VictorJuiz/thesis huggingface dataset:
Energy atlas : machine-learning-based mapping and analysis for sustainable energy and urban systems

Climate change poses increasingly severe threats to the sustainable development of the world. However, vulnerabilities of both human population and the infrastructure they rely on, as well as the abilities to mitigate and adapt to climate change, vary drastically across countries, regions, cities, and even neighborhoods. Their geospatial distributions and temporal variations are critical information for decision making to support sustainability, equity, and climate resilience but are largely unavailable today. In this dissertation, I addressed this gap by developing a set of machine-learning-based approaches towards the construction of "Energy Atlas"—a comprehensive and dynamic geospatial map overlay for distributed renewable energy, infrastructures, and population characteristics. Such approaches to collect granular spatial and temporal information are scalable, non-intrusive, and reliant only on widely-available geospatial data (e.g., remote sensing images, street views) as inputs. In particular, they enable the construction of a nationwide spatiotemporal solar PV installation dataset covering the contiguous US, the fine-grained distribution grid mapping in both the US and Africa, as well as the learning of urban neighborhood characteristics from imagery and textual data. These machine-learning-based approaches drive a closed-loop solution towards customized and evidence-informed decision making for sustainability, resilience, and equity. It begins from observing how our world looks like, to understanding how factors are correlated, and finally to informing what can be done. Specifically, based on "Energy Atlas", I identified certain types of solar energy incentives that are particularly relevant to solar adoption in low-income communities—from both correlational and causal perspectives. Based on "Energy Atlas", I also proposed a cost allocation scheme to make burying wildfire-prone power lines—an effective but costly wildfire mitigation approach—equitably affordable to communities at all income levels. The new methods, new data, and new insights gained in this dissertation can enable other researchers, policymakers, and various stakeholders to further develop econometric and engineering models, conduct in-depth analysis, and inform decision making for developing sustainable, equitable, and climate-resilient energy systems, infrastructures, and communities

Advisor: Majumdar Arunava
Rajagopal Ram
Kiremidjian Anne S. (Anne Setian)
Enfleshing the criminal : producing and policing Black (sexual) difference in the criminological imagination

Enfleshing the Criminal: Producing and Policing Black (Sexual) Difference in the Criminological Imagination scrutinizes the truth claims that undergirded the postbellum emergence of the "criminal" as a coherent object of scientific study. It argues that visual-cultural consensus about the picturability of sexual deviance in the Black female (maternal) body enabled the trajectory of criminological "empiricism" as it migrated from Italian anthropology to U.S. disciplinary practice, satisfying particular postbellum political needs by reinvigorating the logics of antebellum anti-Blackness with positivist rationale. This reliance of empirical analysis on subjective habits of seeing becomes clear when one reads key texts of criminology alongside their contemporary cultural objects. The cultural objects offer insight into the political desires of postbellum publics and cultural habits of seeing through which they were worked through—desires which are far less explicit in the scientific writing but which thoroughly constrained the ways in which the Black female (maternal) body "empirically" appeared. The project simultaneously attends to the ways that postbellum black artists and writers expressively experimented with the terms on which racialized gender subsequently appeared in dominant discourses of knowledge. In so doing, it joins several other works of black feminist and queer theory that use black expressive culture to problematize early professional science's oppressive program of racial-sexual difference. Yet it also complicates this work by carefully attending to the ways that Black writers' and artists' efforts to disentangle Blackness from criminality, though usually motivated by sound political intentions, sometimes recapitulated the violence of these empiricist paradigms and their enabling truth claims—particularly in their imaginings of Black women and queers. Ultimately, the project is invested in deconstructing the coherence of criminal discourse's program of difference by examining its key thinkers' commitments to seeing sexual deviance as the Black female body's pathological inheritance. But the project also insists on seeing the complexity in Black expressive culture, unburdening it of the political desires that engender its overdetermination as an archive of resistance

