VictorJuiz/thesis huggingface dataset:
Better together [electronic resource] : composite plasmonic materials for enhaced upconversion and responsive metasurfaces

Composites can combine the best qualities of multiple materials. In some cases, composite materials can exhibit properties that improve upon their components -- forming a material that is greater than the sum of its parts. In this dissertation, we examine two materials systems wherein combining multiple materials at the nanoscale enhances the resultant properties. We begin by studying upconversion, the conversion of photons from lower to higher energies. Upconversion is a process that promises applications ranging from high-efficiency photovoltaic and photocatalytic cells to background-free bioimaging and therapeutic probes. Existing upconverting materials, however, remain too inefficient for viable implementation. Here, we describe the significant improvements in upconversion efficiency that can be achieved by combining upconverting materials with metallic nanostructures. We review both theoretical underpinnings and experimental demonstrations of plasmon-enhanced upconversion, and elucidate design strategies for optimal enhancements. Then, we demonstrate how plasmonic materials can add new function to upconverting materials by making a transparent upconverting electrode which enhances upconversion emission by 4x. Next, we consider optical materials with dynamic refractive index. Such materials could be transformative, enabling active camouflage, tunable holograms, and novel colorimetric medical sensors. We draw inspiration from chameleons and cephalopods, experts at changing their color, pattern, and reflectivity in response to their environment. Here, we demonstrate a chemically tunable, large-area metasurface with a strong magnetic response. By combining plasmonic nanoantennas with an elastomeric substrate, we can reversibly tune the material's refractive index from positive to negative values. Such a material may provide a new path towards programmable optical elements and responsive light routing.

Keywords: Chemistry.
Advisor: Dionne Jennifer Anne primary advisor. Thesis advisor
Salleo Alberto
Kanan Matthew William
Beyond objectivity [electronic resource] : questioning shifting scientific paradigms in Erwin Schrödinger's thought

Humanistic thinking played a significant role in the thought of one of modern physics' greatest figures, Erwin Schrödinger, whose work extended far beyond his famous cat experiment, for which he is now best well known (not least of which for its continual reinterpretation through popular internet memes). He was also a prolific cultural writer, whose work drew on modernist cultural themes, particularly the critique of Western scientific and objectivist thought, as refracted through his fascination with Eastern Vedic philosophy. I argue that Schrödinger's philosophical interests influenced his scientific thinking, not only in his "native" field of physics, but also in the field of biology, thereby claiming him as modernist figure moving between the "two culture" of science and the humanities. This dissertation is organized around three chapters: 1) I first demonstrate how Schrödinger argued that the debate surrounding the interpretation of quantum mechanics could be understood as a modern metaphysical crisis emerging from conceptual limitations inherent to the Western frame of scientific inquiry. 2) My next chapter explores how he further articulated his cultural criticism of Western thought by turning to a discussion of ancient Indian philosophy to challenge deep-rooted Western theoretical assumptions. 3) In my third and final chapter I argue that Schrödinger's study of ancient Indian philosophy helped shape his ideas surrounding life in the field of biology, particularly in relation to theories of genetic propagation and biological systems. Schrödinger's biological thinking inspired James Watson, Francis Crick and Maurice Wilkins to conduct the research that lead them to the discovery of the double-helical structure of DNA.

Keywords: German Studies.
Advisor: Berman Russell A.
Dornbach Marton
Eshel Amir advisor. Thesis advisor
The BICEP3 millimeter-wave polarimeter [electronic resource] : measuring the cosmic microwave background from the South Pole

