VictorJuiz/thesis huggingface dataset:
Aspects of strongly interacting quantum systems without translational symmetry [electronic resource]
Keywords: Physics.

In this thesis, we study the emergence and dynamics of strongly interacting quantum field theories in a variety of spacetime dimensions, primarily using the holographic duality. We use the duality to probe the low energy dynamics, thermodynamics, and transport properties of such systems, with an emphasis on understanding the implications of translational symmetry breaking. After illustrating the emergence of strong dynamics in a concrete and phenomenologically motivated example, we utilize the duality to study the structure of low energy excitations in holographic systems, in particular finding instances where the low energy spectral weight has non-trivial momentum space structure. With the inclusion of translational symmetry breaking, we find explicit examples where conjectured bounds on the ratio shear viscosity to entropy density are parametrically violated, as well as evidence for new disordered strongly interacting quantum critical points with non-trivial, disorder dependent critical exponents and exotic transport behavior.
Assessing the evolution of written language through data mining in large corpora [electronic resource]
Keywords: Iberian and Latin American Cultures.

Across the centuries, the question of the origin of language has captivated the human imagination. Many theories have been proposed to address fundamental questions such as: Where do languages come from? How do they evolve? What are the societal drivers of this change? Historically, one of the biggest challenges in addressing these questions has been a lack of large-scale empirical data, which has made it difficult to rigorously test hypotheses and correlate language change with cultural patterns. My dissertation research analyzes how written Spanish and Portuguese in the Americas diverged from their European counterparts, focusing on within-language shifts. Methodologically, I carry out this research by data mining in large digitized corpora (~300,000 documents ranging from the twelfth century to today) as well as performing close reading and contextual analysis of selected material. The interdisciplinary nature of my research was carried out as collaborative work between the Division of Literatures, Cultures, and Languages, the Department of Biology and the Stanford Libraries. The breadth of my project requires close attention to historical and social context, which may often be drivers of the written language changes that we trace computationally. For instance, Portugal imposed a 300-year prohibition of the printing press and universities in Brazil, whereas these institutions were introduced into Hispanic America soon after the arrival of Columbus. Accordingly, I found that written Spanish changed relatively "smoothly", reflecting a continuous assimilation of changes in the spoken form, while comparable changes appear much more "abruptly" in written Brazilian Portuguese. This work has an extensive study of personal pronoun evolution in Portuguese, and have found that past prohibition of the printing press, coupled with shifts in literary movements reflecting increased national sentiment, was a major driver of pronoun shift in nineteenth-century Brazilian Portuguese (Chapters 1 and 2). In Chapter 3, I analyze the evolution of personal pronouns in Spanish and show how regional writing styles affected the overall pronoun shift. Finally, I hope that this research will shed light on the main complex socioeconomic and geographical factors that led to divergent evolution of written language between the Americas and the Iberian Peninsula.
Assessing the Role of the p53 Target Gene Pard6g Tumor Suppression
Keywords:  Department of Biology
Biology
Cancer Biology
p53
Tumor Suppression
Stanford
Oncology
Attardi
Thesis

Tumor protein p53 is one of the best known tumor suppressors, controlling various regulatory pathways including apoptosis and cell cycle arrest. Among p53’s main functions is its activity as a transcriptional activator of downstream target genes. Binding of p53 to target gene regulatory regions promotes gene expression and subsequent protein formation. We discovered that Pard6g, the gamma isoform of an apical-basal polarity regulator, was transcriptionally activated by p53, suggesting a potential role of apical-basal polarity maintenance in p53-dependent tumor suppression. Cells lacking Pard6g demonstrate increased anchorage-dependent growth, while not exhibiting significantly different anchorage-dependent proliferation, suggesting that Pard6g functions as a tumor suppressor through mechanisms involving three-dimensional cell morphology or polarity.
Atomic layer deposited protection layers for metal-insulator-silicon water splitting cells [electronic resource]
Keywords: Materials Science and Engineering.

