VictorJuiz/thesis huggingface dataset:
On Stability and Doctor-optimality of Cumulative Offer Process

I study the stability and doctor-optimality of doctors' proposing cumulative offer process in the many-to-one matching with contracts. First, I explore some conventional hospital-by-hospital conditions on each hospital's choice function, and show that unilateral substitutability is equivalent to observable substitutability across doctors combined with cumulative offer achievability, each of which is a necessary condition for cumulative offer process to be doctor-optimally stable in a sense that if a hospital does not satisfy the condition, then we could construct some choice functions for other hospitals such that cumulative offer process is not doctor-optimally stable for some doctors' preference profile. Then, I focus on the joint properties of the choice functions for the entire group of hospitals and introduce two joint conditions---independence of proposing order and group cumulative offer achievability---and show that when these conditions are satisfied, cumulative offer process is always doctor-optimally stable. And it is by far the weakest sufficient condition. Moreover, these two conditions are necessary in a sense that if not, then there exists a doctors' preference profile and a proposing order such that cumulative offer process is not doctor-optimally stable. At last, I also introduce doctor's preference monotonicity and show that when cumulative offer process is doctor-optimally stable, this condition guarantees its strategy-proofness.

Advisor: Shannon, Chris
Quantifying Reproducibility and Bias in Single-Cell Sequencing Analyses of Human Immunity

Single-cell RNA sequencing technologies have evolved rapidly over the past few years, but the newest protocols and platforms are still limited by bias and noise. These technical issues can present serious challenges to downstream data analyses when samples are collected from multiple human donors recruited from multiple sites. My dissertation outlines methods for assessing bias and quantifying reproducibility in single-cell RNA sequencing studies. These tools are applicable to a new class of single-cell studies of human disease that move beyond tissue-level case–control comparisons. I have implemented these methods in two software packages, scone and scRAD, both developed to improve the quality of biological insights derived from single-cell RNA sequencing data.

Advisor: Yosef, Nir
DeWeese, Michael
Social Learning in Health Insurance Choices: Evidence from Employer-Sponsored Health Plans

Research has documented that consumers often have imperfect information about the health insurance plans from which they are asked to choose, but we know less about the sources of that information. Given the difficulty in obtaining reliable information from independent sources, consumers may draw on their peers for recommendations. This dissertation investigates the role of social learning in health insurance selection, using longitudinal data from the University of California on plan choices of employees and peers in their department. The data from 2011 to 2016 span a major change in the insurance choice set, which aids in the statistical identification of social learning effects among both incumbent employees as well as new hires. I start by documenting the high similarity in plan choices within peer groups, suggesting the possibility of strong peer effects, and then use a variety of approaches to test for potential confounding from unobserved heterogeneity. I employ a discrete choice conditional logit estimator to formally model plan choice behavior, finding that a 10 percentage point increase in the share of peers who select a particular insurance plan will lead to a 14 percentage point increase in the probability that an individual will choose the same plan. This large effect on plan choice is equivalent to lowering the monthly premium by 18 percent. I then use this model to simulate employer strategies that could exploit social learning to better promote the employer's insurance objectives. For illustration, I conduct counterfactual analyses of incentives to promote adoption of a new consumer-driven insurance plan. At the actuarially fair premium in this setting, demand for a consumer-driven plan is low, and social learning further discourages take-up. However, with sufficient premium subsidies, the model projects that the social learning effects will become positive and can be harnessed by employers to more effectively achieve their cost and insurance coverage goals.

Advisor: Dow, William H
Addressing Challenges on the Dark Energy Spectroscopic Instrument (DESI)

The Dark Energy Spectroscopic Instrument (DESI) is under construction to measure the expansion history of the universe using the baryon acoustic oscillations technique. The spec- tra of 35 million galaxies and quasars over 14,000 square degrees will be measured during a 5-year survey. A new prime focus corrector for the Mayall telescope at Kitt Peak National Observatory will deliver light to 5,000 individually targeted fiber-fed robotic positioners. The fibers in turn feed ten broadband multi-object spectrographs. This thesis details origi- nal work done in support of the DESI experiment, both for the instrument and survey design and optimization. First, I describe a novel approach for connecting optical fibers using fusion splicing, a method that will be implemented on DESI. Then, I will describe the ProtoDESI experiment, an on-sky technology demonstration with the goal to reduce technical risks asso- ciated with aligning optical fibers with targets using robotic fiber positioners and maintaining the stability required to operate DESI. The ProtoDESI prime focus instrument, which was installed and commissioned on the 4-m Mayall telescope from 2016 August 14 to September 30, consisted of three fiber positioners, illuminated fiducials, and a guide camera. ProtoDESI was successful in acquiring targets with the robotically positioned fibers and demonstrated that the DESI guiding requirements can be met. Finally, I will describe a predictive sky background model for DESI, which is built on the spectra from the 5-year Baryon Oscilla- tion Spectroscopic Survey (BOSS). This dataset consists of ∼1 million unique sky spectra covering 360 - 1040 nm collected in a variety of observational conditions. We measure an inter-airglow line continuum value of ∼ 0.81×10−17erg/cm2/s/ ̊A/arcsec2 in dark time across the full wavelength range, with a variance of ∼ 0.175 × 10−17erg/cm2/s/ ̊A/arcsec2. The de- tailed model, which accounts for 50% of the variance, shows that the dark sky continuum consists of ∼ 30% zodiacal light and is significantly impacted by solar activity. The improved spectroscopic sky background model can be used in simulations and forecasting for DESI and other surveys.

