VictorJuiz/thesis huggingface dataset:
Spherical and Symmetric Supervarieties

We develop and study the notion of a spherical supervariety, which is a generalization of the classical notion of a spherical variety in algebraic geometry. Spherical supervarieties are supervarieties admitting an action of a quasi-reductive group with an open orbit of a hyperborel subgroup. Three characterizations of spherical supervarieties are given: one which generalizes the Vinberg-Kimelfeld characterization of affine spherical varieties, another that extends the ideas of the affine case to the quasi-projective case, and finally one in terms of invariant rational functions which applies to any supervariety. Our characterization of affine spherical supervarieties leads to (non-constructive) existence theorems for finite-dimensional highest weight representations admitting certain coinvariants under spherical quasireductive subgroups./nSeveral interesting examples of spherical supervarieties are given. We present a classification of indecomposable spherical representations (for certain supergroups) and for each the description of its algebra of functions. Adjoint orbits of odd self-commuting elements are shown to be spherical in many cases, in particular for basic simple Lie superalgebras. We study group-graded supergroups and their spherical homogeneous supervarieties, showing in particular that the algebra of functions on an affine homogeneous supervariety is almost never completely reducible for such supergroups./nFinally we study the case of symmetric supervarieties and show that, despite their not always being spherical (in contrast to the classical case), we may under some circumstances guarantee the existence of an Iwasawa decomposition, which implies sphericity. The fixed points of automorphisms of generalized root systems coming from supersymmetric pairs are studied along the way. We use the Iwasawa decomposition to gain partial understanding of the structure of the space of functions as a representation. Finally, the case of a supergroup as a symmetric supervariety is discussed in detail, culminating in a description of the socle filtration and the Loewy layers of its space of functions.

Advisor: Serganova, Vera
Post-fire tree regeneration in an altered disturbance regime: community dynamics and interactions with land management

Fire has long shaped forests across the globe. Anthropogenic forces are reshaping fire regimes, leading to unprecedented forest conditions and unknown long-term consequences. Land management can help mitigate undesired effects of altered fire regimes, but effective management requires information about tree species’ responses to disturbances both historical and modern. In my dissertation, I add to a body of literature examining how novel fire patterns affect tree regeneration and whether forest management strategies can mitigate any undesired effects. I focus on mixed-conifer forests of the Sierra Nevada, where logging, fire exclusion, and climate change have shifted the fire regime from frequent, heterogenous fire to infrequent fire with greater high severity. The tree species that have long comprised these forests are not well adapted to regenerate in large, homogenous fire patches. My dissertation investigates three main questions in three chapters: 1) Can forest management prevent large fire patches and promote post-fire recovery? 2) Will the novel fire regime shift overall species composition toward firs and away from pines? 3) What is the role of post-fire shrub dynamics in determining ecological succession in novel-type fire patches? In Chapter 1, I show that strategically placed fuel reduction treatments effectively reduced fire severity and promoted recovery when burned in a wildfire. In Chapter 2, I explore the idea that the shifting fire regime may lead to regional fir enrichment. I focus on plant interactions following severe wildfire and show that shrub competition affects ponderosa pine more strongly than it affects white fir. However, simulation modeling results in Chapter 3 show that, on net, shrub neighborhood dynamics do not produce an ecological filter favoring firs, though patterns are sensitive to shrub species. These three chapters together illustrate the importance of forest patch dynamics for wildfire resistance and recovery.

Advisor: Battles, John J
Stephens, Scott L
Abstraction, Generalization, and Embodiment in Neural Program Synthesis

Program synthesis, or automatically writing programs from high-level specifications has been a long-standing challenge in computer science and artificial intelligence. Addressing this challenge can help unlock the full power of computing to nontechnical users, assist existing developers on traditional programming tasks, and solve other tasks in artificial intelligence like question answering that are naturally expressible as programs. In recent years, neural methods for program synthesis based on learning have driven significant progress. With this shift, themes like abstraction, generalization, and embodiment that recur in other facets of machine learning provide a natural framework for further improvement. In this dissertation, we present methods to address manifestations of these themes in several concrete instantiations of neural program synthesis./nFirst, we demonstrate how to better synthesize imperative programs by interacting with the program interpreter environment in the form of predicted execution traces, in a challenging domain for program synthesis called Karel. We also show in empirical studies that generating synthetic data for program synthesis requires significant care to enable models to generalize. In an application of program synthesis from natural language, or semantic parsing, we present attention-based neural architectures that can better encode the natural language specification to enable better generalization to new database domains. In this and other code generation domains, we introduce a method for integrating automatically learned code idioms into the synthesis procedure, learning to automatically switch between multiple levels of abstraction.

