VictorJuiz/thesis huggingface dataset:
Effects of Flow Structures on Particle Clustering in Homogeneous Isotropic Turbulence

This work experimentally examines the geometric characterization and spatial distribution of particle clusters and voids in homogeneous isotropic turbulence. Specifically, we analyze the relationship between turbulent flow structures and the spatial distribution of particles. A Voronoi cell analysis and particle number density are used to identify regions of particle clusters and voids. The turbulent flow structures analyzed are vortices, stagnation points, and fast moving jets./nA 40-cm Eaton box is used to generate a homogeneous isotropic turbulent flow with Reynolds numbers ranging from 157 to 319. The first set of experiments examines the geometric characterization of particle voids and clusters by injecting aluminum-oxide particles with dp = 0.5, 1, 3, and 5μm into four turbulence levels. In the second set of experiments aluminum-oxide particles with dp = 1μm and fluorescent polymer microspheres with dp = 12μm are injected into the Eaton box under four turbulence levels. Images of the aluminum-oxide particles are analyzed using planar Particle Image Velocimetry to identify turbulent flow structures. Simultaneously, a second camera is used to capture images through a filter of the fluorescent polymer microspheres to identify regions of particle clusters and voids. The spatial distribution of voids and clusters are compared with the distribution of turbulent flow structures./nThe characteristic length scales for particle voids and clusters vary significantly between the two sets of experiments. The images of polymer microspheres, which have a greater resolution, indicate a characteristic length scale for particle clusters of 10-20η depending on the Reynolds number, which matches the results of previous studies. Similarly, we find the characteristic length scales of particle voids ranges from 10 to 100η. In both sets of experiments, we find the distribution of particle voids, and to some extent particle clusters, follow a power-law fit indicating self-similarity. Results are inconclusive in linking turbulent flow structures to particle clusters and voids, which was unexpected.

Advisor: Savaş, Ӧmer
Hierarchical Deep Reinforcement Learning For Robotics and Data Science

This dissertation explores learning important structural features of a Markov Decision/nProcess from offline data to significantly improve the sample-efficiency, stability, and robustness/nof solutions even with high dimensional action spaces and long time horizons. It/npresents applications to surgical robot control, data cleaning, and generating efficient execution/nplans for relational queries. The dissertation contributes: (1) Sequential Windowed/nReinforcement Learning: a framework that approximates a long-horizon MDP with a sequence/nof shorter term MDPs with smooth quadratic cost functions from a small number/nof expert demonstrations, (2) Deep Discovery of Options: an algorithm that discovers hierarchical/nstructure in the action space from observed demonstrations, (3) AlphaClean: a/nsystem that decomposes a data cleaning task into a set of independent search problems/nand uses deep q-learning to share structure across the problems, and (4) Learning Query/nOptimizer: a system that observes executions of a dynamic program for SQL query optimization/nand learns a model to predict cost-to-go values to greatly speed up future search/nproblems.

Advisor: Goldberg, Kenneth
Integration of Skill Application and Attention Regulation Training to Improve Goal-Directed Cognitive Functioning

Improvement of cognitive function is of great value to many aspects of society. However, identifying robust procedures for training cognitive processes with generalizable benefits remains elusive. Here we present a novel attention regulation training paradigm that incorporates skill application in multiple learning environments. We hypothesized that our training procedure would enhance goal-oriented cognitive function and cognitive control mechanisms. We evaluated training effects using both computerized assessments and self-report questionnaires designed to probe cognitive control in everyday life. We tested for specificity of training effects by employing multiple active control conditions and for generalizability by using assessments that were significantly different from the training tasks as well as a set of secondary self-report questionnaires to explore the extent of far transfer. Training substantially improved performance on multiple tasks that involve goal-oriented cognitive functioning and cognitive control, and these gains were often specific to the group that received attention regulation training and also applied learned skills in varied environments.