BICEP3 is a 52 cm aperture, two-lens refracting telescope designed to observe the polarization of the Cosmic Microwave Background (CMB) at 95 GHz (3.2 mm). By searching for the B-mode polarization pattern of the CMB at degree angular scales, BICEP3 probes signatures of primordial gravitational waves in the early universe that are linked to inflation. Its focal plane consists of modularized detector arrays of antenna-coupled transition-edge sensor (TES) bolometers. All of the detectors and optics are operated at cryogenic temperatures in a single cryostat receiver, with the focal plane held at 274 mK. BICEP3 is currently completing its second observing season from its South Pole observing site. The instrument is an evolution of the previous generation design that expands the per-receiver detector count by 5x to 2560. This thesis covers the design, key technologies, integration, and deployment of BICEP3 through its first two observation seasons, and presents the preliminary detector performance. It details the improvements implemented after the initial engineering season that have increased the CMB observation duty cycle and total instantaneous sensitivity.

Keywords: Applied Physics.
Advisor: Byer R. L. (Robert L.)
Kuo Chao-Lin (Physics professor) primary advisor. Thesis advisor
Irwin Kent
Bioengineered 3D cancer model to decipher brain tumor-niche interactions [electronic resource]

Brain tumors remain as one of the most challenging tumors to treat. A critical barrier to progress in improving clinical outcomes is the lack of faithful experimental models for deciphering brain tumor biology and screening novel drug candidates. By integrating principles from cancer biology, materials science, and tissue engineering, we have developed novel 3D in vitro cancer models using biomimetic hydrogels that may bridge the gap between conventional 2D culture and animal models. Such bioengineered 3D cancer models would enable mechanistic studies to test novel hypotheses for tumor progression and accelerate the discovery of new therapeutics.

Keywords: Bioengineering.
Advisor: Yang Fan (Bioengineering researcher and teacher) primary advisor. Thesis advisor
Grant Gerald
Monje-Deisseroth Michelle
Biogeography of microbial communities inhabiting the human oral cavity [electronic resource]

This thesis is concerned with understanding the biogeography of the human oral microbiota, defining the types and extent of spatial patterns observed in the communities of the oral cavity, as well as the underlying causal mechanisms governing those patterns. First, I provide an overview of spatial ecology and, in a review, discuss how applying the context, principles and methods of spatial ecology to the study of the human microbiota will enable us as a field to move beyond the descriptive statistics that have dominated our biogeographic surveys since the time of Leeuwenhoek (Chapter 1). Second, I review extant literature surveying the biogeography of the human microbiome, of all major body site habitats, providing a critical review that yields insight into the limitations of existing biogeographic surveys (Chapter 2). Third, I identify an ecological gradient that structures the microbial communities that inhabit the exposed surfaces of teeth and which runs between the front of the mouth and its back (Chapter 3). This is the first demonstration of an ecological gradient, that is not a successional gradient, in the human oral cavity, a departure from previous reports that communities are categorically distinct from one another, varying simply by tooth number or tooth class. Fourth, I demonstrate that the anterior to posterior ecological gradient observed for supragingival communities is shared by communities inhabiting multiple tissues, including the alveolar mucosa, keratinized gingiva, and buccal mucosa, highlighting the importance of examining multiple spatial scales in studies of the human microbiota (Chapter 4). Fifth, I tested the hypothesis that reduced salivary flow homogenizes the observed spatial structure of microbial communities (Chapter 5). This is the first demonstration that, in healthy humans, salivary flow mechanistically drives the segregation of human oral microbial communities, maintaining the spatial architecture of bacterial communities across teeth in healthy humans. Taken together, these studies provide novel insight into the biogeography of the human oral microbiota, and how it pertains to human health and disease.

