VictorJuiz/thesis huggingface dataset:
Fluorine passivation of defects in germanium devices [electronic resource]
Keywords: Electrical Engineering.

Today, new materials and structures are being deployed in MOSFET devices as the research/industry is facing challenges to ensure continued scaling for next generation technology. Germanium is one of the promising candidate materials to replace silicon-based devices, having higher mobility than silicon for better MOSFET performance. In addition, its optical operation above 1um wavelength regime makes it a suitable material for opto-electronic applications such as optical interconnects and infrared image sensors. However, due to its low band-gap (0.66eV) and fragile nature, germanium is affected severely by the presence of defects within the crystal and the surface. The effect of these defects mainly results in low n-type dopant activation, high leakage current and low carrier lifetime, which hinder the successful adaptation of germanium devices by the industry. To prevent these defect related degradation in germanium devices, we investigate the effect of fluorine passivation of defect sites. Fluorine, being the most reactive element in the periodic table has high potential to bond with the defect sites, thereby eliminating their degenerate effects. In this dissertation, we will first introduce the effect of defects in germanium. Then we will discuss the effects of fluorine as a passivation element for germanium defects. With this knowledge, we will explain the application of fluorine passivation for the following devices: 1. Forward current enhancement and leakage current reduction in n+/p diode. 2. Source and drain series resistance reduction by defect passivation in Ge nMOSFET. 3. Mobility enhancement by gate-stack fluorine passivation in Ge MOSFET. 4. Carrier lifetime enhancement in n+/p diode. Such applications of the fluorine passivation of germanium defects open new potential for high performance Ge-based devices for both MOSFET and optical devices.
FOMC Responses to Calls for Transparency: Evidence from the Minutes and Transcripts Using Latent Semantic Analysis
Keywords:  Department of Economics
Federal Open Market Committee
Deliberation
NLP
Central Bank
Stanford University
Department of Economics
Thesis

The Federal Reserve has become increasingly transparent in recent years in response to both internal inclinations and external calls from Congress and the private sector, yet it has stopped short of holding open FOMC meetings. Instead, the Fed releases minutes and statements to summarize its policy decisions. This paper applies Latent Semantic Analysis to FOMC transcripts and minutes from 1976—2008 in order to analyze the FOMC’s responses to calls for transparency. It reveals that two notable events explain much of the variation in transparency over this 32-year period. First, the 1978 Humphrey-Hawkins Act increased the degree to which the FOMC used meeting minutes to convey the content of its meetings. Historical evidence suggests that this was done because the Act required the Fed to tie its objectives to short-run Congressional and Presidential economic goals. Second, the 1993 decision to publish nearly verbatim transcripts also increased transparency. However, the cost was a decreasing degree of deliberation at each meeting, as evidenced by lower variance in content disagreement at the member level. By applying LSA to FOMC documents, this study presents a unique way of quantifying transparency and suggests LSA’s usefulness to other empirical studies in Economics.
A freely-moving monkey treadmill model [electronic resource]
Keywords: Electrical Engineering.

Motor neuroscience and brain-machine interface (BMI) design is based on examining how the brain controls voluntary movement, typically by recording neural activity and behavior from animal models. Recording technologies used with these animal models have traditionally limited the range of behaviors that can be studied, and thus the generality of science and engineering research. In this dissertation, I present a freely-moving animal model using neural and behavioral recording technologies that do not constrain movement. The freely-moving rhesus monkey model employs technology that transmits neural activity from an intracortical array using a head-mounted device and records behavior through computer vision using markerless motion capture. This dissertation demonstrates the flexibility and utility of this new monkey model, including the first recordings from motor cortex while rhesus monkeys walk quadrupedally on a treadmill. Using this monkey model, it is shown that multi-unit threshold-crossing neural activity encodes the phase of walking and that the average firing rate of the threshold crossings covaries with the speed of individual steps. On a population level, neural state-space trajectories of walking at different speeds have similar rotational dynamics in some dimensions that evolve at the step rate of walking, yet robustly separate by speed in other state-space dimensions. Freely-moving animal models may allow neuroscientists to examine a wider range of behaviors and can provide a flexible experimental paradigm for examining the neural mechanisms that underlie movement generation across behaviors and environments. For BMIs, freely-moving animal models have the potential to aid prosthetic design by examining how neural encoding changes with posture, environment, and other real-world context changes. Understanding this new realm of behavior in more naturalistic settings is essential for overall progress of basic motor neuroscience and for the successful translation of BMIs to people with paralysis.
From fat to cartilage [electronic resource] : harnessing stem cells to catalyze cartilege regeneration
Keywords: Mechanical Engineering.

