VictorJuiz/thesis huggingface dataset:
Nuclear architecture dynamics in tadpole tail regeneration
Keywords: genetics) degree supervisor.
Genetics.

Mammals possess very limited regeneration capabilities, where the few examples of scarless healing tend to be restricted to early development. In light of this, it is of great interest to study animals that can faithfully regrow complete appendages, and uncover the biological properties that facilitate regeneration. Xenopus tropicalis is an excellent vertebrate model of regeneration, as tadpoles rapidly regenerate amputated tails, a process that has an interesting developmental history that may be widely informative as to why mammals selectively heal through scarring as they age. Though we have some understanding of what processes are required for tail regeneration, we have yet to systematically chronicle the molecular and regulatory events that must set up an apparently coordinated response. In this dissertation, I address two primary questions in the field of regeneration—what molecular events occur in the first 24 hours to set up a potent regenerative bud, and how is this process regulated? In Chapter 2, I chronicle the transcriptional history of tadpole tail regeneration, focusing primarily within the first 24 hours post amputation. In Chapter 3, I describe a novel nuclear morphology I identified in the tadpole tail, detail how nuclei change shape as an early regeneration response, and investigate the relationship between nuclear shape and chromatin state. Finally, in Chapter 4, I address several future directions with respect to this thesis.
Numerical simulation and design of multifunctional structural batteries
Keywords: Aeronautics and Astronautics.

Multifunctional materials have been widely used in electrical applications because it has been demonstrated that high-strength composites can be integrated with active live battery material. This allows high strength and high energy density storage structures that can meet the transportation requirements on mobility and energy density. However, the design of multifunctional material requires fundamental understanding of the mechanical behavior of the integrated structural battery systems under various loading and environmental conditions. Characterization of this new class of multifunctional material becomes challenging without an adequate simulation model to guide the tests and to validate the results. The primary objective of this investigation is to develop the mechanical simulation and design of multifunctional battery systems, in particular Multifunctional Energy Storage Composites (MESC). It consists of multiple thin battery layers, polymer reinforcements, and carbon fiber composites. The combination of them poses significant challenges in simulation and modeling. To tackle these issues, homogenization techniques were adopted to characterize the multi-layer structure of the battery material with physics-based constitutive equations. Non-linear deformation theories are used to handle the interface between the battery layers. Second, mechanical and failure modes among battery materials, polymer reinforcements and composite-polymer interfaces were characterized by developing appropriate models and experiments. The numerical model of MESC has been implemented in a commercial finite element code. A comparison of the structural response and the failure modes between numerical simulation results and experimental test data will be presented. The results of the study have demonstrated that the prediction of elastic and damage responses of MESC at various loading conditions agree with the experimental results. With appropriate material property parameters determined from model calibration, this multi-physics model can be used as a necessary tool to understand and to govern the design of MESC for many applications.
Nutrition for national defense : American food science in World War II and the Cold War
Keywords: History.

"Nutrition for National Defense: American Food Science in World War II and the Cold War" tells the story of how home economists, doctors, food technologists, military strategists, and corporate researchers linked the emerging science of nutrition to the needs of a country at war. In the late 1930's, nutrition experts offered tools to identify and solve new nutrition problems. The still-young discipline of nutrition was catapulted onto the national stage during World War II, when both German and American experts declared that the fate of their nations hinged on the vitamin content of their bread. In the fraught context of the Cold War, the American government sponsored nutrition research both to fashion soldiers' bodies to the needs of war and to direct international politics. Throughout both conflicts, American nutritionists promised that better eating would form the foundation of a strong military, a strong nation, and a strong, democratic world. Nutrition also gave the government a new tool with which to see, assess, and hierarchize citizens. Because hunger anywhere was considered a threat to the nation, the link between nutrition and national defense changed assumptions about the government's responsibility to keep people nourished. The potential malnourishment of different groups—soldiers, war workers, white middle-class consumers, and poor people in the Third World and at home—elicited different responses from the government, from gentle to coercive. Nutrition became a site of conflict and contestation around the rights and privileges of citizens and the duties of the state.
observ - getting the news, first
Keywords:  Department of Communication
observ
Department of Communication
Stanford
MA Journalism
programming
Stanford Journalism School
Journalism
public records
local journalism
Thesis

Observ is an online application designed for local journalists, to help them find public records that are relevant to their beat. With observ, the user can research a database of public records of local municipalities and subscribe to a query of their liking. They will then be notified every hour, day or week if there are new documents in the database that match their query.
Observations of Boundary Layer Dynamics in South San Francisco Bay
Keywords:  Department of Civil and Environmental Engineering
estuary
canopy flow
boundary layer
wave Reynolds stress
stanford university
civil &amp; environmental engineering
cee
sediment transport
cohesive sediment
fluid mechanics
san francisco bay
south san francisco bay
Thesis

