VictorJuiz/thesis huggingface dataset:
Blackboard bodhisattvas [electronic resource] : narratives of New York City teaching fellows
Keywords: Education.

ABSTRACT Since the founding of Teach for America (TFA) in 1990, alternative routes to teaching have proliferated. The New Teacher Project (now TNTP), the consulting and advocacy wing of TFA, has been a key actor behind many Teaching Fellows programs in a number of settings across the U.S., the largest of which is the New York City Teaching Fellows (TNTP website). Using a life history approach (Goodson, 1992), this dissertation investigates the experiences of three New York City Teaching Fellows who have remained in the classroom for eight to thirteen years, well beyond the five-year mark by which point 50% of urban teachers quit. This dissertation argues that the inadequacy of the Fellows' preparation for taking on the challenges of urban teaching speaks dramatically to how the alternative-certification model is far more successful at recruiting and placing young, ill-prepared teachers in classrooms than it is at training or retaining good teachers, with the resulting turnover only leading, in the course of these teachers careers, to more emphasis on recruitment rather than training and retention. The three Fellows in this study, lacking the easy-exit strategy of TFA teachers (who come from the best schools), found the means of becoming better, more engaged teachers by eventually developing a personal point of connection and commitment with the students and the school system. This was despite, and not because of, the system's increasingly bureaucratic efforts at professional development for improved test results. These teachers' stories speak, not only to the difficulty of being an urban teacher in a era of accountability, but the need to provide a more supportive induction process and setting for teachers to find their places and their talents as professionals within the schools and American culture more generally.
Buying suits [electronic resource] : exploring business-to-business financing of American disputes
Keywords: Law JSD.

People litigate for various reasons. Some want to right wrongs, others -- make precedents. But most, at least in the civil realm, sue to protect economic interests; and they are motivated by pragmatic considerations rather than abstract notions of justice. One fruit of the mercantile approach to civil litigation is the nascent market where third parties provide financing for litigants (or their lawyers) and profit from a successful resolution of the funded claims. Through the lens of a third-party funder, justice is a mass-market commodity, and its value depends on laws of men and laws of probability alike. The ways of litigation funders create multiple points of tension for the legal process and its participants, and laws on the book offer little guidance on how third-party interests should be treated. Resulting procedural and ethical dilemmas have stirred a debate among scholars who rushed to offer conflicting opinions and advice. Critics demand that litigation investing be banned, calling it a travesty of justice that turns courts into casinos. Enthusiasts want the practice formally recognized, asserting that it levels the playing field for weaker parties. The discussion on litigation financing does not lack vigor; but it does lack hard facts. Drawing from first-hand empirical data on the practice of litigation funding in the United States, this thesis explores and systematizes the market for legal claims, explaining how it actually works. First, it describes the entire ecosystem of actors who apply the logic of asset management to uncertainties of individual lawsuits. Second, it tackles the question of why commercial disputes get funded. Third, it provides a systematic overview of different models of financing, from secured debt to equity-style investments to attorney's fee-backed securities. Finally, it contemplates funding in the context of complex litigation, and shows various ways used by litigation stakeholders to leverage their resources. Based on the descriptive findings, I claim that modern civil litigation engages multiple, often undisclosed stakeholders with complex financial motivations. I argue that such interests should be recognized by the legal system as legitimate and ultimately regulated.
Candidate and proteomic approaches to study non-histone lysine methylation [electronic resource]
Keywords: Chemical and Systems Biology.

