VictorJuiz/thesis huggingface dataset:
Collaborative musicking on the web [electronic resource]
Keywords: Music.

The Web has evolved far beyond its original function as the vehicle of information sharing through hypertext, but the spirit of collaboration remains central to the Web. With the arrival of HTML5 and new browsers capable of streaming audio and complex graphics, new and unprecedented opportunities have arisen. The advent of Web Audio API in 2010 took real-time audio processing within web browser to a new level, giving birth to a new breed of interactive, visually rich, and networked music software. This thesis investigates the potential of web music technology within the context of collaborative musicking. I adopt the verb `musicking', coined by the late Christopher Small, in the title, to underscore the nature of music as an active process rather than a static object. The dissertation commences with a concise review of the intersections and convergence of the Web and music technology. Following this historical review of web music technology, a theoretical framework is proposed. The subsequent chapters describe technical efforts to implement this theoretical basis and empirical experimentation through a series of `case studies'. We conclude with a critical evaluation of the work and a look toward the future. The work offers a novel model for classification of collaborative computer music production (Chapter 2), and an innovative software framework that facilitates the development of web-based music applications (Chapter 3) that are illustrated in case studies (Chapter 4). Unlike many written dissertations, this thesis documents a living and organic project that is best studied directly engaging with the environment described within. The reader is encouraged to pursue the thesis while directly interacting with this project on the Web. All code examples and operational prototypes discussed in the text are available at \url{https://ccrma.stanford.edu/~hongchan/WAAX} keeping in mind that the very nature of this project is one that enables and encourages collaborative creativity - indeed, `musicking' - on an unprecedented massive scale.
Combined thermal protection and thermal propulsion for aerogravity assist missions [electronic resource]
Keywords: Aeronautics and Astronautics.

The gravity assist maneuver is a way for spacecraft to gain or lose speed without expending any propellant. This technique is an extremely important and commonly used tool in the mission planner's toolbox, and enables some missions that would be impractical to do purely propulsively. Aerogravity assist is an enhanced version of the gravity assist that uses aerodynamic lift in addition to gravity to further increase the momentum exchanged in these maneuvers. It shows significant possible benefits in reducing mission time of flight, lengthening launch windows, and reducing the size (and therefore cost) of launch vehicle required. However, atmospheric flight at interplanetary speeds poses major obstacles, with aerothermal heating and drag loss being two of the most prominent. In the aerogravity assist literature, heating is usually addressed by limiting flight speed to allow use of a radiatively cooled leading edge. Drag loss is addressed by optimizing the vehicle's aerodynamic shape (usually by using a waverider configuration, which is a class of aerodynamic shapes specially designed for hypersonic flight). Both flight speed limitations and achievable waverider lift to drag ratios are important constraints on aerogravity assist. The thermal aerogravity assist concept introduced in this dissertation addresses both problems with a single combined system that turns the heating problem into a solution for the drag loss problem. An active cooling system with a flowing coolant is used to absorb the heat produced by atmospheric entry, allowing the vehicle to withstand higher heat fluxes and permitting faster flight speeds. The heated coolant is then re-used in a thermal propulsion system that makes up for drag losses. The first part of this work is a feasibility study of this thermal aerogravity assist concept, and ends with an example design for a mission to match Voyager 1's solar system escape velocity with a much larger spacecraft (3200 kg compared to Voyager 1's 930 kg) while still using the same launch vehicle. This is intended to illustrate the possibilities of the concept and provide a starting point for future analyses. The second part discusses the design, fabrication, and testing in a miniature arcjet facility of a new kind of actively cooled leading edge that was inspired by the particular demands of thermal aerogravity assist. This leading edge cooling concept takes advantage of the unique thermal properties of highly oriented pyrolytic graphite (HOPG) and the exceptional heat removal capabilities of jet impingement cooling. Both thermal aerogravity assist and the HOPG leading edge concept are novel contributions to the field.
Combining uncertainty and sensitivity using multi-fidelity probabilistic aerodynamic databases for aircraft maneuvers [electronic resource]
Keywords: Aeronautics and Astronautics.

