VictorJuiz/thesis huggingface dataset:
Natural variation and evolved trade-offs in yeast carbon metabolism [electronic resource]

The processes by which the budding yeast Saccharomyces cerevisiae metabolizes carbon sources by both fermentation and respiration have been studied for more than a century. Yeast metabolism has been used both industrially, for the production of important molecules such as ethanol, and as a model for basic scientific research. Applied scientists have studied yeast metabolism to create and optimize novel metabolic phenotypes not naturally found in Saccharomyces yeasts. In parallel, basic scientists have used yeast as a model to understand fundamental processes such as evolutionary adaptation, as well as the pathways of carbon metabolism themselves. There are many unanswered questions in both of these fields, some of which I have addressed in this work. With respect to the industrial importance of yeast, I asked whether there are naturally existing Saccharomyces yeasts that can metabolize the five-carbon sugars important for lignocellulosic ethanol production (such as xylose), and, if so, what is the genetic basis for their phenotypes? Having characterized natural genetic variation in xylose metabolism, I also wanted to understand something more fundamental about how carbon metabolism can adapt, including the molecular nature of adaptations to selection on a limiting carbon source. Specifically, I asked what is the niche breadth of, and are there genetic trade-offs in, yeast that have been evolved under glucose-limitation? I have used a combination of classical genetics, physiology, and high-throughput genomics to answer these two questions. I have discovered novel xylose-utilizing Saccharomyces yeasts and have shed considerable light on the genetic basis for their phenotypes. In addition, I have discovered at least one trade-off for adaptation to limiting glucose, namely that amplification of the hexose-transporter genes HXT6 and HXT7 causes reduced fitness in carbon-rich environments. These two projects highlight two major spheres of Saccharomyces research, and they provide key answers to outstanding questions in both fields.

Keywords: Genetics
Advisor: Sherlock Gavin primary advisor. Thesis advisor
Pringle John
Spormann Alfred M. advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
A necessary condition for robust implementation [electronic resource] : theory and application

Mechanism design theory examines which social objectives (such as efficiency, fairness, stability, and so on) can be achieved when agents have private information. In most of the papers in the mechanism design literature, it has been the standard approach to assume that the agents play a Bayesian-Nash equilibrium (typically with a ``common prior'') to predict the possible outcomes of mechanisms. However, this approach is often criticized due to its sensitivity of prediction to the assumptions on the agents' beliefs. Given these criticisms, some researchers have investigated robust mechanisms to uncertainty about the agents' beliefs, but the standard approach is to restrict attention to dominant-strategy mechanisms. This approach proves to be restrictive, especially in settings that require a balanced budget. In this dissertation, we consider similar robust approaches, but we do not restrict attention only to dominant-strategy mechanisms. In Chapter 2, we provide an example that illustrates a difference between the dominant strategy approach and the other robust implementation approaches. Specifically, we consider expected welfare maximization in a bilateral trading example with voluntary participation and balanced budget. Chapter 3 provides some general findings. First, we show that any social choice correspondence that is implementable in admissibility must have a ``tree dominance property'': For any profile of ``directed trees'' on each agent's type space, the social choice correspondence must have a selection that satisfies dominant-strategy incentive compatibility along all edges of these trees. Also, we discuss the relationships among different robust implementation concepts. In Chapter 4, we apply these theoretical findings to some economic examples. In general, the tree dominance property may not be a sufficient condition. In applications, we guess which tree dominance conditions are the ``binding'' conditions, and solve a relaxed problems subject to those tree dominance conditions. In some cases, the allocation rule that solves the relaxed problem is proved to be dominant-strategy incentive compatible, which means that dominant-strategy mechanisms cannot be robustly improvable. Even if the solution is not dominant-strategy incentive compatible, we can sometimes verify that this allocation rule can be used as a revelation mechanism that actually robustly implements the desired social choice correspondence. As specific applications, we study (i) bilateral trading settings with balanced budget, (ii) quasi-linear environments without balanced budget, and (iii) implementation of unique desirable allocation rules.

