VictorJuiz/thesis huggingface dataset:
Heterogenous dynamics and mechanisms of mammalian primary cilia disassembly

Primary cilia are sensory signaling organelles critical in the regulation of cell proliferation and development. Assembly and disassembly of cilia are complex processes, closely linked with, and essential for, ciliary function and cell cycle progression. However, mechanisms and dynamics of ciliary disassembly are poorly understood in mammalian systems. We characterized dynamics and behaviors of ciliary disassembly in IMCD3 cells. Disassembly behaviors were classified into three major modes, varying in rate by two orders of magnitude -- gradual ciliary shortening, instant loss, and combined behavior consisting of consecutive gradual and instant stages. Surprisingly, instant loss ultimately accounts for a significant majority of disassembly events. We developed two distinct methods of isolating ciliary material from culture media following induction of ciliary disassembly. Consistent recovery of cilia-like structures by both methods demonstrates that instant loss is likely due to deciliation. Two candidate regulators of deciliation were examined -- katanin, and intracellular calcium. Overexpression of the katanin catalytic domain p60 leads to reduced ciliary length and stronger preference toward Instant disassembly dynamics, independently of calcium perturbations. Thus, mammalian ciliary disassembly involves a tunable decision between deciliation and resorption. We propose a model for ciliary disassembly involving two distinct decision points: 1) whether and when to disassemble the cilium, and 2) by which mechanism to disassemble the cilium.

Keywords: Molecular and Cellular Physiology.
Advisor: Nelson W. J. (W. James)
Stearns Tim 
Feldman Jessica L.
O'Brien Lucy
High dimensional dynamics in ecology and evolution

With advances in genomics, the study of evolution is more quantitative than ever. We can now attempt to answer questions like: how fast is evolution in different scenarios? How predictable is it? Why are there so many different types of organisms? In this thesis, we explore three questions in quantitative biology using theoretical approaches. In chapter one, we explore the effect that epistasis - interactions between mutations - has on long-term evolutionary dynamics. In chapter two, we explore models of diversity in ecosystems and show that spatial structure can stabilize such diversity for long periods of time. In chapter three, we develop a model of co-evolution in the context of host-pathogen interactions, and discuss conditions for the generation of diversity.

Keywords: Physics.
Advisor: Fisher Daniel S. 
Ganguli Surya
Kachru Shamit
High fidelity validation of vision-based sensors and algorithms for spaceborne navigation

This dissertation addresses the development of new hardware-in-the-loop testbeds for spaceborne vision-based navigation. The miniaturization of satellites and trend towards distributed space systems place demanding requirements on the navigation capabilities. In particular, next generation miniature space systems requires high levels of autonomy using limited onboard resources. In this context, vision-based sensors play an important role in providing a robust and passive mean to perform both inertial navigation and relative navigation with respect to space resident objects. The characteristic low-cost, low power consumption, small form factor, and high-dynamic range make vision-based sensors the ideal tool to operate in space. Current testbeds used for validation of vision-based sensors and navigation algorithms are affected by a number of limitations such as limited geometric resolution, radiometric dynamics range, or scope in terms of range of operations and functional modes. To overcome these limitations, this research addresses the design, calibration and utilization of two complementary hardware-in-the loop testbeds which make use of a combination of virtual reality and robotics. The virtual reality testbed is a variable-magnification optical stimulator which consists of a pair of actuated lenses that magnify a monitor. High-fidelity, synthetic scenes of the space environment are rendered to the monitor in real-time and closed-loop to stimulate a vision-based sensor test article. This is done using both computer graphics and machine learning techniques. The physical reality consists of a 7 degrees-of-freedom robotic arm, which positions and orients a vision-based sensor with respect to a target object or scene. Custom illumination devices simulate Earth albedo and Sun light to high fidelity to emulate the illumination conditions present in space. After design and calibration, the resulting testbeds are used in conjunction to validate the performance of new navigation algorithms and train neural networks for navigation of the next generation spacecraft.

