VictorJuiz/thesis huggingface dataset:
Transition metal oxides for photoelectrochemical water-splitting and superconductivity
Keywords: Materials Science and Engineering.

Transition metal oxide materials have garnered significant research interest over the past decades due to their diverse chemical and physical properties, ranging from electrochemistry and superconductivity. Moreover, the capability to access vastly different properties with similar crystal structures by controlling the stoichiometry provides a powerful additional degree of freedom in materials engineering for applications. By using pulsed laser deposition, we obtained epitaxial thin films providing a solid platform to investigate and engineer the properties of these oxides. We will first discuss a transition metal oxide, known as pseudobrookite (Fe2TiO5), for photoelectrochemical (PEC) water-splitting. Recently, Fe2TiO5 has emerged as a photoanode for water oxidation due to its chemical stability, scalability, and suitable bandgap. Based on our successful fabrication of epitaxial thin films, we will present our comprehensive characterization of the intrinsic PEC properties. We discovered that Fe2TiO5 exhibits highly efficient charge transfer at the Fe2TiO5-electrolyte interface and deduce a long minority carrier diffusion length of 19 nm, far exceeding that of α-Fe2O3. Furthermore, by forming heterostructures, PEC performance of α-Fe2O3 is enhanced significantly, where photocurrent density increases by one order of magnitude, and the onset potential improves by ∼300 mV. In the second topic, we discuss the infinite layer nickelates, RENiO2 (RE: rare-earth element). Ever since their discovery, superconductivity in cuprates has motivated the search for materials with analogous electronic or atomic structure. Here we present how soft chemistry approaches can be used to synthesize superconducting infinite layer nickelates from their perovskite precursor phase, using topotactic reactions. Following the discovery of superconductivity in Nd1−xSrxNiO2, we find superconductivity in Pr1−xSrxNiO2 and La1−xSrxNiO2
Transnational Senegal River development, 1920-2000
Keywords: History.

Environmental bodies, such as rivers, rebel against political frontiers, and seldom conform to man-made borders. Transnational Senegal River Development, 1920-2000 reveals that regional-level coordination and collaboration between postcolonial African nations in the Senegal River basin was an important strategy for the development and management of the river. Drawing on research in France, Mali, Senegal, and the United States, this research tells a new story of environmental governance in Africa. Chapter 1 looks at French colonial development activities in the Senegal basin. The long afterlife of colonial-era Senegal River development plans calls into question whether a timeline focusing on decolonization is the only salient way to look at West African history, as do continuities in engineering expertise between the colonial and postcolonial eras. Chapter 2 analyzes the appeal of regional and pan-African political organizations during decolonization. It also focuses on the failure of transnational organizations centered on the Senegal River to provide broad regional unification and explicates the formation of an organization named the Organisation pour la Mise en Valeur de Fleuve Sénégal (Senegal River Development Authority or OMVS) in 1972. Beginning in the late-1960s, severe drought and famine ravaged the Sahel. Environmental crisis provided an opportunity for the OMVS. It mobilized concerns about famine to pitch its river development scheme as a long-term solution to food insecurity, and Chapter 3 explains how the OMVS obtained financing for dam projects during the 1970s. Case studies of the construction and consequences of two major dams, Manantali and Diama illustrate gaps between the OMVS' development rhetoric and actual practices, as well as unintended consequences of river management. Chapter 4 focuses on the planning and construction of Manantali Dam and town, the largest and most complex project the OMVS executed. Chapters 5 and 6 investigate the consequences of the integrated Senegal River management plan put forward by the OMVS for river basin populations. Chapter 5 looks at the Manantali Resettlement Program, while Chapter 6 considers downstream effects. The dissertation concludes by explaining how, during the 1990s, the OMVS decentralized due to funder pressures, losing much of its power to shape riverine sovereignty. Nonetheless, it remained a force for transnational river management in West Africa and a global model
Trends in heavy drinking behaviors and hepatitis C virus infection in China : a mathematical modeling study
Keywords: Medicine.