In pursuit of a fully sustainable energy economy, there has been increased effort to develop artificial photosynthesis technologies capable of creating clean fuels and chemicals from greenhouse gases with only the energy of the sun. Photoelectrochemical cells have been developed since the 1970's as all-in-one devices capable of exactly that task, but progress has been impeded by fundamental challenges. Principal among these is the trade-off that the most chemically stable materials due to a wide bandgap are necessarily the most inefficient at converting solar energy. In 2011, our group proposed a novel solution to this problem with a nano-layered composite structure capable of achieving both ends: atomic layer deposited (ALD) metal oxide protected cells where a top layer is chemically passivating and a bottom layer is efficient at solar energy conversion. In this work, I have carried out a rigorous study of ALD-TiO2 protection for metal-insulator-silicon devices, interrogating each layer of the structure and building state-of-the-art analytical models for performance of each component, as well as for the cell as a whole. The catalyst layer was studied first, demonstrating that this protection layer technology is a general solution, applicable with a wide range of catalysts. Second, the protection layer was probed and I discovered bulk-limited leaky conduction for the ALD-TiO2. I proposed a model of trap-mediated hopping conduction in the TiO2 in series with tunneling through the ultrathin SiOx, a model which has become the center point of much ongoing research and remains the accepted theory in the field for the anomalous, hole-conductive TiO2. Third, I probed the SiOx/Si interface, showed that conduction across the SiOx was well described by tunneling, and developed models that investigate the transition from leaky to capacitive structures. From here I developed engineering solutions including ALD-SiO2 and oxygen scavenging methods for fabricating ultrathin SiOx layers in these water splitting devices. In studying the device as a whole, I have developed a general theory for a so-called 'leaky capacitor' and applied this to understand the photovoltage loss observed in insulator-protected devices. This understanding allowed for the development of general design principles for maximizing photovoltage in MIS cells of varying architecture between so-called Type 0 photoelectrochemical cells and fully separated PV-electrolyzer systems. In applying these design principles, I have demonstrated the highest reported photovoltage to date for single junction silicon water splitting cells both in a so-called Type 1 Schottky junction and Type 2 pn junction photoanode. Taken altogether, this work represents a complete scientific investigation and understanding of protected silicon photoelectrode operation, and the corresponding engineering advances culminating in record photoanode performance.
Atomistic and phase field models of catalyzed nanowire growth [electronic resource]
Keywords: Materials Science and Engineering.

Nanowires (NWs) are a type of one-dimensional materials that usually hold a high aspect ratio with a well-defined crystalline structure. This special nanostructure makes NWs promising building-blocks for the next-generation electronic and optical devices. Many techniques have been developed for NW synthesis, among which the vapor-liquid-solid (VLS) growth serves as one of the most commonly used methods. However, many fundamental questions regarding its mechanism, such as the nucleation failure and NW kinking, are still not fully understood. Computational modelings and simulations can provide valuable insights into the study of the NW VLS growth mechanism. In this study, for Au-catalyzed Ge crystal growth, a modified embedded atom method (MEAM) potential is developed, which is well fitted to the Au-Ge binary phase diagram. For the Au-Si system, molecular dynamics simulations at various temperatures and Si fractions in liquid are performed to systematically study the Au-catalyzed Si crystal growth. The observed growth velocity's dependence on temperature is found to have a positive correlation with the surface atom activity's temperature dependence, both following the Arrhenius equation. This study also recognizes very different behaviors between the growth on {111} and {110} substrates, which can be explained by the crystallographic-dependent surface properties: the {111} interface is flat and inert, while the {110} interface is rough and the atoms are more active. For continuum scale modeling, a three-dimensional multi-phase field model is developed for NW VLS growth. This model can capture several important geometric features of the wires grown along different orientations, including the NW tapering, liquid-solid interface morphology and NW sidewall faceting. The model demonstrates the natural kinking of the NW in the steady state growth regime, suggesting a clear wire diameter dependence. Additionally, with phase field modeling, the stability of the droplet on top of the NW pedestal is studied, providing explanations for kinking at the NW base. Coupling with elasticity, the phase field model is further applied to nano-mechanics problems, such as the strain-induced NW surface roughening and the nano-fin pattern collapse.
Atomistic insights into microbial biofilms [electronic resource]
Keywords: Chemistry.