Advisor: Silver, Michael A
Mechanical Energy Storage for Self-Destructing Motes and Jumping Microrobots

Mechanical energy storage has been studied to enable a self-destructing mote and a jumping microrobot. Just as chemical energy stored in batteries can be used for a wide array of devices, so too can mechanical energy stored in beams. In this work various energy storage elements are designed, fabricated, and tested to create these MEMS systems./nAs privacy and data security become increasingly important, new means of keeping that data safe must be developed. A MEMS system has been created to allow a wirelessly enabled mote to destroy itself on command. To achieve this, a cavity is microfabricated, filled with a silicon etchant, and capped with a fracturable membrane. An energy storage device capable applying 100's of milinewtons of force across distances of 10's of microns was designed and fabricated to fracture these membranes. Additionally, an electrostatic latch was developed to electrically trigger the release of the stored energy. The voltage required to keep this latch closed was reduced using a series of lever arms to amplify the electrostatic force./nTwo versions of a silicon jumping microrobots were developed as well. The first microrobot had no active force-producing components and used identical energy storage elements as the self-destructing mote project. In the second microrobot design, the energy storage elements were redesigned and optimized to work with an electrostatic inchworm motor. This motor was combined with a rack and pinion system to create a motor system capable of amplifying the force from a standard inchworm motor by a factor of 10. This microrobot was capable of storing 1.0 uJ of mechanical energy and jumping 1 mm when its motors were actuated electrically through tethered inputs. When the energy storage elements were loaded manually and latched using one of the inchworm motors, 4.0 uJ of energy were stored and the microrobot jumped 6.5 mm./nFinally, a design and simulation library was created throughout this work specifically for microrobots. This library, written in MATLAB, can be used to programmatically generate layout files as well as simulation files. While this functionality exists in other software packages, the MATLAB environment enables calculations to be done in-line with the layout. Users can easily add new functions and build upon the existing software. The simulation environment uses a solid body physics simulator to test functionality of microrobots in software before they are fabricated. This helps ensure that new designs work as intended before going through the time intensive and costly process of fabrication in the cleanroom.

Advisor: Pister, Kristofer S.J.
An Architecture for Network Function Virtualization

Today’s networks provide more than connectivity. Network functions such as firewalls, caches, WAN optimizers play a crucial role in improving security and performance capabilities. Although network functions traditionally have been implemented as dedicated hardware middleboxes, a recent effort commonly referred to as Network Function Virtualization (NFV) promises to bring the advantages of cloud computing to network packet processing by moving network appliance functionality from proprietary hardware to software. However, while NFV has quickly gained remarkable momentum in the industry, accepted NFV approaches are merely replacing monolithic hardware with monolithic software./nIn this dissertation, we argue that current approaches to NFV are ill-suited to the original vision of NFV. Instead, NFV needs a framework that serves as a common runtime for network functions. We present E2 – an NFV framework that provides placement and elastic scaling with high-level network function composition interface. We further consider the privacy challenge of outsourcing NFV deployments in public clouds and present a functional cryptographic technique for privacy-preserving packet classification. Finally, we discuss optimizing NF data-plane scheduling for performance guarantees.