Keywords: Economics
Advisor: Segal Ilya primary advisor. Thesis advisor
Jackson Matthew O. advisor. Thesis advisor
Levin Jonathan D. (Jonathan David)
The neglected role of school district revenue instability [electronic resource] : measurement, causes and responses

Much of the school finance literature has focused on the distribution or equality of resources across school districts. Such literature compares levels of spending between school districts or states. But it has ignored the variability and unpredictability of those revenues within school districts over time. Meanwhile, public finance literature has focused on states or counties, and disregarded school districts as a unit of analysis for responses to fiscal stress. This dissertation addresses these gaps. First, drawing from techniques both within and outside of public finance, I contribute a new measure of fiscal stress based on unpredictability of state revenues. Second, I explicitly assess policy and tax mechanisms that may aggravate revenue instability for school districts and to what extent instability changes over time. Finally, I examine school districts response to chronic unpredictability in state revenues. Despite states' increasing reliance on more volatile sales and income taxes to fund public education, I find that unpredictability in state revenues to districts has declined by one-fourth of a standard deviation over time. In states that shifted to the more volatile sales and income tax base while also centralizing school finance as part of efforts to equalize school funding, unpredictability in state revenues to districts declined by a full standard deviation. In effect, centralization and more equal distribution of funding appears to trump the effects of a volatile tax base, as states have a greater ability to buffer against shocks than local education agencies do. Yet districts still face uncertain and unstable revenues from the states, aggravated by economic downturns. With primary and secondary data, I study the case of California where districts face uncertain cuts to their allocations during the year and between years. I use three key fiscal health measures: average revenue instability over time, whether revenues declined in the prior period, and the experience of the budget officer. I find that highly unstable districts are more likely to raise local revenues, but that cost-cutting is more prevalent that revenue-raising. Experienced budget officers use a greater variety of policy instruments to cope with instability, pointing to the under-explored role of management in the fiscal health of a district. These findings as a whole suggest that revenue instability merits further attention in the school finance literature in particular and public management in general. Unpredictability in states revenues is a phenomenon that concerns school districts, one that changes over time, but one to which they may adapt.

Keywords: Education.
Advisor: Loeb Susanna primary advisor. Thesis advisor
Bettinger Eric advisor. Thesis advisor
Plank David N. (David Nathan)
Negotiating disparate social contexts [electronic resource] : evidence from an interdistrict school desegregation program

This dissertation examines the academic and social effects of an interdistrict desegregation program on transfer students using 10 years of lottery-based data. The goal of the dissertation is twofold. First, I use school district administrative data to estimate the effects of attending better-performing, higher-resourced schools on student achievement. Because of the non-random sorting of students, it is unclear to what extent inequalities in educational outcomes stem from differences in school environments or from differences in family background and other extra-school attributes. To test this, I match transfer application records to student-level administrative records to examine differences in test scores, attendance, special education status, and English language acquisition between students who were lotteried in and those who were lotteried out. Second, I attempt to disentangle the processes that create these school effects. I use both deductive and inductive methods to pull apart structural, organizational, and cultural issues relevant to transfer students' outcomes. I use in-depth interview data from applicants currently in grades 6--12 and their parents to explore non-cognitive, or social, outcomes such as friendship formation, feelings of institutional affiliation in their schools and neighborhoods, and racial identity. Theories that explain the effects of school on students often neglect to consider the degree to which students are embedded in their schools. I introduce the term non-concentric institutions to characterize the non-overlapping nature of these students' environments. This concept contributes to our understanding of the ways in which institutional affiliations, and the potentially disconnected frameworks that emerge out of disparate affiliations, affect individual outcomes. Few scholars have considered the social implications of school choice programs. Moreover, while prior research has focused on African American children, this research sheds light on the effects of school context on Latino children as well, who experience a unique set of challenges including English language acquisition.

Keywords: Sociology.
Advisor: Reardon Sean F. primary advisor. Thesis advisor
Snipp C. Matthew primary advisor. Thesis advisor
McAdam Doug advisor. Thesis advisor
Neural mechanisms and dynamics underlying reaching and decision making [electronic resource]

The ultimate purpose of the motor system is clear: it exists to control the body. However, despite the motor system being among the longest-studied brain structures, it remains unclear how -- mechanistically -- motor cortex performs this function. Here, a mechanistic approach was taken to investigate how primary motor cortex (M1) and dorsal premotor cortex (PMd) control movement. That is, the goal was to elucidate the dynamics of the motor cortex 'machine.' Monkeys were trained in reaching tasks, and neural signals were recorded from their brains as they performed them. Two broad classes of analysis were used. First, cell-by-cell analyses were combined with cell-type analyses, which permitted examining the activity patterns of excitatory and inhibitory neurons separately. Second, techniques based on dynamical systems analysis (such as dimensionality reduction) were applied, which permitted analysis of neural populations as a whole and abstraction to a somewhat higher level of system function. Three major results and a technical advance are presented. Firstly, we investigated how it is possible for an animal to hold still even as neural activity in motor cortex changes drastically during preparation for the upcoming movement. We found that, contrary to common assumptions, there does not appear to be a 'gate' comprised of high inhibition during preparation. Instead, using the dynamical systems perspective, we found that preparatory activity has a special structure such that it remains in intrinsically muscle neutral, 'iso-force' patterns. Secondly, we searched for coherent dynamics in the movement-time activity of motor cortex. We found that motor cortex appears to obey a relatively simple set of dynamics, dominated by oscillatory patterns. Moreover, the exact neural trajectory is heavily determined ('seeded') by the immediately preceding preparatory activity. In order to causally perturb these dynamics with patterned stimulation and cell-type specificity, we then developed a set of optogenetic techniques for use in primates. Finally, we investigated how the dynamics of the decision-making process are reflected in motor cortex. To do so, we combined a novel decision-making paradigm, many simultaneous neural recordings, and single-trial analytical techniques. Preliminary results are given for this final section, demonstrating the presence of vacillation in monkey decision-making. In summary, we found that preparation and movement can be understood as an oscillatory dynamical system seeded by preparatory activity that lives in an iso-force space, that inhibitory and excitatory neurons seem to play more similar roles in the dynamical system than might be expected, and that moment-by-moment processes of motor decision-making can be seen in motor cortex.

