VictorJuiz/thesis huggingface dataset:
One Bird, Several Stones: Investigating Massive Galaxies via Stellar Kinematics, Environment, and Quasar Demographics

Massive galaxies are the end product of a long evolutionary history, impacted by many complex processes. A coupling between quasars and their host galaxies is thought to be an important factor in quenching star formation in these galaxies, although a single unified picture of this process has yet to emerge. The first and smaller portion of this work compares several simple models for quasar demographics, tuning the model parameters to match observations at redshifts from z = 1 to z = 6. A key feature of the models is the enforcement of self-consistent mass growth across time. A variety of models fit the observed luminosity functions, but physical arguments and comparison to additional observations can distinguish among the models. The second and larger portion of this work focuses on two-dimensional stellar kinematics for the most massive local galaxies. The MASSIVE survey is a volume-limited sample of 116 galaxies with absolute magnitude MK < −25.3 mag, corresponding to stellar mass above approximately 10^11.8 M⊙, within a distance of D < 108 Mpc in the northern hemisphere, with observations from the Mitchell Integral Field Spectrograph (IFS) for each galaxy a main component of the survey. The line-of-sight velocity distribution (LOSVD) is extracted from optical spectra over a 107′′ square field of view, with a Gauss- Hermite parameterization up to order 6. After characterizing the statistics of the velocity V , dispersion σ, and higher moments h3, h4, h5, and h6 for the most massive 41 galaxies of the sample, the first two moments (rotation velocity V and dispersion σ) are studied in more detail as a function of galaxy environment. Several measures of environment are calculated, and particular attention is paid to untangling the joint correlations among kinematic properties, galaxy mass, and galaxy environment. The properties of the MASSIVE sample suggest that merger histories and galaxy environment impact galaxy mass and angular momentum in tandem, with no independent correlation between angular momentum and environment once mass is controlled for. The shape of radial velocity dispersion profiles, however, depends on both galaxy mass and environment, with the correlation between dispersion profiles and environment persisting even when mass is controlled for (and vice versa). We include discussion of the kurtosis h4 to distinguish qualitatively between the influence of the total mass profiles and velocity anisotropy on the line-of-sight dispersion profile, and argue that variations from isothermal total mass profiles are very likely in our sample.

Advisor: Ma, Chung-Pei
White, Martin
Modulation of TOR Complex 2 signaling and maintenance of plasma membrane homeostasis in Saccharomyces cerevisiae

Target of Rapamycin (TOR) Complex 2 (TORC2) is a conserved multi-subunit protein kinase associated with the plasma membrane that is an essential regulator of growth. In Saccharomyces cerevisiae, TORC2 regulates the lipid composition and organization of the plasma membrane during normal cell growth and, in turn, responds to environmental insults (such as changes in osmotic conditions) that exert stress on the plasma membrane to maintain homeostasis. Ample genetic and biochemical evidence indicates that TORC2 exerts its effects solely via direct phosphorylation and stimulation of the activity of the downstream protein kinase Ypk1 (and its paralog Ypk2). Ypk1 action modulates plasma membrane lipid homeostasis in multiple ways, including up-regulation of sphingolipid synthesis and inhibition of aminoglycero-phospholipid flipping. Ypk1 also controls glycerol production and efflux, allowing cells to adapt to osmotic changes. Prior work demonstrated that TORC2 phosphorylates Ypk1 at two conserved sequence elements near its C-terminus, dubbed the "turn" and "hydrophobic" motifs. However, this study documents that TORC2 also phosphorylates Ypk1 at four additional C-terminal sites that are also critical for full TORC2-mediated stimulation of Ypk1 activity. Ala substitutions at the four new sites abrogated the ability of Ypk1 to rescue the phenotypes of Ypk1 deficiency, whereas Glu substitutions had no ill effect. Combining the Ala substitutions with an N-terminal mutation (D242A) that has been shown to bypass the need for TORC2 phosphorylation restored the ability to complement a Ypk1-deficient cell. These findings provide new insights about the molecular basis for TORC2-mediated activation of Ypk1. Moreover, TORC2 phosphorylation of Ypk1 changes differentially in response to different plasma membrane stresses; it is elevated in a sustained manner upon sphingolipid depletion, but rapidly and greatly diminished, although only transiently, upon hyperosmotic shock. In this work, new insights were also obtained about how hypertonic conditions influence TORC2. Results described here document that the plasma membrane osmosensor Sln1 is an upstream regulator of TORC2. Inactivation of Sln1, which causes activation of the Hog1 MAPK, leads to loss of TORC2 phosphorylation of Ypk1. This response requires the Hog1 MAPK itself and also the Slt2 MAPK. Upon Sln1 inactivation, Avo2 is hyperphosphorylated at its MAPK phosphoacceptor sites in a Hog1 and Slt2-dependent manner. These findings suggest that MAPK-mediated phosphorylation of Avo2 may provide a mechanism for exerting negative regulation on TORC2 function.

