VictorJuiz/thesis huggingface dataset:
Coded computational illumination and detection for three-dimensional fluorescence microscopy [electronic resource]

In vivo calcium imaging enables the optical monitoring of neural activity at the level of individual neurons in real time, necessitating the development of high speed, three-dimensional (3D) fluorescence microscopy techniques with at least single-neuron spatial resolution. Because a typical widefield microscope intrinsically produces only two-dimensional images, various illumination and detection coding strategies have been implemented to address the challenge of 3D fluorescence microscopy, utilizing either precisely structured and temporally scanned illumination patterns, such as in two-photon laser scanning microscopy or coding of the emission, as in light field microscopy, respectively. However, many single-focal illumination coding strategies have limited acquisition speeds, while detection-coding-only strategies requiring computational reconstruction of the 3D volume are limited by optical aberrations of the tissue. We present a 3D calcium imaging approach utilizing both multifocal scanned two-photon laser excitation for illumination coding and detection coding with the light field microscopy approach suitable for in vivo mammalian calcium imaging. A holographic 3D multifocal illumination pattern is targeted only towards pre-localized neurons avoiding the unnecessary illumination of other regions. The resulting fluorescence emission is coded and detected on an image sensor and deconvolution is used to recover the neural activity at each site. We present the design and optimization of such an imaging strategy, and validate the approach with experimental measurements. Finally, we demonstrate the application of this approach to in vivo mouse calcium imaging. The design and implementation of another technique, frame-projected independent fiber photometry, enabling the optical recording and control of neural activity in freely moving mammals with region-level spatial resolution, is presented in a dedicated chapter as well, including simultaneous recording from multiple brain regions in a mouse during social behavior, two-color activity recording, and optical optogenetic stimulation eliciting dynamics matching naturally observed patterns.

Keywords: Electrical Engineering.
Advisor: Deisseroth Karl primary advisor. Thesis advisor
Horowitz Mark
Wetzstein Gordon advisor. Thesis advisor
Coherent feedback control and nonlinear optics in cavity QED systems [electronic resource]

In order to capitalize on their promise of high-bandwidth, ultra-low power operation, future nanophotonic devices will have to contend with quantum and coherent effects inherent to the small-volume, few-photon limit. The theoretical development of general, systematic frameworks for describing quantum feedback networks enables us to leverage established optical technologies, from single and multi-atom cavity quantum electrodynamics to ultrafast multimode optics, as an essential test bed for establishing direct contact between coherent-feedback control theory and first generation nanophotonic circuits. For interesting regimes for photonic logic, we want to work where switching energies become on the order of attojoules. Within atomic cavity QED systems, this regime occurs where the number of atoms within the typical cavity is on the order of 1-10. In this regime, each atom is a quantum emitter and must be treated with a full quantum model. As the atom number is increased, a mean field theory can be applied and the dynamics can be modeled using the optical Bloch equations. Full quantum modelling of systems with the atom number $> 10$ are not tractable computationally and a simpler semi-classical model does not fully capture the dynamics correctly. Thus we must investigate an intermediate regime where it may not be necessary to keep track of all quantum degrees of freedom and treat them semi-classically. I will present experimental data showing the effects of coherent feedback on a test cavity QED system alongside switching dynamics and other non-linear behavior in a few atom regime. Studying experimental data to help formulate new models will greatly help in the push towards practical optical non-linear systems for ultra low power photonic logic.

Keywords: Applied Physics.
Advisor: Mabuchi Hideo primary advisor. Thesis advisor
Bucksbaum Philip H. advisor. Thesis advisor
Schleier-Smith Monika advisor.
Coherent LQG control, free-carrier oscillations, optical ising machines and pulsed OPO dynamics [electronic resource]

Broadly speaking, this thesis is about nonlinear optics, quantum mechanics, and computing. More specifically, it covers four topics: Coherent LQG Control, Free-Carrier Oscillations, Optical Ising Machines and Pulsed OPO Dynamics. Tying them all together is a theory of open quantum systems called the SLH model, which I introduce in Chapters 1-2. The SLH model is a general framework for open quantum systems that interact through bosonic fields, and is the basis for the quantum circuit theory developed in the text. Coherent LQG control is discussed in Chapters 3-4, where I demonstrate that coherent feedback outperforms measurement-based feedback for certain linear quadratic-Gaussian (LQG) problems, and explain the discrepancy by the former's simultaneous utilization of both light quadratures. Semiclassical truncated-Wigner techniques for quantum-optical networks are discussed in Chapter 5, leading to a thorough discussion of quantum noise in systems with free-carrier nonlinearities (Chapter 6), comparison to the Kerr nonlinearity, and potential applications for analog computing based on limit cycles and amplification (Chapters 7-8). Ising machines based on optical parametric oscillators (OPOs) are discussed in Chapters 9-10, the former focusing on large 1D and 2D networks of OPOs, and the latter on the dynamics of a single OPO in the ultrafast, synchronously-pumped regime. Optical properties and design considerations for silicon photonic waveguides are are treated in Chapter 11.

Keywords: Physics.
Advisor: Mabuchi Hideo primary advisor. Thesis advisor
Ganguli Surya
Hayden Patrick (Patrick M.)
Hwang Harold Yoonsung
Collaborative musicking on the web [electronic resource]

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.

Keywords: Music.
Advisor: Berger Jonathan
Chafe Chris advisor. Thesis advisor
Wang Ge
Combined thermal protection and thermal propulsion for aerogravity assist missions [electronic resource]

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.

Keywords: Aeronautics and Astronautics.
Advisor: Cantwell Brian primary advisor. Thesis advisor
Alonso Juan José
Bell James
Senesky Debbie advisor. Thesis advisor
Combining uncertainty and sensitivity using multi-fidelity probabilistic aerodynamic databases for aircraft maneuvers [electronic resource]

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.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Kochenderfer Mykel J.
Kroo Ilan advisor. Thesis advisor
Combining VEGF Inhibition with Oral Metformin Therapy in a Mouse Model of Type 2 Diabetes

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.

Keywords:  Department of Biology
Biology
Metformin
VEGF Inhibitor
Type 2 Diabetes
Aflibercept
Thesis
Advisor: Kuo Calvin J.
Jones Patricia P.
Compact envelopes [electronic resource] : an efficient and provably safe approach to air and space traffic integration

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.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Close Sigrid
Kochenderfer Mykel J.
Competing in intermediated markets [electronic resource]

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.

Keywords: Management Science and Engineering.
Advisor: Katila Riitta primary advisor. Thesis advisor
Eesley Charles advisor. Thesis advisor
Eisenhardt Kathleen M. advisor. Thesis advisor
Competition and the use of discretion in financial reporting [electronic resource]

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.

Keywords: Business.
Advisor: McNichols Maureen
Larcker David F. advisor. Thesis advisor
Piotroski Joseph D. (Joseph David) advisor. Thesis advisor
Complex adaptation in subdivided populations [electronic resource]

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.

Keywords: Biology.
Advisor: Feldman Marcus W. primary advisor. Thesis advisor
Fisher Daniel
Petrov Dmitri Alex
Rosenberg Noah
Complex Genomic Patterns Characterize Variants in Transcription Factor Binding Associated with Gene Expression

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.

Keywords:  Department of Computer Science
computer science
computational biology
machine learning
genetics
genomics
gene expression
transcription factor
Thesis
Advisor: Kundaje Anshul
Fraser Hunter
Kaplow Irene