parallelization, requiring instead dynamic load-balancing layers. These task-management layers by necessity rely more strongly on communication and synchronization than regular applications do, a problem that is only accentuated by increasing on-chip communication delays. As core counts reach into the hundreds, more careful handling of this synchronization becomes necessary to avoid bottlenecks and load imbalances. We explore solutions to these issues in two dimensions: On the software front, we design a task-stealing runtime layer for irregular parallel applications on hundred-core chips. By setting up fast and efficient ways to share information, the runtime is able to embrace the varying relationship between available parallelism and core count, adapting dynamically to both abundance and scarcity of work. When tested with representative sparse-data and graph-processing applications on 128 cores, runtime overhead is reduced by 60%, simultaneously achieving 15% faster execution and 29% lower system utilization. This is done without hardware assistance, unlike prior solutions. On the hardware front, we address the 'latency multiplying'' effects of relying on coherent caches for inter-core communication and synchronization. Our proposed techniques enable efficient implementation of synchronization and data-sharing by reducing the number and complexity of cache-coherence transactions required. Using ISA hints to express preferred placement of both data access and atomic operations, faster and more efficient communication patterns can result. Our solution is compatible with existing architectures, requires only minimal code changes, and presents few practical implementation barriers. We show experimentally on 128 cores that these tools yield many-fold speedups to benchmarks and cut the optimized task-stealing runtime's remaining overhead, for a 70% speedup to runtime stealing and 18% to actual applications, along with increased energy efficiency. The overall result is to significantly improve the viability of irregular parallelism on many-core chips. We minimize waste and enable faster on-chip communication, by implementing smarter, more context-aware software task management, and by enabling more efficient communication patterns at the cache coherence level.
Amerikanischer Malkasten [electronic resource] : American art and Düsseldorf
Keywords: Art and Art History.

This dissertation examines the group of American painters who lived and worked in Düsseldorf, Germany, in the decades before the American Civil War. By emphasizing that such important works of art as Emanuel Leutze's "Washington Crossing the Delaware, " Richard Caton Woodville's "War News From Mexico, " and Albert Bierstadt's "Roman Fish Market, Arch of Octavius" were all produced in this small city on the Rhine, "Amerikanischer Malkasten" seeks to reframe the historiography of American art before the Civil War by arguing that the American experience in Düsseldorf was not marginal or incidental to that story, but rather essential to it. In recent years Americanists have rejected or refined narratives of American art that assert its isolated, nationalistic character in favor of ones that see American art as deeply engaged with the wider world. However, the American Civil War remains something of a dividing line for many scholars, who view the generation of artists who came to maturity in the 1840s and 1850s as essentially provincial in character, by contrast with later generations of cosmopolitans. Through in-depth case studies of Leutze, Woodville, and Bierstadt, this dissertation upends this tradition periodization in two ways. First, it shows how these individual artists engaged with a wide variety of transatlantic thought, including theatrical meolodrama; the interrelated discourses of "Bildung" and Self-Culture; and the marketing o the Wild West, in particular its American Indian inhabitants. Second, and most importantly, it articulates a vision of American art before the Civil War that emphasizes not only its cosmopolitanism, but also the ways in which these and other artists were possessed of an essentially outward-facing and communal ethos, which I contrast with the more idiosyncratic and personal vision favored by later generations. Ultimately, "Amerikanischer Malkasten" redefines both the history of American art of the antebellum period and how historians of American art conceive of--and speakabout--that history.
An Infrastructural Study of Embeddedness in XXI Century Economies: Personal Networks, Formality, and Informality in Mexico’s Uber X Online-Labor Market
Keywords: social embeddedness
Science Technology and Society
Stanford University
economic sociology
online economies
online labor markets
intermediation
ride-sharing
Uber
informality
development
Mexico
Thesis

The following research study is an empirical examination of the nature and infrastructure of the economic activities carried out in the Online ‘Gig’ Economy (OGE). More specifically, this thesis investigates, through the case study of one singular instance of the OGE (the Uber X market in the city of Guadalajara, Mexico), the role of structures of social relations and institutionalized formal processes with respect to the organization, regulation, transacting, and broader functioning of the OGE. We study these structures and processes through three concrete methods: (1) a series of 15 in-person semi-structured interviews with Uber X drivers and partners in Guadalajara; (2) an online survey distributed through online social networks to a larger pool of Uber X drivers and partners in Guadalajara and (3) the collection (and regression) of data on Uber’s business models and on the economic and social conditions of the countries in which these business models appear. We find: (1) that the operation of the OGE relies on a complexly intertwined dancing around of formality and informality, (2) that the elements of informality in the OGE enhance its social embeddedness, (3) that ‘informal’ workarounds may, paradoxically, have both positive and negative impacts on the formal systems which they underlie, and (4) that on the global scale of Uber’s operations, specific economic and social macro-level affordances correlate with the appearance of informality. We conclude that depending on the context in which it emerges, informality has the potential to impact development both positively and negatively and that its development and impact are closely associated with the affordances and characteristics of structures of social relations.
An Investigation of the use of cQED Systems for Quantum Simulation
Keywords:  Department of Physics
cQED
cMPS
quantum simulation
Thesis

We examine the use of continuous matrix product states (cMPS) as a varia- tional class for estimating properties of the ground state of 1-D quantum fields. In particular, we explore the use of submanifolds of cMPS parametrized by cavity quantum electrodynamic (cQED) systems to perform these variational calculations. Variations over the cQED generated classes could be performed experimentally, and thus provide a means to do quantum simulation - using one quantum system to simulate another. We give a derivation of the cMPS class and describe the correspondence between the cMPS class and cQED systems. Then we perform a variational calculation to find the ground state of the Lieb- Liniger Hamiltonian for several ansatzes from the cMPS and cQED classes. We provide numerical evidence that the correlation functions computed from the cMPS variation are approximately correct. This suggests that the varia- tion over the cMPS class is actually approximating the field ground state and not just approximating the ground state energy. We further compare cQED ansatz-derived energies and correlation functions to those computed from the cMPS ansatz. Our findings suggest that cQED systems can approximate the short range behavior of Lieb-Liniger ground state correlation functions pro- vided they have enough internal degrees of freedom. The simple examples of cQED systems we examine here, however, fail to capture the asymptotic behavior of the correlation functions. In particular, they exhibit too much long range phase coherence and do not exhibit Friedel oscillations. This raises the question of what controls correlation function asymptotics in the cMPS formalism.