VictorJuiz/thesis huggingface dataset:
Investigating Post-translational Modification of p53: Effects on p53 Interaction with the Long Noncoding RNA DINO
Keywords:  Department of Biology
DINO
long noncoding RNA
p53
RNA binding
post-translational modification
tumorigenesis
Biology
Stanford
Thesis

The p53 tumor suppressor is a central component of the DNA damage response, mediating its effect on cell cycle progression and cell death through a myriad of gene expression regulation patterns. A novel long noncoding RNA, DINO, has been recently discovered as an intricate part of the p53 damage response pathway, providing a feed-forward mechanism for p53 activation and stabilization following sustained DNA damage. While DINO promotes post-translational modifications of the p53 C-terminal domain in order to enhance protein stability, it is not yet know whether the post-translation modifications can impact the binding of p53 and DINO. In this study, we set out to identify the amino acid residues critical for p53’s binding of DINO. We were motivated by the observations that the basic residues of the C-terminus, which are likely involved DINO binding, are subjected to extensive post-translational modifications. We generated eighteen point mutations of p53, selectively targeting basic residues in the p53 C terminal domain to identify their role facilitating binding of DINO and p53. Here, we identify six basic lysine residues in p53’s C-terminal domain that we hypothesized to impart critical function in RNA mediated binding of p53. Using site-directed mutagenesis, we successfully synthesized 18 mutant constructs in total, with mutations to alanine, glutamine, and lysine at each of the six lysine residues. To best characterize the functionality of these various p53 mutants, we developed a high-throughput method of RNA immunoprecipitation to characterize their impact on the protein’s ability to bind DINO. qRT-PCR analysis provided us with initial insight into the success of this in vitro RNA binding assay, imparting us with a foundation to better assess the role of post-translation modification of basic lysine residues in p53’s C-terminal domain in the future. A deeper understanding of how p53 modifications impact lncRNA interaction provide a deeper understanding of the mechanism by which p53 post-translational modification “barcode” can elicit distinct cellular phenomenon (1).
An investigation of injectors for use with high vapor pressure propellants with applications to hybrid rockets [electronic resource]
Keywords: Aeronautics and Astronautics.

Interest in nitrous oxide based hybrid rockets is at an all time high. Nitrous oxide (N2O) is a unique oxidizer because it exhibits a high vapor pressure at room temperature (≈ 730 psia or 5.03 MPa). Due to this high vapor pressure, liquid nitrous oxide can be expelled from a tank without the use of complicated pumps or pressurization systems required by most traditional liquid rocket systems. This results in weight savings and design simplicity. Additional benefits of nitrous oxide include storability, ease of handling, and relative safety compared to traditional liquid oxidizers. The design and modeling of injectors for use with high vapor pressure propellants such as nitrous oxide is made complicated due to the possibility of two-phase flow. The operating pressures within rocket propellant feed systems can often drop below the vapor pressure for these unique propellants, especially within the injector. Injectors operating under these conditions are likely to exhibit cavitation, resulting in significant vapor formation and limitation of mass flow rate. A variety of two-phase flow models which attempt to account for this phenomenon are presented and discussed, however none have proven reliable enough to replace traditional experimental injector flow studies. For this reason, a small scale experimental injector cold flow rig was designed, and a test campaign was carried out in an effort to characterize the mass flow rate performance of nitrous oxide rocket injectors over a broad range of operating conditions. Some representative results from this campaign are presented. The Peregrine Sounding Rocket is a hybrid rocket that runs on paraffin wax and nitrous oxide. Its development is a joint effort between NASA Ames Research Center, Stanford University, and Space Propulsion Group, Inc. For years, progress of the Peregrine program has been hampered by combustion instability problems. Based upon results from the aforementioned small scale injector experiments, a powerful, yet simple solution to the so-called feed system coupled combustion instability was discovered, the details of which are presented. This work also led to the invention of a new class of rocket propellant injectors designed specifically to decrease the likelihood of this type of combustion instability. An in-depth discussion of the proposed design and operation of this novel injection scheme is included, along with the presentation of some prototype cold flow testing results which served as a successful proof of concept.
Iran's Nuclear Hedge: The Development of the Iranian Nuclear Program and Why it Keeps the Nuclear Option On The Table
Keywords: Iran
Iranian nuclear program
Iranian foreign policy
US-Iran relations
Nuclear Proliferation
Center for International Security and Cooperation
Thesis

