VictorJuiz/thesis huggingface dataset:
Topographically-mediated variability in fog and belowground moisture and its role in redwood distributions and responsiveness to drought
Keywords: Earth System Science.

Forests cover 30% of the land surface and absorb almost a quarter of annual anthropogenic carbon dioxide emissions, but are vulnerable to increasing drought stress as a result of climate change. Regions of high water availability embedded within topo-climatically diverse forest landscapes could protect forests during drought, but have been understudied. In this dissertation, I sought to develop a nuanced understanding of the role of fine-scale spatial variation in water availability on the habitat distribution and drought responsiveness of coastal redwoods (Sequoia sempervirens), the tallest tree species on earth. In the first chapter, I show that redwood distributions can be mapped at 10 m resolution with demonstrable accuracy over 34,800 hectares and three redwood forests from airborne imaging spectroscopy, field-collected training data, and an optimized machine learning image classification framework. In the second chapter, I found that mapped fog frequency from the MODIS satellite and airborne LiDAR-derived estimates of belowground moisture shaped microscale redwood distributions, and that interpolated height above a stream (IHAS) was consistently negatively related to redwood abundance. These results suggested that fog and topographically-defined gradients of water availability within redwood forests contribute to significant variation in redwood habitat suitability within regions where redwood range contraction has been predicted with coarse resolution data. The third chapter tests the hypothesis that access to moisture from fog and streams have a buffering effect on redwood response to drought. Cores were collected from redwoods across a gradient in fog frequency and at two IHAS positions at Mt. Tamalpais. Annual basal area growth rates calculated from ring width measurements revealed an amplified negative response of redwood annual growth to drought indices at ridge sites with low fog frequency, suggesting that redwoods with access to water from fog and streams were less responsive to drought, as we expected. However, streamside trees under the highest fog frequency regime were the most responsive to precipitation variability, challenging the simple interpretation that redwoods with access to water from fog and streams were always less responsive to precipitation deficits. Analyses of airborne LiDAR-derived tree height data revealed that these trees were significantly taller and therefore exposed to higher leaf water stress. We concluded that biological compensation for higher water availability during mean climate, through increased height growth, might reduce the buffering effect of fog and streams on redwood growth responsiveness to drought.
Toward a predictive composite Higgs model : a dual approach in 5D
Keywords: Toro, Natalia degree committee member.
Physics.

An interesting possibility of explaining the electroweak symmetry breaking is to consider the Higgs boson as a composite particle, i.e. a pseudo-Goldstone boson of a new strong dynamics. Although it is hard to make quantitative predictions under a strong interaction, we can use its dual description in 5D and compute physical observables. In this thesis, I introduce gauge-Higgs unification models in warped 5-dimensional space as a setting for composite Higgs models. Gauge bosons and fermions are in the bulk and the Higgs boson is identified with the 5th component of a gauge field. We formalize the computation of the Coleman-Weinberg potential of the Higgs field and present a simple, general formula. Using this tool, we consider a specific model with SO(5) × U (1) global symmetry and introduce a new fermion multiplet, which competes with the top quark and creates a little hierarchy characterized by a small parameter s = v/f . Using a Green's function method, we compute the properties of the model systematically as a power series in s. We discuss the constraints on this model from the measured value of the Higgs mass, the masses of top quark partners, and precision electroweak observables. Finally, we compute fermion pair creation cross sections in general SO(5) × U (1) models. Our Green's function method provides an analytic understanding of the new physics effects across the parameter space. We find that the predicted effects will be visible in precision measurements and different models of b quark mass generation can be distinguished by these measurements already at 250 GeV in the center of mass.
Toward faster and more data-efficient computational biology
Keywords: Electrical Engineering.

Limited computing power and limited sample size are two central challenges in computational biology. While the next-generation sequencing technology offers a highly scalable way for measuring genomic information, the size of the data for a single biological sample can be as large as tens of gigabytes and presents a tremendous challenge for data storage and processing. At the same time, the data is usually ultra-high-dimensional, e.g., tens of thousands of genes or millions of mutations, requiring a large number of samples for effective inference. In this thesis, I address these two challenges by designing fundamentally better algorithms for several key applications. First, we address the limited computing power problem by presenting two works of algorithm acceleration using a strategy that we call adaptive Monte Carlo computation. Such a strategy first converts the deterministic computational problem into a statistical estimation problem and then accelerates the process by adaptive sampling. Then we move on to the limited sample size problem and consider two aspects, i.e., optimizing the experimental design and borrowing information from other datasets. For the former, we present work on the optimal experimental design for single-cell RNA-Seq. For the latter, we consider multiple hypothesis testing using side information and dimensionality reduction guided by additional datasets.
Towards Broad-Coverage AMR Parsing with Dynamic Continuized CCG
Keywords:  Symbolic Systems Program
semantic parsing
ccg
amr
dynamic continuized ccg
symbolic systems
Thesis

