VictorJuiz/thesis huggingface dataset:
The Polar Bear in the Room: The Role of Institutions in the Changing Arctic
Keywords: Arctic
institutions
international law
cooperation
United Nations Convention on the Law of the Sea
Arctic Council
Center for International Security and Cooperation
Thesis

This thesis focuses on the role of international institutions in the Arctic. Specifically, it examines the two main governance structures in the Arctic—the Arctic Council and the United Nations Law of the Seas Treaty (UNCLOS)—in light of the changing Arctic environment. It evaluates to what extent these two governance structures have been effective at keeping the peace in the Arctic, and whether this cooperation is likely to continue in the future. While the Arctic—and its institutions—are frequently cited as a model for geopolitical cooperation, this thesis finds that predictions that this cooperation will continue are overly optimistic. This conclusion is based on two overall findings. The first is that the Arctic Council, the preeminent forum for cooperation in the Arctic, is unlikely to adapt to upcoming issues, as it is limited by its primarily environmental mandate. The second argument concerns the role of UNCLOS, and finds that, despite its effectiveness in bringing states to the negotiation table for some territorial disputes, it has generally been unable to mandate long-term solutions. By showing the limitations of the Arctic Council and UNCLOS in regards to their ability to provide cooperative governance, this thesis questions the existing literature about the Arctic and raises the question of what other structures—perhaps economic or security related—are needed to ensure that the Arctic remains a peaceful sphere of cooperation in the future. As such, it is valuable for policymakers or academics that have to deal with the Arctic in particular, and for international cooperation literature more generally.
The Role of Neat1 in p53-mediated cell-cycle arrest, apoptosis and senescence
Keywords:  Department of Biology
Biology
p53 tumor suppressor
Radiation Oncology
Stanford
Thesis

Mutations of p53 in over half of all human cancers indicate p53’s critical role as a tumor suppressor. In response to cellular stress, p53 transcriptionally activates a set of target genes to induce cell-cycle arrest and apoptosis. While most known p53 target genes are protein-coding, we have recently discovered that p53 activates transcription of the noncoding RNA Neat1. Neat1 plays a structural role in the formation of paraspeckles, nuclear compartments that regulate gene expression via nuclear retention of mRNA. The role of paraspeckles in cellular functions is not fully understood, and the potential role of Neat1 in tumor suppression mechanisms has not been studied previously. This project illuminates the roles of Neat1 in p53-mediated cell-cycle arrest, apoptosis and senescence. Our data suggest that Neat1 is not necessary for p53-mediated cell-cycle arrest or apoptosis as Neat1-/- mouse embryonic fibroblasts (MEFs) retain the capacity to undergo both G1 cell-cycle arrest and apoptosis in response to DNA damage, although apoptosis is delayed in the absence of Neat1. We additionally show that Neat1 is not necessary for p53 function in senescence as Neat1-/- MEFs retain the ability to senesce. Since Neat1-/- MEFs could upregulate compensatory mechanisms to compensate for the lack of Neat1, we further tested Neat1’s function in cell-cycle arrest using Neat1 overexpression. We found that Neat1 is sufficient for p53-mediated cell-cycle arrest, as Neat1 overexpression was able to induce cell-cycle arrest in p53-/- MEFs. Seeming inconsistency between Neat1 overexpression results and Neat1-/- results is likely due to compensation for the absence of Neat1 in the Neat1-/- MEFs or redundancy of Neat1’s role in p53-mediated cell-cycle arrest. Because Neat1 acts downstream of p53 to promote cell-cycle arrest, further understanding of Neat1’s role in p53-mediated cell-cycle arrest, apoptosis and tumor suppression could suggest Neat1 as a novel target for cancer therapies.
The role of neuronal activity in oligodendroglial cell lineage dynamics and myelination in the healthy and demyelinated mammalian brain
Keywords:  Department of Biology
Biology
Thesis

