VictorJuiz/thesis huggingface dataset:
The mandate of heaven (Tianming) and the Zuo commentary [electronic resource]

The ideology of the Mandate of Heaven, or tianming ,is central to the conceptual framework of the Zuozhuan [Zuo Commentary] and lends coherence to its narratives. The Zuozhuan posits that the Zhou royal house still holds the Mandate of Heaven, despite its decline. At the same time, while Zhou Mandate ideology also explains the rise of other lineages with the potential for obtaining the Mandate and becoming the new royal dynasty, the Zuozhuan suppresses this possibility by suggesting that the greatest achievement other lineages can attain is zhuhou status--that of a regional lord still acknowledging the suzerainty of the Zhou king. The study is divided into three sections. The first section sets the baseline by unpacking Western Zhou period (1045-771 BCE) articulations of the Mandate. It analyzes Shangshu texts, Shijing poems, and bronze inscriptions for this purpose. The second section argues that the Zuozhuan demonstrates the legitimacy of the Zhou royal house in its narratives. The authority of the Zhou has been codified and translated into various practices, customs and institutions that help entrench the Zhou. Even the position of the hegemon, usually regarded as a Spring and Autumn period (770-481 BCE) invention, is subsumed under the rubric of traditional service that the zhuhou provide to the Zhou. The third section examines the Zuozhuan's depiction of several lineages and the limitations the text places on their rise. This is accomplished through an array of tools: predictions and divination, delineation of the origins of various lineages, and descriptions of the behaviors of lineage heads in each generation. The Zuozhuan's position is further supported by the purely historical serendipity of the fall of a few key zhuhou lineages, like the ducal houses of Jin and Qi, at the end of the Spring and Autumn period. Therefore, no other lineage can threaten the Zhou royal position, though the most powerful ones attempt to do so.

Keywords: East Asian Languages and Cultures.
Advisor: Wang John C. Y. (John Ching-yu)
Zhou Yiqun
Dien Albert E. advisor. Thesis advisor
Maximizing the information content of dual energy x-ray and CT imaging [electronic resource]

Computed tomography (CT) has become an essential tool in modern medicine since its introduction in the early 1970s. It generates cross-sectional images of the body's x-ray attenuation by measuring the transmission of x-rays in many directions. Because CT uses ionizing radiation, a governing principle is to use the least amount of radiation dose that still provides diagnostic-quality images. One approach to ensure that dose is appropriately used is to explore the information content of CT scans. This work examines efficient methods for encoding, storing, and extracting information from CT scans, especially as they pertain to spectral x-ray imaging. CT systems that can take advantage of the different attenuation properties of x-rays at different energies can provide additional diagnostic information, known as dual energy imaging. A new technique called Synthetic CT is introduced that enables images from CT protocols other than what was acquired to be retrospectively synthesized. With this tool, the information contained within a dual energy scan can be used to demonstrate the effect of protocol selection on image quality and dose distribution. In addition to experimentally validating the developed synthetic CT theory, further efforts have led to image-based synthetic CT, incorporation of electronic noise models for ultra low dose simulation, and a simple graphical user interface that demonstrates the flexibility of synthetic CT. We also explore an important spectral imaging technology -- photon counting detectors with energy discrimination capabilities. In principle, these detectors capture all the spectral information of transmitted x-rays by counting the number of photons at each energy. Optimal configurations of ideal photon counting detectors are first investigated, leading to the elegant discovery that two energy-dependent weighted counts can form a sufficient statistic for dual energy imaging. In practice, photon counting detectors have count rate limitations and imperfect spectral responses. The performance of realistic photon counting detectors is modeled and compared to conventional dual kV techniques. We find that both optimized photon counting and dual kV systems can significantly increase the dose efficiency of dual energy imaging.