Advisor: Ratnasamy, Sylvia P
Essays in Household Finance

This dissertation seeks to understand what components of household finance are important to consumers. In the first two chapters, we study a natural experiment in Chile where the government introduced legislation to increase financial transparency. In particular, the legislation required banks to include fees in the interest rate and later to provide a standardized presentation of their loan terms. Using administrative data on the universe of consumer loans in Chile, we use a regression discontinuity design to estimate the effect of this transparency reform on loan interest rates. We find that consumers are 50% less likely to default and 100% less likely to be delinquent on their loans. Further, we find that less sophisticated consumers benefited more from transparency legislation that communicated less information than legislation that presented more comprehensive information about their loans. We expand these findings and develop a dynamic structural model in order to explore the link between reduced informational frictions, price-sensitivity in consumer decisions, and welfare in long-term market equilibrium. We find that, after the policy, information frictions fell around 10 percent, which translated into an interest reduction of 180 basis points. We estimate a welfare improvement for consumers of 15 percent in the long run. The last chapter uses tuition freezes on public schools in six states to examine nonprofit universities' tuition reactions to this imposed constraint on their competitor public school. Evidence from both an event study and an instrumental variables approach shows that non-profit universities do not change their prices in response to tuition freezes by comparable public schools. In contrast, for-profit universities decrease their prices by roughly $1,000. This suggests that competition between universities puts downward pressure on prices for for-profit schools but not nonprofit schools. This suggests that an important component of household spending, human capital accumulation, may become increasingly out of reach for households as few determinants cause tuition to go down.

Advisor: Malmendier, Ulrike
Self-Efficacy and Conceptions of Ability of Intelligence, Creativity, and Sport

Dweck (1986) hypothesized that some students believe intelligence is a stable quantity that cannot be altered (i.e., fixed) whereas other students view intelligence as a flexible trait that can be changed with effort (i.e., malleable). Presumably, students with a malleable belief about, or a malleable conception of, intellectual ability will be more efficacious in their academic performance compared to those with a fixed conception. Little research exists on the relationships between conceptions of ability and self-efficacy. Using a sample of 151 predominately Asian and Filipino American middle school students from an urban area, I examined the relationships among domain-specific conceptions of ability and domain-specific self-efficacy in the areas of intellectual, creative, and sport abilities. Participants were recruited from a school in the San Francisco Bay Area of the United States. Results indicated that conceptions of intellectual ability did not predict a meaningful proportion of the variance in academic self-efficacy and conceptions of creative ability did not predict a meaningful proportion of the variance in creative self-efficacy. Conceptions of sport ability accounted for a meaningful proportion of the variance in sport self-efficacy. There were no associations between conceptions of intellectual ability and self-reported grades. Implications of the findings within the field, limitations of the current study, and future directions of research are discussed.

Advisor: Worrell, Frank C.
Living on the Edge of Empire: Edomite Households in the First Millennium B.C.E.

ABSTRACT/nLiving on the Edge of Empire: Edomite Households in the First Millennium B.C.E./nby/nStephanie Hope Brown/nDoctor of Philosophy in Near Eastern Studies/nUniversity of California, Berkeley/nProfessor Benjamin Porter, Chair/nThis dissertation explores the relationship between ancient empires and their peripheries. Due to the uneven distribution of written sources in the ancient world, the narratives describing this relationship are almost always written from the perspective of the imperial core. By ignoring the perspectives of groups living within imperial peripheries, this dissertation argues that these narratives omit a crucial element of the core-periphery relationship. Two such core-periphery relationships existed during the first millennium B.C.E. between the Neo-Assyrian and Neo-Babylonian Empires and the polity of Edom (located in present-day southwest Jordan). As with other core-periphery relationships in the ancient world, scholars have largely relied on sources produced by the imperial cores of the Neo-Assyrian and Neo-Babylonian Empires in order to understand their respective relationships with Edom, ignoring the perspectives and agency of conquered groups living in Edom./nThis dissertation uses a tripartite approach to explore the core-periphery relationships between Edom and the Neo-Assyrian and Neo-Babylonian Empires. This approach gives equal weight to sources produced by the imperial core, the Edomite elite, and the Edomite populace in order to correct the imbalance evident in previous scholarship on Edom. The dissertation employs theories and methods associated with household archaeology and foodways practices in order to discern the actions of the Edomite populace—arguably the least historically-visible people involved in these core-periphery relationships. Because evidence produced through household-archaeological and foodways-based approaches do not rely on logocentric means of communication, they are effective means of elucidating the actions and preferences of individuals and groups about whom there is no written evidence./nThe evidence explored in this dissertation found that during the period of Neo-Assyrian and Neo-Babylonian rule over Edom, life in southwest Jordan changed considerably. Neo-Assyrian political and economic policies throughout the Levant altered large-scale trade networks and forced tribute requirements on conquered peoples. This dissertation argues, however, that while both the Edomite elites and the Edomite populace took advantage of these changing regional systems, there is very little evidence of direct Neo-Assyrian or Neo-Babylonian influence found within the sources produced by both groups of Edomites (until the reign of Nabonidus); rather, the evidence suggests that these groups were closely integrated into local and Levantine social, economic, and political systems.