Mature oligodendrocytes from oligodendrocyte precursor cells (OPCs) have been shown to cause myelination of the central nervous system. In this study, we use optogenetic stimulation of the premotor cortex in awake, behaving mice to demonstrate that neuronal activity causes a robust proliferative response in OPCs and promotes subsequent oligodendrogenesis. Behaviorally relevant activity also increases myelination within the deep layers of the premotor cortex and subcortical fibers entering the corpus callosum. Interestingly, this neuronal activity–regulated oligodendrogenesis and myelination is correlated with improved motor function of the corresponding limb. Inhibition of oligodendrocyte differentiation blocks this improvement in behavior.
The Role of the GABA Antagonist, Pentylenetetrazole, on Augmenting Cognition
Keywords:  Department of Biology
Biology
Circadian Rhythms
Learning and Memory
Neurobiology
Thesis

Previous studies have shown that pentylenetetrazole (PTZ), a GABA antagonist, can ameliorate cognitive defects in both Down Syndrome mice model and arrhythmic hamsters. Starting with the observation that entrained hamsters perform poorly on hippocampal-dependent memory tests in the morning, and well in the afternoon, we sought to see if PTZ improves cognitive performance in normal, entrained animals at both times. To answer this question we performed both an acute injection study and a long-term chronic injection study. Chronic injections of PTZ had no effect on memory test performance in entrained animals, but did increase their exploratory behavior during the tests. Animals treated with acute injections of PTZ or vehicle performed better than control animals in the morning, but worse than controls in the afternoon. However, animals treated with PTZ performed significantly better than Veh animals in the morning. These results suggest that PTZ can rescue a defect, but not augment normal cognition. Further, PTZ may modulate a stress response in acutely injected animals.
The roles of Arabidopsis chaperone J3 and the Xanthomonas type III effector XopX in plant immunity
Keywords:  Department of Biology
Biology
Plant Bacterial Pathogen
Thesis

Xanthomonas euvesicatoria (Xcv) is the causal agent of bacterial spot disease in pepper and tomato plants. Xcv uses its type III secretion (T3S) system to translocate effector proteins into the cytoplasm of plant cells. Although the function of each T3S effector is not well understood, it is known that they are required to collectively suppress innate immune signaling in plants.  In this thesis, I focused on one effector protein, XopX, which has been found to be a major contributor towards Xcv virulence. Using the yeast two-hybrid system and in vitro affinity protein purification, the Mudgett laboratory discovered that XopX physically associates with the Arabidopsis thaliana J-domain protein, J3. Given this finding, I hypothesize that XopX may be directly targeting J3 to alter its function during Xcv infection to promote pathogenesis. Here I studied the role of J3 in plant pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI) by utilizing the heterologous Pseudomonas syringae pathovar tomato (Pst)-Arabidopsis thaliana pathosystem. Arabidopsis j3 mutants were less susceptible to Pst infection than wild-type Arabidopsis lines in PTI assays. By contrast, J3 did not appear to play a significant role in ETI. Studies examining the role of XopX in bacterial virulence in Arabidopsis revealed that both wild-type and j3 mutant leaves were equally more resistant to Pst expressing XopX compared to infection with Pst alone. This suggests that XopX may be triggering Arabidopsis immune responses, possibly in a J3-dependent manner, or that XopX may be interfering with Pst virulence mechanisms during infection. In conclusion, my research identifies J3 as a negative regulator of PTI in Arabidopsis. It is unclear if XopX is directly interfering with J3 function; however, my preliminary findings suggest that J3 is required for XopX-induced resistance in Arabidopsis.
The Structural and Functional Role of Calcium Ions at the Globular Domain of C1Q-Like Proteins
Keywords:  Department of Biology
Stanford
Molecular
Structural
Neuroscience
Biology
Thesis