Keywords: Electrical Engineering
Advisor: Pelc Norbert J. primary advisor. Thesis advisor
Fahrig Rebecca advisor. Thesis advisor
Nishimura Dwight George advisor. Thesis advisor
Maximum-efficiency architectures for regenerative steady-flow combustion engines [electronic resource]

Steady-flow combustion engines currently account for about 20% of world-wide electricity generation (gas turbine engines) and almost all of commercial aviation (jet engines). With growing interest in natural gas as a low-carbon alternative to coal, and the economic opportunity associated with the discovery of potentially large natural gas reserves, steady-flow combustion engines are likely to play a larger role in energy conversion. Evidently, increasing engine efficiency is of primary importance and has been an active topic of research for over a century. On the one hand, many advanced engine cycles (e.g., humidified cycles, oxy-fuel cycles, fuel-cell/gas turbine combined cycles) that promise higher efficiency are being proposed and analyzed. But on the other hand, there is a sense of resignation that raising turbine inlet temperature is our only hope for higher efficiency. Simply stated, we do not know what engine architectures provide maximum efficiency. The objective of this dissertation is to establish maximum-efficiency architectures allowed by physics and implementable by engineering for regenerative, steady-flow combustion engines. The goal is also to advance thermodynamic understanding of the tradeoffs in reducing sources of entropy generation (irreversibility) that are the reason for inefficiency in engines. To do so, an irreversibility-minimization approach is developed that has three stages. First, reactive engine architectures are modeled as sequences of energy transfer and transformation processes, and represented as trajectories traced by the working fluid in thermodynamic state space. Second, total irreversibility in any architecture is calculated as a function of the trajectory that represents it. Third, the extremal trajectory is identified that minimizes total irreversibility while satisfying constraints such as the turbine inlet temperature limit. Two methods are employed for identifying the extremal trajectory: optimal-control theory and attractor-trajectory based methodology. The former is an extension of the calculus of variations. The latter is a physics-based methodology, developed in this work specifically for engine-architecture optimization to overcome some of the challenges associated with obtaining solutions using the former. The extremal trajectory represents the optimal architecture that has efficiency greater than any other conceivable architecture subject to the same constraints, and the attractor-trajectory based methodology provides insights into the thermodynamics of regenerative steady-flow combustion engines.

Keywords: Mechanical Engineering
Advisor: Edwards Christopher
Bowman Craig T. (Craig Thomas)
Gerdes J. Christian advisor. Thesis advisor
Measuring intentional manipulation [electronic resource] : a structural approach

Using a sample of over 1,800 CEOs in the post-SOX period, I estimate the extent of intentional manipulation and manipulation costs using a dynamic structural model that features a risk-averse manager who receives cash and equity compensation. I find that the expected cost of manipulation is low. The probability of detection is 9%, and the average misstatement results in a 1.5% loss in the manager's wealth. According to the estimated parameters, the implied fraction of manipulating firms is around 63% and the value-weighted bias in the stock price is 2.8%. Among five proxies for earnings management used in the extant literature, only performance-matched discretionary accruals have a positive association with the model-implied measure of intentional manipulation.

Keywords: Business.
Advisor: Larcker David F. primary advisor. Thesis advisor
Reiss Peter C. (Peter Clemens) primary advisor. Thesis advisor
Beyer Anne advisor. Thesis advisor
McNichols Maureen
Piotroski Joseph D. (Joseph David) advisor. Thesis advisor
Mechanical control of metal-ligand complexation and catalysis through surface immobilization [electronic resource]