Advisor: Thorner, Jeremy W.
Hybrid Approaches to Bio-Materials and Bio-Inorganic Electrochemical Carbon Dioxide Reduction

Environmental challenges associated with rising atmospheric CO2 concentrations and the promise of CO2 as a cheap and abundant carbon feedstock motivate the search for technologies to transform CO2 into value-added chemical products. The development of stable, efficient, and selective electrocatalysts is challenging, and has traditionally been approached from either a molecular, materials, or biological perspective, each of which have benefits and drawbacks. In order to exploit the benefits of these distinct approaches and minimize their disadvantages, we have directed efforts into exploring hybrid systems for CO2 reduction. This thesis describes a bio-materials strategy designed to synergistically interface living organisms and electrocatalytic materials to achieve artificial photosynthetic transformations. We subsequently describe electrocatalytic CO2 reduction with molecular catalytics that have been inspired by design elements found in bioinorganic systems.

Advisor: Chang, Christopher J.
The Late-Time Formation and Dynamical Signatures of Small Planets

The riddle posed by super-Earths is that they are not Jupiters: their core masses are large enough to trigger runaway gas accretion, yet somehow super-Earths accreted atmospheres that weigh only a few percent of their total mass. In this thesis, I demonstrate that this puzzle is solved if super-Earths formed late, in the inner cavities of transitional disks. Super-puffs present the inverse problem of being too voluminous for their small masses. I show that super-puffs most easily acquire their thick atmospheres as dust-free, rapidly cooling worlds outside 1 AU, and then migrate in just after super-Earths appear. Super-Earths and Earth-sized planets around FGKM dwarfs are evenly distributed in log orbital period down to ~10 days, but dwindle in number at shorter periods. I demonstrate that both the break at ~10 days and the slope of the occurrence rate down to ~1 day can be reproduced if planets form in disks that are truncated by their host star magnetospheres at co-rotation. Planets can be brought from disk edges to ultra-short (<1 day) periods by asynchronous equilibrium tides raised on their stars. Small planets may remain ubiquitous out to large orbital distances. I demonstrate that the variety of debris disk morphologies revealed by scattered light images can be explained by viewing an eccentric disk, secularly forced by a planet of just a few Earth masses, from different observing angles. The farthest reaches of planetary systems may be perturbed by eccentric super-Earths.