Cartilage loss is a leading cause of disability among adults and represents a huge socioeconomic burden. Articular cartilage has limited self-repair potential and damage is often irreversible. Tissue engineering holds great promise for cartilage repair using a combination of cells, biomaterials and/or biological factors. However, one of the key barriers is the lack of abundant cell sources that can effectively regenerate articular cartilage. Conventional tissue engineering strategies for cartilage repair often utilize adult chondrocytes, which is limited by donor site morbidity, the need for multiple surgeries, and tendency to de-differentiate during in vitro expansion. Unlike adult chondrocytes, neonatal chondrocytes (NChons) are highly proliferative, immune-privileged, and can readily produce abundant extracellular matrix with retained articular cartilage phenotype. However, donor availability for NChons is scarce, which greatly hinders their broad application. The goal of this thesis is to examine the potential of ADSCs to catalyze cartilage tissue formation by NChons in 3D hydrogels. Specifically, we explored the feasibility of substituting the majority of NChons with ADSCs, an abundant autologous cell source that can be obtained in a minimally invasive manner. Using three different co-culture models, we demonstrated that the effects of co-culture on cartilage tissue formation were highly dependent on intercellular distance and cell distribution in 3D. Unexpectedly, increasing ADSC ratio in mixed co-culture led to increased synergy between NChons and ADSCs, and robust cartilage formation could be achieved using as few as 2% NChons in the mixed cell population. Cell tracking indicated that the newly formed cartilage was contributed by NChons alone, whereas ADSCs catalyzed such cartilage formation via paracrine signaling. We then demonstrated that catalyzed cartilage formation was retained under hypoxia, supporting the feasibility of translating such therapy for repairing cartilage tissue in situ. Furthermore, we examined the effects of transient priming of ADSCs with transforming growth factor (TGF)-[beta] on their ability to catalyze cartilage formation by NChons. Our results showed that ADSCs with short-term TGF-[beta] priming led to optimal catalyzed cartilage formation. Finally, we validated the efficacy of utilizing a mixed population of ADSCs with a small number of NChons for cartilage regeneration in vivo with robust hyaline cartilage formation over 12 weeks. In summary, the findings of this thesis raise the potential of utilizing stem cells to catalyze tissue formation by NChons, which may accelerate the broad translation of NChons for cartilage repair by alleviating donor scarcity limitation. Furthermore, the concept of harnessing paracrine signaling between two or more cell types in 3D scaffolds to catalyze tissue formation may be broadly applicable to regenerating other tissue types.
The future of terror [electronic resource] : musical settings of the poetry of Matthea Harvey
Keywords: Music.

This dissertation is comprised of two musical works that set the poetry of Matthea Harvey. These songs explore themes of terror, contingency, complacency, and the grotesque. The first musical work presented here is "as if to hold the hemispheres of their own heads together (black; dahlia 1)" for flute, oboe, tenor saxophone, soprano, violin, violoncello, and double bass. This piece sets Harvey's "How We Learned to Hold Hands, " from the poet's collection Modern Life. Ensemble Dal Niente premiered "as if to hold the hemispheres of their own heads together (black; dahlia 1)" in January, 2014. The second musical work presented here is "the future of terror, " for flute and soprano. This song cycle sets Harvey's series "The Future of Terror, " also from her collection Modern Life. Liz Pearse and Élise Roy — for whom this work was written — premiered "the future of terror" in May, 2014.
Generating synthetic noncoding RNAs for programmable and tunable gene control [electronic resource]
Keywords: Chemistry.

The engineering of biological systems offers significant promise for advances in areas including health and medicine, scalable manufacturing, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for genetically encoding molecular sensing, catalysis, data storage, information processing, and gene regulatory capabilities. We describe the development and application of methods for generating and characterizing functional noncoding RNA sequences, including novel biological sensing capabilities and regulatory switches in microbial and mammalian hosts. We developed a surface plasmon resonance-based platform for the rapid characterization of kinetic and equilibrium binding properties of aptamers to small molecules and a high-throughput, quantitative, cell-based screening strategy to support rapid generation of ribozyme-based RNA switches with user-specified regulatory activities. We applied these screening and characterization strategies to construct synthetic RNA regulatory switches to the pharmaceutical drug folinic acid in both microbial and mammalian cells in response to drug administration.
Generation of Induced Pluripotent Stem Cells for Study of MHC I - Mediated Neural Plasticity
Keywords:  Department of Biology
Biology
Neurobiology
MHC I
Neuronal Plasticity
Interferon-gamma
iPSC
Innate immune response
Thesis