Advisor: Brody Jennifer DeVere
Elam Harry Justin 
Robinson Aileen
Scott Darieck 
Wallace Maurice O. (Maurice Orlando)
Engaging agricultural landowners in climate and conservation : California case studies

Human land-use activities have driven widescale environmental collapse, including a global biodiversity crisis and climate change. Given the immense footprint of croplands and rangelands, these landscapes have become the target of new solutions supporting carbon sequestration, reduced greenhouse gas emissions, and habitat conservation. Such government and private sector interventions are predicated on voluntary behavior change by farmers and ranchers, yet little is understood about how these landowners perceive the relevant benefits and risks. To address this research gap, my dissertation uses a social-behavioral approach to policy analysis aimed at identifying the factors shaping land use decisions. My research highlights the importance of distinguishing between rangelands and croplands—and between the types of landowners who manage them—to understand the feasibility of upscaling solutions. I draw on case studies across California, from a Sierra Nevada ranching community to the croplands of the San Joaquin Valley. In each chapter, I investigate the feasibility of a different climate change solution: 1) managed livestock grazing; 2) soil carbon markets; 3) rangeland conservation; and 4) renewable energy production. Using in-depth interviews along with land cover, real estate, and policy-relevant data, I identify the challenges of using managed grazing to sequester soil carbon, the opportunities and risks around payments for ecosystem services, and the role of landscape values and water availability in land use decisions. The empirical findings and recommendations summarized in my dissertation contribute to improved design of environmental policies and corporate sustainability programs targeting farmers and ranchers

Advisor: Huntsinger Lynn
Lambin Eric F.
Cain Bruce E. 
Wong-Parodi Gabrielle
Engaging Ink: The Painting Practice of Zheng Chongbin

This thesis, submitted in partial fulfillment of the requirements for the degree of Masters of Arts, East Asian Studies, examines the painting practice of contemporary multi-media artist, Zheng Chongbin (b. 1961). This study focuses on four other theoretical perspectives that Zheng has variously adapted, reconfigured, retranslated or reoriented to better suit the materiality of his chosen media, the processes of his artistic production, and the expressive, perceptual and intellectual directions of his interests. These include treatises by historical Chinese artists and critics, Shitao and Xie He; the spatial phenomenology incorporated in the architectural paintings of the seventeenth-century Dutch painter, Pieter Saenredam (1597-1665), and the combination of fractal pattern theory with ecological and New Materialism understandings.

Keywords:  Stanford Global Studies
Zheng, Chongbin, 1961-
Ink painting
Text
Thesis
Advisor: Vinograd Richard
Engineered extracellular matrices for modeling patient tumors

The extracellular matrix (ECM) is a dynamic network of proteins, polysaccharides, glycosaminoglycans, and other polymers that provide structural support for tissues and instruct neighboring cells through biochemical and mechanical cues. In healthy tissues, ECM remodeling is a tightly orchestrated process with constant turnover and reorganization of the matrix architecture in response to tissue growth and development, among other stimuli. In disease states, such as cancer, this ECM homeostasis is often misregulated, resulting in tissue disorganization and altered cell-ECM mechanosignaling that can drive disease progression and inhibit treatment strategies. In this thesis, I explore the in vitro culture of patient-derived tumors (termed cancer organoids) within a 3D engineered ECM as a method to understand how this misregulated ECM can influence cancer progression and drug sensitivity. Cancer organoids can be defined as 3D self-organized assemblies of neoplastic cells derived from patient-specific tissue samples that mimic key histopathological, genetic, and phenotypic features of the parent tumor. These organoid models are revolutionizing our understanding of cancer heterogeneity and its implications for personalized medicine, in part, due to their relatively facile genomic and environmental manipulation compared to traditional cancer models (i.e. 2D culture of cancer cell lines, in vivo mouse models). Additionally, as cancer organoids are often grown within 3D matrices that mimic the native ECM, they serve as an ideal model system to explore mechanistic roles of cell-ECM interactions in a dish. Specifically, this thesis contains a review chapter highlighting the current limitations of cancer organoid techniques and future directions to ensure reproducibility of cancer organoid protocols. This thesis also contains primary research focusing on the development of a 3D engineered ECM with tunable biochemical and mechanical properties that models key features of the pancreatic cancer ECM. In particular, I use this engineered matrix to test causal relationships between several ECM properties and pancreatic cancer chemoresistance, with the goal of identifying novel therapeutic strategies for treating this characteristically lethal disease