Elucidation of the molecular mechanisms that regulate synapse formation, maintenance, and homeostasis is required to understand neuron communication and how they contribute to the formation of neural networks and higher cognitive functions. Recent work has shown that C1q-like (C1QLs) are secreted proteins expressed in neurons in specific regions of the brain, and they act as ligands to the postsynaptic brain-specific angiogenesis inhibitor 3 (BAI3) adhesion GPCRs. Although these two proteins have been implicated in synapse development, fundamental questions regarding the calcium-binding properties of C1QL remain unanswered, and little is known about their downstream signaling with BAI3. As such, there is great merit in illuminating their integral roles in synapse regulation.
The globular domain of C1QL (gC1q) binds to thrombospondin repeat domains of BAI3 in a calcium-dependent manner. We generate mutants of calcium sites at the trimer interface of C1QL3. Using X-ray crystallography, we provide high-resolution structures of C1QL3 and its mutants to show changes in structure and ion capacity, which may be relevant for BAI3 receptor binding. We examine folding and stability using circular dichroism (CD) spectroscopy and test calcium affinity using isothermal titration calorimetry (ITC) to narrow down the important calcium sites involved in BAI3 interactions. Together, the results suggest that C1QL and BAI3 mediate synapse homeostasis in the presence of calcium ions bound at specific sites. This research describes the calcium binding properties of the first known ligand to BAI3 and can be applied to the broader regulation of synapses in the brain through the interaction of these two proteins.
Theater and prestige [electronic resource] : the development of the playhouse in Shakespeare's time
Keywords: English.

Early modern playhouses did not exist independently of one another: they constituted a theatrical milieu, and to understand one theater we must understand its relation to other theaters. From the Elizabethan period through the Jacobean and Caroline periods, different theatrical venues occupied different niches in London's playgoing culture and increasingly came to cater to different audiences. This affected the kinds of plays that playwrights wrote and also influenced how playwrights defined themselves as authors. As venues became increasingly differentiated according to their audience and repertoire, literary prestige started to influence the kinds of plays that authors produced. Theatrical venues, authorship, and prestige determined the style of many plays, led to the creation of new genres, and ultimately determined how people conceived of the theater as an institution. We can gain important new insights into early modern drama by looking at how Londoners imagined their array of theatrical venues.
Theme and variation [electronic resource] : essayistic lineages in four 20th century Spanish-American and German novels
Keywords: Comparative Literature.

My dissertation offers a revisionist account of a novelistic tendency generally called "essayism, " in terms of its development vis-à-vis the realist novel and twentieth century literary experiments, within two distinct literary traditions: those of Europe and of Latin America. It explores the insights that essayistic theory can provide into the comparative writing of authority in these contexts, and argues for a more diversified approach than is currently taken to essayistic aesthetics in the study of fiction and other hybrid genres— despite the essay's unmanageable diversity of forms and the impossibly broad set of claims for its uniqueness. My case studies focus on the disjuncture between the much-discussed twentieth-century European essay-novel and its Latin American counterpart, which develops in dialogue with an influential body of essayistic work and tradition. The essayistic novel as seen in this broadened context is symptomatic of an ongoing quarrel between the moral claims of fictional and non-fictional writing.
Theoretical and experimental evolution studies of adaptation under diploidy and epistasis [electronic resource]
Keywords: Biology.

The dynamics of adaptive evolution is explored in the context of diploidy and epistasis. In the first chapter I model the dynamics of adaptation in the framework of Fisher's geometric model for diploids and find that balancing selection due to heterozygote advantage naturally emerges during adaptation. In the second chapter I explore patterns of divergence and adaptation emerging in a model incorporating functional linkage between genes. Finally, in the third chapter I describe an evolutionary experiment where a populations of a diploid yeast strain adapt to glucose-limited continuous cultures by overdominant mutations, result that supports the predictions of the model from chapter 1.
Theory and applications of sparsity for radar sensing of ionospheric plasma [electronic resource]
Keywords: Aeronautics and Astronautics.