Keywords: Microbiology and Immunology.
Advisor: Relman David A. primary advisor. Thesis advisor
Amieva Manuel advisor. Thesis advisor
Loomer Peter M.
Monack Denise M. advisor. Thesis advisor
Biological imaging in a long-wavelength near-infrared window using novel nanomaterials [electronic resource]

Fluorescence imaging in the second near-infrared window (NIR-II, 1000-1700 nm) has attracted increasing attention mainly owing to the advantage of reduced light scattering compared to imaging in shorter wavelength windows such as visible or first near-infrared window below 900 nm. The work in this thesis aims to develop novel nanomaterials with improved optical properties (e.g. high quantum yield and long emission wavelengths) and apply these nanomaterials for biological imaging in live animals, especially imaging in a long wavelength near-infrared window beyond 1500 nm (1500-1700 nm, named NIR-IIb window). Firstly, chirality-pure SWNTs with confined excitation and emission wavelengths were separated from the as-made SWNT mixture using a simple gel filtration method. Due to the strong resonance with the 808-nm excitation widely used for near-infrared imaging, the chirality-pure SWNTs showed much higher brightness compared to the pristine SWNT mixture, which significantly reduced the toxicity concern of using SWNTs for in vivo applications. Secondly, biological imaging in the 1500-1700 nm (NIR-IIb window), long end of the entire NIR-II window, was achieved using a novel large diameter SWNTs grown by laser vaporization method. NIR-IIb imaging is shown to be more advantageous than the traditional NIR-II window, owing to both reduced light scattering and reduced tissue autofluorescence. Thirdly, a bright, NIR-IIb emitting fluorophore, lead sulfide (PbS) quantum dots, was developed for real-time, deep-tissue imaging in the long wavelength NIR-IIb window. Due to the bright emission from the PbS quantum dots in the NIR-IIb region, real-time heart/lung imaging with high frame-rate of ~30 frames/second were performed with high resolution, revealing blood flow and cardiac cycle information useful for imaging heart and lungs.

Keywords: Chemistry.
Advisor: Dai Hongjie
Cui Bianxiao advisor. Thesis advisor
Zare Richard N. advisor. Thesis advisor
Biomedical text mining from context [electronic resource]

Many profound insights from biomedical research and clinical practice remain hidden within the unstructured text of scientific articles and electronic medical records. Extracting structured information from biomedical text could dramatically accelerate the pace of biomedical research, but due to the high variability of natural language, it hinges on our ability to recognize when different-looking statements are saying the same thing. Unfortunately, attempts to address this problem in the biomedical domain usually involve structured lexicons and ontologies, which are expensive and time- consuming to produce. In recent years, a subdomain of natural language processing called distributional semantics has approached normalization in a different way: by learning mathematical representations of words, phrases, and relationships based on their usage patterns in large corpora. These methods can detect that two different strings are semantically related based on how they are used in context, and require little or no human effort. This dissertation illustrates how distributional approaches can be applied to several important biomedical text mining tasks, including gene, drug and disease name normalization, ontology building, and the construction of a structured radiology lexicon from clinical notes. I describe a novel distributional algorithm (EBC) for extracting relationships among biomedical entities, such as chemicals, genes and diseases, and show how it can be applied to learn the structure of chemical-gene, chemical-disease, gene-disease, and gene-gene relationships from contextual usage patterns. Finally, I apply distributional relationship extraction to two inferential tasks: curating pharmacogenomic pathways, and uncovering the mechanisms behind drug-drug interactions.

Advisor: Altman Russ primary advisor. Thesis advisor
Owen Art B. advisor. Thesis advisor
Potts Christopher
Body politics in the postcolony [electronic resource] : global health and local governance in rural Malawi

This dissertation is concerned with the governmental effects of the technocratic, often avowedly apolitical choices that inform the design and implementation of public health initiatives in postcolonial Africa. It seeks to shed light on the interactions between the mutual making of 'global health' and 'local' authority in specific national historical context and the consequences of these processes for ordinary people's lived experiences as beneficiaries, recipients, participants in, 'targets' of health promotion, and as citizens. The dissertation is based on 18 months of ethnographic and archival research on rural health promotion in Malawi. Specific chapters address the intersections of global health initiatives and local governance in the areas of home hygiene promotion and sanitation surveillance, maternal health, community participation in primary health care, and vaccine refusals.