Keywords: Bioengineering.
Advisor: Heilshorn Sarah
Chaudhuri Ovijit
Rankin Erinn
Engineering quantum entanglement by coherent Rydberg dressing

Ensembles of neutral atoms enable state-of-the-art measurements of time, acceleration, and electromagnetic fields. Introducing entanglement among the constituent atoms offers a route to enhancing the precision of these measurements. One proposed approach to generating the requisite entanglement relies on the off-resonant optical coupling of one ground state to a highly excited electronic state. This technique, known as Rydberg dressing, enables local and dynamical control of interactions between neutral atoms. In this thesis, I present the engineering of Rydberg-dressed interactions by single-photon coupling to nP states in a cesium atomic clock. Optimizing the coherence of these many-body interactions is a major challenge; in order to understand and minimize dissipation mechanisms, I show sensitive measurements of percent-level noise processes, comparable to the projection noise of our atomic ensembles. Finally, I present the creation of a squeezed spin state by local interactions that achieves a factor of 0.79(6) reduction in phase variance below the standard quantum limit. The results of this thesis seek to inform the design of future experiments that will use coherent Rydberg-dressed interactions for a wider range of applications in quantum sensing and simulation

Keywords: Applied Physics.
Advisor: Kasevich Mark A.
Schleier-Smith Monika
Safavi-Naeini Amir H.
Engineering Spin Squeezing with Local Interactions

Quantum metrology uses entanglement as a resource to enhance measurement precision, most commonly through spin squeezing. While spin squeezing with all-to-all interactions is a well-studied phenomenon, spin squeezing with local interactions remains a largely open problem. On the other hand, local interactions are indeed more natural to realize in a wide range of physical systems, such as ultracold neutral atoms, Rydberg-dressed atomic gases, electric and magnetic dipolar quantum gases, and solid-state spin ensembles. We provide a general theoretical framework for studying canonical approaches to spin squeezing in the presence of local interactions in terms of spin waves. We propose a gap-protected countertwisting (CT-GP) Hamiltonian, which introduces an isotropic “gap-protection” coupling term to the canonical countertwisting Hamiltonian to mitigate the degrading effect of local interactions. Using the discrete truncated Wigner approximation (DTWA) for simulating dynamics of large spin-½ ensembles, we conduct a numerical study comparing metrological gain attained with the CT-GP (gap-protected countertwisting) and XXZ (gap-protected one-axis twisting) Hamiltonians, with respect to spatial dependence of interactions, spatial distribution of spin-½ sites, and strength of gap protection. We find that CT-GP is advantageous over XXZ in terms of both optimal squeezing and time to optimal squeezing. Furthermore, we find that increasing the strength of gap protection enhances the squeezing, having a similar effect as increasing the interaction range. To obtain the full metrological benefit of the CT-GP Hamiltonian, we propose and analyze an echo protocol that approaches the Heisenberg scaling with system size. We also study how to engineer and trotterize the CT-GP Hamiltonian using different native interaction terms relevant to various physical platforms.