Keywords: Aeronautics and Astronautics.
Advisor: D'Amico Simone 
Macintosh Bruce
Schwager Mac
High-order shock-capturing methods for study of shock-induced turbulent mixing with adaptive mesh refinement simulations

The Richtmyer-Meshkov instability (RMI) and the subsequent turbulent mixing driven by the interaction of shock waves with interfaces separating materials of different densities are commonly found in many natural phenomena and engineering applications with high-speed flows. One of the goals in this thesis is to develop accurate and efficient numerical methods that are suitable for numerical simulations of this kind of flows that involve both shock waves and turbulent motions. A type of high-order shock-capturing schemes that can be in explicit or spatially implicit form is developed to achieve this goal with localized dissipation nonlinear weighting technique. The scheme has the ability to preserve fine-scale features in smooth regions with minimal dissipation while still has the ability to provide sufficient numerical dissipation to capture shocks and discontinuities robustly. The explicit form of the high-order scheme is implemented in an in-house adaptive mesh refinement (AMR) framework which can efficiently employ the computational resources by dynamically allocating fine grid cells only to regions containing features of interest for multi-species Navier-Stokes simulations. As another goal of this thesis, the AMR framework is used to conduct two-dimensional (2D) and three-dimensional (3D) high-resolution simulations for the study of the RMI-induced mixing emerging from the interaction between a Mach 1.45 shock wave and a perturbed planar interface between sulphur hexafluoride and air. The numerical results are used to examine the differences between the development of RMI in 2D and 3D configurations during two different stages: (1) initial growth of hydrodynamic instability from multi-mode perturbations after the arrival of primary shock and (2) transition to chaotic or turbulent state after re-shock. The effects of the Reynolds number on the mixing in 3D simulations are also studied through varying the transport coefficients. An analysis of second-moment budgets for the highest Reynolds number 3D case is also performed. The analysis first addresses the importance of the second moment quantities: turbulent mass flux and density-specific-volume covariance for the closure of Favre-averaged Navier--Stokes (FANS) equations in this type of flow compared to single-species incompressible flows that only require Reynolds stresses for closure. The budgets of different second-moments before and after re-shock are also studied and compared in details. Further analysis is conducted on the post-transition flow to examine the validity of the modeling assumptions in the Besnard-Harlow-Rauenzahn-3 model and its variants for the unclosed terms in the FANS equations.

Keywords: Aeronautics and Astronautics.
Advisor: Lele Sanjiva K. (Sanjiva Keshava)
Alonso Juan José
Iaccarino Gianluca 
Livescu Daniel
High-resolution temperature and acoustic pressure sensors utilizing slow-light fiber Bragg gratings

Slow-light fiber Bragg gratings (FBGs) have attracted interest because they exhibit extremely narrow resonances (~60 fm) on the edge of their bandgap, leading to low group velocities (~290 km/s) and high Q factors (~30 million) in a ~cm-long device. They are fabricated by writing strong index modulations in the core of a single-mode fiber. They can also be used to make fiber sensors with record sensitivities. This work demonstrates how slow-light FBG sensors have pushed the limit of temperature and pressure sensing by at least one order of magnitude over conventional FBG sensors. Specifically, it reports a slow-light FBG temperature sensor with a resolution as high as 0.3 m°C/√Hz, an excellent stability (2 m°C/minute), and a low absorption losses (0.02 m−1 at 1550 nm) as required for negligible self-heating. These sensors were instrumental in recording for the first time the very small temperature changes induced by anti-Stokes fluorescence in optically pumped single-mode fluorozirconate fibers and measuring small absorptive losses with calorimetry. The work also reports a slow-light FBG microphone with a resolution of ~200 μPa/√Hz (100 Hz--20 kHz) and a slow-light FBG hydrophone with a resolution of ~700 μPa/√Hz (2 kHz--100 kHz). Their performance is about one order of magnitude better than that currently reported for conventional FBG sensors, and within two orders of magnitude of that measured by the more fragile membrane-based fiber sensors. With further improvement, slow-light FBGs could be utilized for high-resolution pressure sensing applications such as in the deep sea, structural monitoring, and seismic research.

Keywords: Electrical Engineering.
Advisor: Digonnet Michel J. F. 
Kahn Joseph M. (Joseph Mardell) 
Solgaard Olav
High-speed isotropic resolution and structured illumination using phased arrays in light sheet fluorescence microscopy

This dissertation details the use of high-speed, electrostatically actuated, linear phased arrays of microelectromechanical mirrors for applications in light sheet fluorescence microscopy. First, a phased array is used to demonstrate optical sectioning structured illumination to provide up to two orders of background reduction while maintaining camera-limited frame rates. The illumination is tunable, enabling the user to optimize the structured illumination performance. We then show how to use the phased array for diffraction-limited cylindrical lensing with 90% optical efficiency up to 0.008 numerical aperture (NA) with simultaneous beam steering. Single focus scanning is demonstrated up to a NA of 0.013, at which point the focus splits, creating a multifocal response. Using this lensing method, we show an axially-swept light sheet fluorescence microscope. The phased array allows camera-limited speeds without sacrificing resolution. The narrow focus of the light sheet is synchronized to the rolling shutter of a modern sCMOS camera, enabling isotropic resolution down to 720 ± 55 nm. With an update rates of 2.85 μs, the phased array can track the camera sensor rolling shutter at camera-limited rates at full frame and any reduced the region of interest, which we demonstrate at speeds of 140 frames per second at sub-micron isotropic resolution in GFP-labeled Drosophila.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav 
Contag Christopher H. 
Fan Jonathan Albert
High-stability and temperature-compensated MEMS resonant beam accelerometer