Most microbes live as multi-cellular communities termed biofilms. This lifestyle protects microbes against harsh conditions including antibiotic treatment and host immune responses. Within biofilms, microbial cells are entangled in a self-secreted extracellular matrix (ECM) that is rich in biopolymers such as fibrillar proteins and polysaccharides. This extracellular material is key to the characteristic properties of biofilms. Despite the prevalent roles that biofilms play in infections, a molecular-level understanding of the insoluble matrix components or the interactions between the ECM components has yet to be described. Biofilms and ECM are neither soluble nor crystalline, which poses challenges to analysis by traditional biochemical techniques. Solid-state nuclear magnetic resonance (NMR) is uniquely suited to study such complex systems because it provides quantitative information about chemical composition and also the spatial relationships of the components without requiring degradative sample preparation. Using solid-state NMR, we previously elucidated that the insoluble ECM produced by a uropathogenic strain of Escherichia coli called UTI89 is composed of two biopolymers: a functional amyloid called curli and modified cellulose. The purpose of this study is to elucidate quantitative information about microbial biofilm composition and structural information about biofilm constituents. Additionally, we aim to achieve an understanding of how the chemical and biophysical properties of specific ECM components contribute to the overall ECM architecture. To this end, we pursued three intersecting avenues with a primary focus on the bacterial strain UTI89, although we also determined quantitative parameters of additional microbial biofilms. In the first approach, we explored the dye binding properties of the biofilm constituent and functional amyloid called curli. The ability to specifically stain ECM components has been a key step in traditional investigations of biofilms, and we sought to provide a foundation to similarly study curli. In the second approach, we developed a means to spectroscopically annotate chemically complex ECM composition of the important human pathogens Vibrio cholerae and Aspergillus fumigatus using solid-state NMR. Finally, we provided novel biophysical and structural details of specific ECM components to better understand how these biopolymers interact to form robust ECM networks. Looking forward, we have begun to utilize solid-state NMR to provide a global accounting of the architecture of the UTI89 ECM. Together these studies have provided important quantitative parameters of biofilm composition and structural information of ECM components. Our analysis has wide-ranging implications for understanding the fundamental mechanisms of biofilm formation and for the development of functional biopolymeric materials.
Authenticity's genome [electronic resource] : heredity, conversion, and the adoptability of ethnoracial membership
Keywords: Sociology.

This dissertation explores Jewish converts' search for authenticity in an adopted identity. In examining a highly atypical case in which membership in an ethnoracial is attained through means other than birth, I assess how individuals, groups, and society make sense of a situation of ethnoracial change that is at odds with the typical construction of American ethnoraciality. For converts, there is a looming sense that missing heredity calls the authenticity of one's membership into question, and each of a set of responses -- proving its presence in one's genes, "passing" as having attained membership by birth, or ensuring the heredity of one's progeny -- responds to desiring enhanced authenticity by making heredity palpable. While they focus on different temporal spaces and different subpopulations of converts, heredity is the clear and overarching feature of the authenticity-enhancing strategies identified in all three papers. Balancing being a group that calls heredity's seemingly-uniform role in ethnoracial membership into question against these strategies for achieving authenticity, converts position asking: is heredity surpassable in the politics of ethnoracial groupness?.
Automated air traffic control for non-towered airports [electronic resource]
Keywords: Aeronautics and Astronautics.

The majority of midair collisions involve general aviation aircraft, and these accidents tend to occur in the vicinity of airports. This work proposes a concept for an autonomous air traffic control system for non-towered airports. The system is envisioned to be advisory in nature and would rely on observations from a ground-based surveillance system to issue alerts over the common traffic advisory frequency. The behavior of aircraft in the airport pattern is modeled as a hidden Markov Model (HMM) whose parameters are learned from real-world radar observations. To determine the optimal advisories that reduce the risk of collision, the problem is formulated as a partially observable semi-Markov decision process (POSMDP). In order to address the computational complexity of solving the problem, different approximation methods including exponential sojourn times, phase-type distributions, online algorithms, and particle filters for belief estimation are investigated. Simulation results are presented for both nominal and learned airport models.
B1 estimation using RF coil locators and current sensors measurements [electronic resource]
Keywords: Electrical Engineering.

Parallel transmit (PTx) systems have been proposed to compensate for B1 (RF) field non-uniformity, to improve excitation pulse performance, and to minimize specific absorption rate (SAR), mostly for high field MRI. These systems require prior knowl- edge of the radiofrequency (RF) field of each channel to perform calibration and B1 shimming to cancel out spatial B1 variations. A second class of applications emerging for PTx at 1.5T and 3T is in interventional MRI and implant RF safety. The goal here is to minimize RF coupling to insulated conductive structures such as guide- wires, pacemakers, and deep brain stimulator leads. Lastly, dynamically polarized 13C imaging requires prior knowledge of spatial flip angles to optimize SNR, with flip angle errors resulting in costly re-polarization times. In all these cases, the imaging work-flow would be improved if B1 mapping could be avoided or minimized. Existing B1 mapping methods su↵er from a variety of issues including long scan times, limited B1 dynamic range, and high specific absorption rate (SAR). Moreover, experimental B1 mapping techniques assume nothing about the coil geometry or location, yet the coil structure is known a priori. The goal of this work is to create a "good enough" estimator of B1 fields without mapping, using techniques that enable registration between the physical and simula- tion domains. It is demonstrated that co-registration by fluorine or proton fiducials for coil localization, combined with on-coil RF current sensing, provide the necessary inputs to scale and transform a pre-computed library of B1 simulations into the phys- ical domain to estimate the B1 maps of a known coil geometry with a simple rapid pre-scan calibration. In this dissertation, it is then shown that the estimated B1 maps can be used to calculate complex RF shim weights in an RF shimming application without perform- ing MRI B1 mapping. All the experiments in this dissertation were performed on a GE 1.5T scanner using a Medusa console and a cylindrical four-channel transmit/receive array prototype. Our group is particularly interested in local transmit array applications at 1.5T and 3T for RF implant safety, and MRI interventions, where the intent is to minimize the extent of RF coupling and exposure. In both applications, local transmit arrays could minimize coupling, but the flexible or variable array layouts and load impedance variations call for B1+ calibration aids to simplify their use in setting local RF shim weights. To explore these issues, the feasibility of extending forward and reverse po- larization method is investigated. It is shown that pre-spoiler gradients combined with reverse polarization can significantly suppress the background signal and suc- cessfully visualize the conductive structure inside a body. Finally, it is shown that a 3D model of the conductive structure can be extracted by applying edge detection filter to reversed polarized images.
Baby's first hug: understanding the relationship between embryo biomechanical properties and developmental potential [electronic resource]
Keywords: Bioengineering.