Advisor: Chiang, Eugene
Ambulatory Care Organizations: Improving Diagnosis

Ambulatory care comprises a major and increasingly important part of the U.S. and other countries’ health care sectors. Every year in the U.S., about 80% of the population seeks care at a doctor’s office, amounting to one billion visits. These visits divide almost equally between primary care and specialty clinic organizations. Diagnostic work is part of most ambulatory care, and central to over 40% of patient visits that originate due to a new problem or a flare-up of an ongoing chronic problem. Yet, the risks associated with diagnostic failures have not garnered much attention from health care leaders and policy makers until a recent National Academy of Medicine (NAM 2015) report synthesized research data with the statement that “most people will experience at least one diagnostic error in their lifetime, sometimes with devastating consequences.” This dissertation first reviews organizational theories and measurement challenges relevant to diagnostic safety and quality in the context of ambulatory care, and then presents three papers analyzing specific organizational factors hypothesized to enable or thwart an accurate and timely diagnosis. The first paper targets delayed diagnosis from missed evidence-based monitoring in high-risk conditions (e.g., cancer) within five specialty clinics in an urban publicly funded health system. The second paper analyzes staff-reported office problems that could lead to diagnostic error (e.g., not having test results when needed) in over 900 primary and specialty clinics across the nation. The third paper examines the associations between two types of time pressure (i.e., encounter-level and practice-level), organizational factors, and patient effects including perceptions of missed diagnostic opportunities. The three primary conclusions from this work are 1) organizational vulnerabilities for missed monitoring common to the different clinics included challenges with data systems, communications handoffs, population-level tracking, and patient activities, leading to the development of ‘design seeds’ for context-flexible solutions to improve diagnostic quality; 2) two organizational factors – stage of health information technology (HIT) deployment and patient safety culture are associated with diagnostic-related office problems, and 3) encounter and practice-level time stressors in primary care clinics are associated with perceptions of greater adverse effects on diagnosis and treatment, and worse patients’ experiences of chronic care from the clinic team, respectively, as well as associated with several organizational factors including HIT, patient-centered culture, relational coordination for interdependent teamwork, and leadership facilitation of changes to address frontline practice challenges. Taken together, the dissertation papers also demonstrate the applicability of the NAM Improving Diagnosis Conceptual Framework for research on ambulatory care organizations.

Advisor: Shortell, Stephen M
Lithic Communities of Practice and Daily life in the Northwestern Maya Lowlands during the Late Classic (700-850 A.D.)

This dissertation uses multiple lines of evidence to understand production, exchange and crafting in agrarian societies with a focus on the Northwestern Mayan Lowlands during the Late Classic Period (700-850 A.D). The organization of production in Pre-Columbian times is poorly understood, yet exchange is believed to be critical to the development of sociopolitical relations in ranked agrarian societies, like those in Mesoamerica. This dissertation will examine how the material culture of everyday activities, especially those related to production and exchange, manifests in the archaeological context and reflects communities of practice. It will evaluate two models of control of production and exchange of craft products, primarily lithic products (stone tools) in state-level societies using evidence from regional surveys, household excavation, and archaeometric studies of stone tools. One model proposes that with the development of sociopolitical hierarchies, elites monopolize or centrally control production and circulation of craft goods, even when these productive activities continue to be practiced in decentralized locations, such as dwellings. The second model suggests that craft producers working in decentralized locations may have controlled most or all of the organization of production and distribution of craft products./nThrough extensive regional study, I mapped terrestrial and fluvial communication routes and their relationship to settlement pattern and site distributions. I established the least costly, and thus most likely patterns of travel in the region using analytic tools such as GIS. Including excavation at a major site, Chinikihá. Preliminary research established the presence of areas of production of chipped stone tools in an independent residence outside the palace zone. The excavations sought to understand domestic production and local patterns of production and exchange and tested theories around daily practice and social learning. The study includes a larger sourcing analysis of obsidian stone tools and debitage in done with Energy Dispersive X-RayFluorescence (EXDRF) to reconstruct the movement and exchange distribution. The resulting archaeological analysis and assemblages will reflect local techniques of production, the materials utilized, types of artifacts produced, and consumption practices that will result in a better understanding of the practices of procurement, production, exchange, consumption, social organization, and differentiation, as well as the communal practices in the region.