Silicon-based microelectromechanical systems (MEMS) resonant accelerometers have been regarded as a promising candidate in the field of high precision applications because of their low cost, small size, large dynamic range, and batch manufacturability. However, typical high performance accelerometers are subject to performance limitations due to temperature dependence, aging, and packaging environment degradations. For example, any drift in the system during inertial navigation in the absence of GPS leads to poor tracking accuracy and requires further compensation. This dissertation will present design, fabrication, and implementation of various compensation schemes for achieving highly stable silicon MEMS resonant accelerometers over a large temperature range. First, this work will discuss the hermetic wafer-level encapsulation process that allows fabrication of high performance resonators, and an additional method to achieve degenerate doping for passive temperature compensation. Then, the second part of this work will introduce an accelerometer design that maximizes sensitivity within fabrication constraints and produces a differential output that effectively cancels out common-mode errors such as temperature. Results show sensitivity in the excess of 400Hz/g, bias instability of < 0.5µg, and scale factor stability of < 0.5% over the temperature range from -20ºC to 80ºC. The final chapter will present three different methods of further temperature compensation. A compensation scheme that utilizes the nonlinear amplitude-frequency effect is shown improve the bias stability over the temperature range. Then, the implementation and results from an active compensation method known as ovenization are discussed. By actively controlling the device temperature with an embedded heater, improvements on both bias and scale factor stability over the temperature range are demonstrated. Lastly, a calibration method using in-situ temperature sensing is introduced. Preliminary results show a 0-g bias drift of 38μg over the same temperature range.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Senesky Debbie 
Solgaard Olav
Homer's world at war : cosmic agonism in the Iliad

It is a truism of scholarship on Archaic and Classical Greece that Panhellenic culture prized conflict and contest, that the ancient Greeks were "agonistic" to an extreme degree. Yet theories of why and how the ancient Greeks became exceptionally committed to "agonism" in the first place are seldom offered. This dissertation contributes to a theory of origin for Greek agonism. By agonism, I mean the Panhellenic cultural fascination with the clash of opponents in conflict, contest, dialectic, etc. Rather than attribute agonism's origins to accidents of physical environment (e.g. mountainous terrain separating closely related communities), I locate its roots in the primary narrative poetry of the developing Panhellenic world: Homer's epics, especially the Iliad. I do not assume in advance a distinctive group called the "Greeks" who composed a poem called the Iliad. Instead, I explore how the Iliad's poetic dynamics could transform disparate Greek-speakers into a recognizably agonistic people. I develop in this dissertation an extended and systematic reading of the Iliad focused on its agonism. I show how conflict not only propels the story but creates a coherent Homeric world that embraces human beings, nature, and gods. Part I introduces my concept of Iliadic world vantages, short passages that give the audience stable perspectives on the Homeric world. I consider three world vantages: the golden chain in Book 8, the shield of Achilles in Book 18, and the theomachy of Book 20. I then give a reading of the enigmatic Achaean wall as a poetic construction arising from the heightened agonism of the Iliad's battle books. In the rest of the dissertation, I develop my conception of the Iliadic hero, what I call the "triadic hero" comprising Hector, Patroclus, and Achilles. In Part II, I study the boundary-crossing performed by each warrior apart from the other two. In Part III, I show how the interconnection of these three central figures as a triadic hero test the limits of agonism, bringing the audience into contact with the emerging realms of the Homeric world.

Keywords: Comparative Literature.
Advisor: Gumbrecht Hans Ulrich
Nightingale Andrea Wilson
Anderson R. Lanier 
Martin Richard P.
Homosexuality and the state in cold war Germany

By 1937, Nazi Germany had convicted tens of thousands of men under its anti-homosexuality statute and had begun sending gay men to concentration camps. Eight decades later, with the approval of eighty percent of the population, the German parliament ratified the right of gay marriage. How did this change come about? Looking past vague assumptions about the nature of liberal democracy and the spread of gay rights, this dissertation offers a historical interpretation of the relationship between gay people and the German states that existed between the end of the Second World War and the present. Based on oral histories conducted with period witnesses and files from ten archives in Germany and the United States, it unearths a convoluted past of state persecution and gay liberation efforts.