Advisor: Porter, Benjamin W.
Proposals for a Sustainable Energy Regulatory Framework: The Case of Carbon Pricing in South Korea

This dissertation focuses on analyzing the problems of the institutional structure and the process of energy policymaking for carbon pricing as a domestic implementation scheme of the global climate accord and making proposals for improvement. The case of South Korea illustrates the political and institutional challenges and conflicts that the global climate change scheme faces concerning local implementation. The country has recently experienced continued lower rate of renewable energy generation and acute political conflicts on energy options, despite ambitious commitment to reduce greenhouse gases communicated globally. This study analyzes the political and institutional causes of the current problems with the South Korean energy regulatory scheme as a case study and makes proposals for the institutional and instrumental changes required to mitigate those problems. The goal of the proposals is to build a more efficient energy policymaking process with enhanced transparency in order to make the energy generation and consumption of South Korea more sustainable, which will enable the country to contribute to global efforts concerning climate change mitigation./nThe dissertation begins by reviewing energy policy documents, research papers containing cost-benefit analyses and the carbon pricing created by multiple agencies of the Korean government, which were obtained through official information disclosure requests filed with the Korean government. The analysis focuses on the less refined cost-benefit analysis, the inconsistent and unfounded method of carbon pricing in each document, and the dynamics among relevant agencies by comparing the subtle difference in the way each agency handles energy policy, including carbon pricing. This review further elaborates on the less aligned aspects of the relevant policy instruments, such as the traditional command-and-control style of environmental regulations and the status of their implementation, a newly introduced market-based emissions trading scheme, the wholesale electricity pricing mechanism with the market structure and carbon pricing methodology./nProposals to mitigate those problems based on a comparative review of corresponding U.S. energy policy follow in three aspects, addressing the practicality and the expected political conflicts: (i) instrumental changes in energy policymaking required to make the cost-benefit analysis for energy policies more accountable, efficient, and transparent, reflecting proper carbon pricing; (ii) improvements of the current nation-wide, market-based emissions trading scheme for CO2, with further refinement of the relevant command-and-control type regulations, and the electricity price scheme; and (iii) institutional changes required in the structure of the relevant agencies and the electric power market required to build a more solid institutional infrastructure to effectively implement domestic climate-change policy, securing noticeable independence from political changes.

Advisor: Yoo, John C
Seiberg-Witten and Gromov invariants for self-dual harmonic 2-forms

For a closed oriented smooth 4-manifold X with $b^2_+(X)>0$, the Seiberg-Witten invariants are well-defined. Taubes' "SW=Gr" theorem asserts that if X carries a symplectic form then these invariants are equal to well-defined counts of pseudoholomorphic curves, Taubes' Gromov invariants. In the absence of a symplectic form there are still nontrivial closed self-dual 2-forms which vanish along a disjoint union of circles and are symplectic elsewhere. This thesis describes well-defined counts of pseudoholomorphic curves in the complement of the zero set of such near-symplectic 2-forms, and it is shown that they recover the Seiberg-Witten invariants (modulo 2). This is an extension of Taubes' "SW=Gr" theorem to non-symplectic 4-manifolds./nThe main results are the following. Given a suitable near-symplectic form w and tubular neighborhood N of its zero set, there are well-defined counts of pseudoholomorphic curves in a completion of the symplectic cobordism (X-N, w) which are asymptotic to certain Reeb orbits on the ends. They can be packaged together to form "near-symplectic" Gromov invariants as a map on the set of spin-c structures of X. They are furthermore equal to the Seiberg-Witten invariants with mod 2 coefficients, where w determines the "chamber" for defining the latter invariants when $b^2_+(X)=1$./nIn the final chapter, as a non sequitur, a new proof of the Fredholm index formula for punctured pseudoholomorphic curves is sketched. This generalizes Taubes' proof of the Riemann-Roch theorem for compact Riemann surfaces.

