VictorJuiz/thesis huggingface dataset:
Functional Brain Network Organization Supporting Executive Control Processing

Executive control comprises a set of neural processes that are critical for goal-directed behaviors, such as attention and working memory. Such complex behaviors likely rely on the flexible communication within and between brain sub-networks, or modules. In this thesis, I present several projects that use graph theoretical methods to describe the brain as a complex network and examine the role of brain network organization in supporting aspects of executive control processing. Across these projects, I use a variety of methods, such as functional magnetic resonance imaging (fMRI), functional connectivity, and cognitive training./nThe first chapter of this thesis examines the influence of attention demands on brain network organization. Here, I show that brain network modules become more integrated during the processing of relevant stimuli compared with the processing of irrelevant distractors during a working memory N-back task. The strength of this reconfiguration is related to faster task performance, suggesting its importance in executive control./nThe second chapter of this thesis examines the influence of aging on reconfiguration of brain networks due to executive control (i.e., N-back load) demands. Here, I demonstrate that older adults exhibit changes in brain network organization at lower levels of demand compared with young adults. Further, brain network reconfiguration from a task-free ‘resting-state’ to an N-back task is related to better task performance and greater structural connectivity of a core frontal-posterior white matter tract./nThe final two chapters of this thesis examine how brain network organization can predict gains in executive control processing after cognitive interventions. The first project shows that the extent of segregation of brain network modules (i.e., higher network modularity) is predictive of greater training-related cognitive gains in older adults. The second project extends this predictive framework to healthy young adults./nIn sum, these projects demonstrate that brain networks flexibly reconfigure depending on executive control demands and that aspects of brain networks are predictive of training-related gains of executive control. These findings provide insight into how properties of large-scale brain networks allow for executive control processing.

Advisor: D’Esposito, Mark
Patterns and Processes in Ectomycorrhizal Fungal Ecology

For my dissertation I focused on two key questions central to fungal diversity: the role of/ndispersal in fungal community assembly, and the response of fungi to catastrophic disturbances. As we enter the Anthropocene and catastrophic disturbances are increasing in frequency, it is important to understand how fungi will respond to disturbances since they are major drivers of many ecological processes such as decomposition and forest function. To do this, I utilized large scale-sampling and ITS amplicon-based metagenomics to examine the environmental drivers of ectomycorrhizal fungal spore bank diversity across the North American continent. Two of my study plots were then burned in a catastrophic wildfire. Thus I was able to examine ectomycorrhizal fungal spore bank recovery after the fire, and I made a case for a group of fire fungi, adapted to wildfires./nTo examine the role of dispersal in fungal community assembly, I used a high elevation/nsubalpine basin located in Yosemite National Park where isolated congeneric pine trees have established at varying distances from each other and the forest edge. Since ectomycorrhizal fungi are obligate symbionts of trees, isolated trees are islands from the perspective of the fungi. I used these well-replicated “islands” to test the theory of island biography in host-associated fungi. Moreover, because two distantly related pine species co-occurred in varying distances from each other and the forest edge, I could disentangle host from distance and other environmental factors to determine the drivers of community structure and beta-diversity in the ectomycorrhizal fungi associated with the trees. To do so, I determined fungal community composition with Illumina MiSeq sequencing of ITS amplicons, and applied generalized dissimilarity modeling (GDM), a non-linear form of matrix regression, to test whether total and ectomycorrhizal fungal (EMF)/ncommunities were primarily structured by distance decay, host, seasonality, or edaphic/nenvironmental filtering. I identified soil nutrient environment as a stronger predictor of EMF/ncommunity composition than host identity. I found pH and organic matter to be the strongest predictors of EMF, and total fungal composition. This result fits an emerging paradigm that soil pH is a major driver of microbial community composition.

Advisor: Bruns, Thomas D
Beyond the Initiatives: Developing instructional leadership in school principals as a system-wide effort to improve the quality of classroom instruction.