Since its genesis in 1957, the Iranian nuclear program has been the subject of worldwide attention. Two successive Iranian regimes, Mohammad Reza Shah Pahlavi’s authoritarian monarchy (1941-1979) and the Islamic Republic of Iran (1979-present), have maintained the argument that, as a signatory of the Nuclear Nonproliferation Treaty, Iran has a right to a civilian nuclear program. Evidence suggests, however, that both regimes maintained a nuclear hedging strategy in an attempt to keep the nuclear weapons option open. Iran’s reluctance to cooperate with the International Atomic Energy Agency resulted in international sanctions that have been severely detrimental to both its economy and political standing in the world. This thesis aims to explain why these two regimes sought, and arguably still seek, the nuclear option. In addition to the security model and the domestic politics model, this study will introduce the strategic culture model as a new framework to apply in the Iranian case. For the purpose of this analysis, strategic culture is defined as the set of shared beliefs, assumptions, and narratives that shape the strategic decision-making process of a state. This thesis identifies three key elements of Iranian strategic culture that influence its drive for nuclear technology and a nuclear hedge strategy. These three elements include: [1] Iranian nationalism; [2] a ubiquitous sense of vulnerability; and [3] a love/hate relationship with modernity.
Is science for all? The relationship between middle and high school science students' perceptions of race and their science affinity-identities [electronic resource]
Keywords: Education.

Traditional science assessments and the representation of Blacks in science majors and careers speak to the disparity in science achievement between Blacks and Whites.Some research posits that the establishment of White culture as the cultural norm of science classrooms may create conflict between Black students' development of a science identity (Blickenstaff, 2005; Brown, 2004; Gilbert & Yerrick, 2001). This mixed-methods study explores the relationship that may exist between a sample of Black students' perceptions of their racial identity and science affinity- identity. For this mixed methods study, interviews surveys, and image ranking are used to explore the relationship between students' perceptions of racial and science affinity-identities.
Is the sky the limit? Three papers examining American attitudes toward extremely high pay [electronic resource]
Keywords: Sociology.

This dissertation features three papers examining American public opinion regarding extremely high incomes. Nowadays, a large portion of the top incomes in the United States comes from various sources of employment pay, making the case of salaried high-earners such as Chief Executive Officers (CEOs) of interest. The first paper uses a unique set of data from a national survey experiment specifically designed to study the effects of a CEO`s workplace contributions on the CEO`s perceived fair pay. The three types of contributions examined in this paper are performance, effort, and contribution to society. The second paper juxtaposes two competing accounts of why many Americans find high CEO pay problematic and provides a critical test of these accounts using data from a unique national survey experiment. The third paper uses data from in-depth interviews and addresses the seeming paradox of why, while the general public has shown much grievance regarding extremely high CEO pay, a matching amount of support for policies to address the inequality has not been amassed.
Isotope geochemistry of deep-sea corals [electronic resource] : paleoenvironmental proxy development
Keywords: Environmental Earth System Science.

Inhabiting areas of the ocean where paleoenvironmental records are sparse, deep-sea corals represent valuable yet largely untapped Holocene records of intermediate and deep ocean variability. These archives could give valuable insight into the natural variability of areas of the ocean that play an active role in large-scale climate dynamics. Living in near constant temperature, salinity and pH, and with some of the slowest calcification rates recorded, deep-sea corals can also provide valuable constraints on processes driving mineral equilibrium and disequilibrium signatures. Despite deep-sea corals having been indicated as potential proxies for some time, however, few records of paleoenvironmental conditions have been produced using deep-sea corals. The research covered in this dissertation further develops two methods for extracting temperatures from deep-sea corals. In the first, bulk [delta] 18O and [delta] 13C are explored in a group of calcitic octocorals and a new calibration for temperature extraction in proposed. Secondly, I report new data to further develop "clumped" isotopes as a paleothermometer in deep-sea corals as well as to investigate mineral-specific, taxon-specific, and growth-rate related effects. Carbonate clumped isotope thermometry is based on the abundance of the doubly-substituted isotopologue 13C18O16O2 in carbonate minerals and is a new and exciting method for extracting temperatures from biogenic carbonates. Deep-sea coral records of paleoventilation from the tropical and subtropical Pacific are also presented using paired 230Th-U and 14C measurements.
Issues in global outsourcing [electronic resource] : sustainability concerns and potential of reshoring
Keywords: Management Science and Engineering.

Global sourcing is prevailing in practice because multinational buyers can collaborate with suppliers in emerging economies who are more competitive in production costs than local suppliers. But accompanying the cost savings the buyers obtain through outsourcing, several issues arise. Because of geographical distances and differences in economic and socio-cultural environments, buyers do not have much control over overseas suppliers' social and environmental performance. To achieve lower production costs, suppliers in emerging economies tend to underinvest in socially and environmentally friendly practices. This dissertation first investigates topics related to buyers' auditing and sourcing decisions with emphasis on their suppliers' sustainability practices, and then discusses the potential of different reshoring alternatives from an inventory management perspective.
Justifying political liberalism [electronic resource]
Keywords: Philosophy.