The work covered in this dissertation represents a significant contribution to both the clinical practice of assisted reproduction and to the scientific study of embryo development. It has resulted in the development of a new technology to improve oocyte and embryo viability assessment after in vitro fertilization, which will enable physicians to make more optimal decisions about embryo transfer and improve outcomes for mothers and babies. It has also provided a new tool to scientists wishing to study the fundamental mechanisms underlying oocyte maturation and embryo development. To achieve these contributions, the following studies were performed: (1) An automated robotic device was developed which can noninvasively measure oocyte and embryo biomechanical properties. (2) The ability of oocyte and embryo biomechanics to predict developmental outcomes was validated in preclinical studies using mouse and human research embryos. These were followed by a pilot clinical trial which measured the ability of embryo biomechanics to predict clinical pregnancy in humans. (3) Factors important for successful embryo development were investigated by measuring differences in gene expression between embryos with low and high developmental potential. Experiments were also performed to understand the origin of the link between embryo mechanical phenotype and developmental potential.
Ballistic conduction in graphene heterostructures [electronic resource]
Keywords: Physics.

Electronic transport in a solid is ballistic unless disturbed by disorder. This work describes experiments on a two-dimensional electron system that resides in the heterostructure formed by graphene and hexagonal boron nitride. The ballistic conduction of electrons is probed across micron length scales by examining the transverse electron focusing effect, in which semiclassical electron trajectories emanating from a point on the system boundary are bent by an applied magnetic field and are focused onto another point. Internal reflection at the boundary extends these trajectories into skipping orbits; the observation and analysis of ballistic conduction that proceeds thus characterizes the interaction of an electron in graphene with the edge. Transverse electron focusing is also exhibited in the 14 nm-period moire superlattice, which is formed by the incommensurability and misalignment between the graphene and boron nitride lattices. At low temperatures, ballistic motion exhibits caustics of skipping orbits extending over hundreds of superlattice periods, reversals of the cyclotron revolution for five successive minibands, and breakdown of cyclotron orbits near van Hove singularities. A theory of nearly free Dirac fermions that obey semiclassical equations of motion successfully describes the system. The interlayer interaction parameter and the full miniband structure can be determined quantitatively. Probing such miniband conduction properties is a necessity for engineering novel transport behaviors in superlattices, and the results suggest possibilities for new device functions and more exotic physics in similar van der Waals heterostructures. A direct point-to-point measurement of ballistic transport also enables quantitative measurement of the effect of the electron-electron interaction on the transport of quasiparticles in a clean two-dimensional Fermi liquid, in particular the crossover from the regime of ballistic transport to the viscous and hydrodynamic flow regime as a function of increasing temperature.
Banned books [electronic resource] : medicine, readers, and censors in early modern Italy, 1559-1664
Keywords: History.

Banned Books: Medicine, Readers, and Censors in Early Modern Italy, 1559-1664 examines the censorship of medical books as a lens into debates about the complex relationship between faith and knowledge after the Reformation. I approach the question of censorship from many perspectives: the community of physicians who wanted to maintain access to prohibited medical works; the ecclesiastical and lay censors who both carried out, and in some instances undermined, efforts to expurgate books rather than burn them; the readers licensed to keep prohibited books; and finally expurgated copies of the books themselves that bear the physical marks of censorship. Each of these angles reveals the ways in which the Counter-Reformation project of intellectual and religious control was a human drama defined by institutional ambitions, personal agendas, social constraints, practical realities, and the material form and content of the early printed book. Catholic censorship was a form of promulgation that fostered a community of readers with particular expertise. The consequences of this contradiction included a system of selective expurgation rather than total destruction, an extensive population of licensed readers of prohibited books, and ultimately a selective embrace of Protestant and heterodox medical knowledge in Counter-Reformation Italy.