Keywords: Physics
Quantum metrology
Spin squeezing
Quantum entanglement
Spin waves
Text
Thesis
Advisor: Schleier-Smith Monika
Khemani Vedika
Enhancement of functionality in complex oxides through growth in the [111] direction

Transition metal oxides are a particularly interesting class of materials because they exhibit tunable properties due to the coupling of the lattice, spin, orbital, and charge degrees of freedom. In this thesis, I explore the potential to tune their properties through growth in the [111] direction. The enhancement of functionality of materials grown in the (111)-orientation could expand the current toolbox used to design novel computing devices. The growth of LaNiO3 thin films on (111)-oriented LaAlO3 results in a unique strain state in the first few unit cells at the substrate/film interface. This strain, consisting of an expansion of the out-of-plane lattice parameter in the first few interfacial unit cells, results in insulating behavior at the substrate/film interface, the emergence of the anomalous Hall effect, and changes in the chemical valence. Notably, these changes are distinct from those observed in ultrathin (001)-oriented LaNiO3 films. This makes it clear that the strain introduced by the substrate in (111)-oriented films has the potential to greatly alter the properties of the first few unit cells of film grown on it. These thin films are also indirectly observed to be antiferromagnetically ordered. While antiferromagnetism can be difficult to directly measure, I provide evidence that these films are entirely magnetically ordered and that there is no net ferromagnetic moment. These results suggest growth in the [111] direction alters the magnetic structure of LaNiO3. Next, I explore the enhanced interfacial ferromagnetism enabled in (111)-oriented CaMnO3/CaRuO3 superlattices. These superlattices have a larger total moment and a thicker interfacial ferromagnetic phase present in the CaMnO3 as compared to (001) superlattices as well as the emergence of ferromagnetism in CaRuO3 layers. Further, an enhancement of the Curie temperature shows that growth direction can change this important engineering specification: the temperature at which magnetic ordering occurs. These changes are likely due to the differences in the orbital overlap across the (111) interface and suggest that magnetic structure can be tuned by growth direction--particularly for G-type antiferromagnets. In sum, the superlattices support the conclusion that growth of complex oxides in the (111) orientation results in an enhancement of the functionalities observed in (001)-oriented films

Keywords: Materials Science and Engineering.
Advisor: Suzuki Yuri (Applied physicist)
Wang Shan X.
Dionne Jennifer Anne
Enhancing the safety and efficacy of engineered cell therapies using protease-regulated platforms

Chimeric antigen receptors (CARs) are synthetic modular proteins that allow for directing immune cell reactivity towards a molecular target of interest, such as a cancer-associated antigen. CAR-T cells have demonstrated remarkable clinical activity in patients with refractory hematologic malignancies, leading to ten FDA-approved therapies to date. There is much hope that next-generation platforms leveraging synthetic biology and genetic engineering will expand this class of therapeutics to solid tumors, where toxicity risks and limited efficacy are major barriers to progress. However, current platforms for enhancing CAR potency are at risk for increased toxicity, while those that are designed for safety exhibit diminished potency. In this thesis, I first report on SNIP, an extensively optimized CAR ON switch that dually enhances safety and efficacy of T cells and is regulated by an FDA-approved small molecule. SNIP CARs outperformed conventional CARs in numerous orthotropic solid tumor models. Through phenotypic and functional studies, we show that enhanced activity of SNIP CARs is due to diminished T cell exhaustion and greater generation of memory T cells. In an on-target, off-tumor toxicity model we developed, we show that SNIP CAR activation can be tuned to fall within a therapeutic window in which T cell cytotoxic activity can be directed at tumor cells expressing high levels of antigen while sparing healthy tissue that expresses lower levels of antigen. Next, I report on STASH Tag, a drug regulated system for regulating the subcellular localization of a protein of interest. In order to meet the multiple obstacles facing CAR-T cells in solid tumors, next-generation smart therapies need to be multi-specific, resistant to exhaustion, and maintain their fitness in a hostile tumor microenvironment. Engineering next-generation therapies with these enhanced capabilities will require the introduction of additional genetic modules that often do not fit within the payload capacity of a single vector, or use a combination of gene engineering techniques (e.g. lentivirus + CRISPR), necessitating the use of multiple vectors. For my last thesis project, I report on STASH Select, a simple platform technology for enriching cells that have been engineered with multiple vectors using a single-step selection that results in high purity/yield and is compatible with current GMP cell manufacturing workflows and closed loop systems