I draw on the ideal of political community to defend political liberalism's defining commitment, the Reciprocity Principle. I argue that the Reciprocity Principle is justified by the fact that compliance with the principle promotes an attractive and inclusive form of political community in pluralistic societies. Along the way, I criticize claims that the Reciprocity Principle is self-defeating, that developing a justification of the principle is at odds with the principle's inclusive spirit, and that compliance with the principle is a requirement of respect for the governed.
Kincaid's Carnival: Performance, Identity, and the Reader in A Small Place
Keywords: Postcolonial Literature
Postcolonialism
Colonialism
Kincaid
Bakhtin
Identity Performance
Carnivalesque
Reader-Response
Department of English
Stanford
Thesis

This undergraduate honors thesis, focusing on Jamaica Kincaid’s creative nonfiction memoir A Small Place, shows how readers can be transformed through identity performance in literature. This thesis reads Kincaid’s text as a literary carnival (in the sense described by the literary critic Mikhail Bakhtin) to show how Kincaid forces her Western reader to perceive himself in ways that are uncomfortable and unaccustomed—for the purpose of reconceiving his relationship to postcolonial tourist destinations like the one in which Kincaid grew up. Taking its motivation from Kincaid’s assertion that the English language is inadequate for communicating a critique of colonialism and neo-colonialism, this thesis reads Kincaid’s use of language not as a mere medium, but as a performance that requires the reader’s active involvement. Ultimately, this thesis offers an optimistic stance on literature's ability to engage us in changing ourselves, our perspectives, and our world through imaginative performance.
Knowing the cosmos, growing the person [electronic resource] : faith in a Nigerian Pentecostal church
Keywords: Anthropology.

This dissertation explores how Nigerian Pentecostal Christians understand and perform Christian personhood and its place in the world. Like other evangelical Christians across the globe, Pentecostals in Yoruba-speaking southwest Nigeria view conversion as a sudden shift from non-Christian to Christian status. However, many Nigerian Pentecostals do not approach Christian personhood as complete after conversion -- in fact, they say the Christian person is never whole. During more than one year of ethnographic fieldwork with the Redeemed Christian Church of God (RCCG) in the town of Ile-Ife, Nigeria, I learned that church members defined Christian personhood as the continuous formation of an intimate, sensual relationship with the Holy Spirit, God's earthly manifestation. Redeemers described the process of developing "a relationship with God" as "faith." They explained that faith combined a state of mind -- "belief" -- with the daily and even hourly repetition of practices like prayer, Bible reading, song, and dance. Through faith, Redeemers claimed to cultivate increasingly frequent encounters with God in dreams, voices, and feelings. I examine how Redeemers used faith practices to construct and embody a cosmology, which Stanley Tambiah characterizes as a set of classifications that encompass the entire universe. Drawing on participant observation, interviews, focus groups, and media analysis, I show how Redeemers' cosmology was comprised of a complex web of relationships between the self, God, other Christians, the body and the senses, and time. I argue that faith was for Redeemers an embodied epistemology, a way of relating to the world that was cognitive but also performative. In other words, Redeemers framed faith as inseparable from bodily practice. Redeemers used faith for a central purpose: to become holier, more like God. Day after day, Redeemers practiced faith to shape themselves into moral copies, or icons, of God. I demonstrate the processual character and iconic aim of Nigerian Pentecostal faith by drawing an extended analogy between faith and ethnography. Specifically, I show the ongoing and embodied nature of my analysis. I illustrate how my conclusions emerged over time, through interactions in the field. In this way, I create a written icon of Redeemers' faith. The analytic and representational strategy I flesh out -- a strategy of fidelity -- extends the anthropology of religion by using ethnographic form as well as content to explore religion as an embodied mediating practice.
Knowledge in person [electronic resource] : the socio-literary self-fashioning of the Greek expository author
Keywords: Classics.