Heterogenization, or the covalent immobilization of discrete molecular species to a material surface, is a promising strategy in catalyst design to leverage high selectivity and ligand variability with the practical heterogeneous advantages of catalyst separation and recycling. Moreover, heterogenization can be used as a mechanical means to control intermolecular interactions and thereby probe reaction mechanisms in a way not achievable through purely homogeneous characterization. An ideal immobilization approach needs to be modular, with high degree of control over the total surface loading of a species and its overall surface distribution. Here we report the preparation and application of functionalized mesoporous silica SBA-15 with a silioxypropylazide incorporated through a co-condensation approach. These materials serve as the platform for the heterogenization of ethynylated organic moieties through the copper-catalyzed azide alkyne cycloaddition. Surface loading is controlled by the amount of azide incorporation during co-condensation, and the surface distribution of immobilized species correlates well with a statistically random model. Immobilized manganese complexes demonstrate rapid catalytic epoxidation and C−H hydroxylation with peracetic acid as the terminal oxidant. Through a controlled variation of the surface loading and a quantitative understanding of site-interactions, we examine the impact of multi-ligand binding and site-isolation on catalysis.

Keywords: Chemistry
Advisor: Stack T. (T. Daniel P.)
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Fayer Michael D. advisor. Thesis advisor
A mechanism for the evolution of protein phosphorylation sites and application towards improving phorylation site prediction [electronic resource]

Protein phosphorylation provides a mechanism for the rapid, reversible control of protein function. Phosphorylation adds negative charge to amino acid side chains, and negatively charged amino acids (Asp/Glu) can sometimes mimic the phosphorylated state of a protein. Using a comparative genomics approach, I show that nature also employs this trick in reverse by evolving serine, threonine, and tyrosine phosphorylation sites from Asp/Glu residues. Structures of three proteins where phosphosites evolved from acidic residues (DNA topoisomerase II, enolase, and C-Raf) show that the relevant acidic residues are present in salt bridges with conserved basic residues, and that phosphorylation has the potential to conditionally restore the salt bridges. The evolution of phosphorylation sites from glutamate and aspartate provides a rationale for why phosphorylation sometimes activates proteins, and helps explain the origins of this important and complex process. After using comparative genomics to uncover the evolutionary origins of phosphorylation, I expanded my work to attempt to predict novel phosphorylation sites using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database of proteins and ortholog families. By examining aligned sites within families of proteins for the trends found in my initial investigation, I sought to improve ways of identifying promising potential phosphorylation sites.

Advisor: Ferrell James Ellsworth primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Elias Joshua advisor. Thesis advisor
Media as medium, Raoul Hausmann, 1915-1945 [electronic resource]

This dissertation presents an historical and critical framework for understanding Raoul Hausmann's art and writing from 1915 through 1945. While the confrontational performances, anarchic visual poetry, and boldly discordant photomontages Hausmann produced as a Berlin Dadaist (1918-1921) have long been included in the art-historical canon, his overall project remains largely unexplored. Offering detailed analysis of Hausmann's visual and textual work, I situate him in a "discourse network" that extends well beyond the historical avant-garde as it is normally understood to include theories from the natural sciences as well as both new and outmoded media technologies, which the artist repurposed to subversive effect. This study begins with Hausmann's early work in the applied arts and in German Expressionist circles, then follows his career through his one-man, post-dada "presentist" movement and his experiments as a still photographer. Tracking Hausmann's work across several media, I focus on his project of uncovering and overcoming the deeply ingrained social and perceptual conventions that constrain everyday experience. I situate Hausmann in a tradition of German thought that begins with Ernst Kapp's "philosophy of technology" (1877) and continues in the writings of Walter Benjamin and, more recently, Friedrich Kittler, arguing that the artist's work is best understood through the theory of media it articulates. In so doing, I demonstrate that the crux of Hausmann's project lies in his understanding of sensation as continually renewing human subjectivity, a theoretical gambit that allowed him to avoid the pitfalls of both technological determinism and primitivism. Closely examining the specific challenges that Hausmann posed to audiences through his most important works, this dissertation argues for his central role in the historical avant-garde's critical and creative exploration of media.