Although it has long been known that major histocompatibility complex (MHC) markers play an important role in the adaptive immune system, recent work has implicated MHC Class I in neuronal plasticity in the central nervous system (CNS). However, little is known about the consequences of the innate immune response on neuronal MHC I expression and its subsequent effect on plasticity, an aspect critical to stem cell-derived neurons and their use in transplantation therapy. In this study, we generate neurons from induced pluripotent stem cells (iPSCs) derived from wild type and MHC I – deficient mice to use as a knockout model. We then utilize the inflammatory cytokine interferon-gamma (IFNγ) as a model of the innate immune response to induce MHC I expression in these neurons. We observe that wild type neurons exhibit an increase in MHC I, whereas the knockout-derived neurons display no changes in MHC I levels as predicted. The iPSCs and resulting neurons produced were further characterized for use in future connectivity and transplantation studies to probe the effects of MHC I on stem cell transplant survival and incorporation, with the final goal of employing non-steroidal anti-inflammatory drugs (NSAIDs) to attenuate the inflammatory cytokine effect and increase transplant efficacy. These results provide important insight into the relationship between the innate immune response and stem cell-derived neuronal integration, taking a crucial step toward the future goal of using patient-specific iPSCs in clinical transplant therapies.
Geologic history of the Chukchi Borderland, Arctic Ocean [electronic resource]
Keywords: Geological and Environmental Sciences.

The Amerasia Basin in the Arctic Ocean is one of the least understood tectonic systems on Earth and radically different ideas have been proposed to explain the tectonic development and geologic nature of its intrabasinal ridges. Recently, a push for data collection by Arctic nations for Extended Continental Shelf (ECS) claims under the United Nations Convention for the Law of the Sea treaty has added greatly to the amount of information available about this poorly understood region. Over 380,000 km2 of multibeam bathymetric data were collected between 2003-2012 as part of the Unite States' ECS project as well as 17 dredges, most of which sampled rocks from submarine outcrops within the central Amerasia Basin. Joint operations with the U.S. and Canada resulted in over 15,000 linear km of multichannel seismic reflection data. In order to answer first order questions as to the nature of the bathymetric features within the Amerasia Basin, and their relationship to the surrounding margins, we report on dredged rock samples from the Chukchi Borderland and suggest that this important bathymetric feature is related to Paleozoic mountain belts of the northern Laurentian margin. The multibeam bathymetric dataset and regional muilti-channel seismic transect also documented in this study, are the basis for development of a chronology of sedimentation, deformation, and volcanism that link the geologic history of the poorly known bathymetric features within the Amerasia Basin. Together these data and geologic samples challenge long held ideas about the tectonic history of the Chukchi Borderland and provide constraint for tectonic reconstruction models.
Germanium-tin [electronic resource] : a material and technology for group-IV photonics integration on silicon
Keywords: Electrical Engineering.

The germanium-tin (GeSn) alloy system is a highly engineerable, Group-IV material system that has the potential to yield a useful direct bandgap, making it a desirable material for developing light emitters and other photonic devices. Furthermore, its Group-IV nature makes it electronically compatible with silicon and is important for ubiquitous integration into current silicon-based chips. In this dissertation, we explore several properties, features, design, and integration of GeSn alloys on silicon for photonics. Heterostructure devices with GeSn/Ge are developed in quantum-well microdisk resonators and quantum-well light-emitting diodes emitting beyond 2-[mu] m wavelength. Designs, considerations, and strategies towards developing GeSn-based lasers are presented and discussed.
Ge/SiGe quantum well devices for optical interconnects [electronic resource]
Keywords: Electrical Engineering.

Increasing processing power has been at the heart of technological boom witnessed in the past few decades. However, the communication delay of electrical interconnects poses a fundamental limit to future improvements. On-chip optical interconnects are an alternative solution to allow for continued advancements in processing power. This thesis explores the potential of Ge/SiGe quantum well devices as a candidate for an on-chip optical interconnect system. The Ge and SiGe material system is particularly promising for optical interconnects because these materials are compatible with Si CMOS technology. Our work demonstrates that these devices can perform as light emitters, modulators and detectors—the most important components in an optical interconnect system. Furthermore, we developed vertically coupled waveguide Ge quantum well devices and discuss their performance as well as our efforts to integrate these devices into a functioning optical interconnect system.
Getting a Head Start on Culture
Keywords: Graduate School of Education
Stanford University
Education honors
Head Start
Native American culture
Thesis