Dynamic continuized CCG is a method of compositional parsing that allows indefinites to take scope out of scope islands in a predictable and formalized manner. For example, it allows us to achieve the correct reading of the sentence "If one of my relatives dies, I'll inherit a fortune" (wherein the speaker is identifying a specific relative). At the same time, it prevents the universal from taking wide scope in the sentence "If all of my relatives die, I'll inherit a fortune" - if it did, we would get the reading that as long as any of my relatives die, I will inherit the fortune.
Unfortunately, previous work in dynamic continuized CCG (DC-CCG for short) has not provided a way to allow it to learn from datasets. Rather, it can only be used with a strictly specified lexicon, making it not useful for practical purposes. However, if we were able to reverse the rules of DC-CCG, we would be able to implement lexicon generation, and thus be able to learn from large datasets. As such, this thesis will demonstrate how these rules can be reversed, and how this extended system can be implemented in an existing semantic parsing framework.
Towards Photon-Mediated Creation of Twin Fock States in an Optical Resonator
Keywords:  Program in Engineering Physics
Twin Fock State
Photon-Mediated Interactions
Optical Resonator
Cavity Quantum Electrodynamics
Thesis

This thesis describes the development of experimental tools for preparing many-particle entangled states of cold atoms in an optical cavity. We focus on the illustrative goal of preparing twin Fock states, which requires two key components: coherent photon-mediated interactions and sensitive state detection. We report the development of a phase-locked laser system that provides high power and tunability for driving interactions. Spin-exchange interactions driven by this new laser system demonstrate enhanced coherence compared with past experiments. We also report the design and characterization of avalanche photodetectors for quantum-limited detection, and we present a theoretical analysis of atomic state detection by Faraday rotation. These developments move us towards being able to generate and detect the highly entangled twin Fock state, which ultimately offers the potential for precision sensing near the fundamental Heisenberg limit.
Tracing the moche spectacles of death : performance, ancestrality, and political power in ancient Peru; a view from Huaca la Capilla-San José de Moro (AD 650-740)
Keywords: Anthropology.

The Moche culture thrived in the north coast of Peru between the second and ninth centuries AD. While still a point of debate, many consider the Moche one of the first state-level societies in the pre-Columbian Americas. One fascinating aspect of this society is the elaborate burials, with sumptuous displays of wealth. Traditionally, scholars have envisioned Moche death as an inherent and static manifestation of hierarchy, status, and power. My dissertation moves away from such object-centered approaches, studying death and its effects as a historically and culturally situated phenomenon. My dissertation draws on extensive archaeological excavations conducted in Huaca La Capilla, a monumental adobe structure located within the Late Moche elite cemetery of San José de Moro, Jequetepeque Valley. Based on the striking similarities between the architectural enclosures discovered in this huaca and those represented in the Moche "Burial Theme, " I suggest that Huaca La Capilla was one of the loci where Moche funerary performances systematically occurred. These performances constituted large public spectacles orchestrated around the physical transformation of the corpses of elite individuals and their preparation for their symbolic journey into the afterlife: a process of transformation from a human to a divine entity, of becoming ancestors. Integrating multidisciplinary methods of analysis, my dissertation presents a comprehensive study of Huaca La Capilla, its architectural layout, and its many (and still enigmatic) transformations. I examine the role of Huaca La Capilla within the dynamic deathscape of San José de Moro, providing new insights on the relationship of huacas with death, the regeneration of life, and the cosmological order in the Moche world. In the context of political balkanization that characterized the Jequetepeque Valley during Late Moche times, I argue that the participation in these ritual spectacles was a key means for the creation of political and religious subjectivities. Ultimately, this case study offers novel anthropological perspectives on how the dramatic nature of the rituals orchestrated around the burial of elite individuals (the-body-as-spectacle, sensu Foucault 1977) constituted a means through which pre-modern states were held and constantly reproduced.
Transcribe.it - Audio Transcription Made Simple
Keywords:  Department of Communication
Journalism M.A.
Department of Communication
Stanford University
transcription
audio
newsroom
tool
speech
text
Thesis

Transcribe.it is a tool to help journalists transcribe audio files. This tool is intended to be run locally on a user's machine, in the spirit of tools such as OpenRefine and Tabula. It provides a simple web interface that lets users transcribe audio files using Google Cloud services, and saves the transcription locally. Transcribe.it is one of many solutions journalists can use to transcribe audio files, but this tool aims to simplify the process in a cost-effective way to the user without having to interact directly with Google’s Speech-to-Text API.
Transient fault tolerant asynchronous circuits
Keywords: Electrical Engineering.