Keywords: Art and Art History
Advisor: Lee Pamela M. primary advisor. Thesis advisor
Gough Maria
Levi Pavle advisor. Thesis advisor
Troy Nancy J. advisor. Thesis advisor
Mesograzers of giant kelp (Macrocystic pyrifera) at Hopkins Marine Station, Pacific Grove, CA: community structure and seasonal patterns

This thesis describes the mesograzer community of the Hopkins Marine Station kelp bed canopy. The community is characterized in terms of both taxonomic and size class composition based on data from samples collected monthly from August 2010 to July 2011. Multivariate analysis revealed seasonal variation in community structure driven primarily by high numbers of copepods in the spring and summer. Larger-bodied taxa known to graze significantly on kelp exhibited higher abundances and sizes in winter months, especially the kelp isopod Idotea resecata. These changes in community structure were correlated with the intensity of seasonal upwelling. Changes in food quality associated with nutrients advected into the system by upwelling may have played a role in altering the relative abundances of different taxa. The increased density of large-bodied grazers in months following low upwelling may have been in part an artifact of their high mobility and a lower standing crop of kelp that coincided with these periods. Regardless of its ultimate cause, the co-occurrence of high mesograzer density and low nutrient availability synergistically elevates tissue degradation and loss by Macrocystis at this time of year with implications for both the kelp forest community and neighboring habitats.

Keywords: Hopkins Marine Station
Stanford Biology Department
Marine Life Observatory
MLO
Thesis
Advisor: Micheli Fiorenza
Vitousek Peter
Watanabe James
The microbial ecology of the human nasal cavity [electronic resource]

The establishment and wide acceptance of an abundant and diverse human-associated microbial community has been one of the most important shifts in the field of microbiology in the past decade. From a bacterial perspective, the body is a vast landscape whose shifting geography and fluctuating environmental conditions provide a range of distinct residential possibilities. Some habitats, such as the intestinal tract and the oral cavity, have been characterized more extensively than others; within these environs, an understanding of the interplay between microbial ecology and health and disease has begun to emerge. The nasal cavity, a crucial component of both the respiratory system and innate immune system, has yet to benefit from an exploration of similar depth. Recent examination of the nasal microbial habitat has almost exclusively focused on the anterior nares without examining deeper sites within the cavity which are actively involved in nasal mucociliary clearance and exposed to the efflux of various sinuses. The aim of this work was to explore this biogeography by characterizing the microbial communities in a range of spatial sites along the nasal passageway. Additionally, the nasal cavity has long been a source of pathogens, most notably Staphylococcus aureus. Carriage of S. aureus has been demonstrated to be a significant risk factor for acquisition of antibiotic resistant strains of S. aureus and hospital-acquired infections. The second aim of this project was to understand whether underlying community features may be present that were characteristic of S. aureus carriage. 13 healthy subjects (6 persistent and 7 non-persistent carriers) were sampled weekly at 3 different sites (anterior nares, middle meatus, and sphenoethmoidal recess) within the nasal cavity over a 4-week period. The data shows that biogeographical differences were based less upon spatial factors and more on epithelium type. The data also showed that the S. aureus carriage type of the individual contributed the greatest amount of non-S. aureus variation within the communities. Finally, a carriage-classifying model was generated from the data and examined for important predictive features, revealing a potential intra-genus, interspecific competitive interaction in Corynebacterium with implications on S. aureus carriage. These results highlight the complexity present in human microbial communities even within highly spatially constrained microenvironments.

Keywords: Microbiology and Immunology
Advisor: Relman David A. primary advisor. Thesis advisor
Chambers Henry F. advisor. Thesis advisor
Schneider David (David Samuel)
Schoolnik Gary K. advisor. Thesis advisor
Microfluidic and optofluidic investigation of biological macromolecule phase transistions [electronic resource]