Keywords: History.
Advisor: Daughton J. P. (James Patrick) 
Sheffer Edith
Daub Adrian 
Judson Pieter M.
Sommer Matthew Harvey
Hope among the ashes

This project is an in-depth feature on the series of murals that are located amidst the ruins in Paradise, CA by LA-based artist Shane Grammer. It incorporates a long form narrative article of about 2,300 words, two 360 videos, and several 3D scans of the murals using photogrammetry and drone technology. Although Shane Grammer has received quite a lot of media attention, the 3D photogrammetry shows the murals as they appear surrounded by destruction, a new way of diving in to the story with an approach that uniquely allows viewers to experience the murals and their settings.

Keywords:  Department of Communication
Stanford University
Department of Communication and Journalism
communication
journalism
Thesis
Advisor: Migielicz Geri
Brenner R.B.
Horizons of meaning : explorations of metaphor and the problem of religious language in the hermeneutics of Paul Ricoeur

This dissertation is a philosophical exploration that pursues two distinct lines of inquiry through the development of phenomenology in twentieth-century Germany and France, leading up to the hermeneutics of Paul Ricoeur and his important work on the problem of religious language. The first question is largely thematic: (1) how can we understand the concept of the horizon used as a metaphor within the phenomenological tradition broadly and phenomenological hermeneutics in particular? This question provides the methodological backbone of the project by offering a clear trajectory for working through the philosophy of the study's four central thinkers: Edmund Husserl, Martin Heidegger, Hans-Georg Gadamer, and Paul Ricoeur. The second question constitutes the primary motivating problem driving the study: (2) how do we understand Ricoeur's hermeneutical approach to religious language, and how can we see this work as addressing what I call the modern crisis of religious meaning. My wager is that these two questions are intimately intertwined, and indeed that pursuing the development of the metaphor of the horizon across Ricoeur's vast body of work is the best way to come to a full appreciation of the nuance and value of his theory of religious language. Furthermore, throughout this study I will argue that the deep connection between the question of the horizon and the question of religious language in Ricoeur's thought rests upon the fact that the horizon—as the phenomenological metaphor par excellence—speaks to a set of fundamental experiences that are united by and develop various aspects of the dynamic play of presence and absence found at the heart of Ricoeur's hermeneutical theory.

Keywords: Religious Studies.
Advisor: Sheehan Thomas 
Sockness Brent W.
Bashir Shahzad
Host-centric proteomics : laying the foundation to use human stool proteins as biomarkers of gastrointestinal disease

It is common practice for a physician to request a blood draw at a doctor's visit in order to determine the levels of key molecules in our blood as proxy's for a healthy or diseased state. Though this is a common practice, establishing these molecules' usefulness as diagnostic agents often takes many years. First, it is necessary to determine what molecules are present in blood. Then, extraction protocols for these molecules need to be established in order to ensure reproducible and measurable results. Next, it is necessary to establish the variability of these molecules across healthy people. Finally, it is necessary to ascertain whether these molecules can distinguish states of health or disease based on their abundance or presence in each phenotype. While these steps have been taken countless times in establishing blood biomarkers, thus far human stool has seen limited use as a source of biomarkers. However, new biological discoveries have brought a renewed interest to human stool. In 2013, microbiome sequencing became cheap and high-throughput. The development of this technology allowed researchers to study the microbiome under a multitude of conditions, including how the microbiome changed in the gut. However, these microbes are not living in isolation and constantly interact with and influence the human gut. One avenue through which microbes and their hosts interact is through the use of proteins secreted by cells in the epithelium. Several protein classes are prevalent in stool including structural, immune, and digestion-related proteins. Given the functional importance of gut-related proteins and their relation to the microbiome, it is important to understand their temporal and insult-related changes. The Elias lab has developed a protocol to enrich and purify these proteins from stool and characterize their abundance using mass-spectrometry-based proteomics. Using a mass spectrometer as a diagnostic approach offers the user many excellent attributes in a diagnostic. This host-centric proteomics approach is quantitative, non-invasive, multi-dimensional, and directly gastrointestinally targeted. The goal of this thesis is to further establish the use of human stool proteins as diagnostic markers of gastrointestinal health using mass spectrometry-based proteomics. First, I optimized a protocol focused on human stool that reliably and reproducibly extracts proteins from stool and enables their quantitation on proteomics platform. Next, I describe how these proteins and their relative abundances vary in healthy people. From this study I found that the largest source of variability of human stool protein abundance was between people. This allows us to control for this variability in the future by studying many people to determine "healthy" protein abundance ranges. Finally, I report stool proteins distinguish states of flare or remission in inflammatory bowel disease patients.

Keywords: Chemical and Systems Biology.
Advisor: Wandless Thomas 
Elias Joshua
Holmes Susan
Mallick Parag
Relman David A.