Asynchronous digital circuits are circuits that don't have clocks. They sometimes have advantages including speed, lower power consumption, and relative insensitivity to environmental conditions such as temperature. Transient faults, which are changes in the circuit that do not permanently damage the circuit, are a growing problem in digital circuits. Transient faults are mainly due to radiation effects such as Single Event Upsets (SEUs). These faults occur on the ground and are exacerbated in space. In this work, I present an overview of asynchronous circuits, in particular speed-independent control circuits, and our model for transient faults. I then present a fault-tolerant transformation of the circuit based on duplication. I discuss how to define fault tolerance formally. Then I show using logic and formal methods why the transformed circuit is fault-tolerant to single transient faults.
Transient reprogramming for multifaceted reversal of aging phenotypes
Keywords: Applied Physics.

Though aging is generally associated with tissue and organ dysfunction, these can be considered the emergent consequences of fundamental transitions in the state of cellular physiology. These transitions have multiple manifestations at different levels of cellular architecture and function but the central regulator of these transitions is the epigenome, the most upstream dynamic regulator of gene expression. Reproduction is the only general phenomena in nature where the age of (parental) cells is truly reset - to produce an embryo and ultimately an age 0 offspring - and core to this process is a dramatic reprogramming of the epigenome. Here we present a technology that captures part of this age reset mechanism but using a transient reprogramming - to drive more youthful phenotypes but without the full reset back to an embryo. This reprogramming technology is distinct from previous anti-aging/pro-longevity interventions as instead of just modulating a few identified aging pathways, reprogramming engages a global and balanced state transition, in the case of reproduction, or state perturbation, in our transient approach, which we show leads to a multifaceted age reversal effect at the DNA, metabolic, whole cell and local environmental levels. We further discuss the emergent tissue and organ level benefits when transplanted with cells undergoing this treatment.
Translational Suppression is not an Early Response to Synchronous, Inducible, Intracellular Protein Aggregation
Keywords:  Department of Biology
Biology
proteostasis
AgDD
metabolic labeling
click chemistry
eIF2α
translational suppression
protein synthesis
aggregation
Thesis

Cellular protein homeostasis (proteostasis) is maintained by a complex, adaptive proteostasis network (PN) composed of tightly regulated synthesis, quality control, and clearance systems. Disturbances in the PN that result in the misfolding and subsequent aggregation of proteins are implicated in many neurodegenerative disorders (NDs) such as Huntington’s, Alzheimer’s, and Parkinson’s diseases. While the PN’s late-stage responses to aggregation such as transcriptional changes and deposition of aggregated proteins have been well-documented, there remains a substantial gap in our understanding of the immediate responses of the PN to cytosolic protein aggregation. Elucidating these early responses to aggregation is essential to a comprehensive understanding of ND pathogenesis and can offer insight into previously unknown, potentially therapeutically tractable targets. Previous investigations into the earliest actions of the PN in response to acute shifts in protein solubility were limited by stochastic onset of aggregation in cells overexpressing folding-defective proteins. These models also lacked the synchronicity in aggregation necessary to achieve a temporal resolution capable of characterizing the PN response in the minutes following the onset of protein misfolding. Of particular interest is whether the rapid modulation of protein synthesis, a common fast-acting response to severe cellular stressors that mitigates insults to homeostasis, makes up part of the PN’s earliest response to the aggregation of a single protein in the absence of global stressors. To probe this question, this study used a novel system of inducible, widespread, synchronous aggregation of a single protein in cells, coupled with metabolic protein labeling and click chemistry, to investigate the immediate impact of protein aggregation on protein synthesis rate. The results showed that induced aggregation in our model system produced no significant change in global protein synthesis rate. Furthermore, induced aggregation did not increase phosphorylation of eIF2α, which mediates translational suppression in other models of aggregation.
Treatment of Geometric Constraints in Well Placement Optimization
Keywords:  Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Thesis