Balancing cost and accuracy is a fundamental trade throughout the engineering design process. More accurate results typically take more time or resources to generate. To most efficiently use the resources available, it is critical to understand where the increased accuracy is needed. This thesis covers two major areas of research: developing a framework to quantify the uncertainty over the domain of interest and calculating the sensitivity of some defined performance metric to that uncertainty. Probabilistic aerodynamic databases are functions that store a distribution of possible aerodynamic coefficients over the entire flight envelope. Built with Gaussian processes, an additive correction hierarchical model is applied to combine multiple fidelity levels. Each of these fidelity levels has a subject matter expert (SME) provided error term assigned to each individual sample. Deterministic instances of the database respecting physics and SME uncertainties are created through Monte Carlo sampling to provide inputs to currently used industry analysis tools. By repeatedly running the trajectory analysis with different samples, distributions of the performance metrics are created. In the event these distributions of potential solutions exhibit too large an uncertainty on the quantity of interest, an adjoint-based sensitivity method was developed to guide further analyses. Extended from optimal control theory, sensitivities of the objective function with respect to each aerodynamic coefficient at each time step in the trajectory can be calculated for approximately the same cost as solving the forward trajectory problem. Multiple indicator functions combining the uncertainty and sensitivity were proposed. On a cannon ball example where the drag coefficient was uncertain, these different indicator functions were compared to an exhaustive search of adding a single analysis at each point in the domain. The best performing indicator was then applied to the National Aeronautics and Space Administration (NASA) Common Research Model (CRM). Both the cannon ball and NASA CRM were studied through an adaptive sampling methodology. The cannon ball adaptive sampling, guided by the uncertainty-sensitivity indicator functions, was three-to-four times better than uncertainty-only indicators and one-to-two orders of magnitude better than not adaptive sampling when maximizing accuracy for a fixed cost. When minimizing cost for a tolerable accuracy requirement, the uncertainty-sensitivity adaptive sampling reduced the cost by a factor of two compared to the uncertainty-only sampling. In the CRM case, only one indicator was used. Using 10 percent of the computation budget, a 50 percent increase in accuracy was seen compared to sampling over the entire maneuver domain.
Combining VEGF Inhibition with Oral Metformin Therapy in a Mouse Model of Type 2 Diabetes
Keywords:  Department of Biology
Biology
Metformin
VEGF Inhibitor
Type 2 Diabetes
Aflibercept
Thesis

According to the World Health Organization, more than 300 million people worldwide suffer from type 2 diabetes. Recent studies have demonstrated a previously unsuspected crosstalk between endothelial cells and hepatocytes where Vascular Endothelial Growth Factor (VEGF) maintains the liver vascular network and suppresses hepatic insulin signaling. Conversely, pharmacologic VEGF inhibitors regress the liver sinusoidal vessels, induce relative hypoxia, and increase hepatic insulin signaling through Hypoxia-Inducible Factor (HIF) induction of the insulin receptor adaptor protein IRS2 and suppression of gluconeogenic genes. Here, we explore whether VEGF inhibitors, which potentiate insulin signaling, can be combined with the first-line type 2 diabetes drug metformin, which acts in an insulin-independent manner, to achieve additive or synergistic reductions in blood glucose levels in diabetic db/db mice. Mice treated with combination therapy exhibited improved glucose tolerance in the peripheral blood compared to either single treatment. Moreover, a low dose of the VEGF inhibitor aflibercept was sufficient to induce hepatic vascular regression and to elicit additive improvements in hyperglycemia and glucose tolerance when administered together with oral metformin therapy. However, qRT-PCR analyses of whole liver lysates indicated only mild additive effects at the level of gluconeogenic gene expression; thus, additional mechanisms must contribute to the combinatorial phenotype. These studies suggest that, when given in the context of metformin and at low dosage, VEGF inhibitors may provide a clinically attractive strategy to reduce the pathologically high blood glucose levels seen in type 2 diabetes. This result could be of particular benefit to patients with refractory type 2 diabetes in which metformin is not sufficient for glycemic control.
Compact envelopes [electronic resource] : an efficient and provably safe approach to air and space traffic integration
Keywords: Aeronautics and Astronautics.

Traditional methods for safely integrating space launch and reentry traffic into the National Airspace System use hazard areas (e.g. Special Use Airspaces, Temporary Flight Restrictions, etc.) that restrict aircraft from larger areas, for longer times, than necessary. This can result in significant disruptions to air traffic through increased fuel burn, flight time, and flight delays. This thesis proposes a new class of hazard area that we have named compact envelopes and that guarantees a quantifiable level of risk while dramatically reducing the disruption to commercial air traffic. These compact envelopes are dynamic in time, are described by contours as a function of altitude, and can be constructed for any launch or re-entry vehicle, for both orbital and sub-orbital operations. The generation of these compact envelopes incorporates a probabilistic risk analysis of off-nominal vehicle operations and leverages expected improvements in air traffic management procedures from NextGen; one key assumption is that airborne aircraft can safely react to any off-nominal event given sufficient advance warning. A probabilistic analysis of the disruption to the NAS caused by traditional hazard areas and compact envelopes during space vehicle operations is presented. Quantities of interest include increased flight time, fuel burn, and total distance flown for aircraft that must be rerouted around these hazard areas. The use of compact envelopes for ensuring aircraft safety is shown to produce a near-complete elimination of airspace disruption on average and a dramatic reduction in the worst-case disruptions compared to traditional hazard area methods. It must be noted that the practical implementation of the compact envelope idea only requires improvements to our air traffic control infrastructure envisioned to be part of NextGen by the year 2020.
Competing in intermediated markets [electronic resource]
Keywords: Management Science and Engineering.

