VictorJuiz/thesis huggingface dataset:
High-speed tracer-based PLIF imaging for scramjet ground testing [electronic resource]
Keywords: Mechanical Engineering.

The scramjet engine holds much promise for hypersonic atmospheric flight. In a scramjet engine, fuel is injected into a supersonic stream of air, and this fuel must mix and burn with the air before exiting out the back of the engine. Achieving stable, reliable combustion in a scramjet has been a technical challenge throughout the development of scramjet powered vehicles. The coupling of turbulence and combustion results in a complex non-linear system, prone to several catastrophic failure modes. To better understand the mixing and combustion processes in a scramjet, ground testing facilities are needed to reproduce the extreme conditions in a scramjet combustor, and advanced diagnostics are needed to probe these flow fields. This thesis describes a hypersonic ground testing facility as well as the extension of a laser-based imaging diagnostic to supersonic flows generated in impulse facilities. The thesis is divided into three sections: 1) (Chapter 2) the first section describes the Stanford Expansion Tube Facility, details of its operation, capabilities, and conventional diagnostic capabili- ties, including high-speed schlieren and high-quality pressure measurements; 2) (Chapters 3 and 4) the second section describes the development of toluene planar laser-induced fluorescence (PLIF) temperature imaging in an expansion tube and a rigorous method to correct for background signals in PLIF imaging; 3) (Chapters 5 and 6) the third section describes the application of new, kHz-rate pulsed light sources for tracer-based PLIF imaging, culminating with the demonstration of the technique by visualizing a jet in sonic crossflow in the expansion tube at 20 kHz. An overview of additional scramjet studies conducted at the Stanford Expansion Tube Facility and the application of the diagnostics described within this thesis can be found in the appendices.
Hollywood opera [electronic resource] : envisioning opera for the movies, 1926-1938
Keywords: Music.

While the phenomenon of operatic singing in classical Hollywood cinema is well known, the topic has been marginalized in opera / film studies of the past twenty-five years. Indeed, the very fact that, between 1926 and 1938, all of the Hollywood studios announced plans for full- and feature-length movie operas has escaped historical notice. During the same period, various studios experimented with introducing operatic performances in the context of conventional narrative pictures, as a means of preparing cinema audiences for fully sung opera on screen. Drawing on hundreds of previously unexamined sources, this study reveals the full extent of Hollywood's operatic ambitions during the early sound era, illuminating a phase of cultural development during which opera, in various Hollywood forms, reached a wider audience than ever before. The dissertation consists of five chapters and an epilogue, which proceed in more or less chronological order. Chapter 1 traces the early history of American cinema's relationship with opera, from the visionary projections of Thomas Edison in the late-1880s through the early years of sound. Here I examine the conceptual origins of Hollywood opera, and the various technological and aesthetic barriers to the production of full-length operas on film. Chapter 2 focuses on The Rogue Song (1930), and considers how MGM and various other studios, believing American cinema audiences to be unready for fully sung opera on film, set about cultivating appreciation for the operatic voice in movies. Chapter 3 treats Columbia Pictures' One Night of Love (1934), and the ensuing "opera boom" of 1935-1938, during which Hollywood filmmakers employed opera as a dramatic element in conventional narrative pictures. Chapter 4 explores the emergence of "imaginary" opera—custom-made opera sequences commissioned by the studios to fulfill specific dramatic needs, and as a supplement to the repertoire of well-known and popular (genuine) operatic arias, many of which, by 1936, had already been filmed. Chapter 5 discusses the revival of Hollywood's plans to produce full-length movie operas in 1935, and the subsequent abandonment of those plans with the end of the opera boom in February 1938. In an epilogue I briefly survey the continued presence of operatic performances in Hollywood movies 1939-1962, highlighting two films—Serenade (1956) and My Geisha (1962)—which, respectively, anticipate the techniques of New Hollywood and "art" films, post-1970.
Holography beyond AdS/CFT [electronic resource] : quantum cosmology and black holes
Keywords: Physics.

Inspired by the successes of AdS/CFT, this dissertation is devoted to the study of holography in non-AdS spacetimes resembling patches of our universe. We will consider the universe on large scales and near spinning black holes. In the case of black holes, we will show that holographic entanglement entropy techniques from AdS/CFT prove quantitatively successful when adapted to the spacetime near spinning black holes. In the context of three-dimensional de Sitter spacetime, we will propose a microscopic derivation of the cosmological horizon entropy. For four-dimensional de Sitter spacetime, we shall compute wavefunctionals within a proposed higher-spin holographic duality, in addition to proposing a one-parameter extension to the duality. We will end by analyzing the sharply ultrametric state space of a massless scalar in an FRW background and will propose a holographic duality which relates FRW cosmologies to hyperscaling-violating field theories.
Hopf algebras and Markov chains [electronic resource]
Keywords: Mathematics.