Keywords: Anthropology.
Advisor: Ferguson James
Hansen Thomas
Malkki Liisa H. (Liisa Helena) advisor. Thesis advisor
Body-centric understanding of 3D environments [electronic resource]

Human environments are designed by people to facilitate human actions. Viewing environments as spaces for action motivates the use of an action representation to factor and explain the structure and function of environments. This dissertation proposes to encode human actions as coupled configurations of the body with its surrounding environment in a body-centric representation. By joining these two aspects of human interaction we can analyze 3D scenes through the lens of action, and jointly generate 3D scenes and human poses depicting actions. The body-centric view proposed by this dissertation treats body parts and parts of objects as primitives linked through physical contact, gravitational support, and visual attention in a graph characterizing a given interaction. These primitives and links are encoded in an interaction graph capturing features of the pose configuration and the geometry of the objects present during an action. By recording real-world observations of common actions and converting them into this representation we can obtain aggregate statistics of pose and object configurations under different actions which we summarize in a prototypical interaction graph (PiGraph). The PiGraphs model formalizes a body-centric view of interactions and can be learned directly from observational data captured by commodity RGB-D sensors. PiGraphs can be used to predict the likelihood of common actions occurring over the space of an input 3D environment. They also enable action-based 3D scene synthesis resulting in higher perceived plausibility and quality compared to prior approaches in scene synthesis. Finally, by connecting PiGraphs to natural language we can create an end-to-end text-to-interaction system that jointly generates a 3D scene and human pose depicting an interaction described in natural language.

Advisor: Hanrahan P. M. (Patrick Matthew) primary advisor. Thesis advisor
Agrawala Maneesh advisor. Thesis advisor
Guibas Leonidas J. advisor. Thesis advisor
Bonded metropolis [electronic resource] : race, infrastructure, and the search for capital in San Francisco, 1900-1976

Drawing on trade publications, the personal papers of bankers and municipal officials, credit ratings, annual reports, and bond ephemera, "Bonded Metropolis" offers the first historical account of the tangled trajectories of finance capitalism, race, and metropolitan redevelopment in twentieth century America. With San Francisco as its focal point, this dissertation shows how the municipal bond was at once a debt obligation used by municipal debtors to finance physical infrastructure, a cultural signifier with historically contingent meanings, and the basis of social relations between municipal debtors, bankers, sellers of financial information, and investors. The story begins in 1900, when Progressives repudiated an older logic of fiscal austerity to embrace municipal bonds as tools of progress. In so doing, the city opened itself up to events, processes, and relationships that impinged on the trajectory of public infrastructural development. I end in 1976, when complex structural changes and shattered social relations within the municipal bond market were largely reduced to a simplistic narrative of bad municipal debtors. As New York City's urban fiscal crisis reverberated outwards, an odd tandem of San Francisco liberal Democrats and fiscally conservative Republicans responded by imposing municipal retrenchment. The narrative arc moves from one form of municipal retrenchment to another, but in between I trace the reconstitution of the municipal bond market and situate the construction of public housing, transportation, parks, and schools within the context of rising borrowing costs. Ultimately, this dissertation demonstrates how municipal bonds were central to the production of urban space, how bonds held the potential to undo and remake urban inscriptions of racial inequality, and how the extension of municipal credit allowed geographically distant institutions and individuals to accumulate tax-exempt interest income. By beginning with the municipal bond, this dissertation confronts and reworks familiar narratives about twentieth century American capitalism, the co-creation of cities and suburbs, and layered forms of racial, spatial, and wealth inequality.