Lysine methylation is a chemical modification that occurs naturally in proteins. This post-translational modification is small and preserves the charge on the lysine sidechain, making relatively little chemical difference. However, misregulation of lysine methylation can cause a host of human cancers, developmental disorders, and other diseases. The most prominent example of lysine methylation occurs within histone proteins, but it can also occur on non-histone proteins. The proteomic extent of methylation and the diversity of processes it might regulate were previously unclear. The work presented here focuses on identifying the cellular "methylome" and understanding methylation signaling pathways within cells. I also examine the substrate repertoire of the methyltransferase SETMAR and identify the spliceosome component snRNP70 as a novel SETMAR substrate.
Carbon Cycling in Organic Material Originating from Monospecific Overstories in Hawaiian Lowland Wet Forests
Keywords:  Department of Biology
biology
ecology
hawaii
invasive species
carbon
soil
humus
litter
hybrid ecosystems
Stanford University Department of Biology
Thesis

High levels of invasion and disturbance in the lowland wet forests of Hawaii have led to a need for novel management strategies for the conservation of biodiversity, carbon (C) storage, and other ecosystem services. The hybrid ecosystems approach represents a method by which species traits can be used in the creation of ecosystems which optimize desirable characteristics. In the lowland wet forests of Hawaii, C storage is one of these important traits, given the continual increase in atmospheric carbon and global environmental change. In this study we examined soil humus decomposition and leaf litter decomposition. We asked whether patterns seen in rates of litter turnover across nine species currently present in the lowland wet forests of the big island of Hawaii would be present in the turnover of humus originating from single species stands. We used a soda-lime absorption measurement assay to quantify soil decomposition over a period of four weeks and performed a four-month common site litter decomposition experiment. Total C efflux values for the full four week period ranged from 13.4 – 16.9 g C/kg soil, with little difference among species. Litter decomposition had greater variability. The fastest decomposition occurred in Thespesia populnea (milo) litter, with 17.6% of mass left at the end of the decomposition period, while Persea americana (avocado) litter was the slowest to decompose and maintained 78.6% of its mass. Our results suggest a decoupling of litter and humus decomposition rates. These findings provide additional understanding on the extent to which hybrid ecosystems may be able to influence C storage and turnover through species treatments.
Cas9-Mediated Genome Editing in Mouse Primary Cells
Keywords:  Department of Biology
CRISPR
Cas9
guide RNA
genome editing
embryonic stem cells
toxicity
Biology
Stanford
Thesis

Gene targeting through Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-mediated homologous recombination is a novel and powerful technique with promising applications in human disease modeling and therapeutic development. However, one major factor limiting genome editing efficiency is the time and difficulty of obtaining a transgenic animal, which may require several generations of breeding and expensive maintenance. While the establishment of an animal line with endogenous Cas9 nuclease expression could potentially accelerate the study of both gene knock-out and overexpression models, particularly in primary cells, previous work has yet to test the feasibility of such a system. This project provided the first in vitro proof of concept for a Cas9 transgenic mouse line as a research tool through the generation and characterization of Cas9-expressing mouse cells. In NIH3T3 cells, constitutive expression of either the Cas9 nuclease or nickase resulted in toxicity, with high levels of wild-type Cas9 expression appearing to be lethal over time. Following delivery of a CRISPR guide RNA sequence into cultured Cas9-expressing mouse cells via lentivirus, efficient genome editing was also observed. These findings demonstrate the prospect of high-speed multiplex genome engineering in mouse primary cells with future clinical implications such as cancer modeling and gene therapy. Moving forward, the generation of an inducible Cas9 transgenic animal should be pursued.
Catching Fish With Two Hands: Vietnam's Hedging Strategy Towards China
Keywords: Vietnam
China
hedging
Cam Ranh Bay
bauxite
bauxite mining
Southeast Asia
Center for International Security and Cooperation
Thesis