Keywords: Neurosciences.
Advisor: Shenoy Krishna V. (Krishna Vaughn) primary advisor. Thesis advisor
Huguenard John advisor. Thesis advisor
Knudsen Eric I. advisor. Thesis advisor
Moore Tirin
Neuroanatomical correlates of emotion reactivity and regulation [electronic resource]

Morphometric studies reveal that the volumes of many brain structures differ between clinical and non-clinical populations. Specifically, populations characterized by affective disturbances related to heightened emotional reactivity and diminished emotion regulation have been found to possess smaller volumes of brain structures involved in emotion reactivity and regulation. I sought to determine whether similar associations would be found between brain structure and trait emotion reactivity and regulation in healthy individuals. Specifically, I predicted that emotion reactivity, as measured by negative affect, would be negatively related to the volume of the ventral anterior cingulate cortex, insula, orbitofrontal cortex, and amygdala, and that emotion regulation, as measured by usage of expressive suppression and cognitive reappraisal, would be positively related to the volume of the dorsal and ventral anterior cingulate cortex, dorsolateral prefrontal cortex, hippocampus, orbitofrontal cortex, cerebellar vermis, and anterior insula. I tested these predictions using two complementary methods, region of interest (ROI) and voxel-based morphometry (VBM). In Study 1, which used a sample of healthy adult women, trait usage of expressive suppression was correlated positively with the volume of the middle frontal gyrus and anterior insula, and negatively with ventral anterior cingulate volume. Trait usage of cognitive reappraisal was correlated positively with the volume of the bilateral dorsal anterior cingulate cortex. All of these correlations were found using both ROI and VBM methods. In Study 2, which used a more diverse sample of healthy males and females ranging in age from 10 to 22, self-reported levels of trait negative affect was correlated negatively with posterior insula volume, although this finding was not confirmed using VBM. Both ROI and VBM revealed that trait suppression usage frequency was correlated positively with right ventral anterior cingulate and anterior insula volume. The strength of the relationship between suppression and anterior insula volume increased as subject age increased. Although no ROIs were found to correlate with trait reappraisal usage frequency, VBM found that reappraisal positively correlated with gray matter clusters in the prefrontal cortex. The findings from this dissertation demonstrate that the structural alterations seen in individuals suffering from mood and anxiety disorders may not result from psychopathology per se, but may instead be on the lower end of the continuum of emotion reactivity, emotion regulation, and associated brain structure.

Keywords: Psychology
Advisor: Gross James J.
Knutson Brian advisor. Thesis advisor
McClure Samuel M. advisor. Thesis advisor
A new actuation approach for bio-inspired human-friendly robots [electronic resource]

The increasing demand for physical interaction between humans and robots has led to an interest in robots whose behavior is guaranteed to be safe when they are in close proximity with humans. However, attaining sufficiently high levels of performance while ensuring safety creates formidable challenges in mechanical design, actuation, sensing, and control. To promote safety without compromising performance, a new actuation concept, referred to as hybrid actuation, has been developed. Since low impedance output at high frequencies is essential for robot safety, while optimal passive stiffness is needed for robot performance, the new actuation approach employs a pneumatic artificial muscle as a macro actuator to provide low-frequency torques. Artificial pneumatic muscles provide high force-to-weight ratio and inherent compliance, both of which allow for low impedance actuation. To compensate for the slow and non-linear dynamics of pneumatic actuation, a small electromagnetic actuator collocated at the robot's joint is employed as a mini actuator, which provides high mechanical bandwidth for high performance without increasing the inertia and size of the manipulator. To achieve the appropriate balance between safety and performance, design methodologies were developed that optimally determine key design parameters such as the required mini motor torque capacity, the joint stiffness introduced by an antagonistic pair of muscles, and the pulley radius. Using a testbed, referred to as the Stanford Safety Robot (S2rho), the hybrid actuation was evaluated for position tracking performance, force tracking performance, and impact behavior. The experimental results demonstrate that by significantly improving control performance with the hybrid actuation over performance with pneumatic muscles alone, while reducing the effective inertia significantly, the competing design objectives of safety and performance can be successfully integrated into a single robotic manipulator. As an extension of the hybrid actuation concept, the new design of dual four-degree-of-freedom robotic arms with torso is presented and detailed descriptions of the design are included.