In order to enable flexible high-resolution measurements of ionospheric plasma phenomena, a sparsity-based radar waveform inversion technique is formulated and found to eliminate processing artifacts caused by the standard matched filter approach. Taking direction from the theory of compressed sensing, sparsity of the radar target scene is employed as prior knowledge to successfully perform the inversion. The result is cleaner data that limits self-interference of range-spread targets and enables differentiation in crowded and variable environments. Though the approach has been applied to ionospheric radar, it is generally applicable and especially relevant for radar target scenes with multiple or distributed scatterers. As a basis for the technique, a discrete radar model that captures signal sparsity in a delay-frequency dictionary is developed. This model is shown to have a strong connection to existing methods, resulting in an intuitive interpretation of the inversion technique as an iterative thresholding matched filter. An explicit formulation of the discrete model's representation of arbitrary distributed scatterers is derived, and it shows that sparsity is reasonably preserved in the discrete representation. Building on top of the model, waveform inversion is implemented using modern convex optimization techniques tailored for efficient computation and quick convergence. Finally, the real-world flexibility and effectiveness of the inversion technique is demonstrated by the elimination of filtering artifacts from meteor observations made with a variety of standard radar waveforms.
Theory, design, and demonstration of a new microwave-based undulator [electronic resource]
Keywords: Electrical Engineering.

Synchrotron Light Sources and Free Electron Lasers (FEL) oﬀer great applications in the ﬁelds of metallurgy, biology, chemistry, and archeology etc., by providing a radiation probe for extremely small structures (like molecules, DNAs) and small durations (like timescale of chemical reactions). In these experimental facilities, electrons are accelerated to relativistic energies and then passed through an undulator or wiggler to generate the radiation. The undulator, which is the backbone of such a light source, is conventionally a series of permanent magnets with a strong magnetic ﬁeld, constant in time but alternating in space. These undulators, however, provide limited control over the properties of the generated radiation. Moreover, it is very challenging to scale the magnetic undulators down to smaller undulating periods -- a useful feature to generate shorter wavelength radiation by spending lesser energy in the acceleration of the electrons. Such scaling will also require strict limits on the maximum electron beam aperture, ﬁeld strength, and consequently the radiation brightness. To overcome these shortcomings of the magnetic undulator technology, we have designed a novel short-period microwave undulator and have demonstrated its successful operation at NLCTA, SLAC. This microwave undulator is essentially a Thomson scattering device that has yielded tunable spontaneous emission and seeded coherent radiation. It is about 1 m long axisymmetric, corrugated, copper cavity, resonant at 11.424 GHz with an undulator period of 1.39 cm. The undulator deﬂection parameter (K) of this microwave undulator is tunable and has achieved a value as high as 0.7 (the equivalent ﬁeld strength is 0.55 Tesla). Given the availability of a high power rf source, K = 1 could also be achieved without breakdowns due to high surface ﬁelds in the undulator cavity. Moreover, the design of this undulator is conveniently scalable to smaller undulator periods as the required size of the electron beam aperture does not reduce as sharply as it does for the magnetic undulators. The undulator ends were designed to have tapered ﬁeld to minimize transverse drift and kick induced in the electron beam. For future generation light sources, this device promises shorter undulator period, large aperture, and fast dynamic control. We have also presented a new Finite Element Method (FEM) based implementation that can eﬃciently calculate electromagnetic ﬁelds in general axisymmetric cavities.
A theory of countryside biogeography [electronic resource]
Keywords: Biology.

Humans are the dominant influence affecting patterns of life on the planet. Our demand for food, fuel, and fiber create the countless countryside ecosystems that collectively constitute the majority of the biosphere. Countryside biogeography studies the distribution of biological variation over space and time in human-dominated ecosystems. It explicitly considers all ecosystem components, including: minimally-altered habitats; novel ecosystems; domestic and feral plants and animals; human populations; and the services provided by nature to people, including quality of life. Countryside biogeography also deliberately focuses on forecasting changes in biodiversity and biodiversity-driven ecosystem services under a variety of possible futures. As such, one of the primary aims of countryside biogeography is to understand what kinds of ecosystems will exist in the coming decades and which might merit the most protection through human intervention.
Thermodynamic and kinetic studies of hydrogenenation reaction in magnesium/palladium nanostructures [electronic resource]
Keywords: Materials Science and Engineering.