Population health has drastically changed over time, especially in countries like China where rapid economic and social growth has occurred in the past decades. Economic development in China was paralleled with increase alcohol consumption and an increasing burden of chronic diseases. Empirical studies provide observations on the trends and patterns in health risk behaviors and diseases. Mathematical modelling can further describe dynamics underlying the observed epidemiology and explore evolving disease epidemiology in the population with or without potential interventions. In this dissertation, I apply mathematical models to better understand what drove past trends in high-risk drinking behaviors, hepatitis C virus (HCV) infections, and their interactions among Chinese men in order to project future burden of diseases and potential policy effects. The first chapter of this dissertation shows that inclusion of cohort trends when modeling disease results in different model outcomes and projections than when cohort trend are not included. In Chapter 2, I identify age patterns and cohort trends in high-risk drinking behaviors among Chinese men by applying a model calibration technique to longitudinal data. The constructed model predicts a declining trend in future prevalence of heavy drinking and estimates significant future health benefits of mitigating heavy drinking behaviors among the subpopulation at high risk of heavy drinking. I incorporate the model of heavy drinking behavior into Chapter 3 where I develop a natural history model of HCV infection among Chinese men. By combining sparse data on HCV and HCV-related liver diseases in China, the calibrated model identifies the variation in HCV infection rates by birth cohorts whose risk of infection has changed in response to prior regulations on HCV transmission in China
Two sides of the same coin : separable inhibitory action against GLI and ALDH1B1 activity
Keywords: Chemical and Systems Biology.

Small molecules are powerful tools that enable the interrogation of complex biological questions and provide insights into routes for modulating these processes. Furthermore, small molecules often provide a framework for the design of novel therapeutics with relevant disease targets. In this dissertation, I present my work employing a family of bicyclic imidazolium compounds towards the inhibition of the Hedgehog (Hh) signaling pathway and the aldehyde dehydrogenase ALDH1B1. These studies have enhanced our understanding of specific molecular mechanisms that drive cancer, and potential routes to mitigate tumorigenicity driven by GLI or ALDH1B1
Two-pulse x-ray photon correlation spectroscopy at Linac coherent light source
Keywords: Physics.

Nearly fully transversely coherent femtosecond x-ray pulses produced by x-ray free electron laser sources opened up the possibilities of direct measurement of atomic scale dynamics of complex systems at their native timescales. One area of particular interest is the investigation of noncrystalline matter such as liquids, glasses, amorphous and disordered systems, and holds the promises of unlocking the mysteries behind the glass transition, liquid-liquid phase transitions, fragile-to-strong transitions, etc. A primary methodology with the potential to extend dynamic light scattering to angstrom and femto- to nanosecond timescale is the so-called two-pulse x-ray photon correlation spectroscopy (XPCS) technique, where the dynamics of the scattering object are imprinted onto the fluctuations of coherent scattering intensity distribution. This dissertation focuses on the instrumentation and methodology of two-pulse XPCS, highlighting the challenges and efforts to establish it as a robust technique at x-ray free electron laser facilities towards measuring ultrafast dynamics in complex matter
Ultra low power oven controlled MEMS resonator timing reference
Keywords: Mechanical Engineering.

The main goal of this dissertation is to provide readers with some insights of how silicon MEMS based resonators can be a viable option in making an OCXO-level timing references. We will take a look into the fabrication of such devices using wafer-scale encapsulation techniques, simulation and design of the oven-controlled MEMS resonators, followed by the full characterization
Ultrafast infrared spectroscopy reveals the structural and dynamical heterogeneity of glassy materials
Keywords: Chemistry.

The remarkable properties of glassy materials arise from their complex amorphous structures and dynamics. The heterogeneity of these materials was studied on molecular length scales and picosecond time scales using a combination of polarization-selective IR pump-probe and 2D IR experiments and a vibrational chromophore that is sensitive to local chemical and electrical environments. By monitoring the restricted orientational motion of the chromophore in a polymer, the distribution of sub-nanometer pores could be explored. The same chromophore in a hydrogen-bonding system showed extreme polarization dependence in the 2D line shape, providing evidence for significant dynamical heterogeneity in the supercooled liquid phase
Ultra-Low Latency NIC-CPU Interface Design and Realization
Keywords:  Department of Electrical Engineering
electrical engineering
networking
computer architecture
low latency
NIC
RISC-V
Thesis

This thesis builds off an ultra-low latency network interface device, known as the Lightning NIC (or L-NIC) [7], that opts to bypass the entire processor memory system and cache hierarchy in favor of delivering network data directly into the processor's register file. L-NIC is itself inspired by the J-machine [4], an earlier experimental parallel computer that investigated register-based, rather than memory-based, interactions with data. We expect a particular class of self-contained, granular, cache-resident, sub-microsecond applications, known as nanoservices, to enjoy a substantial performance benefit from the lower latency this approach provides. In turn, nanoservices, by allowing for much finer-grained parallelism than has been previously possible, can be used to significantly accelerate many existing distributed applications.
In "The nanoPU: From Microservices to Nanoservices" [6], our group presents a modified RISC-V processor, known as a nanoPU, that supports this L-NIC approach to network data and is optimized for running nanoservices. We also present a set of candidate nanoservice applications, demonstrate an order of magnitude performance improvement over a baseline NIC, and discuss how other distributed applications with a high degree of parallelism might stand to benefit from a nanoservice-focused refactor and a network of nanoPUs.
Here, I expand upon several complete components of this larger effort, focusing specifically on the design and development of the nanoPU's hardware-software interface — that is, on the particular instructions and registers relevant to the integration of the L-NIC into the processor. This is itself a novel undertaking. The challenge, at its core, is to design a system that supports easily usable software interfaces in an environment where each individual instruction constitutes a noticeable latency increase and a single DRAM access in an executing nanoservice introduces an unacceptably high delay.
Ultraviolet light-induced genome instabilities
Keywords: Biology.