Keywords: Mechanical Engineering
Advisor: Cutkosky Mark R. primary advisor. Thesis advisor
Khatib Oussama primary advisor. Thesis advisor
Roth Bernard advisor. Thesis advisor
New methods for extracting ultrafast water dynamics at interfaces [electronic resource]

Water dynamics near interfaces and in confined systems, as manifested by vibrational relaxation, orientational relaxation, and spectral diffusion of the water hydroxyl stretch (5% HOD in H2O), are measured via infrared (IR) pump-probe and 2D IR vibrational echo techniques. It is shown that a two component model for population and orientational relaxation accurately describes the dynamics for systems comprised of two types of hydrogen bonding ensembles: waters that are hydrogen bonded to other waters and waters at an interfacial region. Through a combination of spectroscopic and data analysis techniques, the dynamics of these two environments become separable. This two component model is successfully applied to binary mixtures of water and tetraethylene glycol dimethyl ether. The effects of confinement on water dynamics are studied by examining water inside of reverse micelles made with the surfactant Aerosol-OT (AOT), which contains charged head groups. Large reverse micelles (diameter [greater than or equal to] 4.6 nm) can be decomposed into two separate environments: a bulk water core and an interfacial water shell. Each region has distinct dynamics that can be resolved experimentally using the two component model. The core follows bulk water dynamics while interfacial water shows slower dynamics that are independent of size for large reverse micelles. To explore how the chemical composition of the interface influences dynamics, the dynamics of water in AOT reverse micelles are compared to water dynamics in reverse micelles made from the neutral surfactant Igepal CO-520. It is found that the presence of an interface plays the major role in determining interfacial water dynamics and not the chemical composition. A two component model is also developed for spectral diffusion. The two component model for spectral diffusion is an extended version of the center line slope (CLS) analysis procedure, originally developed for single ensemble systems. The modified two component CLS procedure allows the CLS behavior of water at the interface to be back-calculated from known parameters. From the interfacial CLS, the interfacial frequency-frequency correlation function, which describes spectral diffusion, can be determined. It is found that, similar to orientational relaxation behavior in large AOT reverse micelles, the interfacial FFCF does not vary with increasing reverse micelle size.

Keywords: Chemistry
Advisor: Fayer Michael D. primary advisor. Thesis advisor
Dai Hongjie
Pecora Robert
A new way to think about press freedom [electronic resource] : networked journalism and a public right to hear in the age of "Newsware"

This dissertation presents a new way to think about press freedom in the context of online, networked news production. Essentially, if individual freedom means something other than just being left alone, and if press freedom is anything other than an anachronism from a time when only a privileged few could print or broadcast, then there is a democratic reason to defend press freedom and networked press dynamics to be discovered. To be free, people still need relationships with others and a right to hear -- conditions that are, ideally, guaranteed in part by an autonomous press. The need for freedom remains, but the press is negotiating its autonomy in new ways: distancing itself from and depending upon publics, markets and states through online networked infrastructures I call "newsware". I begin by unpacking the idea of autonomy as a general philosophical and democratic concept. I trace autonomy through a number of democratic rationales and situate it within an institutional understanding of the democratic press and an affirmative interpretation of the U.S. Constitution's First Amendment. I then use Bourdieu's Field Theory and New Institutionalism to show how the press can be understood as a field and use this model to trace how the mainstream press has historically negotiated its autonomy. Focusing on contemporary dynamics of online news production, I identify a new type of infrastructure called "newsware" through which the press negotiates its autonomy today. My empirical investigation focuses on one type of newsware: news organizations' application programming interfaces (APIs) that give publics access to their content. I present what I believe to be the first integrated account of three leading news organizations' APIs (The New York Times, The Guardian, and National Public Radio) and identify three ways in which they use them to negotiate distance from and dependences upon software programmers and internet users. I conclude by claiming that this new way of thinking about press autonomy--as a set of negotiated separations and dependencies among distributed actors connected through newsware infrastructures--better lets us both define and defend the press as an ideal networked institution that ensures a public right to hear.

Keywords: Communication.
Advisor: Glasser Theodore Lewis
Bailenson Jeremy advisor. Thesis advisor
Jain Sarah S. Lochlann
Turner Fred advisor. Thesis advisor