China’s dramatic economic growth and ascendance onto the world stage has had large implications for neighboring Southeast Asian states that, while enthusiastic about growth opportunities, are still apprehensive of Chinese dominance in the region. As a result, most scholars maintain that states in the region have chosen to “hedge” against China by cultivating positive relations with all large states involved in the region. Current literature on hedging is insufficiently nuanced since it treats hedging as a fixed foreign policy strategy in between balancing and bandwagoning. Furthermore, existing explanations generally consider only one plane of hedging, namely how small states cultivate relations with other powers to hedge against a threatening state. This paper contributes to existing literature on hedging in two ways. First, it proposes a three-dimensional approach for understanding hedging that considers how domestic, foreign, and sectoral factors affect small-states’ hedging strategy. Second, this thesis examines two cases of Vietnamese foreign policy towards China in the 21st century using this three- dimensional framework. More specifically, this paper analyzes one case study in the economic realm, bauxite mining in the Central Highlands, and one in the security sphere, the open port policy of Cam Ranh Bay. Ultimately, this thesis demonstrates the fluid processes of hedging across issues and the need for a better understanding of these dynamics in the Southeast Asian context.
Cellular composition of cerebral arteriovenous malformations: determining the presence and characterization of progenitor cells
Keywords:  Department of Biology
Stanford University Department of Neurosurgery
Biology
Cerebral arteriovenous malformation (AVM)
progenitor cell
Thesis

Cerebral arteriovenous malformations (AVMs), although rare, are a leading cause of intracerebral hemorrhage and stroke in young adults and children. Due to a poor understanding of the formation and cellular makeup of AVMs, available treatment options are complicated and invasive, and AVMs can regrow in some cases. Progenitor cells have been implicated in AVMs, possibly functioning in the abnormal growth characteristic of this lesion, but their physical presence has not been directly confirmed. By analyzing the protein expression in human AVM tissue in vivo and cells isolated from AVMs in vitro, this project works to clarify a potential progenitor presence and associated differentiation potential. First, Ki67 and CD133, accepted markers for cellular proliferation and stem cells respectively, were analyzed by immunohistochemistry in 29 human AVM tissue samples. In conjunction with previously identified expression patterns, the co-expression of progenitor-associated proteins in AVM tissue strongly indicates a progenitor presence. Second, two progenitor cell lines were successfully isolated from human cerebral AVMs by enrichment under progenitor conditions. The protein profile of these cell lines was then explored by immunocytochemistry to determine their in vitro differentiation potential. These cell lines maintain several characteristics of progenitor cells, including proliferation and expression of progenitor-associated proteins. Importantly, they have a unique protein signature, and the cells proliferate independently of growth factors. Additionally, human serum causes proliferation rather than differentiation. This project augments understanding of the fundamental nature of cerebral AVMs by identifying the presence of progenitor cells. Future research should extend these findings to determine the full characterization of these novel progenitors and their role in AVM formation and/or maintenance.
CEO Overconfidence: An Alternative Explanation for Corporate Financing Decisions
Keywords:  Department of Economics
Stanford Department of Economics
Thesis

In the well-established trade-off capital structure model, a rational CEO
chooses to issue debt and equity depending on the costs and benefits of each.
In this model, the optimal amount of debt and equity financing occurs when
the dead-weight costs of bankruptcy exactly offset the tax saving benefits of
debt. However, this rational decision-making theory does not provide an
adequate explanation for empirical findings that companies often deviate
from the presumably optimal levels of debt and equity issuance. As an
alternative explanation for these capital structures, we examine the additional
impact that CEO overconfidence appears to have on financing decisions. In
order to measure overconfidence of CEOs, we employ a measure based on
the percentage of optimistic press coverage a CEO receives relative to the
percentage of optimistic press coverage that the company itself receives. We
then gather data on net debt issuance and net equity issuance under the
governance of each CEO, and regress these financing decisions on our
measure of CEO overconfidence. We find weak evidence that what we term
overconfident CEOs deem equity financing relatively more expensive than
debt financing, and thereby maintain higher than expected leverage ratios.
We focus our data analysis on financing decision data from the decade 1997-
2007, and examine capital structure decisions arising from CEO overconfidence in conjunction with differentials by industry and the effects of the dividend tax cuts from the 2003 Jobs and Growth Tax Relief Reconciliation Act.
Characteristics and implications of brief duration hydrodynamic forces in the intertidal zone [electronic resource]
Keywords: Biology.