The factors affecting the formation rate and stability of metal hydride thin films, so crucial for hydrogen storage applications, are not well understood. The low equilibrium hydrogen pressure, hence high stability, of metal hydride inhibits easy charging/discharging for fuel cell applications. The significant increase of equilibrium hydrogen pressure observed in Mg/Pd thin films is encouraging, but has been mistakenly attributed to mechanical and not chemical factors. Our experiments prove that mechanical strain is present only in the Pd layer and cannot significantly affect the hydride stability. However, a simple thermodynamic analysis suggests that an intermixing layer of Mg and Pd will destabilize the hydride enough to account for the observed increase in equilibrium hydrogen pressure. We used TEM and XPS to look for this layer and found it, as expected. We show that the equilibrium pressure increase can be further enhanced by increasing the amount of intermixing. Having determined the effect of intermixing on the hydride thermodynamics, it is still unclear how the diffusion of hydrogen and propagation of the hydride phase boundary occurs in the metal hydride. We next characterize hydride formation from isolated points of nucleation in a simple morphology in order to develop design rules for more complicated hydrogen storage structures. In order to physically control the nucleation, we only permit hydrogen to enter the magnesium through sparsely distributed Pd ``nanoportals.'' Because the Pd nanoportals are far apart, we are able to study hydride nucleation one site at a time. We are able to measure the nucleation time constant and the diffusion constants of hydrogen in the hydride by fitting data to a modified Avrami model. We observe that the morphology of grown hydride and the growth rate of hydride are prominently affected by the crystal structure of the magnesium film. However, continuous oxidation of the Mg film pinches off the Pd portals and slows the hydride formation. Better control of the sample structure and chemical state is needed to extract the kinetic parameters correctly and understand the reaction kinetics. By doing so, we hope to provide new ideas and design rules for future storage materials.
Thunderstorm-induced enhancements in the E-region ionosphere [electronic resource]
Keywords: Aeronautics and Astronautics.

The purpose of this study is to understand the coupling between convective phenomena in the lower atmosphere and the Sporadic-E anomaly observed in the E-region of the ionosphere. The ionosphere is a region of partially ionized air in the upper atmosphere created by solar radiation. It has often been observed that Sporadic-E, an anomalous ionization enhancement occurring in the E-region of the ionosphere, often disrupts satellite-earth communications at the MF, HF and even in the VHF frequency bands and that this anomaly is thought to be fairly prevalent during thunderstorm activity. However, very little is known about the mechanisms behind Sporadic-E formation, though multiple theories that attempt to explain the physics behind this phenomenon are topics of ongoing research. This study attempts to explore the theory of indirect enhancement of the E-region ionosphere through the launching of atmospheric gravity waves (AGWs) and the subsequent formation of traveling ionospheric disturbances (TIDs) through two observational experiments. In the first experiment, two dual-band GPS receivers were used to measure fluctuations in total electron content during thunderstorms. This experiment was aimed at providing insights into whether or not thunderstorms were always associated with AGWs and TIDs. As part of the second experiment, a stellar radio source was observed within a range of output radio frequencies from the Long Wavelength Array (LWA) at Datil, NM, during both stormy and fair weather days. Preferential blockage of the lower stellar frequencies could then be used to suggest that the E-region has been enhanced to 'cutoff' the low frequency stellar radiation. Although the experiments themselves were conducted successfully on multiple occasions, there is insufficient data for conclusions regarding the correlation between thunderstorms and the formation of Sporadic-E. Nonetheless, some encouraging conclusions and recommendations are discussed and the study is hoped to serve as a stepping stone for future research.