Advisor: Schlegel, David
Perlmutter, Saul
Expansion of the Surrogate Method to Measure (n,xn) Cross Sections and Fission Neutron Multiplicity Distributions

In addition to \textsuperscript{235,238}U and \textsuperscript{239}Pu, \textsuperscript{241}Pu is considered a major actinide in regards to nuclear fuel and systems. Despite contributing up to $\sim$10$\%$ of energy generated in nuclear reactors towards the end of a cycle, nuclear data for this isotope is limited. Due to its 14 year half-life, target manufacturing for this isotope is difficult, and as a result the (n,xn) cross section and fission neutron multiplicity as a function of incident neutron energy for $^{241}$Pu does not exist in the published literature. Using the surrogate ratio method, experimental difficulties associated with target manufacturing can be circumvented in measuring n + $^{241}$Pu reactions by using inelastic scattering of $\alpha$ particles incident on $^{242}$Pu to create the same compound nucleus. The NeutronSTARS detection array in Cave 4 of the Texas A$\&$M Cyclotron was commissioned specifically for experiments of this nature. The target chamber consists of three large area silicon detectors: two serve as a silicon telescope to determine the energy of the scattered alpha particle, and one fission detector to gate on fission events by detecting fission fragments. A segmented cylindrical array consisting of ~2.2 tons of gadolinium doped liquid scintillator is used to detect emitted neutrons. By relating the detected recoiled alpha energy to an equivalent neutron energy, detecting fission fragments to separate neutron evaporation events from fission, and detecting emitted neutrons in close time coincidence; an attempt to measure the (n,xn) cross section and prompt fission multiplicity for $^{241}$Pu was made. The prompt fission neutron multiplicity was fit to a skewed Gaussian distribution, while the average neutron multiplicity was recorded. Due to the large contribution of oxygen and carbon in the target, relatively low neutron detection efficiency, and inadequate background rejection for non-fission events; the (n,xn) cross section measurement was difficult to extract.

Advisor: Norman, Eric B
Surround integration during active sensation in the mouse barrel cortex

Organisms scan their sensors around their environment to build an internal representation of that environment in a process known as active sensation. The integration of information across time and space is critical to providing context as to what is the organism is perceiving. However, the neural circuits that encode and underlie the integration of incoming sensory information have predominantly been studied in the context of passive sensation. Studying these circuits in the context of active sensation is imperative to generating a better understanding of how the brain naturally encodes sensation. This would have profound impacts on understanding the mechanisms of a number of neural disorders, including autism and attention-deficit/hyperactivity disorder, as well as how to improve the acuity of artificial sensation implanted into disabled individuals./nTo better understand how the mammalian brain encodes and integrates information during active sensation, my collaborators and I developed several novel paradigms to study surround integration in the mouse barrel cortex during active whisking. In Chapter 1 I establish why this is an important problem, and briefly summarize what is already known about sensory coding in the mouse whisker system. In Chapter 2 my collaborators and I probe how mice represent the location of an object within its whisking field, and how the integration of information across surround whiskers affects this representation. In doing so we discover a novel thalamocortical transformation where surround integration in the cortex suppresses activity in layer 4 of the cortex, ultimately generating a smooth map of scanned space in cortical layer 2/3. In Chapter 3 I utilize a novel tactile display to better understand the logic of multi-whisker integration in two cortical layers. In this unpublished work, I show that contrary to the previous literature in anesthetized mice, cortical neurons in awake, whisking mice powerfully summate specific whisker combinations supralinearly, generating a sparse code representing the entire combinatoric space of whisker touch. In Chapter 4, I conclude with some closing thoughts and propose some future lines of inquiry to further this research.