The hydrodynamic forces produced by breaking waves make the rocky intertidal zone one of the most physical stressful environments on Earth. Although the classical in-line hydrodynamic forces are well studied and characterized, an undescribed force -- known as the impingement force -- may be the largest hydrodynamic force in the intertidal zone. Impingement is characterized by a sharp, transient spike in force at the instant of wave arrival, and very few measurements of it exist. I measured impingement in the laboratory, using a gravity-driven water cannon to simulate waves and tested which variables affect impingement magnitude. I show that impingement is likely drag, rather than an undescribed hydrodynamic force; it likely occurs due to brief increases in flow velocity at the front of a wave. To assess the frequency and magnitudes of impingement events in the field, I built a force transducer to record high-frequency forces in the intertidal zone. Impingement events occur in 2-7% of waves in the field, but surprisingly, the average magnitude of impingement events is lower than the average maximum force produced by all recorded waves in this study. This suggests that impingement is not the largest hydrodynamic risk to organisms, and future work measuring flows in the intertidal zone should focus on identifying large transient forces regardless of where they occur in a wave. Using these measurements, I explore the likely effects of brief forces on intertidal organisms in two ways: first, I model a limpet as a mechanical spring-mass-damper system and show that its foot has the capacity to reduce the effective force on the animal. I also predict dislodgment rates of three species of gastropod using the maximum forces recorded in my field study. At my site, snails are very susceptible to wave-induced dislodgment. This dissertation illustrates the necessity of recording high-frequency flows when studying intertidal hydrodynamics.
Characterization and application of vertical nanopillar-based sensors for probing cellular functions [electronic resource]
Keywords: Chemistry.

Vertically aligned nanopillars can serve as excellent electrical, optical and mechanical platforms for biological studies. To date, the interface between cells and nanopillars, particularly the conformation of the cell membrane and nucleus, has not been well characterized despite its importance to the choice of feasible applications for nanopillar substrates to cellular studies. We characterized the cell-nanopillar interface by fluorescence, scanning electron and transmission electron microscopy on nanopillars with a range of diameters, pitch and heights. We found that the cell membrane wraps around the entirety of the nanopillar without loss of membrane integrity, contrary to prior suggestions. We also observed that the membrane-surface gap of both cell bodies and neurites is smaller for nanopillars than for a flat substrate. These results support a tight interaction between the cell membrane and the nanopillars and previous findings of excellent sealing in electrophysiology recordings using nanopillar electrodes. Subsequently, we took advantage of the cell-nanopillar interface to develop applications of nanopillar arrays to mechanical and optical measurements in living cells. We observed that vertical nanopillar arrays significantly deform the nuclear envelope, and the extent of deformation is sensitive to both the stiffness of the nucleus and the stiffness of the cytoskeleton. Thus, nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and open up exciting new possibilities for the study of nuclear mechanotransduction in live cells. In addition to serving as mechanical probes, we developed a nanopillar-based platform for single molecule measurements in live cells. With a diameter much smaller than the wavelength of visible light, a transparent silicon dioxide nanopillar embedded in a nontransparent substrate restricts the propagation of light and affords evanescence wave excitation along its vertical surface. We showed that nanopillar illumination can be used for in vitro single molecule detection with high background. In addition, the tight interface between vertical nanopillars and live cells allows them to function as highly localized light sources inside the cell. Overall, nanopillar arrays are a powerful platform for studying cell function through electrical, optical and mechanical measurements.
Characterization of Lin28-RNA interactions in human embryonic stem cells [electronic resource]
Keywords: Genetics.