Estuarine sediment transport is an important process in determining the fate and transport of contaminants. While physical models exist to describe spherical non-flocculating particles in a fluid, cohesive sediments are poorly modeled from first principles. We conducted field work in South San Francisco Bay during the summer of 2018 to take detailed observations of sediment and water motion near the bed in the shallow eastern shoals. Data collected by a Nortek Vectrino Profiler provides insight into the patterns of flow in the wave-current boundary layer and nearby log layer, as well as the physical forcing behind bed behavior. I compare these profiles with accepted fitting models for flow over a canopy and with measurements taken higher in the water column by an Acoustic Doppler Profiler deployed at the same site. Velocity profiles at 64 Hz for 12 minutes every hour at a 1 mm resolution for 2 mm overlapping the bed are highly detailed in space and time relative to previous field measurements of similar variables, and permit the study of friction velocity and turbulent Reynolds stress in and above the wave-current boundary layer. Velocity profiles in the shallow shoals of South Bay are modeled by the canopy log law. Waves are a major contributor to instantaneous velocity profile deviations from the 12-minute mean profile, and cause corresponding variations in turbulence Reynolds stress and friction velocity. Phase-averaged velocity profiles and turbulence statistics are presented for different tide and wave environments to describe the results of complex wave-current interactions in the boundary layer. This work has implications for interpreting time-averaged velocity profile measurements and presents detailed measurements of parameters relevant to understanding sediment transport in an economically important estuary system.
Observing structures and dynamic behavior in biological cells using single-molecule based super-resolution fluorescence microscopy
Keywords: Applied Physics.

For the last three decades, the ability to detect single molecules at high spatiotemporal resolutions has revolutionized the way we observe and understand the cells that harbor life. This research uses super-resolution imaging and single-molecule tracking to uncover nanoscale structural details and dynamics for mammalian cells and bacteria. By optically separating out each individual emitter in time using an active-control mechanism, every localization provides spatial information with a resolution much better than the diffraction limit to yield super-resolution microscopy. To address the fact that biological systems are inherently three-dimensional, the microscope detection path is further extended to include a "4f system" configuration, which provides easy access to the conjugate back focal plane. By strategically placing a phase mask here, the emission can be optically transformed in way which breaks the symmetry of the detected intensity profile of a single-molecule emitter above and below the focal plane to give precise axial positions. However, it still remains a challenge to obtain a clear picture of the surface features of small, crowded biological structures in their natural habitat in both a non-invasive and precise manner. This dissertation describes how super-resolution fluorescence microscopy and surface meshing algorithms are used in conjunction to quantify the surface topology of two main biological systems: the primary cilium of mammalian cells and the surface of the bacterium, Caulobacter crescentus.
Oceanic rumblings : midtrophic responses to oceanographic variability observed through acoustic and diet analyses
Keywords: Biology.

Open ocean ecosystems are the largest on the planet, containing an enormous diversity of organisms boasting incredible adaptations to life in a mostly dark, seemingly featureless habitat. Despite the heavy reliance on marine resources by countries across the globe, there remains a large gap in our basic understanding of marine ecosystems, particularly with respect to the organisms at the center of open ocean food webs: micronekton. These small, swimming animals are notoriously difficult to quantify, commonly avoiding conventional sampling methods and occurring across large areas that are costly to sample. In this dissertation I collaborated with existing monitoring programs to generate timeseries that capture variability in the composition, abundance, and distribution of micronekton communities with respect to environmental variability. I examined changes in diet composition and prey availability for Humboldt squid, Dosidicus gigas, in the Gulf of California (GOC), Mexico between 1996 and 2017. Humboldt squid in this oceanographically-variable region have exhibited a large range in mature size (15-85 cm mantle length) associated with the El Niño Southern Oscillation (ENSO), but it is unclear how their role in the ecosystem changes with respect to body size or how their prey respond to ENSO. I demonstrated that Humboldt squid diet in the GOC is more different between squid collected in different environmental conditions than between individuals of different sizes. Prey responses to environmental variability were directly assessed with nighttime acoustic observations in the same region. In conjunction with strong El Niño events, I observed significant reductions in forage biomass, which remained depressed for 2-3 years following the event regardless of subsequent environmental conditions. I also described variability in the diet of longnose lancetfish, Alepisaurus ferox, across the central North Pacific Ocean using specimens collected by federal fisheries observers in the Hawaii-based deep-set longline fishery, and demonstrated that continued monitoring of lancetfish diet could be used to quantify environmental responses of their diverse micronektonic prey. My work provides unique insights into large-scale spatiotemporal variability in two open ocean forage communities and contributes to our understanding of the role micronektonic organisms will play in mitigating or exacerbating the effects of ocean warming on marine resources.
Octans, chart your constellation of support: A web platform for adolescents to identify and expand their social support networks to explore interest-driven learning pathways
Keywords: Learning Design and Technology
Graduate School of Education
social networks
social capital
social support
high school students
marginalized youth
mentoring
advising
learning experience design
Thesis