Exposure to the ultraviolet (UV) radiation in sunlight creates DNA lesions, which if left unrepaired can induce mutations and contribute to skin cancer. The two most common UV-induced DNA lesions are the cis-syn cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts (6-4PP), both of which can initiate mutations. Interestingly, mutation frequency across the genomes of many cancers is heterogenous with significant increases in heterochromatin. Corresponding increases in UV lesion susceptibility and decreases in repair are observed in heterochromatin versus euchromatin. However, the individual contributions of CPDs and 6-4PPs has not been systematically examined in specific genomic and epigenomic regions. In this study, we generated a genome-wide map of 6-4PP lesion abundance in primary cells and conducted a comprehensive analysis to determine the genetic and epigenetic features associated with 6-4PP susceptibility. We found high degree of similarity between 6-4PP and CPD formation, with enrichment of both in heterochromatin regions. However, when examining the relative levels of the two UV lesions, we found that bivalent and Polycomb repressed chromatin states were uniquely more susceptible to 6-4PPs. Interestingly, when comparing UV susceptibility and repair with melanoma mutation frequency in these regions, disparate patterns were observed in that susceptibility was not always inversely associated with repair and mutation frequency. Functional enrichment analysis hint at mechanisms of negative selection for these regions that are essential for cell viability and immune function and induce cell death when mutated. Ultimately, these results reveal both the similarities and differences between UV-induced lesions that contribute to skin carcinogenesis
The uncensored man : Leonid Tsypkin, Russian writer and Soviet jew (1926-1982)
Keywords: Ilchuk, Yuliya degree committee member.
Slavic Languages and Literatures.

This dissertation introduces the reader to the uncensored Russian writer Leonid Tsypkin (1926-1982) and his unique mode of creation. A doctor by profession, Tsypkin was too afraid of the possible ramifications on his career to publish and instead "wrote for the drawer." It was not until he was denied an exit visa and became a "refusenik, " that he decided to finally seek publication in earnest. Tsypkin carried with him a consciousness of his marginal position in Russian literature, as well as the peripheral position of Jews in Russian culture and in contemporary Soviet society. I argue that not only do his texts' orientation toward the drawer endow them with a unique orientation toward history, but the lack of an obvious interlocutor contributes to what I have termed Tsypkin's act of "co-creation." Through a series of encounters with material objects, photographs, or literary texts, Tsypkin is able to forge his texts in dialogue with other voices and perspectives, thus gaining a new understanding of himself at the same time. The four chapters of this dissertation move chronologically through Tsypkin's work, offering close readings and analysis of three major prose works and one collection of photographs. They trace Tsypkin's search for material which reflects him and can thus provide a view on the self from the outside. To this end he uses photography, autobiographical fiction, and the travel narrative. His most successful attempt at achieving that view on the self from the outside comes from the act of reading -- and, in particular, reading the Dostoevskys, both Fyodor Mikhailovich and Anna Grigorievna (née Snitkina). Identifying with these writers and their characters during the act of reading gives Tsypkin the means to fashion himself into what I call an "uncensored man, " in the vein of Dostoevsky's "Underground Man, " who also wrote as if he had no reader. When Susan Sontag eventually discovered Tsypkin's novel in translation and helped to bring it to attention, she was drawn to the "Tsypkin sentence" that can extend for pages and unite a multitude of characters, places, and epochs. Tsypkin's unique form encapsulates an understanding of history as non-linear. I argue that his texts' mode of existence as unpublished literature, their distinctive sentence structure, and their transgressive content allow readers to feel as if they are in two places at once - a feat of escapism and a necessary skill for the new type of "underground man, " the "internal emigre, " or the Jew in the late Soviet Union
Unconventional shale gas field development under price uncertainty
Keywords: Energy Resources Engineering.