How do low-power actors compete in intermediated markets? Prior research on intermediated markets has often taken the perspective of powerful intermediaries. In this dissertation, I take the perspective of low-power actors and examine how they compete. Three distinct papers constitute the core of this cumulative dissertation. In the first paper, a conceptual analysis, I examine how complementors manage their dependence on platform owners in platform-based markets. In the second paper, I examine how sellers resolve the "big fish, big pond" dilemma in their choice of intermediaries. In the third paper, I conduct an empirical analysis of how competition in the intermediary portfolio affects the success of employees' intra- and entrepreneurial activities. Taken together, I examine the antecedents and consequences of the strategies that low-powered actors can use to compete in intermediated markets.
Competition and the use of discretion in financial reporting [electronic resource]
Keywords: Business.

The purpose of this dissertation is to explore the use of discretion in financial reporting when firms are faced with an increase in the threat of competition. I use state-level changes in branching regulation under the Interstate Banking and Branching Efficiency Act (IBBEA) of 1994 to obtain variation in the threat of competition. Regulation was passed by the state legislature or announced in the press one to two years before it became effective, allowing for separation of the threat of competition from an actual increase in competition. Findings suggest that banks increase their loss provisions and appear less profitable under the threat of competition. Additional tests indicate that both managers' and regulators' use of discretion in financial reporting may be driving the results. Survey based evidence supports the premise that banks prefer to locate in markets where incumbents have high profitability and low credit losses, and that banks use competitors' financial statements in analyzing their competition.
Complex adaptation in subdivided populations [electronic resource]
Keywords: Biology.

Adaptations that give rise to new biological functions are often complex, emerging through the interaction of multiple mutations. A complex adaptation may require a set of mutations that are beneficial only in combination. To adapt, a lineage must acquire mutations that are individually neutral or deleterious before gaining the beneficial combination, thereby crossing a plateau or valley, respectively, in the mapping from genotype to fitness. This thesis explores how spatial population structure affects the rate at which populations adapt across fitness valleys and plateaus through the analysis of theoretical models of populations that are subdivided into discrete subpopulations linked by migration.
Complex Genomic Patterns Characterize Variants in Transcription Factor Binding Associated with Gene Expression
Keywords:  Department of Computer Science
computer science
computational biology
machine learning
genetics
genomics
gene expression
transcription factor
Thesis

Although allele-specific transcription factor (TF) binding has been identified at a large number of human genetic variants, known as TF binding quantitative trait loci (bQTLs), very few bQTLs are also linked to detectable changes in gene expression. Classifying the bQTLs that are also gene expression QTLs (eQTLs) is a challenging problem with the potential to illuminate broad patterns underlying TF involvement in gene regulation and the implications for downstream phenotype. We were able to use a machine learning classifier to predict bQTLs that are also eQTLs with high performance using a relatively small number of functional genomics features. We show that linear and three-dimensional proximity between a bQTL and its target gene are most indicative of an association with expression, followed by complex interactions involving genomic structure, multiple TFs, and epigenetic modification, while also showing that bQTLs can mediate gene co-expression and long-range effects on transcription. Our results suggest that bQTLs are marked by diverse yet consistent genomic signatures that elicit future inquiry into the broader regulatory and functional significance of TFs.
Compliance and fragmentation [electronic resource] : who pays for public goods in China
Keywords: Political Science.