Keywords: History.
Advisor: Camarillo Albert primary advisor. Thesis advisor
Connolly N. D. B. advisor. Thesis advisor
White Richard
Boundaries of nature [electronic resource] : national parks and environmental change at the Argentine-Brazilian border, 1890-1990

"Boundaries of Nature" investigates the creation of the Iguazú National Park in Argentina (1934) and the Iguaçu National Park in Brazil (1939), analyzing the geopolitical reasoning and the spatial practices behind the establishment of these two protected areas. Located at the Argentine-Brazilian border around the famous binational Iguazu Falls, the two national parks were initially envisioned as tools for the nationalization of the border. In Argentina, park proponents innovated by engaging the country's national park service in the promotion of settler colonization in national park lands. The Argentine national park agency traced street grids, parceled and sold lots, and implemented urban infrastructure inside park boundaries. Brazilian officials in turn, partially inspired by the Argentine example across the border, engaged in more modest efforts to use national park policy in the development of their side of the border. Brazil's weak control of public land, however, resulted in thousands of contested settlements inside its own border national park. In the 1960s and 1970s, the consolidation of an international paradigm of national parks as spaces devoid of dwellers and the strengthening of state tools to manage land and people led the military regimes in the two countries to engage in conflictive processes of settler eviction. This study employs space as a crucial dimension in the reconstruction of the history of Iguazú and Iguaçu, showing the spatial practices that helped to define these protected areas: mapping, demarcation, zoning, parceling, patrolling, eviction. It also demonstrates how settlers, poachers, and heart-of-palm harvesters contested the enforcement of national park rules in the space of the parks. The result was the establishment of landscapes of protected nature that were socially and politically constructed through spatial processes.

Keywords: History.
Advisor: Frank Zephyr L.
White Richard
Wolfe Mikael advisor. Thesis advisor
Breathing Soils: Topographic and Biologic Controls on Seasonal Soil CO2 Respiration in a Rocky Mountain Subalpine Meadow

Soil carbon accounts for roughly 80 percent of carbon in terrestrial ecosystems. Respiration of carbon dioxide (CO2) from plant roots and soil organisms is one of the largest fluxes of CO2 from the land surface to the atmosphere (Lal, 2008). Increasing temperatures and changes in the timing and amount of precipitation can potentially affect soil moisture, temperature, plant primary productivity, and microbial productivity. Measurements of the response of soil respiration to climate change forcings are often based on point measurements, then extrapolated to the landscape scale without much consideration of small-scale variation. Although both root and microbial soil CO2 respiration are known to be sensitive to changes in temperature and soil moisture, relationships derived from either point measurements (meter-scale) or laboratory experiments have not been tested over larger spatial domains (kilometer-scale), where competing factors may interact with the relationships observed at smaller scales. To determine how CO2 fluxes vary across scales, I examined the relationship between soil CO¬2 respiration and landscape metrics of soil moisture, such as topographic wetness index (TWI), across a subalpine meadow in the Colorado Rockies (East River, CO) from late May through August 2016. To identify the scales of spatial and temporal variation in soil properties (moisture and temperature) that have been found to control soil CO2 fluxes, I measured surface soil moisture and CO2 respiration rate at spatial scales of 0.5-40 m across a grid of 74 points within a 625 m^2 area of meadow-dominated hillslope. The magnitude of variability in both soil moisture and respiration slightly increased later in the growing season, but remained consistently small for spatial separations <50 m. Soil CO2 respiration is not well correlated with soil moisture. Further, neither soil moisture nor soil CO2 respiration correlate with TWI, indicating that this metric of topography does not capture the key drivers for either at our site. Expanding upon these observations, I used remotely-sensed multispectral data to determine that soil respiration is not correlated with plant primary productivity as represented by the Normalized Difference Vegetation Index (NDVI). Combining these observations, I found that the limited correlations between soil respiration and topographic or multispectral indices present challenges for extrapolating meter-scale measurements of soil moisture, temperature, and respiration to the catchment scale (km).

Keywords:  Department of Geological Sciences
Soil respiration
Soil moisture
spatial variability
NDVI
TWI
subalpine soils
soil microbes
Department of Geological Sciences
School of Earth Energy and Environmental Sciences
Thesis
Advisor: Maher Katherine
Sperling Erik
Chadwick K. Dana