This thesis introduces a way to build Markov chains out of Hopf algebras. The transition matrix of a Hopf-power Markov chain is (the transpose of) the matrix of the coproduct-then-product operator on a combinatorial Hopf algebra with respect to a suitable basis. These chains describe the breaking-then-recombining of the combinatorial objects in the Hopf algebra. The motivating example is the famous Gilbert-Shannon-Reeds model of riffle-shuffling of a deck of cards, which arise in this manner from the shuffle algebra. The primary reason for constructing Hopf-power Markov chains, or for rephrasing familiar chains through this lens, is that much information about them comes simply from translating well-known facts on the underlying Hopf algebra. For example, there is an explicit formula for the stationary distribution (Theorem 3.4.1), and constructing quotient algebras show that certain statistics on a Hopf-power Markov chain are themselves Markov chains (Theorem 3.6.1). Perhaps the pinnacle is Theorem 4.4.1, a collection of algorithms for a full left and right eigenbasis in many common cases where the underlying Hopf algebra is commutative or cocommutative. This arises from a cocktail of the Poincare-Birkhoff-Witt theorem, the Cartier-Milnor-Moore theorem, Reutenauer's structure theory of the free Lie algebra, and Patras's Eulerian idempotent theory. Since Hopf-power Markov chains can exhibit very different behaviour depending on the structure of the underlying Hopf algebra and its distinguished basis, one must restrict attention to certain styles of Hopf algebras in order to obtain stronger results. This thesis will focus respectively on a free-commutative basis, which produces "independent breaking" chains, and a cofree basis; there will be both general statements and in-depth examples.
Hormonal Regulation of Prostaglandin F2α Receptor Expression: Identifying Mechanisms of Female Reproductive Behavior in a Cichlid Fish
Keywords:  Department of Biology
Biology
prostaglandin F2α (PGF2α)
receptor
social behavior
reproductive regulation
teleost
17α
20β-dihydroxy-4-pregnen-3-one (DHP)
Thesis

Several hormones work in concert to mediate female reproduction, a behavior that drives evolution. Previous studies in mammals have identified the ovarian steroids estradiol and progesterone as hormones that act together to induce female mating. In other organisms, the identity of and relationship between reproductive hormones can vary, and this divergence is informative from an evolutionary and molecular standpoint. For example, though ovarian steroids are involved in the reproduction of teleost fish, the post-ovulatory hormone prostaglandin F2α (PGF2α) is sufficient to induce spawning (mating) behavior in females of many teleost species. PGF2α thus activates a distinct, important pathway for reproduction. However, the regulation of this pathway has yet to be defined. Here, we sought to address whether and how ovarian steroids regulate PGF2α-mediated female reproductive behavior. To do so, we used the African cichlid fish Astatotilapia burtoni, a model organism for the study of social behaviors and neural plasticity. In female A. burtoni, the PGF2α receptor (Ptgfr) is expressed in a behaviorally relevant brain region, the preoptic hypothalamus (POA), and increases expression during spawning. This spatio-temporal expression pattern implicates the POA as a locus of PGF2α signaling during reproductive behaviors. We investigated the mechanism of PGF2α-mediated spawning by searching for the regulators of POA Ptgfr expression in female A. burtoni. We hypothesized that ovarian steroids account for the observed variation in Ptgfr mRNA expression. Using in situ hybridization, we demonstrated upregulated POA Ptgfr expression in ovariectomized females treated with teleost progesterone 17α,20β-dihydroxy-4-pregnen-3-one (DHP). We further demonstrated that DHP receptors are expressed in the POA, suggesting DHP directly regulates Ptgfr expression in that region. These results are consistent with a model where DHP-regulated PGF2α signaling mediates reproductive behavior. This model can help identify conserved PGF2α pathways in other vertebrates or track the diversification of PGF2α’s reproductive role over evolutionary time.
How Toxoplasma gondii induces c-Myc, a pivotal host oncogene [electronic resource]
Keywords: Microbiology and Immunology.