We all belong to social networks. A social network is comprised of the set of social actors and relationships among these actors. Social capital refers to the embedded resources in these social networks that an individual actor can access, build and utilize to achieve personal interests. Hence, social capital is a key determinant in our academic and career trajectories. However, social capital is not evenly distributed across individual actors. Historical and institutional processes have resulted in unequal opportunities for different social groups based on characteristics like gender and race. Fortunately, social networks are dynamic, and we can learn to recognize, nurture, and employ social capital to improve these networks.
Octans seeks to empower high school students, particularly marginalized youth, by raising their awareness of the importance of social capital and guiding them to notice, act upon and expand their surrounding resources. As a web platform, Octans features (1) interactive narratives of how relevant role models have used social capital, (2) a visualization tool that helps students identify and reflect on their social networks, and (3) a goal-setting and action-planning journal with prompts and strategies to build social capital. Along with other mentoring resources, Octans aspires to prepare learners to pursue interest-driven learning pathways using their social networks.
Interviews and user testing with target learners have shown that after using Octans, learners are more aware of and grateful for their social networks. Learners are better able to articulate the types of support they encounter in their social networks. Finally, they feel a greater sense of agency to work towards their goals knowing that they have the support from these bonds and the possibility of building new ones.
Offset and noise behavior of microfabricated aluminum gallium nitride-gallium nitride two-dimensional electron gas hall-effect sensors
Keywords: Electrical Engineering.

Magnetic sensors are quite common in everyday life, with a variety of uses in mobile devices, electric machines, cars, motors, navigation, and planetary exploration. They are incredibly useful due to their non-perturbing nature. For example, they infer information about position, velocity, and current in power systems. Silicon Hall-effect sensors are popular for many applications due to their low cost and ease of integration with silicon circuits. However, silicon Hall-effect plates cannot operate at extreme temperatures (below -100 degrees C or above 300 degrees C) due to carrier freeze out or intrinsic carrier leakage, respectively. In addition, Hall-effect plates have challenges with thermal drift, offset, and flicker noise. In this PhD thesis, I start with an in-depth focus on the fabrication of high aspect ratio trenches (18.5:1) in 4H-SiC for potential use in direct hot-spot cooling of GaN-on-SiC power devices as well as extreme environment SiC microelectromechanical system (MEMS) applications. I then switch gears and describe an AlGaN/GaN 2DEG Hall-effect plate with ~100 ppm/K constant-current sensitivity drift, 0.5 micro-Tesla offset, and 200 Hz corner frequency. These metrics surpass state-of-the-art silicon Hall-effect sensors with a larger temperature operation range, stability of sensitivity, and lower offset and noise floor. I then describe the fundamental limits of offset in GaN devices and present an examination of the flicker noise of these devices. Through this work, I have achieved a record-low offset in GaN 2DEG Hall devices, presented the first framework for studying noise in GaN Hall sensors, and have demonstrated a world record aspect ratio in bulk 4H-SiC machining. These contributions will enable a future monolithically integrated GaN-on-SiC platform for extreme environment sensors and power electronics. I conclude with proposing future work, including a path forward for implementing these devices in extreme environment systems.
On applications of Szemerédi's regularity lemma
Keywords: Mathematics.