We present an optimization framework for unconventional shale gas resource development under price uncertainty. Shale gas developers must balance the ability to implement price-reactive actions with the operational and financial constraints of long-term service agreements. Both can improve project NPV, but they typically act in opposition to one another. We represent gas price uncertainty with a Ornstein-Uhlenbeck stochastic natural gas price model. We develop a mixed-integer linear program (MILP) framework to define optimal month-to-month field development decisions based on current gas prices and future expectations. Our workflow then provides the optimal set of long-term upstream and midstream agreements based on NPV and NPV-risk preferences. Using two case studies, we illustrate both how a field developer can leverage flexible on-demand services, as well as the restrictive effect of long-term agreements on price-reactive actions. For the financial parameters and natural gas price uncertainty used in one of our case studies, a stochastic solution that utilizes on-demand services is, on an NPV basis, equivalent to a 3.1% reduction in the field development costs associated with long-term agreements. Larger cost savings would be achieved in cases with greater price volatility, weaker reversion speeds, and increased availability of on-demand services
Uncovering natural variation in root system architecture dynamics
Keywords: Biology.

The plant kingdom contains an immense array of complex morphologies that provide adaptive advantages for life on Earth. While we can easily observe the stunning diversity of plant form in the above-ground portions of plants, it is much more difficult below ground. As the interface between the soil environment and the shoot system, roots play a key role in plant anchorage and resource uptake. The distribution of roots, termed root system architecture (RSA), is determined by root growth and branching and is influenced by the surrounding environment. GLO-Roots (Growth and Luminescence Observatory for Roots) is a new soil-based root imaging technology, which enables detailed observations of Arabidopsis thaliana root system growth in soil. Expanding upon this system using automation, we developed GLO-Bot, a linear-rail robot designed to accurately manipulate the position of plants, which enables automated watering and treatment of plants, and time-lapse imaging of root luminescence reporters. To take advantage of this technological improvement in plant growth and imaging, I improved and further developed a data analysis pipeline to extract root traits from these images in order to quantitatively describe changes in RSA. I examined architectural diversity amongst six diverse accessions and observed differences in how the spatial distribution of roots within the soil changed over time. I then characterized a larger diverse population of 93 Arabidopsis accessions and found root angle to be a major driving force in determining RSA diversity. I uncovered correlations between traits and climate variables which suggested that roots with shallow angles are found in climates with larger diurnal changes in temperature. Finally, I performed multiple genome wide association (GWA) analyses, which identified putative alleles involved in controlling RSA. Future experiments simulating stressful environmental conditions could elucidate how these factors aid in plant fitness
Uncovering the role of biochemical ligands in modulating stem cell mechanotransduction and differentiation : a biomaterials-based approach
Keywords: Bioengineering.

The extracellular matrix (ECM) is comprised of different types of proteins and adhesive ligands, which change in composition and ratios during morphogenesis and disease progression. ECM proteins provide cell adhesion and impart mechanical cues to the cells. Increasing substrate stiffness has been shown to trigger Yes-associated protein (YAP) translocation from the cytoplasm to the nucleus, yet the role of ligand parameters in modulating mechanotransduction and stem cell fate remains largely unexplored. Studies of stem cell mechanotransduction and fate have widely used polyacrylamide hydrogels. However, conventional methods of conjugating biochemical ligands to polyacrylamide hydrogels suffer from low efficiency and heterogeneous protein incorporation, making studies of ligand effects on cellular mechanotransduction difficult. Here we report a method that enhances the conjugation of biochemical ligands to polyacrylamide hydrogels, enabling a greater incorporation and tunability of the amount incorporated. Using this method, we studied the effect of ligand density, ligand type, and ligand solvent on modulating cellular mechanotransduction. We showed stiffness-induced YAP translocation occurs only at intermediate ligand densities, whereas at low or high ligand densities, YAP localization is dominated by ligand density independent of substrate stiffness, mediated by cytoskeleton tension and integrin binding. We further showed that, comparing four major ECM proteins: fibronectin, collagen I, collagen IV, and laminin, the density required for such biochemical ligand-induced YAP translocation differs across ECM types. While stiffness-dependent YAP translocation can be induced by all four ECM types, each ECM requires a different optimized ligand density for this to occur. Finally, we assessed the effect of ligand solvent on modulating collagen coatings and downstream cell response. We found that collagen I coatings are highly dependent on solvent pH and composition, with solvents of pH from 3.4 to 8.5 leading to different conjugation efficiencies and distributions. We found that acetic acid of pH 3.4 led to the highest conjugation efficiency and most homogeneous coating, and induced robust MSC spreading and nuclear YAP localization across the broadest range of densities and stiffnesses, as compared to coating solvents such as PBS. The hydrogel platform with enhanced conjugation efficiency of biochemical cues provides a powerful tool for uncovering the role of biochemical cues in regulating mechanotransduction of various stem cell types. Together, results from this work highlight the important role of ligand density, ligand type, and type of ligand solvent as important parameters in studies of mechanotransduction and differentiation, and call for future mechanistic studies to further elucidate the role of changes in ECM compositions in mediating mechanotransduction during morphogenesis and disease progression