Keywords: Bioengineering.
Advisor: Cochran Jennifer R.
Mackall Crystal
Majzner Robbie 
Qi Lei (Professor of Bioengineering)
An enriched-basis high-order method for wall-modeled large eddy simulation

Turbulent flows occur in a wide variety of engineering applications from flow around an aircraft to internal combustion engines. However for most applications, the computational cost of a direct numerical simulation (DNS) is prohibitive because of the large range of scales of motion. Large eddy simulation (LES) is a more cost effective method where only the large scales of motion are resolved and the smaller scales are modeled. High-order methods, such as the spectral element method (SEM) and the discontinuous Galerkin method (DG), are well suited LES applications because their dissipation and dispersion properties. One limitation of high-order methods is that their polynomial basis cause unphysical oscillations when high-gradient features are under-resolved. For wall-bounded flows, even LES is too expensive for most applications because a large number of elements are needed near the wall to resolve the boundary layer. Wall-modeled LES (WMLES) addresses this challenge by modeling the near wall region while using an LES level of accuracy away from the wall. Traditionally, wall-models use an analytical model to compute the a modeled shear stress on the wall and enforce it as a boundary condition. While shear stress wall-models have shown success, they creates an unphysical solution in the near-wall region. Additionally, these methods are primarily designed for low-order methods and have not been integrated with the advantages of high-order methods. In this thesis, I discuss the development of a solution enrichment method for the spectral element method that augments the polynomial solution with a problem specific non-polynomial enrichment function. This method enhances the ability of SEM to model the targeted feature without unphysical oscillations. The framework is designed to be easily implemented in existing solvers to make it more easily usable for industrial applications and the method is implemented in the open-source solver Nek5000. The enrichment framework is then used to develop a turbulent wall-model for WMLES that maintains a physical solution and turbulent fluctuations throughout the domain. The wall-model enriches the polynomial solution representation with a law-of-the-wall enrichment function so that the large gradients in the near-wall region can be captured with large elements without oscillations. In comparison to traditional shear stress wall-models, the enrichment wall-model is able to better capture the mean velocity profile with larger elements

Advisor: Ihme Matthias
Alonso Juan José
Lele Sanjiva K. (Sanjiva Keshava)
Environmental change and human health : studies on vector-borne disease transmission and wildfire smoke pollution

While there is widespread recognition that anthropogenic global changes are leading to human and planetary health crises, we often lack nuanced, causal estimates of these effects and do not fully understand their magnitude or extent. In this dissertation, I focus on two particular effects of environmental change on human health: vector-borne disease transmission and air pollution from wildfire smoke. In the first chapter of this dissertation, I focus on spillover of yellow fever virus in Brazil. I parameterize a mechanistic model of spillover and find environmental risk, based on the ecology of sylvatic vectors and non-human primates, distinguishes between locations and times with spillover better than risk metrics incorporating vaccine coverage or human population density. In my second chapter, I examine the effect of gold mining on malaria transmission in the Brazilian Amazon, using data on reported cases of malaria and gold production inferred from financial asset taxes from 2010 to 2015. I find that gold mining increases malaria transmission both in the municipality in which production occurs and up to 250km away. In my third chapter, I predict fine particulate matter (PM2.5) from wildfire smoke in the US. Using data from ground monitors, satellite imagery and global reanalyses, I calculate anomalies in PM2.5 that can be attributed to smoke and train a model to predict smoke PM2.5 to produce daily estimates of wildfire smoke over the contiguous US from 2006 to 2020. Concentrations of smoke PM2.5 have grown by up to 5μg/m3 in some areas of the Western US and the number of people living in locations with extreme smoke days over 100μg/m3 has grown 27-fold in the last decade. These chapters contribute to our understanding of the important linkages between environmental change and human health

Advisor: Burke Marshall
Mordecai Erin
LaBeaud Desiree
Luby Stephen