Advisor: Son, Dawn
Identification of a function for the zinc coordination center of Shh and mechanisms of Smo inhibition by Ptch1/2 activity

The Hedgehog (Hh) signaling pathway is critical for patterning during embryonic development in most animals. The three key components in mammals are the ligand Sonic Hedgehog (Shh), its receptors Patched1 and -2 (Ptch1/2), and the pathway activator Smoothened (Smo). In the absence of Shh, Smo is inhibited by a small antagonist that is thought to be transported across the cell membrane by Ptch1/2. In the genetic and functional analyses of single pathway components, three-dimensional aggregates of cells with varying genotypes pose a valuable proxy for the in vitro study of signaling events. I describe a protocol for the generation and analysis of such in vitro organoids where specific roles (like producing and responding cell) can be assigned to a fraction of the cells based on their genotype. Release of the ligand Shh from producing cells and the inhibition of Smo by Ptch1/2 in responding cells in the absence of Shh are central aspects of this thesis. I demonstrate a function for the zinc coordination center of Shh in the release of the protein from the cell into the extracellular matrix. Furthermore, I present the known Smo inhibitor 7-Dehydrocholesterol (7DHC) as a putative cargo for Ptch1/2. Ptch1/2 are not only required for 7DHC to be inhibitory but also exacerbate the Smo inhibitory effect of 7DHC.

Advisor: Roelink, Henk
Magmatic Architecture of Hotspot Volcanism and Large Igneous Provinces

Volcanoes are an important part of the Earth system - supplying volatiles (e.g., H$_2$O, CO$_2$, SO$_2$) to the atmosphere, as well as nutrients to the oceans (e.g., Fe, other trace elements), and producing subaerial and submarine topography. In particular, flood basalt events are some of the largest magmatic events in Earth history, with intrusion and eruption of millions of km$^3$ of basaltic magma over a short time period ($\sim$ 1-5 Ma). They are hypothesized to be the result of the emergence of a mantle plume head - which frequently forms the start of a hotspot track. Flood basalt eruptions are associated with significant perturbations to the Earth’s climate and biosphere, including mass extinctions. This link is generally hypothesized to be due to the emission of climatically active volatiles, such as CO$_2$ and SO$_2$. In this thesis, I utilize fluid dynamics and mechanical theory from Earth-science, astrophysical, and engineering sub-disciplines to develop intermediate-complexity models for hotspot volcanism and flood basalt eruptions./nI analyze how the mantle partial melt gets mobilized and transported in the asthenosphere before feeding the crustal magmatic system. For this, I used natural modern day occurrences of where a mantle plume interacts with a nearby mid-ocean ridge e.g., Gal\'{a}pagos and Iceland. My results suggest that plume-ridge interaction in general, possibly including transport of plume-derived material along ridge axes (e.g., Iceland), may involve transport in high-melt-fraction channels, as opposed to just solid-state mantle flow. With regards to the crustal magmatic system, I analyze how the loss of volatiles from a magma reservoir affects the magmatic overpressure responsible for driving ground deformation and eruptions. I developed a fully coupled poro-thermo-elastic framework to account for both the flow of volatiles as well as associated effects on the stress state of the crust and calculate an analytical solution for spherical geometry./nI utilize these ideas to understand the eruptive dynamics and magmatic architecture of continental flood basalts (CFB). I used a new volume-averaged visco-elastic mechanical model for an ellipsoidal magma reservoir coupled to a dike-shaped erodible conduit to calculate how eruptive fluxes (km$^3$/year) and volumes vary as a function of reservoir geometry and crustal properties for a single magma reservoir, as well as multiple connected reservoirs. I found that the presence of just a few large crustal magma reservoirs is inconsistent with observational constraints. Instead, I propose that CFB eruptions are fed from a number of smaller ($\sim$ 10$^2$ - 10$^{3.5}$ km$^3$) interconnected magma reservoirs present throughout the crust consistent with the paradigm of a trans-crustal magmatic system./nThis work has important implications for interpreting a CFB's potential to cause environmental change.

Advisor: Richards, Mark A
Island City: Urban Development, Planning, and Real Estate in Jakarta