RNA binding proteins (RBPs) play essential roles in the post-transcriptional regulation of gene expression. The RBP Lin28 is highly expressed in human embryonic stem (hES) cells and is known to play important roles in hES cell self-renewal and pluripotency. However, it is not completely understood how Lin28 contributes to the regulation of stem cell properties. This dissertation aims to advance our understanding on the molecular mechanisms Lin28 utilizes to influence stem cell biology. The first goal of the study was to systematically identify the full complement of Lin28-associated RNAs in hES cells. Using crosslinking and immunoprecipitation (CLIP) in combination with other genome-wide in vivo and in vitro techniques, we discovered that Lin28 interacts with the large majority of cellular RNAs, including all major functional classes of cytosolic RNAs in hES cells. Among the large number of targets preferential association occurs with tRNAs and mRNAs. The high abundance of Lin28 in hES cells is sufficient to allow binding of multiple Lin28 molecules to most of its mRNA targets. The second goal of the study was to uncover Lin28 recognition sequences on the identified RNA targets. Bioinformatic analysis and in vitro testing of Lin28 binding regions showed that Lin28 recognition of RNA targets occurs through interactions with low complexity nucleotide motifs that vary among RNA classes. The motif preference was clearest in mRNAs where Lin28 bound preferentially but not exclusively to the 3'UTR and favored interactions with AU rich sequences. The third and final goal of the study was to better understand Lin28's role in regulation of its mRNA targets. The data showed that in hES cells Lin28 appears to play no more than a minor role in regulating mRNA stability. However, Lin28 binding is strongly associated with a Lin28-dependent decrease in the density of ribosomes associated with its mRNA targets. The multiplicity of Lin28's interactions with diverse functional classes of RNA in hES cells, and the evidence that these interactions systematically alter translation of its mRNA targets, suggest that Lin28 may have a general transcriptome-wide regulatory role in hES cells.
Characterizing, identifying, and using tree-like structure in social and information networks [electronic resource]
Keywords: Electrical Engineering.

In this work, a detailed empirical analysis of two kinds of tree-like structure, in a variety of real and synthetic networks, is presented. The two types of tree-like structure computed are Gromov hyperbolicity, originated from geometric group theory, and the tree decomposition, an object common in theoretical computer science. The relationship between these structures and core-periphery structure, measured using the k-core decomposition, is also presented. The computational methods for each of these measurements are discussed, including timing results using OpenMP in several different implementations of the algorithm for computing Gromov hyperbolicity. The results show that tree-like structure is present in many real networks, but, because of the inherent fragility of the measurements, that modified definitions (which are scale-sensitive) are required to identify meaningful structure. Additionally, it is shown that there is a strong connection between the core-periphery structure and both Gromov hyperbolicity and the structure of the resulting tree decompositions. The final chapter of this work is separate and self-contained. It describes a novel method for using persistent homology (a technique of computational topology) to classify computed tomography (CT) scans of hepatic lesions.
Characterizing sensory cell regeneration by facultative Lgr5+ cells in Mus musculus utricle
Keywords:  Department of Biology
Biology
Otolaryngology
regeneration
Wnt
Thesis

Recruitment of endogenous progenitors is critical during tissue repair. In the mammalian cochlea, damaged hair cells are not regenerated. As a result, hearing loss is permanent and negatively impacts the quality of life for over 48 million Americans. Adjacent to the cochlea in the inner ear are the vestibular organs responsible for our balance functions. Of the vestibular organs, the utricle requires mechanosensory hair cells to detect linear acceleration. After damage, non-mammalian utricles regenerate hair cells mitotically and non-mitotically. By contrast, mammalian utricles exhibit limited non-mitotic regeneration, with the source of regenerated hair cells currently unknown. Here, we used Lgr5-EGFP reporter mice to show that hair cell damage in neonatal mouse utricles activates the Wnt target gene, Lgr5, in supporting cells, which normally do not express Lgr5. Lineage tracing and time-lapse microscopy in utricles from Lgr5-EGFP-CreERT2; Rosa26R-tdTomato mice reveal that Lgr5+ cells non-mitotically become hair cell-like cells in vitro, a process termed “direct transdifferentiation.” Thus, Lgr5 marks damage-activated HC progenitors and may help reveal factors necessary for mammalian hair cell regeneration.