Regulation of host transcription is a common strategy of intracellular microorganisms to control their host cell. The obligate intracellular parasite, Toxoplasma gondii, secretes specific effectors that alter host transcription and regulate various cellular processes. This thesis explores a novel interaction of this apicomplexan with its host that involves the induction of one of the most pivotal host transcription factors, c-Myc. Given the far-reaching role of c-Myc in essential host processes, e.g. cell cycle, apoptosis, metabolism, and immune function, it is likely that the regulation of this protein has profound consequences on the cell and is therefore one of the factors determining the outcome of Toxoplasma infection. This thesis presents evidence that Toxoplasma dramatically increases the expression of host c-Myc in infected cells and that this induction likely alters the host transcription program as numerous c-Myc targets are regulated during Toxoplasma infection. Moreover, a genetic screen that led to the isolation of Toxoplasma mutants defective in c-Myc induction and subsequent identification of a novel Toxoplasma effector, MYR1 (MYc Regulator 1), is described here. The data strongly suggest that MYR1 controls not only the expression of c-Myc, but also carries an additional function in regulating the expression of Major histocompatibility complex (MHC) class II in infected cells. Remarkably, MYR1 mutants (although derived from a highly virulent strain of Toxoplasma) exhibit decreased virulence in mice showing that this parasite factor has an evident effect on the outcome of the infection. Finally, an intriguing observation that the infection by a closely related parasite Neospora caninum leads to a completely opposite effect on c-Myc levels is presented, offering an insight into how these two parasites have evolved to control their cell and revealing a potential explanation for their distinct host range and immunopathology.
Human development and disease [electronic resource] : lessons from induced pluripotent stem cells with X chromosome aneuploidies
Keywords: Genetics.

1 -- 2% of all human fetal conceptions result in Turner syndrome -- the complete or partial loss of the second sex chromosome (45, X karyotype). 90% of Turner cases terminate in spontaneous abortion during the first two trimesters; however, those who survive have a wide array of clinical characteristics. Infertility is very common in Turner syndrome women, making a link between the X chromosome and causes of infertility. Induced pluripotent stem cells (iPSCs) offer a means of obtaining insight on the genetic requirements of germ cell development. I have used iPSCs to characterize XIST, a non-coding RNA that initiates X chromosome inactivation (XCI), and shown that newly reprogrammed female iPSCs reflect the developmental state of the preimplanation embryo following embryonic genome activation. From the generation of iPSCs from four Turner syndrome, one premature ovarian failure and a control female, I demonstrated that two X chromosomes are not necessary for reprogramming to pluripotency. Single cell analysis of genes that escape XCI within control, Turner syndrome and Triple X iPSCs revealed minimal expression differences when compared to a female human embryonic stem cell (hESC) line. Next, I investigated the ability of X chromosome aneuploidy and control iPSCs to form germ cells by differentiating iPSCs and analyzing single cells and populations throughout a differentiation protocol using BMP4/8 and Retinoic acid. An increase in germ cell associated genes was not observed, but rather a loss. Finally, xenotransplantation was used to assess germ cell formation across different X chromosome aneuploidy states. All lines were capable of forming early germ cells in vivo, independent of their X chromosome composition. These results demonstrate that two complete X chromosomes are not necessary for the formation of early germ cells, and X aneuploidy iPSCs are amenable for the study for germ cell formation.
Human reproduction and low fertility in urban Taiwan [electronic resource]
Keywords: Anthropological Sciences.

From an evolutionary perspective, this research asks whether human beings have any natural inclination to reproduce. By examining biological, social, and interpersonal influences on women's reproductive behavior, the study argues that fertility outcomes result more from social influences than from a "maternal instinct" to want children. The absence of a biological basis for human desire to bear children is a primary cause of the ubiquitous fertility decline in the modern world.
Hybrid organic-inorganic films for high-performance adhesive bonding [electronic resource]
Keywords: Materials Science and Engineering.

Hybrid organic-inorganic materials can be engineered to exhibit unique property sets intermediate to oxides and polymers by the intermixing and covalent bonding of organic and inorganic chemical components at the molecular scale. This class of materials has enabled a range of new technologies in diverse applications including protective coatings, adhesion promoting layers, ultra-low-k dielectrics and optical waveguides. This dissertation presents results from several studies investigating the correlation between hybrid molecular structure and fracture properties. A low-cost, low-temperature sol-gel approach is utilized to synthesize ZrOx/epoxysilane hybrid films for adhesion promoting applications across a wide range of metal oxide / epoxy interfaces. XPS depth profiling reveals a unique compositionally graded structure capable of forming durable bonds between metal oxides and structural adhesive organic resins. The influence of the underlying substrate isoelectric point on the synthesis and deposition of compositionally graded hybrid networks is investigated. Subsequently, linear elastic fracture mechanics experiments are utilized to develop a correlation between substrate isoelectric point and fracture properties, showing increasing adhesion with decreasing isoelectric point. Using bulk metallic glass substrates, the fracture properties of hybrid organic-inorganic films are optimized by investigating variations in sol-gel synthesis parameters. In addition to significant increases in adhesion strength, the efficacy of hybrid layers in mitigating moisture-assisted debonding is demonstrated. Finally, the application of hybrid organic-inorganic adhesion promoting layers is explored in titanium composite (TiGr) aerospace laminates. The roles of mode mixity and fiber orientation under monotonic and fatigue loading are investigated, revealing critical effects on failure pathways and resultant fracture resistance.
Hydrodynamics within the reef [electronic resource] : a closer look at flow-coral interactions
Keywords: Civil and Environmental Engineering.