Advisor: Adesnik, Hillel
Punishing Play: Policing of Entertainment Activities in Oakland, California, Lima, Peru, and Stockholm, Sweden

Despite a general pattern of decarceration occurring in US prison rates, an equivalent realignment has not developed around policing policy in cities across the US. This is despite the fact that in recent years, police departments throughout the country have faced intense public scrutiny for issues of misconduct and police violence. At the same time, a divide seems to be underway globally in which some cities and municipalities are adopting US-style, order-keeping policing policy, while others are reconsidering the conventional wisdom around the methods and goals involved in crime control. This dissertation investigates police practices aimed at “disorderly” activities on the margins of the law. It consists of a comparative ethnographic study of three restricted forms of entertainment in Oakland, California, Lima, Peru, and Stockholm, Sweden to investigate how different societies police activities deemed disorderly and how targeted groups respond to these interventions. Although prior penology scholarship has centered the discussion of punitive penal systems on larger political economic projects (e.g. neoliberal vs. social democratic) or solely at the site of the carceral state, this study shows how two mid-level factors—external, key government actors and internal police organizational logics—gives way to punitive practices described as dissonant disciplining. While dissonant disciplining in Oakland involved raids, surveillance, and racial profiling practices, in Lima, incosistent organizational logics made dissonant disciplining largely informal, consisting primarily of intimidation and physical violence handed out on the street. Repressive practices in these two sites threatened public safety and fueled direct acts of resistance directed at the police. Contrasting these findings, in Stockholm, policing reforms brought about by the central government paved the way for dialogue policing reforms. Dialogue policing suspended enforcement of nuisance laws in exchange for stronger relationships with policed groups, reduced incidence of violence, and diminished resistance to police efforts. The findings of the dissertation suggest the need to place greater focus on policy domains and institutional arrangements taking shape around penal organizations. Additionally, the research has policy implications as it pertains to policing reform. Namely, reform efforts aimed at reducing danger and racial bias in police practices would be served to target government actors which place untethered power in the hands of police organizations.

Advisor: Enriquez, Laura J
Harding, David J
American Graphic

This dissertation theorizes the “graphic” as a term seemingly at odds with itself. On one hand, “graphic” demarcates the provocative, upsetting excess of visual and/or verbal works that inadequately temper their taboo-violating content. This graphic is gross, sticky, shocking. On the other hand, “graphic” promises the geometrically streamlined—information mastered on a coordinate plane or in sleekly simplified visuals, through which people and places can be appraised from a comfortable distance. This sort of “graphic” is about calculations and schematics, detachment and diagrams, and disinterested evaluation. I examine twentieth-century American texts (primarily post-45) that perplexingly and provocatively encompass these extremes of the graphic at the same time. These are texts at once viscerally grotesque and coolly clinical. In them, readers are forced into the affective bind of a mode of identification that is simultaneously classificatory and empathic. It is only when we think about famously graphic twentieth-century American literature as disinterested and disgusting at once that we can expose the unseemliness of the lust, in our contemporary culture of information, for epistemological mastery of the bodies of others./nI analyze the “double graphic” along three specific axes: the ethnographic, the pornographic, and the infographic. Whether dealing primarily with race, sex, or data, each manifestation is marked by the discomfiting affective ambivalence of coercive identification. We both empathize with and clinically document other people in moments of taboo overexposure. So we see the conflation of racial classification and racial violence in Edgar Alan Poe’s Tslalians in The Narrative of Arthur Gordon Pym (1838), later reimagined by Mat Johnson in Pym (2011), and evident in the visual work of Kara Walker. In these texts, uncannily animated ethnographic silhouettes—racial others reduced to flat icons—become available for both classification and laceration: produced by cutting and perhaps apt, too, to cut back. I uncover the antiseptic titillation of pornographic sex dolls in Vladimir Nabokov’s Lolita (1955), Fran Ross’s Oreo (1974), and the work of contemporary “avant-porn” performance artist Narcissister. The sex doll—which can be uncanny, repulsive, erotic, or hilarious—materializes the lust for “the ‘knowledge-pleasure’ of sexuality” that Linda Williams locates at the core of the pornographic, replacing complex people with fully knowable things. Finally, the peripatetic protagonists of Thomas Pynchon’s Crying of Lot 49 (1966) and Teju Cole’s Open City (2011) each engage in an infographic mode of tangential narration that becomes grossly parasitic on the intimate stories and secrets of others, transcribing personal trauma into cool data. In the graphic moment, I argue, people shift unsettlingly into and back out of things—be they flat black silhouettes, hollow dolls, or dimensionless sets of data points—and we don’t quite know how we are meant to feel about it.