This design research effort implemented a series of intervention activities designed to support a small group of elementary school principals improve their instructional leadership practices. The purpose of this research was to improve the skills of principals to lead instructional improvements identified through classroom observations, work with their school-level Instructional Leadership Team (ILT) to create teacher professional development that addresses the instructional improvement, and implement the leadership moves necessary for leading instructional change in their context./nA sample of three principals with more than 3-years principal experience and those who were participating in the Balanced Literacy Cohort were asked to participate in this design challenge. Principals participated in the Instructional Rounds (IR) process over a 6-week span, received pre-training, participated in three IR sessions to collect base-line data on their Problem of Practice, identified and designed a Next-Level Work Plan, collaboratively implemented teacher professional development with their Instructional Leadership Teams (ILTs), and reflected on their progress./nData were obtained from principals and from teachers on the Instructional Leadership Teams (ILTs) to provide a description of how principal instructional leadership behaviors faired while participating in Instructional Rounds and how this process shaped professional learning. Participants completed pre and post surveys, interviews, IR sessions, and created teacher professional development plans. These data were analyzed against an instructional leadership rubric and evaluated how the Instructional Rounds process shaped instructional leadership behaviors in participating principals.

Advisor: Trujillo, Tina
Fake Federalism: How American "Federalism" Works and Why It Doesn't

My dissertation introduces a new, positive theory of federalism that explains that the divergence of institutional and individual interests is an important cause of instability in federal systems. This is because, when the interests of state institutions and individual politicians differ, rational, self-interested politicians will pursue their individual interests at their states’ expense. My dissertation then applies this theory to the United States. I use two qualitative case studies, education and crime control, to show why this “interest gap” between states and state politicians developed, and further, how the short sighted, self-interested decision-making of state actors contributed to American federalism’s decline.

Advisor: Feeley, Malcolm M.
Precision Measurement in Atom Interferometry Using Bragg Diffraction

We experimentally and theoretically study Bragg diffraction as a tool for large-momentum transfer beam splitters in atom interferometry. A theoretical framework is developed to quantify the diffraction phase systematic caused by Bragg diffraction and experiments are performed to confirm these predictions using a Ramsey-Bord\'e atom interferometer. We then develop methods to systematically cancel and reduce the diffraction phase systematic by carefully selecting Bragg diffraction parameters and utilizing Bloch oscillations. These techniques are then applied to an ongoing precision measurement of $h/m_\text{Cs}$ for cesium, with the end goal of measuring the fine structure constant $\alpha$. We demonstrate a high contrast simultaneous conjugate Ramsey-Bord\'e interferometer using 5th order Bragg diffraction and 25 common mode Bloch oscillations which achieves $2.5\times 10^6$ radians of phase. We also demonstrate an interferometer with a statistical uncertainty of $\delta \alpha/\alpha=0.25$ ppb after 25 hours of integration time that has diffraction phase systematic error of around 1 ppb. Other sources of systematic uncertainty are also thoroughly explored and determined to better than 0.1 ppb. The techniques and theories developed in this thesis will hopefully help enable future precision measurements based on Bragg diffraction.

Advisor: Mueller, Holger
Adult Exploration Support Schema: Validation of a New Father Attachment Measure

In this study, a new adult attachment scale, the Adult Exploration Support Schema (AESS), is presented. The AESS was based on the concept of the exploratory behavioral system, unlike most existing adult attachment measures that are grounded in the availability of attachment figures for the purpose of protection. Specific attention is given to the father version of the scale—Adult Exploration Support Schema–Father (AESS–F)—which is examined using a factor analytic approach to data from a racially and ethnically diverse sample of undergraduate students from a large urban American university in a Western state. Exploratory and confirmatory factor analyses supported the structural validity of AESS–F scores and the construct of secure adult-father attachment tied to the exploratory behavioral system. Associations between the AESS–F and existing adult attachment measures supported the convergent and divergent validity of AESS–F scores. Hierarchical linear regressions involving AESS–F and constructs of secure exploration (i.e., academic self-efficacy, work ethic, educational engagement, curiosity, and hope) provided support for the predictive validity of AESS–F scores, with AESS–F scores explaining more of the variance than an existing adult-father attachment measure rooted in secure base conceptualizations of attachment. These results suggest that an updated conceptualization based in the exploratory behavior system might be a useful addition to the literature on adult-father attachment.