In well placement optimization, the goal is generally to determine the well configuration that maximizes a profitability or productivity measure. An important requirement in these optimizations is the satisfaction of geometric constraints that limit the locations where wells can be placed. In this work, we introduce and test new constraint-handling treatments within the context of particle swarm optimization
(PSO), a stochastic global search method. These treatments enable the satisfaction
of three types of constraints, namely maximum well length, minimum inter-well distance, and minimum well-to-boundary distance, during the PSO run. Our treatment 'repairs' infeasible solutions by projecting them into feasible space. The repair procedure entails the application of alternating projection using sequential quadratic programming (SQP), along with a perturbation step. This perturbation step acts to shift infeasible solutions out of poor local minima found by SQP. 'Post-evaluation' treatments are also required to handle solutions, within the optimization, that remain infeasible after repair. Three types of post-evaluation treatments are considered in this work - the filter method, and static and dynamic penalty treatments.
The performance of our treatments is assessed for optimizations involving the
placement of multiple deviated wells in 3D models. Two cases (one with 18,225 active cells and one with 42,886 active cells), with irregularly shaped boundaries, are considered. In both cases, PSO without the repair procedure has difficulty finding
reasonable feasible solutions. The repair procedure is shown to render feasible the majority of infeasible solutions, thus providing substantial improvement in optimizer
performance. For the first case, we assess the impact of the parameters in the repair procedure and in the (post-evaluation) penalty treatments. The effect of each
parameter is evaluated based on the resulting median objective function value over
five PSO runs. We observe that the use of smaller-magnitude perturbation, and the
replacement of all infeasible PSO solutions by their repaired versions, leads to the
best overall performance. In addition, the penalty treatments are found to outperform the filter method if suitable penalty parameters are assigned. For both models, the use of the constraint-handling treatment greatly improves optimizer performance compared to PSO without the repair procedure. This is observed over a wide range of parameter values, and for all post-evaluation treatments considered.
TREM1 and TREM2 in the Maladaptive Microglial Inflammatory Response in Alzheimer's Disease
Keywords:  Biology
Biology
Neurology
Alzheimer's Disease
microglia
inflammation
TREM1
TREM2
Thesis

Alzheimer's disease (AD) is a debilitating neurodegenerative disease currently afflicting millions for which no disease-modifying treatments exist. Neuroinflammation has been heavily implicated in AD progression and is a potential therapeutic target. In addition to the neurotoxicity caused by amyloid beta (Aβ) and tau, microglial activity causes secondary toxicity and may exacerbate Aβ and tau pathologies. Triggering receptor expressed on myeloid cells 2 (TREM2) promotes phagocytosis and has been identified as a risk variant associated with AD using genetic approaches, but its role is not fully understood. TREM1 signals via the same pathway, and it has been identified as a potent amplifier of toxic immune responses in acute inflammatory settings but remains relatively unexplored in AD. Using immunohistochemistry, we examined microglial activity and TREM1 and TREM2 expression in mouse brain tissue with intracerebroventricular Aβ delivery. We measured microglial activity by examining process length, number of processes, and CD68, a phagocytosis marker. We also developed and verified a monocyte-derived, microglia-like cell (MDMi) model to provide more direct evidence of the microglial response to Aβ. We carried out an Aβ-dosing study where we examined the response of TREM1 and TREM2 in MDMi cells with exposure to escalating levels of Aβ. We additionally developed an IHC protocol to examine human brain tissue from AD patients and confirmed TREM1 expression. Our results support increased microglial activity upon exposure to Aβ, as well as an increase in TREM1 and decrease in TREM2 with Aβ. These data have led us to propose a model whereby TREM1 activity promotes the maladaptive immune response by decreasing expression of protective TREM2. With further exploration, the regulatory roles of TREM1 and TREM2 in development of pathologic inflammation could be fully revealed and hold clinical and therapeutic relevance.
Trust in a Digital Age: Overcoming Systemic Difficulties in Returning Unclaimed Property
Keywords:  Department of Communication.
Unclaimed Funds
Thesis

Each year, in California alone the state government takes in almost 9 billion dollars of unclaimed property from its residents. Unclaimed property can be defined as any property that is left to a specific person without their knowledge, most likely money given to an individual based on a will or a old bank account that had been closed. The process of identifying the owners of unclaimed funds as well as claiming funds once the owner has been found has been notoriously difficult with little changes made by the government to make the process easier for citizens to claim their property.
In this paper, I will examine the history of unclaimed funds and ways in which the government has systematically made it difficult for this property to be returned to its rightful owner. I will acknowledge the reasons that people’s lack of trust in government leads them to avoid searching for their funds on their own. I will also describe the ways in which modern financial scamming has only increased the difficulty for citizens to find these funds while navigating the online financial scams that exist.
Finally, I will propose an alternative method of reaching out to individuals who have unclaimed property, describing a business model that people can trust to help them get this money back. By relying on some psychology, I will focus on the trust that people inherently have in charities to describe a partnership with my business and charities in order to effectively return this unclaimed property back into the hands of its rightful owner.