Advisor: Hutchings, Michael
Decoding the mechanisms of cancer and stem cell immortality

Telomeres are the repetitive sequences at the ends of linear chromosomes. The/nkey functions of telomeres are to protect the cells from losing genomic information and to/nprevent chromosome ends from being repaired by the double strand break repair/nmachinery. To counteract loss of telomeric DNA, cells can express a reverse/ntranscriptase, telomerase, that synthesizes telomeric repeats de novo. In humans,/ntelomerase activity is mostly restricted to germ and stem cells, so the telomeres of most/nsomatic cells progressively shorten with each cell division. Once telomeres become/ncritically short, they are recognized as sites of DNA damage and cells cease to proliferate./nBy this mechanism, telomere shortening functions as a tumor suppression mechanism./nTERT, the protein component of telomerase, becomes silenced once stem cells/ndifferentiate. However, in 90% of cancer cells, TERT is transcriptionally re-activated./nThus, telomerase regulation is crucial for our understanding of telomere length regulation/nin stem cell maintenance and tumorigenesis. To understand how telomerase acts on/ntelomeres, I attempted to endogenously tag telomerase. To do this I inserted epitope tags/nat the endogenous TERT locus in hESCs using genome editing. However, I found that all/nthe tested tags cause defects in telomere maintenance, which was previously not/nappreciated in experiments using exogenous overexpression./nRecently, point mutations in the TERT promoter were identified as the most/nfrequent non-coding mutations in cancer. To elucidate the role of TERT promoter/nmutations (TPMs) in tumorigenesis, I genetically engineered these TPMs into human/nembryonic stem cells (hESCs) using genome editing. Using the resulting isogenic hESC/nlines, I demonstrated that TPMs lead to a failure of TERT silencing upon differentiation/nfrom stem into somatic cells. To understand role of TPMs in tumorigenesis, I monitored/nlong-term telomere maintenance and proliferation in human fibroblasts engineered to/ncarry TPMs. I found that TPMs immortalize cells but do not prevent telomere shortening/nand telomere fusions. In vitro, around the time when telomere fusions occurred, TERT/nexpression was gradually increased. Thus, TPMs are required, but not sufficient, for/ncancer cell immortality and contribute to tumorigenesis in two steps. First, TPMs expand/nproliferation capacity of a cell by elongating only the shortest telomeres but do not/nprevent overall telomere shortening. In the second step, TPMs fuel tumorigenesis by not/nfully suppressing genomic instability. In order for cells to immortalize they need to/nupregulate TERT during this second step.

Advisor: Hockemeyer, Dirk
Statistical and computational methods for single-cell transcriptome sequencing and metagenomics

I propose statistical methods and software for the analysis of single-cell transcriptome sequencing (scRNA-seq) and metagenomics data. Specifically, I present a general and flexible zero-inflated negative binomial-based wanted variation extraction (ZINB-WaVE) method, which extracts low-dimensional signal from scRNA-seq read counts, accounting for zero inflation (dropouts), over-dispersion, and the discrete nature of the data. Additionally, I introduce an application of the ZINB-WaVE method that identifies excess zero counts and generates gene and cell-specific weights to unlock bulk RNA-seq differential expression pipelines for zero-inflated data, boosting performance for scRNA-seq analysis. Finally, I present a method to estimate bacterial abundances in human metagenomes using full-length 16S sequencing reads.

Advisor: Dudoit, Sandrine