This dissertation investigates how Hellenistic and Imperial-Greek 'expository' authors fashion a textual persona, as well as the consequences that persona holds for the reception of their works. I define the term 'expository' to identify a style of writing that expounds knowledge on an abstract theme, presents it from a unified point-of-view, and grounds authority in an author's intelligence, diligence, or research acumen. The category thus encompasses texts from the exact sciences, medicine, history, and numerous technical or specialized treatises. Through five chapters the disseration demonstrates how social and literary forces jointly shape the Greek expository persona, arguing that beyond its function as a device for asserting didactic authority, the persona emerges as a vivid, elite identity that was felicitous in the Greek cultural context. The first three chapters offer a general account of the textual persona and show, respectively: 1) how prefaces feature a vividly rendered first-person persona, resonant with Greek performance culture, in works that may otherwise suppress that persona; 2) systemic differences in how authors present themselves in relation to patrons and other types of addressee; 3) how chronological changes in third-person naming practices indicate the increasing importance of a literary canon for authorial self-fashioning. Chapters four and five are case studies of Claudius Ptolemy: chapter four connects scientists with civic benefactors, showing how Ptolemy uses the rhetoric of euergetism to construct a unique model of virtual collaboration with past authorities and future readers. Chapter five shows how Ptolemy creatively alludes to Plato's Phaedrus through expressions of a 'desire for knowledge', which in this respect situates him closer to contemporary literary-stylists than to predecessors in the exact sciences. In conclusion, I argue that the authorial persona emerges to establish a place for an expository text in elite, Greek literary culture. It thus serves as a bridge between specialized, non-canonical texts, which largely comprise the 'expository' corpus, and the literary canon: it offers a flash of vivid personality, a moment of performance, an evocation of literary ghosts, for works that may otherwise seem impersonal, unperformable, or non-literary.
Large-eddy simulation of a body-junction flow [electronic resource]
Keywords: Mechanical Engineering.

Wall-junction flows are common in engineering applications but corner flow physics near the junction is not well understood. Moreover, the performance of the subgridscale (SGS) models frequently used for large eddy simulation (LES) is not well characterized. For this reason we have focused on LES simulations of a wing-body junction experimentally studied by Devenport & Simpson (1990). First, we have performed LES with the Vreman model, and analyzed the simulation results with respect to three specific goals: compare the computed and measured turbulence statistics in the junction region, investigate the corner vortex dynamics, and characterize why the SGS model shows inaccurate predictions near the corner. In order to improve the prediction ability of LES, we have developed two SGS models by focusing on two critical components: the mathematical operator that connects the resolved and subgrid stresses, and the determination of the model coefficient. The resulting models, volumetric strain-stretching based SGS eddy-viscosity model and residual stress based dynamic Vreman model are presented. The two SGS models are first validated in LES of two typical flows: decaying homogeneous isotropic turbulence and turbulent channel flows in compressible and incompressible regimes. Based on the improved wall-behavior of the proposed SGS models, we carried out additional LES of the wing-body junction case.
Lateral interactions in organic functionalization of semiconductor surfaces [electronic resource]
Keywords: Chemical Engineering.

As the size scale of current electronic devices is reaching a fundamental physical limit, new and innovative materials solutions are required for continuous progress of semiconductor technologies. Moreover, the development of nanotechnologies comprised of nanoscale materials is burgeoning in various fields. Nanomaterials often show completely different properties compared to their bulk, dominated by surfaces or interfaces. Given the importance of these interfaces, organic functionalization of semiconductor surfaces, or direct attachment of organic molecules, is a topic of increasing interest. By creating interfaces between inorganic and organic functionalities, we may be able to tune the properties of the surface with the versatility and tailorability of organic molecules. In order to utilize organic functionalization in such applications, a deep understanding of the adsorption of the molecules on the surfaces is necessary. In this work, we focus on the fundamental aspects of the adsorption chemistry of organic molecules on a semiconductor surface, and on the lateral interactions between the adsorbed molecules. We explore several molecules' adsorption chemistry on the Ge(100)-2×1 surface. Experimental techniques such as infrared spectroscopy, X-ray photoelectron spectroscopy, and temperature programmed desorption, in addition to theoretical methods including density functional theory calculations and Monte Carlo simulations, are utilized. The strongest interaction that drives the adsorption of the molecules on the surface is local bond formation between the molecules and "dimers" of the Ge(100)-2×1 surface, such as C-dative bonding of isocyanides, dissociative adsorption of phenols, and cycloaddition of nitrobenzene. However, weaker lateral interactions between the adsorbates or between adsorbates and the surface are also present, and they significantly affect the adsorption of the molecules, especially at higher coverages of the adsorbates. In studies of adsorption of small molecules that interact with one dimer, we observe a coverage-dependant spectral shift of tert-butyl isocyanide, and explain self-assembly of methanol and ethylene that had been reported in the literature. Slightly larger molecules can interact with other neighboring dimers: we show that phenol undergoes a shift in molecular orientation due to non-covalent adsorbate-surface interactions, and we determine that coverage-dependent evolution of dual and single adsorption products of benzenediols originates from inter-adsorbate interactions. Overall, this dissertation provides new insights toward the organic functionalization of semiconductor surfaces.