Advisor: Worrell, Frank C
Subphonemic Teamwork: A Typology and Theory of Cumulative Coarticulatory Effects in Phonology

In this dissertation, I argue that phonology is ---at least partly--- grounded in phonetics, and that the phonetic information that is relevant to phonology must be given dedicated scalar representations. I lay out the foundations of a theory of such representations, which I call SUBFEATURES. A typology and case-study of SUBPHONEMIC TEAMWORK, a kind of multiple-trigger assimilation driven by partial coarticulatory effects, serves as the empirical basis of this proposal. I argue, on the basis of instrumental evidence, that such partial coarticulatory effects are relevant to the phonological grammar, and must accordingly be represented in it./nIn doing so, I take a stand in several debates that have shaped phonology. First, the debate surrounding phonological substance: I argue against a substance-free approach (cf. Blaho 2008 and references therein) by showing that some phonological phenomena (here, subphonemic teamwork) require a phonetically grounded, or ``natural", approach. Furthermore, within the field of phonetically based phonology, I argue in favor of maintaining a separation between phonology and phonetics, which are conceived of as distinct components of the grammar that communicate through the mediation of abstract phonetic knowledge. Finally, the theory I propose is representational: phonetic knowledge, which is what allows phonology access to some phonetic information, is reified into subfeatural representations that can be manipulated by the phonological grammar.

Advisor: Hyman, Larry M
Inkelas, Sharon
Electron Dynamics in Solids Studied by Attosecond Extreme Ultraviolet Spectroscopy

The creation of attosecond pulses using high harmonic generation (HHG) to produce extreme ultraviolet light (XUV) pulses has enabled table-top core-level spectroscopy in both the gas and solid phase. Because HHG relies on a near infrared (NIR) driver pulse to create the XUV radiation, it is readily incorporated into pump-probe transient absorption and photoelectron spectroscopy experiments, giving way to measurements with unprecedented temporal resolution. The ability of attosecond XUV pump-probe spectroscopy to study solid state semiconductor materials allows for the interrogation of carriers on the timescales where a separation between electronic and lattice dynamics can occur. This will have far reaching implications addressing the fundamental carrier physics that govern the next generation of hot carrier charge transfer devices, which are at the forefront of photocatalytic and electronic device development./nIn this dissertation, a literature review of XUV transient absorption on solids using HHG is presented in Chapter 1. This chapter details the progress from femtosecond experiments on metal-oxide thin films to attosecond time-resolved experiments on semiconductors. In Chapter 2, the design and construction of the attosecond transient absorption apparatus capable of studying ultrafast dynamics in both solid state and gas phase samples using a near infrared (NIR) pump and an extreme ultraviolet (XUV) probe is presented. Chapter 3 presents transient absorption experiments done on germanium thin films, which measure both electrons and hole dynamics simultaneously in a single measurement. These results are supported by work from a theory collaboration. in Chapter 4, preliminary work on silicon germanium alloys is presented. While the results need further confirmation by additional experiments and characterization, it is clear that signals from hot carrier relaxation are present. Chapter 5 presents a theoretical investigation of a future experiment on silver nanoparticles using a velocity map imaging (VMI) device. The key feature of this theoretical study is the identification of a metric to follow the near-field of the plasmon, isolated from the electric field of the exciting laser pulse.

Advisor: Leone, Stephen R.
Neumark, Daniel M.
The Organizational Weapon: Ruling Parties in Authoritarian Regimes

This project examines party building in authoritarian regimes. The overarching puzzle I seek to address is: why are some autocratic ruling parties stronger organizations than others? What explains variation in the institutional capacity of autocratic rule? The collection of three essays in this dissertation outline the strategic logic of party institutionalization, in addition to providing new and original ways in which to measure this key concept of authoritarian party strength. It tests previously untested hypotheses about the origins of strong autocratic parties and provides insights on the conditions under which leaders will be incentivized to rule through binding institutions. The first paper conceptualizes autocratic party strength as institutionalization and provides new ways of measuring this variable. The second paper describes the strategic logic of party institutionalization in autocracies and explains why and when some autocrats choose to tie their own hands. The third paper evaluates the thesis that parties emerging out of revolutions and independence wars tend to be more durable by examining parties that emerged out of independence struggles in Africa.

Advisor: Arriola, Leonardo
Powell, Robert
Optimization and Design for Automation of Brachytherapy Delivery and Learning Robot-Assisted Surgical Sub-Tasks