Advisor: Joyce, Rosemary A.
Shackley, Steven M.
Set in Motion: Dance Criticism and the Choreographic Apparatus

This dissertation examines the multiple functions of dance criticism in the 20th and 21st centuries in the United States. I foreground institutional interdependencies that shape critics’ practices, as well as criticism’s role in approaches to dance-making, and the necessary and fraught relations between dance criticism and higher education. To challenge the pervasive image of the critic as evaluator and of criticism as definitive, Set in Motion focuses on conditions that produce and endorse certain forms of criticism, and in turn how this writing has gained traction. I employ the concept of a choreographic apparatus to show shifting relations amongst writers, artists, publications, readers, institutions, and audiences. Their interactions generate frameworks that influence dance’s history, canon, and disciplinary formations. I propose a way of situating criticism as a form of writing that intersects with, informs, and influences both history and theory./nSet in Motion expands discourse on writing by examining the continuities and discontinuities in practices over the course of a century. Chapter 1 focuses on articles by John Martin in the New York Times the late 1920s and early 1930s. Chapter 2 analyzes how artists in the 1960s, in particular Yvonne Rainer, took hold of the choreographic apparatus to redirect discourse about their projects. In Chapter 3, I expand my analysis from methodologies to the study of educational institutions. Chapter 4 turns to the question, “where is criticism today?” and investigates how digital technologies in the 21st century inform and inflect our engagements with criticism. Set in Motion contributes to dance studies discourses, disciplinary formation, and histories of professionalization by noticing ways in which criticism and theory function less often as opposing forces and primarily as reciprocal and interconnected partners. By recognizing the ways criticism has functioned as a fulcrum to legitimate and leverage particular approaches to dance, this project highlights artists’ and critics’ modes of production that generate and redesign our definitions of dance writing.

Advisor: Jackson, Shannon
Temporal Constraints on Saccadic Eye Movements

Although we are rarely aware of it, our ability to visually perceive and successfully interact with the world depends on a rapid and carefully orchestrated sequence of eye movements. Roughly three times a second, large high-velocity movements known as saccades drastically alter the spatial and temporal stream of visual input. To investigate the temporal constraints on saccadic eye movements and identify biases in oculomotor behavior, I developed a simple but novel task: rapid alternating saccades (RAS). Human participants are asked to make a series of eye movements back and forth between stationary targets as quickly as possible./nIn Chapter 2, I investigate the characteristics of one of the most prominent and well-known biases in eye guidance, inhibition of return. Participants made RAS between two targets or following an “hourglass” pattern in which the same location is only sampled every fourth eye movement. The experiments revealed that both saccade dwell times and secondary saccade characteristics were dramatically altered when the eye returned directly to a previously viewed location. The effects depended on the direction of movement and the angular difference between subsequent saccades. The results further explicate the inhibition of return phenomenon and provide novel insight into motor and attentional constraints governing the rate of sequential eye movements./nChapter 3 explores interactions between the eye and the hand. Findings indicate that the maximum rate of RAS increases when concurrent and directionally compatible hand movements accompany the eye movements. The increase is the result of shorter dwell times, higher saccade peak velocity, and a decrease in secondary saccade occurrence. The findings occur independently of changes in saccade amplitude or direction. Hand movements in the opposite direction of the eye result in longer dwell times and more frequent secondary saccades. The experiments illustrate the tight temporal coordination between saccades and arm motor systems during sequential movements.

Advisor: Olshausen, Bruno A
Theory of Real Bundles on the Projective Line

In this thesis we discuss the theory of vector bundles with real structure on the projective line. This extends classical work by Grothendieck classifying complex vector bundles on the projective line. In particular, we show that vector bundles with real structure can be classified in terms of the coroot lattice of GL(n), similarly to the complex case. In addition, we provide a comparison of a certain K-group of sheaves on the moduli space of vector bundles to a K- group of sheaves on the moduli space of local systems, a kind of Langlands duality statement for real bundles, and give a uniformization of the moduli space.