Szemeredi's regularity lemma is an important and powerful tool in graph theory. One of its prevalent application is the graph removal lemma, which has numerous applications to extremal problems for graphs and hypergraphs, additive combinatorics, discrete geometry, and theoretical computer science. In this thesis, we initiate and prove a new removal lemma with respect to a stronger metric on graphs, which is a strengthening of the usual graph removal lemma. We also prove a new application of the regularity lemma. The Ramsey number r(H) of a graph H is the minimum integer n such that any two-coloring of the edges of the complete graph Kn contains a monochromatic copy of H. Determining the Ramsey number for all graphs is a famously difficult question. A more general question is to study the minimum total number of monochromatic copies of H over all two-colorings of Kn. When n = r(H), this quantity is referred to as the threshold Ramsey multiplicity of H. Addressing a problem of Harary and Prins forty years ago, we proved the first quantitative sharp bound for cycles and paths. This thesis describes the work for path and even cycles. Although the regularity lemma is powerful, a notable drawback is that applications of the regularity lemma will result in very weak quantitative estimates. One important application of the regularity lemma is the field of property testing, whose goal is to very quickly distinguish between objects that stratify a certain property from those that are epsilon-far from satisfying that property. Some of the most general results in this area give ``constant query complexity" algorithms, which means the amount of information it looks at is independent of the input size. These results are proved using regularity lemmas or graph limits. Unfortunately, typically the proofs come with no explicit bound for the query complexity, or enormous bounds, of tower-type or worse, as a function of 1/epsilon, making them impractical. We show by entirely new methods that for permutations property testing, such general results still hold with query complexity only polynomial in 1/epsilon.
On manifold bundles over classifying spaces
Keywords: Mathematics.

This thesis comprises the results of three independent research projects in high-dimensional geometric topology. The first one exhibits, for various manifolds as fibers, smooth bundles over the classifying space of SU(2) not induced from an action. The second project is joint work with M. Krannich. It gives conditions on when a manifold is, up to bordism, the total space of a fiber bundle over a surface with highly-connected and almost-parallelizable fiber M, including a computation of the corresponding characteristic numbers. As a corollary, we determine an explicit basis for the second integral cohomology of BDiff(M) up to torsion in terms of generalized Miller—Morita—Mumford classes. Finally, the third project analyzes models for higher parametrized cobordism categories, with a special focus on the case where the parametrizing space is a circle.
On the arithmetic of weight two Eisenstein series
Keywords: Mathematics.

This thesis contains two separate results on the arithmetic of Eisenstein series. The first is a new proof of theorems of Merel and Lecouturier on the relationship between Mazur's Eisenstein ideal and special values of Dirichlet L-functions. The second is a computation of the Galois representations and mixed Hodge structures associated to certain Eisenstein series on Hilbert modular varieties.
On the methods of construction and evaluation of reaction coordinates from direct dynamics
Keywords: Chemistry.

With the emerging interest in using non-linear dimensionality reduction (NLDR) methods to study and generate meaningful reaction coordinates for complex dynamical systems, it is important not only to find methods most suited for these types of data but to have methods of evaluating the quality of these different mappings. Methods that perform well for lower energy, simpler ground state reactions are not necessarily suitable for describing the reaction path of more complex ground state reactions or high energy excited state reactions. NLDR is a good candidate for finding reaction coordinates for excited such systems where assumptions used to generate reaction coordinates for ground state reactions do not hold. In this dissertation we explore how different data featurizations and NLDR methods affect the mapping quality of excited state dynamics simulation of ethylene and RPSB analogue. We also introduce techniques to determine the quality of these mappings using several existing, general techniques for comparing the different NLDR mappings and by adapting those general techniques to specifically evaluate the mappings of molecular dynamics simulation data. Having a metric to compare the quality of different NLDR mapping allows us to approach the construction of reaction coordinates in a systematic way.
On the orderability up to conjugation of certain open contact manifolds
Keywords: Mathematics.

In this thesis, we define and study the orderability up to conjugation problem for groups of compactly supported contactomorphisms of certain open contact manifolds. In particular, we show that the groups of compactly supported contactomorphisms of certain subsets of odd-dimensional spheres are orderable up to conjugation. This class of manifolds has recently showed its importance in the flexible side of contact topology. Along the way, we prove non-squeezing-type results for prequantizations of hyperboloids in the product of an even-dimensional Euclidean space with a circle, which may be of independent interest. The main tool is an equivariant version of contact homology, adapted to subdomains of the product of an even-dimensional Euclidean space with a circle.
On the scale dependence of flow structures and transport in chaotic electroconvection
Keywords: Mechanical Engineering.

Electroconvection (EC) is a hydrodynamic instability that occurs when dissolved ions are driven from a bulk fluid towards an ion-selective surface under a sufficiently large applied voltage. When the applied voltage exceeds a threshold, chaotic features arise from the coupling between ion-transport, fluid flow, and electrostatic forces near the ion-selective interface. This greatly enhances ion transport, impacting mass transfer and ion residence times and plays a significant role in a wide range of electrochemical applications. Simulating EC in regimes relevant to industrial applications is challenging; its wide range of spatiotemporal scales requires costly computations with extremely high resolutions. This dissertation considers aspects of electroconvection that would inform future modeling of these complex flows in the highly chaotic regime.