In the past three decades, private real estate projects have proliferated across the Jakarta metropolitan region, with new towns in the outskirts of the city, superblocks in the city center, and land reclamations on the northern coast. This dissertation examines the roles of private real estate developers and government planning agencies in the transformation of Jakarta through real estate development, and how this development reshaped not only urban space, but also urban governance. I argue that national planning institutions in Indonesia promoted the rise of a capitalist real estate sector in Jakarta, but doing so, they tied urban planning and development inexorably to private growth in spatially discrete enclaves. The government promoted private real estate to grow the economy and also to improve the city’s infrastructure and urban space. Planning agencies relied on the private real estate industry to provide public goods—to improve the urban environment, to provide public space, and to add infrastructures like electricity, water, roads, and even a seawall to address flooding. However, private development also led to a fragmented urban system, the proliferation of elite enclaves and disjointed infrastructure, a city of islands. This research spans two eras, from 1988 to 1998, the final decade of Suharto’s authoritarian government, and the subsequent democratic era, from the 2000s to the present. The private real estate sector first emerged in the late 1980s under the authoritarian government of Suharto, when the government liberalized the economy and promoted the rapid growth of an urban land market. Development slowed during the Asian Financial Crisis, but it began again in the mid-2000s and boomed throughout the following decade. In spite of the reforms associated with democratization and anti-corruption reform, private real estate development continues to be a complicated problem for the city and national governments. National planning agencies have attempted to construct a coordinated and transparent development planning system, particularly through a mechanism that requires development firms to contribute specific elements to the city’s infrastructure projects in exchange for development rights. However, planning agencies still struggle to coordinate across a wide range of agencies at multiple scales of government, and also to reconcile the goals of growth with transparent regulation in a way that serves the public. Despite a growing economy and improvements in the city’s infrastructure, private real estate development continues to exacerbate the city’s island geography.

Advisor: Caldeira, Teresa
Fabrication of Extremely Soft Cellular Hydrogels for Vascular Modelling

In the past three decades, microtissue models grown inside miniaturized fluidic systems fabricated using soft lithography, were probably the most widespread form of engineered cellular structures. This conventional methodology has now been challenged by biofabrication techniques that offer shorter lead times and greater three-dimensional design freedom, while circumventing the manual alignment and inter-layer bonding challenges of soft lithography. As a result, attention has moved towards additive fabrication solutions./nFused deposition modelling (FDM), inkjet, and stereolithographic projection-based 3D-printing solutions have demonstrated the possibility of printing master molds and sacrificial structures as well as encapsulated fluidic networks directly. As an example, we will briefly explore one such indirect fabrication strategy that we have developed for large area fabrication of multi-material soft structures (Multi-layered Micro-casting). Despite the simplicity and cost-efficiency of such indirect methods, an alternative direct bioprinting technique would overcome the geometrical limitations and enable better automation and process yield. However, direct printing in extremely soft hydrogels has its own diversity of challenges. These techniques typically require the use of support structures when printing overhanging features such as encapsulated fluidic networks. This support material is, in some cases, entirely impractical to remove from small-scale channels. Additionally, due to the material deformation during printing, most existing printing techniques are limited to materials that are orders of magnitude higher in elastic modulus than biological tissue./nIn contrast, we introduce a new additive technique, computed axial lithography (CAL), which enables volumetric 3D-printing by illuminating a rotating volume of photosensitive material with a 3D light intensity map constructed from the angular superposition of many 2D projections. Oxygen inhibition-induced thresholding of the materials’ dose response enhances patterning contrast. We report the application of CAL to fabricate structures in methacrylated gelatin with elastic moduli as low as 100 Pa, as well as stiffer acrylates. Uncured resin provides mechanical support during printing, eliminating the need for solid support. Among other advantages are print durations as low as a few minutes and the possibility to overprint gels on/in other structures.

Advisor: Taylor, Hayden
Data-Driven Decision Analysis in Electric Power Systems

This dissertation describes tools and techniques for applying data to inform decisions made in electric power systems. We explore how limitations inherent to data sets can contribute to model uncertainty, and formulate quantitative methods for issuing recommendations that are robust to uncertainty. The work provides a basis for justifying advancements in data collection and monitoring to increase confidence in decision-making outcomes./nData about the past can offer valuable insights about the present and future. Data can improve the fidelity of simulations for characterizing performance, and can shed light on emerging risks. Data offers a basis to validate performance, to inform targeted maintenance, and to predict the outcome of candidate decisions./nThough data can be a powerful tool, our interpretations of data and even the data themselves are subject to error. Data analysts must judge whether the data are sufficient to answer the question at hand, whether the questions themselves are well-posed, or whether more suitable data should be sought after. The current work describes methods to inform these judgements by exploring how they could alter interpretations of risk and performance, contextualizing these different interpretations in terms of recommendations issued to decision-makers./nThe work centers around three case studies that apply imperfect data to inform such recommendations. We consider data sets where relevant information is lost, where observational history is sparse, and where spatial coverage is limited. We synthesize data using exploratory data analysis, hierarchical modeling, and Bayesian optimization. These methods internalize what is known about the limitations of underlying data sets to examine uncertainty in decision-making outcomes. Each case study formulates a quantitative decision-support model, and offers a quantitative basis to inform the collection of new information that could help decision-makers to act with greater confidence.