Advisor: Serpell, C. Namwali
The Cultural Politics of Water Privatization in an Arab-Israeli Town

From Theodor Herzl’s utopian novel Altneuland, to Seth Siegel’s recent bestseller, Let There be Water, Israeli water development has preoccupied the Israeli and Jewish imagination. Traditional scholarship on water in Israel focuses on high politics and international relations; official policy and its associated techno-logics; or views water problems through a purely economic lens. My dissertation takes a “bottom-up” ethnographic approach to examining water politics. It offers a new framework for thinking about natural resources, and “nature” in Israel by demonstrating the role of struggles over “nature” in linking and shaping two processes that are often assumed to be separate and opposed: nation building on the one hand, and global capitalism on the other./nDrawing on five years of ethnographic and historical research in Israel, my dissertation, The politics of water privatization in an Arab-Israeli town, argues that local struggles over access to water in the context of water privatization, reveals the contradictory relationship between nation building with its rigid delineation of territorial boundaries on the one hand, and global capitalist development on the other. I show how connections between processes of water privatization and ongoing discrimination in the realm of planning have come together in distinctive ways in Kafr-al-Bahar, the Israeli-Arab town where I conducted my research. These convergences are forged at the level of ordinary practices. I emphasize, in particular, the way that notions of "nature" are central to these processes and connections. For instance, I focus on alternative local water histories that residents have revived in the context of water cutoffs and indebtedness, and how they provide a framework for understanding, contesting and engaging with water privatization and the notions of nature that inform these policies. Such notions include taken-for-granted assumptions about the nature of Arab political culture, of national service, and of market logic. The alternative water histories that residents have revived, challenge the national narrative about the nature of Kafr-al-Bahar’s relationship to water and to the nation. Such an approach to water politics in Israel advances emerging scholarship on the interconnections of nationalism with globalization in Israel by bringing it into conversation with geographical and anthropological literature on the cultural politics of nature and difference in Israel./nEveryday water politics, homely as they may seem, are forcing front and center the issue at the heart of Israel’s current legitimation crisis; namely, the tensions between the values and institutions of liberal egalitarianism and the ongoing realities of dispossession, exclusion, and segregation.

Advisor: Kosek, Jake
Structure and Function of Fungal Polysaccharide Monooxygenases

ABSTRACT/nStructure and Mechanism of Fungal Polysaccharide Monooxygenases/nby/nElise Arielle Span/nDoctor of Philosophy of Biophysics/nUniversity of California, Berkeley/nProfessor Michael A. Marletta, Chair/nPolysaccharide monooxygenases (PMOs) are a newly discovered and growing superfamily of secreted copper catalysts found in nature. Initial PMO discoveries were made in 2011 describing the role of these enzymes in the cellulolytic machinery of fungi. Since then, additional families predominantly from fungi and bacteria have been characterized as having oxidative activity towards a variety of polysaccharide substrates. Chapter 1 introduces these enzymes and describes their origins, structure, function, as well as what can be surmised about their mechanism./nChapter 2 describes a study that probes PMO mechanism in a system utilizing insoluble (and non-quantifiable) cellulose as a substrate. A combination of in vitro assays and electron paramagnetic resonance studies of a panel of single amino acid variants illustrates the function of the secondary coordination sphere in O2 activation by a cellulose-active PMO. This study bears directly on the recent controversy over the co-substrate of PMOs: although under some conditions PMOs can utilize peroxide, there is clearly a pathway for O2 utilization./nAn example of discoveries that are on the horizon in the PMO field is described in Chapter 3. Genetic experiments and biochemical characterization of a homologously expressed PMO from Neurospora crassa shed light on a new family of PMOs that represents a significant departure from those studied previously. These enzymes are necessary for hyphal homing and fusion in filamentous fungi.

Advisor: Marletta, Michael A.
Chemical tools to design and study microbial communities

Techniques for the design and study of microbial cocultures may enable the development of bioproductions from more sustainable feedstocks. Furthermore, designed microbial communities could enable insights into a variety of fields including environmental bioremediation, microbial bioproductions or the microbiome. Each chapter of this dissertation describes the development of microbial cocultures or chemical tools to study microbial cocultures. In Chapter One, the development of a microbial coculture where one partner ensnares the other in a secreted biopolymer is described and characterized. In Chapter Two, a microbial coculture that produces the bioplastic polyhydroxybutyrate with no fixed carbon or nitrogen inputs is described. A strategy to improve the performance of this coculture using a spatially-constrained hydrogel is also discussed. Chapter Three delves into various strategies that have been developed to pattern microbes via DNA-based hybridization. This includes the description of a new oxidative coupling strategy that has been developed to pattern DNA on surfaces and its application towards the study of specific microbes and microbial communities.

Advisor: Francis, Matthew B