Phase transitions are ubiquitous in nature. Fundamental study of phase transition phenomena is a cornerstone of condensed matter physics, and theoretical results in this area guide technology development in material science. Phase transitions also play an important role in biology. Biological macromolecule phase transitions occur in many biological processes, for example the gel-liquid transition in lipid bilayers and amyloid formation in protein aggregation disease. From a technological standpoint, the ability to crystallize proteins has enabled one of the most important advances in biology of the last century: protein structure determination with X-ray crystallography. However, biological macromolecule phase transitions often display stark phenomenological differences from their inorganic analogs. This owes to the sheer size and complexity of proteins and nucleic acid complexes. Macromolecular phase transition theory is rich in subtleties, anecdotal & counter-intuitive results, and often diverges from predictions of classical theory. In addition to developing theory, fundamental study in this area is also critical for improvements in high-throughput crystallography efforts and in understanding mechanisms of devastating neurodegenerative diseases. This thesis approaches the study of macromolecule phase transitions through the development of new measurement technology. In this work, spectroscopic and imaging techniques are combined with microfluidic systems to provide insight into three areas of macromolecule phase transitions. First, dynamic light scattering and microscopy are integrated onto a microfluidic platform to study and optimize protein crystallization. Additionally dynamic light scattering is combined with fluorescence spectroscopy to investigate amyloid fibril aggregation. Finally, a new technology is presented that demonstrates high-throughput mapping of macromolecule structure by integrating single-molecule fluorescence resonance energy transfer spectroscopy with a microfluidic mixing platform. This lab-on-a-chip platform enables examination of conformational transitions in nucleic acids in response to changes in the chemical and molecular environment in order to create a conformational "phase diagram". In addition to presenting new insight into the mechanism of protein crystallization and protein aggregation, this thesis introduces new technologies for studying biological macromolecule phase transitions.

Keywords: Applied Physics
Advisor: Quake Stephen Ronald primary advisor. Thesis advisor
Doniach S. advisor. Thesis advisor
Kopito Ron Rieger
Microfluidic chromatin immunoprecipitation [electronic resource]

Protein--DNA interactions are responsible for numerous critical cellular events: for example, gene expression and silencing are mediated by transcription factor protein binding and histone protein modifications, and DNA replication and repair rely on site specific protein binding. Chromatin immunoprecipitation (ChIP) is the only molecular assay that directly determines, in a living cell, the binding association between a protein of interest and specific genomic loci. It is an indispensible tool in the biologists' toolbox, but the many limitations of this technique prevent broad adoption of ChIP in biological studies. The typical ChIP assay can take up to one week to complete, and the process is technically tricky, yet tedious. ChIP assay yields are also low, thus requiring on the order of millions to billions of cells as starting material, which makes the assay unfeasible for studies on rare or precious samples. Cancer stem cells (CSCs), for instance, are obtained from primary tumors, and FACS sorting of the dissociated tumor cells rarely yields more than ~100,000 CSCs per tumor. This thesis describes the microfluidics-based strategies for performing ChIP. The first design for a microfluidic ChIP design utilizes the automation and scalability aspects of microfluidics to reduce both total and hands-on assay time, and improve throughput. It can take chromatin prepared using any existing ChIP protocol as input, and generate ChIP-qPCR results in just 1 day. The device is shown to be comparable to existing ChIP protocols, and can detect cellular epigenetic changes induced by external cytokine stimulants. It was used to investigate transcription factor binding dynamics in an aging-related pathway, and was able to link transcription factor binding to local changes in histone modifications. The second design of the microfluidic ChIP platform focuses on addressing the cell number requirements of ChIP. In addition to reducing assay time through automation, this design incorporates microfluidic designs that allow whole fixed cells as input, and enables automated ChIP from as few as 2,000 cells. Finally, using this high-sensitivity ChIP device in conjunction with next-generation sequencing technology, a protocol for determining genome-wide epigenetic landscapes from as few as 2,000 cells is developed, with the ultimate goal of performing protein-DNA association studies on CSCs.

Keywords: Bioengineering.
Advisor: Quake Stephen Ronald primary advisor. Thesis advisor
Chang Howard
Felsher Dean (Dean Walton) advisor. Thesis advisor