When a government does not strictly enforce its policies, there will likely be non-compliers. What explains why some agencies and citizens comply with the state more than others? This dissertation explores the variation in compliance with public goods contribution targets in China. Although the Chinese regime is relatively capable of eliciting local contribution for public works projects, it rarely coerces compliance on a big scale due to concerns over political stability. Instead, it mostly relies on giving selective incentives, such as cutting funding and policy privileges for a few laggards. In this institutional context, theories of cooperation that emphasize the free-rider problem cannot explain compliance, because the temptation to free-ride on public goods is not sufficient for a subject to defect when the state may punish laggards. To understand compliance with public goods contribution targets in China, I present a theory of quasi-voluntary compliance: the subjects comply with the state to avoid the risks of losing resources from the state in the future; and the subjects will only offer as much contribution as their peers do to avoid punishment. This theory explains why both compliance and noncompliance could be contingent behaviors. It also implies that the state may encounter a problem of coordinated inaction—it cannot effectively use the threat of punishment to induce cooperation in a community where the majority of the members have reached a low-cooperation equilibrium. In addition, I argue that coordinated inaction is harder to sustain in fragmented bureaucratic systems or social communities, because the subjects in fragmented networks have more difficulties in predicting the strategies of their peers. This argument is in contrast with the "fragmented authoritarianism" model and social solidarity theories for explaining compliance in Chinese bureaucratic systems and rural villages. This dissertation offers two empirical tests of the relationship between organizational fragmentation and quasi-voluntary compliance. First, I use water infrastructure provision records to compare compliance from agencies in centralized and fragmented bureaucratic systems. Second, I use water tax records to compare compliance from rural households in single and multi-lineage villages. Empirical results show higher compliance for subjects in fragmented bureaucratic or social organizations. This study thus provides a cautionary tale regarding reforms that favor more centralized bureaucratic control or more small-scale social solidarity.
Composition and mechanics of the Gram-positive bacterial cell wall and implications for cell division [electronic resource]
Keywords: Chemistry.

Most bacteria are under significant turgor pressure and surround themselves with cell walls to withstand it. This thesis mainly explores the mechanisms by which bacteria grow and divide their cell wall in the context of turgor pressure. I first discuss the plasticity and robustness of cell wall synthesis in Chapter 2 by describing the finding that the Gram-positive pathogen Staphylococcus aureus changes its cell wall composition in response to nutrient conditions. In Chapter 3, I present a collaborative study in which we characterized the cell cycle of S. aureus at single cell level and discovered a novel mechanical mechanism of daughter cell separation by which the coccoid shaped S. aureus is able to harness its turgor pressure to drive ultrafast daughter cell separation. In Chapter 4, I explore the mechanisms of daughter cell separation in a variety of bacterial species and describe the surprising observation that the fast mechanical daughter cell separation is unique to the Staphylococcaceae family in Firmicutes yet widespread in the other Gram-positive phyla Actinobacteria. In Chapter 5, I characterize the growth and division of the cell envelope in Corynebacterium and Mycobacterium, both of which polar-growing Gram-positive rods with an "outer-membrane like" mycomembrane. Finally in Chapter 6, I discuss our efforts in dissecting the roles of cell wall hydrolases in the mechanical daughter cell separation in S. aureus.
Comprehensive image and transcriptomic analysis of circulating tumor cells [electronic resource]
Keywords: Electrical Engineering.

The presence of circulating tumor cells (CTCs) in the blood of metastatic cancer patients can be an indicator of poor prognosis and survival. However, CTC detection assays that enable non-invasive "liquid biopsy" are generally limited by the lack of high-throughput, high-efficiency enrichment of CTCs from whole blood and rapid, accurate enumeration of the collected CTCs. Moreover, molecular analysis of single CTCs, which may recapitulate primary and metastatic tumor biology, remains challenging because current platforms have limited throughput, are expensive, and are not easily translatable to the clinic. This doctoral dissertation describes research work that aims to address these challenges by enabling a comprehensive image and transcriptomic analysis of CTCs from cancer patients. Image analysis of CTCs by immunocytochemistry comprises the immunofluorescent staining of CTCs followed by image analysis to identify CTCs. After CTCs were immunomagnetically enriched from whole blood samples by MagSifter and immunofluorescently stained, fluorescence microscope images of CTCs were then acquired on prepared cytospin slides. To achieve automated image cytometry of CTCs, CTC candidate images were first identified using an automated cell image segmentation method. Subsequently, a Random Forest machine learning algorithm was developed to classify each CTC candidate image as positive or negative, based on parameters such as size, shape, and fluorescence intensities in different channels. This approach was applied to identify and enumerate CTCs enriched from non-small cell lung cancer (NSCLC) patients' blood samples with high correlation to pathological assessment. This approach for automated image cytometry has demonstrated high-throughput CTC identification with excellent accuracy and reproducibility. For downstream molecular analysis of CTCs at the single-cell level, a massively parallel, multiplex gene expression profiling platform has been developed to enable compartmentalization and analysis of hundreds of single CTCs. After magnetic collection of CTC from blood, a single-cell Nanowell assay performs CTC mutation profiling using modular gene panels. Using this approach, multigene expression profiling of individual CTCs from NSCLC patients has been demonstrated with unprecedented sensitivity. These results represent the first demonstration of a high-throughput, multiplexed strategy for comprehensive single-cell mutation profiling of individual lung cancer CTCs toward non-invasive cancer therapy prediction and disease monitoring.