Advisor: Moura, Scott J
Post-fire succession of plants and soils in chaparral shrublands: the role of ephemeral herbs and mammalian herbivores

Understanding the drivers of ecological succession requires linking ecological interactions and biodiversity to ecosystem soil processes. California’s widespread chaparral shrublands provide an ideal setting to investigate mechanisms linking plant and soil dynamics during succession. Periodic crown-fire in chaparral temporarily removes all living shrub cover, deposits mineral N on soils, and allows functionally diverse herbaceous communities to dominate the landscape for 3-5 years. In many areas, chaparral stands are bordered by non-native grasslands and fire can facilitate invasion of chaparral by grasses. Herbivorous small mammals in chaparral have been previously demonstrated to impact the composition of the chaparral understory and consume non-native grasses at the grassland-chaparral border. Herbivory may also impact soil N and C cycling through changes to plant community composition and direct additions of herbivore feces and urine. The composition of post-fire herbaceous communities, whether influenced by herbivory or another factor, may itself impact soil nutrient cycling. In particular, N-fixing and non-N-fixing herbs can have functionally distinct effects on ecological and ecosystem processes, influencing herbivore feeding preferences, competitive or facilitation relationships between plants, and litter decomposition rates./nIn this dissertation, I conducted three field experiments in Northern California chaparral. In Chapter 1, I established an herbivore-exclosure experiment at chaparral-grassland borders to investigate how mammalian herbivores impact invasive grasses and general understory herb composition, as well as how this effect was mediated by wildfire. In Chapters 2 and 3, respectively, I manipulated herbivore abundance and the biomass of N-fixing and non-N-fixing herbs to investigate how these factors influence soil C and N cycling in post-fire chaparral during the first two years after fire./nMammalian herbivory reduced herbaceous abundance post-fire, particularly non-native grasses, suggesting herbivores limit grassland invasion into chaparral. However, herbivore exclosures did not measurably impact N and C cycling during the first two post-fire seasons. Removing N-fixing and non-N-fixings herbs dramatically influenced soil N and C dynamics in the same system. Two years after fire, plots with all herbs removed had significantly lower soil N and C than any treatment with herbs. Post-fire herbs do appear to enrich soil in C and N, which may benefit recovering shrubs even after herbaceous communities die back.

Advisor: Sousa, Wayne P
Total Synthesis of Topologically Complex Natural Products: Aconitine-Type Diterpenoid Alkaloids, Simplified Analogs and Sesterterpene Somaliensene A

The synthesis of aconitine-type diterpenoid alkaloids and analogs thereof has been completed. The first chapter of this dissertation introduces the diterpenoid alkaloid natural products and seminal studies toward their synthesis. The second chapter details strategies used to construct the polycyclic scaffolds of these highly bridged molecules, including both previous synthetic work and our own total synthesis of weisaconitine D. The third chapter focuses on the biological activity of these natural products and synthesis of analogs thereof to enable structure–activity relationship studies. The final chapter details ongoing studies regarding the rearrangement of strained [3.1.1] bicycles for use in terpene synthesis./nChapter 1 includes discussion of the classification and biological activity of these topologically complex natural products. Seminal syntheses by both Nagata and Wiesner of two relatively simple diterpenoid alkaloids, atisine and garryine, are discussed alongside Wiesner’s later synthesis of the more highly bridged talatisamine./nChapter 2 details how the use of bond-network analysis can provide clues on how to put together these highly caged scaffolds. The efficacy of this approach is evaluated in the context of eight modern syntheses of hetidine- and hetisine-type diterpenoid alkaloids. Bond-network analysis is then applied to the retrosynthesis of the aconitine-type diterpenoid alkaloids, identifying key disconnections that were ultimately applied successfully in the total synthesis of weisaconitine D. Two late-stage bicyclization strategies—the originally planned meta-pi-arene photocycloaddition and an alternative Diels–Alder cycloaddition/Wagner–Meerwein rearrangement sequence—are discussed./nChapter 3 includes further discussion of the biological activity of the aconitine-type diterpenoid alkaloids, focusing on their modulation of voltage-gated sodium ion channels. The effects of two representative compounds, aconitine and lappaconitine, were evaluated in collaboration with Dr. David Hackos of Genentech and used as the starting point for structure–activity relationship studies using simplified analogs of these diterpenoid alkaloids. The design and synthesis of these analogs is discussed./nChapter 4 focuses on the synthesis and rearrangement of strained [3.1.1] bicycles as part of an ongoing effort to synthesize terpene natural products. Discussion includes synthetic progress toward the sesterterpene somaliensene A from carvone using a strategy featuring cyclization and deoxygenation, as well as toward the diterpene xishacorene B from verbenone using a strategy featuring rearrangement and ring expansion.

Advisor: Sarpong, Richmond