Head Start is a government pre-school program run through the United Stated Department of Health and Human Services. Head Start’s goal as an organization is “Helping people. Changing lives. Building communities” and it primarily serves low socio-economic communities and the children that live within them. Head Start has a long history of improving academic success by correcting or buffering against the negative effects of poverty so children coming through its program are developmentally on par with their peers. However Head Start has vested interest in many other non-academic areas of development, such as cultural development. Head Start has long worked with ethnically dense and diverse communities to encourage the cultural growth of its students and local community. However, fostering cultural development is a difficult task as there are many sensitive issues, rules, and obligations that any organization should adhere to when trying to improve cultural development. One particular area of Head Start where the teaching of culture is especially difficult is within Native American reservation centers. The Office of Head Start (OHS) regularly encounters requests for assistance from reservations in improving their ability to support children’s cultural development, which is understandable considering the fact that Native American culture has a long history of mistreatment in this nation and is severely damaged. The goal of this particular thesis is to explore how parents and teachers within one reservation community want their children to develop culturally. I asked three particular questions regarding the relevance of traditional culture, perceived cultural needs, and the efficacy of Head Start in meeting those needs. The questions are as follows. In the minds of parents and teachers, how relevant is teaching Native American culture at the pre-school? What are the cultural needs, as perceived by parents and teachers, of the children within the Head Start program? How do parents and teachers perceive the efficacy of Head Start’s approach to teaching culture within the classroom? Through this research I hope to contribute to a growing body of literature on culturally-minded teaching and Native American identity formation.
Gibbs measures and phase transitions on locally tree-like graphs [electronic resource]
Keywords: Statistics.

In this thesis we consider Gibbs measures defined on sparse, locally tree-like graphs. We investigate the asymptotic behavior of these measures in the limit of graph size tending to infinity. In the first part we study replica symmetric heuristics for the asymptotic free energy density. We develop an interpolation scheme for proving replica symmetric bounds, and apply it to establish new results on the free energy of some classical models of statistical physics, including the Ising, Potts, and hard-core models. In particular, for d even we explicitly determine the asymptotic free energy density of ferromagnetic Potts models on graphs converging locally to the d-regular tree. This result covers, for example, any sequence of d-regular graphs with diverging girth. In the second part of this thesis we study random constraint satisfaction problems in which replica symmetric heuristics are expected to fail. For a large class of these problems, the one-step replica symmetry breaking cavity heuristic yields exact predictions of the satisfiability transition. We give the first rigorous confirmations of this prediction for two problems in this class, not-all-equal-SAT and maximum independent set, both in the setting of random regular graphs. In the second problem we furthermore establish tight concentration of the maximum independent set size.
Global civil society [electronic resource] : altering pathways to empower the marginalized
Keywords: Sociology.

Increased cross-national exchanges and the rise of global civil society have captured the attention of scholars and practitioners alike. In the three papers that comprise this dissertation, I use different analytic and methodological approaches to explore the features of global civil society and its effects on domestic civic and political affairs. The central focus is on the ability of global civil society actors and agendas, and transnational movements to reshape domestic contestations and empower those who are generally among the most marginalized: minority groups, indigenous peoples, and women and girls. Two important trends emerge from the research. First, NGOs, as key actors of global civil society, may strengthen local civil society organizations generating new systemic and sustainable opportunities for marginalized communities. The political economy of aid, though, remains a predominant feature of global civil society, strongly influencing where NGOs locate and biasing who is—and is not—supported. Marginalized groups, thus, have new pathways to recourse, but those opportunities may be constrained by geopolitics and global hierarchies.
Global quantification of proteostasis regulation [electronic resource]
Keywords: Chemical and Systems Biology.

Protein homeostasis, or proteostasis, is the result of protein synthesis, folding, degradation, and other quality control mechanisms which work in unison to establish and maintain desired levels of proteins. Deficiencies in proteostasis have been linked to aging and a number of diseases such as Alzheimer's disease, Huntington's disease, and cancer. Although individual mechanisms within the proteostasis network have been studied at length, the extent to which each process is responsible for overall protein maintenance has yet to be uncovered. Genomic and proteomic techniques developed in the last decade and are now capable of measuring proteostasis regulation, particularly protein synthesis and degradation. Chapter 1, the introduction to this dissertation, covers the techniques currently available for studying the dynamics of proteostasis on a systems-level. These techniques were applied in Chapters 2 and 3 to explore proteostasis regulation. Chapter 2 includes a global analysis of four aspects of proteostasis regulation -- transcript abundance, translation, proteins abundance, and degradation. This four dimensional approach to characterizing proteostasis under unperturbed conditions allowed for the detection of several distinct modes of regulation that reflect underlying biological mechanisms notably, non-degradative ubiquitination and mTOR-dependent translation regulation. Expanding our fundamental and quantitative understanding of these and other processes will support future mechanistic studies and will aid in the development of predictive models of proteostasis dynamics. Chapter 3 describes a project, in collaboration with the Kim lab at Stanford, aimed characterizing the aging proteome. Proteostasis collapse has been linked to aging in several of model organisms, however research focused on the systems biology of aging has largely relied on genomic and transcriptomic techniques. Here, we used mass spectrometry to quantify the changes in protein abundance that occur from adulthood to old age in the nematode, C. elegans. We identified over three thousand proteins and reproducibly measured changes in protein abundance for over 60 proteins. Some of these proteins were previously shown to play a role in the aging process, thus supporting our results. Proteins that signify the aging phenotype will serve as candidates for future experiments toward deciphering the mechanisms of aging.