The goal of this dissertation is to enhance automation in healthcare applications, specifically: brachytherapy delivery for cancer treatment and robot-assisted surgery, used for over 500,000 procedures annually in US alone. Brachytherapy uses cutting-edge computer-assisted planning, but assumes a fixed hardware design. On the contrary, Robot-Assisted Surgery uses high-precision state-of-the-art hardware under complete manual control with little automation. This dissertation is a step towards addressing this gap using a combination of optimization and design. Case studies show that performance of autonomous systems can be improved by leveraging the interaction between optimization based algorithms and the design of hardware systems./nFor Brachytherapy, this dissertation has developed a new approach for treatment delivery in Intracavitary Brachytherapy using patient specific 3D printed implants and implemented it on a clinical case of oral cancer. I present an algorithm to quantify reachability with straight-line needles for a given anatomy in prostate cancer. I integrate optimization based needle and dose planning algorithms in interstitial brachytherapy for prostate cancer using two methods of skew-line needle configuration implants: robot-assisted procedures and customized needle guides. The procedures are demonstrated on physical phantoms and performance is compared with an expert physician./nFor Robot-Assisted Surgery, this dissertation highlights the interplay between the design of/nhardware to reduce uncertainty and optimization based motion planning to enable automated multi-throw suturing . A novel algorithm, Transition State Clustering (TSC) extracts the latent task structure from task demonstrations by segmenting robot trajectories using hierarchical clustering and fitting Gaussian mixture model to identify transitions. I extend TSC with deep learning to perform trajectory segmentation for multi-modal data consisting of kinematics and videos.

Advisor: Goldberg, Ken
Atamturk, Alper
Enhancing Bioproduction with Enzyme, Compartment, and Pathway Engineering

Microbial fermentations are often the most efficient and environmentally friendly option for producing valuable chemicals. However, producing the correct molecule without losing material to side products and spontaneous degradation can prove challenging, especially working within the constraints of a living organism. To address this problem, we present three separate strategies for directing flux and controlling reactions, each operating on a different pathway. We apply enzyme-level engineering to enhance the benzylisoquinoline alkaloid (BIA) pathway, where a cytochrome P450 is responsible for both product formation and degradation. Next, we demonstrate compartment engineering by sequestering prodeoxyviolacein (PDV) pathway enzymes in the peroxisome to control the flow of intermediates and reduce side products. Finally, we rearrange pathways themselves by using biological protecting groups to protect reactive and unstable molecules, producing stable indican from unstable indoxyl in the indigo pathway. These three strategies – enzyme, compartment, and protecting group engineering – can be applied individually or together to enhance microbial yields of valuable products while minimizing byproducts.

Advisor: Dueber, John E
The Masses and Orbital Dynamics of Exoplanets

We live in a golden era of exoplanet discovery and characterization. Since its launch in 2009, the Kepler Mission has discovered over 4000 exoplanets, enabling detailed studies of their physical and orbital properties. These include empirical studies of the prevalence of planets of various sizes and orbital distances. In some of the Kepler systems, the compositions of the planets have been determined. Other studies include empirical, analytical, and numerical constraints on the formation and evolution of planetary systems./nThis thesis focuses on two aspects of the Kepler revolution. The first focus is on the masses and densities of small planets. Planets smaller than Neptune span a variety of compositions. Some of them are rocky and potentially habitable. The diversity of compositions among sub-Neptunes offers clues to planet formation and evolution. To determine the compositions of small planets, it is necessary to compute bulk densities from measurements of the planet radii and masses. While Kepler has determined the radii of thousands of planets, only a handful of the small planets are amenable to mass measurement techniques. Using the results from two mass measurement techniques, called the radial velocity (or Doppler) method and the transit timing variation method, a detailed study of the masses and compositions of more than 65 small planets was conducted. This study determined empirical relationships that describe the average masses and densities of exoplanets smaller than Neptune as a function of planet radius. Such exoplanets achieve a peak bulk density of 7.6 grams per cubic centimeter at a physical size of 1.5 times the radius of Earth. This peak density corresponds to a rocky composition; rocky planets smaller than 1.5 Earth radii are less compressed and less dense, whereas planets larger than 1.5 Earth radii have thick envelopes composed of volatile gases that lower their bulk densities./nThe second focus of this thesis is on the masses and orbital dynamics of planets in multi- planet systems. Multi-planet systems represent the end-states of planet formation. Their orbital dynamics and planet compositions are a fossil record of how they arrived at their present configurations. The systems studied herein include 3 multi-planet systems: KOI- 94, Kepler-10, and Kepler-11. KOI-94 is a system of 4 planets including a warm Jovian world. Kepler-10 contains a scorched rocky planet, a cooler gas-enveloped world, and a likely third planet. Kepler-11 has six small planets with fluffy hydrogen-rich envelopes, all contained within the equivalent orbital distance of Venus. Measurements of the compositions and orbital dynamics of these planets offer valuable steps toward characterizing the possible formation and evolutionary histories of these planetary systems.

Advisor: Marcy, Geoffrey W