Advisor: Nadler, David
Microaggressions in the Context of Conflict: A Study of Perceived Discrimination among Israeli Adolescents

Ethnic microaggressions refer to subtle slights or mistreatments that can occur in regard to someone’s ethnicity. This study tests the validity of an adapted measure of racial microaggressions among a sample of Israeli students in order to understand which ethnic microaggression dimensions emerge from adolescent self-reports. It uses those dimensions to assess how they correlate with general perceptions of discrimination and with reports of psychological distress. It then seeks to understand how overall reports of microaggressions vary by ethnic identity and geographic locality. Cross-sectional data were collected from high school students throughout Israel (N =1,031). An exploratory factor analysis revealed four dimensions of microaggressions: (1) Invisible Ethnicity, (2) Criminalized Ethnicity, (3) Disadvantaged Ethnicity, and (4) Homogenized Ethnicity. The Invisible and Criminalized dimensions corresponded closely to dimensions identified in prior United States-based, adult-focused research, suggesting that those dimensions may be valid cross-nationally and with both adolescent and adult populations. An ordinal logistic regression revealed that Disadvantaged Ethnicity was the only dimension to significantly correlate with more general perceptions of discrimination. A multiple linear regression revealed that Invisible Ethnicity and Criminalized Ethnicity both significantly correlated with higher levels of psychological distress. Via a two-level hierarchical linear model, it was found that identifying as Arab, Palestinian-Israeli, Ethiopian, or Bedouin significantly correlated with higher reports of microaggressions. However, differences in geographic-locality did little to explain variance in microaggression reports./nFindings from this study suggest that microaggression reports may vary by ethnicity, Israeli identity, level of religiosity, and mother’s education level. They additionally reveal that decreases in exposure to microaggressions related to Disadvantaged Ethnicity is associated with a decrease in perceptions of discrimination; decreases in exposure to microaggressions related to Invisible and Criminalized Ethnicity is associated with a decrease in psychological distress. Decreasing psychological distress could also be associated with decreased perceptions of discrimination. This study is the first to examine reports of microaggressions among Israeli adolescents, and to establish the relationship between microaggression reports, perceptions of general discrimination, and psychological distress. By building on social, political, and developmental psychology theories, it employs a unique approach to understanding how minority adolescents in Israel experience discrimination in their daily lives.

Advisor: Segal, Steven P.
Architecting for Performance Clarity in Data Analytics Frameworks

There has been much research devoted to improving the performance of data analytics frameworks, but comparatively little effort has been spent systematically identifying the performance bottlenecks of these systems. Without an understanding of what factors are most important to performance, users do not know how to choose a software and hardware configuration to optimize runtime, and developers do not know which optimizations are most important to implement./nThis thesis explores how to architect systems for performance clarity: the ability to understand where bottlenecks lie and the performance implications of various system changes. First, we focus on incrementally adding performance clarity to current data analytics frameworks. We develop blocked time analysis, a methodology for quantifying performance bottlenecks in parallelized systems, and use it to analyze the Spark framework’s performance on two SQL benchmarks and one production workload. Contrary to commonly-held beliefs about performance, we find that (i) CPU (and not I/O) is often the bottleneck, (ii) improving network performance can improve job completion time by at most 2%, and (iii) the causes of most stragglers can be identified./nBlocked time analysis helped to understand performance bottlenecks in today’s frameworks, but fell short of enabling users to reason about the impact of potential hardware and software configuration changes. Given the challenges to providing performance clarity in current architectures, the second part of this thesis focuses on a new system architecture built from the ground up for performance clarity. Rather than breaking jobs into tasks that pipeline many resources, as in today’s frameworks, we propose breaking jobs into units of work that each use a single resource, called monotasks. We demonstrate that explicitly separating the use of different resources simplifies reasoning about performance without sacrificing fast runtimes. Our implementation of monotasks provides job completion times within 9% of Apache Spark, and leads to a model for job completion time that predicts runtime under different hardware and software configurations with at most 28% error for most predictions.

Advisor: Ratnasamy, Sylvia