Coral reefs are valuable marine ecosystems. Moreover, their importance extends beyond the oceans, as they protect coastlines and are a source of income for coastal communities and fisheries. The decline of reefs over the past decades has led to the need for bettering our understanding of the processes that take place on the reef, as we strive to conserve and restore them. Small-scale hydrodynamics are vital to survival within the reef canopy and enhance mixing to ensure the high productivity of this benthic community. By supplying nutrients, removing waste material and applying forces to coral colonies, influencing their distribution and growth, flows within the reef canopy determine its shape. However, there is still much to be learned about the role of small-scale hydrodynamics in sustaining coral health and facilitating the biological processes needed for survival. The interactions between flow on the reef and individual coral colonies forms a feedback loop where flow affects coral morphology and as the corals adapt and grow, they in turn affect the flow. This dissertation focuses on deepen our understanding of how this feed-back loop works through a series of laboratory experiments. The work here addresses inaccuracies in using simplified geometries, cylinders and spheres, to model the forces on coral colonies as well as how colony position in the reef affects the forces it experiences. Additional work also examines the downstream evolution of flow after it has passed a colony and its role within the reef canopy as well as how nighttime polyp tentacle extension affects the floe in the boundary layer. The implications of these results on the colony dislodgment, biological processes and mixing within the reef are also presented.
Identification of deer antler proliferation genes for accelerating the growth of hMSCs
Keywords: hMSC
proliferation
RNA-Seq
deer antlers
tissue engineering
bone regeneration
Thesis

Deer antlers are fascinating models for mammalian epimorphic appendage regeneration, and their meticulous study could provide insight for addressing the unmet medical need of regenerating skeletal defects and losses. In this study, RNA-Seq was used to compare differentially expressed genes in human mesenchymal stem cells (hMSCs) and fallow deer reserve mesenchyme cells (FDRMCs) under proliferating conditions. Over 40 genes uniquely upregulated in proliferating FDRMCs were identified, and 2 gene candidates—esm1 and has2—were successfully subcloned from FDRMC cDNA. These genes were transfected into mouse mesenchymal fibroblasts to determine if their proliferation rate could be accelerated, as a mouse model for hMSCs. Although the transfection of these candidates into mouse mesenchymal fibroblasts did not result in any change to their doubling time, semi-quantitative non-competitive RT-PCR results suggest that the genes may not have been expressed at high enough levels to cause changes in the cells’ behavior. Additionally, ALP staining conducted on BMP-2 transfected cells confirmed that transfection did not significantly alter the cells’ differentiation behavior. In summary, the developed in vitro methodology developed in this project allowed for the identification of genes involved in FDRMC proliferation separately from other antler growth-related processes, and this work opens future avenues for investigating the successful expression of subcloned FDRMC genes for the acceleration of hMSC growth.
Identifying oncogenic attributes and protein binding partners of the NKX2-1 lung cancer oncogene
Keywords:  Department of Biology
lung cancer
NKX2-1
co-immunoprecipitation
oncogene
protein cofactors
Department of Pathology
Department of Biology
Stanford University
Thesis

Lung cancer is the leading cause of cancer death in the United States, and the oncogene NXK2-1 has been previously been implicated in a subset of lung cancers. NKX2-1 encodes a transcription factor known to be important in controlling normal lung development. However, NKX2-1 is also found to be amplified and overexpressed at the DNA and protein levels, respectively, in approximately 15% of lung cancers, where it contributes to abnormal cell proliferation and survival, and thus it is classified as an oncogene. Although it is presumed that NKX2-1 must be behaving differently in cancer compared to normal cells, the mechanisms by which it increases cancer cell proliferation are not well understood. Possible mechanisms include altered NKX2-1 transcriptional activity by expression of distinct NKX2-1 protein isoforms, or by NKX2-1 association with distinct protein binding partners. Here, we examined the phenotype of lung cancer cells overexpressing different NKX2-1 isoforms, to better understand the protein’s function. We also used co-immunoprecipitation to isolate proteins that associate with NKX2-1 in lung cancer cells, and then employed mass spectrometry to identify the co-immunoprecipitated proteins. The resulting findings provide unique and novel insight into the mechanisms of NKX2-1 oncogenic activity, which may lead to future efforts in targeted molecular therapy for these lung cancers.